pax_global_header00006660000000000000000000000064135037061640014517gustar00rootroot0000000000000052 comment=b0234647d9429328afa5393caf22e0d95ae3326e adapterremoval-2.3.1/000077500000000000000000000000001350370616400145305ustar00rootroot00000000000000adapterremoval-2.3.1/.gitignore000066400000000000000000000000451350370616400165170ustar00rootroot00000000000000.vscode build googletest-release* *~ adapterremoval-2.3.1/.travis.yml000066400000000000000000000012441350370616400166420ustar00rootroot00000000000000language: cpp dist: trusty compiler: - clang - gcc os: - linux - osx addons: apt: packages: - zlib1g-dev - libbz2-dev - python3 - python3-pip before_install: - if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then python3 -m pip install --user cpp-coveralls; fi install: true script: - make - if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then make test COVERAGE=yes; fi - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then make test COVERAGE=no; fi - make regression - PATH=$PATH:$PWD/build/ make -C examples after_success: - if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then python3 -m coveralls --exclude tests --gcov-options '\-lp'; fi adapterremoval-2.3.1/AdapterRemoval.1000066400000000000000000000436731350370616400175350ustar00rootroot00000000000000.\" Man page generated from reStructuredText. . .TH "ADAPTERREMOVAL" "1" "Jun 23, 2019" "2.3.0" "AdapterRemoval" .SH NAME AdapterRemoval \- Fast short-read adapter trimming and processing . .nr rst2man-indent-level 0 . .de1 rstReportMargin \\$1 \\n[an-margin] level \\n[rst2man-indent-level] level margin: \\n[rst2man-indent\\n[rst2man-indent-level]] - \\n[rst2man-indent0] \\n[rst2man-indent1] \\n[rst2man-indent2] .. .de1 INDENT .\" .rstReportMargin pre: . RS \\$1 . nr rst2man-indent\\n[rst2man-indent-level] \\n[an-margin] . nr rst2man-indent-level +1 .\" .rstReportMargin post: .. .de UNINDENT . RE .\" indent \\n[an-margin] .\" old: \\n[rst2man-indent\\n[rst2man-indent-level]] .nr rst2man-indent-level -1 .\" new: \\n[rst2man-indent\\n[rst2man-indent-level]] .in \\n[rst2man-indent\\n[rst2man-indent-level]]u .. .SH SYNOPSIS .sp \fBAdapterRemoval\fP [\fIoptions\fP…] –file1 <\fIfilenames\fP> [–file2 <\fIfilenames\fP>] .SH DESCRIPTION .sp \fBAdapterRemoval\fP removes residual adapter sequences from single\-end (SE) or paired\-end (PE) FASTQ reads, optionally trimming Ns and low qualities bases and/or collapsing overlapping paired\-end mates into one read. Low quality reads are filtered based on the resulting length and the number of ambigious nucleotides (‘N’) present following trimming. These operations may be combined with simultaneous demultiplexing using 5’ barcode sequences. Alternatively, \fBAdapterRemoval\fP may attempt to reconstruct a consensus adapter sequences from paired\-end data, in order to allow the identification of the adapter sequences originally used. .sp If you use this program, please cite the paper: .INDENT 0.0 .INDENT 3.5 Schubert, Lindgreen, and Orlando (2016). AdapterRemoval v2: rapid adapter trimming, identification, and read merging. BMC Research Notes, 12;9(1):88 .sp \fI\%http://bmcresnotes.biomedcentral.com/articles/10.1186/s13104\-016\-1900\-2\fP .UNINDENT .UNINDENT .sp For detailed documentation, please see .INDENT 0.0 .INDENT 3.5 \fI\%http://adapterremoval.readthedocs.io/en/v2.2.3/\fP .UNINDENT .UNINDENT .SH OPTIONS .INDENT 0.0 .TP .B \-\-help Display summary of command\-line options. .UNINDENT .INDENT 0.0 .TP .B \-\-version Print the version string. .UNINDENT .INDENT 0.0 .TP .B \-\-file1 filename [filenames...] Read FASTQ reads from one or more files, either uncompressed, bzip2 compressed, or gzip compressed. This contains either the single\-end (SE) reads or, if paired\-end, the mate 1 reads. If running in paired\-end mode, both \fB\-\-file1\fP and \fB\-\-file2\fP must be set. See the primary documentation for a list of supported formats. .UNINDENT .INDENT 0.0 .TP .B \-\-file2 filename [filenames...] Read one or more FASTQ files containing mate 2 reads for a paired\-end run. If specified, \fB\-\-file1\fP must also be set. .UNINDENT .INDENT 0.0 .TP .B \-\-identify\-adapters Attempt to build a consensus adapter sequence from fully overlapping pairs of paired\-end reads. The minimum overlap is controlled by \fB\-\-minalignmentlength\fP\&. The result will be compared with the values set using \fB\-\-adapter1\fP and \fB\-\-adapter2\fP\&. No trimming is performed in this mode. Default is off. .UNINDENT .INDENT 0.0 .TP .B \-\-threads n Maximum number of threads. Defaults to 1. .UNINDENT .SS FASTQ options .INDENT 0.0 .TP .B \-\-qualitybase base The Phred quality scores encoding used in input reads \- either ‘64’ for Phred+64 (Illumina 1.3+ and 1.5+) or ‘33’ for Phred+33 (Illumina 1.8+). In addition, the value ‘solexa’ may be used to specify reads with Solexa encoded scores. Default is 33. .UNINDENT .INDENT 0.0 .TP .B \-\-qualitybase\-output base The base of the quality score for reads written by AdapterRemoval \- either ‘64’ for Phred+64 (i.e., Illumina 1.3+ and 1.5+) or ‘33’ for Phred+33 (Illumina 1.8+). In addition, the value ‘solexa’ may be used to specify reads with Solexa encoded scores. However, note that quality scores are represented using Phred scores internally, and conversion to and from Solexa scores therefore result in a loss of information. The default corresponds to the value given for \fB\-\-qualitybase\fP\&. .UNINDENT .INDENT 0.0 .TP .B \-\-qualitymax base Specifies the maximum Phred score expected in input files, and used when writing output files. Possible values are 0 to 93 for Phred+33 encoded files, and 0 to 62 for Phred+64 encoded files. Defaults to 41. .UNINDENT .INDENT 0.0 .TP .B \-\-mate\-separator separator Character separating the mate number (1 or 2) from the read name in FASTQ records. Defaults to ‘/’. .UNINDENT .INDENT 0.0 .TP .B \-\-interleaved Enables \fB\-\-interleaved\-input\fP and \fB\-\-interleaved\-output\fP\&. .UNINDENT .INDENT 0.0 .TP .B \-\-interleaved\-input If set, input is expected to be a interleaved FASTQ files specified using \fB\-\-file1\fP, in which pairs of reads are written one after the other (e.g. read1/1, read1/2, read2/1, read2/2, etc.). .UNINDENT .INDENT 0.0 .TP .B \-\-interleaved\-ouput Write paired\-end reads to a single file, interleaving mate 1 and mate 2 reads. By default, this file is named \fBbasename.paired.truncated\fP, but this may be changed using the \fB\-\-output1\fP option. .UNINDENT .INDENT 0.0 .TP .B \-\-combined\-output Write all reads into the files specified by \fB\-\-output1\fP and \fB\-\-output2\fP\&. The sequences of reads discarded due to quality filters or read merging are replaced with a single ‘N’ with Phred score 0. This option can be combined with \fB\-\-interleaved\-output\fP to write PE reads to a single output file specified with \fB\-\-output1\fP\&. .UNINDENT .SS Output file options .INDENT 0.0 .TP .B \-\-basename filename Prefix used for the naming output files, unless these names have been overridden using the corresponding command\-line option (see below). .UNINDENT .INDENT 0.0 .TP .B \-\-settings file Output file containing information on the parameters used in the run as well as overall statistics on the reads after trimming. Default filename is ‘basename.settings’. .UNINDENT .INDENT 0.0 .TP .B \-\-output1 file Output file containing trimmed mate1 reads. Default filename is ‘basename.pair1.truncated’ for paired\-end reads, ‘basename.truncated’ for single\-end reads, and ‘basename.paired.truncated’ for interleaved paired\-end reads. .UNINDENT .INDENT 0.0 .TP .B \-\-output2 file Output file containing trimmed mate 2 reads when \fB\-\-interleaved\-output\fP is not enabled. Default filename is ‘basename.pair2.truncated’ in paired\-end mode. .UNINDENT .INDENT 0.0 .TP .B \-\-singleton file Output file to which containing paired reads for which the mate has been discarded. Default filename is ‘basename.singleton.truncated’. .UNINDENT .INDENT 0.0 .TP .B \-\-outputcollapsed file If –collapsed is set, contains overlapping mate\-pairs which have been merged into a single read (PE mode) or reads for which the adapter was identified by a minimum overlap, indicating that the entire template molecule is present. This does not include which have subsequently been trimmed due to low\-quality or ambiguous nucleotides. Default filename is ‘basename.collapsed’ .UNINDENT .INDENT 0.0 .TP .B \-\-outputcollapsedtruncated file Collapsed reads (see –outputcollapsed) which were trimmed due the presence of low\-quality or ambiguous nucleotides. Default filename is ‘basename.collapsed.truncated’. .UNINDENT .INDENT 0.0 .TP .B \-\-discarded file Contains reads discarded due to the –minlength, –maxlength or –maxns options. Default filename is ‘basename.discarded’. .UNINDENT .SS Output compression options .INDENT 0.0 .TP .B \-\-gzip If set, all FASTQ files written by AdapterRemoval will be gzip compressed using the compression level specified using \fB\-\-gzip\-level\fP\&. The extension “.gz” is added to files for which no filename was given on the command\-line. Defaults to off. .UNINDENT .INDENT 0.0 .TP .B \-\-gzip\-level level Determines the compression level used when gzip’ing FASTQ files. Must be a value in the range 0 to 9, with 0 disabling compression and 9 being the best compression. Defaults to 6. .UNINDENT .INDENT 0.0 .TP .B \-\-bzip2 If set, all FASTQ files written by AdapterRemoval will be bzip2 compressed using the compression level specified using \fB\-\-bzip2\-level\fP\&. The extension “.bz2” is added to files for which no filename was given on the command\-line. Defaults to off. .UNINDENT .INDENT 0.0 .TP .B \-\-bzip2\-level level Determines the compression level used when bzip2’ing FASTQ files. Must be a value in the range 1 to 9, with 9 being the best compression. Defaults to 9. .UNINDENT .SS FASTQ trimming options .INDENT 0.0 .TP .B \-\-adapter1 adapter Adapter sequence expected to be found in mate 1 reads, specified in read direction. For a detailed description of how to provide the appropriate adapter sequences, see the “Adapters” section of the online documentation. Default is AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG. .UNINDENT .INDENT 0.0 .TP .B \-\-adapter2 adapter Adapter sequence expected to be found in mate 2 reads, specified in read direction. For a detailed description of how to provide the appropriate adapter sequences, see the “Adapters” section of the online documentation. Default is AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT. .UNINDENT .INDENT 0.0 .TP .B \-\-adapter\-list filename Read one or more adapter sequences from a table. The first two columns (separated by whitespace) of each line in the file are expected to correspond to values passed to –adapter1 and –adapter2. In single\-end mode, only column one is required. Lines starting with ‘#’ are ignored. When multiple rows are found in the table, AdapterRemoval will try each adapter (pair), and select the best aligning adapters for each FASTQ read processed. .UNINDENT .INDENT 0.0 .TP .B \-\-minadapteroverlap length In single\-end mode, reads are only trimmed if the overlap between read and the adapter is at least X bases long, not counting ambiguous nucleotides (N); this is independent of the \fB\-\-minalignmentlength\fP when using \fB\-\-collapse\fP, allowing a conservative selection of putative complete inserts in single\-end mode, while ensuring that all possible adapter contamination is trimmed. The default is 0. .UNINDENT .INDENT 0.0 .TP .B \-\-mm mismatchrate The allowed fraction of mismatches allowed in the aligned region. If the value is less than 1, then the value is used directly. If \fB\(ga\-\-mismatchrate\fP is greater than 1, the rate is set to 1 / \fB\-\-mismatchrate\fP\&. The default setting is 3 when trimming adapters, corresponding to a maximum mismatch rate of 1/3, and 10 when using \fB\-\-identify\-adapters\fP\&. .UNINDENT .INDENT 0.0 .TP .B \-\-shift n To allow for missing bases in the 5’ end of the read, the program can let the alignment slip \fB\-\-shift\fP bases in the 5’ end. This corresponds to starting the alignment maximum \fB\-\-shift\fP nucleotides into read2 (for paired\-end) or the adapter (for single\-end). The default is 2. .UNINDENT .INDENT 0.0 .TP .B \-\-trim5p n [n] Trim the 5’ of reads by a fixed amount after removing adapters, but before carrying out quality based trimming. Specify one value to trim mate 1 and mate 2 reads the same amount, or two values separated by a space to trim each mate different amounts. Off by default. .UNINDENT .INDENT 0.0 .TP .B \-\-trim3p n [n] Trim the 3’ of reads by a fixed amount. See \fB\-\-trim5p\fP\&. .UNINDENT .INDENT 0.0 .TP .B \-\-trimns Trim consecutive Ns from the 5’ and 3’ termini. If quality trimming is also enabled (\fB\-\-trimqualities\fP), then stretches of mixed low\-quality bases and/or Ns are trimmed. .UNINDENT .INDENT 0.0 .TP .B \-\-maxns n Discard reads containing more than \fB\-\-max\fP ambiguous bases (‘N’) after trimming. Default is 1000. .UNINDENT .INDENT 0.0 .TP .B \-\-trimqualities Trim consecutive stretches of low quality bases (threshold set by \fB\-\-minquality\fP) from the 5’ and 3’ termini. If trimming of Ns is also enabled (\fB\-\-trimns\fP), then stretches of mixed low\-quality bases and Ns are trimmed. .UNINDENT .INDENT 0.0 .TP .B \-\-trimwindows window_size Trim low quality bases using a sliding window based approach inspired by \fBsickle\fP with the given window size. See the “Window based quality trimming” section of the manual page for a description of this algorithm. .UNINDENT .INDENT 0.0 .TP .B \-\-minquality minimum Set the threshold for trimming low quality bases using \fB\-\-trimqualities\fP and \fB\-\-trimwindows\fP\&. Default is 2. .UNINDENT .INDENT 0.0 .TP .B \-\-preserve5p If set, bases at the 5p will not be trimmed by \fB\-\-trimns\fP, \fB\-\-trimqualities\fP, and \fB\-\-trimwindows\fP\&. Collapsed reads will not be quality trimmed when this option is enabled. .UNINDENT .INDENT 0.0 .TP .B \-\-minlength length Reads shorter than this length are discarded following trimming. Defaults to 15. .UNINDENT .INDENT 0.0 .TP .B \-\-maxlength length Reads longer than this length are discarded following trimming. Defaults to 4294967295. .UNINDENT .SS FASTQ merging options .INDENT 0.0 .TP .B \-\-collapse In paired\-end mode, merge overlapping mates into a single and recalculate the quality scores. In single\-end mode, attempt to identify templates for which the entire sequence is available. In both cases, complete “collapsed” reads are written with a ‘M_’ name prefix, and “collapsed” reads which are trimmed due to quality settings are written with a ‘MT_’ name prefix. The overlap needs to be at least \fB\-\-minalignmentlength\fP nucleotides, with a maximum number of mismatches determined by \fB\-\-mm\fP\&. .UNINDENT .INDENT 0.0 .TP .B \-\-minalignmentlength length The minimum overlap between mate 1 and mate 2 before the reads are collapsed into one, when collapsing paired\-end reads, or when attempting to identify complete template sequences in single\-end mode. Default is 11. .UNINDENT .INDENT 0.0 .TP .B \-\-seed seed When collaping reads at positions where the two reads differ, and the quality of the bases are identical, AdapterRemoval will select a random base. This option specifies the seed used for the random number generator used by AdapterRemoval. This value is also written to the settings file. Note that setting the seed is not reliable in multithreaded mode, since the order of operations is non\-deterministic. .UNINDENT .INDENT 0.0 .TP .B \-\-deterministic Enable deterministic mode; currently only affects –collapse, different overlapping bases with equal quality are set to N quality 0, instead of being randomly sampled. .UNINDENT .SS FASTQ demultiplexing options .INDENT 0.0 .TP .B \-\-barcode\-list filename Perform demultiplxing using table of one or two fixed\-length barcodes for SE or PE reads. The table is expected to contain 2 or 3 columns, the first of which represent the name of a given sample, and the second and third of which represent the mate 1 and (optionally) the mate 2 barcode sequence. For a detailed description, see the “Demultiplexing” section of the online documentation. .UNINDENT .INDENT 0.0 .TP .B \-\-barcode\-mm n .TP .B Maximum number of mismatches allowed when counting mismatches in both the mate 1 and the mate 2 barcode for paired reads. .UNINDENT .INDENT 0.0 .TP .B \-\-barcode\-mm\-r1 n Maximum number of mismatches allowed for the mate 1 barcode; if not set, this value is equal to the \fB\-\-barcode\-mm\fP value; cannot be higher than the \fB\-\-barcode\-mm\fP value. .UNINDENT .INDENT 0.0 .TP .B \-\-barcode\-mm\-r2 n Maximum number of mismatches allowed for the mate 2 barcode; if not set, this value is equal to the \fB\-\-barcode\-mm\fP value; cannot be higher than the \fB\-\-barcode\-mm\fP value. .UNINDENT .INDENT 0.0 .TP .B \-\-demultiplex\-only Only carry out demultiplexing using the list of barcodes supplied with –barcode\-list. No other processing is done. .UNINDENT .SH WINDOW BASED QUALITY TRIMMING .sp As of v2.2.2, AdapterRemoval implements sliding window based approach to quality based base\-trimming inspired by \fBsickle\fP\&. If \fBwindow_size\fP is greater than or equal to 1, that number is used as the window size for all reads. If \fBwindow_size\fP is a number greater than or equal to 0 and less than 1, then that number is multiplied by the length of individual reads to determine the window size. If the window length is zero or is greater than the current read length, then the read length is used instead. .sp Reads are trimmed as follows for a given window size: .INDENT 0.0 .INDENT 3.5 .INDENT 0.0 .IP 1. 3 The new 5’ is determined by locating the first window where both the average quality and the quality of the first base in the window is greater than \fB\-\-minquality\fP\&. .IP 2. 3 The new 3’ is located by sliding the first window right, until the average quality becomes less than or equal to \fB\-\-minquality\fP\&. The new 3’ is placed at the last base in that window where the quality is greater than or equal to \fB\-\-minquality\fP\&. .IP 3. 3 If no 5’ position could be determined, the read is discarded. .UNINDENT .UNINDENT .UNINDENT .SH EXIT STATUS .sp AdapterRemoval exists with status 0 if the program ran succesfully, and with a non\-zero exit code if any errors were encountered. Do not use the output from AdapterRemoval if the program returned a non\-zero exit code! .SH REPORTING BUGS .sp Please report any bugs using the AdapterRemoval issue\-tracker: .sp \fI\%https://github.com/MikkelSchubert/adapterremoval/issues\fP .SH LICENSE .sp This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 3 of the License, or at your option any later version. .sp This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. .sp You should have received a copy of the GNU General Public License along with this program. If not, see <\fI\%http://www.gnu.org/licenses/\fP>. .SH AUTHOR Mikkel Schubert; Stinus Lindgreen .SH COPYRIGHT 2017, Mikkel Schubert; Stinus Lindgreen .\" Generated by docutils manpage writer. . adapterremoval-2.3.1/CHANGES.md000066400000000000000000000443041350370616400161270ustar00rootroot00000000000000### Version 2.3.1 - 2019-06-23 * Added --preserve5p option. This option prevents AdapterRemoval from trimming the 5p of reads when the --trimqualities, --trimns, and --trimwindows options are used. Neither end of collapsed reads are trimmed when this option is used. * Fixed Ns being miscounted as As when constructing consensus adapter sequences using --identify-adapters. ### Version 2.3.0 - 2019-03-12 * Fixed --collapse producing slightly different result on 32 bit and 64 bit architectures. Courtesy of Andreas Tille. * Added support for output files without a basename; to create such output files, use an empty basename (--basename "") or a basename ending with a slash (--basename path/). * Added support for managing file handles to allow AdapterRemoval to run when the the number of output files exceeds the number of file handles, e.g. when demultiplexing large numbers of samples. * Reworked demultiplexing to improve performance for many paired barcodes. ### Version 2.2.4 - 2019-02-10 * Fixed bug in --trim5p N which would AdapterRemoval to abort if N was greater than the pre-trimmed read length. * Fixed --identify-adapters not respecting the --mate-separator option. ### Version 2.2.3 - 2019-01-22 * Added support for trimming reads by a fixed amount: --trim5p N --trim3p N. Different values may be given for each mate: --trim5p N1 N2. Trimming is carried out after adapters have been removed and reads have been collapsed, if enabled, but before quality trimming (Ns and low qualities). * Added option for determistic read merging (--collapse-deterministic). In this mode AdapterRemoval will set a merged base to 'N' with quality 0 if the corresponding bases on the two mates differ, and if both have the same quality score. The default behavior is to select one of the two bases at random. * Fixed reporting of line numbers in error messages. * Added conda installation instructions, courtesy of Maxime Borry (maxibor). * Fixed reading mate 2 adapters specified via --adapter-list. Adapters would be used in the reverse orientation compared to --adapter2. Courtesy of Karolis (KarolisM). * Fixed various typos and improved help/error messages. ### Version 2.2.2 - 2017-07-17 * Made gzip and bzip2 support mandatory. * Added support for Intel compilers, courtesy of Kevin Murray (kdmurray91). ### Version 2.2.1a - 2017-05-17 * Fixed compilation on OSX. ### Version 2.2.1 - 2017-05-15 * Numerous spelling errors fixed courtesy of Andreas Tille. * Added support for specifying multiple filenames after --file1 and --file2, in which case the files are treated as if they were concatenated. This is supported for all operations. Special thanks to Stephen Clayton. * Added additional run-time checks to catch race-conditions. * Progress messages written to STDERR no longer cause subsequent error messages to be written to the same line. * Implemented quality trimming using a sliding window approach inspired by sickle (https://github.com/najoshi/sickle). Special thanks to Kevin Murray. * Fixed miscounting of the total number of retained nucleotides, where mate 1 reads were being counted twice instead of counting both mate 1 and mate 2. ### Version 2.2.0 - 2016-10-27 * AdapterRemoval now requires a C++11 compliant compiler; furthermore, multithreading is no longer an optional feature, as this is now implemented using the C++11 instead of directly calling pthreads. * Add explicit message not to use the results after failed runs. * Minor changes to .settings: Adapter numbers now 1-based; the 'Number of reads with adapters' is changed to 'Number of read pairs with adapters' when trimming PE reads; the 'Average read length of trimmed reads' is changed to 'Average read length of retained reads' for clarity. * Dropped the undocumented 'poor' classification for alignments; for statistical purposes, reads are either counted as aligned or not aligned. This ony changes how results are presented in the .settings files. * Rework selection of nucleotides at overlapping positions with the same quality, in order to prevent potential data-races during tie-breaking, when running in multi-threaded mode. * Added support for reading FASTQ files using Windows-style newlines (\r\n). * AdapterRemoval will not print a warning to STDERR if the same command-line option is specified multiple times. * Reworked handling of barcodes to avoid unnecessary memory allocations, which would cause problems when using long barcodes. * Added support for combining output files; this is enabled using the --combined-output option, and ensures that all reads are written to the same file, or pair of files (for non-interleaved PE reads). The sequence of reads that fail are replaced with a single 'N' with quality score 0. * Fixed bug in the counting of singleton reads used in '.settings' files. * Fixed mis-placement of underscore when pretty printing adapter sequences that included barcodes. * Fixed misprinting of mate 2 adapter sequences in the .settings file; these would be printed in the reverse complemented orientation, relative to how they were specified on the command-line. ### Version 2.1.7 - 2016-03-11 * The mate number is now stripped from collapsed reads, where previously this would always be '\1' (if set). However, if meta-data is present in the reads, that found in the mate 1 read is retained. * The value used for --mate-separator is now written to the 'settings' file. * Improved 'make install'. This command now makes use of a PREFIX value to determine the installation destination (defaults to /usr/local), and includes the 'README.md' file and 'examples' folder in the installation. * Improved 'make test'. This command now attempts to download the required testing library automatically, using either wget or curl if available. ### Version 2.1.6 - 2016-03-03 * Added support for reading / writing interleaved FASTQ files; this is enabled by the options --interleaved-input and --interleaved-output, respectively, or by setting --interleaved option which implies both of the former options. See the README for an example. * Fixed bug in a sanity check meant to detect if the mate 1 and mate 2 files were of unequal length. This is now correctly detected in all cases. * Expanded README with information about reading / writing FASTQ files with different PHRED encodings / maximum quality scores. ### Version 2.1.5 - 2016-02-19 * Added the --mate-separator option, which specifies the character separating the mate number; by default this is '/', and AdapterRemoval will therefore identify mate numbers if read-names end with "/1" or "/2". * Fixed race condition which could result in premature termination when using --gzip or --bzip2 together with the --threads options. * Improved checks during compression and sanity checks following processing. ### Version 2.1.4 - 2016-02-09 * Fixed bug which could occasionally result in failure when bzip2 compression was enabled, by attempting to compress empty buffer. * The following was contributed by Hannes Pétur Eggertsson: * Wrapped code in 'ar' namespace, and made it possible to compile AdapterRemoval as a static library (via the command 'make static'), allowing it to be used as part of other projects. * Updated instructions for installing GTest library using new repository. * Fixed typos. ### Version 2.1.3 - 2015-12-25 * Added option --minadapteroverlap, which sets a minimum alignment length when carrying out trimming of single-end reads. The default (0) may result in an excess of false postiives around (1 - 2 bp long), which may be mitigated by running AdapterRemoval with '--minadapteroverlap 3'. * Greatly expanded README.md, adding several examples with test data included in the 'examples' folder, demonstrating common usage of the program. * Updated man-page with missing information and rewrote several parts. * Updated the help-text for several command-line options. * Avoid writing information to stdout, so that (SE) trimming can be piped. This can be accomplished by using the option --output1 /dev/stdout. * Fixed the --seed option, which was not properly applied during runtime. ### Version 2.1.2 - 2015-10-08 * Changed the way "full-length" and "truncated collapsed" reads are counted in the .settings file; previously, all collapsed reads were counted, even if these were subsequently discarded (due to the length). Now only retained reads are counted, matching the behavior of AdapterRemoval v1.x. * Added setup instructions when running 'make test' for the first time. ### Version 2.1.1 - 2015-09-14 * Fixed broken assert preventing the use of --adapter-list. * Fixed bug using --qualitybase-output for both input and output. ### Version 2.1.0 - 2015-09-08 Major changes: * Support for (transparently) reading and writing bzip2 files. * Parallelization of adapter trimming and identification using pthreads; the number of threads used is specified using --threads. Note that only one thread is allowed to perform IO (reads / writes) at a time, to prevent clobbering the disk, but compression (if enabled) is performed in parallel. * Support for combined demultiplexing and adapter-removal using the --barcode-list command-line option; when demultiplexing, the barcodes identified for a given read is added to the adapter sequence, in ordre to ensure correct trimming of the reads. * Features depending on external libraries (gzip, bzip2, and threading support) can be disabled in the Makefile on systems lacking these libraries. Other changes / bug-fixes: * Display currently specified --adapter1 / adapter2 sequences for comparison when attempting to infer adapter sequences. Only the first pair is used, if multiple adapter pairs are specified. * Sites with no majority-base during adapter-identification are set to N. * Fixed failure to read of barcode sequences (--5prime / --5prime-list). * Progress report now shows total number of reads processes, for both single ended and pair ended analyses. * FASTQ reads with Solexa scores are now output as Solexa scores by default, rather than Phred+64. Note that the program represents quality scores using Phred scores internally, resulting in a lossy conversion. It is therefore recommended to convert to Phred scores rather than use Solexa scores. ### Version 2.0.0 - 2014-03-10 Version 2.0.0 of AdapterRemoval is a near complete rewrite, with the goal of improved safety, increased speed, fixing a number of minor issues with previous versions of AdapterRemoval, and adding a few new features: Compatibility changes: * Command-line arguments --pcr1 and --pcr2 have been deprecated in favor of --adapter1 and --adapter2. While --pcr1 and --adapter1 are equivalent, --adapter2 expects the adapter sequence which may be observed in raw mate 2 reads, unlike --pcr2 which expected the sequence which could be observed in the reverse complement of mate 2 reads (cf. the README). * The use of --file1 and (optionally) --file2 is now required; reads will not be read from STDIN, nor written to STDOUT by default. To approximate the previous behavior, the following command may be used: $ AdapterRemoval --file1 /dev/stdin --output1 /dev/stdout * Per-read statistics of adapter / low-quality base trimming using --stats is no longer supported. Major changes: * Strict validation of input FASTQ records, to ensure that records are well formed, that quality scores fall within the expected range given the specified format/offset, and more. * Limited support for Solexa quality scores; these are converted to and saved as Phred+33 or Phred+64 encoded scores. * Improved handling of asymmetric read-pairs, in which the length of the mate 1 read differs from the length of the mate 2 read. * Significant improvements in performance, resulting in a ~5x increase in the rate of adapter trimming in basic version, and a ~20x increase in the rate of adapter trimming in the SSE enabled version (the default). * Support for multiple adapter sequences as well as multiple barcode sequences; AdapterRemoval will favor the highest scoring alignment, favoring longer alignments over shorter alignments with the same score, and favoring alignments with the fewest ambiguous bases (N) involved if the score and length is identical. * If --collapse is set in single-ended mode, "collapsed" reads will be identified using the same criteria as for paired-ended mode, i.e. requiring that at least --minalignmentlen bases overlap, and written to .collapsed and .collapsed.truncated. This allows for the identification of reads that are complete inserts. * Added the ability to identify adapter sequences for paired-ended reads, by identifying reads which extends past the ends of the template sequence, and extracting the adapters from these. * Added support for reading / writing gzipped compressed FASTQ files; if enabled (using the --gzip flag), the ".gz" extension is added to filenames, unless the filenames are explicitly specified by the user. * Length distributions are now calculated per read-type post-trimming (mate 1, mate 2, collapsed, etc.) and written to the .settings file. Other improvements / bug-fixes: * Barcodes may now contain Ns. * Fixed underestimation of error-probabilities during sequence collapse. * Fixed (futher) underestimation of error-probabilities of bases during collapsing, for conflicting base-calls with the same Phred score. * Fixed the maximum number of mismatches for alignments in the range of 6 .. 9 bases always being 1, even if --mm was set to 0. * Fixed the maximum number of mismatches for alignments being calculated based on the length of the alignment including ambiguous bases (N), thereby inflating the number of mismatches allowed for poor alignments. * Replaced use of lower bits of rand() calls with random(), as the former generates low entropy bits in that range on some (non-Linux) platforms. * Fixed well-aligned reads being discarded due to the minimum-length requirement after trimming not being counted as well-aligned, resulting in the total number of alignments not matching the total number of reads. * Fixed bug in shifts for PE reads, which was causing some alignments to be missed for adapter-only (i.e. no insert sequence) sequences. * Improved input validation and sanity checks for command-line parameters. * It is now possible to explicitly specify the RNG seed, to allow individual runs to be reproduced; the seed is also written to the .settings file. * Seed is now initialized using a mix of seconds and microseconds, instead of the current time in seconds, to reduce the risk of multiple instances spawed within a short timespan from using the same seed. * An (optional) progress report is printed during usage, incidating the run-time and number of reads processed. ### Version 1.5.4 - 2014-04-23 * Fixed bug in which collapsed reads would not be considered truncated if bases were trimmed from the 5' end. * Fixed bug in which the quality bases used for mate 2 during collapsing of overlapping read pairs made use of quality scores with a wrong orientation. * Reduced the amount of IO operations during trimming. ### Version 1.5.2 - 2013-10-22 Two changes to the program: * I have added a reference to the paper to both the man page and the help text. * I fixed a minor bug in the collapse code where two very low quality bases might give rise to a third low quality base being called. For example, a C with quality " and a T with quality ! would result in an A with quality #. This has been fixed so that the the result is now C with quality ". ### Version 1.5.0 - 2013-04-29 Small update: Due to user feedback, the program now outputs collapsed pairs in two files: One contains full-length collapsed pairs constituting the full insert, the other contains collapsed pairs that have been truncated due to low qualities or Ns in the reads. ### Version 1.4.0 - 2013-03-24 I have made some fixes to the program: * The program can now handle the use of '.' instead of 'N' to encode undefined nucleotides. * There was a typo in the adapter sequence used for PCR2! * Some minor changes to output etc. ### Version 1.3.0 - 2013-02-10 I have updated AdapterRemoval and released version 1.3. These changes are based on feedback from users of the program that had some very specific and well- founded suggestions. Some of these changes are minor, others will have more dramatic effects on the use of the program so please read these notes carefully: Minor changes: * I fixed an occasional segmentation fault. * Collapsed reads are now names "@M_...". * Collapsed reads are put in a separate file with extension ".collapsed". Important changes: * The sequences PCR1 and PCR2 are now used as-is without reverse- complementation. You have to make sure that the sequences you search for are correct. * The default PCR1 and PCR2 sequences are now: PCR1: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG PCR2: AATGATACGGCGACCACCGAGATCACACTCTTTCCCTACACGACGCTCTTCCGATCT * I have changed the way PCR1 and PCR2 are used to make the program consistent. Now, you always search for the sequence PCR1 in READ1 (whether single end or paired end), and you search for PCR2 in READ2. In single end mode, this corresponds to having an empty READ2 and ignore PCR2 as illustrated below: * For paired end data, PCR2-READ1 aligned to READ2-PCR1. * For single end data, READ1 aligned to PCR1. As always, please contact me with any questions or comments. Stinus ### Version 1.1.0 - 2012-05-01 * It is now possible to look for adapter in the 5' end of reads using the --5prime parameter. * Updated trimming of qualities. * Added option for discarding reads with too many gaps using --maxns max. * The programs handles lower vs upper case issues by translating all sequences to upper case. * The program now checks for inconsistent parameters. * Fixed some typographical issues with output. adapterremoval-2.3.1/LICENSE000066400000000000000000001045131350370616400155410ustar00rootroot00000000000000 GNU GENERAL PUBLIC LICENSE Version 3, 29 June 2007 Copyright (C) 2007 Free Software Foundation, Inc. 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But first, please read . adapterremoval-2.3.1/Makefile000066400000000000000000000155451350370616400162020ustar00rootroot00000000000000############################################################################### # Makefile options: Edit / comment / uncomment to change build behavior # # Installation destinations PREFIX := /usr/local # Default compilation flags CXXFLAGS := ${CXXFLAGS} -std=c++11 -O3 ## Optional features; comment out or set to value other than 'yes' to disable # Hide individual commands during build; only shows summaries instead. QUIET_BUILD := yes # Use of colored output during build COLOR_BUILD := yes # Debug build; adds warnings and debugging symbols DEBUG_BUILD := no # Include coverage instrumentation in build COVERAGE := no ############################################################################### # Makefile internals. Normally you do not need to touch these. # Libraries required by AdapterRemoval LIBRARIES := -pthread -lz -lbz2 # Build directory; modified depending on build options BDIR := build/main ifeq ($(strip ${QUIET_BUILD}),yes) QUIET := @ endif ifeq ($(strip ${COLOR_BUILD}),yes) COLOR_YELLOW := "\033[0;33m" COLOR_GREEN := "\033[0;32m" COLOR_CYAN := "\033[0;36m" COLOR_END := "\033[0m" endif ifeq ($(strip ${COVERAGE}), yes) $(info Building AdapterRemoval with coverage instrumentation: yes) CXXFLAGS := ${CXXFLAGS} --coverage DEBUG_BUILD := yes else $(info Building AdapterRemoval with coverage instrumentation: no) endif ifeq ($(strip ${DEBUG_BUILD}), yes) $(info Building AdapterRemoval with debug information: yes) CXXFLAGS := ${CXXFLAGS} -g -pedantic -Wall -Wextra -Wcast-align -Wcast-qual \ -Wctor-dtor-privacy -Wdisabled-optimization -Wformat=2 -Winit-self \ -Wold-style-cast -Woverloaded-virtual -Wredundant-decls -Wsign-promo \ -Wstrict-overflow=2 -Wswitch-default -Wundef -Weffc++ -Wdeprecated else $(info Building AdapterRemoval with debug information: no) endif PROG := AdapterRemoval LIBNAME := libadapterremoval LIBOBJS := $(BDIR)/adapterset.o \ $(BDIR)/alignment.o \ $(BDIR)/alignment_tables.o \ $(BDIR)/argparse.o \ $(BDIR)/barcode_table.o \ $(BDIR)/debug.o \ $(BDIR)/demultiplex.o \ $(BDIR)/fastq.o \ $(BDIR)/fastq_enc.o \ $(BDIR)/fastq_io.o \ $(BDIR)/linereader.o \ $(BDIR)/linereader_joined.o \ $(BDIR)/main_adapter_id.o \ $(BDIR)/main_adapter_rm.o \ $(BDIR)/main_demultiplex.o \ $(BDIR)/managed_writer.o \ $(BDIR)/scheduler.o \ $(BDIR)/strutils.o \ $(BDIR)/threads.o \ $(BDIR)/timer.o \ $(BDIR)/trimmed_reads.o \ $(BDIR)/userconfig.o OBJS := ${LIBOBJS} $(BDIR)/main.o DFILES := $(OBJS:.o=.deps) .PHONY: all install clean test clean_tests static regression docs all: build/$(PROG) everything: all static test regression docs # Clean clean: clean_tests clean_docs @echo $(COLOR_GREEN)"Cleaning ..."$(COLOR_END) $(QUIET) rm -f build/$(PROG) build/$(LIBNAME).a $(QUIET) rm -rvf build/regression $(QUIET) rm -rvf $(BDIR) # Install install: build/$(PROG) @echo $(COLOR_GREEN)"Installing AdapterRemoval .."$(COLOR_END) @echo $(COLOR_GREEN)" .. binary into ${PREFIX}/bin/"$(COLOR_END) $(QUIET) mkdir -p ${PREFIX}/bin/ $(QUIET) mv -f build/$(PROG) ${PREFIX}/bin/ $(QUIET) chmod a+x ${PREFIX}/bin/$(PROG) @echo $(COLOR_GREEN)" .. man-page into ${PREFIX}/share/man/man1/"$(COLOR_END) $(QUIET) mkdir -p ${PREFIX}/share/man/man1/ $(QUIET) cp -a $(PROG).1 ${PREFIX}/share/man/man1/ $(QUIET) chmod a+r ${PREFIX}/share/man/man1/$(PROG).1 @echo $(COLOR_GREEN)" .. README into ${PREFIX}/share/adapterremoval/"$(COLOR_END) $(QUIET) mkdir -p ${PREFIX}/share/adapterremoval/ $(QUIET) cp -a README.md ${PREFIX}/share/adapterremoval/ $(QUIET) chmod a+r ${PREFIX}/share/adapterremoval/README.md @echo $(COLOR_GREEN)" .. examples into ${PREFIX}/share/adapterremoval/examples/"$(COLOR_END) $(QUIET) mkdir -p ${PREFIX}/share/adapterremoval/examples/ $(QUIET) cp -a examples/*.* ${PREFIX}/share/adapterremoval/examples/ $(QUIET) chmod a+r ${PREFIX}/share/adapterremoval/examples/*.* static: build/$(LIBNAME).a # Object files $(BDIR)/%.o: src/%.cpp @echo $(COLOR_CYAN)"Building $@ from $<"$(COLOR_END) $(QUIET) mkdir -p $(BDIR) $(QUIET) $(CXX) $(CXXFLAGS) -pthread -c -o $@ $< $(QUIET) $(CXX) $(CXXFLAGS) -w -MM -MT $@ -MF $(@:.o=.deps) $< # Executable build/$(PROG): $(OBJS) @echo $(COLOR_GREEN)"Linking executable $@"$(COLOR_END) $(QUIET) $(CXX) $(CXXFLAGS) ${LDFLAGS} $^ ${LIBRARIES} -o $@ # Static library build/$(LIBNAME).a: $(LIBOBJS) @echo $(COLOR_GREEN)"Linking static library $@"$(COLOR_END) $(AR) rcs build/$(LIBNAME).a $(LIBOBJS) # Automatic header depencencies -include $(DFILES) # # Unit testing # TEST_DIR := build/tests TEST_OBJS := $(TEST_DIR)/main_test.o \ $(TEST_DIR)/debug.o \ $(TEST_DIR)/alignment.o \ $(TEST_DIR)/alignment_tables.o \ $(TEST_DIR)/alignment_test.o \ $(TEST_DIR)/argparse.o \ $(TEST_DIR)/argparse_test.o \ $(TEST_DIR)/barcodes_test.o \ $(TEST_DIR)/barcode_table.o \ $(TEST_DIR)/fastq.o \ $(TEST_DIR)/fastq_test.o \ $(TEST_DIR)/fastq_enc.o \ $(TEST_DIR)/fastq_enc_test.o \ $(TEST_DIR)/strutils.o \ $(TEST_DIR)/strutils_test.o TEST_DEPS := $(TEST_OBJS:.o=.deps) TEST_CXXFLAGS := -Isrc -DAR_TEST_BUILD -g test: $(TEST_DIR)/main @echo $(COLOR_GREEN)"Running unit tests"$(COLOR_END) $(QUIET) $(TEST_DIR)/main clean_tests: @echo $(COLOR_GREEN)"Cleaning tests ..."$(COLOR_END) $(QUIET) rm -rvf $(TEST_DIR) $(TEST_DIR)/main: $(TEST_OBJS) @echo $(COLOR_GREEN)"Linking executable $@"$(COLOR_END) $(QUIET) $(CXX) $(CXXFLAGS) ${LIBRARIES} $^ -o $@ $(TEST_DIR)/%.o: tests/unit/%.cpp @echo $(COLOR_CYAN)"Building $@ from $<"$(COLOR_END) $(QUIET) mkdir -p $(TEST_DIR) $(QUIET) $(CXX) $(CXXFLAGS) $(TEST_CXXFLAGS) -c -o $@ $< $(QUIET) $(CXX) $(CXXFLAGS) $(TEST_CXXFLAGS) -w -MM -MT $@ -MF $(@:.o=.deps) $< $(TEST_DIR)/%.o: src/%.cpp @echo $(COLOR_CYAN)"Building $@ from $<"$(COLOR_END) $(QUIET) mkdir -p $(TEST_DIR) $(QUIET) $(CXX) $(CXXFLAGS) $(TEST_CXXFLAGS) -c -o $@ $< $(QUIET) $(CXX) $(CXXFLAGS) $(TEST_CXXFLAGS) -w -MM -MT $@ -MF $(@:.o=.deps) $< # # Validation # VALIDATION_BDIR=./build/regression VALIDATION_SDIR=./tests/regression regression: build/$(PROG) @echo $(COLOR_GREEN)"Running regression tests"$(COLOR_END) @mkdir -p $(VALIDATION_BDIR) @$(VALIDATION_SDIR)/run $(VALIDATION_BDIR) $(VALIDATION_SDIR) # Automatic header dependencies for tests -include $(TEST_DEPS) # # Documentation # SPHINXOPTS = -n -q SPHINXBUILD = sphinx-build docs: $(QUIET) @$(SPHINXBUILD) -M html docs build/docs $(SPHINXOPTS) $(QUIET) @$(SPHINXBUILD) -M man docs build/docs $(SPHINXOPTS) $(QUIET) cp -v "build/docs/man/AdapterRemoval.1" . clean_docs: @echo $(COLOR_GREEN)"Cleaning documentation ..."$(COLOR_END) $(QUIET) rm -rvf build/docs adapterremoval-2.3.1/README.md000066400000000000000000000500301350370616400160050ustar00rootroot00000000000000# AdapterRemoval [![Travis](https://img.shields.io/travis/MikkelSchubert/adapterremoval/master.svg)](https://travis-ci.org/MikkelSchubert/adapterremoval) [![Coveralls](https://img.shields.io/coveralls/MikkelSchubert/adapterremoval.svg)](https://coveralls.io/github/MikkelSchubert/adapterremoval) This program searches for and removes remnant adapter sequences from High-Throughput Sequencing (HTS) data and (optionally) trims low quality bases from the 3' end of reads following adapter removal. AdapterRemoval can analyze both single end and paired end data, and can be used to merge overlapping paired-ended reads into (longer) consensus sequences. Additionally, the AdapterRemoval may be used to recover a consensus adapter sequence for paired-ended data, for which this information is not available. For comments, suggestions and feedback please contact Mikkel Schubert (MikkelSch@gmail.com) and Stinus Lindgreen (stinus@binf.ku.dk). If you use AdapterRemoval v2, then please cite the paper: Schubert, Lindgreen, and Orlando (2016). AdapterRemoval v2: rapid adapter trimming, identification, and read merging. BMC Research Notes, 12;9(1):88 http://bmcresnotes.biomedcentral.com/articles/10.1186/s13104-016-1900-2 AdapterRemoval was originally published in Lindgreen 2012: Lindgreen (2012): AdapterRemoval: Easy Cleaning of Next Generation Sequencing Reads, BMC Research Notes, 5:337 http://www.biomedcentral.com/1756-0500/5/337/ ## Overview of major features - Trimming of adapters sequences from single-end and paired-end FASTQ reads. - Trimming of multiple, different adapters or adapter pairs. - Demultiplexing of single or double indexed reads, with or without trimming of adapter sequences. - Reconstruction of adapter sequences from paired-end reads, by the pairwise alignment of reads in the absence of a known adapter sequence. - Merging of overlapping read-pairs into higher-quality consensus sequences. - Multi-threading of all operations for increased throughput. - Reading and writing of gzip and bzip2 compressed files. - Reading and writing of interleaved FASTQ files. ## Installation ### Installation with [Conda](https://conda.io/docs/) If you have Conda [installed on your system](https://conda.io/miniconda.html): ``` conda install -c bioconda adapterremoval ``` ### Manual installation To install, first download and unpack the newest release from GitHub: $ wget -O adapterremoval-2.1.7.tar.gz https://github.com/MikkelSchubert/adapterremoval/archive/v2.1.7.tar.gz $ tar xvzf adapterremoval-2.1.7.tar.gz $ cd adapterremoval-2.1.7 or $ git clone https://github.com/MikkelSchubert/adapterremoval.git $ cd adapterremoval To compile, run $ make The resulting binary and man page is located in the "build" folder. To install, run $ sudo make install It is also possible to compile AdapterRemoval as a static library: $ sudo make static Note that AdapterRemoval requires that the zlib library and headers (www.zlib.net) are installed, that the bzlib2 library and headers are installed, and that the compiler used supports c++11. Please refer to your operating system documentation for installation instructions. ## Documentation For detailed program usage, please refer to the manual page. If AdapterRemoval has been installed, this may be accessed using the command "man AdapterRemoval". If AdapterRemoval has not been installed, the manual page may be read using the command "man build/AdapterRemoval.1" in the source folder once "make" has been run. Alternatively, the manual may be read online: https://github.com/MikkelSchubert/adapterremoval/blob/master/AdapterRemoval.pod ## Examples The following examples make use of the data included in the 'examples' folder: ### Trimming single-end reads The following command removes adapters from the file 'reads\_1.fq' trims both Ns and low quality bases from the reads, and gzip compresses the resulting files. The --basename option is used to specify the prefix for output files. $ AdapterRemoval --file1 reads_1.fq --basename output_single --trimns --trimqualities --gzip Since --gzip and --basename is specified, the trimmed FASTQ reads are written to 'output_single.truncated.gz', the discarded FASTQ reads are written to 'output_single.discarded.gz', and settings and summary statistics are written to 'output_single.settings'. Note that by default, AdapterRemoval does not require a minimum number of bases overlapping with the adapter sequence, before reads are trimmed. This may result in an excess of very short (1 - 3 bp) 3' fragments being falsely identified as adapter sequences, and trimmed. This behavior may be changed using the --minadapteroverlap option, which allows the specification of a minimum number of bases (excluding Ns) that must be aligned to carry trimming. For example, use --minadapteroverlap 3 to require an overlap of at least 3 bp. ### Trimming paired-end reads The following command removes adapters from a paired-end reads, where the mate 1 and mate 2 reads are kept in files 'reads\_1.fq' and 'reads\_2.fq', respectively. The reads are trimmed for both Ns and low quality bases, and overlapping reads (at least 11 nucleotides, per default) are merged (collapsed): $ AdapterRemoval --file1 reads_1.fq --file2 reads_2.fq --basename output_paired --trimns --trimqualities --collapse This command generates the files 'output_paired.pair1.truncated' and 'output_paired.pair2.truncated', which contain trimmed pairs of reads which were not collapsed, 'output_paired.singleton.truncated' containing reads where one mate was discarded, 'output_paired.collapsed' containing merged reads, and 'output_paired.collapsed.truncated' containing merged reads that have been trimmed due to the --trimns or --trimqualities options. Finally, the 'output_paired.discarded' and 'output_paired.settings' files correspond to those of the single-end run. ### Multiple input FASTQ files More than one input file may be specified for mate 1 and mate 2 reads. This is accomplished simply by listing more than one file after the --file1 and the --file2 options. For single-end reads: $ AdapterRemoval --file1 reads_1a.fq reads_1b.fq reads_1c.fq And for paired-end reads: $ AdapterRemoval --file1 reads_1a.fq reads_1b.fq reads_1c.fq --file2 reads_2a.fq reads_2b.fq reads_2c.fq AdapterRemoval will process these files as if they had been concatenated into a single file or pair of files prior to invoking AdapterRemoval. For paired reads, the files must be specified in the same order for --file1 and --file2. ### Interleaved FASTQ reads AdapterRemoval is able to read and write paired-end reads stored in a single, so-called interleaved FASTQ file (one pair at a time, first mate 1, then mate 2). This is accomplished by specifying the location of the file using --file1 and *also* setting the --interleaved command-line option: $ AdapterRemoval --interleaved --file1 interleaved.fq --basename output_interleaved Other than taking just a single input file, this mode operates almost exactly like paired end trimming (as described above); the mode differs only in that paired reads are not written to a 'pair1' and a 'pair2' file, but instead these are instead written to a single, interleaved file, named 'paired'. The location of this file is controlled using the --output1 option. Enabling either reading or writing of interleaved FASTQ files, both not both, can be accomplished by specifying the either of the --interleaved-input and --interleaved-output options, both of which are enabled by the --interleaved option. ### Combining FASTQ output By default, AdapterRemoval will create one output file for each mate, one file for discarded reads, and (in PE mode) one file paired reads where one mate has been discarded, and (optionally) two files for collapsed reads. Alternatively, these files may be combined using the --combined-output, in which case all output is directed to the mate 1 and (in PE mode) to the mate 2 file. In cases where reads are discarded due to trimming to due to being collapsed into a single sequence, the sequence and quality scores of the discarded read is replaced with a single 'N' with base-quality 0. This option may be combined with --interleaved / --interleaved-output, to write a single, interleaved file in paired-end mode. ### Different quality score encodings By default, AdapterRemoval expects the quality scores in FASTQ reads to be Phred+33 encoded, meaning that the error probabilities are encoded as (char)('!' - 10 * log10(p)). Most data will be encoded using Phred+33, but Phred+64 and 'Solexa' encoded quality scores are also supported. These are selected by specifying the --qualitybase command-line option (specifying either '33', '64', or 'solexa'): $ AdapterRemoval --qualitybase 64 --file1 reads_q64.fq --basename output_phred_64 By default, reads are written using the *same* encoding as the input. If a different encoding is desired, this may be accomplished using the --qualitybase-output option:: $ AdapterRemoval --qualitybase 64 --qualitybase-output 33 --file1 reads_q64.fq --basename output_phred_33 Note furthermore that AdapterRemoval by default only expects quality scores in the range 0 - 41 (or -5 to 41 in the case of Solexa encoded scores). If input data using a different maximum quality score is to be processed, or if the desired maximum quality score of collapsed reads is greater than 41, then this limit may be increased using the --qualitymax option:: $ AdapterRemoval --qualitymax 50 --file1 reads_1.fq --file2 reads_2.fq --collapse --basename output_collapsed_q50 For a detailed overview of Phred encoding schemes currently and previously in use, see e.g. the Wikipedia article on the subject: https://en.wikipedia.org/wiki/FASTQ_format#Encoding ### Trimming paired-end reads with multiple adapter pairs It is possible to trim data that contains multiple adapter pairs, by providing a one or two-column table containing possible adapter combinations (for single-end and paired-end trimming, respectively; see e.g. examples/adapters.txt): $ cat adapters.txt AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCACCTAATCTCGTATGCCGTCTTCTGCTTG AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT AAACTTGCTCTGTGCCCGCTCCGTATGTCACAACAGTGCGTGTATCACCTCAATGCAGGACTCA GATCGGGAGTAATTTGGAGGCAGTAGTTCGTCGAAACTCGGAGCGTCTTTAGCAGGAG CTAATTTGCCGTAGCGACGTACTTCAGCCTCCAGGAATTGGACCCTTACGCACACGCATTCATG TACCGTGAAAGGTGCGCTTAGTGGCATATGCGTTAAGAGCTAGGTAACGGTCTGGAGG GTTCATACGACGACGACCAATGGCACACTTATCCGGTACTTGCGTTTCAATGCGCATGCCCCAT TAAGAAACTCGGAGTTTGGCCTGCGAGGTAGCTTGGGTGTTATGAAGAACGGCATGCG CCATGCCCCGAAGATTCCTATACCCTTAAGGTCGCAATTGTTCGAGTAAGCTGTACGCGCCCAT GTTGCATTGACCCGAAGGGCTCGATGTTTAGGGAGGTCAGAAGTTGAGCGGGTTCAAA This table is then specified using the --adapter-list option: $ AdapterRemoval --file1 reads_1.fq --file2 reads_2.fq --basename output_multi --trimns --trimqualities --collapse --adapter-list adapters.txt The resulting .summary file contains an overview of how frequently each adapter (pair) was used. Note that in the case of paired-end adapters, AdapterRemoval considers only the combinations of adapters specified in the table, one combination per row. For single-end trimming, only the first column of the table file is required, and the list may therefore take the form of a file containing one sequence per line. ### Identifying adapter sequences from paired-ended reads If we did not know the adapter sequences for the 'reads\_*.fq' files, AdapterRemoval may be used to generate a consensus adapter sequence based on fragments identified as belonging to the adapters through pairwise alignments of the reads, provided that the data set contains only a single adapter sequence (not counting differences in index sequences). In the following example, the identified adapters corresponds to the default adapter sequences with a poly-A tail resulting from sequencing past the end of the insert + templates. It is not necessary to specify this tail when using the --adapter1 or --adapter2 command-line options. The characters shown under each of the consensus sequences represent the Phred-encoded fraction of bases that differ from the consensus base, such that a high Phred score indicates a strong consensus. In the examples below, adapter 1 is observed to contain the index CACCTA: $ AdapterRemoval --identify-adapters --file1 reads_1.fq --file2 reads_2.fq Attemping to identify adapter sequences ... Processed a total of 1,000 reads in 0.0s; 129,000 reads per second on average ... Found 394 overlapping pairs ... Of which 119 contained adapter sequence(s) ... Printing adapter sequences, including poly-A tails: --adapter1: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG ||||||||||||||||||||||||||||||||||******|||||||||||||||||||||||| Consensus: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCACCTAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAA Quality: 55200522544444/4411330333330222222/1.1.1.1111100-00000///..+....--*-)),,+++++++**(('%%%$ Top 5 most common 9-bp 5'-kmers: 1: AGATCGGAA = 96.00% (96) 2: AGATGGGAA = 1.00% (1) 3: AGCTCGGAA = 1.00% (1) 4: AGAGCGAAA = 1.00% (1) 5: AGATCGGGA = 1.00% (1) --adapter2: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT |||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Consensus: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA Quality: 525555555144141441430333303.2/22-2/-1..11111110--00000///..+....--*-),,,+++++++**(%'%%%$ Top 5 most common 9-bp 5'-kmers: 1: AGATCGGAA = 100.00% (100) No files are generated from running the adapter identification step. The consensus sequences inferred are compared to those specified using the --adapter1 and --adapter2 command-line options, or with the default values for these if no values have been given (as in this case). Pipes (|) indicate matches between the provided sequences and the consensus sequence, and "*" indicate the presence of unspecified bases (Ns). ### Demultiplexing and adapter-trimming As of version 2.1, AdapterRemoval supports simultaneous demultiplexing and adapter trimming; demultiplexing is carried out using a simple comparison between the specified barcode (a sequence of A, C, G, and T) and the first N bases of the mate 1 read, where N is the length of the barcode. Demultiplexing of double-indexed sequences is also supported, in which case two barcodes must be specified for each sample. The first barcode is then compared to first N_1 bases of the mate 1 read, and the second barcode is compared to the first N_2 bases of the mate 2 read. By default, this comparison requires a perfect match. Reads identified as containing a specific barcode(s) are then trimmed using adapter sequences including the barcode(s) as necessary. Reads for which no (pair of) barcodes matched are written to a separate file or pair of files (for paired end reads). Demultiplexing is enabled by creating a table of barcodes, the first column of which species the sample name (using characters [a-zA-Z0-9_]) and the second and (optional) third columns specifies the barcode sequences expected at the 5' termini of mate 1 and mate 2 reads, respectively. For example, a table of barcodes from a double-indexed run might be as follows (see examples/barcodes.txt): $ cat barcodes.txt sample_1 ATGCGGA TGAATCT sample_2 ATGGATT ATAGTGA sample_7 CAAAACT TCGCTGC In the case of single-read reads, only the first two columns are required. AdapterRemoval is invoked with the --barcode-list option, specifying the path to this table: $ AdapterRemoval --file1 demux_1.fq --file2 demux_2.fq --basename output_demux --barcode-list barcodes.txt This generates a set of output files for each sample specified in the barcode table, using the basename (--basename) as the prefix, followed by a dot and the sample name, followed by a dot and the default name for a given file type. For example, the output files for sample_2 would be output_demux.sample_2.discarded output_demux.sample_2.pair1.truncated output_demux.sample_2.pair2.truncated output_demux.sample_2.settings output_demux.sample_2.singleton.truncated The settings files generated for each sample summarizes the reads for that sample only; in addition, a basename.settings file is generated which summarizes the number and proportion of reads identified as belonging to each sample. The maximum number of mismatches allowed when comparing barocdes is controlled using the options --barcode-mm, --barcode-mm-r1, and --barcode-mm-r2, which specify the maximum number of mismatches total, and the maximum number of mismatches for the mate 1 and mate 2 barcodes respectively. Thus, if mm_1(i) and mm_2(i) represents the number of mismatches observed for barcode-pair i for a given pair of reads, these options require that 1. mm_1(i) <= --barcode-mm-r1 2. mm_2(i) <= --barcode-mm-r2 3. mm_1(i) + mm_2(i) <= --barcode-mm ### Demultiplexing mode As of version 2.2, AdapterRemoval can furthermore be used to demultiplex reads, without carrying out other forms of adapter trimming. This is accomplished by specifying the --demultiplex-only option: $ AdapterRemoval --file1 demux_1.fq --file2 demux_2.fq --basename output_only_demux --barcode-list barcodes.txt --demultiplex-only Options listed under "TRIMMING SETTINGS" (see 'AdapterRemoval --help') do not apply to this mode, but compression (--gzip, --bzip2), multi-threading (--threads), interleaving (--interleaved, etc.) and other such options may be used in conjunction with --demultiplex-only. AdapterRemoval will generate a '.settings' file for each sample listed in the --barcode-list file, along with the adapter-sequences that should be used when trimming reads for a given sample. These adapters correspond to the adapters that were specified when running AdapterRemoval in demultiplexing mode, with the barcode prefixed as appropriate. An underscore is used to demarcate the location at which the barcode ends and the adapter beings. It is important to use these, updated, adapter sequences when trimming the demultiplexed reads, to avoid the inclusion of barcode sequences in reads extending past the 3' termini of the DNA template sequence. ## A note on specifying adapter sequences Please note that the --pcr1 and --pcr2 options used with AdapterRemoval v1.x have been deprecated in favor of options --adapter1 and --adapter2. For both --adapter1 and --adapter2 the adapter sequence are expected to be observed in the raw mate 1 and mate 2 reads respectively, exactly as specified on the command-line, which corresponds to the behavior of most adapter trimming programs. Default adapter #1: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Default adapter #2: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT Assuming these were the adapters used to generate our data, we should therefore see these in the FASTQ files (assuming that the read lengths are sufficiently long and that insert sizes are sufficently short), typically followed by a low-quality A-tail, when ignoring any difference in case and treating Ns as wildcards: $ grep -i "AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC......ATCTCGTATGCCGTCTTCTGCTTG" file1.fq AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCGATGAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAACAAGAAT CTGGAGTTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCGATGAATCTCGTATGCCGTCTTCTGCTTGAAAAAAA GGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCGATGAATCTCGTATGCCGTCTTCTGCTTGCAAATTGAAAACAC ... $ grep -i "AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT" file2.fq CAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTCAAAAAAAGAAAAACATCTTG GAACTCCAGAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTCAAAAAAAATAGA GAACTAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTCAAAAACATAAGACCTA ... The options --pcr1 and --adapter1 are functionally equivalent, while the option --pcr2 expects the reverse complement of the --adapter2 sequence. Thus, the default for --pcr2 is AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, the reverse complement of the default for --adapter2. adapterremoval-2.3.1/benchmark/000077500000000000000000000000001350370616400164625ustar00rootroot00000000000000adapterremoval-2.3.1/benchmark/README.md000066400000000000000000000050161350370616400177430ustar00rootroot00000000000000=========================== AdapterRemoval - Benchmarks =========================== Running the 'benchmark.sh' script from the 'benchmarks' folder will execute one or more sets of analyses, after checking that all required software is available in the ./bin/ folder. The following software is expected: - AdapterRemoval v1.5.4, located at 'bin/AdapterRemoval-1.5.4' - AdapterRemoval v2.1.0, located at 'bin/AdapterRemoval-2.1.0' Source: https://github.com/MikkelSchubert/adapterremoval - leeHom rev. dfca9e6, located at 'bin/leeHom_patched' Source: https://github.com/grenaud/leeHom Apply patches/leeHom.patch - Skewer v0.1.127, located at 'bin/skewer' Source: https://github.com/relipmoc/skewer - AlienTrimmer v0.4.0, located at 'bin/AlienTrimmer' Source: ftp://ftp.pasteur.fr/pub/GenSoft/projects/AlienTrimmer/ Note: Compile AlienTrimmer using GCJ! - Scythe 0.991, located at 'bin/scythe' Source: https://github.com/vsbuffalo/scythe - Cutadapt 1.8.3, located at 'bin/cutadapt' Source: https://code.google.com/p/cutadapt/ - FASTQ-MCF v1.1.2, located at 'bin/fastq-mcf' Source: https://code.google.com/p/ea-utils/ - Flexbar v2.5, located at 'bin/flexbar' Source: http://sourceforge.net/projects/flexbar/ - pIRS v1.1.1, located at 'bin/pirs_patched' Source: ftp://ftp.genomics.org.cn/pub/pIRS/ Apply patches/pIRS_111.patch - Trimmomatic v0.33, located at 'bin/trimmomatic-0.33.jar' Source: http://www.usadellab.org/cms/?page=trimmomatic - PEAT rev. 4e9ebf3, located at './bin/PEAT' Source: https://github.com/jhhung/PEAT - PEAR 0.9.6, located at 'bin/pear_patched' Source: http://sco.h-its.org/exelixis/web/software/pear/ Apply patches/pear.patch - Minion (from Kraken), located at 'bin/minion' Source: http://www.ebi.ac.uk/research/enright/software/kraken Additionally, the script expects a Java JRE ('bin/java') and the GNU 'time' command (located in PATH). As noted above, patches are supplied for the following programs: - leeHom: Disable gzip-compression and mark merged reads with "M_", to simplify analysis. - PEAR: Marks merged reads with "M_", to simplify processing. - pIRS: Adds support for user supplied adapter sequences and barcodes, allow zero length inserts. To process results generated by 'benchmark.sh', use the following scripts: - scripts/tabulate.py, call with arguments 'basic' or 'throughput' on the tables written to 'results/', for MCC and other statistics, and for data- processing throughput, respectively. adapterremoval-2.3.1/benchmark/adapters/000077500000000000000000000000001350370616400202655ustar00rootroot00000000000000adapterremoval-2.3.1/benchmark/adapters/adapter_1.fasta000066400000000000000000000001201350370616400231360ustar00rootroot00000000000000>mate1_adapter AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCACCTAATCTCGTATGCCGTCTTCTGCTTG adapterremoval-2.3.1/benchmark/adapters/adapter_1.pairs000066400000000000000000000001031350370616400231570ustar00rootroot00000000000000N AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCACCTAATCTCGTATGCCGTCTTCTGCTTG adapterremoval-2.3.1/benchmark/adapters/adapter_1.txt000066400000000000000000000001011350370616400226560ustar00rootroot00000000000000AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCACCTAATCTCGTATGCCGTCTTCTGCTTG adapterremoval-2.3.1/benchmark/adapters/adapter_2.fasta000066400000000000000000000001111350370616400231370ustar00rootroot00000000000000>mate2_adapter AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTadapterremoval-2.3.1/benchmark/adapters/adapter_2.txt000066400000000000000000000000731350370616400226670ustar00rootroot00000000000000AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT adapterremoval-2.3.1/benchmark/adapters/adapters.fasta000066400000000000000000000002221350370616400231040ustar00rootroot00000000000000>adapter/1 AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCACCTAATCTCGTATGCCGTCTTCTGCTTG >adapter/2 AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT adapterremoval-2.3.1/benchmark/adapters/mixed.fasta000066400000000000000000000014241350370616400224140ustar00rootroot00000000000000>adapter_orig/1 AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCACCTAATCTCGTATGCCGTCTTCTGCTTG >adapter_orig/2 AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT >adapter_rng_1/1 AAACTTGCTCTGTGCCCGCTCCGTATGTCACAACAGTGCGTGTATCACCTCAATGCAGGACTCA >adapter_rng_1/2 GATCGGGAGTAATTTGGAGGCAGTAGTTCGTCGAAACTCGGAGCGTCTTTAGCAGGAG >adapter_rng_2/1 CTAATTTGCCGTAGCGACGTACTTCAGCCTCCAGGAATTGGACCCTTACGCACACGCATTCATG >adapter_rng_2/2 TACCGTGAAAGGTGCGCTTAGTGGCATATGCGTTAAGAGCTAGGTAACGGTCTGGAGG >adapter_rng_3/1 GTTCATACGACGACGACCAATGGCACACTTATCCGGTACTTGCGTTTCAATGCGCATGCCCCAT >adapter_rng_3/2 TAAGAAACTCGGAGTTTGGCCTGCGAGGTAGCTTGGGTGTTATGAAGAACGGCATGCG >adapter_rng_4/1 CCATGCCCCGAAGATTCCTATACCCTTAAGGTCGCAATTGTTCGAGTAAGCTGTACGCGCCCAT >adapter_rng_4/2 GTTGCATTGACCCGAAGGGCTCGATGTTTAGGGAGGTCAGAAGTTGAGCGGGTTCAAA adapterremoval-2.3.1/benchmark/adapters/mixed.table000066400000000000000000000011541350370616400224050ustar00rootroot00000000000000AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCACCTAATCTCGTATGCCGTCTTCTGCTTG AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT AAACTTGCTCTGTGCCCGCTCCGTATGTCACAACAGTGCGTGTATCACCTCAATGCAGGACTCA GATCGGGAGTAATTTGGAGGCAGTAGTTCGTCGAAACTCGGAGCGTCTTTAGCAGGAG CTAATTTGCCGTAGCGACGTACTTCAGCCTCCAGGAATTGGACCCTTACGCACACGCATTCATG TACCGTGAAAGGTGCGCTTAGTGGCATATGCGTTAAGAGCTAGGTAACGGTCTGGAGG GTTCATACGACGACGACCAATGGCACACTTATCCGGTACTTGCGTTTCAATGCGCATGCCCCAT TAAGAAACTCGGAGTTTGGCCTGCGAGGTAGCTTGGGTGTTATGAAGAACGGCATGCG CCATGCCCCGAAGATTCCTATACCCTTAAGGTCGCAATTGTTCGAGTAAGCTGTACGCGCCCAT GTTGCATTGACCCGAAGGGCTCGATGTTTAGGGAGGTCAGAAGTTGAGCGGGTTCAAA adapterremoval-2.3.1/benchmark/adapters/mixed_1.fasta000066400000000000000000000006311350370616400226330ustar00rootroot00000000000000>adapter_orig/1 AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCACCTAATCTCGTATGCCGTCTTCTGCTTG >adapter_rng_1/1 AAACTTGCTCTGTGCCCGCTCCGTATGTCACAACAGTGCGTGTATCACCTCAATGCAGGACTCA >adapter_rng_2/1 CTAATTTGCCGTAGCGACGTACTTCAGCCTCCAGGAATTGGACCCTTACGCACACGCATTCATG >adapter_rng_3/1 GTTCATACGACGACGACCAATGGCACACTTATCCGGTACTTGCGTTTCAATGCGCATGCCCCAT >adapter_rng_4/1 CCATGCCCCGAAGATTCCTATACCCTTAAGGTCGCAATTGTTCGAGTAAGCTGTACGCGCCCAT adapterremoval-2.3.1/benchmark/adapters/mixed_1.txt000066400000000000000000000005051350370616400223540ustar00rootroot00000000000000AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCACCTAATCTCGTATGCCGTCTTCTGCTTG AAACTTGCTCTGTGCCCGCTCCGTATGTCACAACAGTGCGTGTATCACCTCAATGCAGGACTCA CTAATTTGCCGTAGCGACGTACTTCAGCCTCCAGGAATTGGACCCTTACGCACACGCATTCATG GTTCATACGACGACGACCAATGGCACACTTATCCGGTACTTGCGTTTCAATGCGCATGCCCCAT CCATGCCCCGAAGATTCCTATACCCTTAAGGTCGCAATTGTTCGAGTAAGCTGTACGCGCCCAT adapterremoval-2.3.1/benchmark/adapters/mixed_2.txt000066400000000000000000000004471350370616400223620ustar00rootroot00000000000000AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT GATCGGGAGTAATTTGGAGGCAGTAGTTCGTCGAAACTCGGAGCGTCTTTAGCAGGAG TACCGTGAAAGGTGCGCTTAGTGGCATATGCGTTAAGAGCTAGGTAACGGTCTGGAGG TAAGAAACTCGGAGTTTGGCCTGCGAGGTAGCTTGGGTGTTATGAAGAACGGCATGCG GTTGCATTGACCCGAAGGGCTCGATGTTTAGGGAGGTCAGAAGTTGAGCGGGTTCAAA adapterremoval-2.3.1/benchmark/benchmark.sh000066400000000000000000001141641350370616400207570ustar00rootroot00000000000000#!/bin/bash # # Copyright (c) 2015 Mikkel Schubert # # Permission is hereby granted, free of charge, to any person obtaining a copy # of this software and associated documentation files (the "Software"), to deal # in the Software without restriction, including without limitation the rights # to use, copy, modify, merge, publish, distribute, sublicense, and/or sell # copies of the Software, and to permit persons to whom the Software is # furnished to do so, subject to the following conditions: # # The above copyright notice and this permission notice shall be included in # all copies or substantial portions of the Software. # # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR # IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, # FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE # AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER # LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, # OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE # SOFTWARE. set -o nounset # Fail on unset variables set -o errexit # Fail on uncaught non-zero returncodes set -o pipefail # Fail is a command in a chain of pipes fails ############################################################################### ## BENCHMARK PARAMETERS # Number of replicates per test NUM_REPLICATES=10 # Read lengths to examine # Lengths > 100 use an interpolated profile, and should therefore not be used # to estimate anything other than runtime (see 'simulate_reads'). READ_LENGTHS=(100 200) # Insert sizes of reads to simulate for adapter ID ADAPTER_ID_INSERT_SIZES=($(seq 250 5 350)) # Maximum number of threads to use (testing 1 .. max) where supported MAX_THREADS=4 # Number of read (pairs) to simulate using pIRS for each replicate SIMULATED_NREADS=1000000 REFSEQ="results/reference.fasta" SIMULATED_PREFIX="results/simulated/reads" SIMULATED_MIXED_PREFIX="results/simulated/mixed" SIMULATED_ADAPTER_ID_PREFIX="results/simulated/adapter_id" ############################################################################### ## PRE-BENCHMARK CHECKS function check_for_executable() { echo -n "Checking for $1 executable '$2': " > /dev/stderr if [ -x "$2" ]; then echo -e "OK" > /dev/stderr elif which "$2" &> /dev/null; then echo -e "'$(which "$2" | head -n1)'" > /dev/stderr else echo -e "ERROR, NOT FOUND!" > /dev/stderr exit 1; fi } function check_for_jar() { echo -n "Checking for $1 jar at '$2': " > /dev/stderr if [ -e "$2" ]; then echo -e "OK" > /dev/stderr else echo -e "ERROR, NOT FOUND!" > /dev/stderr exit 1; fi } EXEC_ADAPTERREMOVAL1x="bin/AdapterRemoval-1.5.4" check_for_executable "AdapterRemoval v1.x" "${EXEC_ADAPTERREMOVAL1x}" # https://github.com/slindgreen/AdapterRemoval/raw/master/AdapterRemoval-1.5.4.tar.gz EXEC_ADAPTERREMOVAL2x="bin/AdapterRemoval-2.1.3" check_for_executable "AdapterRemoval v2.x" "${EXEC_ADAPTERREMOVAL2x}" # https://github.com/MikkelSchubert/adapterremoval EXEC_LEEHOM="bin/leeHom_patched" check_for_executable "leeHom" "${EXEC_LEEHOM}" # https://github.com/grenaud/leeHom # -- Apply patches/leeHom.patch EXEC_SKEWER="bin/skewer" check_for_executable "Skewer" "${EXEC_SKEWER}" # https://github.com/relipmoc/skewer EXEC_ALIENTRIMMER="bin/AlienTrimmer" check_for_executable "AlienTrimmer" "${EXEC_ALIENTRIMMER}" # ftp://ftp.pasteur.fr/pub/GenSoft/projects/AlienTrimmer/ EXEC_SCYTHE="bin/scythe" check_for_executable "Scythe" "${EXEC_SCYTHE}" # https://github.com/vsbuffalo/scythe EXEC_CUTADAPT="bin/cutadapt" check_for_executable "Cutadapt" "${EXEC_CUTADAPT}" # https://code.google.com/p/cutadapt/ EXEC_FLEXBAR="bin/flexbar" check_for_executable "Flexbar" "${EXEC_FLEXBAR}" # http://sourceforge.net/projects/flexbar/ EXEC_PIRS="bin/pirs_patched" check_for_executable "pIRS (with adapters)" "${EXEC_PIRS}" # ftp://ftp.genomics.org.cn/pub/pIRS/ # -- Apply patches/pirs.patch JAR_TRIMMOMATIC="bin/trimmomatic-0.33.jar" check_for_jar "Trimmomatic" ${JAR_TRIMMOMATIC} # http://www.usadellab.org/cms/?page=trimmomatic EXEC_PEAT="./bin/PEAT" check_for_executable "PEAT" ${EXEC_PEAT} # https://github.com/jhhung/PEAT EXEC_PEAR="bin/pear_patched" check_for_executable "PEAR" ${EXEC_PEAR} # http://sco.h-its.org/exelixis/web/software/pear/ # -- Apply patches/pear.patch EXEC_MINION="bin/minion" check_for_executable "minion (kraken)" ${EXEC_MINION} # http://www.ebi.ac.uk/research/enright/software/kraken EXEC_FASTQ_MCF="bin/fastq-mcf" check_for_executable "fastq-mcf" ${EXEC_FASTQ_MCF} # https://code.google.com/p/ea-utils/ EXEC_TIME=/usr/bin/time check_for_executable "GNU time" ${EXEC_TIME} # Needed for time / RAM usage EXEC_JAVA="bin/java" check_for_executable "Java JRE" ${EXEC_JAVA} # Needed for Trimmomatic # Script for evaluating trimming / collapsing RESULTS SCRIPT_EVALUATE="./scripts/evaluate.py" check_for_executable "Evaluation script for read trimming / merging" ${SCRIPT_EVALUATE} # Script for evaluating trimming / collapsing RESULTS SCRIPT_EVALUATE_ID="./scripts/evaluate_id.py" check_for_executable "Evaluation script for adapter identification" ${SCRIPT_EVALUATE_ID} # Script for merging tables generated by ${SCRIPT_EVALUATE} SCRIPT_MERGE="./scripts/merge_tables.py" check_for_executable "Table merging script" ${SCRIPT_MERGE} ############################################################################### function shuffle_and_run() { echo > /dev/stderr echo "Shuffling batch ..." > /dev/stderr python -c "import sys, random lines = sys.stdin.readlines() random.shuffle(lines) sys.stdout.write(''.join(lines))" | while read command; do ${command}; done } function do_run_piped() { DST=$1 DST_TIME=$2 DST_STDOUT=$3 DST_STDERR=$4 shift 4 if [ -e "${DST}.table" ]; then echo "Skipping ${DST}.table" > /dev/stderr else echo "Building ${DST}.table" > /dev/stderr rm -rf "${DST:?}/" mkdir -p "${DST}/" if ! ${EXEC_TIME} --verbose --output "${DST_TIME}" "$@" \ > "${DST_STDOUT}" 2> "${DST_STDERR}"; then echo "Error running command!" > /dev/stderr exit 1 fi fi } function do_run() { DST=$1 shift 1 do_run_piped "${DST}" "${DST}/time" "${DST}/stdout.txt" "${DST}/stderr.txt" "$@" } function do_evaluate() { DST=$1 if [ ! -e "${DST}.table" ]; then ${SCRIPT_EVALUATE} "$@" fi } ############################################################################### function fetch_reference() { echo "------------------------------------------------------------" > /dev/stderr echo "Fetching reference sequence ..." > /dev/stderr if [ -e "results/reference.fasta" ]; then echo "Reference sequence found; skipping ..." > /dev/stderr echo "" > /dev/stderr else echo "" > /dev/stderr wget -O results/reference.fasta.gz http://hgdownload.soe.ucsc.edu/goldenPath/hg38/chromosomes/chr1.fa.gz gunzip results/reference.fasta.gz fi } function simulate_reads() { echo "------------------------------------------------------------" > /dev/stderr echo "Simulating reads ..." > /dev/stderr echo "" > /dev/stderr for readlen in ${READ_LENGTHS[*]}; do INSERT_MEAN=$(((${readlen} * 3) / 2)) INSERT_SD=$((${INSERT_MEAN} / 2)) if [ "${readlen}" -gt 100 ]; then # Use fake profiles, built using scripts/extend_profile.py PROFILE_CLI="-b profiles/phixv2.InDel.matrix -s profiles/humNew.PE100.matrix.gz" else PROFILE_CLI= fi for run_n in ${REPLICATES}; do DST="${SIMULATED_PREFIX}_${run_n}_${readlen}" if [ -e "${DST}.read.info" ]; then echo " Skipping ${DST}.*" > /dev/stderr else echo " Simulating reads run=${run_n}, l=${readlen}, m=${INSERT_MEAN}, v=${INSERT_SD} ..." > /dev/stderr rm -rf "${DST:?}/" mkdir -p "${DST}/" # -c 0 = uncompressed output if ! ${EXEC_PIRS} simulate ${PROFILE_CLI} -x "${SIMULATED_NREADS}" -l "${readlen}" -i "${REFSEQ}" -c 0 -m "${INSERT_MEAN}" -v "${INSERT_SD}" -Q 33 -o "${DST}/reads" \ > "${DST}/reads.stdout" 2> "${DST}/reads.stderr"; then echo "Error simulated reads ..." > /dev/stderr exit 1 fi gunzip "${DST}/reads_${readlen}_${INSERT_MEAN}.read.info.gz" ln -sf "$(basename "${DST}")/reads_${readlen}_${INSERT_MEAN}_1.fq" "${DST}_1.fq" ln -sf "$(basename "${DST}")/reads_${readlen}_${INSERT_MEAN}_2.fq" "${DST}_2.fq" ln -sf "$(basename "${DST}")/reads_${readlen}_${INSERT_MEAN}.read.info" "${DST}.read.info" fi done done echo > /dev/stderr } function simulate_mixed_reads() { # Random adapter pairs generated as follows: # # $ scripts/shuffle_fasta.py adapters/adapter_1.fasta # Seed = 209548449294681565 # Seq = AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCACCTAATCTCGTATGCCGTCTTCTGCTTG # New = AAACTTGCTCTGTGCCCGCTCCGTATGTCACAACAGTGCGTGTATCACCTCAATGCAGGACTCA # New = CTAATTTGCCGTAGCGACGTACTTCAGCCTCCAGGAATTGGACCCTTACGCACACGCATTCATG # New = GTTCATACGACGACGACCAATGGCACACTTATCCGGTACTTGCGTTTCAATGCGCATGCCCCAT # New = CCATGCCCCGAAGATTCCTATACCCTTAAGGTCGCAATTGTTCGAGTAAGCTGTACGCGCCCAT # # $ scripts/shuffle_fasta.py adapters/adapter_2.fasta # Seed = 1852992042931739018 # Seq = AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT # New = GATCGGGAGTAATTTGGAGGCAGTAGTTCGTCGAAACTCGGAGCGTCTTTAGCAGGAG # New = TACCGTGAAAGGTGCGCTTAGTGGCATATGCGTTAAGAGCTAGGTAACGGTCTGGAGG # New = TAAGAAACTCGGAGTTTGGCCTGCGAGGTAGCTTGGGTGTTATGAAGAACGGCATGCG # New = GTTGCATTGACCCGAAGGGCTCGATGTTTAGGGAGGTCAGAAGTTGAGCGGGTTCAAA echo "------------------------------------------------------------" > /dev/stderr echo "Simulating mixed reads ..." > /dev/stderr echo "" > /dev/stderr for readlen in ${READ_LENGTHS[*]}; do INSERT_MEAN=$(((${readlen} * 3) / 2)) INSERT_SD=$((${INSERT_MEAN} / 2)) if [ "${readlen}" -gt 100 ]; then # Use fake profiles, built using scripts/extend_profile.py PROFILE_CLI="-b profiles/phixv2.InDel.matrix -s profiles/humNew.PE100.matrix.gz" else PROFILE_CLI= fi for run_n in ${REPLICATES}; do DST="${SIMULATED_MIXED_PREFIX}_${run_n}_${readlen}" if [ -e "${DST}.read.info" ]; then echo " Skipping ${DST}.*" > /dev/stderr else echo " Simulating mixed reads run=${run_n}, l=${readlen}, m=${INSERT_MEAN}, v=${INSERT_SD} ..." > /dev/stderr rm -rf "${DST:?}/" mkdir -p "${DST}/" # -c 0 = uncompressed output # -x ${NREADS} if ! ${EXEC_PIRS} simulate ${PROFILE_CLI} \ -x "${SIMULATED_NREADS}" -l "${readlen}" -i "${REFSEQ}" \ -c 0 -m "${INSERT_MEAN}" -v "${INSERT_SD}" -Q 33 \ -o "${DST}/reads" \ -1 AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCACCTAATCTCGTATGCCGTCTTCTGCTTG \ -1 AAACTTGCTCTGTGCCCGCTCCGTATGTCACAACAGTGCGTGTATCACCTCAATGCAGGACTCA \ -1 CTAATTTGCCGTAGCGACGTACTTCAGCCTCCAGGAATTGGACCCTTACGCACACGCATTCATG \ -1 GTTCATACGACGACGACCAATGGCACACTTATCCGGTACTTGCGTTTCAATGCGCATGCCCCAT \ -1 CCATGCCCCGAAGATTCCTATACCCTTAAGGTCGCAATTGTTCGAGTAAGCTGTACGCGCCCAT \ -2 AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT \ -2 GATCGGGAGTAATTTGGAGGCAGTAGTTCGTCGAAACTCGGAGCGTCTTTAGCAGGAG \ -2 TACCGTGAAAGGTGCGCTTAGTGGCATATGCGTTAAGAGCTAGGTAACGGTCTGGAGG \ -2 TAAGAAACTCGGAGTTTGGCCTGCGAGGTAGCTTGGGTGTTATGAAGAACGGCATGCG \ -2 GTTGCATTGACCCGAAGGGCTCGATGTTTAGGGAGGTCAGAAGTTGAGCGGGTTCAAA \ > "${DST}/stdout.txt" 2> "${DST}/stderr.txt"; then echo "Error simulated reads ..." > /dev/stderr exit 1 fi gunzip "${DST}/reads_${readlen}_${INSERT_MEAN}.read.info.gz" ln -sf "$(basename "${DST}")/reads_${readlen}_${INSERT_MEAN}_1.fq" "${DST}_1.fq" ln -sf "$(basename "${DST}")/reads_${readlen}_${INSERT_MEAN}_2.fq" "${DST}_2.fq" ln -sf "$(basename "${DST}")/reads_${readlen}_${INSERT_MEAN}.read.info" "${DST}.read.info" fi done done echo > /dev/stderr } function simulate_adapter_id_reads() { echo "------------------------------------------------------------" > /dev/stderr echo "Simulating reads for adapter identification ..." > /dev/stderr echo "" > /dev/stderr readlen=100 for INSERT_MEAN in ${ADAPTER_ID_INSERT_SIZES[*]}; do for run_n in ${REPLICATES}; do DST="${SIMULATED_ADAPTER_ID_PREFIX}_${run_n}_${readlen}_${INSERT_MEAN}" if [ -e "${DST}.read.info" ]; then echo " Skipping ${DST}.*" > /dev/stderr else echo " Simulating reads run=${run_n}, l=${readlen}, m=${INSERT_MEAN}, v=75 ..." > /dev/stderr rm -rf "${DST:?}/" mkdir -p "${DST}/" if ! ${EXEC_TIME} --verbose --output "${DST}/time" ${EXEC_PIRS} simulate -x "${SIMULATED_NREADS}" -l "${readlen}" -i "${REFSEQ}" -c 0 -m "${INSERT_MEAN}" -v 75 -Q 33 -o "${DST}/reads" \ > "${DST}/reads.stdout" 2> "${DST}/reads.stderr"; then echo "Error simulated reads ..." > /dev/stderr exit 1 fi gunzip "${DST}/reads_${readlen}_${INSERT_MEAN}.read.info.gz" ln -sf "$(basename "${DST}")/reads_${readlen}_${INSERT_MEAN}_1.fq" "${DST}_1.fq" ln -sf "$(basename "${DST}")/reads_${readlen}_${INSERT_MEAN}_2.fq" "${DST}_2.fq" ln -sf "$(basename "${DST}")/reads_${readlen}_${INSERT_MEAN}.read.info" "${DST}.read.info" fi done done echo > /dev/stderr } ############################################################################### function run_pear() { NTHREADS=$1 DST=$2 FQ_INFO=$3 FQ_MATE1=$4 FQ_MATE2=$5 shift 5 do_run "${DST}" ${EXEC_PEAR} paired -j "${NTHREADS}" -t 0 \ -f "${FQ_MATE1}" -r "${FQ_MATE2}" \ -o "${DST}/reads" "$@" do_evaluate "${DST}" "${FQ_INFO}" --read-mode PE --collapsed } function run_adapterremoval() { MODE=$1 EXECUTABLE=$2 NTHREADS=$3 DST=$4 FQ_INFO=$5 shift 5 if [ "$NTHREADS" -eq 1 ]; then NTHREADS_CLI="" else NTHREADS_CLI="--threads ${NTHREADS}" fi if [ "${MODE}" = "COLLAPSE" ]; then MODE="PE" COLLAPSE_CLI="--collapsed" else COLLAPSE_CLI="" fi do_run "${DST}" "${EXECUTABLE}" --basename "${DST}/reads" ${NTHREADS_CLI} "$@" do_evaluate "${DST}" "${FQ_INFO}" --read-mode "${MODE}" ${COLLAPSE_CLI} } function run_peat_se() { NTHREADS=$1 DST=$2 FQ_INFO=$3 FQ_MATE1=$4 shift 4 do_run "${DST}" ${EXEC_PEAT} single -q SANGER -n "${NTHREADS}" \ -a "$(cat adapters/adapter_1.txt)" \ -i "${FQ_MATE1}" -o "${DST}/reads.fastq" "$@" do_evaluate "${DST}" "${FQ_INFO}" --read-mode SE } function run_peat_pe() { NTHREADS=$1 DST=$2 FQ_INFO=$3 FQ_MATE1=$4 FQ_MATE2=$5 shift 5 do_run "${DST}" ${EXEC_PEAT} paired -n "${NTHREADS}" \ -1 "${FQ_MATE1}" -2 "${FQ_MATE2}" \ -o "${DST}/reads" "$@" do_evaluate "${DST}" "${FQ_INFO}" --read-mode PE } function run_trimmomatic_se() { MODE=$1 NTHREADS=$2 DST=$3 FQ_INFO=$4 FQ_MATE1=$5 FQ_EXT=$6 shift 6 if [ "${MODE}" = "MIXED" ]; then ADAPTERS="adapters/mixed.fasta" else ADAPTERS="adapters/adapters.fasta" fi do_run "${DST}" ${EXEC_JAVA} -jar ${JAR_TRIMMOMATIC} SE -phred33 -threads "${NTHREADS}" \ "${FQ_MATE1}" "${DST}/reads${FQ_EXT}" "$@" \ "ILLUMINACLIP:${ADAPTERS}:2:7:10" do_evaluate "${DST}" "${FQ_INFO}" --read-mode SE \ --dimers-are-discarded } function run_trimmomatic_pe() { MODE=$1 NTHREADS=$2 DST=$3 FQ_INFO=$4 FQ_MATE1=$5 FQ_MATE2=$6 FQ_EXT=$7 shift 7 if [ "${MODE}" = "MIXED" ]; then ADAPTERS="adapters/mixed.fasta" else ADAPTERS="adapters/adapters.fasta" fi do_run "${DST}" ${EXEC_JAVA} -jar ${JAR_TRIMMOMATIC} PE \ -threads "${NTHREADS}" -phred33 \ "${FQ_MATE1}" "${FQ_MATE2}" \ "${DST}/reads.1${FQ_EXT}" "${DST}/reads.1.singletons.${FQ_EXT}" \ "${DST}/reads.2${FQ_EXT}" "${DST}/reads.2.singletons.${FQ_EXT}" \ "ILLUMINACLIP:${ADAPTERS}:2:30:7:1:true" "$@" do_evaluate "${DST}" "${FQ_INFO}" --read-mode PE \ --dimers-are-discarded } function run_flexbar() { MODE=$1 NTHREADS=$2 DST=$3 FQ_INFO=$4 shift 4 do_run "${DST}" ${EXEC_FLEXBAR} -m 0 -t "${DST}/reads" -n "${NTHREADS}" "$@" do_evaluate "${DST}" "${FQ_INFO}" --read-mode "${MODE}" } function run_skewer() { MODE=$1 NTHREADS=$2 DST=$3 FQ_INFO=$4 shift 4 do_run "${DST}" ${EXEC_SKEWER} -o "${DST}/reads" -l 0 -t "${NTHREADS}" "$@" \ do_evaluate "${DST}" "${FQ_INFO}" --read-mode "${MODE}" } function run_scythe() { DST=$1 FQ_INFO=$2 FQ_MATE1=$3 shift 3 do_run "${DST}" ${EXEC_SCYTHE} -M 0 "$@" \ -a "adapters/adapter_1.fasta" \ -o "${DST}/reads.trimmed" \ "${FQ_MATE1}" do_evaluate "${DST}" "${FQ_INFO}" --read-mode SE } function run_alientrimmer_se() { DST=$1 FQ_INFO=$2 FQ_MATE1=$3 shift 3 do_run "${DST}" ${EXEC_ALIENTRIMMER} -l 0 "$@" \ -i "${FQ_MATE1}" \ -o "${DST}/reads.trimmed" do_evaluate "${DST}" "${FQ_INFO}" --read-mode SE } function run_alientrimmer_pe() { DST=$1 FQ_INFO=$2 FQ_MATE1=$3 FQ_MATE2=$4 shift 4 do_run "${DST}" ${EXEC_ALIENTRIMMER} -l 0 "$@" \ -if "${FQ_MATE1}" \ -ir "${FQ_MATE2}" \ -os "${DST}/reads.trimmed" \ -or "${DST}/reads.trimmed.mate1" \ -of "${DST}/reads.trimmed.mate2" do_evaluate "${DST}" "${FQ_INFO}" --read-mode PE } function run_cutadapt_se() { DST=$1 FQ_INFO=$2 FQ_MATE1=$3 shift 3 do_run "${DST}" ${EXEC_CUTADAPT} "$@" \ -o "${DST}/reads.trimmed" \ "${FQ_MATE1}" do_evaluate "${DST}" "${FQ_INFO}" --read-mode SE } function run_cutadapt_pe() { DST=$1 FQ_INFO=$2 FQ_MATE1=$3 FQ_MATE2=$4 shift 4 do_run "${DST}" ${EXEC_CUTADAPT} "$@" \ -o "${DST}/reads.trimmed.1" \ -p "${DST}/reads.trimmed.2" \ "${FQ_MATE1}" \ "${FQ_MATE2}" do_evaluate "${DST}" "${FQ_INFO}" --read-mode PE } function run_leeHom() { MODE=$1 DST=$2 FQ_INFO=$3 shift 3 if [ "${MODE}" = "COLLAPSE" ]; then MODE="PE" COLLAPSE_CLI="--collapsed" else COLLAPSE_CLI="" fi do_run "${DST}" "${EXEC_LEEHOM}" "$@" -fqo "${DST}/reads" do_evaluate "${DST}" "${FQ_INFO}" --read-mode "${MODE}" ${COLLAPSE_CLI} } function run_fastq_mcf_se() { DST=$1 FQ_INFO=$2 ADAPTERS=$3 FQ_MATE1=$4 shift 4 # -0 to disable quality trimming do_run "${DST}" ${EXEC_FASTQ_MCF} -0 \ "${ADAPTERS}" \ "${FQ_MATE1}" \ -o "${DST}/reads.trimmed" "$@" do_evaluate "${DST}" "${FQ_INFO}" --read-mode SE \ --dimers-are-discarded } function run_fastq_mcf_pe() { DST=$1 FQ_INFO=$2 ADAPTERS=$3 FQ_MATE1=$4 FQ_MATE2=$5 shift 5 # -0 to disable quality trimming do_run "${DST}" ${EXEC_FASTQ_MCF} -0 \ "${ADAPTERS}" \ "${FQ_MATE1}" \ "${FQ_MATE2}" \ -o "${DST}/reads.trimmed.mate1" \ -o "${DST}/reads.trimmed.mate2" \ "$@" do_evaluate "${DST}" "${FQ_INFO}" --read-mode PE \ --dimers-are-discarded } ############################################################################### function run_minion() { DST=$1 FQ_MATE1=$2 FQ_MATE2=$3 shift 3 if [ ! -e "${DST}/DONE" ]; then echo "Runing ${DST} ..." > /dev/stderr rm -rf "${DST:?}/" mkdir -p "${DST}/" ${EXEC_MINION} search-adapter -show 5 -i "${FQ_MATE1}" \ > "${DST}/mate1.txt" ${EXEC_MINION} search-adapter -show 5 -i "${FQ_MATE2}" \ > "${DST}/mate2.txt" touch "${DST}/DONE" fi } function run_adapterremoval_id() { DST=$1 FQ_MATE1=$2 FQ_MATE2=$3 shift 3 if [ ! -e "${DST}/DONE" ]; then echo "Runing ${DST} ..." > /dev/stderr rm -rf "${DST:?}/" mkdir -p "${DST}/" ${EXEC_ADAPTERREMOVAL2x} --identify-adapters \ --file1 "${FQ_MATE1}" --file2 "${FQ_MATE2}" \ > "${DST}/mates.txt" touch "${DST}/DONE" fi } ############################################################################### # Common replicates strings REPLICATES=$(printf "%03i\n" $(seq 1 ${NUM_REPLICATES})) function benchmark_se() { simulate_reads echo "------------------------------------------------------------" > /dev/stderr echo "Running SE benchmarks ..." > /dev/stderr echo "" > /dev/stderr for readlen in ${READ_LENGTHS[*]}; do for run_n in ${REPLICATES}; do { # Shuffle each individual run SIMULATED_MATE1="${SIMULATED_PREFIX}_${run_n}_${readlen}_1.fq" SIMULATED_MATE2="${SIMULATED_PREFIX}_${run_n}_${readlen}_2.fq" SIMULATED_INFO="${SIMULATED_PREFIX}_${run_n}_${readlen}.read.info" RESULTS="results/se/${readlen}_${run_n}" # -mm 3 corresponds to AR 2.x defaults echo run_adapterremoval SE ${EXEC_ADAPTERREMOVAL1x} 1 \ "${RESULTS}/adapterremoval1x_mm3" \ "${SIMULATED_INFO}" \ --file1 "${SIMULATED_MATE1}" \ --mm 3 # -mm 3 --minadapteroverlap 3 (test) echo run_adapterremoval SE ${EXEC_ADAPTERREMOVAL2x} 1 \ "${RESULTS}/adapterremoval2x_min3_mm3" \ "${SIMULATED_INFO}" \ --file1 "${SIMULATED_MATE1}" \ --minadapteroverlap 3 --mm 3 # -mm 5 --minadapteroverlap 3 (test) echo run_adapterremoval SE ${EXEC_ADAPTERREMOVAL2x} 1 \ "${RESULTS}/adapterremoval2x_min3_mm5" \ "${SIMULATED_INFO}" \ --file1 "${SIMULATED_MATE1}" \ --minadapteroverlap 3 --mm 5 for nthreads in $(seq 1 ${MAX_THREADS}); do AR_PREFIX="${RESULTS}/adapterremoval2x" echo run_adapterremoval SE ${EXEC_ADAPTERREMOVAL2x} "${nthreads}" \ "${AR_PREFIX}_t${nthreads}" \ "${SIMULATED_INFO}" \ --file1 "${SIMULATED_MATE1}" \ echo run_skewer SE "${nthreads}" \ "${RESULTS}/skewer_t${nthreads}" \ "${SIMULATED_INFO}" \ "${SIMULATED_MATE1}" echo run_flexbar SE "${nthreads}" \ "${RESULTS}/flexbar_t${nthreads}" \ "${SIMULATED_INFO}" \ -a "./adapters/adapter_1.fasta" \ -r "${SIMULATED_MATE1}" echo run_trimmomatic_se SE "${nthreads}" \ "${RESULTS}/trimmomatic_t${nthreads}" \ "${SIMULATED_INFO}" \ "${SIMULATED_MATE1}" \ ".fastq" echo run_peat_se "${nthreads}" \ "${RESULTS}/peat_t${nthreads}" \ "${SIMULATED_INFO}" \ "${SIMULATED_MATE1}" done echo run_cutadapt_se "${RESULTS}/cutadapt" \ "${SIMULATED_INFO}" \ "${SIMULATED_MATE1}" \ -a "$(cat adapters/adapter_1.txt)" echo run_scythe "${RESULTS}/scythe" \ "${SIMULATED_INFO}" \ "${SIMULATED_MATE1}" echo run_alientrimmer_se "${RESULTS}/alientrimmer_q00" \ "${SIMULATED_INFO}" \ "${SIMULATED_MATE1}" \ -c "adapters/adapter_1.txt" \ -q 0 echo run_leeHom SE \ "${RESULTS}/leeHom" \ "${SIMULATED_INFO}" \ -fq1 "${SIMULATED_MATE1}" echo run_leeHom SE \ "${RESULTS}/leeHom_ancient" \ "${SIMULATED_INFO}" \ -fq1 "${SIMULATED_MATE1}" \ --ancientdna echo run_fastq_mcf_se "${RESULTS}/fastq_mcf" \ "${SIMULATED_INFO}" \ "./adapters/adapter_1.fasta" \ "${SIMULATED_MATE1}" } | shuffle_and_run done done ${SCRIPT_MERGE} results/se > results/se.table } function benchmark_pe() { simulate_reads echo "------------------------------------------------------------" > /dev/stderr echo "Running PE benchmarks ..." > /dev/stderr echo "" > /dev/stderr for readlen in ${READ_LENGTHS[*]}; do for run_n in ${REPLICATES}; do { # Shuffle each individual run SIMULATED_MATE1="${SIMULATED_PREFIX}_${run_n}_${readlen}_1.fq" SIMULATED_MATE2="${SIMULATED_PREFIX}_${run_n}_${readlen}_2.fq" SIMULATED_INFO="${SIMULATED_PREFIX}_${run_n}_${readlen}.read.info" RESULTS="results/pe/${readlen}_${run_n}" DEFAULT_ARGS=("${SIMULATED_INFO}" "${SIMULATED_MATE1}" "${SIMULATED_MATE2}") # -mm 3 corresponds to AR 2.x defaults echo run_adapterremoval PE ${EXEC_ADAPTERREMOVAL1x} 1 \ "${RESULTS}/adapterremoval1x_mm3" \ "${SIMULATED_INFO}" \ --file1 "${SIMULATED_MATE1}" \ --file2 "${SIMULATED_MATE2}" \ --mm 3 for nthreads in $(seq 1 ${MAX_THREADS}); do AR_PREFIX="${RESULTS}/adapterremoval2x" echo run_adapterremoval PE ${EXEC_ADAPTERREMOVAL2x} "${nthreads}" \ "${AR_PREFIX}_t${nthreads}" \ "${SIMULATED_INFO}" \ --file1 "${SIMULATED_MATE1}" \ --file2 "${SIMULATED_MATE2}" \ echo run_skewer PE "${nthreads}" \ "${RESULTS}/skewer_t${nthreads}" \ "${DEFAULT_ARGS[*]}" echo run_flexbar PE "${nthreads}" \ "${RESULTS}/flexbar_t${nthreads}" \ "${SIMULATED_INFO}" \ -a "./adapters/adapters.fasta" \ -r "${SIMULATED_MATE1}" \ -p "${SIMULATED_MATE2}" echo run_trimmomatic_pe PE "${nthreads}" \ "${RESULTS}/trimmomatic_t${nthreads}" \ "${DEFAULT_ARGS[*]}" \ ".fastq" echo run_peat_pe "${nthreads}" \ "${RESULTS}/peat_t${nthreads}" \ "${DEFAULT_ARGS[*]}" done echo run_cutadapt_pe "${RESULTS}/cutadapt" \ "${DEFAULT_ARGS[*]}" \ -a "$(cat adapters/adapter_1.txt)" \ -A "$(cat adapters/adapter_2.txt)" echo run_alientrimmer_pe "${RESULTS}/alientrimmer_q00" \ "${DEFAULT_ARGS[*]}" \ -cf "adapters/adapter_1.txt" \ -cr "adapters/adapter_2.txt" \ -q 0 echo run_leeHom PE \ "${RESULTS}/leeHom" \ "${SIMULATED_INFO}" \ -fq1 "${SIMULATED_MATE1}" \ -fq2 "${SIMULATED_MATE2}" echo run_leeHom PE \ "${RESULTS}/leeHom_ancient" \ "${SIMULATED_INFO}" \ -fq1 "${SIMULATED_MATE1}" \ -fq2 "${SIMULATED_MATE2}" \ --ancientdna echo run_fastq_mcf_pe "${RESULTS}/fastq_mcf" \ "${SIMULATED_INFO}" \ "./adapters/adapters.fasta" \ "${SIMULATED_MATE1}" \ "${SIMULATED_MATE2}" } | shuffle_and_run done done ${SCRIPT_MERGE} results/pe > results/pe.table } function benchmark_collapse() { simulate_reads echo "------------------------------------------------------------" > /dev/stderr echo "Running collapsing benchmarks ..." > /dev/stderr echo "" > /dev/stderr for readlen in ${READ_LENGTHS[*]}; do for run_n in ${REPLICATES}; do { # Shuffle each individual run SIMULATED_MATE1="${SIMULATED_PREFIX}_${run_n}_${readlen}_1.fq" SIMULATED_MATE2="${SIMULATED_PREFIX}_${run_n}_${readlen}_2.fq" SIMULATED_INFO="${SIMULATED_PREFIX}_${run_n}_${readlen}.read.info" RESULTS="results/collapse/${readlen}_${run_n}" DEFAULT_ARGS=("${SIMULATED_INFO}" "${SIMULATED_MATE1}" "${SIMULATED_MATE2}") # -mm 3 corresponds to AR 2.x defaults echo run_adapterremoval COLLAPSE ${EXEC_ADAPTERREMOVAL1x} 1 \ "${RESULTS}/adapterremoval1x_mm3" \ "${SIMULATED_INFO}" \ --file1 "${SIMULATED_MATE1}" \ --file2 "${SIMULATED_MATE2}" \ --mm 3 --collapse for nthreads in $(seq 1 ${MAX_THREADS}); do AR_PREFIX="${RESULTS}/adapterremoval2x" echo run_adapterremoval COLLAPSE ${EXEC_ADAPTERREMOVAL2x} "${nthreads}" \ "${AR_PREFIX}_t${nthreads}" \ "${SIMULATED_INFO}" \ --file1 "${SIMULATED_MATE1}" \ --file2 "${SIMULATED_MATE2}" \ --collapse echo run_pear "${nthreads}" \ "${RESULTS}/pear_t${nthreads}" \ "${SIMULATED_INFO}" \ "${SIMULATED_MATE1}" \ "${SIMULATED_MATE2}" done echo run_leeHom COLLAPSE \ "${RESULTS}/leeHom" \ "${SIMULATED_INFO}" \ -fq1 "${SIMULATED_MATE1}" \ -fq2 "${SIMULATED_MATE2}" echo run_leeHom COLLAPSE \ "${RESULTS}/leeHom_ancient" \ "${SIMULATED_INFO}" \ -fq1 "${SIMULATED_MATE1}" \ -fq2 "${SIMULATED_MATE2}" \ --ancientdna } | shuffle_and_run done done ${SCRIPT_MERGE} results/collapse > results/collapse.table } function benchmark_mixed_se { simulate_mixed_reads echo "------------------------------------------------------------" > /dev/stderr echo "Running mixed se adapters benchmarks ..." > /dev/stderr echo "" > /dev/stderr for readlen in ${READ_LENGTHS[*]}; do for run_n in ${REPLICATES}; do { # Shuffle each individual run SIMULATED_MATE1="${SIMULATED_MIXED_PREFIX}_${run_n}_${readlen}_1.fq" SIMULATED_MATE2="${SIMULATED_MIXED_PREFIX}_${run_n}_${readlen}_2.fq" SIMULATED_INFO="${SIMULATED_MIXED_PREFIX}_${run_n}_${readlen}.read.info" RESULTS="results/mixed_se/${readlen}_${run_n}" DEFAULT_ARGS=("${SIMULATED_INFO}" "${SIMULATED_MATE1}" "${SIMULATED_MATE2}") AR_PREFIX="${RESULTS}/adapterremoval2x" # -mm 3 --minadapteroverlap 3 (test) echo run_adapterremoval SE ${EXEC_ADAPTERREMOVAL2x} 1 \ "${AR_PREFIX}_min3_mm3" \ "${SIMULATED_INFO}" \ --file1 "${SIMULATED_MATE1}" \ --adapter-list ./adapters/mixed.table \ --minadapteroverlap 3 --mm 3 # -mm 5 --minadapteroverlap 3 (test) echo run_adapterremoval SE ${EXEC_ADAPTERREMOVAL2x} 1 \ "${AR_PREFIX}_min3_mm5" \ "${SIMULATED_INFO}" \ --file1 "${SIMULATED_MATE1}" \ --adapter-list ./adapters/mixed.table \ --minadapteroverlap 3 --mm 5 for nthreads in $(seq 1 ${MAX_THREADS}); do echo run_adapterremoval SE ${EXEC_ADAPTERREMOVAL2x} "${nthreads}" \ "${AR_PREFIX}_t${nthreads}" \ "${SIMULATED_INFO}" \ --file1 "${SIMULATED_MATE1}" \ --adapter-list ./adapters/mixed.table echo run_trimmomatic_se MIXED "${nthreads}" \ "${RESULTS}/trimmomatic_t${nthreads}" \ "${SIMULATED_INFO}" \ "${SIMULATED_MATE1}" \ ".fastq" done echo run_alientrimmer_se "${RESULTS}/alientrimmer_q00" \ "${SIMULATED_INFO}" \ "${SIMULATED_MATE1}" \ -c "adapters/mixed_1.txt" \ -q 0 echo run_cutadapt_se "${RESULTS}/cutadapt" \ "${SIMULATED_INFO}" \ "${SIMULATED_MATE1}" \ $(for seq in $(cat adapters/mixed_1.txt); do echo "-a ${seq}";done) echo run_fastq_mcf_se "${RESULTS}/fastq_mcf" \ "${SIMULATED_INFO}" \ "./adapters/mixed_1.fasta" \ "${SIMULATED_MATE1}" } | shuffle_and_run done done ${SCRIPT_MERGE} results/mixed_se > results/mixed_se.table } function benchmark_mixed_pe { simulate_mixed_reads echo "------------------------------------------------------------" > /dev/stderr echo "Running mixed pe adapters benchmarks ..." > /dev/stderr echo "" > /dev/stderr for readlen in ${READ_LENGTHS[*]}; do for run_n in ${REPLICATES}; do { # Shuffle each individual run SIMULATED_MATE1="${SIMULATED_MIXED_PREFIX}_${run_n}_${readlen}_1.fq" SIMULATED_MATE2="${SIMULATED_MIXED_PREFIX}_${run_n}_${readlen}_2.fq" SIMULATED_INFO="${SIMULATED_MIXED_PREFIX}_${run_n}_${readlen}.read.info" RESULTS="results/mixed_pe/${readlen}_${run_n}" DEFAULT_ARGS=("${SIMULATED_INFO}" "${SIMULATED_MATE1}" "${SIMULATED_MATE2}") for nthreads in $(seq 1 ${MAX_THREADS}); do AR_PREFIX="${RESULTS}/adapterremoval2x" echo run_adapterremoval PE ${EXEC_ADAPTERREMOVAL2x} "${nthreads}" \ "${AR_PREFIX}_t${nthreads}" \ "${SIMULATED_INFO}" \ --file1 "${SIMULATED_MATE1}" \ --file2 "${SIMULATED_MATE2}" \ --adapter-list ./adapters/mixed.table echo run_peat_pe "${nthreads}" \ "${RESULTS}/peat_t${nthreads}" \ "${DEFAULT_ARGS[*]}" echo run_trimmomatic_pe MIXED "${nthreads}" \ "${RESULTS}/trimmomatic_t${nthreads}" \ "${DEFAULT_ARGS[*]}" \ ".fastq" done echo run_alientrimmer_pe "${RESULTS}/alientrimmer_q00" \ "${DEFAULT_ARGS[*]}" \ -cf "adapters/mixed_1.txt" \ -cr "adapters/mixed_2.txt" \ -q 0 echo run_cutadapt_pe "${RESULTS}/cutadapt" \ "${DEFAULT_ARGS[*]}" \ $(for seq in $(cat adapters/mixed_1.txt); do echo "-a ${seq}";done) \ $(for seq in $(cat adapters/mixed_2.txt); do echo "-A ${seq}";done) echo run_fastq_mcf_pe "${RESULTS}/fastq_mcf" \ "${SIMULATED_INFO}" \ "./adapters/mixed.fasta" \ "${SIMULATED_MATE1}" \ "${SIMULATED_MATE2}" } | shuffle_and_run done done ${SCRIPT_MERGE} results/mixed_pe > results/mixed_pe.table } function benchmark_adapter_id { simulate_adapter_id_reads echo "------------------------------------------------------------" > /dev/stderr echo "Running adapter id benchmarks ..." > /dev/stderr echo "" > /dev/stderr readlen=100 for INSERT_MEAN in ${ADAPTER_ID_INSERT_SIZES[*]}; do for run_n in ${REPLICATES}; do SIMULATED_MATE1="${SIMULATED_ADAPTER_ID_PREFIX}_${run_n}_${readlen}_${INSERT_MEAN}_1.fq" SIMULATED_MATE2="${SIMULATED_ADAPTER_ID_PREFIX}_${run_n}_${readlen}_${INSERT_MEAN}_2.fq" SIMULATED_INFO="${SIMULATED_ADAPTER_ID_PREFIX}_${run_n}_${readlen}_${INSERT_MEAN}.read.info" RESULTS="results/adapter_id/${readlen}_${INSERT_MEAN}_${run_n}" run_minion "${RESULTS}/minion" \ "${SIMULATED_MATE1}" \ "${SIMULATED_MATE2}" run_adapterremoval_id "${RESULTS}/adapterremovalv2" \ "${SIMULATED_MATE1}" \ "${SIMULATED_MATE2}" done done ${SCRIPT_EVALUATE_ID} results/adapter_id > results/adapter_id.table } cd "$(dirname "$0")" mkdir -p results fetch_reference echo > /dev/stderr if [ "$* " = "all " ]; then benchmark_se benchmark_pe benchmark_collapse benchmark_adapter_id benchmark_mixed_pe benchmark_mixed_se elif [ "$* " = "se " ]; then benchmark_se elif [ "$* " = "pe " ]; then benchmark_pe elif [ "$* " = "collapse " ]; then benchmark_collapse elif [ "$* " = "adapter_id " ]; then benchmark_adapter_id elif [ "$* " = "mixed " ]; then benchmark_mixed_pe benchmark_mixed_se else echo "Usage: benchmark.sh " > /dev/stderr echo "Commands: all se pe collapse mixed adapter_id" > /dev/stderr fi adapterremoval-2.3.1/benchmark/patches/000077500000000000000000000000001350370616400201115ustar00rootroot00000000000000adapterremoval-2.3.1/benchmark/patches/leeHom.patch000066400000000000000000000022261350370616400223450ustar00rootroot00000000000000diff --git a/src/leeHom.cpp b/src/leeHom.cpp index 14ff31d..ae83533 100644 --- a/src/leeHom.cpp +++ b/src/leeHom.cpp @@ -449,7 +449,7 @@ int main (int argc, char *argv[]) { }else{ if(result.sequence != ""){ //new sequence - onereadgroup.single<<"@"< max(fo1->getSeq()->length(),fo2->getSeq()->length()) ){ mtr.incrementCountmergedoverlap(); diff --git a/libgab/gzstream/gzstream.C b/libgab/gzstream/gzstream.C index 8cb4590..4de5c09 100644 --- a/libgab/gzstream/gzstream.C +++ b/libgab/gzstream/gzstream.C @@ -54,8 +54,10 @@ gzstreambuf* gzstreambuf::open( const char* name, int open_mode) { char* fmodeptr = fmode; if ( mode & std::ios::in) *fmodeptr++ = 'r'; - else if ( mode & std::ios::out) + else if ( mode & std::ios::out) { *fmodeptr++ = 'w'; + *fmodeptr++ = '0'; + } *fmodeptr++ = 'b'; *fmodeptr = '\0'; file = gzopen( name, fmode); adapterremoval-2.3.1/benchmark/patches/pIRS_111.patch000066400000000000000000000401641350370616400223360ustar00rootroot00000000000000diff -rwu pIRS_111_original/src/pirs/src/global.h pIRS_111/src/pirs/src/global.h --- pIRS_111_original/src/pirs/src/global.h 2013-09-26 14:52:51.000000000 +0200 +++ pIRS_111/src/pirs/src/global.h 2015-09-30 15:39:16.000000000 +0200 @@ -4,6 +4,8 @@ using namespace std; using namespace boost; +#include + typedef struct{ int Read_length; @@ -17,7 +19,7 @@ int Q_shift; int Mask_quality_mode; int Output_type; - double Coverage; + int NPairs; double Error_rate; string Input_ref1; string Input_ref2; @@ -25,6 +27,10 @@ string GC_depth_profile; string InDel_error_profile; string Output_prefix; + vector adapter_1; + vector adapter_2; + vector barcode_1; + vector barcode_2; }PARAMETER; #endif diff -rwu pIRS_111_original/src/pirs/src/simulate_Illumina_reads.cpp pIRS_111/src/pirs/src/simulate_Illumina_reads.cpp --- pIRS_111_original/src/pirs/src/simulate_Illumina_reads.cpp 2013-09-26 14:52:52.000000000 +0200 +++ pIRS_111/src/pirs/src/simulate_Illumina_reads.cpp 2015-09-30 15:39:16.000000000 +0200 @@ -15,6 +15,30 @@ using namespace std; + +// Barcode: +// NNNNNN +const std::string ADAPTER_1 = "AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCACCTAATCTCGTATGCCGTCTTCTGCTTG"; +const std::string ADAPTER_2 = "AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT"; + + +void add_adapter(const std::string& adapter, int length, std::string& dst) +{ + if (dst.size() < length) { + dst.reserve(length); + + for (int pos = 0; dst.size() < length; ++pos) { + if (pos < adapter.size()) { + dst.push_back(adapter.at(pos)); + } else { + dst.push_back('A'); + } + } + } +} + + + /*parameter variable: int Read_length; @@ -28,7 +52,7 @@ int Q_shift; int Mask_quality_mode; int Output_type; - double Coverage; + int NPairs; double Error_rate; string Input_ref1; string Input_ref2; @@ -37,7 +61,7 @@ string InDel_error_profile; string Output_prefix; */ -PARAMETER InputParameter ={100,500,-1,1,0,1,1,1,64,0,1,5,-1,"","","","","","Illumina"}; +PARAMETER InputParameter ={100,500,-1,1,0,1,1,1,64,0,1,10000,-1,"","","","","","Illumina"}; int Ref_Base_num = 0; //ATCG: 4 int Statistical_Cycle_num = 0; //the cycle number in Base-calling profile @@ -94,13 +118,19 @@ cout<<"you can get another diploid genome sequence by the command \"pirs diploid\", but remember that heterozygosis SNP rate and heterozygosis Indel rate only exist in diploid. \n"; cout< Adapter sequence appended to mate 1 reads,default:"< Adapter sequence appended to mate 2 reads,default:"< Barcode sequence appended to mate 1 reads"< Barcode sequence appended to mate 2 reads"< input_ref1, input reference genome sequence *.fa/*.fa.gz, no default vaule"< input_ref2, for diploid genome, input another reference genome sequence which was generated by command \"pirs diploid\""< Base-calling profile, input Base-calling profile for simulating substitution-error and quality score,default: (exe_path)"< GC content-coverage profile, input GC content-coverage file for simulating GC bias, the default profile are determined based on the twice of read length"< InDel-error profile, input InDel-error profile for simulating InDel-error of reads, default:(exe_path)"< read_len, set length of read, read1 and read2 have the same length,default:"< coverage, set the sequencing coverage(sometimes called depth),default:"< number of reads-pairs to generate,default:"< insertsize_mean, set the average value of insert size,default:"< insertsize_sd, set the standard deviation of insert sizes, default:insertsize_mean/20"< substitution-error rate, set the average substitution-error rate(0 or 0.0001~0.63) over all cycles, default=average substitution-error rate of Base-calling profile"< 0.63 ){cerr<<"Error: error_rate should be set 0 or between 0.0001 and 0.63, you can also set -1 to simulate default error rate according with error profile, please check option -e !"<seqlen){pair_count--;continue;} - //get insert seq - string sub_str=seq.substr(pos,insertsize); - map > indel1; map > indel2; int r1_slen = 0; @@ -714,27 +750,36 @@ if(InputParameter.Is_simulate_InDel) { get_reads_indel(InputParameter.Read_length, indel1, indel2, r1_slen, r2_slen, InDel_max_len, InDel_error_matrix, InDel_num); - //fixed in v1.1.1 - if(InputParameter.Read_length-r1_slen > sub_str.size() || InputParameter.Read_length-r2_slen > sub_str.size()) - { - pair_count--;continue; - } } string ref_read1, ref_read2; int selection=int(rand()%2); //0 or 1, for selecting output file randomly and deciding read +/- int read1_pos, read2_pos; + + const int barcode_idx = rand() / (RAND_MAX / InputParameter.barcode_1.size() + 1); + const std::string barcode_1 = InputParameter.barcode_1.at(barcode_idx); + const std::string barcode_2 = InputParameter.barcode_2.at(barcode_idx); + + //get insert seq if(selection == 0) { + const string sub_str = barcode_1 + seq.substr(pos,insertsize) + reversecomplementary(barcode_2); + const string sub_str_rev(sub_str.rbegin(), sub_str.rend()); + ref_read1 = sub_str.substr(0, InputParameter.Read_length-r1_slen); - ref_read2 = sub_str.substr(insertsize-InputParameter.Read_length+r2_slen, InputParameter.Read_length-r2_slen); + ref_read2 = sub_str_rev.substr(0, InputParameter.Read_length-r2_slen); + ref_read2 = std::string(ref_read2.rbegin(), ref_read2.rend()); read1_pos = pos+1; - read2_pos = pos+insertsize-InputParameter.Read_length-r2_slen+1; + read2_pos = pos+ref_read2.size()+1; }else{ - ref_read1 = sub_str.substr(insertsize-InputParameter.Read_length+r1_slen, InputParameter.Read_length-r1_slen); + const string sub_str = barcode_2 + seq.substr(pos,insertsize) + reversecomplementary(barcode_1); + const string sub_str_rev(sub_str.rbegin(), sub_str.rend()); + + ref_read1 = sub_str_rev.substr(0, InputParameter.Read_length-r1_slen); + ref_read1 = std::string(ref_read1.rbegin(), ref_read1.rend()); ref_read2 = sub_str.substr(0, InputParameter.Read_length-r2_slen); - read1_pos = pos+insertsize-InputParameter.Read_length-r1_slen+1; + read1_pos = pos+ref_read1.size()+1; read2_pos = pos+1; } @@ -747,8 +792,10 @@ //simulate GC bias if(InputParameter.Is_simulate_GC_bias){ string check_seq = ref_read1+ref_read2; + if (!check_seq.empty()) { if(simulate_GC_bias(check_seq,GC_bias_abundance)){pair_count--;continue;} } + } //insertsize statistics if(InsertSize_distr[insertsize]>0) @@ -790,6 +837,10 @@ exit(-1); } + int adapter_idx = rand() / (RAND_MAX / InputParameter.adapter_1.size() + 1); + add_adapter(InputParameter.adapter_1.at(adapter_idx), InputParameter.Read_length - r1_slen, ref_read1); + add_adapter(InputParameter.adapter_2.at(adapter_idx), InputParameter.Read_length - r2_slen, ref_read2); + bool* Is_insertion_pos1; bool* Is_insertion_pos2; Is_insertion_pos1 = new bool[InputParameter.Read_length]; @@ -1234,7 +1285,9 @@ } } - Infor_outfile<data); - fprintf (fd[0], "%s\n", fwd[i]->header); + fprintf (fd[0], "@M_%s\n", fwd[i]->header + 1); if (!bothOut) { fprintf (fd[0], "%s\n", fwd[i]->data); adapterremoval-2.3.1/benchmark/profiles/000077500000000000000000000000001350370616400203055ustar00rootroot00000000000000adapterremoval-2.3.1/benchmark/profiles/humNew.PE100.matrix.gz000066400000000000000000042340761350370616400241610ustar00rootroot00000000000000/UhumNew.PE100.matrix[${v^'?@$;(%5@6e6 [~zIwl5MBTDheīW7qZq;mGhOh}BLhOOxqiڎ9yר rNS~ƁT0qj6'Qp#kϯ[q8G؜{xkWcN"~I~_#]|썰WWGvW s"g8&N]8ųId߸Pp&GWx5/8礬trܟ}8Χ8;rrۺf/Q }_8q~8cdWku/~+Y9/wMGxzYZeOdW)c.3{uyy|̱ktm{D^ܻq5\%zue5zＢQ^=S0؍3tGFp{#cZ-bjYű4"L.T#W#Br#|IDoǍH4GDWa<Y} CHs>0}nǩjGE')" b8[YqD"um.*bDɢ0z?(8E|+Biţ<ݩ%GgxJ}Ңxk4_+Gt7:( K+߻v1O+a/M JZTASR@p@G]Th8P!~C0FjQ"#^IV7?}-uF n u.\DAL hP)u /C6"yr5G[`!?0rvY1efz>#: 9*8CgRs 6Yq99&E۷ͷ=/+CuV|/)T+L7bY0xOh1 j|hz$9YC-'}3'CiVLt{@Ju8˷GE1$S}c#mHDq ܰ*.NwNsMwÐ|buT;աo,8\̨Sg0%bQp| /WqBv5c3~(\ H8z''ʓC~Mu Det`6{~45}tb}^e'^ߩ聈8Z|b~A)>fѭEQQ .C8׫ј/MһD0LJDxeiTC%:9zz8RAqyWHf[\{q}{MX,v&>y%.8a4W]UO\ŋXS6Yn1nw<oEen>}N WG-Ju\3M$Fq/.`a 'zD0m^qУM8oQ@cľ8~j9:0\u,.Rq* O.ז,ڪ!BUܣ%˱Nܥ xh9sQy#hx6'_47mϠMVhJaHJ9vF|V".'F'.ês>jٜ3T9h; 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(tn_.M΃07{7#mE/8RclXL2<%l=//OINGpSq^czi|HcǤ,(Q7 щ;>3Ikʧds '9Ώ - |{D [^\񺡀:9:_=':a$G :tp!8vG/ZQ'żHBc m:S#ig9e FdEH&.Rbw_!˗®Q<| iG距Đ@_ U?}~6۟[lWCȥAVtbn;skLkΌս\u?ۑ;[-p#E&g%I" QdOIdXb;00s0K=oHdoK%a'd~"/a/aa/d/KaIYz> M|ɰddK!|_2l= {0_Ɨ ]|ɰ$|#Ä~H"2} !Iadapterremoval-2.3.1/benchmark/profiles/phixv2.InDel.matrix000066400000000000000000000242701350370616400237520ustar00rootroot00000000000000[Info] File = 110416_I327_FCB008GACXX_L1_PHIXCONTROLv2.sam.gz Read_Length = 200 Read_1_Count = 147091454 Read_2_Count = 145785569 MaxInDel_Length = 3 < # # Permission is hereby granted, free of charge, to any person obtaining a copy # of this software and associated documentation files (the "Software"), to deal # in the Software without restriction, including without limitation the rights # to use, copy, modify, merge, publish, distribute, sublicense, and/or sell # copies of the Software, and to permit persons to whom the Software is # furnished to do so, subject to the following conditions: # # The above copyright notice and this permission notice shall be included in # all copies or substantial portions of the Software. # # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR # IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, # FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE # AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER # LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, # OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE # SOFTWARE. import os import sys import bz2 import math import gzip import argparse import itertools import collections def open_ro(filename): """Opens a file for reading, transparently handling GZip and BZip2 compressed files. Returns a file handle.""" handle = open(filename) try: header = handle.read(2) if header == "\x1f\x8b": handle.close() # TODO: Re-use handle (fileobj) handle = gzip.open(filename) elif header == "BZ": handle.close() handle = bz2.BZ2File(filename) else: handle.seek(0) return handle except: handle.close() raise def parse_timelog(filename): if not os.path.exists(filename): return float("nan"), float("nan") total_time, total_ram = 0.0, 0.0 with open(filename) as handle: for line in handle: key, value = line.lower().strip().split(": ") if "(wall clock)" in key: mult = 1.0 for field in reversed(value.split(":")): total_time += float(field) * mult mult *= 60.0 elif key == "maximum resident set size (kbytes)": total_ram += float(value) return total_time, total_ram class Summary(object): def __init__(self): self.true_pos = 0 self.false_pos = 0 self.true_neg = 0 self.false_neg = 0 self.cpu_time = 0.0 self.max_ram = 0.0 @property def total(self): return self.true_pos + self.false_pos \ + self.true_neg + self.false_neg def print_summary(self, args, stattype, header=True): stat = self _summary_stats = [ ("Reads", args.read_mode, None), ("Metric", stattype, None), ("Name", args.name, None), ("Threads", args.threads, None), ("Total", stat.total, None), ("TP", stat.true_pos, None), ("FP", stat.false_pos, None), ("TN", stat.true_neg, None), ("FN", stat.false_neg, None), ("SEN", stat.true_pos, stat.true_pos + stat.false_neg), ("SPC", stat.true_neg, stat.true_neg + stat.false_pos), ("PPV", stat.true_pos, stat.true_pos + stat.false_pos), ("NPV", stat.true_neg, stat.true_neg + stat.false_neg), ("MCC", (stat.true_pos * stat.true_neg - stat.false_pos * stat.false_neg), math.sqrt((stat.true_pos + stat.false_pos) * (stat.true_pos + stat.false_neg) * (stat.true_neg + stat.false_pos) * (stat.true_neg + stat.false_neg))), ("WallTime", "%.3f" % (stat.cpu_time,), None), ("MaxRAM", "%.3f" % (stat.max_ram / (2.0 ** 10),), None), ("Rate", ("%.1f" % ((stat.total / (stat.cpu_time or float("nan"))) / 1e3)).rjust(6), None) ] row = [] if header: args.out.write("\t".join(name for (name, _, _) in _summary_stats) + "\n") for (_, numerator, denominator) in _summary_stats: if denominator is None: value = str(numerator) elif not denominator: value = "NA" else: value = "%.4f" % (float(numerator) / float(denominator),) row.append(value) args.out.write("\t".join(row) + "\n") def missing_reads(expectations, se_mode): if se_mode: reads = [(key, [pair[0], None]) for key, pair in expectations.iteritems() if pair[0] is not None] else: reads = [(key, pair) for key, pair in expectations.iteritems() if pair != [None, None]] max_errors = 0 for name, mates in reads: for mate, record in enumerate(mates, start=1): if record is not None: if max_errors > 4: sys.stderr.write(" ...\n") return True sys.stderr.write(" Read not found: %s/%i\n" % (name, mate)) max_errors += 1 return bool(reads) def pop_expected_read(expectations, record): is_collapsed = False name = record["name"] if name.startswith("M_") or name.startswith("MT_"): name = name.split("_", 1)[1] is_collapsed = True expected = expectations[name] if is_collapsed: expectations[name] = [None, None] return expected[0] or expected[1], True mate = expected[record["mate"] - 1] expected[record["mate"] - 1] = None return mate, False def _perf_trimming(args, expectations, stat, record): ins_length, collapsed = pop_expected_read(expectations, record) obs_length = record["obs_len"] if args.barcode_len and obs_length == args.read_len: # Barcode not correctly identified / trimmed stat.false_neg += 1 return read_len = args.read_len - args.barcode_len if not collapsed: if ins_length >= read_len: if obs_length != read_len: stat.false_pos += 1 else: stat.true_neg += 1 elif obs_length == ins_length: stat.true_pos += 1 elif obs_length < ins_length: stat.false_pos += 1 elif obs_length > ins_length: stat.false_neg += 1 else: assert False, record else: # If collapsed, the read accounts for 2 sequences if obs_length == ins_length: # Merged reads containing adapters are considered positives if ins_length >= read_len: stat.true_neg += 2 else: stat.true_pos += 2 else: stat.false_pos += 2 def _perf_collapsed(args, expectations, stat, record): ins_length, collapsed = pop_expected_read(expectations, record) obs_length = record["obs_len"] if ins_length and ins_length < args.read_len * 2: if collapsed: if obs_length == ins_length: stat.true_pos += 2 else: stat.false_pos += 2 else: stat.false_neg += 1 elif collapsed: stat.false_pos += 2 else: stat.true_neg += 1 return collapsed def evaluate(args, expectations, trimmed_reads): stat = Summary() if args.collapsed: eval_func = _perf_collapsed eval_title = "Collapsed" else: eval_func = _perf_trimming eval_title = "Trimmed" for record in trimmed_reads: eval_func(args, expectations, stat, record) if args.dimers_are_discarded: for key, pair in expectations.items(): if args.read_mode in ("SE", "MIXED_SE"): pair[1] = None for mate, read in enumerate(pair, start=1): if read is not None: record = {"name": key, "mate": mate, "obs_len": 0} eval_func(args, expectations, stat, record) cpu_time, max_ram = parse_timelog(args.time) stat.cpu_time += cpu_time stat.max_ram += max_ram stat.print_summary(args, eval_title) return not missing_reads(expectations, args.read_mode in ("SE", "MIXED_SE")) def find_fastq_files(root): results = [] for filename in os.listdir(root): fpath = os.path.join(root, filename) if os.path.isfile(fpath): with open_ro(fpath) as handle: header = handle.readline() handle.readline() seperator = handle.readline() if header.startswith("@") and seperator.startswith("+"): results.append(fpath) return results def read_fastq(filename): if not os.path.exists(filename): sys.stderr.write(" Skipping %r ...\n" % (filename,)) return counter = 0 sys.stderr.write(" Reading %r ...\n" % (filename,)) with open_ro(filename) as handle: while True: header = handle.readline() sequence = handle.readline() _ = handle.readline() # Seperator _ = handle.readline() # Qualities if not header: break fields = header.split(None, 1) result = {} # Split is needed for ARv1x discarded name = fields[0].split("__")[0] if name[-2] == "/" and not name.startswith("M_"): result["name"] = name[1:-2] result["mate"] = int(name[-1]) assert result["mate"] in (1, 2), result["mate"] else: result["name"] = name[1:] result["mate"] = None result["obs_len"] = len(sequence.rstrip()) yield result counter += 1 sys.stderr.write(" Read %i records\n" % (counter,)) def read_expected_lengths(args): header = None results = collections.defaultdict(lambda: [None, None]) for line in open_ro(args.read_info): if line.startswith("@"): record = dict(zip(header, line.rstrip().split('\t'))) name = record["readId"][1:] name, mate = name.split("/") results[name][int(mate) - 1] = int(record["insertSize"]) elif line.startswith("#read length: "): args.read_len = int(line[14:]) elif line.startswith("#readId"): header = line[1:].rstrip().split('\t') return dict(results) def parse_args(argv): parser = argparse.ArgumentParser() parser.add_argument('root') parser.add_argument('read_info') parser.add_argument('--read-mode', default="PE", choices=("SE", "PE", "MIXED_SE", "MIXED_PE")) parser.add_argument('--time', default=None) parser.add_argument('--name', default="NA") parser.add_argument('--collapsed', default=False, action="store_true") parser.add_argument('--threads', default=1, type=int) parser.add_argument("--dimers-are-discarded", default=False, action="store_true") parser.add_argument("--keep", default=False, action="store_true") parser.add_argument("--barcode-len", default=0, type=int) return parser.parse_args(argv) def main(argv): args = parse_args(argv) args.name = args.root.rstrip("/").rsplit("/", 1)[-1] name = args.name.rsplit("_", 1) if name[-1].startswith("t") and name[-1][1:].isdigit(): args.name = name[0] args.threads = int(name[1][1:]) if args.time is None: args.time = os.path.join(args.root, "time") args.out = open(os.path.join(args.root, "table"), "w") expected = read_expected_lengths(args) fastq_files = find_fastq_files(args.root) trimmed_reads = [] for filename in fastq_files: trimmed_reads.append(read_fastq(filename)) if not evaluate(args, expected, itertools.chain(*trimmed_reads)): return 1 args.out.close() os.rename(os.path.join(args.root, "table"), args.root + ".table") if not args.keep: for fpath in fastq_files: os.remove(fpath) return 0 if __name__ == '__main__': sys.exit(main(sys.argv[1:])) adapterremoval-2.3.1/benchmark/scripts/evaluate_dmux.py000077500000000000000000000064031350370616400233740ustar00rootroot00000000000000#!/usr/bin/python # -*- coding: utf-8 -*- # Copyright (c) 2014 Mikkel Schubert # # Permission is hereby granted, free of charge, to any person obtaining a copy # of this software and associated documentation files (the "Software"), to deal # in the Software without restriction, including without limitation the rights # to use, copy, modify, merge, publish, distribute, sublicense, and/or sell # copies of the Software, and to permit persons to whom the Software is # furnished to do so, subject to the following conditions: # # The above copyright notice and this permission notice shall be included in # all copies or substantial portions of the Software. # # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR # IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, # FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE # AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER # LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, # OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE # SOFTWARE. import argparse import bz2 import gzip import os import sys def open_ro(filename): """Opens a file for reading, transparently handling GZip and BZip2 compressed files. Returns a file handle.""" handle = open(filename) try: header = handle.read(2) if header == "\x1f\x8b": handle.close() # TODO: Re-use handle (fileobj) handle = gzip.open(filename) elif header == "BZ": handle.close() handle = bz2.BZ2File(filename) else: handle.seek(0) return handle except: handle.close() raise def read_barcodes(filename): header = None results = {} for line in open_ro(filename): if line.startswith("@"): record = dict(zip(header, line.rstrip().split('\t'))) name = record["readId"].split("/")[0] results[name] = "_".join((record["barcode_1"], record["barcode_2"])) elif line.startswith("#readId"): header = line[1:].rstrip().split('\t') return dict(results) def parse_args(argv): parser = argparse.ArgumentParser() parser.add_argument('info') parser.add_argument('files', nargs="+") return parser.parse_args(argv) def main(argv): args = parse_args(argv) expectations = read_barcodes(args.info) total = 0 correct = 0 for filename in args.files: basename = os.path.basename(filename) # Implicitly handle unidentified, will be "unidentified_1", etc. barcode = basename.split(".")[1] with open_ro(filename) as handle: header = handle.readline() while header: name = header.split(None, 1)[0].split("/")[0] if expectations[name] == barcode: correct += 1 else: print expectations[name], barcode total += 1 handle.readline() handle.readline() handle.readline() header = handle.readline() print total, correct return 0 if __name__ == '__main__': sys.exit(main(sys.argv[1:])) adapterremoval-2.3.1/benchmark/scripts/evaluate_id.py000077500000000000000000000132401350370616400230100ustar00rootroot00000000000000#!/usr/bin/python # -*- coding: utf-8 -*- # Copyright (c) 2014 Mikkel Schubert # # Permission is hereby granted, free of charge, to any person obtaining a copy # of this software and associated documentation files (the "Software"), to deal # in the Software without restriction, including without limitation the rights # to use, copy, modify, merge, publish, distribute, sublicense, and/or sell # copies of the Software, and to permit persons to whom the Software is # furnished to do so, subject to the following conditions: # # The above copyright notice and this permission notice shall be included in # all copies or substantial portions of the Software. # # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR # IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, # FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE # AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER # LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, # OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE # SOFTWARE. import os import sys import argparse import collections import numpy def parse_args(argv): parser = argparse.ArgumentParser() parser.add_argument('root') parser.add_argument('--adapter1', default="AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCACCTAATCTCGTATGCCGTCTTCTGCTTG") parser.add_argument('--adapter2', default="AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT") return parser.parse_args(argv) def cmp_pcr(obs, ref): ncorrect = 0 for ref_nt, obs_nt in zip(ref, obs): if ref_nt == obs_nt: ncorrect += 1 else: break return ncorrect class evalulate_minion(object): def __init__(self, pcr1, pcr2): self._pcr1 = pcr1 self._pcr2 = pcr2 self._results = collections.defaultdict(dict) def __call__(self, readlen, insert_mean, replicate, fpath): prefix = os.path.join(fpath, "mate") for method, result in self._parse_report_minion(prefix).items(): self._results[(readlen, insert_mean, method)][replicate] = result def finalize(self): return dict(self._results) def _parse_report_minion(self, prefix): results = collections.defaultdict(dict) for result in self._parse_report_minion_part(prefix + "1.txt"): key = "minion:%s" % (result["criterion"],) results[key]["PCR1"] = max(results[key].get("PCR1", 0), cmp_pcr(result["sequence"], self._pcr1)) for result in self._parse_report_minion_part(prefix + "2.txt"): key = "minion:%s" % (result["criterion"],) results[key]["PCR2"] = max(results[key].get("PCR2", 0), cmp_pcr(result["sequence"], self._pcr2)) return dict(results) @classmethod def _parse_report_minion_part(cls, filename): results = [] with open(filename) as handle: result = {} for line in handle: line = line.strip() if not line: if result: results.append(result) result = {} else: key, value = map(str.strip, line.split("=", 1)) result[key] = value if result: results.append(result) return results class evalulate_adapterrm(object): def __init__(self, pcr1, pcr2): self._pcr = [pcr1, pcr2] self._results = collections.defaultdict(dict) def __call__(self, readlen, insert_mean, replicate, fpath): prefix = os.path.join(fpath, "mates.txt") self._results[(readlen, insert_mean, "adapterremovalv2")][replicate] \ = self._parse_report(prefix) def finalize(self): return dict(self._results) def _parse_report(self, fpath): result = {} with open(fpath) as handle: key = "Consensus:" counter = 1 for line in handle: line = line.strip() if line.startswith(key): adapter = line[line.index(key) + len(key):].strip() result["PCR%i" % (counter,)] \ = cmp_pcr(adapter, self._pcr[counter - 1]) counter += 1 if counter > 2: break return result def print_rows(program, results): rows = [] for (readlen, insert_mean, method), replicates in sorted(results.items()): mean_pcr1 = numpy.mean([repl["PCR1"] for repl in replicates.values()]) mean_pcr2 = numpy.mean([repl["PCR2"] for repl in replicates.values()]) rows.append((method, readlen, insert_mean, mean_pcr1, mean_pcr2)) for row in sorted(rows): print "\t".join(map(str, row)) def main(argv): args = parse_args(argv) eval_funcs = { "minion": evalulate_minion(args.adapter1, args.adapter2), "adapterremovalv2": evalulate_adapterrm(args.adapter1, args.adapter2), } for run in os.listdir(args.root): readlen, insert_mean, replicate = map(int, run.split("_")) for program in os.listdir(os.path.join(args.root, run)): if program in eval_funcs: fpath = os.path.join(args.root, run, program) eval_funcs[program](readlen, insert_mean, replicate, fpath) print "\t".join(("Method", "ReadLen", "InsertMean", "PCR1", "PCR2")) for program, func in sorted(eval_funcs.items()): print_rows(program, func.finalize()) return 0 if __name__ == '__main__': sys.exit(main(sys.argv[1:])) adapterremoval-2.3.1/benchmark/scripts/extend_profile.py000077500000000000000000000070351350370616400235420ustar00rootroot00000000000000#!/usr/bin/python # -*- coding: utf-8 -*- # Copyright (c) 2014 Mikkel Schubert # # Permission is hereby granted, free of charge, to any person obtaining a copy # of this software and associated documentation files (the "Software"), to deal # in the Software without restriction, including without limitation the rights # to use, copy, modify, merge, publish, distribute, sublicense, and/or sell # copies of the Software, and to permit persons to whom the Software is # furnished to do so, subject to the following conditions: # # The above copyright notice and this permission notice shall be included in # all copies or substantial portions of the Software. # # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR # IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, # FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE # AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER # LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, # OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE # SOFTWARE. import sys import bz2 import gzip import argparse def open_ro(filename): """Opens a file for reading, transparently handling GZip and BZip2 compressed files. Returns a file handle.""" handle = open(filename) try: header = handle.read(2) if header == "\x1f\x8b": handle.close() # TODO: Re-use handle (fileobj) handle = gzip.open(filename) elif header == "BZ": handle.close() handle = bz2.BZ2File(filename) else: handle.seek(0) return handle except: handle.close() raise def parse_args(argv): parser = argparse.ArgumentParser() parser.add_argument('file') return parser.parse_args(argv) def try_cast(value): try: return int(value) except ValueError: return value def main(argv): args = parse_args(argv) rows = [] in_table = False in_table_header = None with open_ro(args.file) as file_in: for line in file_in: line_s = line.rstrip() if in_table: if not in_table_header: in_table_header = line_s.split('\t') if line_s.startswith("#"): in_table_header[0] = in_table_header[0][1:] if "Cycle" not in in_table_header: in_table = False in_table_header = None elif not line_s or line_s.startswith("#") or line_s == "< # # Permission is hereby granted, free of charge, to any person obtaining a copy # of this software and associated documentation files (the "Software"), to deal # in the Software without restriction, including without limitation the rights # to use, copy, modify, merge, publish, distribute, sublicense, and/or sell # copies of the Software, and to permit persons to whom the Software is # furnished to do so, subject to the following conditions: # # The above copyright notice and this permission notice shall be included in # all copies or substantial portions of the Software. # # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR # IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, # FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE # AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER # LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, # OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE # SOFTWARE. import os import sys import argparse def parse_args(argv): parser = argparse.ArgumentParser() parser.add_argument('root') return parser.parse_args(argv) def main(argv): args = parse_args(argv) keys = [] rows = [] for run_info in os.listdir(args.root): readlen, replicate = run_info.split("_") for filename in os.listdir(os.path.join(args.root, run_info)): if not filename.endswith(".table"): continue fpath = os.path.join(args.root, run_info, filename) with open(fpath) as handle: line = handle.readline() header = line.rstrip().split('\t') if keys is None: keys = header elif header != keys: if set(header).issubset(keys): pass # Fewer keys elif set(keys).issubset(header): keys = header # More keys else: assert False, fpath for line in handle: rows.append(dict(zip(header, line.rstrip().split('\t')))) rows[-1]["Nth"] = str(int(replicate)) # Strip leading zeros rows[-1]["ReadLen"] = readlen keys.insert(0, "Nth") keys.insert(0, "ReadLen") print "\t".join(keys) rows = ["\t".join(row.get(key, "NA") for key in keys) for row in rows] rows.sort() for row in rows: print row return 0 if __name__ == '__main__': sys.exit(main(sys.argv[1:])) adapterremoval-2.3.1/benchmark/scripts/shuffle_fasta.py000077500000000000000000000043351350370616400233450ustar00rootroot00000000000000#!/usr/bin/python # -*- coding: utf-8 -*- # Copyright (c) 2014 Mikkel Schubert # # Permission is hereby granted, free of charge, to any person obtaining a copy # of this software and associated documentation files (the "Software"), to deal # in the Software without restriction, including without limitation the rights # to use, copy, modify, merge, publish, distribute, sublicense, and/or sell # copies of the Software, and to permit persons to whom the Software is # furnished to do so, subject to the following conditions: # # The above copyright notice and this permission notice shall be included in # all copies or substantial portions of the Software. # # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR # IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, # FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE # AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER # LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, # OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE # SOFTWARE. import sys import random import argparse def parse_args(argv): parser = argparse.ArgumentParser() parser.add_argument('file') parser.add_argument('--seed', default=None, type=int) parser.add_argument('--replicates', default=5, type=int) return parser.parse_args(argv) def read_fasta(fpath): with open(fpath) as handle: header = handle.readline().rstrip() sequence = handle.readline().rstrip() assert not handle.readline() assert header.startswith(">") header = header.split("/", 1)[0].split(None, 1)[0] return header, sequence def shuffle(rng, seq): seq = list(seq) rng.shuffle(seq) return "".join(seq) def main(argv): args = parse_args(argv) if args.seed is None: args.seed = random.randint(0, sys.maxint) rng = random.Random(args.seed) name, sequence = read_fasta(args.file) print "Seed =", args.seed print "Seq =", sequence for _ in xrange(args.replicates - 1): print "New =", shuffle(rng, sequence) return 0 if __name__ == '__main__': sys.exit(main(sys.argv[1:])) adapterremoval-2.3.1/benchmark/scripts/tabulate.py000077500000000000000000000134421350370616400223330ustar00rootroot00000000000000#!/usr/bin/python # -*- coding: utf-8 -*- # Copyright (c) 2014 Mikkel Schubert # # Permission is hereby granted, free of charge, to any person obtaining a copy # of this software and associated documentation files (the "Software"), to deal # in the Software without restriction, including without limitation the rights # to use, copy, modify, merge, publish, distribute, sublicense, and/or sell # copies of the Software, and to permit persons to whom the Software is # furnished to do so, subject to the following conditions: # # The above copyright notice and this permission notice shall be included in # all copies or substantial portions of the Software. # # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR # IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, # FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE # AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER # LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, # OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE # SOFTWARE. import sys import argparse import collections import numpy def parse_args(argv): parser = argparse.ArgumentParser() parser.add_argument('filter', choices=("basic", "throughput"), type=str.lower, help="TODO") parser.add_argument('table', help="Benchmarking results", nargs="+") return parser.parse_args(argv) def read_table(fpath, filter_func): results = [] with open(fpath) as handle: header = handle.readline().rstrip().split("\t") for line in handle: fields = line.rstrip().split("\t") assert len(fields) == len(header), (header, fields) row = dict(zip(header, fields)) name = row["Name"] if name.endswith("_gz") or name.endswith("_bz2"): row["Name"], row["Compression"] = name.rsplit("_", 1) else: row["Compression"] = "NA" if filter_func(row): results.append(row) return results def _filter_basic(row): return int(row["ReadLen"]) == 100 \ and int(row["Threads"]) == 1 def _filter_throughput(row): return int(row["ReadLen"]) >= 100 \ and int(row["Threads"]) >= 1 _FILTERS = { "basic": _filter_basic, "throughput": _filter_throughput } def _collapse_basic(rows): max_nth = 0 keys = ("Name", "ReadLen", "Reads", "Metric", "Compression") results = collections.defaultdict(dict) for row in rows: key_row = tuple(row[key] for key in keys) key_nth = int(row["Nth"]) max_nth = max(max_nth, key_nth) subdd = results[key_row] assert key_nth >= 1, (row, subdd) assert key_nth not in subdd, (key_nth, subdd) subdd[key_nth] = row for key, values in results.iteritems(): assert len(values) == max_nth and max(values) == max_nth, values collapsed_rows = [] value_keys = ("SEN", "SPC", "PPV", "NPV", "MCC", "Rate") for rows in results.itervalues(): result = {} for key in value_keys: if any((key in row) for row in rows.itervalues()): values = tuple(float(row[key]) for row in rows.itervalues()) result[key] = "%.3f" % (numpy.mean(values),) for key in keys: result[key] = rows[1][key] collapsed_rows.append(result) return ("ReadLen", "Reads", "Name", "Metric", "Compression") + value_keys, \ collapsed_rows def _collapse_throughput(rows): max_nth = 0 keys = ("Name", "Reads", "Metric", "Compression") rate_keys = set() results = collections.defaultdict(dict) for row in rows: key_row = tuple(row[key] for key in keys) key_nth = int(row["Nth"]) assert key_nth >= 1, (row, key_row) max_nth = max(max_nth, key_nth) subdd = results[key_row] subdd.setdefault(key_nth, {}) subdd = subdd[key_nth] if int(row["Threads"]) == 1 and int(row["ReadLen"]) == 100: subdd.update(row) key = "%03i/%i" % (int(row["ReadLen"]), int(row["Threads"])) rate_keys.add(key) subdd[key] = row["Rate"] for key, values in results.iteritems(): assert len(values) == max_nth and max(values) == max_nth, values collapsed_rows = [] value_keys = tuple(sorted(rate_keys)) for rows in results.itervalues(): result = {} for key in value_keys: if any((key in row) for row in rows.itervalues()): values = tuple(float(row[key]) for row in rows.itervalues()) result[key] = "%.1f" % (numpy.mean(values),) for key in keys: result[key] = rows[1][key] collapsed_rows.append(result) return ("Name", "Metric", "Compression") + value_keys, \ collapsed_rows _COLLAPSERS = { "basic": _collapse_basic, "throughput": _collapse_throughput, } def get_output_keys(rows): keys = ["Name", "ReadLen", "Reads", "Metric", "Compression", "SEN", "SPC", "PPV", "NPV", "MCC"] max_threads = 1 for row in rows: rate_key = "Rate(%i)" % (max_threads,) if rate_key in row: keys.append(rate_key) max_threads += 1 return tuple(keys) def main(argv): args = parse_args(argv) rows = [] for fpath in args.table: rows.extend(read_table(fpath, _FILTERS[args.filter])) keys, rows = _COLLAPSERS[args.filter](rows) output_rows = [] for row in sorted(rows): output_rows.append(tuple(str(row.get(key, "NA")) for key in keys)) print "\t".join(keys) for row in sorted(output_rows): print "\t".join(row) return 0 if __name__ == '__main__': sys.exit(main(sys.argv[1:])) adapterremoval-2.3.1/docs/000077500000000000000000000000001350370616400154605ustar00rootroot00000000000000adapterremoval-2.3.1/docs/README.rst000066400000000000000000000077211350370616400171560ustar00rootroot00000000000000AdapterRemoval v2 ================= .. image:: https://img.shields.io/travis/MikkelSchubert/adapterremoval/master.svg :target: https://travis-ci.org/MikkelSchubert/adapterremoval :alt: Travis-CI .. image:: https://img.shields.io/coveralls/MikkelSchubert/adapterremoval.svg :target: https://coveralls.io/github/MikkelSchubert/adapterremoval :alt: Coveralls AdapterRemoval searches for and removes adapter sequences from High-Throughput Sequencing (HTS) data and (optionally) trims low quality bases from the 3' end of reads following adapter removal. AdapterRemoval can analyze both single end and paired end data, and can be used to merge overlapping paired-ended reads into (longer) consensus sequences. Additionally, AdapterRemoval can construct a consensus adapter sequence for paired-ended reads, if which this information is not available. If you use AdapterRemoval v2, then please cite the paper Schubert, Lindgreen, and Orlando (2016). AdapterRemoval v2: rapid adapter trimming, identification, and read merging. BMC Research Notes, 12;9(1):88 http://bmcresnotes.biomedcentral.com/articles/10.1186/s13104-016-1900-2 AdapterRemoval was originally published in Lindgreen 2012: Lindgreen (2012): AdapterRemoval: Easy Cleaning of Next Generation Sequencing Reads, BMC Research Notes, 5:337 http://www.biomedcentral.com/1756-0500/5/337/ Overview of major features ========================== - Trimming of adapters sequences from single-end and paired-end FASTQ reads. - Trimming of multiple, different adapters or adapter pairs. - Demultiplexing of single or double indexed reads, with or without trimming of adapter sequences. - Reconstruction of adapter sequences from paired-end reads, by the pairwise alignment of reads in the absence of a known adapter sequence. - Merging of overlapping read-pairs into higher-quality consensus sequences. - Multi-threading of all operations for increased throughput. - Reading and writing of gzip and bzip2 compressed files. - Reading and writing of interleaved FASTQ files. Installation ============ For detailed installation instructions, please see the `Installation `_ section of the online documentation. Installing AdapterRemoval using `Conda `_ ----------------------------------------------------------------- If you have Conda `installed on your system `_, you may install AdapterRemoval using one of serveral unoffical recipies:: conda install -c bioconda adapterremoval conda install -c maxibor adapterremoval2 Installing AdapterRemoval on Debian based systems ------------------------------------------------- Users of Debian Stretch or Ubuntu Artful Aardvark may install AdapterRemoval using Apt:: sudo apt-get install adapterremoval adapterremoval-examples Building AdapterRemoval from scratch ------------------------------------ Compiling AdapterRemoval from scratch requires a C++11 compliant compiler, and that the zlib and bz2lib headers are installed:: make sudo make install Getting started =============== To run AdapterRemoval, specify the location of pair 1 and (optionally) pair 2 FASTQ using the --file1 and --file2 command-line options:: AdapterRemoval --file1 myreads_1.fastq.gz --file2 myreads_2.fastq.gz By default, AdapterRemoval will save the trimmed reads in the current working directly, using filenames starting with 'your_output'. See the `Input and Output `_ files section for more information about files generated by AdapterRemoval. More examples of common usage may be found in the `Examples `_ section of the online documentation. Documentation ------------- For a detailed description of program usage, please refer to the online `online documentation `_. adapterremoval-2.3.1/docs/conf.py000066400000000000000000000121531350370616400167610ustar00rootroot00000000000000# -*- coding: utf-8 -*- # # AdapterRemoval documentation build configuration file, created by # sphinx-quickstart on Sun Sep 17 15:00:32 2017. # # This file is execfile()d with the current directory set to its # containing dir. # # Note that not all possible configuration values are present in this # autogenerated file. # # All configuration values have a default; values that are commented out # serve to show the default. # If extensions (or modules to document with autodoc) are in another directory, # add these directories to sys.path here. If the directory is relative to the # documentation root, use os.path.abspath to make it absolute, like shown here. # # import os # import sys # sys.path.insert(0, os.path.abspath('.')) # -- General configuration ------------------------------------------------ # If your documentation needs a minimal Sphinx version, state it here. # # needs_sphinx = '1.0' # Add any Sphinx extension module names here, as strings. They can be # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom # ones. extensions = [] # Add any paths that contain templates here, relative to this directory. templates_path = ['_templates'] # The suffix(es) of source filenames. # You can specify multiple suffix as a list of string: # # source_suffix = ['.rst', '.md'] source_suffix = '.rst' # The master toctree document. master_doc = 'index' # General information about the project. project = u'AdapterRemoval' copyright = u'2017, Mikkel Schubert; Stinus Lindgreen' author = u'Mikkel Schubert; Stinus Lindgreen' # The version info for the project you're documenting, acts as replacement for # |version| and |release|, also used in various other places throughout the # built documents. # # The short X.Y version. version = u'2.3.0' # The full version, including alpha/beta/rc tags. release = u'2.3.0' # The language for content autogenerated by Sphinx. Refer to documentation # for a list of supported languages. # # This is also used if you do content translation via gettext catalogs. # Usually you set "language" from the command line for these cases. language = None # List of patterns, relative to source directory, that match files and # directories to ignore when looking for source files. # This patterns also effect to html_static_path and html_extra_path exclude_patterns = [] # The name of the Pygments (syntax highlighting) style to use. pygments_style = 'sphinx' # If true, `todo` and `todoList` produce output, else they produce nothing. todo_include_todos = False # -- Options for HTML output ---------------------------------------------- # The theme to use for HTML and HTML Help pages. See the documentation for # a list of builtin themes. # html_theme = 'alabaster' # Theme options are theme-specific and customize the look and feel of a theme # further. For a list of options available for each theme, see the # documentation. # # html_theme_options = {} # Add any paths that contain custom static files (such as style sheets) here, # relative to this directory. They are copied after the builtin static files, # so a file named "default.css" will overwrite the builtin "default.css". html_static_path = ['_static'] # Custom sidebar templates, must be a dictionary that maps document names # to template names. # # This is required for the alabaster theme # refs: http://alabaster.readthedocs.io/en/latest/installation.html#sidebars html_sidebars = { '**': [ 'about.html', 'navigation.html', 'relations.html', # needs 'show_related': True theme option to display 'searchbox.html', 'donate.html', ] } # -- Options for HTMLHelp output ------------------------------------------ # Output file base name for HTML help builder. htmlhelp_basename = 'AdapterRemovaldoc' # -- Options for LaTeX output --------------------------------------------- latex_elements = { # The paper size ('letterpaper' or 'a4paper'). # # 'papersize': 'letterpaper', # The font size ('10pt', '11pt' or '12pt'). # # 'pointsize': '10pt', # Additional stuff for the LaTeX preamble. # # 'preamble': '', # Latex figure (float) alignment # # 'figure_align': 'htbp', } # Grouping the document tree into LaTeX files. List of tuples # (source start file, target name, title, # author, documentclass [howto, manual, or own class]). latex_documents = [ (master_doc, 'AdapterRemoval.tex', u'AdapterRemoval Documentation', author, 'manual'), ] # -- Options for manual page output --------------------------------------- # One entry per manual page. List of tuples # (source start file, name, description, authors, manual section). man_pages = [ ('manpage', 'AdapterRemoval', u'Fast short-read adapter trimming and processing', [author], 1) ] # -- Options for Texinfo output ------------------------------------------- # Grouping the document tree into Texinfo files. List of tuples # (source start file, target name, title, author, # dir menu entry, description, category) texinfo_documents = [ (master_doc, 'AdapterRemoval', u'AdapterRemoval Documentation', author, 'AdapterRemoval', 'One line description of project.', 'Miscellaneous'), ] adapterremoval-2.3.1/docs/examples.rst000066400000000000000000000356721350370616400200450ustar00rootroot00000000000000.. highlight:: Bash Example usage ============= The following examples all make use of the data included in the 'examples' folder. Trimming single-end reads ------------------------- The following command removes adapters from the file *reads_1.fq* trims both Ns and low quality bases from the reads, and gzip compresses the resulting files. The ``--basename`` option is used to specify the prefix for output files:: AdapterRemoval --file1 reads_1.fq --basename output_single --trimns --trimqualities --gzip Since ``--gzip`` and ``--basename`` is specified, the trimmed FASTQ reads are written to *output_single.truncated.gz*, the discarded FASTQ reads are written to *output_single.discarded.gz*, and settings and summary statistics are written to *output_single.settings*. Note that by default, AdapterRemoval does not require a minimum number of bases overlapping with the adapter sequence, before reads are trimmed. This may result in an excess of very short (1 - 3 bp) 3' fragments being falsely identified as adapter sequences, and trimmed. This behavior may be changed using the ``--minadapteroverlap`` option, which allows the specification of a minimum number of bases (excluding Ns) that must be aligned to carry trimming. For example, use *--minadapteroverlap 3* to require an overlap of at least 3 bp. Trimming paired-end reads ------------------------- The following command removes adapters from a paired-end reads, where the mate 1 and mate 2 reads are kept in files *reads_1.fq* and *reads_2.fq*, respectively. The reads are trimmed for both Ns and low quality bases, and overlapping reads (at least 11 nucleotides, per default) are merged (collapsed):: AdapterRemoval --file1 reads_1.fq --file2 reads_2.fq --basename output_paired --trimns --trimqualities --collapse This command generates the files *output_paired.pair1.truncated* and *output_paired.pair2.truncated*, which contain trimmed pairs of reads which were not collapsed, *output_paired.singleton.truncated* containing reads where one mate was discarded, *output_paired.collapsed* containing merged reads, and *output_paired.collapsed.truncated* containing merged reads that have been trimmed due to the ``--trimns`` or ``--trimqualities`` options. Finally, the *output_paired.discarded* and *output_paired.settings* files correspond to those of the single-end run. Multiple input FASTQ files -------------------------- More than one input file may be specified for mate 1 and mate 2 reads. This is accomplished simply by listing more than one file after the ``--file1`` and the ``--file2`` options. For single-end reads:: AdapterRemoval --file1 reads_1a.fq reads_1b.fq reads_1c.fq And for paired-end reads:: AdapterRemoval --file1 reads_1a.fq reads_1b.fq reads_1c.fq --file2 reads_2a.fq reads_2b.fq reads_2c.fq AdapterRemoval will process these files as if they had been concatenated into a single file or pair of files prior to invoking AdapterRemoval. For paired reads, the files must be specified in the same order for ``--file1`` and ``--file2``. Interleaved FASTQ reads ----------------------- AdapterRemoval is able to read and write paired-end reads stored in a single, so-called interleaved FASTQ file (one pair at a time, first mate 1, then mate 2). This is accomplished by specifying the location of the file using ``--file1`` and *also* setting the ``--interleaved`` command-line option:: AdapterRemoval --interleaved --file1 interleaved.fq --basename output_interleaved Other than taking just a single input file, this mode operates almost exactly like paired end trimming (as described above); the mode differs only in that paired reads are not written to a 'pair1' and a 'pair2' file, but instead these are instead written to a single, interleaved file, named 'paired'. The location of this file is controlled using the ``--output1`` option. Enabling either reading or writing of interleaved FASTQ files, both not both, can be accomplished by specifying the either of the ``--interleaved-input`` and ``--interleaved-output`` options, both of which are enabled by the ``--interleaved`` option. Combining FASTQ output ---------------------- By default, AdapterRemoval will create one output file for each mate, one file for discarded reads, and (in PE mode) one file paired reads where one mate has been discarded, and (optionally) two files for collapsed reads. Alternatively, these files may be combined using the ``--combined-output``, in which case all output is directed to the mate 1 and (in PE mode) to the mate 2 file. In cases where reads are discarded due to trimming to due to being collapsed into a single sequence, the sequence and quality scores of the discarded read is replaced with a single 'N' with base-quality 0. This option may be combined with ``--interleaved`` / ``--interleaved-output``, to write a single, interleaved file in paired-end mode. Different quality score encodings --------------------------------- By default, AdapterRemoval expects the quality scores in FASTQ reads to be Phred+33 encoded, meaning that the error probabilities are encoded as (char)('!' - 10 * log10(p)). Most data will be encoded using Phred+33, but Phred+64 and 'Solexa' encoded quality scores are also supported. These are selected by specifying the ``--qualitybase`` command-line option (specifying either '33', '64', or 'solexa'):: AdapterRemoval --qualitybase 64 --file1 reads_q64.fq --basename output_phred_64 By default, reads are written using the *same* encoding as the input. If a different encoding is desired, this may be accomplished using the ``--qualitybase-output`` option:: AdapterRemoval --qualitybase 64 --qualitybase-output 33 --file1 reads_q64.fq --basename output_phred_33 Note furthermore that AdapterRemoval by default only expects quality scores in the range 0 - 41 (or -5 to 41 in the case of Solexa encoded scores). If input data using a different maximum quality score is to be processed, or if the desired maximum quality score of collapsed reads is greater than 41, then this limit may be increased using the ``--qualitymax`` option:: AdapterRemoval --qualitymax 50 --file1 reads_1.fq --file2 reads_2.fq --collapse --basename output_collapsed_q50 For a detailed overview of Phred encoding schemes currently and previously in use, see e.g. the Wikipedia article on the subject: https://en.wikipedia.org/wiki/FASTQ_format#Encoding Trimming paired-end reads with multiple adapter pairs ----------------------------------------------------- It is possible to trim data that contains multiple adapter pairs, by providing a one or two-column table containing possible adapter combinations (for single-end and paired-end trimming, respectively; see e.g. examples/adapters.txt):: cat adapters.txt AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCACCTAATCTCGTATGCCGTCTTCTGCTTG AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT AAACTTGCTCTGTGCCCGCTCCGTATGTCACAACAGTGCGTGTATCACCTCAATGCAGGACTCA GATCGGGAGTAATTTGGAGGCAGTAGTTCGTCGAAACTCGGAGCGTCTTTAGCAGGAG CTAATTTGCCGTAGCGACGTACTTCAGCCTCCAGGAATTGGACCCTTACGCACACGCATTCATG TACCGTGAAAGGTGCGCTTAGTGGCATATGCGTTAAGAGCTAGGTAACGGTCTGGAGG GTTCATACGACGACGACCAATGGCACACTTATCCGGTACTTGCGTTTCAATGCGCATGCCCCAT TAAGAAACTCGGAGTTTGGCCTGCGAGGTAGCTTGGGTGTTATGAAGAACGGCATGCG CCATGCCCCGAAGATTCCTATACCCTTAAGGTCGCAATTGTTCGAGTAAGCTGTACGCGCCCAT GTTGCATTGACCCGAAGGGCTCGATGTTTAGGGAGGTCAGAAGTTGAGCGGGTTCAAA This table is then specified using the ``--adapter-list`` option:: AdapterRemoval --file1 reads_1.fq --file2 reads_2.fq --basename output_multi --trimns --trimqualities --collapse --adapter-list adapters.txt The resulting .summary file contains an overview of how frequently each adapter (pair) was used. Note that in the case of paired-end adapters, AdapterRemoval considers only the combinations of adapters specified in the table, one combination per row. For single-end trimming, only the first column of the table file is required, and the list may therefore take the form of a file containing one sequence per line. Identifying adapter sequences from paired-ended reads ----------------------------------------------------- If we did not know the adapter sequences for the *reads_*.fq* files, AdapterRemoval may be used to generate a consensus adapter sequence based on fragments identified as belonging to the adapters through pairwise alignments of the reads, provided that the data set contains only a single adapter sequence (not counting differences in index sequences). In the following example, the identified adapters corresponds to the default adapter sequences with a poly-A tail resulting from sequencing past the end of the insert + templates. It is not necessary to specify this tail when using the ``--adapter1`` or ``--adapter2`` command-line options. The characters shown under each of the consensus sequences represented the phred-encoded fraction of bases identical to the consensus base, with adapter 1 containing the index CACCTA:: AdapterRemoval --identify-adapters --file1 reads_1.fq --file2 reads_2.fq Attemping to identify adapter sequences ... Processed a total of 1,000 reads in 0.0s; 129,000 reads per second on average ... Found 394 overlapping pairs ... Of which 119 contained adapter sequence(s) ... Printing adapter sequences, including poly-A tails: --adapter1: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG ||||||||||||||||||||||||||||||||||******|||||||||||||||||||||||| Consensus: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCACCTAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAA Quality: 55200522544444/4411330333330222222/1.1.1.1111100-00000///..+....--*-)),,+++++++**(('%%%$ Top 5 most common 9-bp 5'-kmers: 1: AGATCGGAA = 96.00% (96) 2: AGATGGGAA = 1.00% (1) 3: AGCTCGGAA = 1.00% (1) 4: AGAGCGAAA = 1.00% (1) 5: AGATCGGGA = 1.00% (1) --adapter2: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT |||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Consensus: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA Quality: 525555555144141441430333303.2/22-2/-1..11111110--00000///..+....--*-),,,+++++++**(%'%%%$ Top 5 most common 9-bp 5'-kmers: 1: AGATCGGAA = 100.00% (100) No files are generated from running the adapter identification step. The consensus sequences inferred are compared to those specified using the ``--adapter1`` and ``--adapter2`` command-line options, or with the default values for these if no values have been given (as in this case). Pipes (|) indicate matches between the provided sequences and the consensus sequence, and "*" indicate the presence of unspecified bases (Ns). Demultiplexing and adapter-trimming ----------------------------------- As of version 2.1, AdapterRemoval supports simultaneous demultiplexing and adapter trimming; demultiplexing is carried out using a simple comparison between the specified barcode (a sequence of A, C, G, and T) and the first N bases of the mate 1 read, where N is the length of the barcode. Demultiplexing of double-indexed sequences is also supported, in which case two barcodes must be specified for each sample. The first barcode is then compared to first N_1 bases of the mate 1 read, and the second barcode is compared to the first N_2 bases of the mate 2 read. By default, this comparison requires a perfect match. Reads identified as containing a specific barcode(s) are then trimmed using adapter sequences including the barcode(s) as necessary. Reads for which no (pair of) barcodes matched are written to a separate file or pair of files (for paired end reads). Demultiplexing is enabled by creating a table of barcodes, the first column of which species the sample name (using characters a-z, A-Z, 0-9, or _) and the second and (optional) third columns specifies the barcode sequences expected at the 5' termini of mate 1 and mate 2 reads, respectively. For example, a table of barcodes from a double-indexed run might be as follows (see examples/barcodes.txt):: cat barcodes.txt sample_1 ATGCGGA TGAATCT sample_2 ATGGATT ATAGTGA sample_7 CAAAACT TCGCTGC In the case of single-read reads, only the first two columns are required. AdapterRemoval is invoked with the ``--barcode-list`` option, specifying the path to this table:: AdapterRemoval --file1 demux_1.fq --file2 demux_2.fq --basename output_demux --barcode-list barcodes.txt This generates a set of output files for each sample specified in the barcode table, using the basename (``--basename``) as the prefix, followed by a dot and the sample name, followed by a dot and the default name for a given file type. For example, the output files for sample_2 would be * output_demux.sample_2.discarded * output_demux.sample_2.pair1.truncated * output_demux.sample_2.pair2.truncated * output_demux.sample_2.settings * output_demux.sample_2.singleton.truncated The settings files generated for each sample summarizes the reads for that sample only; in addition, a basename.settings file is generated which summarizes the number and proportion of reads identified as belonging to each sample. The maximum number of mismatches allowed when comparing barocdes is controlled using the options ``--barcode-mm``, ``--barcode-mm-r1``, and ``--barcode-mm-r2``, which specify the maximum number of mismatches total, and the maximum number of mismatches for the mate 1 and mate 2 barcodes respectively. Thus, if mm_1(i) and mm_2(i) represents the number of mismatches observed for barcode-pair i for a given pair of reads, these options require that 1. mm_1(i) <= ``--barcode-mm-r1`` 2. mm_2(i) <= ``--barcode-mm-r2`` 3. mm_1(i) + mm_2(i) <= ``--barcode-mm`` Demultiplexing mode ------------------- As of version 2.2, AdapterRemoval can furthermore be used to demultiplex reads, without carrying out other forms of adapter trimming. This is accomplished by specifying the ``--demultiplex-only`` option: AdapterRemoval --file1 demux_1.fq --file2 demux_2.fq --basename output_only_demux --barcode-list barcodes.txt --demultiplex-only Options listed under "TRIMMING SETTINGS" (see *AdapterRemoval --help*) do not apply to this mode, but compression (``--gzip``, ``--bzip2``), multi-threading (``--threads``), interleaving (``--interleaved``, etc.) and other such options may be used in conjunction with ``--demultiplex-only``. AdapterRemoval will generate a *.settings* file for each sample listed in the ``--barcode-list`` file, along with the adapter-sequences that should be used when trimming reads for a given sample. These adapters correspond to the adapters that were specified when running AdapterRemoval in demultiplexing mode, with the barcode prefixed as appropriate. An underscore is used to demarcate the location at which the barcode ends and the adapter beings. It is important to use these, updated, adapter sequences when trimming the demultiplexed reads, to avoid the inclusion of barcode sequences in reads extending past the 3' termini of the DNA template sequence. adapterremoval-2.3.1/docs/getting_started.rst000066400000000000000000000066401350370616400214070ustar00rootroot00000000000000.. highlight:: Bash Getting started =============== To run AdapterRemoval on single-end FASTQ data, simply specify the location of FASTQ file(s) using the ``--file1`` command-line options:: AdapterRemoval --file1 myreads_1.fastq.gz To run AdapterRemoval on paired-end FASTQ data, specify the location of the mate 1 and mate 2 FASTQ files using the ``--file1`` and ``--file2`` command-line options:: AdapterRemoval --file1 myreads_1.fastq.gz --file2 myreads_2.fastq.gz The files may be uncompressed, gzip-compressed, or bzip2 compressed. When run in this manner, AdapterRemoval will save the trimmed reads in the current working directly, using filenames starting with 'your_output'. This behavior may be changed using the ``--basename`` option, or using specific options for each output file. See the :doc:`input_and_output` section for more information about files generated by AdapterRemoval. More examples of common usage may be found in the :doc:`examples` section of the documentation. A note on specifying adapters ----------------------------- AdapterRemoval relies on the user specifying the adapter sequences to be trimmed, using the ``--adapter1`` and ``--adapter2`` command-line options. By default, AdapterRemoval is setup to trim Illumina Truseq adapters, corresponding to the following command-line options:: --adapter1 AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG --adapter2 AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT It is therefore extremely important to specify the correct adapter sequences when running AdapterRemoval on a dataset that does not make use of these adapters. Failure to do so will result in the wrong sequences being trimmed, and actual adapter sequences being left in the resulting "trimmed" reads. Adapter sequences are specified in the read orientation when using the ``--adapter1`` and ``--adapter2`` command-line options, directly corresponding to the sequence that is observed in the FASTQ files produced by the base calling software. If we were processing data generated using the above TrueSeq adapters, then we would therefore expect to find those sequences as-is in our FASTQ files (assuming that the read lengths are sufficiently long and that insert sizes are sufficiently short), typically followed by a low-quality A-tail:: $ grep "AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC......ATCTCGTATGCCGTCTTCTGCTTG" file1.fq AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCGATGAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAACAAGAAT CTGGAGTTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCGATGAATCTCGTATGCCGTCTTCTGCTTGAAAAAAA GGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCGATGAATCTCGTATGCCGTCTTCTGCTTGCAAATTGAAAACAC $ grep "AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT" file2.fq CAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTCAAAAAAAGAAAAACATCTTG GAACTCCAGAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTCAAAAAAAATAGA GAACTAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTCAAAAACATAAGACCTA The ambiguous bases representing the mate 1 barcode (the six Ns) have been replaced by single-character wildcards (dots) in the above grep commands, corresponding to how AdapterRemoval itself treats such characters. For paired-end data, the ``--identify-adapters`` mode may be used to verify the choice of adapters, by attempting to reconstruct the adapter sequence directly from the FASTQ reads. See the :doc:`examples` section for a demonstration of this functionality. adapterremoval-2.3.1/docs/index.rst000066400000000000000000000023761350370616400173310ustar00rootroot00000000000000AdapterRemoval ============== AdapterRemoval searches for and removes remnant adapter sequences from High-Throughput Sequencing (HTS) data and (optionally) trims low quality bases from the 3' end of reads following adapter removal. AdapterRemoval can analyze both single end and paired end data, and can be used to merge overlapping paired-ended reads into (longer) consensus sequences. Additionally, Additionally, AdapterRemoval can construct a consensus adapter sequence for paired-ended reads, if which this information is not available. If you use AdapterRemoval v2, then please cite the paper: Schubert, Lindgreen, and Orlando (2016). AdapterRemoval v2: rapid adapter trimming, identification, and read merging. BMC Research Notes, 12;9(1):88 http://bmcresnotes.biomedcentral.com/articles/10.1186/s13104-016-1900-2 AdapterRemoval was originally published in Lindgreen 2012: Lindgreen (2012): AdapterRemoval: Easy Cleaning of Next Generation Sequencing Reads, BMC Research Notes, 5:337 http://www.biomedcentral.com/1756-0500/5/337/ .. toctree:: :maxdepth: 2 :caption: Contents: installation getting_started examples manpage misc Indices and tables ================== * :ref:`genindex` * :ref:`modindex` * :ref:`search` adapterremoval-2.3.1/docs/input_and_output.rst000066400000000000000000000001121350370616400216050ustar00rootroot00000000000000Input and output files ====================== Output files ------------ adapterremoval-2.3.1/docs/installation.rst000066400000000000000000000032351350370616400207160ustar00rootroot00000000000000.. highlight:: Bash Installation ============ Installing on Debian based systems ---------------------------------- Debian users on Stretch, Buster, or Sid, or using Jessie-backports, as well as Ubuntu users on Zesty or Artful, may install AdapterRemoval using apt:: apt-get install adapterremoval For other distributions, or to get the latest version of AdapteRemoval, please see the `Installing from sources`_ section below. Installing on OSX ----------------- MacOSX users may install AdapterRemoval using Homebrew:: brew install homebrew/science/adapterremoval Please see the Homebrew website for instructions on how to install and use Homebrew: https://brew.sh/ Installing from sources ----------------------- Installing AdapterRemoval from sources requires the presence of libz and bz2 headers. On Debian based systems, these may be installed as follows:: sudo apt-get install zlib1g-dev libbz2-dev In addtion, a C++11 compatible compiler and basic build-tools are required. On Debian based systems, these may be installed as follows:: sudo apt-get install build-essential To compile AdapterRemoval, first download and unpack the newest release from GitHub, and then run the 'make' command:: wget -O adapterremoval-2.2.2.tar.gz https://github.com/MikkelSchubert/adapterremoval/archive/v2.2.2.tar.gz tar xvzf adapterremoval-2.2.2.tar.gz cd adapterremoval-2.2.2 make The resulting 'AdapterRemoval' executable is located in the 'build' subdirectory, and can be run as-is. It is also possible to perform a system-wide installation of the AdapterRemoval executable, man-page, and examples using the following command:: sudo make install adapterremoval-2.3.1/docs/manpage.rst000066400000000000000000000374441350370616400176360ustar00rootroot00000000000000AdapterRemoval manpage ====================== Synopsis -------- **AdapterRemoval** [*options*...] --file1 <*filenames*> [--file2 <*filenames*>] Description ----------- :program:`AdapterRemoval` removes residual adapter sequences from single-end (SE) or paired-end (PE) FASTQ reads, optionally trimming Ns and low qualities bases and/or collapsing overlapping paired-end mates into one read. Low quality reads are filtered based on the resulting length and the number of ambigious nucleotides ('N') present following trimming. These operations may be combined with simultaneous demultiplexing using 5' barcode sequences. Alternatively, ``AdapterRemoval`` may attempt to reconstruct a consensus adapter sequences from paired-end data, in order to allow the identification of the adapter sequences originally used. If you use this program, please cite the paper: Schubert, Lindgreen, and Orlando (2016). AdapterRemoval v2: rapid adapter trimming, identification, and read merging. BMC Research Notes, 12;9(1):88 http://bmcresnotes.biomedcentral.com/articles/10.1186/s13104-016-1900-2 For detailed documentation, please see http://adapterremoval.readthedocs.io/en/v2.2.3/ Options ------- .. program:: AdapterRemoval .. option:: --help Display summary of command-line options. .. option:: --version Print the version string. .. option:: --file1 filename [filenames...] Read FASTQ reads from one or more files, either uncompressed, bzip2 compressed, or gzip compressed. This contains either the single-end (SE) reads or, if paired-end, the mate 1 reads. If running in paired-end mode, both ``--file1`` and ``--file2`` must be set. See the primary documentation for a list of supported formats. .. option:: --file2 filename [filenames...] Read one or more FASTQ files containing mate 2 reads for a paired-end run. If specified, ``--file1`` must also be set. .. option:: --identify-adapters Attempt to build a consensus adapter sequence from fully overlapping pairs of paired-end reads. The minimum overlap is controlled by ``--minalignmentlength``. The result will be compared with the values set using ``--adapter1`` and ``--adapter2``. No trimming is performed in this mode. Default is off. .. option:: --threads n Maximum number of threads. Defaults to 1. FASTQ options ~~~~~~~~~~~~~ .. option:: --qualitybase base The Phred quality scores encoding used in input reads - either '64' for Phred+64 (Illumina 1.3+ and 1.5+) or '33' for Phred+33 (Illumina 1.8+). In addition, the value 'solexa' may be used to specify reads with Solexa encoded scores. Default is 33. .. option:: --qualitybase-output base The base of the quality score for reads written by AdapterRemoval - either '64' for Phred+64 (i.e., Illumina 1.3+ and 1.5+) or '33' for Phred+33 (Illumina 1.8+). In addition, the value 'solexa' may be used to specify reads with Solexa encoded scores. However, note that quality scores are represented using Phred scores internally, and conversion to and from Solexa scores therefore result in a loss of information. The default corresponds to the value given for ``--qualitybase``. .. option:: --qualitymax base Specifies the maximum Phred score expected in input files, and used when writing output files. Possible values are 0 to 93 for Phred+33 encoded files, and 0 to 62 for Phred+64 encoded files. Defaults to 41. .. option:: --mate-separator separator Character separating the mate number (1 or 2) from the read name in FASTQ records. Defaults to '/'. .. option:: --interleaved Enables ``--interleaved-input`` and ``--interleaved-output``. .. option:: --interleaved-input If set, input is expected to be a interleaved FASTQ files specified using ``--file1``, in which pairs of reads are written one after the other (e.g. read1/1, read1/2, read2/1, read2/2, etc.). .. option:: --interleaved-ouput Write paired-end reads to a single file, interleaving mate 1 and mate 2 reads. By default, this file is named ``basename.paired.truncated``, but this may be changed using the ``--output1`` option. .. option:: --combined-output Write all reads into the files specified by ``--output1`` and ``--output2``. The sequences of reads discarded due to quality filters or read merging are replaced with a single 'N' with Phred score 0. This option can be combined with ``--interleaved-output`` to write PE reads to a single output file specified with ``--output1``. Output file options ~~~~~~~~~~~~~~~~~~~ .. option:: --basename filename Prefix used for the naming output files, unless these names have been overridden using the corresponding command-line option (see below). .. option:: --settings file Output file containing information on the parameters used in the run as well as overall statistics on the reads after trimming. Default filename is 'basename.settings'. .. option:: --output1 file Output file containing trimmed mate1 reads. Default filename is 'basename.pair1.truncated' for paired-end reads, 'basename.truncated' for single-end reads, and 'basename.paired.truncated' for interleaved paired-end reads. .. option:: --output2 file Output file containing trimmed mate 2 reads when ``--interleaved-output`` is not enabled. Default filename is 'basename.pair2.truncated' in paired-end mode. .. option:: --singleton file Output file to which containing paired reads for which the mate has been discarded. Default filename is 'basename.singleton.truncated'. .. option:: --outputcollapsed file If --collapsed is set, contains overlapping mate-pairs which have been merged into a single read (PE mode) or reads for which the adapter was identified by a minimum overlap, indicating that the entire template molecule is present. This does not include which have subsequently been trimmed due to low-quality or ambiguous nucleotides. Default filename is 'basename.collapsed' .. option:: --outputcollapsedtruncated file Collapsed reads (see --outputcollapsed) which were trimmed due the presence of low-quality or ambiguous nucleotides. Default filename is 'basename.collapsed.truncated'. .. option:: --discarded file Contains reads discarded due to the --minlength, --maxlength or --maxns options. Default filename is 'basename.discarded'. Output compression options ~~~~~~~~~~~~~~~~~~~~~~~~~~ .. option:: --gzip If set, all FASTQ files written by AdapterRemoval will be gzip compressed using the compression level specified using ``--gzip-level``. The extension ".gz" is added to files for which no filename was given on the command-line. Defaults to off. .. option:: --gzip-level level Determines the compression level used when gzip'ing FASTQ files. Must be a value in the range 0 to 9, with 0 disabling compression and 9 being the best compression. Defaults to 6. .. option:: --bzip2 If set, all FASTQ files written by AdapterRemoval will be bzip2 compressed using the compression level specified using ``--bzip2-level``. The extension ".bz2" is added to files for which no filename was given on the command-line. Defaults to off. .. option:: --bzip2-level level Determines the compression level used when bzip2'ing FASTQ files. Must be a value in the range 1 to 9, with 9 being the best compression. Defaults to 9. FASTQ trimming options ~~~~~~~~~~~~~~~~~~~~~~ .. option:: --adapter1 adapter Adapter sequence expected to be found in mate 1 reads, specified in read direction. For a detailed description of how to provide the appropriate adapter sequences, see the "Adapters" section of the online documentation. Default is AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG. .. option:: --adapter2 adapter Adapter sequence expected to be found in mate 2 reads, specified in read direction. For a detailed description of how to provide the appropriate adapter sequences, see the "Adapters" section of the online documentation. Default is AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT. .. option:: --adapter-list filename Read one or more adapter sequences from a table. The first two columns (separated by whitespace) of each line in the file are expected to correspond to values passed to --adapter1 and --adapter2. In single-end mode, only column one is required. Lines starting with '#' are ignored. When multiple rows are found in the table, AdapterRemoval will try each adapter (pair), and select the best aligning adapters for each FASTQ read processed. .. option:: --minadapteroverlap length In single-end mode, reads are only trimmed if the overlap between read and the adapter is at least X bases long, not counting ambiguous nucleotides (N); this is independent of the ``--minalignmentlength`` when using ``--collapse``, allowing a conservative selection of putative complete inserts in single-end mode, while ensuring that all possible adapter contamination is trimmed. The default is 0. .. option:: --mm mismatchrate The allowed fraction of mismatches allowed in the aligned region. If the value is less than 1, then the value is used directly. If ```--mismatchrate`` is greater than 1, the rate is set to 1 / ``--mismatchrate``. The default setting is 3 when trimming adapters, corresponding to a maximum mismatch rate of 1/3, and 10 when using ``--identify-adapters``. .. option:: --shift n To allow for missing bases in the 5' end of the read, the program can let the alignment slip ``--shift`` bases in the 5' end. This corresponds to starting the alignment maximum ``--shift`` nucleotides into read2 (for paired-end) or the adapter (for single-end). The default is 2. .. option:: --trim5p n [n] Trim the 5' of reads by a fixed amount after removing adapters, but before carrying out quality based trimming. Specify one value to trim mate 1 and mate 2 reads the same amount, or two values separated by a space to trim each mate different amounts. Off by default. .. option:: --trim3p n [n] Trim the 3' of reads by a fixed amount. See ``--trim5p``. .. option:: --trimns Trim consecutive Ns from the 5' and 3' termini. If quality trimming is also enabled (``--trimqualities``), then stretches of mixed low-quality bases and/or Ns are trimmed. .. option:: --maxns n Discard reads containing more than ``--max`` ambiguous bases ('N') after trimming. Default is 1000. .. option:: --trimqualities Trim consecutive stretches of low quality bases (threshold set by ``--minquality``) from the 5' and 3' termini. If trimming of Ns is also enabled (``--trimns``), then stretches of mixed low-quality bases and Ns are trimmed. .. option:: --trimwindows window_size Trim low quality bases using a sliding window based approach inspired by :program:`sickle` with the given window size. See the "Window based quality trimming" section of the manual page for a description of this algorithm. .. option:: --minquality minimum Set the threshold for trimming low quality bases using ``--trimqualities`` and ``--trimwindows``. Default is 2. .. option:: --preserve5p If set, bases at the 5p will not be trimmed by ``--trimns``, ``--trimqualities``, and ``--trimwindows``. Collapsed reads will not be quality trimmed when this option is enabled. .. option:: --minlength length Reads shorter than this length are discarded following trimming. Defaults to 15. .. option:: --maxlength length Reads longer than this length are discarded following trimming. Defaults to 4294967295. FASTQ merging options ~~~~~~~~~~~~~~~~~~~~~ .. option:: --collapse In paired-end mode, merge overlapping mates into a single and recalculate the quality scores. In single-end mode, attempt to identify templates for which the entire sequence is available. In both cases, complete "collapsed" reads are written with a 'M\_' name prefix, and "collapsed" reads which are trimmed due to quality settings are written with a 'MT\_' name prefix. The overlap needs to be at least ``--minalignmentlength`` nucleotides, with a maximum number of mismatches determined by ``--mm``. .. option:: --minalignmentlength length The minimum overlap between mate 1 and mate 2 before the reads are collapsed into one, when collapsing paired-end reads, or when attempting to identify complete template sequences in single-end mode. Default is 11. .. option:: --seed seed When collaping reads at positions where the two reads differ, and the quality of the bases are identical, AdapterRemoval will select a random base. This option specifies the seed used for the random number generator used by AdapterRemoval. This value is also written to the settings file. Note that setting the seed is not reliable in multithreaded mode, since the order of operations is non-deterministic. .. option:: --deterministic Enable deterministic mode; currently only affects --collapse, different overlapping bases with equal quality are set to N quality 0, instead of being randomly sampled. FASTQ demultiplexing options ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. option:: --barcode-list filename Perform demultiplxing using table of one or two fixed-length barcodes for SE or PE reads. The table is expected to contain 2 or 3 columns, the first of which represent the name of a given sample, and the second and third of which represent the mate 1 and (optionally) the mate 2 barcode sequence. For a detailed description, see the "Demultiplexing" section of the online documentation. .. option:: --barcode-mm n Maximum number of mismatches allowed when counting mismatches in both the mate 1 and the mate 2 barcode for paired reads. .. option:: --barcode-mm-r1 n Maximum number of mismatches allowed for the mate 1 barcode; if not set, this value is equal to the ``--barcode-mm`` value; cannot be higher than the ``--barcode-mm`` value. .. option:: --barcode-mm-r2 n Maximum number of mismatches allowed for the mate 2 barcode; if not set, this value is equal to the ``--barcode-mm`` value; cannot be higher than the ``--barcode-mm`` value. .. option:: --demultiplex-only Only carry out demultiplexing using the list of barcodes supplied with --barcode-list. No other processing is done. Window based quality trimming ----------------------------- As of v2.2.2, AdapterRemoval implements sliding window based approach to quality based base-trimming inspired by ``sickle``. If ``window_size`` is greater than or equal to 1, that number is used as the window size for all reads. If ``window_size`` is a number greater than or equal to 0 and less than 1, then that number is multiplied by the length of individual reads to determine the window size. If the window length is zero or is greater than the current read length, then the read length is used instead. Reads are trimmed as follows for a given window size: 1. The new 5' is determined by locating the first window where both the average quality and the quality of the first base in the window is greater than ``--minquality``. 2. The new 3' is located by sliding the first window right, until the average quality becomes less than or equal to ``--minquality``. The new 3' is placed at the last base in that window where the quality is greater than or equal to ``--minquality``. 3. If no 5' position could be determined, the read is discarded. Exit status ----------- AdapterRemoval exists with status 0 if the program ran succesfully, and with a non-zero exit code if any errors were encountered. Do not use the output from AdapterRemoval if the program returned a non-zero exit code! Reporting bugs -------------- Please report any bugs using the AdapterRemoval issue-tracker: https://github.com/MikkelSchubert/adapterremoval/issues License ------- This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 3 of the License, or at your option any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this program. If not, see . adapterremoval-2.3.1/docs/misc.rst000066400000000000000000000044771350370616400171610ustar00rootroot00000000000000Miscellaneous ============= Window-based quality trimming ----------------------------- As of v2.2.2, AdapterRemoval implements sliding window based approach to quality based base-trimming inspired by `sickle`_. If ``window_size`` is greater than or equal to 1, that number is used as the window size for all reads. If ``window_size`` is a number greater than or equal to 0 and less than 1, then that number is multiplied by the length of individual reads to determine the window size. If the window length is zero or is greater than the current read length, then the read length is used instead. Reads are trimmed as follows for a given window size: 1. The new 5' is determined by locating the first window where both the average quality and the quality of the first base in the window is greater than ``--minquality``. 2. The new 3' is located by sliding the first window right, until the average quality becomes less than or equal to ``--minquality``. The new 3' is placed at the last base in that window where the quality is greater than or equal to ``--minquality``. 3. If no 5' position could be determined, the read is discarded. Migrating from AdapterRemoval v1.x ---------------------------------- Command-line options mostly behave the same between AdapterRemoval v1 and AdapterRemoval v2, and scripts written with AdapterRemoval v1.x in mind should work with AdapterRemoval v2.x. A notable exception is the ``--pcr1`` and ``--pcr2`` options, which have been replaced by the ``--adapter1`` and ``--adapter2`` options described above. While the ``--pcr`` options are still supported for backwards compatibility, these should not be used going forward. The difference between these two options is that ``--adapter2`` expects the mate 2 adapter sequence to be specified in the read orientation as described above, while the ``--pcr2`` expects the sequence to be in the same orientation as the mate 1 sequence, the reverse complement of the sequence observed in the mate 2 reads. Using the common 13 bp Illumina adapter sequence (AGATCGGAAGAGC) as an example, this is how the options would be used in AdapterRemoval v2.x:: AdapterRemoval --adapter1 AGATCGGAAGAGC --adapter2 AGATCGGAAGAGC ... And in AdapterRemoval v1.x:: AdapterRemoval --adapter1 AGATCGGAAGAGC --adapter2 GCTCTTCCGATCT ... .. _sickle: https://github.com/najoshi/sickleadapterremoval-2.3.1/examples/000077500000000000000000000000001350370616400163465ustar00rootroot00000000000000adapterremoval-2.3.1/examples/Makefile000066400000000000000000000033331350370616400200100ustar00rootroot00000000000000 TARGETS := single_end paired_end phred_64_encoded phred_33_encoded \ collapsed_q50 multiple_adapters identify_adapters \ interleaved_input interleaved_output interleaved_input_and_output \ demultiplexing demultiplexing_only .PHONY: all ${TARGETS} all: ${TARGETS} single_end: AdapterRemoval --file1 reads_1.fq --basename output_single --trimns --trimqualities --gzip paired_end: AdapterRemoval --file1 reads_1.fq --file2 reads_2.fq --basename output_paired --trimns --trimqualities --collapse interleaved_input: AdapterRemoval --interleaved-input --file1 interleaved.fq --basename output_interleaved_input interleaved_output: AdapterRemoval --interleaved-output --file1 reads_1.fq --file2 reads_2.fq --basename output_interleaved_output interleaved_input_and_output: AdapterRemoval --interleaved --file1 interleaved.fq --basename output_interleaved_both phred_64_encoded: AdapterRemoval --qualitybase 64 --file1 reads_q64.fq --basename output_phred_64 phred_33_encoded: AdapterRemoval --qualitybase 64 --qualitybase-output 33 --file1 reads_q64.fq --basename output_phred_33 collapsed_q50: AdapterRemoval --qualitymax 50 --file1 reads_1.fq --file2 reads_2.fq --collapse --basename output_collapsed_q50 multiple_adapters: AdapterRemoval --file1 reads_1.fq --file2 reads_2.fq --basename output_multi --trimns --trimqualities --collapse --adapter-list adapters.txt identify_adapters: AdapterRemoval --identify-adapters --file1 reads_1.fq --file2 reads_2.fq demultiplexing: AdapterRemoval --file1 demux_1.fq --file2 demux_2.fq --basename output_demux --barcode-list barcodes.txt demultiplexing_only: AdapterRemoval --file1 demux_1.fq --file2 demux_2.fq --basename output_only_demux --barcode-list barcodes.txt --demultiplex-only adapterremoval-2.3.1/examples/adapters.txt000066400000000000000000000011541350370616400207130ustar00rootroot00000000000000AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCACCTAATCTCGTATGCCGTCTTCTGCTTG AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT AAACTTGCTCTGTGCCCGCTCCGTATGTCACAACAGTGCGTGTATCACCTCAATGCAGGACTCA GATCGGGAGTAATTTGGAGGCAGTAGTTCGTCGAAACTCGGAGCGTCTTTAGCAGGAG CTAATTTGCCGTAGCGACGTACTTCAGCCTCCAGGAATTGGACCCTTACGCACACGCATTCATG TACCGTGAAAGGTGCGCTTAGTGGCATATGCGTTAAGAGCTAGGTAACGGTCTGGAGG GTTCATACGACGACGACCAATGGCACACTTATCCGGTACTTGCGTTTCAATGCGCATGCCCCAT TAAGAAACTCGGAGTTTGGCCTGCGAGGTAGCTTGGGTGTTATGAAGAACGGCATGCG CCATGCCCCGAAGATTCCTATACCCTTAAGGTCGCAATTGTTCGAGTAAGCTGTACGCGCCCAT GTTGCATTGACCCGAAGGGCTCGATGTTTAGGGAGGTCAGAAGTTGAGCGGGTTCAAA adapterremoval-2.3.1/examples/barcodes.txt000066400000000000000000000001131350370616400206640ustar00rootroot00000000000000sample_1 ATGCGGA TGAATCT sample_2 ATGGATT ATAGTGA sample_7 CAAAACT TCGCTGC adapterremoval-2.3.1/examples/demux_1.fq000066400000000000000000003265041350370616400202520ustar00rootroot00000000000000@read_150_1/1 ATGGATTTTTGCATTCAAATTTCTATCCATCTGGAATTGATTTTTGTGTTATTCCGAGTTGGGGATTTGATCTTTTTCCCACGTGGATAACCAGTTGTTG + GGGGGGFHHHHHGGG?FEEHGHHHGFF@EEAFFEEGGFGHHHF=FFHHHFHHHHHEEFHHFE?BHFHHHHEHHFBEEE?CEHHHHHHFFGEHHHHEE?@E @read_150_2/1 ATGGATTGGTACTTGGGAAGCATTTAGTTCTTGTTGAAAGAATGAATGAGTGGATGAATGAATGAATGAGATGGCCCTTGAGCTGAGTCGTATCACTATA + HHGGGGGHHHHHHHHHHHHHHHHHHFGGFD@2CFGHHHHHHHHHE@FHH<=4@ABA3=4(,'-321+7D0/25<8%''%9DA @read_150_5/1 CAAAACTAGGGCCCGTGGACTGAGCCAGGGAGAGAGGCACCAGGAAATACAGGGCTGCACGTTTCCTTGTGGGCCACTGTGTGTTTGCTATCTGCACTGC + HHHHHHHHEFGHHHHHHHHHEEHHHD>GBEGBFHHHEEEEHHHHHFHHHHHFEEHHHHHHFHFB=@FBB?%04:8DBC<>B2EG5<5CD5*<5EBGGGGF @read_150_6/1 ATGGATTAAAAAAAACAAAAAAACTAAACAAAAAAACAAAAGAAAAGAAAAAAGAAGGTACACGGATAATTTTTTTTCTTTCTTCTGAGGTTTTTCTCTT + HHHHHHHHHHHHHHHHHHHGGGGGHFGHFHFHHHGHHHHFEEHHHGCGFHF@+73B:BBFHHHBHHFFHFHHFED1/;EGHHGHEFFFHHHHFFECDBCC @read_150_7/1 ATGGATTCAGGCGCGGTGGCTCAAGCCTGTAATCCCAGCACTTTGGGAGGCTGAGGCCGGTGGATCACTTGAAGTCAGGAGTTCGAGACCAGCCTGGCCA + HHHHHHHHHHHHHHHHGGFHHGHHHHHHHHHGDABCEEGHHHHHHHHGEEFB@:FB>-@DE86?DHFF:4D@4/97@:9-15<5GF7/36ACCFHHHHH= @read_150_8/1 CAAAACTAGCTAGGATTTGAATCTAGATCTGCCTGACTCCAAGACTACTGCACTTTTAAGAGGCAAAAGGAAAAAGTGTTGATAAAATATAGAATGAGAG + HHHHHHHHHHHHHHHHHHHHEEGHHHHFHFHHHHHFBGF98DBDEBDFFFFHHHHHGFHE7EGHHCFFF9/--;14-/EFHHHHHHHHHHHFFEHHHHFFHHHHHHHHHHHDHDHCFBEEA5>A>?HHHHHHHHHHFFEBBFHHHHEHEFEE: @read_150_12/1 ATGCGGACTAGCTGTTGCTTCTGCTGCTGGCCTGAGGCCTATACTTTAAGAACCTTTGGACTCGATGATGTTTAAGCTCCCATCCAGAACCAACATTCTG + HHHHHGGHHHHHHHCE@FEGGHHHHHFHHHFCCD(6*1CGGBFF?G@FHHHFHHHHE7DGFFGGHHHFFFED @read_150_13/1 ATGGATTTATTATGTTAGGCTTGAGAAAATTTAAGAAAGGAAATATAAGAATAGACATTTCTAGGTACTTTGGTCTAAATTCAATACCAATCCTTAAAGG + HHHHHHHHHGHHHFGDEBFFFEEDHGBDFGGHEEEFFFDEFFFEHHHHFEEDFBHFFFGHC?DDFHFFBFFDCFFFHFH6*;4,(7A1.:FEBCDHHHFH @read_150_14/1 CAAAACTCAAATCAGAGTGAACTGGAGAAGAGGGTGAGGACATTATAGAGGTAAGCATCGCAGCGAAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC + HGGFFHFCBHHHGEFEEEFGEF?E7@<;FDF;FHHHHHF=FHHFDCA@DBCFEHHHHHHHHEE??45;><9<53D==81/8?0DA>>@<<@CCD;@EEGF @read_150_15/1 ATGGATTCTCCAGGCCCTCGGGACGCGGCTTCAGCGTCCCTCGCTTTCCTCTCCCTGGCTCCGCTCCGGCCTTCGGGCCTCCTGTCTGCTCCTGGAGACT + FFDHHHHHHHHHHHGHHHHHHHHHHDEGGEF<@GGHHHHHHHHHHHHFGGFHHHFCEGDFFGE@DGEF=EHGFHHHHHHHHHHHHHHFFIGGEGEGGEFF @read_150_16/1 ATGCGGATCTCTCATCTGATATGATCCTACTTGCAGGGGGCAAGGGAAACTACATTAAGTATAGTACACCTGTTCTGAAATGACTTTGCCTCCCAATAAT + HHHHHHHHG.><:@@@GGHHEAHHHHHHHHHGFFHHEFFHGGFFFGFHGGHH:*,CFHHHHHFHHHFEGH?DHHFGHHHHHHHDA@FGHHHHHHGHGH@1 @read_150_17/1 ATGGATTCATTTTACTAGTCAATTTTTCTAAGTGCTTGAAGGGGGAACAAAAATATTTGGTTTCTGGCAATAATAACTATGACAGTAGCATAGAGTTTTA + C@CDHHHHEGGGGHHHHHHHGEFHGHFFGFHHHHHDADHHFHFHHHHHHHHHHHHHHHHHC90-<066BBGGGGGGGHHGG@FHGHHEFFFHHFDFHHE96.BEHHHHHGFHHF;EGHHHHHHFFGFEE @read_150_19/1 ATGGATTATAGATTGCAGTGAAAATAAAGCAGGGGGACCAAGCCCTTACCTGAGTGTCAATGCCTCCCTGGTGAGAGCTTTGCTCCATCACATTCAAAGA + GFGGFG?BGGHHHHG-@DF?FE.<>FHFHHDGFD@?@=@GEEEFFEEB@CFHHHHHFHHHFHHF=EFC@B75>.A@@AD?EEGGB@=EED6*735<7?DDFHHFF @read_150_21/1 ATGGATTGGAGGCTGAGGCAGGAGAATCGCTTGAACCTGGGAGGTGGAGGTTGCAGTGAGCCGAGATCACGCCATTGCATTCCAGCCTGGGCGACAGAGT + HHHHHHHHHHHHHHHHHHHHHFGHGHHHEFHHHHGHHGBFFGEHFHHHHFHHHHHFFB86EHHHHFFEFFHHHHHHHHHFHHDHHEHGGGBHHHHHB.*+ @read_150_22/1 ATGCGGATGTTCTAAAAGGTACATTTCAGCGATTGGGTAGAAAAGGGATTGTATGGAGAAATAGGCTGACTGGTCAGGTGAACAGGGCAATCTGGGAAAG + HHHHHHHHHHHHHHHHHGCCFHFHFFFFHHGB?BFFHHHGB9<7=>7C<;1130 @read_150_23/1 ATGGATTTGAGTTGGAAAATAAATAAATGAATGAATATAAATAATTGTAAAATAAAAATTCATAAGGTATACAGTAATCATACAGATGCACAACAATGAA + HHHHHHHHHHHGG==GEGHHHHHHGGGGEEEFHHHHHHHHHHHHHDFHHHFBGHHHHFEED5:ADFFFFHF@>EEBDEG@FFBDCH:E>A9?7.56/=BE @read_150_24/1 ATGCGGACCTTTCTTTTCATAGAGCAGTTAGGAAACACTCTGTTTGTAAAGTCTGCAAGTGGATATTCAGACCTCCTTGAGGCCTTCGTTGGAAACGGGA + FEGFGHFEEEB4@C=EEEFHHHHHFBCDHHHHHHHHHHHHBGG93?AABDFHHHECGGHFHHHFFFBHFFB<3:.6>AC>DGFFGHHFFHHHDFF@EDDD @read_150_25/1 ATGGATTTCTCAATCTCCCCACAGAGTGAGAGCCTGGCCTCCGTTGCTCTCAGTACATCAGAAGACACAATGACTCTGGTGCCCAGGTCCCAACCTACCA + GGGGGGGHHHHHHHHFHHHGDE=HHHHE=B=FF?5;BBEFDHHHHHHHHHHGHHHHHFFF5:FCDE6*6?DEHHDEEEF?-.&;=?DE;CE>EEEEHHBF @read_150_26/1 ATGGATTCTGTATTCTTTTGGCCCCGGTGATTGGTCCAGGGATAGGCCTGTGAGTTAATAAGATCCTTCATATTTATTATATGGACATTAGAGGAAAGAC + HHHHHHHHHGBEGHHHHHFGDCGGE;?C5GHEBEDHGGGEFFEEGDCD>E:.909CEEEFFCC@DEFGHHFFHFGGGGGHHEFGEFFGBFHFBCEEEDDF @read_150_27/1 ATGCGGAGTGCCTAACATGAACTAGTTTAAGAAACTTGAGGAATCCACATAACTATCCTTGGTTCCAATTTTTTAATTAAAAAGTTTAGACTAGAGCAGT + HHHHHGHHHHHHHHHHHHHHHFHG@=GFGHHFFFEFFHHHHGHHEE:?BFHHHHEEAEFFHHHHHHDDGGFDD?AHHHHHHHHHHHHGHHFFFEHGEE8= @read_150_28/1 ATGGATTGTTGGGCACGGTCGCGGGTGCCTGTAATTCCAGCTACTCAGGAAGCTAAGGCAGAAGAATTGCTTGAACCCAGGAGATGGAGGTTGCAGTGAG + DCCDFHHHHHHHHHHHHHFFFFGHHHHGGFGGGGHHHHHEDFFHHHHHHHHHHHHHHHHHHFHHHEDHFEFHHFFDB8>7C @read_150_30/1 ATGCGGAAAGGACACTTATATACAAACAGGAAGAGGTTCCCTGCTCTGAGCAGGTGCAGCCCCCATGATGTTTTAGTGCAAAGAAAAAGACTCCCTTTAT + E6BEDGEFGGFFCFFEBE=EHHHHHHDE78>=BGHHHHHHHHHHHFHHH:EDGHHHHHHHH=FHBCBDBHHHFFCGGGGFHHGDFFHHHHCEFGE7;7,* @read_150_31/1 ATGGATTAGATTATAAGTGATCTGATTGTATGCTCTAATCTTCCAAGTTGTTTTGAGAAAGATCTTCAAAGTTGTTTTAAAAGATCATTCTCATAGGAGA + @=EEEHHHHHGGFHHHHHHHHHHHHHHHHCFFHHHHHHHHHGGGGHFHFCFHHHHDHHHEFDFEEDFHBEBEFHFHGGFHHEBHHHFGEDHHDDF?:ACE @read_150_32/1 ATGGATTTATATGTCATAACCTCAAATGTCAGGAAAAGGAGATGGAAACTCACTATAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCACCTAATCT + EEEFFFFD5CECCCD9>BHHHHHHHGGGEBEE=@B@???,;>EB>ECCF?FFEHHFEDFHHHHFHGEHHHHFFFFHHHHEEEEGG @read_150_33/1 ATGGATTAACAAGTTATCAGAGGAAAAACATGTGGGAAAAGATTGAGAACAGAAGTAACATCTAGCTATCCAATACGAGAGAGAGAAGCCACTGAAAGTA + GGHHGFHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHE=EFBFHGHHHFHHHFFHHHFFF>AHHHHE66AGFHHABHHHHHHHHHHHGGGDCDDCGGGAB @read_150_34/1 CAAAACTACCATGCCAAAGGCACCGCCTCACCGAAAGGGATGATTAAGCATCTTTCCGAAAGAAAAACTAACCTCCACATGTTTTCTGTTTCTGCAGCGA + FFFFDFFHHGG?FHHHHHHHGGHHFD>77GHHHHFEHHHHHHEHHHFBH?HHHHFEFFHHGG?5ADFFFFFFEEEGGHHHHFBEBECEGFHABEGFB@>> @read_150_35/1 CAAAACTTTTAAAGGAGTAGAAAATAATAAGACTGATGATGAAATGGTGCCATATTATGAGATTTTAGAATGGTTTGCTGAGAATTGGTTTCAGCCATTG + HHHHHHHGGGGGGHHHGGFHHFEHHGFGFHHHHHGHHHHHHHHHHHF;:EGFHFFHHFACEDHHHFFHHH;;;@AFFFHHGFFD,BE;EEFFEBHHFHHH @read_150_36/1 ATGGATTTTGTTTCCACTTTTTGGCTATTATGAACAGTGTTGCTACAAACATGTATGTAGAAGTATATGTGTGGACATATGTTTTCATTTCTCTCAGGTA + HHHHHHHHHHHHHHHHHHHHHHHHHGFHHHFFE=GD?AEGHEEFGGGHHHEFHHHFFF;D2DDAAEEFFGF>:CCGGGGGHFHGFEA@DHHEGGGEHHHH @read_150_37/1 ATGGATTAAGCCAGTTCTCTCTGTGAAATATTTCTAAGCAGCCCTCAACCACCAGGTCTATGAGGGTCCCTGTTGTCCCTCAGCCAAGGCTGCTCTCTCC + AADDDEEHHHHHHE6EGHHHHHGB>@DAFHDCC @read_150_39/1 ATGGATTATCCTCCCACCTTGGCCTCCCAAAGTGCTGGGATTACAAGTATGAGCAGCTGCGCCTGGCCTGAAAGGTTTTGCACAATGATTTTGTTTCTTA + E=CDFHHHGEFFHHHHGHHGGD>CCBGGEGHHHHHHHHHHFFHHHHHHHHHHGGGFHHHHFFBGHFGGFFHDDDFFEHHD?@DFGG<@@EFFFEHE=>9: @read_150_40/1 CAAAACTTTGAACTATTCATATAATTGAAATAGAAGTGGTTTTCTTGGCCTAAATTGTCAAGAAACTCTCAGTTCTCCATTTCACTTGCTTCCCCAGGGA + GHHHHHHHHHHHHHH8=3DE>>><3=9<:DGGGFHHHHHHHHDEHHFAA:517D5CHHHHFBGHHHFHHHEHHF?HHGHHEEABDFBHHEGFHFEEE99/ @read_150_41/1 ATGCGGAACTGGAAGACTTAATATTGTTAAGGTGTCAATACTGCCCAAAGTGATCTGTAGATTCAATGAAATCCTTATGACATTTCAATGTCAATGAAAA + FBGGGFFFE=EFGGGHEHHHHHHHHHHHGHHDDDEFFGHHHHHHHHHHE;DDEEEFFFFHFHHDDHHBFHHHHE>FEGFHHHHHGBEEHHHHBBHADGHH @read_150_42/1 ATGCGGATGTGTATTGTGTATCACCCACGATACATACCACGTTCCCAATTCCTGCCTTGAGAAAAAACAAAACAGGGATTGTGAGTGGGGTTTCATGGAG + GHHHHHHHHHHHHHHHHHGHHHFEDFHHHHGFFFFFFHHHHHGFGBEEE @read_150_43/1 ATGCGGACTCAGGTGCAGGAGACCCCGGGCCATGCATCCTTCCGGGCAGGAAAATGTCAGCCAGCGCTCGCCGGCCGCTTTCAGATTCAAGATCGGAAGA + HGGEGGGHHHHHHHGHHHHHHGGGAEHHHHHHHHFHHHFFHFC=DFFGGHHHHHHAFFHHHHHHHEBBHE:>B@D9FHHHHFDHFC95DHHHG?BCHFHDBFFBFGFFFGEFHBBHFFEEEEEEDAEHGHHHFFHHG@EE?DD @read_150_48/1 ATGGATTAAAAATCACTGGTAGAGGATAAGAAAGTGAGACAGGGAGAGAAAGAAGCCAACAATGGGTGTATTACCAAGCAACTTACACCAGAGGTAACTG + HGGHHHHHHHHHHHHHHHHHHHDHHHHFHHHHHHHHHFFDCEEFDGFGFHFHHHHHHHEEFFEHHHHHHEEB?AEGGDDE1,56669EEFFGGHGB;=28 @read_150_49/1 ATGCGGATAATTGAAACAACTCAATTCTTGCTTTTTTTTTTTTTTTTTAGATGGAGTCTCACTCTGTCGCCCAGGTTGGAGTGCAGTGGCACAATCTTGG + HHHHHHHHHGGGHEFHHHHHHHGGGGGE@GGEFGGFFFEDDB;C>DD=EHHGGHHHHHHHHDFBHHHFDDEFHFFHHHHHHGGEFFGGGF@EBBA@@A@F @read_150_50/1 ATGGATTTCTTTTTCTTCTTTACGTTAATGCTGAATCTTTGGTTTTATGGTGATGTGTGTAATTCCAGTATAGAAGTTGGAACATTATAAATGGCTTTTA + EE;=@F?:?FEHHHHHGHHHHHHHHHGDHHHFHEHHGFHHHHHHBEHHHHCFCGGBFFHFFDAEE>DEHFCCFD?>4;><.:/2@CDEEHHHFCFEDGDD @read_150_51/1 CAAAACTGCAGCGAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCACCTAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAA + HHHHHHHFEGHHHHHEEFHHHHHHH@DDGHFGHHHHHHHFHHHHHHHFFFEBEFHHEFDEDHHHHHHHHHHFFHFGBGFFHHH?5=FDCGGFDFBHHFDD @read_150_52/1 ATGCGGAATCATCACAAAGCAGTTTCTGAGAATGCTTCCATGTAGCTTTTAGGAGAAGATATTTCCTTTTCCACCCCAGGCCTCGAAGCCCTCCAAATGT + HHHHHHHHHHHHHFEGEEHHHHEEE@CCBADBDDEGB>E @read_150_53/1 CAAAACTGTAGAGATGGGGTTTTGGCATGTTGGCCAGGGTAGTCTTGAACTCCTGACTTCAGGTGATCTGCCAGCCTCGGCCTCCCAAAGTGCTGGGATT + HHHHHHHGHHHHHHHHHHHHHHCBA??CEHHFG@E:<46EGGFFHHHEHFGEEBBFF;-19'6DCFEFHHHHFCFGHHHHHHGHGHF@D=FBAFFDAEBG @read_150_54/1 ATGCGGACAAGGCGGACAGATCATGAGGTCAAGAGATCGAGACCATACCAGCCAACATTGTGACACCCTGTCTCTACTAAAGATTCAAGATCGGAAGAGC + HHHHHHHHHHHFFC7*4BHHHHHHHGFEHHGFGDEFHHHHHHHEEHHHHHHHHHHEGEHHFFAFHHHHHHHFFAEFHHGGGHHHHHHH?GHHDFFEHHHE @read_150_55/1 ATGCGGATCTACCAATTTTTTTTTTTAATTTAGCCAAGCGTGGTGGCGCGTGCCTGTTGTCACAGCTATTTAGGAGGCCGAGGTGCGAGGAGCGCTTGGG + FHHHHHHHHHFGFFHHHHEEHHHHGHGGHHHHHHHHHHHHHFHHHHHHFHHHFBEHFGEBGGFF9;>ECDD>50GHHHHGDF8FH?HHEEA4D=>=FGBH @read_150_56/1 ATGCGGACCATCTCATCCTCCATCCAGTTCTGCACCCTTGCTGGAGAACTGTTGTTAACATTTGGAGAAGATGGACTCTGGCCTTTTGAGTTTTCAGCAT + GHHHHHHHHHHHHHHHFGHHHHHHGHHHHHFHEHHHGFFFDHEEHHGFFEHDGGHHHHHHHEHHHDFHHHHB@ADFHFDHFFGFHHGEHHFACE@;::DH @read_150_57/1 ATGGATTCATTTGAATTGCACATTTAACATATTGAAAGATATTAAGAATTTTAAGGTGGAAAACAAGAAAATATATAGTCCATATGTAATGAGGAATACT + FFHHEHHHHHGHGHHHCCEGFFG=?EF@HHHHFFFB@EEFHHHGGEE?FDDFHHHEFHHHHHHHHHHHHHH;AEDGGEEECB8DBC@C=(BC@E?CC@>?@?>DFCDC(>DEHEFHGCFHFFG?D=3+ @read_150_59/1 ATGGATTGGTTTATTTTCTATTTTTAAACATTTCTGCTTCACTATAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCACCTAATCTCGTATGCCGCC + HHHHHGGHHHHHEFHFFEGHHHHHHHCEHHGGDHHEAFA@ABFGFHHFGGEEDDHAHHHGFFFFFFFFDB@@AAACA8&*38;FHHHHHFHECBCF7>,7 @read_150_60/1 CAAAACTACTTTTATGGAAAAGCATAGGAGTAAATTTTGTGGACCAGTGATTTGGTGAACACATTTTAGACATAATGCCAAAGGCTTGATCCATAAAAGG + HHHHHHHHGGGFGE?CDDGHBE?BGFEGGFHHHHFC@@BHHEHHHHFHHHHHHHHHHE<.B;BG9AC:FHHFE@EEFHHHHHHHHHHEEEGEFFHHGHC@ @read_150_61/1 ATGGATTGGTAACTGTTGACATGTTTCCTCCAAGTCCATACCAATGCATTTGTTAGTAATATATTCACTATAGATCGGAAGAGCACACGTCTGAACTCCA + HHHHHHHHHFFFBHHHHHHFGHHHHHHHHHFGCCHHHHHHEHHHHFFFHDEBFHHDFFFHHHHHHHFHFFDECA9EGFHHHHHHEFDCECFHHHFGGB@F @read_150_62/1 ATGCGGAAACTTACTTCAACATTTCTAAACATAAAGTTTTGACAAAACAAAGCATTTAGAAATAGGTATCACTCAAATAGTGACAATACAATGTCACATG + HHHHHHHHGGGFHHHHHHHHHHHHHEGGFBGGDEEGBCB@HHHHFGGGFHEFHHHHHFFCFHFCBCCBFFCHHHHHGE@HHHHHHHHHHHHHHHHHHHHHHHHBAA=.29<9@705::>9<>.FEDEGEFFHHHHG @read_150_66/1 ATGCGGAACAGAGAGAGAACAGATATTCTTGCACAACTTACAAGAATTGGTGGCCTAGTGGATGAGAAGAATAAAGGAGAGGGAGGAATCTGTTTCTTTT + >9735B@?,;ABBEEDHHEHHHHFGFGBGGEEEFHGGGDHHHHHHHHHHFHDA@EEDCCDEGFHHHBE?+6CABFHHHHFG=8>EDGHHFFEEF?EFHHH @read_150_67/1 CAAAACTCTTGCCAGTCAAATGTTCTAGTTGCCATATTGCAAGTAGAGACAGGGAAACATAGAGCTCAAGTAACTGGATCAATTAGTGCAACAGGCATGA + HHHHHHHHHHHHHBD@CHHHGGHHFHHHHGHHHEDAFCDDEEHFEGC?DFHFHHHFDHEBFGHFFHHHHD>C==6.C.5.>FHHHFHFEHHHDDF;5>DD @read_150_68/1 CAAAACTCCAGTAATTAGAAAAGGGCAAATTACTCTGAGTCAATTGTGAATTGAGATGGTTCAAGTCAGTTTCAGGTTTATATGAGTTGGTTAATTTCTA + HHHHHHHFHDHHHHHHFHHHHHHHHHHHHHHHHHHHHHHHHHHHHD+2,8>?AAEEFEGGE @read_150_69/1 ATGGATTTGGCCGCTGCCTGCCTCACCAGCCTCATCTCAGGCCACTCAAGCCCTCATGCTCTGTGCTGCAGAGGCCCCAGGCCTCTTTCTGCTCAGGTAG + HHHHHHHHFBFFFFHHHHHHHHHHGGHHDDGFDGGFHGFFHDBFHHHHHF;FGGFHDEGBFGGDAEFHDEBDHHHGFFDBEGEBGFEHHHHHHHHHFFHH @read_150_70/1 ATGGATTCCTCTGTCCTTTTCCTCCTCTTCTCTTCATTTCCCCTGTGAGTGCTCTTTTACATTCTCTTCCTTCTTCATCTGTCTCTCATATTTTCTGTCT + HHHHDDDDFFFB@;AFADFHHHHHHHHEEBBDDA=@@6ADHHHHEAHHFFHHHHHHHHHHHHHHHHHHHHHHFFDHGHGHHHHFGHGGABGHF;>EF?A@ @read_150_71/1 ATGCGGAAGGGTAGGGAACAGCCCTTTCATTATGGCCACGTTTAAGTGTGGAATATAAGGAATAAAGAAACTCTATTTGAAGTTGGCCTTTCCAAAAATT + GHHHHHHHHHHHHHHHHHHHHGGFGHGEGHHHHHHEAEBEE5/.;GGGGHHHHHH?EBCEHEEHFHHHFHHHFDDGGGGGFGHHHHGGE@;>F?A.:CED @read_150_72/1 ATGGATTATGTTAATTTTAAGATGGCAGCATTTGGGGACATTTCATTATTTCCCATTAGGACACTGAAAGAGCATCAAGTATTTTAATCTGGGGGACTGA + HFFD@@FFHHHHHHGBFGGGHGCCHGHHHFHHHHHHCDBEHHHEFGHHHHHHGGFHHHFHHHHFHFHHHDHHEHHHHHHHHHHHHHHHHHEHFF?GGGD9 @read_150_73/1 ATGCGGATCTTTGTGCAAAATGGGTCCCACAGCTTCCTTCATTATAACTGCTCTTCACTGCTTGTTAGCGGCCTGTGAAAATTTGATTGAATTAATTCAA + HHHHHHHHHHG8ED@AB>?CGGHGGHHHHHHFFFFEEFBGHHHHHHFHHHHHHGHHFDD>HHHHFFCFHHDBFHDGGFFEFEHCAFEHHB:@CA?CFFHH @read_150_74/1 CAAAACTTGAGTGAGAACATGCGGTGTTTGGTTTTTTGTCCTTGCAATAGTTTACTGAGAATGATGATTTCCAATTTCATCCATGTACCTACAAAGGACA + HHHHHGGDCHHHHHHHHHHHHHHHHHHHHGEF6CHHHHHF@DEHHHHGCFFHHHHFHHHH@A?EHEHFEEHHHHHHHHGGHHHHFB//2,>?=EHE<766 @read_150_75/1 ATGCGGAATTGGCTGGGCTTCTGCATTCCTGTTCTTCTAGTTCCTATTTCATTTTCAAGTTAAGTTAAATGTCAAAGGGAAAGATTCAAGATCGGAAGAG + EBBGEHHHHHHHHHHGHHHHHHHHHHEHHHGGABC868+BHHFFD@99DHFHHHHHFGE?'>CDEEAD6><< @read_150_77/1 ATGGATTCAAAAAATATGTTTAAATAATGAATGAATGAATGTAAAGGACTGAGCCATAAGAATTCAGCACAAATCAAAAGGGCCACAGAGCTCAATATAG + HHHHHHHHHGGHHHEFHHHHHHHFBEHHHGGEFHF=CEBFGEHHHHDDHHBCFBEHHHHFHHHHHFCDGHHBFFDFGFFFEGHHHHHFHHHHGDDF?EHH @read_150_78/1 CAAAACTTCCCTGGGACAGTAAGAGGGAGGAGAGAGAGAGAGAGAGAGAAGAGAGAGGAGAGAGAGAATGTGTGAACGTGTAGCAAGATGATTTATTCTC + GHHHHHHHHHHHHHHHHFF4>@BEEGGHDHHHHHHHHHHHFHHHFHHEBEFDHHEE@;;><878?EEHHHHHFHD848);<@CFHFHHHHHHGHFHHHHH @read_150_79/1 ATGCGGAATGTTTCATATATTTTGAGTTAATTTTGATATTTGGTGAAAGGTAGGATTCCAGCTTCAATTTTCTGCATATGGCTAGCCAGTCATTCCAGCA + =BC@58DGHH5>6@@GHHGGFGGHHHHHHHHHHHGHHHHHHHHHHHHHC@A+)7EHHGFHHHHHF=A?A(2,4DDHHHHFHHHHHGHEHHFGHHDCEF6+ @read_150_80/1 ATGGATTGCATGTGATAAAACGTTTCTGTGAAAGATTTATGTCTGCATAATATTTCATCATATGAATGTACCAAGGTTTATTTAACCATTCCTATTCTGC + HHHHHHHHGHHEEGGDDEGGHFHHHHHHHHHHHHEFHBBFGEFHFFHHEEFFFHHHHHHEFEHFH?FBB7DFFDCHHHHHHHEGHHHHHDGBDDE=:EAD @read_150_81/1 ATGGATTCTCTTCCATTACAGTATAATGCTTTATCTACCTTCAATCATAACTCAGTCTAATCCAATATGCTTTGATTGTTATACTCTCTGCATTTCCAGT + HH@BEGHHHHHEE8DEDDBFGHFEHGGB?G<@7<80842.:=79BF9CEEEGEGHFGGGEHHA;=>?2)7*7?;>DEEFFFGEHHHEHFGFDEB7<.9<= @read_150_82/1 ATGGATTGATTGATGGACTGGTTTCTCAGTTAGGAGAGCGAATTGAGAAGTTGTGGAAACGAGATGAAGGAGGCACAGGAAAATATCCTCCTGCTAGTCT + GGGHHGDG@DFGHHD=EGGHEHHCFHHFFHHEGACD=@CFFHHFFFEC778EFHHHGHHHHEEEEHFEB@GBDDDGGGGGHHHEFHFEFDEHHBE02'>@ @read_150_83/1 ATGGATTCCAGTTATTGTTTACCAGAAACAAAACATGCTTCACTTCTCCCCACACTCTCCATTTGAATTATCATTTATACAACTAACACATAACATCTTT + HHHHHHHHGHHGGGHHHGGGHHHHHHHHHHGGHHHHHHGFFHHBFHHHHHHHHHHFFHHHHHHHHHHHHHFFHHHHFHGHHFH@BGDECFHFHHHHG?;FDEFCEFHHHHHHHFD?EEDGGGHHHHHHHHHFFFFHHHHHHFF>,:CFHFHFFHEE<4DCECCFGEEBDD?7DFF;DB:4DD>;;7.1 @read_150_85/1 CAAAACTATCCTCTGGGTGGGGCTGACTGCGCGGCACCAGCACAGTCCGCAGTCCTTCCCACGCAGGACCTTCATTTTTCCCAGTCCAGTCATTCAGCTA + HHHHHHHHHHHHBBBDGGGHHEEDFHHHGFEECGGGBB?DHFFFFGADFFF<9>EH?CHHFHFFHDFFFB@B:?EGGFEDBGHHDGGEEFGGGGEHHEEE @read_150_86/1 ATGGATTCTACTTTGAAGACATACTCTTAAGCAATCTGGATCTTAAATTTATGTGAATACATTTTTAGAAAATGATAAAGAAAAATGGAATTACTTCAAA + CCA8>-?@@DDEEGGGGDDCGDHHHHF2/*((19:GHHHHHHEHHFEFHHHDBGFH;:=>HHHHHHFHHFCEEHHFEHEG5CCBHHHHHHCFFGGE<:>4=,>>;6 @read_150_88/1 CAAAACTAATGCATTTAAAGTTGGGAGGAAAACAAAACACTACAGCAAGAAGAAAAAGGAGAAAATGCAGAGATGGAAATATGGAGGCCCACCTCTTCTA + HHHHHHHGHHHHHHFE@HE>E8DDDHHHGHHHHBHHGGEF?FFFFHHHHEC;>;>DEGHHGGFBHHEHCD;8/*3EDFEEHHHHHHHHCC9=HF-7?FBH @read_150_89/1 ATGCGGAGACAGATCAACGAGACAGAAAGTTAAAGATTCAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCACCTAATCTCGTATGCCGTCTTCTG + HHHGHHHHHHGHHHCFHHHHHHHHFBFFFFHHHHHHHHGFHHHHHDCFHHHEHHEBHF=:<7)3;:11C(;9DAHHHHHHHHFEEH@1CA2*=:1<497F @read_150_90/1 ATGGATTATAGCAAAGACCAGGAACCAACCCAAATGTCTATCAGTGATAGACTGGATTAAGAAAATTCACTATAGATCGGAAGAGCACACGTCTGAACTC + HHHHHHFGHHGGC@@8>=FHHHHHHGGHHFGGGFCFFHHFHHHHHHHHHHHHFHHGEEHHHHEGGHHECEBDD?9<:8@>ADCCFFFHHFGEFFHGF @read_150_91/1 CAAAACTGCAAAGCCACTGTAGCCAGACTGCCTCTCTAGATTCCTCCTTTTTGGCCAGGGCATCTCTGAAAAAAAGGCAGCAGCCTGTAGTCCCAGCTCC + HHHHHHHHHHHHHHHHHHHHHHHHHHHEEHHHFEHHHHHHHHHHHG8-.8DEGHFGGDCFBFGCCBFHHHECBD>CD?ACCHHHHHHHBEBFFFF><-&' @read_150_92/1 ATGCGGACCCATCAAAGTCAAGGAGCATCTGTATCTTCATAACAGTATATTTTATAATAAAATGGGATAGATTCAAGATCGGAAGAGCACACGTCTGAAC + GFFFGGGGGHHHHHHHHHHHEEFGHHGGHHHHEFHFFHHF9<47ADDCDHHHFFFFCDFDEEBDFHHHHEAFEHHHHFBBFHHHHHFBFHDA?AD?@@HH @read_150_93/1 ATGCGGAACACTGGGGCCTGTCAACGGGTGGGGGGCAAGGGGAGGAATAGCATTAGAAGAAATACCTAATGTAGGTGATGGGTTGATGGGTGCAGCAAAC + FFFGGEEEEFHHHHHHHHHHHFEEEGHHHHH?FHHHC6DFHHFHF?FHFHFHHHGGHHHFFHHHGFFFFBDE48+077(/DGGGGFHHG2@GGHHD1AAF @read_150_94/1 ATGGATTGCAAAGGTTGCAGTGAGCTGAGATCACACCACTGCATTTCAGTCTGGGTGACCGATCGTGACTCTGTCTAAAAAAATAAGAAAGGAAAAAAAA + EEFFHHHHHHHHHHHHHHHHHEGGHHHE@D;AGHHHHHHHHHHHHHBHHHHHHHHF;9A?EEGGAEABBAEHFEFEFHHHHHHHHHHEED9EEEHGFF=/ @read_150_95/1 CAAAACTGGAAGCCCCTGAGTCCCCCTGGTTGGGCATTGGCACAGAATGGGGTGGGTACCCAGCCTCTGTCCCTGCCATCCCCTCGTTGTGACACCTGCC + GGHGGFGHHHHHHHHHHGEEEEFHHHHFEGHHHHHHHHHHHHHHFEFDGGCF?@@=;EHHHHFDBFCCFGEDDFFDABAB>B@@>(43?DHHH@>FFGHG @read_150_96/1 ATGCGGACTGCAGGGCCCAGCACTGTGGAATAATAGTGCTGTGTGCCTCAACTCTTCCCCATCCTGGTGGCAAAGAGGAAACAAGGGAGAAGGATATGGT + HHHHHHGEFHHHHGDHHHHE@EEEABGFGGGFGGCFFHHFGHHHHHHHHHHHHD?FEDBFFE9EFEFHFE?CEFFHHHHHFGGGHFGFEBD.=EHHFHG'.:>@D55?AEDBEDFHFDC4ADAF@FDEHHEFDGEEFFHHHHHHHHHHHHFFEFFFHHFFHCH @read_150_99/1 CAAAACTCTAGCTATTCACTTACTGGTATGATGGTTATTTTTACCTGTCAAGTTCACTGGGCCATGGGGTCCCCAAATTAAATATTATCCTGGATGTGTC + HHHHHHHHHGGGHHHEDFEHHEHHHHHHHHGGEFHFEFFHHHHHHHGFDDGHHHHGFECFHHHHHHHFEHHHHHF@=FFCFFHG=DBB4DC??CEHFFHH @read_150_100/1 CAAAACTATAATAAATCTATTTTTGTATGCCTACCTTGCTAGACATTCTACCCTTTTTGCTGCGCAGCGAAGATCGGAAGAGCACACGTCTGAACTCCAG + GGHHHHHHHGHHHHHHHHHHGHCHEHHHHHGC:BFGHHHHGGHHHHHDDCFFEEFHFEFGHHHHHHHHHHHGGFHHHHHFHFFBE;7,,: @read_150_104/1 ATGCGGAGCGTTGTTAGGTGCCTAGGGAAACAAAGACAAATCATTGCTTCCTGTCTCCAAAAAGTTCCCCATTGAGCAAGCAGGTGAGCTACAATAAAAG + HHHHFGHHHHHHHFHHHHHHHHGFHHHHGFHHHHFGGHF<@FHHHHFHFFEFHFHHHFHHH=E;AD>E;>BHD>49>>>@DDFHHHHFHHHHFBGEHFFE @read_150_105/1 CAAAACTTGCAGCTGACATGATCGTGGCTCACTGCAGCCTCAGCCTTGCAGCGAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCACCTAATCTCG + DFGGGHHHHHHE867++GDE?FFHHHGGGGHEGGEEEFHH?HFHHHFFHHHFFFHHHHHEFFHFFE?C?A5338AHFFGGHGHHHHHDHEEHHGFEGHHF @read_150_106/1 ATGCGGAAAGCCATGGCTTACTTTCTTCCTATAGACAGTCCAGGGCACATGCTAGCCATGGACTTTAGCTGCTGACACCCAGGTATGAAACTAAAATGAA + HHHHHHHHHHGGFFGEGGGGFGGFGGHHHHHHFF@<,5*0+(38FEA7C904)1>DBFEC;EBFHHHHFHFFFHGF>D9FFHHHHHHFFHHHBICE94+21031,-.EEECFHHHGHFFGFDGBFF5ACCCC @read_150_109/1 ATGGATTTGACATTATACCTCCCCTTCTGGCCATTATGCTAGTGTTGTCATGTAATTTGATTTTAGACATGTTACAAACCCCAGAATCCATTATTATTGC + HHHHHHGHHHHHHHHHHHGGEFHHHDHHHHGGGHHHHHHHGGFBHFHEGHGG?@EGHFFFDA??EGGFEBD@EEHHGHFFHHHH?FFBGHGG=6>85EEEHHFHHBHFFG?5EFEFHHFDAB=6:8+39EFGEBCDFFHHHFHHFHHHHHHFF9B @read_150_111/1 CAAAACTCAGGCTGGTCTCAAACTCTTGGCCTCAAGTGATCCACTCGCCTCAGCCTCCCAAAGTGCTGGGATTCCAGGTATAAGCCACCGTGCCCGGCCA + GGGE=/BA>@><>268BECCGGF=;=EHHHHH=G @read_150_112/1 CAAAACTAATACACACACACCCCCCATGTACACACACTACACACACACTCCCCACATGTACACAAACACTACACACACACACGCCCCCCCACATGTACAC + HHHHHHHHHHHGHHHHHHHGHHHHHGGFEEHHHHHHHHHHHHFGHHHHGGHC:>BEHHHFEFCHHFHHE>;>AFHHEFECFHEHHF?;DFEHHF?DCD?>@>AEBHD>*8)6DFFFEBBCFDBEEGGHHHGHHHHGFHHHHEA;+0 @read_150_114/1 CAAAACTAAGGACTACTATAACAACTTACCACAAACTTGGTATCTTAAAAACAACAGAAATGTATTCTGTCAAAGTTCTAGAGGCCAGAAGTCTGAAATC + HHHHGGE@DDEC4BGHHHEDHC9EFHCCHHHHGFB @read_150_118/1 CAAAACTAGATTCTCGTTCTATATCTCATCACAGTGCCAGCCCTGTTTTTAGCCGGAAAGGATTCAGGAGAAACATTATTATGCATTCTGAACTGGATGC + GGGBDBBGGEHHHHHGGFFFHHHHHHHHGFB9>7)1;D@FFHFFHHHFHHHHGHFD:@68DFHHHHHHHFFDBBFHHGGE@ACFFGHHEFGHHFEHH?@5 @read_150_119/1 ATGCGGAGCAATTTGGGAGGCCGAGGTGGGCGGATTGCCTGGGGTCAGGAGTTCAAGACCAGCCTGGCCAACATGGTGAACCTCTGTCTCTACTAAAAAC + GGHHHHHHHHHHHHGFGEHHHHHHHHHHHHGGB79FFHHHEHHFHHHGGHHHDDEAEFHH6*/-:&7CDCEFHHEFFGHHHHHGFDGFHHHHFE@CCEED @read_150_120/1 CAAAACTATTATAGGACTTCTAATTAATGTTCGAATCCTTGGTTCACAATCCGGTTTTGACACTCCCTAGGTACTATTGCATTTGGCTTCACTTTCCTCA + HHHHHHHHHGHHGGECC@GGGGEHHHHHHHGHHHFHHHHHEGGHHFHHHHC5;)4>@FBCEEHFFGBDDEFBE.=?@>72CEEEAC9CGG<>ACEDBEFH @read_150_121/1 ATGCGGAGAATGACCAGTTGTATTTGGGTGGGATGTTGCTCAGAAAGGTTTTGTAACAATAAATGATGCTTGAGGAAAGTCTTCATTAGGTATTATAAAG + HHHHHHHHHHHHHHHDEFCCCBEFGE@EGHHHHHHHHHHHHGHHDBEDAAFBEDHDD6@EFH @read_150_123/1 ATGGATTTATAAAATTAAAAGAGAAGGCAGGCTAGGGTAAACCCTGAAAAACATCAGCATTTAAAGACAACCTGAGGAGGAGGAGGAGCCAGCCAGCAGA + HHHHHHHHGHHHHHGHHHHHHHHHHHHHHHHHHHHGEFGH>-1DDCGFHEGC?FA?C@@HFFFH>*@;BEGFEHHGHHEDHFFFEHHHHHFHFF?EE4A: @read_150_124/1 CAAAACTAAGATAAGTAGGTTTTGCTCTTTGCCTCAGTGGTCTTTGACGGACTCTGGGTACTAAAGCTAAGATGGAATTGAGGGAAGCTCCTAATGCCTC + GHHGHHHHHHHHHHHHHHHFEGHHHHFGGGBCDBEBCFBDEHEHFFFFGFFGHECDDC?EEB@CD7FHBFFFBBFFGHFHHHHHEHHHF8EEHG?DDHHH @read_150_125/1 ATGCGGACATAAGCCAAAGTCCTATTGCACACTAGTACAAGAGAAGAACCTTCTGAATAAGCTAGTTCAAAAAACCCAATATTCTGAGGTCATTATATGG + CCDFHHHHHHFFGGHHEFEEGGHHHGFGGFFHHHHHHHHH>EEFHHHHHHHHHHFEE?AAFHBGEHF?7>)(><<>ACACHHHEEEFBEEHHHHHFFFEG @read_150_126/1 CAAAACTTGTTTGTTTTTTAAAGCAACATATAGTTGTTTACCAGCTGCATACTATTACTAGATTCCAGCCTCTTTGCTTTTACATCTCTAGGTTTGGTCA + HHHGEGFFF=DDFFEFFHHHHHHHHGFHHHHHFFHGHHHHHHHHHHEFHHHHHHHGFCCFBFEEHHEE=BEEEEBEC?<43%/@@>.2?>4FFAB<8HHDGFBBFGDGFHHHHHHDHHEHHHHHHHHFEFFGHFHHGE>EED:9EHGFEEBBCF?DCED8).@EEFBAEGHHHGBEGHFFHHHFEHH @read_150_128/1 ATGGATTAGTGGTTGGTGCCTCGGCTCTCCTGAAGTTGAAGCCAAAAGTGAACCCAAACGCCTACGCTGCACTCCATCTCCTCCCAGCTGAAAGCCCCAC + HHHHHHHHHHHHHHHHHEFG@HGFHEAGGHFB-CHHHEFEHHFDCFGFFFHHHE=@@73@@5>9,7>87?4@:CEEE90DHHFGFFGHHHFFHHFGIGCC @read_150_129/1 ATGCGGATAAAATGTTTAGAGATTTGTCTCTATATTTTATTTTCACTTGGACAGTATGAAGTATTCACCAAACACACTTACTTATCAGGATGATGATCAG + HHEHHHHHHHFEEEFBE@C4DFHGEHFFFEFFEFDFHHEEGHFFFHFGGFFFAHHHHFFE?;D=BG?:%.446CCGGDCEDBEGHEHHHHHHEEFBFF== @read_150_130/1 CAAAACTTAAACAGAATACAAATTGTGTACACAGATGGGTGTGTCACTATTGCACTGTCACTTATGTAAGTGCAGTTTAGCATTTCTTCTTTCCTTTTAA + HHHHHGGFDAECCGCDHHHHHHHHHHHGHHGGGHHHHHHHHHHFHHGHHBFGGHHHCEHFFHFHHEEHHHDEADBFDACDGGEGHHFFHHFHHHHHHBFA @read_150_131/1 ATGGATTAGCCCAGCAGAAGCTGTGTTGCTTTGTATGATGTAGTCTTAGAAGTCACCTGGTATCATTCTGTCACATTCTGTTGGTCAAGACAGTTACAAA + HG;AADBDHHHHHHHHHGFABEGGFFGFGGGFGGFHFGD=FHHHHHHHHE??DFF?<<(12=?FEBEGEFHHHHEBAEFHHHHGGHE8)4EEE=DDBD41 @read_150_132/1 ATGCGGATCCCAAAGATTCAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCACCTAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAA + HHHHHHHHGGHHHHHHGHHGGGF@DCGHHHHHHHHHHHHFE>CHHFBHHHFBDFBFHHHHHHHEFHHHDCE@EHHGHHHHGEHGGH@*@EE:>HE8ACC?HHEAFFHHHHADBEAHHHFHHFHHEEBDEEGHFHECDDDADFB=;8>F?78FHFEE@GHHH @read_150_134/1 ATGCGGAATTTACAGATTCAATGCTATTCCCATCAAGCTACCAGTGACTTTCCTCACAGAATTAGAAAAAATTACTTTAAATTTTACATGGAACCAAAAA + GHHHHGGHHHHHHHHHHHEGFFEHFGGHGGEGGGECDD@57ADBFDHHHHDHHFFBBE<@D783@BC5DE @read_150_136/1 CAAAACTTATATTATTTTTCTTTGTCTTATTATATTTTCAAACATTAAACCATCCTTGCATTTTAAGAATAATATTTAATGATGTGTCGGGAGACAATTC + HHHHHHHHHHHHHFFHHHHGGHHHHHHHHHHHFHHGHHHHHHFHHGHHHHFHHHHHHHFEHHHHHHFFEEEFFEGGFFHHHHFGHHHGGHHHHHEGECB? @read_150_137/1 CAAAACTTGGAAGGCCCCTACCCACCATTCCAAGGCCTTTCAATCTTACTCGGACCCAGTGTCTCCAAATCTTAGCCATGAAGTTCCTCCTCACATCAAA + HHHHHHHFHFBDABE>>C>EEGHHFHGGHHHHHHHHFFHFFFHHHFHHHHHHGBCAFEECB8CFFDFFEHHFDDFFB/72DFFFHHHHHEHFCFHHHH?E @read_150_139/1 ATGCGGAAGGGTGGAAAGACTGAGGCCCAGAGCAGTTAATCAACTTGCCTAAGGTCACACAGTTAATACATGGCACAGGTAGAATCTGAACTCAGCCCTT + HHHHHHHHHHHHHHHHHHHHGGHHHHHHHHGFHHFFGDBFFGBGDFBCFEEBFGFHHHHHHCECEHHHHHFFFHEHHEGHHHHGGHHFG&1AA@+>=GGHHHHHFBFH=EHGGCBHDDD74CD4 @read_150_142/1 ATGCGGAAGAGTAAATGAAGTGGGAATGAAAGAATAATTCATAGGTGGATGGATGGAAAGATAGATAGATAGATGGATAGATAGATAGATAGATAGATAG + HHHHHHHHHHHHHHHGHHHHHGHHHHHHGGHHHHHHHHFFHEHHFHHHHFFFGFHEGFHFFHHHHHGHHHHHFFHFFFGD?@B?EHFFHFGDFGGGGHGG @read_150_143/1 ATGGATTCACAAATGATGTCAAATATCTATGCAGATTAGAGATCATAGATGAAAAGATACAAAAGTAGACAAAAGTTTGGGTAAGAGAATTAAAGCTCTA + FFGGGGHHHFHHHHHHHHHEGHHHHHHHHHHHHHHHHFHHHHHEC?@=E2DFEEHHHHHFFHHEE9ABDCBFBG=?BBEHFGDFB=)&16>BBEG?E51A @read_150_144/1 CAAAACTTGCTCTATGAAAAGCAAGGTTAAAGTCTGGGAGTTGAACACATGCCTCACAAAGAAGTTTCTGAGAAGGCATCTGTTTACTCTTTAAGTGAAG + HHHHHHHHHHHHHHG;BF8=HHGGED9BABCC=>=>FHHHHHHHEHHHHHFFFHHHHHGGGDDFFHHHGFHHGGFHGGHFFCBFGAFEBDFGHHHHHDEF @read_150_145/1 CAAAACTCAAACCAAGTTTTGAATAAGTCAACTTGTTTATAATTATATATTCCTTGACAAAAAAAGCAATGTATTATAAAGTGAATTCAATTACACTCCT + HHHHHHHHFHHHHHFFGGGDGGHHGGC>DGHHHHHEBFHHHHHHHHHHHFB?DB<9?DHHHHFHHFEFHBGFDEDGCC<4DECBEEDFGGFGD(-:-20/ @read_150_146/1 CAAAACTGTACCATATACACCGATTCTGAGGATTAGGAGGGAGACACCTTCGGGGGACCATGATTCTTCCTACCATACTCTGGATATTAGCAGGAGGGGT + HHHHEFFGGDDDDEHHHHHHHFHHHHGHFFDGHHHHHHFHHG?DDAEE5BBEGHH=CCCA8;GEBBGFHHHHFECGGFFHHGFEGFHHHHHHGHBGHHFDHFFGDHHFH@6?A.DGEEBBCBDCCBD;;DGHHHHFFCBH @read_150_148/1 ATGGATTTTTTCCTCCCTATTCCCTTATCCCAGCTTTCGTGAATTTCCACCAGTGCCTTCGGACTACAGCTGTGTCGCACTTCCTGCTGAATATTTCCTT + HGGHHHHHHHHHHHFHHHFFGBHHHHHHHFFHFHHHHHHHHHHHGEFFHHHHHHHFHHHHHHHHDADDABCFEHFEA@AAGHHFGHHHHHHHHFHHFB>? @read_150_149/1 CAAAACTATGTCATCCCTGTGACTAGGAGTCTAATCTTTGGGCCAGCAGCAAAACAGGGGAGCTAGCAGCGAAGATCGGAAGAGCACACGTCTGAACTCC + G8EEDFHHHHHHHHG?BDC/)>:?FEEGGE>AA?FHHHHHEFBBFEEBEBFHHDFHFBHFFD?8=CEB?5>>.GFBHHHHHDHFFHHHHFHHHHHHFFF@7.DHHHHHHGG @read_150_151/1 CAAAACTATTTTCTCCCCCAAATCAGACCTATGACTAGCAGTGTTGTTGCAAGACACCACACTAGATAGTATCACCACACTAGATACCGCAGCGAAGATC + HHHHGGGHHHHHEBFFFFFGHHHHHHEEHHHHHHHHHDDDBHHHHHDGGHFB>-*5@>A2+DEHFHHHFFGA6FBFHHHHHHHEFCC=<B5?8<> @read_150_152/1 ATGCGGAACTATTTTTTCCCAGTGAATTGTCTTTGCACCTTTATCAAAAATCAGTTGTCTCTATGTGTGGGTCTATTTCTAGACTCGCTTCTGTTCCTTT + HHHHHHHHGFFEEGFHHHHHGHHGGHHHHABDC@GGF@BEB=GGDFHHGGGFHHEA?DF @read_150_156/1 ATGGATTCCTTTCTGATAGTAGGACATTCTGACAACAATGACTTTGCAGGAGGTTTGTTTCAAATACTTACACCAGTAAGAAGGTATTTTGCATTTCCTA + HHHHHHHHHFGGEFFHEHHHHHHHHHHFFEGEEGHHFBGHHHHH>>DBF@BA@BFGGHHHHHHHHGGFGFHHHHE.<@:9D>?EBEED==:74?GFB?E8 @read_150_157/1 CAAAACTCTTGCCACTGCCCAGGATGCGGTCACCGCTCTGCATTACTCAGGAGAAGGACCAGAGAGTGGAGAGTAGAAATGGGAAGGAGGAAGAGGATCA + HHHHHHHFFE@GEEFHHEGGHHHHHGHHHHHHGHHHHFHHHHHHHHHHHFGGGHHHHFFFHHHHHHEEADFCBE@E;4?EGHFGGHHHHHGCBGGHFHFF @read_150_158/1 ATGGATTGAGAGCAAGGAAGTCGGCAGAGGCGGCGACCCTGGCGAGGAAACTTCCCAGTAGCTTTGTTCAGCGGTAAGGACCGGATCCCTGAGAGACAAA + HHHHHHHHHHHHHHHHHHGGBE@FFHHFHHGGGGGHHHFCDDA?5//-=GHHHFHFFHHFFDAAFHFFHHFCC?EHFGGGHHHHHFBB<EEFHHHHHHHHHHGGHHDHFHFHHHFHHFC/>:=EEHHCBFFFHFE?>ACE @read_150_160/1 ATGCGGAACTCTTTCCCTTTTCCGAAAACTTGATATCTTTTCTGCAAGCTTAAGCTCATCTTCTTAGCTCCCCCTTGGACTTTGCCTTATTTTTCCCCAA + HGGFFFHHHHHHHGHHHHHHHHHHHHHHBD:DDAGHHFHHEDEFHHHHHHHHEHHHHGEHHHHHHHFFB?HFHFEHHHDGHHC27AFFDH@/C0/=<:78 @read_150_161/1 CAAAACTGTCAGTAGTACTACCCACCTACCCCTACTCCCAAACTTTTTTTTTAAAGACAGGGTCTCACTCTGTCACCCAAACTGGAGTGCAATGGCACAA + HHHHHHHHHHHFHHHHHHHHD:2AHHHHHHHF7C>DGGHHHHHHGFFHBFHHBCEFEEB.*;>9 @read_150_163/1 CAAAACTGAACTGGGACTATACAGGTGCGTGCCAGTACCCCTGGCTAATTTGTTTGATTTTTAGTAGAGACAAGGTCTTGCTATATTGCTCAGGTTGGGT + GGHGHHHHHHHHHHHHHEHHHHHFHHHHHHHEB8=FFGEEHHHFFHFHHHBEHFFHHHHE@22CEEB:,1>:9C.8DFFHGHFFFHHCCHEBEHHHHHHF @read_150_164/1 ATGGATTAGTCCACTGTTTCTGGGCCTAGTTCAGCACTAGGACTCACCTAAGAGTTGCAGTCATTATGGCCTAGAATGCCTTTCAAGTTTACTTGGAGAC + HHHHHHHHHHGGHHHHHHHHHHHF;/5DDEGGGHGH@FEEB:*6E8D;>AEE @read_150_165/1 ATGCGGATACATGCACCACAGACACATGAATGTGTAAATACACACAAATACACAACCCACACACACCAGCTTCCAGTCATGCCACTATGTGTGAATTATG + EEEEFHHHHHHHHHHHHHHHHHHHHFHHCHHHHFCDDHHHEHHEHHHEHHHHHHGHHHHHFBGFHEECFFHFDCCEDAACGHHEGGGBCC.-6EDBEE@A @read_150_166/1 ATGGATTTAAAATCCAAGGGAATCTGAATAAAGTATGGACTTTAGTTAGTACCAGTATATCAATATTGGTTCATTAATTGTAATAATGCACCATACTAAT + HHHHHHHHHGDEF?BFGHHGGGDAD@B7GHHHHHHGGDDD5/287AAA,-CCBHHFB?HHHHHHDHGFHHE?CECDHHHHEHHHHHHHGGGGGHCFHHFE @read_150_167/1 ATGCGGAGTCAGGAGTTCGAGACCAGCCTGACCAACATGGTGAAACCTCGTCTCTACTAAAAATGCAAAAATCAGCCGGGCATGGTGGTGTGTGCCCATA + HHHHHGGHGHHHHHHHHHHHHHHHFGHHHFHHGEHHHHHHFFFFAGGFFF==EHHHFFHFHFFHHHHHHFA>AA?FHGGFGGFGG?;C4DHBF@.),>:) @read_150_168/1 CAAAACTCTTTGGCTACAAAGGTTAATAACAAAAGTAGTCAGTCTAAAGTTGCACAAGCAGTTGCTAGGCAGATGTCCTTACAGTAGTATTTTTGCATAA + BFFHHHHHHHGHHHHFHHHHHEDFGGECGHHHHHGE?DGDDBHHHHHHHHHEFCFHF<>;C56FFCCHFFD><: @read_150_170/1 ATGGATTCCTCTGCATTTATAAAAGAGCAGGGGGCTGGGTGCAGTAGCTCATGTCTGTAATTGCAGCACTTTGGGAGGCTGTGGCAGGAAGATTGCTTGA + HHHFB===GGFFGEGGHHHHHHHFHHEEEHFEEAEGGCGEFFGEFHHHHHHHFFHHHA<>EFHHHHHFHGHHHHFFFHHHHHFDE?=CDGHFHHHFGGGG @read_150_171/1 ATGCGGATGGCCAATATTTCCCCAAGTATGCTTTTGCCCATTCTCTCTCTTCTCTCCTTCTAGGACCCCCACTCTGCCTTTGTTGGTATGCTTGATGGCA + EEFGFFGGGFHHHHHHHHHEDGGGGGHHC+4:?CDAA?@FHHHHHHHFHFHCC2./1;<5BEEGG:=A=CA=C,;C02/EFEEGA4DHHHHHA=32EGHFGHDGCDFHHHFFHHHHHHHHHHHFHFHFHHHHHHHHHHFFHHFFHBGFFF>@@>:9==D?GHHHHFHGBHFHFGD= @read_150_174/1 ATGCGGAATACTCTATCTCAATACCTCACAATTTTGTAGAAGAGACGGACAAGTAAGCAAATAATTGCAAATCCTATATGAAGAGTGATATAATGGAGGA + HHGDFHHHHHHHHHHHHHHHHHHHGHHHEGHHGGGFHHHHHHH@CFFHHHFHHEEBGFHFDFHHFFDEFFFFCAD647@BCEFDFGEEHH@FEEFFBEBHH @read_150_176/1 ATGGATTCTGGACCTGGCCCATGAAACCTTTCTTCCCTCTTAGTCCTCCAGGCCTGTGATGGGAGGGGCTGCCACAGAGGTCTCTGAAATACCTTGGAGG + GGHHHHHHHHHHHHHHHHHHHHHHHHHHHHFHHHHHHHHHFFFHHEHFAHHFGCCDFFBDHFFHEDDCEBB1%'50&,66>FFHFHHHFGHHHHHHFEAH @read_150_177/1 ATGGATTTGCAGGCAAGACAGCTAGATCTTAAGCTCCATGAAGGCAGCCAGTGCCTGAACCATGGAAGTAACTTAATAAATACCTGAATGAATGAATCAA + GGHHHHHHEEHHHHHHHHHHHHHHHHFBFEGBFF94DHHHHHHHHHHHHHFDFHHFHHHHHEFFFFFFFEEA:>CBD@<>8.+EECBB4GA@=C5DDDD+ @read_150_178/1 ATGGATTAGTTGAGTTACAGAAGAGTAAAGAAAGTTATTATCGTTATTATTTTGCACATTTGGATCATGTAACTTGCAAATTGAGTATTTTCAGCAGCCA + HHHHHHHHHHFFD@@BGHHHHGGEFFHGB3AGGGHHHHHHHFHHEEFHHGEDBAE4D?= @read_150_179/1 CAAAACTAGAATGACTTGAACTCGGGAGGCGAAGGTTGCAGTGAGCCAAGATCGTGCCATTACACTCCAGCTTGGGCAACAGAGTGAGACTGTCTCAAAA + HHHHHEDFEHHHHHHHHHHGHHHHHHHHHHHHHGHHFHHGHHHHHHHHDFEHHHHHHHHFGFHHHFFFHHCCCEFEDE?CFDDHFHHHA1;9???78>:9 @read_150_180/1 ATGCGGATCTAGGTTTGTGTAAGTACACTCTATGATACCCGCACAATGATGAAATCACCCACTGATGATTTTTTCAGAATGTATCCCTGTTGTAATGCAA + HHHHHGEEEHHHFFG>@4:FGHHHHGGGHHFBA1@BC<<@EGEFEE:8EEHHFGFBHHDFHHEDABCEBCDABBAC@-*4DCAGDGFGGGGGFFH=:1/= @read_150_181/1 ATGCGGATGCGGTGGCTCATGTCTTTCATCCCAACATTTTGGGAGGCTGAGGTGAGACATGGCTTGAGCCTAGGATTTCAAGACCAGCCTGGGCAACATA + HHHHHHHHHHHGHHHHHHHHHFHFHGHHHEHHHHHEEDGCFEHHHHHHHEBDFHHDEFHHHHGBCAAABB:BE8EHHGEEHDGGHHGGFFFFHHHDHHDB @read_150_182/1 CAAAACTAGTTATTTGTTCTTCAAGGTGCAGCTCAGGGGCCACCTCCTCCAGAAATGCCGCCTCTTCTCCAACCCAGCTGGAGGAAGTGAGGCACCTCTG + HHHHHHHHHHHFHHHHHHHHHHFHHHHHHE@@3:>:>HHHHHFHHHHHHHA?6&/EEHFHHGFHHGGFHFHHHEFBBB6FFDCDDGHFE>EAEEFFGFFF @read_150_183/1 CAAAACTGGGATTACAGGTGTGAGCCACCGCACCCAGCCCTAAAGAGAAAAATTTCTAAACTTTACTTTCTGACAGAAATATTTGGTAGGCAAGCATTCA + EEFHHHHHHHGGGGGHHHFHHHHGGCDE@9;5*2AHHBHHHFHHHHHHHHHHHHHEHFFGGHHH@EEC>?CHHHHHHHHHHHHHFFBF=BFCHHC44:7E @read_150_184/1 ATGGATTTTAAGAATGTTGAATATTGGCCCCCACTCTCTTCTGGCTTGTAGAGTTTCTGCCGAGAGATCAGCTGTTAGTCTGATGGGCTTCCCTTTGTGG + GGFHHFEEED=FFFFHHHBEHGGGHHFHHHHHEEFHHHHHHHGGEG<>63DHHGFC5>6+4AAFHHHHHGC(CE<.03AAEHH@@GGIGIHDGG@:C5/0;>D>DFHHHHHFHBFHC.? @read_150_189/1 CAAAACTTCCTGCCTCGGCCCCCCGAGTAGCTGGGATTATAGGCACCCACCACCACGCCCAGCTAATTTTTGTATTTTCAGTTGAGATGGGGTTTCACCA + HHHHHHHHHC@B?EEEDEGFBGHHHHHHHHFEFFHFEEFHFFHHHHHHHHHHHHHEE?AEE=GA?D9B??7EHGHHFHHHHEFFDGFHHHHFC?'9FHHHGBFFGGGHHHHHHCCEEEH?DDCCHHH @read_150_192/1 CAAAACTGCATTTTAGGAAGCATTTAAATCCACCATCTAGGCTGGGCACAGTGGCTCATGCCTGTAAGCCCAGCACTTTTTGGGAGGCTGAGGTGGCCGG + DGGGGHHHHHEGGECFHHHHHHHHFEHHHHHHHHCBEFFFCF?BFEEEFF @read_150_195/1 ATGCGGACTGATGAATTCTGGAGCAGTGAAAAAGGGTTCTTACTTGGTTTCAAATAGTTTTCCTAGGACTTCTTGAGATTCAATAAAGCTTTAAAAAATA + HHHHHHHHGGEFGFFF2CDFGDDHGEEBHHHHHHHHHHHHHHHHHHHEFHHHHHHHHCHB=DFHHHHHFDGGG68;<6DEHHHEEFEFF@45FB;86:BG @read_150_196/1 ATGGATTATTGCCTTGATATTTAAAAAAATCAATTGACCACAAAGATAAAGATTTATTTCTGGACCTTATATTCTGTTTTACTGATCTATATGTCTATCC + GFFBBFHHHHHHHHHHHHBHHHHHGHHHF@FHHGGHHHHHHC@FEHHHDHGF>F9EFFHGHHHFFFFFFHBB5@>><9DFFGHHHHHHHHHHHHHHHHFFGHFCHHHHHHHFHHGGHHHHFHHHHHHFH7D@HFHHHHHHHEHHHHHFEFHHEDDGD?EFDG>0(D?? @read_150_204/1 ATGGATTCAGAATTTATGTTGCTCTGATAGGGGCTCTTTTCAAATTGATGTCTTATCTTTCTTACTGCCCCAAACTAGTTCCTGTTCAGACATGTTATAA + DDDE=EFBEDFE=AD@5?;=DHHHHHFGFHHHHHHHHHHFDFHHHHHHHHEFA?FCCDFFHHHHHEAFFDCEHHHHHHFHHHFHHHHHHHHHDDHHHHHHHGGF=45&9EFE @read_150_206/1 CAAAACTACGTGTTGTGCAGCACATGGTTCTGCAAGATTACCAAACATGCCCCTATGATCAAATCCAACTATGATTTTCAAAATCTTTTTGGACCTCTCC + HGGHGD>FFGEGGBCHHHDDEGGHEGHGHHEGFHEFHHHHHHHHHFHHFFHHH=CHHHGB9<6;>BEBCB;DA>A?DEDDEG=;GCGGEEEC>ACEFEA? @read_150_207/1 ATGGATTTCTGCCTAACCCTGAGGGTCTATGTTTTATGTAGTTTTAGGAGTGGCGATGCATCTAAACACATTTTATTTGTTTAATTCGTACACCTGTAAT + DDDGHHHHHHHHHHHHHHHHHHHHHHGHHHGGHHHHHHHHHHHFFHHFHFHHHHFBDFFHHHHHHHB94AHBFF=9.-8BEDEDGFDFBCEFHDBDGBGG @read_150_208/1 ATGGATTGTTCAACATCAATAATCATCAGGGAAATGCAAATTAAAGCCACAATGAGATACCATCTTACTCCTGCAAAAATGACCATAACTAAAATGTCAA + FFCDCD@:946,4>7') @read_150_209/1 CAAAACTCCACTGCTCACTTCCTGCTGTGTGGCGCTTTTCCTAACAGGCCGTGGACCAGTGCCAGTCCGCAGCCCGGGGGTTAGGGAATCTCTGTCTCGG + HHHHHHHHHHHHHHHHHHHHHHHHHFGHEA=FFEFHHHHHHHHHHEHHHHFGHFDHEFHHHHFEADE&?FFHHHHHHEH9EF3;EFHF @read_150_213/1 ATGGATTGGAAATATAAATATCTATAGAAAATGAAAAAGAAGCCGGGTGCGGTGGCTGACGACTGTAATCCCAGCACTTTGGGGGGCCAAGGCAGGCAGA + HHHHHHHHHHHGGHHHHHGGFHHHHHHHHHHHFGG677<75*AFH01:AB69,,@ACFHHHEEFHEHHFGHBDHHEDCGGHHHF=CHH @read_150_214/1 ATGGATTAAGATGCTTGACTGTGCATTGTGTATAATGGCAAATAAATATATGAATTAGTAAAACATTATGAATTATTACAGGTAAGGTAATATATAAATA + HHHHHGGHHHHHHHHHHHHHHHHHHHHA=GHHHHFAEFHH?ADEHHHHHDEHEGFFFFD=EEAF?6A;A+?4421:6-354>>A-F?D/.6A>;@FHHHH @read_150_215/1 ATGCGGAAGGGAGGTGAGTCAAAGGGTCAGCCCCATTGCCAGCCCCATGAGCTGCAGGGAAGACTTTTGCTTGTGGTCCATGAACAGGTTCCCAGTAAAC + HHHGGHHHHHHHHHHHHHHHHHHHFHHHHGGHHHFHHHFDHHHHHHHFFHGG;@F>DEHHFGCB?EHFHHGHFBHD @read_150_219/1 CAAAACTAAAGTATTTCTTTTTTCTTTTTTTATTTTTGGAGACAAGGTCTTGCTCTGTCACATAGGGCAGCGAAGATCGGAAGAGCACACGTCTGAACTC + HHGDCEEHHHHHHHHHHHHHHDGGEGGGGGHHHHHHHHHHBFHHHHHEHHHHHHHF0198DFD5:HHHHFHHFHHFGCGGHHHHDFHHFHFEEECD8D*. @read_150_220/1 CAAAACTGACAGGTCTGACTTCTGAGAAGGGAAAGTGGTAAAAGTATTGTCCAGTCCTTTTTAAGTTGGTGGCTGAGCTTGGTGAGGTGTGTTTTTAAAA + HDCBGEGHGDGHHHHHGG<= @read_150_221/1 CAAAACTGCTCCTTATATTCAACTACTTTTTAGAAAGTGATTCCTGTTGGTATCAAATCCTCCCCAGCTGGTCTTTCCAGACATTTATTTGAGGCACCAA + GHHEHHHHHHHGGGGGFHHHGGBEFFED4@@@HHHDHHHEFFHHFFC?55;;:@E<6BHDCEEEC@DEGHC?EBHHGGHHHHHHHHHHHHEDHFHGHHFH @read_150_222/1 CAAAACTTTCACTCTCCCCAATCCCTCCCCCTGAAAAAAAGTAGACTTCTCTTTCTGGACTACTTGTGATAACTAATTACCTAAGGCTGGAGTAATTTTT + HHHGGFEEEFFHHGED==>>GDHFHHHHHHFFHHHHHHHHHHHHDHHHDHHHGFFB9CBFHHHHFHHFFHFHHHEGEBD9'&2CFHHHHHFFFHHFFHHHHHHHHHHHHHHBBE:E8AAD?EEEHHHHE @read_150_224/1 ATGCGGATTGTTTCTTACTGAAAGGGAGGTTGGTCAAGGTAACCCATCACAGATTCAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCACCTAATC + HHHHHHHHHHHHHHFFHHHHEHHGGGEBBDGFFGGHHHHHHHHHHGGCG087019>@@=DHFF?@C+92;:H//;6.GFEFHHHH98;C@GDFHEFHDHHGFFGHHGEGFBE6F86>/),6DE @read_150_227/1 ATGCGGAGTGAGCATCTGACAAGATTCAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCACCTAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAA + HHHHHFHHDGHGGGFGBDEBEABFHHHHHHHHHD>BFEHHBHFHHHFB5E>FFBFHFHHHHHHHBDDCE?D?9?BGGGEGFGGG?FFHHHHGGF@E>CA? @read_150_228/1 ATGGATTGGCTGGGAGGCAAGGCCCGTCTCTCCCTTTCACGTTTTTCTGCCTGCTTTATATTCGCTGGGAGCTGATTAGATTGTGCCCACCAGATTCAGG + GFFFGHHHHHHHHHHHHHHHHHHHHFHHHHHHHHHHHHHEFGFHHHDD:HHHHEEGD<3EFFEDFF9%4DFHHHHBFHHGFDCCHHHHHGGHHGHHHFGFGEDBHFFCD @read_150_231/1 ATGGATTGTGGAGAAAGGACAGTCTTTTCAACAAATGAAGATGGAGTAGCTAGAATTCTACATGGTGACAAGGTGAATTTAGACAGAGATGACACTTTTC + EHHHHHHHHHHHHHHHHHHGGHHGGGHHHFFHHHHHHHHHGEGGFFHDEEFHHHHHHHFEFDA*6CFHEFHHHHFHGDDA?;3;FHHEB7,(3389>98; @read_150_232/1 CAAAACTTTAGAATTTGAATGGGAATAGAACATATAGAACATGAACCAATAGATCTTAGAGACCATATATTATTCTCTATTCACAGAAAGCAGACTACAC + HHHHHGHHHHHHHHHHGFFGHHFFGGBD@8EHH=FHHGFFHHFGGFHHHHHHHHHHHHCC7EFEHHDABDHFF?3;@@>@AFDEDEBFHGHEFGGHHDB@ @read_150_233/1 CAAAACTAGGCTGGTGGGTTAGTGGCTGGATAATCTCGCTGGGCTTCCTCACCCGTTCTGCACGCAGCAGACCATCGGCCAGGGCTCCCCAGTTCTCCCC + GHHHHHHHHHHHHHHHHHHHHFDDE@EGD@EGHHFDE:A:FHHHGFFGEFEDDDFHCDBF>;9C?HHHHFHHFFFHHHFEFHHHHGEGHHF?DEDBFCEB @read_150_234/1 ATGGATTAAACTGTATAAACAGGTAATGAAGGGACAATTCTGTAGAAAATCCCTCTGAATGCCATTAATAGCATGAACACTTTAAAAGCCTCCAAGGTTC + HHGGHHHHHHHHHHHHHHHHHHHHHHHHFFFHHHGHF?B:CBG7?EEGGG9:@?HEEFC3EHEECHHHFB9>>+%*/.7>9CDFDDADDHHHF=@;?EEH @read_150_235/1 ATGGATTTCTGAGCAGCTGTGTTTGAAGAAAGCTAGTGGGAAAAGTTCCAGGATTACATGTCAGGAAACTACAAGAGGTAGAAACCTTTGTTGATTTACC + HHHHHHGGGGEGHHFFFFFFHHG=)BEEE@7:@5GFGHHHGHHDEHFFHFHHFE@+<>B2<84@>B4>D(5+4<>='7EFFFB?473D @read_150_238/1 ATGGATTACACAAGTGAGTTTTAATAATTTTTATTATCAAATTTCACTTAAATAAATTGAACGTAATATCTAATACTTGTGATGTCAGTTTTGTTACCTG + GGGHHEEGGHHHFHGEGHHHHHHHGGHHHHHHHHGGD@:6C:BGHHHHHGHHHFA@585D@1/AACDDFFHHFFB?@@EFDFFBHDGGGF18.'*9:-*E @read_150_239/1 CAAAACTGATCTCTTAGATCATCCGACAGTCAGCTGCCCCCAGGCACAAGGGTGAGCCCAGTCAAGATCTGCAGTCATCGGCTAGGCGTGATGGCTCATG + HHHHHHHHHHHHEEEHHHGHHHHHHHHEGGDGEFFEBCGFHHHHHHHHHHFBEDCFHHHHHFFCFFHHFEFFHHFCC5)6BFGHHEFGHHEHHHHFEHHH @read_150_240/1 ATGGATTTCAAATTAGAACTTGGGATTAAGAAACTCACTCAAAACCACACAACTACATGGAAACTGAACAACCTGCTCCTGAATGACTACTGGGTAAATA + HGGGFFFHHGGHGHBGHHHHGHHHGHHHGHGHHHHHHHBEHHHFDGGGFHHHHHHCEBFBEEHHHHEEFBEEBCDGB?5A+7<@8BFBBHFEEFFDFEFH @read_150_241/1 ATGCGGAAATGTTCATAATAAGAAAATACACAGAAAAGAAAGTAGATTTGTGGTTGCCTAGGGCTGGGGCTGGTAGGAGGGGGATAGAGAAATGACTGCT + DEEGCEEFFHHHEEFFC@CHHHHHHGHHFFEGGFHHHHHHHHHHHHHHHHHHHFGHGHHHHHHEHHA>>HHGGDEEHGGGHFHHEC@GGGEBCC5>5;@F @read_150_242/1 CAAAACTATGAGCTATAATTTGAAGGTAAATTGAAAAAAATCTTGCCTCACGTGAATTCCATTATTAATGTTGAGGTTAATAGGAAAATAACAGATGCTT + HHHHHHHHHFFEGGFGHHHHHHHHHFDGHHHGHHGFFG@BEHHGHFFHHHEEHHEFFHHHHGB19EECAA%,?@DBHHFFHHGGHH?/D5:5/*-;BCFE @read_150_243/1 ATGGATTAGGCTGAGGCGGGTGGATCCCAAGGTCAGGAGATCGAGGCCATCCTGGCTAACACCGTGAAACCCGTCTCTACTGAAAATACAAAAAATTAGC + GGHHHHHHHHHHHHHHHHHHHHHHHHGEFHGFGEEHHHFHHHEGGGHHHHHEDHHHHHFBHHHHHHHFFFFBEEEFHHHHHHHHH;@6)2%2;<>3*?BE @read_150_244/1 ATGGATTCCTCAAACAAGAAAATCACTTCTAAAGGGGAAGGAGAAGTCTGAGGCTCTCTACAAAATATTTTCTATCTGAACTAGTTTTATGGTGGTCGAG + HHHHHHHGADFFFGHHHHHHHHHHHHDC@?<70@>FEBBFGD=GGEFEHFG=CFBHGEDEHGFHGHHHHHEFFFFEGEEE=3:=GHFHH@D;>FFFDB>AFBDE @read_150_248/1 ATGCGGATTCTTTCTATCCCTATTCCCTTCTTTAAAATTCCCCAGAGTGTCCAAAGATTCAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCACCT + EEEFGHHHFEEECBHHHHFGGGFGFGHHHHHGHGHHFFFEEBGGHHHFGGHHHHHHEGGHDE=CBBCFHFD=ECHHGGFGHHGEGCEFFFC8139+:+7* @read_150_249/1 ATGCGGATACAGCAAAGTTAGTAAAAGATGAAATATACTGTCTCCCAGATAACAGAGATTCAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCACC + HHHHHHHHHHHHHHHFFFHHFDCFAGEHFFFCFFHHHHHHHHHHEHHHFHHG=9:HHHHFFFHFH86/<<@::=FHHHHHHHHHHHHHHHHFAA5EEB;A @read_150_250/1 ATGGATTAGAAAAAAAGAAATATCTCCACTCTTATAGTCATTGAAGCATAATTAACAATAACCAAGCTATGAAATCAATGTAAGTGCCCATCAATGGATG + GHGFGGGFGFHGHHHHEEGFF8EEEGGHGBFFBEEFHHHHHHGAHHGGCDDEDFFFDEFBEDBFFHHHHHCC96DHHFGGHGGGAHHHHHHHHHEHGEB< @read_150_251/1 ATGCGGACTAATTCTGGAACATTTTTATCACCCAAAAAGGAGCCCAGCACCCATTAATCAGCCACTTGTGTTCTCCTCTTCCCCCTTGGCAACCACTAAT + HGFGFEHHHHHHHHHHECBGGCDBFEHHHHHHHHHEECHHHHHEFGFHHHHEFHGHHHF9CA?CHHHHED69AA>BFGGHHFHHHHH@EGC?ADHHGE/3 @read_150_252/1 CAAAACTCTAATCAATAGTAAATAGTAAGTCAAACAAAAGTACCTTCCCTTAGAGAGTTAAAAAAAGATTTGGTGGTTTGTTAGGCAACCTTCCAGTATG + HGHHHGB@@GHHH?<@;@DFEFD9EHHHFHHHFFGEEDGGDDFFFHHHHECHHHHHHHEHHEEF=6&&4:;,>EGFEEFFFBEEFFFHGEHDHHHHHHHDD64-.32DBBFHHHHHHGHHEEGFEEECDBEFFHHGFHHHFF>7=:>8DDD4 @read_150_254/1 CAAAACTAGGGACTCTGTATCTAGTTAGGGATCTAGAACAGATGGAGAACATTCACCCAGCAATATACATTTGCGTGTAGGTTCCCACACTGCTTATCAT + HHHHHHHHHHHHHHHHHHFBFCHFHHHHHHHHHHHHHHHHHHHHHHCFFEE?HHHHHHDEFHFFFHEB<;08431*)@FEDGFFFFHHHHHHHHHHE@DE @read_150_255/1 CAAAACTCCAACATGGTGAAACCCTGTCTCTACTAAAAATACAAAAATTAGCCGGGCATGGTGGCACACGTCTATAATCCCAGCTACTTGGGAGGCTGAG + FEEGD55CBFGD==@FHHHHHHEHHHHHEHGBDHHHHHFFFGFFHHHFB9>C?HHFFFGDHFEFEACDBDFFFFHGGGGGHDEB95EGDDDADFEFF835 @read_150_256/1 CAAAACTTGGTCCCAGCTACTTAGGAAGTAGGTCTTGAACACCTGGCATTAAGGGATCCTCCTGCCTCGGCATTCCAAAGTGCTAGGATTACAGGTGTGA + HHHHHHHGFFHHHHHHHHGGGFHGFGHHHHHHHHHHHHHHHDEFFHHHHHHHFHHHDHFEBEFHE5>569@)3=EHHFFFC:8>EFDADEC@=DFGGHHH @read_150_257/1 ATGCGGAGATATTCTTTGGTTTGCATCTCAGAACCAAGGGTGAAATATCCCCATTCTGGTAGATCGTTATCCCAAAATCACTTATAGATTCAAGATCGGA + FFGGGGHHHHFG@FGHEGHHHHHHHGEGHEGHHHGHHG@CHHHHHHHHHEHHHHHHHHHHFB=+/;5DECB=BEFHHHHHHEFEFHHHHHHHHEEBDED; @read_150_258/1 ATGCGGAAATAATTATAATAATAATAAAAAGAGTCAAAAAGGAGGAGAACCAGGAATGCACAAAGAAAGATACAGAAAATAAAAGTTTCAAGAAGAGAGA + HHHHHHHHHHHHHHHHHHHHHHHGGDGGGGBBDDBBGBEEHGFFFHHHHHHE?FC?E@BFEHFFBC @read_150_259/1 ATGGATTGAGAACAGGAAGGAGAGAGGTGAGCAATGGAGAGGCACACCAAAAATGGAAATAAGACGGAGACAGACCAGTATAAAAATAGGGAAGAGGTGA + FFGGGG;BDGGHHHHHHHHHHHHHHFEEHHHHHHHHHFHEEHHHHHHHHHHHBCF7?65??DEDFFFFEHFGGFCDDCBGHHHHHGEEEFGGGB@HHHHH @read_150_260/1 ATGCGGATTGCCCAAAATTCCTTGTGCAATGCCTATGCACAGAAACTTAGGGCATAAATATGTTAAGTATGTCATTCCCCCCCACCCTTCCCCTAGTTTC + HHEHHHFHHHHCHFGHHHHEFFHHFEBBFFGGGHHHHFFFHHHHHHHGEHHHHHHFF1AFFHHHBEHGFHEEEEFHHHHHHHHH:895@A<@DABGGHHHHHHHHFHFFHHHHHHHEGEEHHHHHFHHHHHHHFFF6DBAGGGEDFHHHFHHFHHD77?FGFFEHBEFHFFBDFBCFHHHFHHGDGGAEBFHFFBFHFHF @read_150_265/1 CAAAACTAGGCTCTGTAAAAGCATCCAGCAGAGGAAGCATAGGCTGGAAGCAGCGAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCACCTAATCT + HHHHHHHGGG@B;EEEHHGHGFFBED=CCDGF=C69;0:FHHHDDACEHGGGHEEFHDEEEFHHHFDDA==FFHFEEHHHHHHEGHHHHHHGHHHHEGGF @read_150_266/1 CAAAACTTCAAACCCAAATGCGTAGAACCCCCATTTTTATCCACTACAACTCCTTTACACCTACGTACCGTATGCACGCATGTGTTTATTACCCTAAGGG + HHHHHHHHGHHHGFEGB3)8FFEFBGGEEDCHGDE@BEHFHHHHHHHHHHFHHHHFHFHHHFHHDEBFHHEEEEB?93?EFED@B.@BGEHHHHHHFHFG @read_150_267/1 CAAAACTAAAGCACCTTTCCTGTCTGTGATCTAAGCCTATTTTTACTAATAGAGAAAGAGGCCAAGAGAAATCAAATGATCCCAGGACCCTTACCACAAA + HGGGGHHHHHFA:3.9:?GHHHHHHHHFHHHHHHHHHHHCHHHDCGHFGGGA?G@9?12@BFGGC'*(>>EDFFD?;><<9GGGFFFBGF6?BGDH?DC=C @read_150_269/1 CAAAACTATGGTATTTGTTAATTGAGTACTTTTAAAAATGTTTTTCATAATAATTAGAATAATGTTTTATTCTGGCAACAAAAGAAATATAAATTAATTA + HHHHHHHHHHHHHHHHHHGGGE8=CEHHHHHHHHEEA>B@FHHHHHHHHDFEFDADDDFBEEED@BB>FHHHHHBGFHHHHHHHGEHGHHHHFHHHEBGH @read_150_270/1 CAAAACTTCCAAGTTCACGGGGATGCTGACAACGTGTTGTCCCAGACCTACATGAAAGAAAAACGTCTGGCCTTATCCCAAACCCATTGCATACTTTTCC + HGGHDCB@@DCFFEDCDD @read_150_271/1 ATGGATTAACAAAAATAACCAACTTTAGCCAGACTAAGAAAAAAGAGAGAAGATACAAATAAATGAAATCAGAGATTAAAAAGGAGACGTTACAACTGAT + ECDFFCEGFFHHDDBFHHHHHHHGGGHHHHHFHHHHHHHHFFDHFHFDDHHHHHFFHFHA9>.=D7E4CHHFHFHHHHGGGFF?HFFFFGF>DDDHHHHB @read_150_273/1 CAAAACTTTAGACCGTTCACTTCCAGGTGATGAGTGATGTGGTAAGACCAGTTAATTCCATGGGAATCAGCCCACTTTTACATTTCCTTTGTTGTGAAAT + GGHHHE=EFHHHHHHHHHHHHFEBECFFGEE?HB?@>5''06@6=EEGGGFEHHBGHFD @read_150_274/1 ATGGATTTCATTTTATGTTCCCAATTTGGTTTCTACCACTGATGCCTCTGGCATCTTTGTGTTTTAGATGAAGACTGGGAAGCTGATGGAAGGCAACATT + HHHHHHHHHHHCCEDEA@GGEHHHHHHHHHHHDHHHHHFEFGHHHFHHHHFGEHACCDBAA7:6;FHC?BEHFFECDEEEFGHEEDFEDDCEBFGFFFDC @read_150_275/1 ATGGATTGGCCTGAAAGCCATACTGGAGTTGGTTCCAAGGAGTCTGAGAGGGGAATATAAGGAGCAATGAGGTCACTATAGATCGGAAGAGCACACGTCT + BE8FFEGGDCFGD=EGHHHHHHHFGGGDFEFHHEFC=CDD<6>?FEDC;/<*'4?DEEFFB1BFBHHFFD?EEEFHHHHHHHFBEDEEHEABFHHHHHHH @read_150_276/1 CAAAACTGGAGGGGGAGGGAGAGGGAGAGGGAGAGGGAGAGTTCCCAGGTGATTTCAATGTGTAGAACTGGGGATAGCAACTCTGAGCGCCAACCTCTTA + EHHHHGEEFHHHFHGHHHHHHHHGHHHE/19@GHG2=DFHHHHE@B8EFG@+0(1=,.BAEFF @read_150_277/1 CAAAACTGACCATTTAAGAATCTATTTTAAAATGTGAGAAAAATGTAGCTATTGATTAAACTGTGCATGATTAAGATTTCAGAAACTGAAGTCAAAGCAG + HHHHHHHHHHHFFGGE>)::<17FHHHHHHHHBHHHFEHFEFCAEFHHHHHFHHEA=FHHFHFF;6@:>:EBFHHHHHHDGD@FF>A766:;+':DC7@G @read_150_278/1 CAAAACTCCACTCTCTCGCTGCAATCTCACTAGAGACACTTGAGCAAGAACTGTCTCACTGACCCCGTCAAACCTCAGATTTATTAACAAAATTAATGTG + HHHHHHHHHGGHHHHHHHHHGGHF?CBEGGED=DBEEE67AEHDDHHHHHHHDGEHBDDEFFEHBEFHHD@C=>>*701()8EGHFFHGGHHHFHHFHHH @read_150_279/1 CAAAACTACCCAGGCTGGAGTACAGTGGTATGATCTTGGCTCACTGCAACCTCCACCTCCCGGATTCAAACAATTGTCCTGCCTCCGCCCCCCGAGTACC + GGHHHHHHHHHHHHHHHHGGHHHHDCABGGHFHFFHHHDD=EBEAEHHHHEBBBFHHG46HHHEGF?9CFEHA=78+417DB@805:;)6=CDDFHHHHH @read_150_280/1 ATGGATTGCTTTATATCCTATCCCTGTTTCTCCAAACTCAGTGATGGCATCAACATCTCTCGAGTTGTTCAAGCTTGAAATCATCACTATAGATCGGAAG + HHHHHHHHHHHEEHHHHGHHHEEHHHHHHHFFFFFGGGGFBFHHHHFGDGHHHHHHHHBHHHHD@FB<9AFEEEBGGGHHHHHHHHD5?FHHEEHHHHHH @read_150_281/1 ATGGATTCAACTGCAGCCCTGGCCACAGCCCCAGCTCTCCCTTCTGCACTTAGCACCATCTGACACACTACATGTTTTACTTAATATCACTATAGATCTG + B;BEGGGHHHDFEEFGGE@@=-84<=>@B9@FHB2ADDDFFFHHHF@C65//=FBAEEHEFHHDFFHFEFHHHBCFFGGHHHCEEHHHHHHHHE7A.;'3 @read_150_282/1 ATGCGGAAGCCCAGCCCTCACCTTACTTTGTAATGTAGGCCTGATTTCTTTCAGTGAAACCTTGACCTTAACCTTGAGAAAAATTACACCCTCAGTAGTT + GHHHHHGEEEEHHHHHHHHHHHHHFHFEHHHHHHHHFGFFEADHHHHHHA-:9>D?FHHFFHHHHHHHHHFFEBC?DDDD>67DDED@B=),3A?4@HHH @read_150_283/1 ATGGATTATATATGTGATTGGGCTCGAGCAGGTCCTGAAGGCACAAGTAAGTTACATGAGGAAGTGGCTCAAATGCCTATGGTCTCCACTCCTGCCACCC + HHHHHHHHHHGHHHHHHHHHG@BE;EGF:>B=DCAFFGGHHHHHHHHEHHHHFHH/@EEC8/DFHCGGEED7A?AB78;9CC?8863'4HHHHD5/:(DG @read_150_284/1 ATGGATTACAGAGCAGGACTCTGTCTCAAAAAAAAAAAAAAAAAAAGATTTGAAGGGAGCCCAGGGGGCAGGACTGGGTTCACTATAGATCGGAAGAGCA + HHGHGHHHHHGGEDDHHFEGHHHHHGFHGHHHHHEHHFGHHGGE@CEEED?5?>FHHHHHHHEEFHHFHHFHHHHGGFFFDFGFFDHHFFHHHHEBGFBB @read_150_285/1 ATGGATTTTTATTTTTTTTTGAGATGGAGTCTCACTCTGTCACCCAGGCTGGAATGCAGTGTCACTATAGATCGGAAGAGCACACGTCTGAACGCCAGTC + FFE/=B;A;A@CFHHHHHGGHHHHHHHHHHGEE?BGGGHHH@57:FHGGHHHHHFFE89BEHHGB8?EEE>;DGHHHHHDFFDDFD?FFFFC5&%/BEG? @read_150_286/1 ATGGATTTATTAGTCCTTTGTCACATGTATAAATTGTGAAGATTTTCTCCTACTCTGTGGGTTGTCTATTTACTCTGCTGACTGTTCCTTTTGCTGTGCA + EHHHHHHHHHHHGHHEHHHHHHEEHHHHHGHHHHGHHHEHGHHHHGAEHHHFHHFFCCHGGFFFFCHHF6@=5ECDD;-?DDDEFHHHEEDHFHGGFHHH @read_150_287/1 ATGGATTACATCATCATATTATTTTTGTTTTGTTTCGTTTTTTGTTGTTTTGAAACAGAGTTTCGCTCTTGTCAGCCAGGCTGGAGTGGAATGGCACAAT + HHHHHHHHHHHHHHHHHHHHFFHHDGGFGEFGEEEHHHHHHHFFFBDAFGE64>=@@,/6.>)*%5513@ @read_150_288/1 ATGCGGATCAGGTGATCCGACTGGCTCCGCCTCCCAAAGTTCTGGGATCACATCAGCCACTGTGCTTGGCCACAGTGAAAGGTTTTGTGTGGAGAGCATG + HHHHHHHHHHEBDEGGHHHHHHHHHHHFHHHHHHEGHGGGFHECHHHHFHHHFHFHHHHHHHH@FDD?@FHFCBFHHGGDGCC>2A?5AGFFFEHHBB8= @read_150_290/1 CAAAACTGGCCTCGTAGGTGACCAGGACATCAGAGACGAGAAGAGGAAAGCCTCGTAGGTGACCAGGACATCAGAGATGAGAAGAGGAACCCCTCTTAGG + HHHHHHHHHHHHHHHHHHEEGHHHHHHHFFBE>FDDEHHHHFHFHFEHHHFFF;E?AAFHFEDDCEHHHHBEHHHHHHHGHHDGFGHAB4&*1:8(>;EF @read_150_291/1 ATGCGGATGAATGCTCAAATGTTCAAGTACCTTTTTCTACATTTATCTGAATGATCACACAAGTATCATTTTACTTTTAATGTGGTGGAATACATTGGCT + HHHHHHH=DGADHHFGFHHHHFEGFBGGGEHHHHGFHHHHF87FFFHHHHHHHHHHHHHHEEEF>6>ACBHHFE?GEEEDEDDD2//%3%64-2&@?F=6 @read_150_292/1 ATGGATTGTATTAGGCTGACTTGTTCCAGAGGCAGCAATGAGCACAGCCCAGACCCAGGGAAAGTCTTGATAATACTATCTAAGGAGCCAGGACACAAAG + GBGGFGGE@DFHHGHHHHHHHHHHHHHHCC@DFHGGHD@@7D??HE??DHHHEDDHHFHHHD3D@HHEE:9>@)2EFGBEHHHHHHHE=CGECC @read_150_297/1 CAAAACTGAATGGCACCTCTCAGAATTTGGTAAGAGCCATTCAATTGTCAGAACTAGGTGGCATCTTAAAGGTGTCTTTTCCTCAGCCTCTGAAGTTGAG + HGGGGHHGFGGHHHHHHHGEED==:CFHFHGGGEEGGBDFGHHHFFHHHBHHHBDHHHHFHHHHHFFF<6(03((A>;@HHG>CBCFB@DEGDB*=CEDA@CFCBFHDEEFBGFFHHHHHEHHHFEEEE*, @read_150_300/1 ATGGATTATAGAAATATATCAGTAGTATGTGTTCATAAATACACATAGGTGGGAATTGAGCAATGAGAACACTTGGACACAGGGTGGGGAACATGACACA + HHEEEEGHHHHHGGFFDBFFHGGDEHHHGHDGHFA>EBFGGGBHHHEHHHHHFGEFHHEDEFHEHFDAFGFFDE@DFGG?BEG5>CBBA@CC8',>@EF? @read_150_301/1 ATGCGGACCAAACATAAACTACACTAACACTAATAGTAGCTGATGAGCTTTAAAAGTTGCAAAAAAAATCTTGTAATGTTTTAAGAAAGTTTACAAATTT + HGGGGHHHGHHHHHHHCB?CGHGGGGGEGGHGHHHFHGDEDHEG@EHHHHHHHHHHHFFFFHHHHHHHFFHHFBEFGHHHHHHHGBDF;EEDHHHHHHHH @read_150_302/1 ATGCGGATCAACCCCCTAAACCTACAGGCACCCCTGTCATAATCTGTTGTCATACTATATGCTTTTCCTTTGTAATACTTATCACAATTTGTCTTTATAT + HHHHGGHHHHHHHFEDD=EHHEHHHHGGFGFBEC9BEEFHHHEDDEHHECFFFHB?CFGHHECEFFGDGFHHHEDEHHHHC.5EFBCD2@<57@DCCFFHDAAA?EECCA?F?< @read_150_304/1 ATGCGGATTTTCTTTAGACTGTTGTGACTTCACTTGATATTCTATGCTAAAATGTGACAAAAAGAAAAAAAAGGCTTGCGAAGTTTTTAAGAAGAGAATT + HHHHHHHHHHHHHGFFFGGHHHHHHHHHHHHEEHGHFHHHHHHHHHH?BDBHGGFHCCCCD>CCCCBFHHHFEB.48C=DCBB4&3> @read_150_307/1 ATGGATTAAGAAGGAAAAGGAAATTTATACTAGTTTTGCTGTCATACCTCAAACTTTATTATTATGCATAGGAAAAACATTGTGTATATCGGGATCGTTA + HHHHHHFHHHEGGHHHHHGGGIIIGHHHHHHHHFBGEEBGDAHFFHBEHEFEEHFHHFHHE<23*;FFFHHHHHHHHHDBHHHHF?E55&*8&13BFGEE @read_150_308/1 ATGGATTACATTTTTGCATGTCAAATATATCTCAATAAAGCTGTTAAGGGCTGGGCGAGGTGGCTCACGCCTATAATCCCAGCACTTGGGGAGGCGGAGG + HHHHHHHGHHHHHHHHHHHHHHHHHHHHHHHHHGFHHHHHFHHHFHHHHFHFD?HHFGFFFBFGDFHHHHFFEEFHHHHHHHHH=C7&%AFFHHHHHHGF @read_150_309/1 ATGCGGACTGTATGGTTTGTGTTGCAAACATTTTCTACCAGGCTGAATTTTTTTTTTTTTTTTTTTTGAGAAGGAGTTTCACTCTTGTTGCCCAGGCTGG + HHHHHHHHEHHHHHHHHHFGGHHHHHHGGGHHHHHGHHHCFEHHHHFHHHHHHHHHGFHHE?CAHHHCHGBFHEEHHHHHHHHFCDDDFFHHEFDCD=6E @read_150_310/1 CAAAACTCCCGCGCCTGGCCAATATTCAATTTTTTAAACTGTTTTCATAACTCTTAAAGGTATGTTTGTTTTATAATTTTAAAAATTAATTAAATTGCCA + HHHHHHHHHHHHHD8GGHHHHEFHHHHHFHHDB?DGGGF@DDHHHEGHHHHE8>EE75A6:>EFB?EEEEBEEHHHHHFFFBEFEA>DDC2:><<<>:BD @read_150_311/1 CAAAACTAGTTGGACAAGCATGTTGTACAGTATTCATATCTTTAGTTTAATTTCAGTGTATATCCTATTGCAGTTTTATGTACAGGTGGGATTTACCAAA + HHHHHHHHFFGGGGGHHHHHHGHHGHHHHHHHHHFHHHHHHHHHHHFFDD9BDFFHHGHHHFEFFEFHHHBDECC><->AHHEHHHHFEFDD?BFFHHFF @read_150_312/1 ATGCGGACCTTTGCCTCCATGTGTGTCCCAAACCAATTCCCTGTCATCTTCCCCAACCCAAATGATTGGGGGGACTGTGTGTCTACATGTGGGCTCTGGC + HHHHHGFHHHHHHHHHGDDGGFFGGDHHG@HGBGFEE@EDHFFE6=EFFEEFHHE4+?D49;?<>2@2,7CC:9,6669.EEHH?9?HHF;=37/CFFBE @read_150_313/1 ATGCGGATACTTTCTCTTTGGCCACCTACTCACATCTGAAACCTGCTCCTTCTCCAAGAGCCTGGGTATACGACAAAGACCCAGGTCACGAGACATCCCT + HHHHHHHHFCCFEHHHHHHHHHHHHHHHBA=3:HHHHADHECFEEE=DBCEFHFF=5;BHHHHHFCD;GDEBFEGEBBFBHHHHFFGFHFDDCDD;>CFHHHHHHHHH?EEEBHFFCD @read_150_315/1 ATGCGGAACGCGCTGGTGAGACCAAGGAACACCAAAGTCAGTGAGGAGATAGATTCAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCACCTAATC + FFFHHHHHHHHHHHHHHGGHHHHHGDGGEE78EEHFHHFCDGHHHHFFGGFFFDHF?CFBFHFE?ACEFGGG<.'3<<BD>A?DEBFF@>CDDDHHHHHGHHHF@BFFFHGGGFFHHGF @read_150_318/1 ATGCGGATATGTTAAGTTTCAGCAAATCTTAATTTTGGAATAAGTTAGCCTTGATATTACTTTTTACCCCTAGTACATTTCATTACCATTACCCTGCAAA + HDEEFHHGGGHHEFFFHHHHHHHG=<0,?>D8@7GGHHHHHGFHHFFHHHHEGGHHHHHHHHFCGHHHHHHHHEEHHHHHHHHHHHHHHHHHHHHHEBDH @read_150_319/1 ATGCGGATAGAATTTTCTGTAGTCTACTATACATTTCTCTTGAAATGCTTCTTCCTAGATTTTTGTTTTACTTCACCATTCTGGCTTTCTTTCTGTTTTC + GGGHGHHHHHHHHHHHHHHHGB>>@EEGGHHHHHHGBCCDHHHHFHHHHFHHGHHHHHHHHHFHEF@@DCFFFGGHHFFDHHHHHHHHHHHHHHHHHHHF @read_150_320/1 ATGCGGACAAATGTGTAGCAAATGAATGATTGCACACCCAGCACTCCTGTCGTTCCTGAGATTCAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACC + HH=<7905DEBFHHHHHHHHHHHHFGHHHHHHHGEHHHHHHHFEFHHHHHHFFFBBGBEHHBF?CEECDFEHHHFEEEDAHHHHFHHFFHFC93=+=DFF @read_150_321/1 ATGGATTGGGGCCAAGGTGGGCAGATCACGAGGTCAGGAGATCAAGACCATCCTTGCCAATATGGTGAAAACCCGTCTTTACTAAAAATACAATAATTAG + HHHGGHHHHHHHHHHHHHHHG?EDGGHGDHFGGHHHFAC?HHHHHC@FC?HECDFHHHHHHHHHHGHHAE?D.BFGGGGFFHGFGFHHHGFHHHHH??A/ @read_150_322/1 ATGGATTCATCAGTTTGTAAAGGCTATCTATAAGAATAATCCTTTGCCTAATATGTTTTGTTGGAAATTTCTCCTAAACTTTCCATCTGCTATCTAAATT + HGHGGGHHHHHHHHHHHHHHHHHGHHHHG7AEBBD?FHBHB:EEFFHEDDEFHHHHHHHHGGHHFHHHHDHEHHHHHHHHHHHFGFEHHHHHHFHGBA?> @read_150_323/1 ATGCGGAAAATAAATCCCTTCTTCAAGTCCCACCTCACTGGCTTCTCCAATGTCTTTTATAGGGCGAAAATGATTGGTCAAGATTCAAGATCGGAAGAGC + HHBB?FFEF@F9+5DEE?DEDDFFHHHHGHHHHHHHHHHHHHHHFHFFHHHHEEEDDFFCBFHFBFHHGGHHFEHHHHHHHHFHHHHGGHHFHHHHHHEF @read_150_324/1 ATGCGGAGAGAAACTTGTTGGGAACTGGAGCAAAGGTGATGCTTGTTATGTTTTAGCTAAGAGACTGGTGGCATTTGTACCTGCTCTAGAGATTTGTGGA + EDFHHFGHHHGGGGGHHHHHHHHHHHHHHHHFE7?=E@69=BFHHHHHHHHFHH?FFDFHHHHHEFHHFCEFHHFGGGGEDD@ADFFGHHHHHHHHEHHH @read_150_325/1 ATGGATTAACTCCCTACTCTCCATCCCCCACTCGTAGGAAACTAAGGTAAGGGAACTCATATTTACAGAGTACCTCCTGGGGTGCCAGGCACTGTGCTTC + HHGEHHHGGFH@DDC?GGHHHFGGHHHEHHHHHHHHHFHHHHHHHHHHHHHHDGFHHHHHHHHHHHHHHHFHHFHHHHEG@><;BFFFGHHFGGBGFDHH @read_150_326/1 CAAAACTCACCCAGTTTAATCATTTCTAGCTTTAAATTTAAAATGAGAGATGTGGTTCTATCTTTCACCTAAACACTTACAGGCCATTGTAGGGTTGGCC + HHFHGGGF@?HHHHHHHHHGHFHHHHHHHHHHHHHHHHFFGFBFHHHHHHHCCDBDHEEFHHCEFFFCHHEHC4=EFDDEGFGHHHHHHHEE<3<;A@@H @read_150_327/1 CAAAACTATGTTCTGTGATAAGGACAAAAATCACACTTTCTCCTACTTCTCAATATAAGTTCAAGCACTACTAATAAAGGTTGGAAAATGTGGTATTTAT + HHHGEFEEHHHHHHHHHHHHHGGHGHHHHHHHGHHHHGEEEEAEEBBEGGGFFHHHFDEFHHHHHFHFCFDFEE@DFGHHBC9-5EHFH??@DB=DEHHH @read_150_328/1 ATGGATTAGAGGATTTTCAAAGTGCTTTATCAGTACCATAACTTTGCTGAAAATATGGTGTTGCCTTCTTGTTATTACGTTTTCTAGGATGTTGCCTTTA + HHHHEFHHHHGFGGGDDDGGGHFHHHHEHHGB@GGGHHHHHHFFHEEBHHECEHFHHHHBCDDDHEDE@6'((.?FFE*&*0&*'-2 @read_150_330/1 CAAAACTATAAGAAAAGACCTATCTTGGAATTTGTATTGGTGATTATTTGCATTTTCAAAAAGCTTATGAATTTAATGGTGACTTTAAAAACAGAACCTC + GFDGGGGHHHHHHGHHHHHHHHEAFGGGHHFGFFGHHHHGGFFFFHFHHHHGGE8EFFFFHHFEHHFHH;D@FA@HHHHHHGHGHGFHFHHH>:+078EE @read_150_331/1 ATGGATTATCTTTAGAATTTTCTAAGAGAGGAATAAAACAGAGAAACAGAAGAAAATGAGAGAGTTGACTTCAGATAAATATAAAATTATCACCTTAAAA + HHHHHHHHHFFGFHHGHHHGGEG@>GHHHHHGHHB&2>FHF?HHHFHHHHGGFBG>E*CFHFFHGGF?C?F>?:FGHHHBC?DCGGHHG?ADDEFG?ECC @read_150_332/1 CAAAACTGAATATATATTTATATCTTTTTCCTTCTTCCCTTCCCATTGCAATTATCTTATTATATCATTTGCTTATTAAATCCGTATTGCCATATACTTG + HHHHHHHHHGGGHHHHHHHHHHFHHHHHFHHHHHHHFGHHHEEFDACFHCDA;ECCFECEFHHBF>9BCC@BB:EBHHHHEFFHHDF?FEHHHHHHFHHH?CCDBAHGGGHHHHDD>DDHBCEHHHEGFBH @read_150_334/1 ATGCGGACCTGCCGAAAAGGAAAAAAGATATGTTGTATTAAAAATATACCCCCAAAATGCATTCCTGAAATGTTAATTGTATCCCGAAAAAACACATAGT + HHHHGHHHHHHHHDAEBEDDGHHHHFFBFFFHHFHGGFHHHHFFFB6&,GGGHHHHHFGHBEEFEHHHFFFFBDDDAADGFFBF?:>>3GHHHHHHHHHH @read_150_335/1 ATGGATTATAAACTGCACAGCAAACATTAATAAATTCTTACAACAACTTTGTGAACTATAATTTTTATGTGCATATAGTAAATGAATCACCGAAAGACCA + FGGGBEFFHHHHHHFHHHHGFH<9D@EGEE934>>FHHHHFFFEFGFHHHHHHHHHHHHFHHHHHHHFHHF@FFFGGEGGEGFGFHHHHHC75@=9A>BB @read_150_336/1 ATGCGGAGGCGAAGTAACAGGTTTTTTCCCCTTTGGATGCATATTTTTTTCTGTTTGTTTGACCTGAATCTGGGAACTAGTCAGTCGAGATTCAAGATCG + BFFFEBDEB6<+9>=;B@BGHHDD5EBFHHHFHHBDGHHGHHB?FHHHHHHHFFEGHBDCFEFHHHFFF9=8>BAHEGEHHHHHFHFHHHHHHGF?A?DF @read_150_337/1 ATGGATTCCAAATCTACGTCTGATTGGTGTACCTGAAAGTGATGGGGAGAATGGAACCAAGTTGGAAAAAACTCTGTCACTATAGATCGGAAGAGCAGGC + HHHHHHHHHHHHHHHHHHFDGHHHDHHHHHBGGHGG;B@>CEHHH?FHHHHHHFBEEF?BFEBDA+7AHHHHHDFFFFE6=DHHHHHHHHHHHHED7*%: @read_150_338/1 ATGCGGAGAGAATCACTTGAACCCAGGAGGTGGAGGTTGCAGTGAGCCGAGATCATGCCATTGCACTCCAGTCTGGGCAACAAGAGCAAGACTCTGTCTC + HHHHHHHHFFF@>FGGB@D8@FDGGFBFEDB<1-BDHHFHHHHHHGFHCBHHFEEBEEHHHFEFDHHFEA;ECC@<5<8>9D55/61EHFAEFHHFHHHFFHHFFFGFHHGGHHHHHHGB;:2-BF @read_150_340/1 ATGCGGATGGTGCCAGTGGATTGGACGGGCTCCAGCTTCTTACTCTTAGCGACCTTGTTCTGCCATTTGATGTTAAATATAGAATGTAAGGGGCAGGGTG + HHHGFBA<:;=DEEEHHHHHHEDBEHHHHEHHHHHEFFGHHEFFHHHHHHHHHGG?DEEEEHHHHHHHFHFHHHBFDBB@FDA+:BGHHDFHHHHHDBHH @read_150_341/1 ATGCGGACCACTTTTCCTAATTTGAAATCACTGAAAACTAAGCTGTGCTTTCTTAAAGACCTGCAAACTGAAGCTAGACAACAAATTTCCAAAGCAAATA + HHHDEBCEFFBGGHGFEEHHHHHEEE=DDDGGHHHHHHHHHFEEHHDE?9:;;DHHHHFFHHHHE?FEFBD9AAFHHHHHHFHHHHHF@FHC89)=5BDB @read_150_342/1 ATGCGGATTCTTTACTGACACAAAATATTGTTTGACACCATGGTTGAAACATTGGTCTTAGGCCAACACTCTCCATTATCTGTTGTTGCCAAGCCTTTGA + HHHHHHHHHHHGGGGHHHHFHHHGGHHHEECEHHHHHHHHHHHHHFFHHFHFCHHHHHHHD>DHFHHHE?:C7EHHHHHFGHHHEEGHHHHHHHHFEEEEBA @read_150_344/1 CAAAACTCCAATAACAGACAAACAGAGAGCCAAATCATGAGTGAACTCCCATTCACAATTGCTTCAAAGAGAATAAAATACTTAGGAATCCAACTTACAA + HHHHGHHHHHEFFFADDCEEGEGGHHEBEGHFHHFFHHE@))6D=EGHHHFFFFEBE@?5ACEHHHFFAA=EHFHHGGFFHHHHHFHG@DFHEFHCEFHH @read_150_345/1 ATGCGGACTCATTCTGTTCATCTCTCAGATCAGTGCTGGACCAGGGGAAGGCACCACAGAAGCTACCTCCTCTCTCCTTTCAAAGATGTGGTGTTTGTTT + HHHHHHGHHHHHHFHHHHHHHHHFBEEHFABFGGEHHGHFDGBHHFHDDFFHHHDEEGEHHHHHHFFEDE>?AC@9:.--@D?))?EH5))6;99BDEDE @read_150_346/1 ATGGATTGTGTGAAGGTGGCCAAGAAGTTGCCCCAGGCCCTCCAGCGGCACCCACCCTCCTCCAAACACATTCCTTACACCCAGACACCCACCCCTCAGG + FFDGHHHHHHFHHHGHHFHHHFDFGFHHHHHHD89FGGEEE@:2;>9FCEGHHHHHGHHHFEHHGFHHHHHFEDHHHHHEEFFFHB9BHHHFHHHHDECF @read_150_347/1 ATGCGGACAATAAAAATTCACAAAACACAGGCATGGATAAATTACGGCACGCCAGCTGGATAAATATACCACTGAAGGCATGATTTTTCAAGATTGTATT + GGGGGEGHHEGHHHHHHHGHHGHHHFHFHHH=BC@HHHHHHHEHHHHHFHHHHHE?GFFGHHHFHHFEDHD@EBFBB6;:A>EEBHHHEFHEDDDFFHFD @read_150_348/1 ATGGATTGCTTGTCTAAAGCTGACTAATTATTAGAATTTATTTATAAACTTCCTGTGATGATTTCACTTGCCAATCAGCCCCTGCCTTCTTTCAGCAATT + HHHHHHHHHHHHHHHEDHHHHHGHHHEEGFHHHHHGGFFHHHHHHEHHHHHEGADCFFB/DHHFGHBBFFHEEFFGGGGGHHEFGHHHHFGFFFHHHBBE @read_150_349/1 ATGCGGACCCACCGTTGGACATTTAGATTGTTTTCAATGTCACACAAATAGAAACAATGATGAAACTGATATCTTGATGCATAAAGCTTTTGCTGTATTT + HHHHHHHHHHHHFHHHHHHHHHHHHHHCAF5EHFF5CBE@ @read_150_353/1 ATGCGGACTCTGCAGCCATAAAAAAGGATGAGTTCATATCCTGTGCAGGGACATGGATGAAGCTGGAAACCATCATTCTCAGCAAACTATCATAAGGACA + HHHHHHHHHHHHHEGHHHHHHHHHHHHHHHHHHHHHHHHHHFFDFHHHHFHHHHHECHHHHD;D@ABBHHHHEEFDHHGHHHHHHHHHFHGHFHHGFBFD @read_150_354/1 ATGGATTAAAGGCACATGCAAATGCATAGATTTATTTATTTAGATTTCAATTGAAATTTTTCATTATGTTTATTATTTGTAAACACAGGCATCTGCTTGG + HHEEGGGGGHGHHHHFHGGGFHHHHFHHHHHHHHHHFHFFHED?DDBFHHHGGFFHHHFBGGBFFEEFGEFHHFHFFHFFEEGEEGGHHFBHHHFHEFFH @read_150_355/1 ATGCGGATTCTGTCCCTCAGTGCCTAAGACAAAACTGAGGCACATAAACTGACAAATACATGTGTATCTACAAGGGTAATGGGGCAAAATATTTTAAACT + GGDA6B@FHHHHHHHHHH@>DHHHHFFFFFDEFHHHHHHHHGHHHHFHFHFHFGG5>+?8EGBHHEEEEFFHHHEGGEE@:@D@ABDHHHHGHFBDDEEFBD?EHGGFFE@8@57>@:F@39>.6=CHHFFHGDEFFECCB?HFFDFEFFCHHHHHHEHHHHHFCGHFHHHCA @read_150_358/1 ATGGATTGTAGGGACCCAGAATTTATAGAATAAAGGGAATGTCTAACAGAGATCTCGGGGCAGCAATCTAGCTGACGCTCTCTCCTATGTAACAAGCAGA + HHHHGGHHHHHHHHG@ADDHHHGBBFFHHHHHHHHHHHHHHHHHFD3A>HHHHHEEEGFHHHFECGGGGGB;6;FGFFBAFFEB>ADFFHFHFFE?BBBB @read_150_359/1 ATGGATTTGAGATTTGGGGATTACTTTTTATGTGGCATCATCACAACAAAGCCTGACTAATATATTGTATAAAGTTAATTGAGTACTAACAACATAAGAG + HHHHFFGHHHHHHHHHHHGHGHHHHFF=2GF@360D?66@?DFFGFGGFDHFHHHDEHHFHHHHFFFFD???;,8043&0&,5-(26EGEGF<8%%')77 @read_150_360/1 ATGGATTCACTGAGATGTTTATGTAAAGTTAAACATAAATCTAGCCTATGTGCACATCCAGGCACAGCACCTTTCCTTAGACTTATTTATGACACAGATT + HHHHHHHHHHHHHHHHHHHHHHGHHHHHHHGHGDFHHHHHHHHEGFED=FHHHHHFFDGFGFFFF@:?DDFFEHHHGGGGGHHHHHHFF>CFHHGHHHHB @read_150_361/1 CAAAACTTATTTTATTCTCTTTGCAGTGGTTGTAAATGGGAGTTCACTCATGAATTGGCTGTTTGTCTTTTATTGGTATATAGGAGTACTTGTGTATTTT + GGHHHHHGGHHFEEDHFFBHHHHHHHFHHHHHGGBGGGC>>DA>DEEHHHEDDFHE=HHHHHHEFHHHHEE?FEGE:1<6CE@EEECBFEEHFFHHGHHF @read_150_362/1 CAAAACTTGGCAATTTGACCTGGATCTTGAAGGATGGTTAAGATTTACAAGATGGATTAAAAGATGGGGATAAAGGGAAGGGATTCCCGGGCAGCGAAGA + HHHHGGGHHHHHHHHFFHB>GDGHHHHHHGGGHHHHHFEFHHHHHHHHHHHHFHHEHFCFFHHHCFCC255@.EED?2::EFHFGFF<DFHFHHHFDBDBFHHHHHHHHHGHHHHHHFHHHFFCDCEEEEHG @read_150_365/1 ATGGATTTTGTATATATAATGTGATTTCTAATGCTGCATTTAAAAAATTTTATTGAAACACCTTGTCCTTGTTTAAAATTTTTAAAATATAACCAAATGA + HEGEEEFGFHHHHHHHHFHHHHHHGEHHHHHGFG>+:,47DEDDHHGFHEAFGHHHGEGHHHHHFGBEGHFFHHHE @read_150_366/1 ATGGATTGGGCGCCCCTCCCCCAGCCTCGCTGCCGCCTTGCAGTTTGATCTCAGACTGCTCACTATAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC + F8<>=GHHHHHHHHHHHHHHHHHHHHHHGHHFHHGHHHFEFBGGGGGGEDHHHHHHEGHEHFHHHHHFHHHHHHHHHHCCEHHHHHHHGHHHHHCGEHGGEHHHHHHHHEFFEHHGGG?FHHHHHHHHH<;65EAE98ACEHHHHHHHEHHHHHH@EHHHHHE;9 @read_150_368/1 CAAAACTGCATGGGGATTAAGCCCAGGAAGATAATTACCAGAATATCAGACTCCAAACCGTAATCACATCTATTAAAAATGACACGCGGCAGCGAAGATC + HHHHHHHHHHHHHHHHHHHEGHHHHHHHHHHHHHHHHGG@FFHHHHHEHHHGDCEEFEDCHFGGFEHHHHHFHFDEE<8.BD;;8+@CDEBFGGGHHBBC @read_150_369/1 CAAAACTACAAACCCCAACTGAGGGACATACTGACCTGCAGTCTTCAAGTGTCAAGATCGTGTCAAGGAAAGACTGATGAACTCTTCCAGATGGAAGAGA + HHHHHHHHHHHHHHHHHHHHHHHHGEGBGHHHHFGHHHHHHHHEAEA>*3)=3+-;>>F@@DDDHHHHHHHDFEDHFHHHHHHHFB;EEFHHHEEHGD@? @read_150_370/1 ATGCGGACTGTAATTCCAGCTACTCGAGAGCCAAAGCAGGAGACTCGCTTGAACCCAAGAGGCAGAGGTTGCAGTGAGCCAAGATTGTGCCACTGCACTC + HHHHHGHHGFFFFHHHHHDBA?B?AEGHC8/*'1(1<*135>FG8=DHEEFFHH@;AEGH @read_150_371/1 ATGGATTAAATCTCAGCAATAGAATTGCACAGGTAAAGAAAGAACTTCAGAGCTTGAAGACGAGGCTTTAGAATTAACCCAATCTAACAAAGACAGAAAA + HHHEGFFFGGGGGGFGGGBEBGFFFFHGHHHHHFFHHHHHHHHGDEGECDDHFHHHHEFEFFHHHHFDFFE?6>DGGGGHHHGGGHHHHHHHHHHGHF?E @read_150_372/1 CAAAACTCACCTTGCCCCACAGCCCCTGACAGGCCCCTGTGCGTGATGATCCCCTCCCTGTGTCCATGTGTTCTCATTAGTCAACTCCCATTTATGTGTG + HHHHHHHHHHGGHHHHHHD=GFFHGHHHHHGGG=@@DCDBFHFFHHHHHHFBEEF59DFCFFD2-:;FFHFBFFGHHHFGC@@EFHHHFFGGGHEFFBCH @read_150_373/1 ATGGATTTCCCCACGTCCATGTGTTCTCATTGTTCAGCTCCCACTTACGAGTGAGAGCATGTGGTGTTTGGTTTTCTGTTCTTGTGTTAATTTGGTGAGA + HHHHHHHHGGHHHHHHE@@B=BDFEGHHHHGFF=DDCFCEE?CCEFFFHECHHHHEFFHHBGGHFHHHDDEBA@@(*97&5BI?=6>95&(15();A<6@ @read_150_374/1 ATGGATTGGTCCTACAATTCAATGTATTTAAAATCTACCATGCAATATTTCAATATTTCTACAAAAAACTTGACCTCCTCTAATCAGCTCCATTCCAACA + GHHHHHHHHHGDEHHHHHHHHHGHHGEGGDHDHEFHHHHHB>7>7*7@EA2EEHHHHHHHHHHHHHHHFHFFEE8=@@<,8DEHHHHFHHHHBGFFEEHB @read_150_375/1 ATGGATTGGGCTTTTTAATCACATCAGCTGGCTTGCTTTTATTTGAAGTTATTGTAATTTCCATCTTCTTCATTCCTCCTTTTAGCCATTCTCGATTTGA + D?CGFEEFEHHGHHHHHHHH??BDDFGD=G=FEGHHHAHHHHHHHHHHHHHHHDCEE9DFFFCFDGGGFHFFEE401'+EHHHB=?EFHHHHE6.;@C?H @read_150_376/1 ATGCGGATAAGTTCCTCTTGACTGCATACATGCAGTAGTCAAAGATTCAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCACGTAATCTCGTATGC + HHHHHHHHGEGGGGHGGHHGHHHHC>/@FFEFHHFHHHFFHHHGGFGGF;<@@=-65EEEFDHHGDHFHHFGGGGHHHHHHF=FB5)+%/ED67@EFFEH @read_150_377/1 CAAAACTCTGCCTAGGCTGGAGTGCAGTGGTGTAATCTTGGCTCAATGCAACCTCCGCCTCCTGGGTTCAAGCCATTCTCCTGCCCAGATTCTCAGCTGG + D=GGGGGHHHHHHHHHHHHHHHFB>EGHHECGGGHHFEEHEFHHHBEHHHHHHHHHHHGFFFHHHFFFFEBFFEEHHH?GBDEDHHFCDCA=@GHEGEHH @read_150_378/1 ATGGATTCTGAGGCAGGAGAATTGCTTGAACCCGGGAGGTGGAGGTTGCAGTGAACCGAGATCGCACCACTGCACTCCAGCCTGGGTGACAGAGCAAGAC + HHHHHHHHDD55@FHHHFGGFFHHHHHHHGGHHFGGGGFE8??DGGFHHHHBFEDHHHFHHFHHFA2;>GHHHHHHGFGHHHFHHHHHHFHHFE@EFHHHHHHD79'BC9/89'/-7.3@DFFGAAADCBGDD?;,6CHFFEFH @read_150_380/1 ATGCGGAACAATCATGTCGTCTGCAAACAGGGACAATTTGATTTCCTCTTTTCCTAATTGAATACCCTTTATTTCCTTCTCCTGCCTAATTGCCCTGGCC + HHHHHHHHHHHHHEFGGHEGHHHHHHHHHHDDHHHHHHHHHHHHHEG?HHHFHHHHHHHHHHHHHHCDDFFDFBF797*2-3CBFDEEGGGGGHFDFEHHGC7;0%%. @read_150_383/1 ATGGATTACTGCTCTATGAAAAGAAAGGTTAAACCCTGTGAGTTGAACGAAAACATCACAACGCAGTTTGTGGGAATGATTCTGTCTAGTTTTTATATTC + HHHHHHHHCC97<8GGGBABB3=B>;:; @read_150_384/1 CAAAACTGTTATTTGTGTCCTTTTACTGTTAAATTGCAAGAGGAAAGTCTTTTTAAGGGAGCAAAAATAATATTTGTGGGGAGGAGACAGCAAGCAGCGA + HHHHHGHHHHHFFHHHGGGGHGGHHEHHHHHHHHHGEG@=DFHHHE>=BFHFHHB3);%87<*D@FHHHHHHHHHHHDGGC.6>9BGDEFEE;>:@C7(- @read_150_385/1 ATGCGGAAATTTGATCACTGTATTTATGATGCCACTCAGCCAATTAGTAGGAGATCAAAGACCAGTTTTCATTTTCTGACTATGATGATCTGTTTGGTTT + HHHHHHGGFHGFHHHHHFFFHHHHHHHEGHHHHHEGHHHHHHHHHHHHDHHHHFFGHHHH?CDHDDHHHHFFFFFHHEGGHHFFHHBC93BHFFHGGHHH @read_150_386/1 ATGCGGACCTTTTAATCTCAGTCGGTGAGTCTTATTTGTTTAAAGTGCTTTTGTGGTTGGTTGCTTTTGTGAACTGACCTAGTTTATTAAAATGATAATA + HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHDDGGFFHHEFG?DE:29.EFHHHEHGHHGEBAEEHFBFFC;ADDEFEHHHHHHGHGED?E<8DDEFGFGF @read_150_387/1 ATGGATTGCCTGGGCATACCTCTGTCGCACAGCCTAGGTTCAAATCCTGGCTCTGTCACCTAGCGCTCTGCAGCCTTGGGCAAGACACTTCACCTCTCTG + HHHHHGGHHHHHHHHHHHHHHGHHHGEEEH>@FDEGCFGHHEHGHHHFHA1,=CFHGE@ @read_150_388/1 ATGGATTGGAATCTCAGATATCACTATAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCACCTAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAA + GGFD@FHHHHHHHHHFEHHHHHGGED=BHHEGGGHHHHHHHHHHFGF=;FFDCFEBFHHHHHHFHHHHHDFHHHHHHHHHHHHHHEEHHHEE=BD=FCEF @read_150_389/1 ATGGATTTTTTGCCTTCTTATTTGTCAATACTCTTACTCTGGATGAGTCCTACAGTTTACTCTGTTTGTCACTGATACCACAAACTGAAAGTTCCAGAAG + HHHHGEFHHHHHHHHHHGGHGGGDFHHHHHGHHHHHHGHHBEHGGGHHHHHHFHEEDBBBBFHHHFBDFHE?DED=?GGF/-:1(:8DD@CD=FHHHHHH @read_150_390/1 ATGCGGATTTTTTTTGAGATGGAGTCCCACTCTGTTGCACAGGCTGGAGTGCAGTGGCATGATCTCAGCTCACTGCTGCCTCCGCCTCTCGGGTTCAAGC + HHHHHHFFHHHHHHHGGHECGGHFFFBGEEGHHFFEFHHH7@@BFCCDFHHHH?FHFGFHHFFE/-?HH@BBEEDEEBBF;>63**=>>EE=DA50:64CFHBFFFFHHHBDDCHHHHFDHHHHHHFFE:4EGHHGHEFED>=BBFFFFH @read_150_392/1 ATGCGGAGTGAGACCCTATCTGTACAAGATTTTTTTTTTTTTTCCATTAAAACAGGCAACAGGGCCATCTAACTGGAGATTCAAGATCGGAAGAGCACAC + HHHHHHHHHHHHFFGEFFGFHHHHHHHHGFBBGEFHHECDBCGE+BFFFHHHHHHHHHHF@D@E@DF@?E?)=CCEEEEEGHCHHFDHGGHHG@@A@BFH @read_150_393/1 ATGGATTTATCCCTGTCCTCATGAAGCTTACCTTCTAGTGGGTGAAGCAGGTAATAAACAATATAAGTAAGTAAAAATAAGTATGTTAGGTACTGGTTAG + GHHHHHHHHHHHHHHHHEF=F@8EHHHGDD2>9A=HGCC?HEHB;4?CF;EHFHHHHHHHHFFCB?FHHHFFE=2>=BCFFBE??31-3.9FHHF.A>:; @read_150_394/1 ATGGATTGCTTGGCCTCAGCGGGCCATGGGAGACCCAGGGAAACGACTCTAGTGTGAGGCAGTGGTCCTGCCAGTGACTGACAAACCCTCTTTGTAAGCA + DDDFFFBB=;DBFHHHHHHHB-DGDDGFGHHHFBEHHHHHHHHHHHEFHGFGGGFHHFDBFGBEHHHEEEEFE>HGGGFGHHHFF;CA88DEEHFEFFBHFBHE@,8CD?D@DGGD?BEFGHHHGC @read_150_397/1 ATGGATTCTCAAATCATATTAGAATCTATAGATATGCCTCTGTTATAACAATCCTGTACCCACATAAAACCTGCATTTTTAATAGGAGATACAAAGGTAT + HHHGFHBGGGEHHHHHHHHHHHHHHHHHFGDHHHGGECFHHHHCBFDEGGDHFHFHHGFHHHHHEHHFHHFEFFFHHHGBHFFEEGHHHHHHHHDFFE;E @read_150_398/1 CAAAACTAATGTCAAGTAATTATTCATTAAATGAATGAAAAAATATTATTCATGTTATTCATTAAAGTATCTAGTGAATCCATAGGCAATAATTTCCTAA + HHGGGHHHHHHHHHHHHHEDD9=GEGHHHHHHHGFF@=1@@CDDDEFDFDCEBFFHHBHHHHHH @read_150_400/1 ATGGATTTCATTGTATTGCTGTCTATTTTACCCTTCATCACTATAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCACCTAATCTCGTATGCCGTCT + GHHFEE;@=FEGGHHHEHHHHHHHHHHGEEB=D=3E<2'1FHH??>CHHHHHFHHHHHCEHHHHFHHFHHHHHHHFFGGF>DHHFC6E:?@-2BF4)*/1=*1,6 @read_150_402/1 ATGCGGAGCCTGAGTTTTTCTTCACTTCCTGGGTTTGTTTTTGTTTGTTTGTTTTTGAGACGGAGTCTCGCTCTGTCCCCCAGGCTGGAGTGCAATGGCG + HHGFGDEHHHHHHHHHHHHHHHHHHHHID='?HHHHGHHHHHHFFBEDEEA:;,)/*9EBCFHEEEEFD@D765ECGGFEGGGHHHHHHHHHFFFEFCCB @read_150_403/1 ATGCGGATTCAGAGCTGGAGCAGAGGATCCCCAGGAGGCTATGACAACTTCACAGGCACCCCCAGTGCCTTGGGGATCACTTGATAAAGGTTCAGGAGTA + GEFBBFHHHHHHHHHHHHFFHHHH?AEEHHFD6439AEFHHGFFFFHHC?FGGHHHHFHHHGHHHHA:0<1*:?EHHHHHHHGE@.3+,-<=DDCFF?=B @read_150_404/1 ATGCGGACCCGACCCAAATTGACAAACCTATACCCAAACAGTGCTCTGAACCACCTACATTTCCCTGCTTGGCTCAAACTCTCTCTCTCTGTGTGTGTGT + HHHHHHHHHHHHHHHGGGHHHHHHHGGGGGFFGHFGGHHEHHADHHHHHHHHHDCEGGHHHHHF:>>;>@DD773?AEADBFHHHHFBF:7.=?GFFFFD @read_150_405/1 ATGCGGAGTTGAAGGTCCCACCGTGTCAGGCCCTCTGGGTGAAGATTCAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCACCTAATCTCGTATGC + HHHHHHHGGHHHHHHHGG=DGGHFHHHHHHHHHFHHHHHHHHCCFEBFHHGFCBB8==DHHHHHHGEDAFFHHHHFEGFFH @read_150_408/1 ATGGATTAGATTAACTATGATTCACTATAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCACCTAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAA + HGEDB09DD?D<>64:5>?HGHH? @read_150_409/1 CAAAACTTTTTTATCCTCAGCCTTTCCGAATTTGCTTATCAGTTCTAATAGGTTTTTGGTAGAATCTTTAGGTTTTTCCAAATATAAGATCCTATTGTCT + EGGGGEFEHHHHHHHHHHHHHHHHHHHHEBGDFFGHHHHHFHGGGGFHHHHEEBDFHHFEEEGBFHHHHHHHHFFGGGGDHHHAC?:F7GADEBEFFFHH @read_150_410/1 ATGCGGACCTGTAATCCAAGAACTTTGGGATGCTGAGGCTGGTGGATCACTTGAGGTCAGGTGTTTGAGACCAGCCTGGCCAACATGGTGAAACCCTGTC + HHHHHFGHHHHHHHHHHFHGHHHHGHHH?EGBEEGHHHHHHHHHHHHEEBDGHHHHHHFC?FFFFHHHD:6'2CEHHGHHHHHHH?EBCEAE=B=EDHH@ @read_150_411/1 ATGCGGAAGGTTCCAATGCGTGGAACCTGTAAATATTGCCTTATTTGGATAAAGGGTCTCTGCAGGTGTGAAGATTCAAGATCGGAAGAGCACACGTCTG + HHHHHFEHFHDCGHHHHHHHGGGGGCBCD@EFFFEHHHEB5DFHHGGF2:@EDFE?3.,C>DDDHFHHFDEHHHHHHHGHHGHEEHGEGGGHHHFHHHGE @read_150_412/1 ATGGATTATAGCCTGGGTGACAAAGTGAGACTTGGTCTCTATCAAAAACAAACGAACAAACAAATTCATTCCTTAAATCACTATAGATCGGAAGAGCACA + G8@@>8/@GFEDDHHFEDBBC@?DBGGFHHHHHFFFFEHHHHHHHHHHHFBEFFEC?4;?AFHGHHHHHHHHFHG=;7DHGGEHHHFHHFD>>9CHFFEBGGEEEEFFBFBBA<>56(62@:9 @read_150_416/1 ATGCGGAGTGAGGGGGCAGGAGCTTAAGAAGGCCATGGCCAGAGCAGCACAGAATTCAGTGAATACTCCAGGGAAGGGCGTAGCCTTTGAGATTCAAGAT + HHHHGGEDHHHHHHHFDEDB5ADEEEEHHHHHHHFDHHHHHHECHE6FHHEGGHHHHHHDB38=9FF@:.('*3C?@:>:1*DFADHBFEHGHHEFEFGG @read_150_417/1 ATGGATTAGGAACCACTGAAGATTCAGAGCTAGGAAATCTGATGAGAAGTAGACAGCGTGGGAAGAATGAATTTAACAAAGTTACAGACCATGCCTAAGA + HHHHHGGGDDE:<9FFGHHHHHHHHHHGBB;@EHHHHHHEFGGHHHDBEDFHHHHHHHFFCAE955EEHHGGGHHFHHEHHH @read_150_418/1 ATGGATTTTGTATTAATCAAAAGACCATTACTAATTTCAGGGAAGCCTCTTGATTCACTATAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCACCT + GGGFEEBA?;@=FBF9>CGGHHHHHHHHHHHHH2?FB8>>:7EEHDFGFFGF<@DFBDCBFHHHC.DFFFFF @read_150_422/1 ATGGATTAAAAACCAGTGCCAGGGCCCACTACAAAGGTTTTAATCCCCTTGTTCTTGAGTGGGGGCCTAGGCATCATCATTTTCCAAACCTTTCTGGTTG + GGFEGHHHHGHHHHHHHHHGHHEFFGHACHHHHGFHFHFEHHHHHHE>DFGHHHHHHEGFHFHHAEEFDEDFGFEGGD:?C74EFGGGCBBFC>DHHFBG @read_150_423/1 CAAAACTCAGCAAATATTTTTAGATAAATAAATGGTCTAGGACAAGTTAGTAGAATGTTTTGAACCTCACTTTCTGGTATGTAACATAGGGATACCAATA + HHHHHHHHHHHHHHHHHHHHGHHHHHFGGHHHHHHHHHHGHHGGE587-<0(?CEE;BC2)/7*@FAAD;:>>69EGG;BEHEGG?EA79BDEF.6AHEHFHHFHHF;<>G,8@AAFFGGG<)%''%/5@,:).,9DDC59 @read_150_425/1 ATGGATTAGGAGGAGATGGGAGCAAAGGTAAAATGCGGTAAGTAGAAAGATGGGGCCCAGTGCTGGGGTGGAGAGAGCTCTTGGAGAACTGGGTGCATAT + GFFHHHHHHHHHHHHCCEHGGFHHHHE/'-4:EEBFE@GFHHHFHHF;-=886352::*=BFHHHHEHHHFFECBGGGFHHHHFGHEFHHHCC3)4=CAH @read_150_426/1 ATGCGGAGTAAAACACAAAAGGCCACTATCACATGTAATTCACCAAGACTGAATTCTAGAATTATAATACAACTAAAACAGTCATTTAAGTTTCATCATT + HHHHHHHHHHHHHHHHHHHHHHHHH7>DCDFB?DD>:BHHHHHHHHHHEGGA:DEE?FEHHFHHHHGBHHC>DDDE77ACBGGC>?BDDBDHE?EEECBFGFFHHHF<=>+@BEC/3>6=@>?F=FHHHHGFD7,,;F @read_150_429/1 CAAAACTCCTCATTGGCGCTTCCACGGATCATCTCCAAAAAAACTACTTGTATCCAAGTGTTGCAGCGAAGATCGGAAGAGCACACGTCTGAACTCCAGT + HHHHHHHHHHHHHHFGHGHHHFFFGHHHHHHHHHHCDDFGGGE:<@ED5DCE?CEEHHGGA9>D@BEDCBDEEDCEBFFFHHHDDEEHHB=CA@C?EED9 @read_150_430/1 ATGGATTCTATCATCACAAGTTATTCCCTCCGGCCGACCCATCCTGCCGATTACCACCTGGCCTGTAGGTTAACTTCATGTAGCCAATTCTGTGCCATGA + HHHHHHHHHHHHHHHGGEDCFFGDF?=GCHHHHHFEFFFFHHHHFHHGGHBD:D=7>CFEHHGHC88?EEFFFHHHGGA=CFHHHHHHHHDEGFFCBHH@ @read_150_431/1 ATGCGGAAGTTCCTTGGCTTCTACTGATTTCCTTTTCTTATCCTGGACATTCAGGGCTGGCTTGGAGAGACCCGGATTAGAAATCTAGAGAAGAAAAGAG + FFHHHHHHGFHHHHHF@@/DDAGGGGAHDGHHGFFHGHHHHHHFFFFFE+:?FHHHHHHHHHHHHHFBHHD76D?EHHGHHHHFCE?HF=EHHEEGD7AA @read_150_432/1 ATGCGGATGTATGGTCTGCAATAAAATAAAAATATTAAATTTTTACTATCTGCCCATTTACAGAAAAAGTTTGCCAACTCCTATTCTAGACATCTAAAAG + HHEEDHHHHHHHHHHHHHEHHHHHHHHFB?FHEHH?@:B:+.EFHFHHH?HHHHBHHEF=?DBEBEFFHHHHHEBHHHHHHHEHGHGFHHHHGGGFBDFH @read_150_433/1 CAAAACTGATGCTAATGTAGCATTTCATGAAATTCAACAATCTTTTGGATTTTTAAAAAATCACACAATAATTTAGTCATAGATAAATACTTCCTTAACA + HHHHHGGGFDCBEF9FGHHHHHHHHHGH.CB@;8EFFHHHHHHHFHHFHGGGG<+6EC>4CDD@E@>CFFHFFDA@C=;9B?D=B?CC?@FCFD@FHHHE @read_150_434/1 ATGGATTAAAGCCAGGCCTGTTGGTGCACATCTATAATCCCAGTTACTTGGGAGGCTGAGGTGGGAGTATTGCTTGAACCCAGAAGGTCAAGGCTGCCTC + BC?GEHHHHHEBE<@EGGGHHGGE/FHHHHHHGHHHHHHHHHHDHHEHHFHFHHHHEFCC6D??HHHHHHHBDEHFGGGFEHHHHGGGFGG<(152%'+9 @read_150_435/1 ATGGATTGAGAAATAAAAATAGAAGTATAGTGTGATGAGTTCTGTGGTCAAGTTCTGTGTTGGGGGACATGGGAGCAGCATGGCAGAATCACTATAGATC + DCFFHHHHHHHHHHHHHHHHHHGFHDHHEGHGEEHHHHHF==DFFC>CCHEHHHGADHAHHFFBHHHFD:AEFHDHFEHHGHHHHHHGGGE>DDGGGGGE @read_150_436/1 ATGCGGACTCCTGGGTTCAACCTCTGCCTCCGGGGTTCAACCTCTGCCTCCTGGGTTCAAGCAATTTCCCTGCCTCAGCCTCCCAAGTAGCTGGGATTAT + FCCD=EFHHHHHHHHHDHH/DCHGDADDB<<%GHHHFHHHEB7>DFH?A;FB@CFFF?==DCDBGEHHHHHHHHEFD?;D+7@EHHFGEHFHHHHHHH@::?EFHH @read_150_440/1 ATGGATTAGTAATTGTTTTATAAATTTGGGAGCTCCAGTGTTAGGTGCATATATGTTTAGGATTGTGATATTTTCCTGTTGGACAAGGCCCTTTACCATT + HHHHHHHHHHHHHFEBFGHHHHHGHHGGGGEE;<FE6?DGGGGHDG=)9<35>FEFFHFFGG5 @read_150_441/1 ATGCGGAAGAAAACCCGTCATGGTACGGATGTATATCCAGGGGAGACACAAGATGTCATGGGAGGTTCCCATGGGAGGTTCACAGGATTTGAAGGACGGC + HHHHGGHHHHHHD=GFGGGGGGGHHHHEHFC@EBHHHGGFHHHBHHHHFHEF=EFHHHEBF???EC?1AB;@2/-,6:=BGFHHG?338BGEFHHHHHHHHHHHHGE<48:CAFDBEH?DDA@DFBCBFFFFAEFDEEHHHHCHHHHFGGEBB @read_150_443/1 ATGCGGACAGCATCAGAATCCTGTGGACGGCAAGCCCAGGTTTCTGAGCCCCACCTGGGCCTCTGACTCAGAATTCCAGGCATGGGCTTGGGAATCTGCA + HGHHHHGGDDHHHHGGHHHHHHHHHHHFGDDCFFEBCEHFEGB.,?DCFFHHHHHHHGGHHHHHHEHGFFHHCEHE;ABDBE?.&,@D;',<@;BHHHDFHHHHHFHHHHFGDEFFHFFC?34,85@DFCCEEHHAFHFFFFCEE%,;BBF=CGGFHHHHHHHDEFDDEFEHHHFEB33)5;CF?8@6AFHHFAC;FFBDDHGEF@D?D38B?BEHA= @read_150_447/1 CAAAACTACTAGCGAACAGAAGAAACTGAATGTTGATGATTAGATGGGTTACAATGACAAAAGACCTGGCAATTTAACAAGAAGGCATCTTCTGTAGGGA + HHHHHHHHHGGGGHHHHHHHHHHHHHHHGHHEEF?FEFHHHHHHHHFFHFHHGGGA?FFHHDGHHHHHHFFFFHFGFEDGHFFGG;+0<5>B@BEFGGHG @read_150_448/1 CAAAACTTATGTGTTACATGAATGTAACATATAATTAACACAACTATCATTACATTTGCTGTACTATACTTGGAATAAAATAGCATTTGGACAAACTGGA + HHHHHHHGGGGGGFEB>C@DFHHHEDFDDDCA@B@DEEF>E?HHHHHB82DCHE=EEEFFHHFFHFHHHDCBEHHEEGFHHHHG?BCFHHHHHDDFDECF @read_150_449/1 ATGGATTGGTGCTATGCCGCCCGCTGTCCTGGATATAGTGAATGAGCAGGGCTCGGAAGTAGCCGCTGTTAGCAAACAAAATGTTCCTGTGGGCCTTGAA + HGFFGGHHHHHHGGBEFHHFEEEE8=BCDECDDHHHHEFEHHFEE557=FFB=>BDEEFHGEBHHHFEDD?D@9DHHHHHFFEHHHHHGGGHHHFD>?:@ @read_150_450/1 ATGGATTTGAGAGAAGAGCAGATGGAGGGTTCACTATAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCACCTAATCTCGTATGCCGTCTTCTGCTT + HGHHHHHHHHHHHHHHHFCCDGHHHGHHHHHBB>FFCHHHHGEFFDEEAD@DCEFHHHHBGC55?HEHHHHHHHHHHHGBCGHBFHFDBEC9@DFHHHHH @read_150_451/1 ATGCGGAAAAGAAATGTTCAAATCTGTGAGTTGAATGCAATCATCACAGAGAAGTTTCTGAGAAGGCTTCTGTCTAGATTTTATGTGAAGATATACCTGT + EGGEGFGFDGGHEGGG8<<@BB?BB?<;:FGHHHHHHHHHHHFHHHHHFBGFHHFDADE;;?HHHEFFFFFC2?4?FFFDEFA@CEBFD<< @read_150_452/1 ATGGATTCATTCTACCTCTATAATATTTCTCCTATCTTTTCTCTTTTGTTCATTTTCACTATAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCACC + HHHHHGFFFHHHGGHHHGGGGGFGGGHHHHHHHHHHHHHFGHHHHHHHFFHHHEABBCC>24C?AFD?CHECC@6AAA@D83()08%.EHHHHFGHHEB@ @read_150_453/1 ATGCGGATGCAGGTCTCTGTGAAGTCTGCCTGCAGCCTCTGATGCTTTGTTTGACAATGTGCCCTGCAAGACTTTCCACCTGCTCCTCTATCTCCCCTTC + HHHHHHHHHFHHHHHHHHHHHHHGEHHHHHFHHBEADBHHH@>>61:>89>@CHDFHHC?ABBEBHGGHHHHHHHFFF;AFA<@B@@E>+6.+?AEGGFH @read_150_454/1 CAAAACTGTTCGGCTGTTAACCGAAAGGTTGGTGGTTCGAGCCCACCCAGGAACGGTTGTTCGAGCTTTTAAAGTATTCATGCATTGTCAATCACTAGAT + HHHHHGHHHHHHHHGHHHHHHF>777>GHHHHFFBEEGFHHHHHHHHHFHHHHCA@BCC??E87FHHHHFEEBFEGHHHGBFHHHHHHHHHGGGHHFEE, @read_150_455/1 ATGCGGAGTCTACTGTAGAACAAGCATTGTGGTTGGTACTTTACATATTACTTCAGGGAGGAAGCAGGAAGTAGTTGCCGGGCACCTGCTAGTTTCTCCC + DDFFGHHHHHHHHHHHHHHHHHHHHHHFGGE@6?CDH??AFHHFFEHHHHHH7FFCEEB:6=DFEH@2D?DCB<8+9:'(8(BB,;EEGHHFFHDEEEEF @read_150_456/1 CAAAACTCATAGGTAACATTGGTTTAAGGAGAGAGACCTGTGATCGAACAGTGTCTTGTGTCTAATCTGAGAAAGAAAGCATCCAGTCTTATCATCATGT + DEEHHHHHHHHHHHEEEEGFFB?EHHHH::FGGGDHHEBEGFE;9ADBGHHHHHHHHBFEHHHHH?FFEEFHHECHHHDDFHFHHHHHHGFHFFEFAB>5 @read_150_457/1 ATGCGGATGAGAATCATTGGGAGGGCAAACTTGCAGAACTAGGCTGAGTTTCCAGGAATGGCTCACAAAACAGAATTTCCTGGGACTGCCAAGGAGCTGT + HHHHHHHHHHHGFGGGHHHHHHHHHHHHDGFG::CCCA:'*'DBHHFF<.;;HEFHE>3 @read_150_460/1 ATGGATTTTCGTTTCTGATTATGGTTCATAGTCTGGGTGGTGTTGTTTTATCCCATCTCACCTCCCACATAGAGATCCTCATTGATAGACCCTGGATCCT + HHHHHHHHFGHHGFHHHHHHFHHHHHHHHHFHHHEEHHHHHEHHHHHHHHHFBD7:=FFHHHHH?EFH@>DFFHHGDGEGHF<-64:9BFHFFHHHHHHG @read_150_461/1 ATGGATTCAACTATTACTTGTCACATGATTTGGGGCAATTCATTAATCTTTCAATTCTTTGGTTTCCTCATTTGAGAATATGGGTTATAATAGCATCCAT + GGHHHHE8HHHHHHHHHHHGEFEHGGFEE@GFHGEFHHHHHHHFHHHHHHFHHHFGBEDFHHHFHHHHFHB:A>=CGGEEEHGFGFHHHHFFHEGEECCD @read_150_462/1 CAAAACTTGAAGATTTTTGCATCAATATTTATCAGTGATATTGCCCTGTAGTTTTTTGTTTTTTGTTTTTGTTTTTGTTTTTTTGATGCGTCTTTGGTTT + HHGGGEBFFGGHHHHFE@HHHHFEHHHHHHHEFEE?HHHHHHHHHGFHFFHHHFD?AA=HHHHFFHFHHHHHHHECCFHGGGHHHFGGDC5?=D=A?BE= @read_150_463/1 ATGCGGAGTTTAAATTTTCTACCTTCAAATATTGAAATAAAAATATTATCAAGCAATCTCTACTGGCAAATGACAGAGGGGAAATTATATTTTATTTCAA + @B86EDDEEBFHHHHHHHFHHHHHEGHHHFGGHHHHHHFEHHHHHHHHHHHFFFG?83<=C@C>AFHFFFFBFEFDEEFDGGGEHHHHEBFBFD@GE@5B @read_150_464/1 CAAAACTTCATTGTCAGGAGGATTCTCATCTACAAGTCTCAAATTTGTTTTTGCTTCTCAAACTTGTTTTGTTTTGTGCTGTTGTTTCTAGCCTGTTTTA + HE@CE@D@>FGFHHHHHHFFEEE8EHGGEACHHHHFCDAGGHB9DGGGGBEGHGHHHHHHHHD=EHHFHHFHEHHHEGHHHHHHHHGBFFGGGFHHHHHF @read_150_465/1 ATGCGGAGTCTCTTCAAACTTTACTTTTTTTTTTTGCATTCGATAAAGGTACGCAATTCAATGCAAAGAAGAGCTAGGGAGGAAAATTGAGAGCATTTTA + GGGFFFFFFHHHHHHHHHHGEGGGHHHHHHHHFFHHGBBDHHHHHHHHHHHHH=HHHHHFHHHHHGF?EHHHBE?91?AFHHHHHHHFFGHFH@>?HFHH @read_150_466/1 CAAAACTACTCCCTTGACTGGCAGTTGAAGCCCCATCCACTATCTGCCCTCGTCCTCCCTCCTAATCTCTCCACATTTCTCCATATGCCCTAGGCTCATT + FFEFGFHHHHHHHHHHHHHHHHHHGGGGGHHHHHGHHHHHHHHHHHHHHFFEEEBHHHE?):CFFFEEB @read_150_469/1 ATGGATTCATCCTAGCCCTGGACTGTAAATACATTGCTGGTCACTGAAATGCTCAGTATTAAAGTAATCTGTATAGCATATAAAACATCTGTGGGTCCAG + HHHHHHHHHHHHHHHGHHHFBGHHHGGEHGFHFFGGH?EHHHHHHHDEDFFDEDD:>CCAE=EEHHHFHHEFFHHHGFBEEFFHHHGFDCHHHHFED?=C @read_150_470/1 ATGGATTTCCATTTGTTTGTGTCATTTCTGATTTCATTGAGCAGTGGTTTGTAGTTCACCTTGAAGAGGTCCTTCATTTCCCTTAGCTTTTTGCTTTGTA + HHHHHHHHHHGHHHHHHHEGHHHHHGGH?GE79;/?DCAEHHECF?A@>;CFFHGFDDDDBFDEDDEEFEFGEDB6%5@/7:@@A5>>E:DADDEEFCFH @read_150_471/1 CAAAACTGTCACCAGGCTAGAGTGTGGCGGCACGATCTTGGCTCACTGCAATCTCTGCCTCCAGGATTCACGTCATTCTCCTGCCTCAGCCTCCCAAGTA + GHHHGGGHEEFHFGE=@@FFB<;BCDEHGGGEFFHHEGFFDFEEHEECFFFEHHHHFHHHHHFFHHHHHHHFHHHFHHHHFF57CFEE;5CF @read_150_472/1 CAAAACTAAAAAAAAAAAGAAAAAAAAAAAAAGCCGGGTGCGGTGGCTCACACCTGTAATCCTAGCACTGTGGGAGGCCGAGGCGGGTGGATCCCAAGGT + HHHHHHHHHEHHHGHHHHHHHGGGEHHHHHHFFHHHHHHHHHHEEHHHHDACF?9FEEB?EFBFHFHHHHHHFFFHHGGGGEHFFFAFH?@C@<5.;>>> @read_150_473/1 ATGCGGACAGATTCAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCACCTAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAA + HHGGGGFGGHHEDDHHHHHHHHHGGHHHFFGE@C;A@HH?AHHBFEFGCEH @read_150_474/1 ATGCGGAGGACAAGGGAGTCAGGAAGGGCAGGTCTGACCGAAGGTCCTCTGTGGCAGGCACAAACACCAGTGCCAAGGGAGAATCCAGTGGGTGGTCACC + GGGGGHGHHHHHHEECCCEEA<9GHHHEEBBE@:HHFEGGHHHHHFFHGFF>A?;5CFHHDDFFHFBE:DHHFEE@CDA?GHHHHHHF>FFHHE9EFDHH @read_150_475/1 ATGCGGATTCACATTGTTTTGTCTCTTATTTCCTAACTTTTTAATCTTTTTATTACATTTTCTAGAAGGCTTCCACAAAATTATCTTCCAATTTGTTAAT + HHHHHHFFGDHHHHHHHHHGHHHHHHHGHHHHHHHFFEEBFF<:9EB<:?DFHHHHHHHHFB6&&-+<

1<,AADDB97-0?D5(033;CEBGCC?FHHHBFHHHHEHHHHHHHAAHHHHFEFHGGGHHDHFFFGF?ACFEEBC.8A@ @read_150_479/1 CAAAACTTGGGTCTGATAACTTGAGAAATGCAGGGCAGGTGTGATTAATGAAAGGTCCTCCCTCTTTTTTCCTCTCAGGGGAGTGTTTAAAGACACCAGC + GGEGGGDFDDGGHHHHHHBDFHHHHFHGFFGADGHHHHHHEFGDEHHHHHFHHHECEHHFHHHHHHHHHBEFFFFHGEHHHHHGGHHHF@5)233CDEE5 @read_150_480/1 ATGCGGAAGATTCAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCACCTAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAA + GDEEHHHHHGHHHHHHHHHHHHHHEHDBFHHHHHHFFGGFGGGF@9EEEEBF?GDBHH @read_150_481/1 ATGGATTGGCACGGACTTAGGGACCGAGTACCTTCGAGGGCAGATCTCTTTCCATTCAAGCTCGAACATTCTGGGTGCTCGGAGAAGGCTTCTTCTATCT + HHHHHHHHHHHHHHHGHHHHCGHGGGDHHHHHHHHHHF6DGFHHEHHHHFHF;CGF6'13;=ADF8=6BFHHHHHHE>CDFFEBEEGFHEHE=+( @read_150_482/1 ATGGATTAAAACCCAATACCTATAATATTCCTGGCTAGTACTCTTCACATCTATATCATCAAAAACAAAGAAAGTATGTGAAACTGACACAGCCAAGTGG + GGFGGGHHHHHHGEEFGGHHHHGGE5EEEHHHFADDHHHHHHHHHHHBGGFHHHFFFFHHHHFHHFHHHHHEGGHHHHG@C833EEFFEBFB7/%8 @read_150_483/1 CAAAACTTTTGTGGGTAACCCGACTTTTCTCTCTGGCTGCCTTTAACAATTTTTCCTTCATTTCAACTTTGGTGAATCTGACAATTATTTGTCTTGGGGT + HHHHHGFFGGHHHHHHHHHBHHHHHHHHHHEGHHHHFE5EHFGFFGH9?ABHHHHHHHHHHHHHHHHHFFB4@BEEHHHHFFGFFHHGGEHHFHHEEHGF @read_150_484/1 ATGGATTAACAGACAGATCTTCTATTATCCTTTCTTCTGAATCATGACAACCAGAATCATGACAATCTGAATCATGACAATCAGAGCATCTTAATCTATT + HHHGHHHHHHHHHHHHHHEEFFFFFGDFHGGFHHGHFFFBC?<45=762*,AEHHHHHHFEEEC>)5BHHHHFHHHHHHHHFHHGFEADFAEEHHHHHFD @read_150_485/1 ATGCGGAGCAACTGAGATGGGATTTATCTGCTATTTTATGTGGCCTAGATTCAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCACCTAATCTCGT + HHHFEBEEGGGGGGEFGGHHHHHHHHGHHH8@CHHHHHHHHHGGHGGFBHHFGBFBGHHFDGHFHHHHHHHHHHHEEEEDF?FHHHEEHFGF?FHHHFF? @read_150_486/1 CAAAACTATCACTGTAGGAGAAGTGGGCCCTTGTGCAGAAGTTCTGCCCAGGAGGGAAGGAAGGCCTGAAGAATGAAGAGCTCCAAAGCTCTGCCTGAGA + HHHHHHHHHHHHHHHFHHHHHFGGDEC:@DDFHHFHFHHHHHHHFHHHHHHFHHHHEHHHHHHHFHEHHHHEFBFCGFFFFHHFF>AD6<;E??GGHHHHHHHBFFHFFDDFDEHH @read_150_489/1 ATGCGGATGTCCTCTTGGAGATGTCCATCCCATTAGCATCCACACACGGCCCTAATGGGCTTCAGAAGGCCAATGCCAACAGTCTTGTCTTCACTCCGCA + HFGHEEHHGCCDD==BB?@C6:,A:6@BGFFHHHHHFGE7=9GFHHGFFBFHHHDEFHHHHDBDEBFE7EA?958FE=20@FG @read_150_491/1 CAAAACTCACCAAGGTAAGATGGAAATGGTGGGGGCACTGAAGGAAGATTGCAACTTGTTCAGCCTCTGGGTGCCCAACATGCATACCAAAGCCTCAAGA + HHHHHHGBFFDDDHHFHHHHHHBHHHGCHHHGGFGHHHHHHHHHHHDFF>DFHGGFFFFHHFHHH2BFHGBBF @read_150_492/1 ATGGATTGCAATTTTCCGTAATATTTGTATAGTATGAAGTAAAAATGTTTGCTTTAAGAGACATCTGCTATAAATAAAATGACAGTGTAAATTTTCAAGA + HHHHHHGHHHHHHHHHHGEDEFHHHFGGGHGFFFFC>>:7?FHE@DEHHHCGFFHHHHHHHHHHHHGGGFFDHGFCHHHHHHEFHHFDD@FHG>2=GHHHFCCCBDEEBB @read_150_495/1 CAAAACTTGATTTTTAACAAAAGATAACAGCAAAACCCCAGATAAATTAGCAAACTACCTTCACAGCTCGATGTGAGAACTCTCTTAGTTTTATTTATTT + HHHHHHHHEDFHHDDCGEHHHHHHHHHHHHHHGGGDD?BDFDFEFF>:;HHHHFC=>EEGGCCFHHHECDHHHHHHHFFHHHHFG?CCDD @read_150_496/1 CAAAACTCTGTCCCTAGGGAAGGGACGATGAACGAGCTTACTGTGTGTTTGTTCACTCACTGGTCACTCTGATCATCCGTGCATCTCTGCAGTCAGCAGA + EDDDFFEHHHHHHHHHHFEEHFHHHHGHHHGDBEDEHEHHHHHHEDDFHCFFHHHHHHHHHDHFHFHHHEFFEDHFFF@2AEEFDB?A1AAFD/DGFF5F @read_150_497/1 ATGGATTGGAAGAAGCTGTAGGACTAAGGACTGAGGATCCTGGGGTGTCCCCCACCACTTTCCCCTGCCCTGTCGCAGGGGCAAGTGAGGAGGGGGAATC + HHHHHHHHHHHHGHHHHHHHC@@EHEBGD=@CFEEGGEHHHHFHHHHHHHHHHHFGGHHHHFBHDDHB=>CCCCEHHHHGB@CGHHHHHHEFGHHHB928 @read_150_498/1 ATGCGGAACTCTTGAGATTCAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCACCTAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAA + HHHHGGGGGHHHHFHHHDEHHHHHHHHHHHHHHHHHHHHHHHFEB;GHDFCCEFHHHHHF?CCFHHHFEHHHHFFGGBGEFEEEAADDG=GGGGAFFFFG @read_150_499/1 ATGGATTAAAAAAATTAGCCAGATGCAGGGTAGGTGGGGTGTGCCTGTAGTCTCAACCACCCAGGAGATTGAGGCAGGAAGATTGCTTGAACCCAGGAAG + HHHHHHHGGGGFGHHHHFF8BGHHGFEGHEHHB6;9=>9CBBAEFFGFHHHFFHHHECHGHGGGGGHHHHHHFHHBFHEEEFHHHFFHCGFHFFDE<:DGGEHHEGGC7@=GF@B@FHHHD/A5<>/ adapterremoval-2.3.1/examples/demux_2.fq000066400000000000000000003265041350370616400202530ustar00rootroot00000000000000@read_150_1/2 ATAGTGACAGTGGAAGAGAGTGGGTGTCCAGAAACCCTTGCATATGGAAAGTGTATATCATGCGGCTGTCGTTGCAGACCAGCGGGGAAAATGTGGACCA + HHHHFFFHHEGGGHHHHHHHHHHEB<2->A263=A<&7EEHHHHHF=C==;DDGEHHHEGHHHHHHGBCHEDEEGHHFEEDCCEHHHHFFHHHHFHFHFA @read_150_2/2 ATAGTGATACGACTCAGCTCAAGGGCCATCTCATTCATTCCTTCATCCACTCATTCATTCTTTCAACAAGAACTAAATGCTTCCCAAGTACCAATCCATA + BHHHHHHHHHHHHHHHHHHFGGGDHHHFHHGGGB==@@@:-6-34?C8A@0+.<<;9@FHH?@,--37EDEEDFHFHHHHFFFFD>>CDDEBBFF>>BEE @read_150_3/2 TGAATCTTCTTGCTTTGTCACCCAGGCTACAGTGCAGTGGCATGATCATAGCTCACTGCAACCTCAACCTCCTAGGCTCAAGTGGTCCTGCCACCTCTGC + HHHHHHHHBHHHHHHHHHHHHHHHHHHHGGBCCEEFHHHHHHHHHHH99BBGGE8?5.<9>BHFGGHF@:.D9HHFFHHH @read_150_5/2 TCGCTGCAGCGTAGACCCTAGTTGAGGACATAAAATGTGTAATAATACAAAACATGCAGTGCAGATAGCAAACACACAGTGGCCGACAAGGAAACGTGCA + HHHHHHHFHHHHHHHE=@BHHHHFHHFFHHHHHHHHHE@<@>?GHHFFHHHHHHHHHHHGEC@HHDEHHHHHHHHHHGFHHFHHHGFEEC66CBCDEDDF @read_150_6/2 ATAGTGAAATACAAAGATGAATGGTAAAATTCATGCTAATAATTTAAATTTTTAATTTTTCCTTACTTAGAACCACATAAATCGCCAATACATAAAACAC + HHHHHHFHHHHHHHGEF?@D@5=HHHHHHEEE@BHHHHHHHEFHHC@8DHHHHHGGGGGFBHD/@995=HGGG>@@AECDC7-2DHHFG4%/%&&-:;47 @read_150_7/2 ATAGTGATTTGTATTTTTAGTAGAGATGGGGTTTTGCCATGTTGGCCAGGCTGGTCTCGAACTCCTGACTTCAAGTGATCCACCTGCCTAAGCCTCCCAA + GGGHHHHHHGHHHHHHHHHHHHHHHHHFEGEBCDEHHFFFGCHHEHHFECEHHHHHHHHHHHHHHDC7DHHHHHEGHHFFGFFH>F<@5.7BBEBEHEE< @read_150_8/2 TCGCTGCGCACCAAGCACACAATGATGAAATACAGACGCTCCCTTGGTGGCATAAACACGGTGCCAGTCAGCTCCACGCTCTTTCCCATCTTATTCCAAT + HHHHHHHHHHFGHHHHHEHHHHGHHHHEE@5CFFGHHHFFHHDEHHHFF@526,+(<<<=5EC6BDFHHHHHHHHFEEHHHHHGGGHFHHHHHFFGGHHFCDHHHHGDFHHHHHEEEECB@FGFFGHHHHH @read_150_10/2 TGAATCTCTCTGGTCCCATGTAACAAATCTTAAAAGTCGTATGCAAGAAGATCAACTGTTTCTAAGTAACATAACTGCATGCCAAAAGAAAGCTCAAATC + F=EDFBBGEFFFHHEHHHHHGGGGGBDHHHFFDEHBGGHHHHHHHHGH=BB>.GGHHGGFGGHHGHHHHHF@DEHH>CBD8.CCFE;?E<5<>.4;845 @read_150_12/2 TGAATCTGGGATAGAACAGAATGTTGGTTCTGGATGGGAGCTTAAACATCATCGAGTCCAAAGGTTCTTAAAGTATAGGCCTCAGGCCAGCAGCAGAAGC + HGFEHHHHHHHFEEHGHGHHHHHHGBADDHHHHHHHHHHHHHE?3:BAA=>5:+8;:<963<36A=/DAC@FHHHHHHHHHHHFHHHFHHHHEGHH:;EFEEF@3&338GHHHFHHFHHFGHFC2.<@=6BEG?GHGGEEGDDHHFFEFHGFFE @read_150_14/2 TCGCTGCGATGCTTACCTCTATAATGTCCTCACCCTCTTCTCCAGTTCACTCTGATTTGAGTTTTGAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA + HHHHHHHHHHHGEEHHHHHHFHHHFHHFFDHHHHEHHHHHHHHHHHHE=:=A@7@>95<2=84.6DFFFHHHHHGCEE93(CBGGEE6&01,2;?G8?EFEF. @read_150_17/2 ATAGTGAAGAGCATAGCCATGAACCTCAGAGTAAACATTCAGAAAATTACTTCAATGAGTGCATAGTTATTGTAATGTAGTAAGCAGTAAGGTCATTGCA + IHHHHHHHHHHHHGBHHHHHHHHHHHHHHHHHHHG??8BBCGA4=CDEEHHHHFHE@CFHGGFFHGHHEHHHEGGGB>A@EEDFEGGHHHHFHHED=5*2 @read_150_18/2 ATAGTGAGGGCCCGCTGACAGCGCGCCCAGTAGAATATTGTATTAGTTGGTAGTGAGCTGTGTTCTCGTCAGGGTATCTGAGTTTCACAGAACAGACGGG + GEFGGEEEF=GHHHHHHHHHGHHHHHHFBEEEGGGHHHEDEEEEBGED22,(//7.16GGF=8@GG?;EBCDB3?FFD?AEE(FHHHHHHHFFHHHHHHH @read_150_19/2 ATAGTGAGTCTTCACTTATTGAGTTTATCTTTGAATGTGATGGAGCAAAGCTCTCACCAGGGAGGCATTGACACTCAGGTAAGTGCTTGGTCCCCCTGCT + HHHHHHHHHHHHHHHHGGHHHHHHHGHCFHHHHHHHHHHF@==HHFEEEHHHHHHHHHHEDHFHHHHHHGHHGDDDE;GEGD*+5)'+=:C8DEBB>?AD @read_150_20/2 ATAGTGAAGGAAAAACGTAATCTCTTTTTTCCATACCTACATTACAATGCAAAATTAATTGGTAAGTCAAAGAAATTTCAAAGAATTAGAGAGAGTTTGT + @=FEGFFCEGGI8=EG<6-.:6916@CEEFHHFDC871*:9>395@AEEGFHF><;HE73+1.=5.;-,0)3C890&9C(.. @read_150_22/2 TGAATCTTAGCTATCACCCTACTATACCAAGCCACTTTTCATCTCTTTCCCAGATTGCCCTGTTCACCTGACCAGTCAGCCTATTTCTCCATACAATCCA + HHHHHHHHHHHHHHFGHHFHHGBBFEFGFGHHHHHGEEHHHHEGGHHHHDD8@FHHHGBCHHDC:?DHHHHHHHHFGGDHHHHHHHHHHFEDEEB@--,5 @read_150_23/2 ATAGTGAACCTCCTACCACCACAGAGTTTAAAAAAAGACAATGAAACATATGGTGGGCTCACTGAGCACTTTCCTACAGAATTGTTCATTGTTGTGCATC + DGHHHHHHHHHHHHCHHHHEFHHHHHHDDFGFHGGGHEGEHHHHFHHHEDDB;@GFGFFFGFBHGCDHHHHHHHHHHHFGEEHHFBECB@627.;??5EF @read_150_24/2 TGAATCTTCTCCACTTGCAAATTCCACAAAAACAGTGTTTCAAATCTGCTCTCTCTAAATGAAAGTTCAATTCTGTCAGTTGAATACACACAACACAAGG + HHHHGHFHHHHHHHHHHHHHEBGHHHHGDHHHGDFFHHHHHFC=5AAEHHHHHDCFHEFHDBHGGEEBD?EEFGG;;=/,;>C@CDHC<A913:>FFCEEEEGHHHHGD?>CHEHBHEFHHHHHHHF<8=B?FFG@:5(02?FG6CHF @read_150_26/2 ATAGTGAGTGAGCGGGAAGGAAAAGAGAGAGAGACCGTCTTTCCTCTAATGTCCATATAATAAATATGAAGGATCTTATTAACTCACGGGCCTATCCCTG + HHHHHHHHHHHEEHGHHGGFHHHHHHHDBHHHHEFHHHHHHHHHFHHBDD@:@EBEA<<@BEG77@HGGCDFHHD?3-394>97GFB,CCFFFH=AF=FF @read_150_27/2 TGAATCTCCACTAAATACTGTGCTTACAAACTGATAATGGGTTGGAAATCACAATTTGAAAAGCACTGCTCTAGTCTATACTTTACAATTAAAAAAGTGG + D@B@HEGFEEGHHHHHHHHHFEFGIGHHHHHHHHHFCGBBBDBBHHHFCGB4D>@506???:5:.-9:BB*2,6.<<:*),+//).=>D=DHFC4;,2>+ @read_150_28/2 ATAGTGATCTTAGTTCTGAGTTATCATTTCCGGCTAGGGCATCAATTCTCCTAACTCGGGGACACAGACATTTGCACCAGTCTTTGGCAGTAATTATGTT + HHHHHGHGHHHHHHFGHEHHHHHG@DGHHHHFF?BECB@GGFHHHHFHHECBGIGFEFGEHFFFEHHHHFHHHE/GGBFEGFHFHH>;FDFFFH?GC80C @read_150_29/2 TCGCTGCGGGTAGTATGGACACTTTAACAATATTAATTCTTCCAATCTATGAACATGGGATATCTTTTCATTTATTTATGTCTTCAATTTTTTTCATCAA + 5002.579BEGHHHHGGGHHHHHHHCFGFDFFGGGGHHHHHFFFGHHHHFGDHHHHHHGEHHHHHHHDCHHFCE/12EHHHHFBEFHHHHHF?F>?A;9; @read_150_30/2 TGAATCTGGGGTAGATCTGGCCTTGGCCTGTGCTCTGCTCACTGAGCCTTGTGCCCTGGCATAGGCTAGATTGCGCTTAGGCGCAAGGGAGTCTTGTTCT + HHHHHHGGHEGHGHHHC.51>1@/1/6;.CHHHHHGGHHHHEEEEHHHFHHHA<9:''-;ACDEHHHHHHHHHHFEGHHG:-*3?EEDHFDA@8='4>EH @read_150_31/2 ATAGTGACTCTCCTATGAGAATGATCTTTTAAAACAACTTTGAAGATCTTTCTCAAAACAACTTGGAAGATTAGAGCATACAATCAGATCACTTATAATC + HHHHHHHHHHFFEHHFDHHHHFHHHHHHGGFFGGHHHHFHHHFHFHHHHHHHHGHHHHHHHGHHHFE8HHHHHHHDCHBEHEHFFDDA; @read_150_32/2 ATAGTGAGTTTCCATCTCCTTTTCCTGACATTTGAGGTTAAGACATATAAATCCATAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTG + HE@BHHHHGGGHHHHHHHEDHHHHHE=BDBD:/C=AHHHHHHHCAEG>?DGCHHHHHDCCHHHHG97 @read_150_33/2 ATAGTGAAACACTCACATTGGTAACATGACACAGCTGACTTTAGATGGGCCATGGCCTCTCCAGTCTCCACAACTCCCTAACGCTTACCACTGGACCACT + EGC>=EGHHHHHGBBBFHHHFDIGFF??5;GGEEC7880;05>BCDGHHHGGFBBEGIGE38EAHHHHHHDCGFFHHHH=?GHHHHHHHHEDE68799?D @read_150_34/2 TCGCTGCAGAAACAGAAAACATGTGGAGGTTAGTTTTTCTTTCGGAAAGATGCTTAATCATCCCTTTCGGTGAGGCGGTGCCTTTGGCATGGTAGTTTTG + FEHHHHHHHFEEFGHHHHHGHEDD4-6.>EDGGGDHHHFFHHFHHHHHHFHHHHHHHHHHHHHHG<>?EEC?=CC@DDBBF @read_150_35/2 TCGCTGCATAGGGTGGGGCCCCACTTCAATATTTTTAAGAGTCACCACAGGATTGGGAATCAATGGCTGAAACCAATTCTCAGCAAACCATTCTAAAATC + HHHHDHGEHHHHHHHHEEEGEGHHHHFHHHHHHHGEHHHHFHEBFHE@>HHHHHHDGBCGHHHHHHFHHHC;5A5BB=DH@>5BBEEEBE?815?E;BFD @read_150_36/2 ATAGTGATTGGAGCTCTCATACGCTGCTGGTAAGAATGTAAAATGGCACGATTGCTTTGGAAAACAGTTTGGCAGGTCATTAAAAGATTAAACACAAAAT + HHFHHFGGGGHHHHHHHHHHHHHHHHGEHHG@GGHHBCCHHHHHHHHFFEHHHHFGGFEHHHHHFGGH?EGGHHHDGGGGHHHHH3CE=HEGFB@CDHHF @read_150_37/2 ATAGTGATCACAGACTGTGCTAAAACTTTACATACATTACCTCATCCTCACAACAACCAGTAGGTACTCAGTAAATGTTAGCAGCTTTAATTGTATTGCA + HEEEECGGCDGHHHGGG=@<.8)+C3*08F@DHHHFGHHHHHHHFDAHHHEEB@CDHHDFFF.BGFD@HHHHFFGHHHHG@CDA@DBHHBEHGGGBFEFF @read_150_38/2 TCGCTGCAGGGATTTTTGCCATGTTGGCCAGGCTGGTCTCGAACTCCTGACCTCAGGTGATCCACCCACCTCGGCCTCATAAAGTGCTGGGATTACAGGC + FHHHD?CG?BHHHHHHHHHHHHHFHHEFHHHHBFHFDFGGHHHEEGGGHHHHHHHHHGGGHHHHHHHFGE-18A<.6+,->*EFGHFHHHED04DB@DFE @read_150_39/2 ATAGTGATGAGTAAGGATCACTATTACCCTTACAGACTGGATAAAACCCTAAGAAACAAAATCATTGTGCAAAACCTTTCAGGCCAGGCGCAGCTGCTCA + GHHHHHHHHHHHHGHGGDDFHHHHHGHFFE>AEHHFFFFDHHED?CCFHHHHF=9>?>@>4<<.65>4;FEDBEFCAA>>D?HHHD?A0.@FHHHHHGGF @read_150_40/2 TCGCTGCTAGCCTTTAGAATTGTGAAAAATAAATGTTTGTTGCACAAGCCACCTTTTCTATGGTAATTTGTTATAGCAATACAGACTGACTAAAACAAGC + FEGHHHHHHHHHDGFFCGFFHHHHHHHHHHFFFDGFFHHHFD9:7<@FHHHHGHHHHHHHHHGHEFF=EHHHHDF@1133)7?FHDHDDGHHHFEFFFD> @read_150_41/2 TGAATCTTAGCTTTGTAGTAAGTTTTGAAATCAGGAAATGTCTTTCAACTTTGTTCTTCTTTTTCAAGACTGTTTTTGGCTATTTGGATTCCTTTGCAAT + HHEEEHGHHHHHHH>DFHGGEHHHHHHHHHHHHBDDEBHCHHHDBABEEEGD669;.?GEBBFHHHHHHFEH?4FHHFF@FIFHHHHHHHGGHHB??DFF @read_150_42/2 TGAATCTTTATCAACCAAGTGCCAAGATCCCCTCCACCACCAAACAAGATGAAAACCCAAAAACTTTGCTCAGGATCTCAGAGCTTCACTGTCTTTCCAT + HHHHHHB@EHHHHGHHHHD=>@<:)'%'3%6822@ @read_150_43/2 TGAATCTGAAAGCGGCCGGCGAGCGCTGGCTGACATTTTCCTGCCCGGAAGGATGCATGGCCCGGGGTCTCCTGCACCTGAGTCCGCATAGATCGGAAGA + HHHHGEEECFHEFHGHGGGHHHHHEHHHF@8>@B@HHHHHHHHHBEHHHFHGGFDEGEEEHHGGIFEFHHHHHHHHH4=<'2DBEGE9/>AGDDF@CHFF @read_150_44/2 TGAATCTAAAACAAGTATGTCACAGACTTTAAAGCCTCCAGAGTTATTTCTTCCAGCCTCTGATCTCCAAATCTCCAGCAACTCAACAGTAATAGAATCT + HHFHHHHHHEBGHEHEBAHGFDDDDEGGFFCBEG=BCBBHHGGEGEFHHHFDGHHHHHGGFFDCBFFEFC>=:<>7;?BCBCDGDFFHHFEHGHHHFEHHGFHHHHFHHFCCEHHGFGHHHHGF<@C@536<=A08EHHHHFFHHGDEFGGHDEFFGGGGHHCCD/EDHHHEGHHHHFFHHHHFFA@GHHFEA;:(:<5.=D @read_150_48/2 ATAGTGACTGAGGAGTACATTCTACACTGGCTGGCAGAGTTTAAGCTCCAGTTACCTCTGGTGTAATTTGCTTGGTAATACACCCATTGTTGGCTTCTTT + HHHHHHHHHFHHHHHHHHGGHHHHHHHHGE?FGFHHHFHHHHHDF/DFFGGGGGGHHHHHHHHHHHHHHFDDGHF@9DEEHHEDGHHHHEHHGEFDDFBB @read_150_49/2 TGAATCTGAGAATGGCGTGAACCCAGGAGGCGGAGGTTGCAGTGAGCCAAGATTGTGCCACTGCACTCCAACCTGGGCCACAGAGTGAGACTCCATCTAA + HHHHHGEEGGGHHGHFHHHHHGGHFGHHHHE=;29DGGFBHHHHHHHHHHHHHHHHHHHHFDGGGHH=6*D8EFHG;@-6AAA@@GHFHHFHHFHDAE<8 @read_150_50/2 ATAGTGAAGAACACAAGACAGTAATAAAAGCCATTTATAATGTTCCACCTTCTATACTGGAATTACACACATCACCATAAAACCAAAGATTCAGCATTAC + /,,5-GHH@DHHHHHHHGEBC>C57DDEEBGHHHHHHHHHHFB7::<333<;@@@BHFDG.);@;/1:9>C@>7@B@@ECEFHHFGCFHFHHHHHBF?10 @read_150_51/2 TCGCTGCAGTTTTGAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATAATTAAAAAAAAAAAAAAAAAAAAAAAAAAAA + HHHHHHHHFHHHHHHHEFHHHHHHHEFHHGCAHH?GGGGGGEHD?ED@@=GGFFHHHHHGEE=A629@>>9<7:DEGEFFHFGFHDHFEEHFEB<+BH?F @read_150_52/2 TGAATCTTGCAAGGGGACATTTGGAGGGCTTCGAGGCCTGGGGTGGAAAAGGAAATATCTTCTCCTAAAAGCTACATGGAAGCATTCTCAGAAACTGCTT + AAHHHHHHHHHHHHHFGHHHGDCG?DDHHHHHHHHEFFHB5;EHHHHHHHHHHHHHE?EDBC89:?8>@CDD8:5)-'1FGHGGDFGGFDGB5B8,;<<: @read_150_53/2 TCGCTGCATTAAGACATTTATTTTGGCCACGCGCAGTGGCTCATGACTGTAATCCCAGCACTTTGGGAGGCCGAAGCTGGCAGATCACCTGAAGTCAGGA + HHHHHHHHHHHFHHHHHHHGHHHHHHHHHHFHHHHHHHHHHHHHHEBE=FHHDDDGGEBHHHHEGGGFEDBEC4,9@EHGGGGGGDFHHHHFHHHFFHHF @read_150_54/2 TGAATCTTTAGTAGAGACGGGGTGTCACAATGTTGGCTGGTATGGTCTCGATCTCTTGACCTCATGATCTGCCCGCCTTGTCCGCATAGATCGGAAGAGC + HHHHHHHHHHHHHHHHHHHHHHHHGFFEDDDEGEHFCEEHHHHEFHHAF@554>:97@HHHHBGGGGFFF:65855>54>:DBG@+DFHHFHFHGGHFF7:B4>.(:@@DHHFHHHHHHHHHHH@FHHE<,1-5DHHHFBE @read_150_57/2 ATAGTGAGGGACCAAGATGTGGACATTAATTTGATTCCACATGGGTTTTTATTCCTATTACTTATATATAGCTATTTTTCTAGTAATATTGCTACATCTG + HHHHHHHHHHHFGEEGGHHHHHHFHFGEFD+/BEEHHHB8@BCFHHHHHHHHBDCHHEEEHHHEECEB><')+?DABBHFHHHHHDG?EGEEHHHHHHHH @read_150_58/2 ATAGTGAATTTTGGAGGTAAGGAAATTAAGGCTCTAACAAGGTAAAGAATGTAACATGCTTGAGGGCAGGTGGCAAGAGGAAGGTAGAGCCTAGAGGTTC + HHHHHH=GFDD887/B;CEEEEEHHHHEGE@HGCC.:1-0?469?BFEHGHGHHHGGHGHHHHEHHHHGGGGB,:CBF?EGHHHHHHGCCAFGA;BAD?H @read_150_59/2 ATAGTGAAGCAGAAATGTTTAAAAATAGAAAATAAACCAATCCATAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATC + HHHHHHHGGGBCHH?HHHHHHHEBB-=CBEEDCHHHHHHHHHF@AFGFHE@CCC7BF<@=A@ADHHB;@AAGHHHGHHHHHHHGFGEFFB?70<;6F@@/:7;7CHFHHHEGH;EHEHHGHGGBGEFHHDHHHHFHHHHHHHHH=. @read_150_61/2 ATAGTGAATATATTACTAACAAATGCATTGGTATGGACTTGGAGGAAACATGTCAACAGTTACCAATCCATAGATCGGAAGAGCGTCGTGTAGGGAACGG + HHHHHHHHHHHGFFEBEEFFFFHHHHHHHHHHHHHFHHHEHHHHFHFG?EHHHHHHHHFHHHFFB=BHHFHHHHHHHF?EEGFGHHFFHHH@5448;.2) @read_150_62/2 TGAATCTATAGCTGTGTCATTGTACAGACCATAAGCCTGTGTTTTCCAGGTCTAGAATGACACACTTGACATTGTATTGTCACTATTTGAGTGATACCTA + HHHHHHHHHHHHHGHHGEEBGGE=E@69))0>FGHGHHHHHHHFFFGIGAGFFFFHGGD=B-&>-14/8:@BEEE=GE=EFAFGGHHHHCEGFHHHH@C5 @read_150_63/2 TGAATCTCCAGCAGGACCTGCACCTTTGGGAATCACCCAGGCCCCTGCCATCTTCCCTCCTGAGACTGCTTTTGCCACCTTACTGTCTCCGCATAGATCG + DDEE/B/87?GE@FFGHHHHFHHHHHEGGGGGEEFC5DHHH @read_150_65/2 TCGCTGCAGCCCTCATGGAGATCCTCTACTAGGGCAATGCAGATGGGAAATATGGGGTTAGAGCCCCCACACAGAGTTCCCAATGGGGAGCCTAGTGGAA + HHHEEHHHHHHHHHHEEHHHHHHHGFFFFDGEFADGEGHEHHHGE:;FEHGGGGGGGEEEGE@EGGHHHGBEGGGFHEEF/7DGFB>49:FE:@EBHHBF @read_150_66/2 TGAATCTAGAGGGAGGAATCTGTTTTTGGTCTAAAATAGGTACGCAATAAATATGTTAAGGATAAAAAACAAAGAAACAGATTCCTCCCTCTCCTTTATT + HFHHHHHHHHHHGEE@BGHDBFDDDFHHHHEGHFEBFHHHHHBEHHDFEB6>BBHHHGGFHFHHHHHD@))1';FHHHHFEHDGHHHHFFFE:B:3@EHH @read_150_67/2 TCGCTGCAAAACTCTCCACAGCACATGTTCAAATACTTGAGGTATGTGTTTCAAACTACAGGGAGAAACTTACGTAAGACAATGACCCTCATAGCTGGTA + HHHHGDDFHHHHHGEBFHHCHHHHHBCF<@DBGGGHGG@DBFGFG;@DBEGGGGHGBBGGHHHHHF@GFEHHHHHEEEGD;?=8FHHHHE6:5%'&)%8< @read_150_68/2 TCGCTGCTACTAGAATGAGAGGCTGAGAATTCAAGTAGAAAATAGGTATTAAATGGCTACAAATGCAAGAAAAAATTTTGTAAGCTGTTTTTAGTATAAA + HHHHHGFFHHHHHGGDD@GDGGDFHHGFHHHFHHHHHHHFBBDDBEFBHHHHHHFEFCE?=CED6>?GGFBBHHFHH @read_150_69/2 ATAGTGAATTAGAAAAAGCAGACAAGAAGAGGGTTTCAAACAAAGGCATTATGCAAAGGTCCTGGGGCCAGTAGGAAAGTTGCCTACCTGAGCAGAAAGA + EEHHHHHHHHGHHGEEGH@884EHHHHHGHHDFFHHFGEHHHFHD7<@/CFFGGHGGDHHHHG95CGHHG@ADFEGGHHGH@61(>BDF<1.?BEHHHED @read_150_70/2 ATAGTGATGAGCACAAGCCCAAGCGACAAGAAGCAAAGACAAGAGAAGGAAAAGGGAGTTCAGGAGAAGATAAGAGAGAGTAAGAGGCTGAGGAAGGGAA + HHHHHHHDBCC@GHECCBBGBHHHHBGHFEBF?7CEHHHFBFHHHHHHHFHHHFHHHHHHE+9@EDDD<;DEEFEB?@;CFGGGC?DD@CBGA=>388EE @read_150_71/2 TGAATCTACTACAATAGCAGACCCTCCTAAATATTTGAAATGTTACAGGTCAAGTTAACCAACTGTTAAATATGTTTTATGCTTCTGCAATGACAAATAT + HHHHHHHHFHHHHHFHHHHHHHHHHHHHHHDBEEBAHHFFHHFHHFHFHFHHHFFHEDD=FHHHHHHHHEHHHDBIE<-1'.;D><:A730)46931:;8 @read_150_72/2 ATAGTGAAAGAAAGGGGAAGCATATTTCATTAGGCACGTCAATGCCAGACCCTAAATAATTCAGTCCCCCAGATTAAAATACTTGATGCTCTTTCAGTGT + HFDBGHDGFGGHHEEHHHHGHHBCEBBCGFEHHECDGGDFFFEEFD?GFHHHHHH8*,BBCC<:.)+,6*84GGAEFHHHHHHEECE=>0+)'.>5<&77 @read_150_73/2 TGAATCTCAGCATGGGTGAATAGGACTCGTTTTGTTAGCAACGTTTGAATTAATTCAATCAAATTTTCACAGGCCGAGAACAAGCAGTGAAGAGCAGTTA + HHHHGHHHHDDDB?DHHHHHHHHHHHHBEEGGGHHHHHHHHHFD@EGEGHHGGHHHGGG?E=BHGD56;7:6,;6+%%44GG=BECEFHHHHHGH:0=EG @read_150_74/2 TCGCTGCCATGTATGTTTATTGCGGCACTATTCACAATAGCAAAGACTTGGAACCAACCTACATGTCCAACAATGATAGACTGGATTAAGAAAATGTGGC + D=759A<5969:@:>DHHHHHHHHHHHFHHHHHGGFHHHHHHHHFFFFHHHHFHEHHHHHHF@'%%*) @read_150_76/2 TCGCTGCAATTGACACCCTAACATCACAATTAAAAGAACTAGAAAAGCAAGAGCAAACACATTCAAAAGCTAGCAGAAGGCAAGAAACAACTAAAATCAG + HHHHHHHHHGGGHHHHHHHHHHHHHHHHHHHHHHEHHHHHHHHHHHEHHHHHHHHHHHHHHHHHBHHHHEF>=DDBEHHHEFBGFEHHA@EGCFFHHHHF @read_150_77/2 ATAGTGATTACAAGTACTTTCATGGTTCATGATCTATCAAGTTTCTGAGAGTTAATGCAATTTCTCCTGGGGTGTAGGAACACCACATTGGGATACTGGG + HHHHHHEHHHHHHHHHHHHHHHHEHGGFHHHF?@<+::.>HHG.5EFABEHHEFCGHHHHHHHHHHHHHHHFHE<>>5CB+7.:CGDEHH:.8CED@BFHFG @read_150_79/2 TGAATCTAAATAGAGGACTCAGAAATAAAACTGCACACCCACAACCATCTCATCTTTGACAAAGCCAATCAAAACAAGCAATGGTAAATGGACTACCTAT + HHHHHHHHHHHHHDF=@@7<1?ADFHHFHHHHHFEHFGHHHHHHHHGFHHFHHHGHHHFEBDF@DHHHHG@BFHGHHHHHHEDGGDFGIFGHE>/577)) @read_150_80/2 ATAGTGAAGGAATAAGTTACAAAGCAAAAGGAAATGGAGAAACTTGGACAGAAATTTATACAAAGAAACATCTAAACATAGAGCAGAATAGGAATGGTTA + HHHHHHHEDGHHHHHHHEGHHHEEHHHFF@FHHFGHHHHHHHHHHHHBGFF@>@FEGGFEHHGGGHHHHHHHH=??BFHHHHGGGHHHGG>1-0>'?FFF @read_150_81/2 ATAGTGAAAAAGCACTGTCTTCAGCAAATGTGTATTGTACCTGTCCTTGCAAGAGGCTACTACCATATTAGTTACTGGAAATGCAGAGAGTATAACAATC + HHHHHHHHHHHHHHHHHHHHHGE@CHHCEGHHHHHHEDBAF=HHHGHHHHHHHFFDHHHHHHHHHHGGHHHHHHD<;5,CDE>?CF=GFGE=BD.-1D@E @read_150_82/2 ATAGTGAATTACTGCAAACCTACATGCAGACTAGCAGGAGGATATTTTCCTGTGCCTCCTTCATCTCGTTTCCACAACTTCTCAATTCGCTCTCCTAACT + @FFGADEGDBEHHHHHHHHHHHBGGFDGHHHHH@@EEEEF89DAGHE?EEHHCFEGHGHHFGD;0FFFHFFE@,==HFHBFEEEEHHHHHHFFGHFFEBH @read_150_83/2 ATAGTGAAAAGATGTTATGTGTTAGTTGTATAAATGATAATTCAAATGGAGAGTGTGGGGAGAAGTGAAGCATGTTTTGTTTCTGGTAAACAATAACTGG + HHHHGHHEHHHHHHHHHHHHHHHHHHFHHHHHHHF?EEFDD;>>=FB/B7C@GFEEBB1:;?DEFDEFHE @read_150_84/2 TGAATCTGCCTGCCTCACTCTCCATGGAAAGCCTCATTATATGAGTTGTAGCCCTTTCAATACCCTCTTAGTGCAGGTGTGCAATCATCAGTCTCAACAG + HHHHGHHHHHDGGHHHHHHHHHHAAGGHHHGFGGFHHHHHFHHHHHEE?83.<96D:'(-985BCEEEC>>:EGHGHHHHHHHHHD=,?BHHHHHEE>:12@@>H?@EEGFGEFHHHHHEBFFGHHHHHHEE4?AHHHHHHEGHHHFFEE>D=.).)'0 @read_150_86/2 ATAGTGATCATTTGGTTACAGTTTTAAACTAGCAAACCATTGCCCTATAAGAGGAGCTAAACTAAACTGTAACACTACACAAACTTCCCAAGGAAGGTAA + HHHHHEEGHHFFHHHHHHHHHFGGGFGHGB@/3;EDGFG?:GCCGHHHHHHHHHHHHGGFFCD?BEFFEDE..1+4@B?BFB=EDGGEGGHGFCF<>4@> @read_150_87/2 ATAGTGATCTCTTTTATAGATGTGGTAACTGAAGCACGTAAATTTAAGTAGCTTGTCCAATACCACAAAGGTAGTAAGCGGTAGAACCAAGAAATCCATA + HHHHHHHHHHH@<.9?<+=>EGEFGGHHFFHGFHFHHHHHHHHHHHG9CFHHHHHHFHHH;*22,,2(4FFHHHHHEBGGEDDDEGCGDA?@FHEEHHFC @read_150_88/2 TCGCTGCAACGGAAACATTCATTCATGAAGCAGTCCTGCTTGTGAAAATTCATTGTGCTGTATACTCAGGAGATGACCACTTTTCTGCATGTATATTCTA + HHHHFHHHHHFGGHHHHHGEHHHHHFDEEFHHHFFHHHHHHHE@?,:GFHHHHHFHGEGHHHHHHHD=GGFDCHEGHHHGGHHHHEDEHHHHFCAFF=,0 @read_150_89/2 TGAATCTTTAACTTTCTGTCTCGTTGATCTGTCTCCGCATAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGATGGTCGCCGTATCATTAA + GGGFHHHHHHGFDFHGDFHHHGGGF>?FHHHEHHHHGGHHHGHHHHHBCCHHHHHGFHHHHHHHHHHGEHHHHBDGFD(7-+7EHD?BBBFFFHFHHHEH @read_150_90/2 ATAGTGAATTTTCTTAATCCAGTCTATCACTGATAGACATTTGGGTTGGTTCCTGGTCTTTGCTATAATCCATAGATCGGAAGAGCGTAGTGTAGGGAAA + HFFGGHHGHHHHHHHGEHHHHHHGHHHHFGEFAFDCC?DG@GHHHHHHHHHHHFCD?E?BBBGGHHHHHEGGHHHHFHHFFF@11)13''CDDEFEDD2. @read_150_91/2 TCGCTGCATGCCATTCTCCTGCCTCAGCTTCCCGAGTAGCTGGGACTACAGGCTGCTGCCTTTTTTTCAGAGATGCCCTGGCCAAAGAGGAGGAATCTAG + HHHHHGF@@BGGDGFBEBB<<;?<>7ACAE@BHHHHEFFBFHHHFCEFCGDEEHHHHHHGHHHHHHHFHHHHHHHHHHHHEGFFHHHHHHHGEBHHGCFG @read_150_92/2 TGAATCTATCCCATTTTATTATAAAATATACTGTTATGAAGATACAGATGCTCCTTGACTTTGATGGGTCCGCATAGATCGGAATAGCGTCGTGTAGGGA + HHHHHHHGHHHHGGGHHH8:<.0.>8C@:0)<@>BHHHHGGHHHFHHHHHHGED?GHHHGGEHHFHHHHHHHHHEFHHHHHHHHGFHHHHHFFFHHHHFHHHHHECDGGBDHB?5+3C;>@DEBBD @read_150_94/2 ATAGTGAGATTTGTCTTGTTTTTCTAGTTTCTCTAGGTGTGGTGTTAGGTTGTTAGTTTGGGATTGCTCTTAACTTTTCTATTAATACTGTTTTAGCTGT + HHFE=GGHHHHHHHHHHHHHHHHHHGE>=E?:,8,46?GBFHHHHHBHHHHHEGHHHHEGGG?@DFHGEEGDDDB@CHFBCCEE?EEFEEHHHCHGHHHE @read_150_95/2 TCGCTGCCTCCCTCTGCCTAGTCCTCAGAGTGGGTGGGACAGGAGACAGGCCCACCTCGTCAGTTGCTGGGCTGCCTCCAGGCTGGGCACAGTGGGCAGT + HHHHHHHHHHHHHHGHHHHHHHGHG>=@BHHHGIGHHHHHHHHHHB>=FG=DGECHHFEE@C@FD?:::;D@BGGHFHCCF<EFHHHHHHH=FEEE? @read_150_96/2 TGAATCTCATCTCCTCCCTGGTCAAGCTGGGCACACACAGGCCCTGTTTAATGGGCACCTGGTTTTAGACCCTCACTCCCCCAGTTCCCTGCACCACCAT + HHHHGHHHFCHHHHHHHHHHHHHHGHGFHHHHDDGHHFHHHHHHHHHEHFHHHHHHHHGHEHHHFGHHHHHE@@@5:G3>@6@%?8DA:,ABEEHHGGGFA,0*0ABG@D @read_150_98/2 TCGCTGCTTTCTCCTGGAGCTCACTTTCTATTGGGGAGAAAAAGTAGTTAAATAAGTAAACAAGCAACAAATTTAGGCCAGGTAACTCGATTGTGACAAG + EHHHEBBDCCEEE<=@FEHEEFHHHHHHCEHC8E@FHHHHHHHFHFHF:>6AEEADDFGFEHHHHGB@DCGGDDEC+9*:@AGGEGGHFD<3/2>=<>--6=:*8ADHHHHBBFGEEHHGCHCEGFHHHHHFHHHHHB@GFEGHFEGGHHEGBFGEFEFDDHH @read_150_101/2 ATAGTGAGATCCCTGTCCAGCTTTTTCTCAAGACTTGCTCTGCTTGCAGGACTTGCTTTACCACGGTTCCTGCCTTCCTGTAACCACTTAGTTCAGCTTT + HHHHHHHE24EEGHHGGE63846:*=AA6;FDHHFFHHHDD-0153 @read_150_102/2 TGAATCTTGATTCTGCCAGTGTGTGGGATTTGGGAACTAGTGGGGAACAATTCATTTTCGGAAGAGAAGATGATCAATACATTGAGACATTAAAGCAAAT + HHHHHFHHHHHFFD>@;?>ICD=99DBD><?>>DDCHHHHHHHHHH?A6;FHHHHHHHHHHHHHFHHHHHFB?65EC45>ABBFGHF?'.8GEBBHE63@61<7CH7 @read_150_104/2 TGAATATAGTGGAATTTATCACACTCTCCTCTGGATTTGCCCAGGCCTTTGTTAATAAGACCTGTTGCTTTTATTGTAGCTCACCTGCTTGCTCAATGGG + 25376+6>.:CCEE>EGHHHHEHHHHHHHEHF@.<33/+:.3(90@?@<@@D@BCC@CBDDGEBF5@A@GE<=?HHFCFGEE<=EDEFFGHHHHH@5=;5 @read_150_105/2 TCGCTGCAAGGCTGAGGCTGCAGTGAGCCACGATCATGTCAGCTGCAAGTTTTGAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGT + HHHBGFHFDC5CA=DD/85=+=EEHFC@EED?@@ @read_150_107/2 TGAATCTATTGACCCGGAGATTTTATTTGTTGATGTCAAGAAAATGCATATTATACTATATTTGAGGCTAGCATTGTATCAATTAGCCAATGTTTAACTG + HHHHHHHHHHHHHHHHHHHHGCA:FFFFGGGHHHHFFEHHGHE>GEDB@>GFFGGHHDDGHHHHHFIB.5BED5=EHHGEFFGBGFHHGHEGFA.9ECFG @read_150_108/2 TGAATCTTTCCAGCCCAGCCCTGACTGTGGACCAGAAAGCAAGAATTAGTGAGGACTCAGAGCGTGCCAGGTTCAGGTGCCCAGCACCCATTCTGTGCCT + 7760.6::16>@CBGHHDHHDEGAA=CFFDBFFGFHFFFHF=:11DDD?B@=ABCEHHHEBCDHHDD=?<>C8=B?@D890').)/@=ADDCDD?D<=GG @read_150_109/2 ATAGTGATTAAATATATATGTTCTTATTATATAAATCTTTTAAAATAATTTGACCGATTAAACAAAAGCAATAATAATGGATTCTGGGGTTTGTAACATG + DDBGFD=DDDGHHHHHHH@@HHHHHGHHGGADFHHHHHHDEFE*>.DDHFHHHGG@@@;35365CBEGHFHDC.@FGEEDHHGHHHHHHEDHHHHHGEFF @read_150_110/2 TCGCTGCATGGAGGTAACCTCCAGAAGTTAGAAAATGAAAGAAAATGAATTCTCCCCTAGAGACTCCAGAAACGTCACAGACCTTCCAACACCTTAATTT + HHHEBDCBE@)'271AGGGGHHHHEBHH@@GF8;AHHHE?CFHHFFHFHHHHHGGHHHHHHHHHHHF?AC?=GHFEE=DDGFDGHGHFGH.38FHC5EHH @read_150_111/2 TCGCTGCTTTTCCACTTCAAATTTATCCCTACTCTTTGGCCGGGCACGGTGGCTTATACCTGGAATCCCAGCACTTTGGGAGGCTGAGGCGAGTGGATCA + HHHHHHHEGEGEGEGHHHHHEFAGEFDHHFHHHHHIGFHHFHHHHEHHFCCDDDDFEHHHFFFBEFAADDFEED?DGEGFE@<<)>=FAGBEFHHHGHHHHHHHHHEHHEE=?E=.BHHHHHFADGACCDGGGFBEDDFGGGHHHFGGE73?ADE=D<)0-;=3684<0BE?E @read_150_113/2 TCGCTGCGCTGGTCTTCAACTCCTGGACTCAAGTGATCCTCCCACCTTAGCCTCCCAATGTGCCGGTATTATATGCCTGCAAAACTGTACCTGACCACCT + HHHHHHHHHHHHHHHHHFEGFFHHHGFE@@5?DHHHHHHFEHHHHHHGHFGHHGGHHFHFG@;82.::..20:><@BC6,8;87DEHHHHDBEB> @read_150_116/2 ATAGTGAGTCTCAGAAGGAAGAGTGACACCAAGATGAAAACAGCATTAAAACAAAGCCACAAAGAGACAAAGGCAAATCAATGCCCAGAAAATGAAGTCT + HHHHHHHFCEEEFHHHHHHHHHEFHHHHHHHHHHHB8@ @read_150_117/2 TGAATCTCCACATATCTCATTTGTTCCTTTCCACATTCATTTTCCTGCCACATTCCTGCTAAATTTCCTCTTTCATATGGCAGGTCAAGTAAACTAAATC + HHHHHFHHHFGGG@GHHFEEHHHEEEGGFFG=,A5EHHHHHHHHHHHHHHHHHHEHHHFGHHGHGHHHHHHHD @read_150_118/2 TCGCTGCCTTTATTATTAATACTCAGGACATTAGGAATTTCCAGATTTTTTTCAGTAGCATTTGTAGAACCACTTTTGGTAACAAATACAGTAGTTAGGA + HHGGGHHHHHHHHHHE@EBGGGBCBHHHHGGFFHHFHHHFHEHHHHFDFEGGGGGHHHHHBFDEFHHGFGHHHHGHB5AHHHFFECB@FFDB2:0'6@76 @read_150_119/2 TGAATCTTACTGCAACCTCTGGCTCCCGAGTTCAAATGATTCTCCCGCCCCAGCCTCCCGAGTAGCTGGGACTACACGTGCACACCACCACGTCCAGCTA + HHHFGEFDGEHHHEHHHHHHHHHGGHHHHHHGEFF39DHFHEHHHHHHHFGGGGGHHHHHHGFHFHHHHHHHHHHEGHHGGDGBFFFHHFEHHFCBHHB= @read_150_120/2 TCGCTGCATTCTACTAATCCTTATGACTGGCTTTGAGGAAAGTGAAGCCAAATGCAATAGTACCTAGAGAGTGTCAAAACCGGATTGTGAACCAAGGATT + GEEEDDCGGCFHGEHHHHHFGHHHHHHHHFFF657=CHHHHG?DDDDA<6(GGHGFHHHGHBD?>B/(*.=));70>;@5>CC@FHHHHHEFD?HEDDEE @read_150_121/2 TGAATCTTAATGGAAATAATCTTTGTTCATGCTTCTTGGATCACCTTTCCTAACTTTATAATACCTAATGAAGACTTTCCTCAAGCATCATTTATTGTTA + HHHHHHHHHG@D866BHHHHHCEGECFGHHGGFFFHHHHHHHF>A68&,A@D/6B0*ECDFFHHHHGEGDHHHHHBHHHHHHHFEGGBBGFGBEFGF@D@401.;B;DDDDAHHGGC>9FHFFFEFFGD@C=<GEGHHHHHHHHHHHHHHHHHHHHHHEHEEFH==>/+89:?@EHHHEDCGFGGHHHHHGHE?EA:CBCCEAGHHHHHHFHHFHHHGFHFFH=17;591?D;@9422>6=BHHHHHHHFFEEBEEFHGEGHHHHHFFGEEDBD@FHHHHHHFHHFHHGHHHFH=E@31:<59.>?B<+ @read_150_125/2 TGAATCTTGTCAGGAATCTTATGATCTTTAACCATATATATTTTGTCTTATAGCTAATGTAATAAAGATATTTAAATACTTTCTCCGTCCATATAATGAC + GGFHGEBB:=FHHHHHHHHHHHHHHGFGFDBCFFD59@63BHHHHHEEB>EFFGEHHHHHB<2.?EB@6A@HHHF=HBCFEGEHHD;8>AGG=6@5.DEHGEFFGGGHGGDFB @read_150_127/2 TCGCTGCGATGCTATAATTTTGTGTTATTTCTGATTGTAGAGCTGCTCTGTCCAGCATAGTAGCCACTAGCAATATATGGCTATTTATATTTGAATTTAA + HHHHHHHHGG?:608DEEHHHHHHHHE>+;5.:.>BF@FFDDDG<--FHFHG=4@F6<:EHEFGEFFHGHHH @read_150_128/2 ATAGTGACTGAGGGACTGACCATTAAAACCTACCAAGAGTTAGCTCAGCTGTGGTGGGGCTGGGCCGGAGCGCTAATCAGAGTGCATTCACCTCTGGCTA + HHHHHFGEEHHHHHHHDHEFHHGGGHCCGHHGHGGHHHHHHHHDCEFEHE>@CDGGHHGFHFE<9*86FEHHHHHGBD*GGAC@BCEA??5?BFF<3;3= @read_150_129/2 TGAATCTAAGAATTTTCAAGAAATGATTCCTGCCTTTGGAATTTTCAGACTGCTGATCATCATCCTGATAAGTAAGTGTGTTTTGTGAATACTTCATACT + HHGHHHGGD:27@HHEGHHHHHHHHHHHHHHHHHHHHH?GHFHHHFFB>>?=FD=0<61368DBCHF?E?AFGFHHHHHFHBBEFH6><<*91,2)*(C> @read_150_135/2 TCGCTGCCAAATCAAAACTACGATGAGATATCATCTCACCCCAGTTTAAATGGCGTTTGTCAAAAAGTGAATAACAGAAGTTGGTGAGGATGCAGAGAAA + HHHHHHHHHHGHGGGFGEFEHHHHHHHHHHGE?D@BF?BBDDFHHHHHHHHHHHHFEFHHGGEGGBGEHG=BDFF=.>>4-55=9@ECBEB=:ABDGHFF @read_150_136/2 TCGCTGCCAGTCAGTGCCTGTGCTCACAAGGAGTACAGAAATGTGAGAGACCCATGGAGAATTGTCTCCCGACACATCATTAAATATTATTCTTAAAATG + HHE@>EHHHHHHHHHHHHGDBD8@@DD4FFHHHHGGDDBG5G;GHHHHFHHHEHHDEEHHHHHHHHFB=DFHHHHHHHHEGGHHGGBFFHHFFDEB=26; @read_150_137/2 TCGCTGCCCAGACAGGCAGACCCCAAAGCCCCATTCTCAACATCCATCCTCTAAGGTCAAAGGTAACGGGGAAGCTGCTGCTCAAAACACAGCCGCGACA + EHHGE@?GGHFFEHHHHFEC.6EECDFHHDA/@?3=@CEFEB>D?.-+=>F @read_150_138/2 TCGCTGCTTTGAAAAATGATGGAAGTTGCTTTTTTAAATTAAGGTGGCAACACCACTGATAATTTAAACATTGCAGGCATTCCAAAATGCTGTGATTTGC + HHHHHEEGGHHHFBFHHHHFE8;;=CEF5:?FF6;ADHHFFF>.<.5(FFHHHGGFFEFFGHDEEE@>@=85:..)+9349GFEDAD=A==-3>>5+DD. @read_150_139/2 TGAATCTGATGGGCTTTAAAATGAGAAGGGCTGAGTTCAGATTCTACCTGTGCCATGTATTAACTGTGTGACCTTAGGCAAGTTGATTAACTGCTCTGGG + HHHHHHHHHGGHHHHHHHHHHFHHHHHHHHFHHGGHHHHGHHHHHHHHHGGBEDDEHHHHHHHHHHEEEGFFHHB?HHGHFFBCHFHHHHFEEFFEHFFH @read_150_140/2 ATAGTGAGACCACAGGCTTATTTTGAGGATCAAGATAATGCATGTAAAATGGCTCTAAATTCTTTAAAGCAATATACAGATGCAGATATTAATTTATATC + GBDFHHHHHF>-5@@C@6:AGHHHHFD=DBHFFHHHHFHHHHH@CEFFIFHHHHHHHFHDGFEFDHFHHHHHHFF>AA;1))225<9>:DF??244%.>HHHHEGHEEFHHCBABDDDHHCEF;@5%.7. @read_150_142/2 TGAATCTGTAGGAAAGAGGTTCTATCATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCCATCTATCTATCTATCTTTCCATCCATCCAC + HHHHHFFHHHHHG=FHHHHHHHHHHHHHFGHHHFHIGEFBEHHHHHHHFFEG./DHFGFFDDDE>5EEEGGGHEHHEHHEEABGHHCB6+A8EFCFGGE> @read_150_143/2 ATAGTGAGCCACATGAAAAGTTAGAGCTTTAATTCTCTTACCCAAACTTTTGTATACTTTTGTATCTTTGCATCCATGAGCTCTAACGTGCATAGATATT + GGGHHHHHHHHHHHHHHHHHHHHFHHE;DD?16><7B>FFHHHEEEFGHHHHHHGFHHG@HHH9/')*1;<>>CCHHHCH @read_150_144/2 TCGCTGCTTTTGAAACTCTCTTTTTTCTGGAATCTGCACGTGGATAGGTGGAACTCTGTGAAGGTTTCCTTGGAAACGGGTATATCTTCACTTAAAGAGT + HHHHHHHHHHHHHHHHHEEEHBBBE?19=@BGGHHFFEHHHHHHHGFHHHHHHHHEFHHHHHHHFGHFFHHFDF4>>>DDHHADEEHGHEEFEGCHHHFB @read_150_145/2 TCGCTGCTTATTTATGAGTTTTATCCATATAAAATTTGCTGGTAATCTGCTCTCCCCACAGTTTTTTTTTTTATTGCTGACAATTGAAAGAGGAGTGTAA + 55>6:>;5:>FDFHEGGGHHHHHEHHHGDHHHHHHHHHFGHHBGGD@EEB<<>:023::*6?BFBEEHFHHHBF49DEHHHEE@;>?@DDEDA@C@>@HE @read_150_146/2 TCGCTGCGAATGCCTGCCTAGATCACAAAAACCCCTCCTGCTAATATCCAGAGTATGGTAGGAAGAATCATGGTCCCCCGAAGGTGTCTCCCTCCTAATC + B723.@GFHHHHGHEDHHHHE8>.;FHHEEHHGBHHHFFHFFBB:GF=BFGFGHHHHHHHHHHHF?BDFGFFGHHGFFDDHHHHGGHDED@CDCFFHHHE @read_150_147/2 TGAATCTCTATTGACTGTATTTTGTCTTGATAATGAGTTATATTTCCTGTGCATTTTCATGCCTACTAGTCTGATTTTATCCTGGATATTCTGGATGACA + HHHHHHHFHH=;:40/=FHHHHHHFHHEEBHF=CEFCDFFHFHHHFD;@AEEHGGFEGHEEGFFDHFGHFHHHHFE?,>>BBEHHHHHHCBHHHHFFCEF @read_150_148/2 ATAGTGATTCAACTCCCCTCTCTTCCTCAAGGAAGGAAATATTCAGCAGGAAGTGCGACACAGCTGTAGTTCGAAGGCACTGGTGGAAATTCACGAAAGC + HFHHHHHHHHHHHHHHHHHHHHGHHHHHHHHHHBEEC:6@DEECFHHHGG?BGGEHFGHHGGEGFHGDE=(957@HHHHHHHFC91.8==DBDA>),;@/ @read_150_149/2 TCGCTGCTAGCTCCCCTGTTTTGCTGCTGGCCCAAAGATTAGACTCCTAGTCACAGGGATGACATAGTTTTTAGATCGGAAGAGCGTCGTGTAGGGAAAG + HHHHHHHHHHHHHHH>?@CHHHHFBFHHHEHEEHHHFEEEHHHHHEGBB9BCCEE;C@DGDC5>.@DGG=:./DAA>=DH@>:?HHFHFED927@@FHHH @read_150_150/2 TCGCTGCCATTGTTTCTAGGAAGTAACTAACTTCCTTTTGATTTTACAGTCTCATAAGCAGAAGGGACCTGCGTTGTTTTTGATGGGACATTGGACTGTG + HHHHHHHHHHEBGHFGGHHHHHHHHHGGGEFHHHEDEECBFGHFHHHHHEECEGHHHHHHHH@=?A72/8EBFGEHHFFE9<<9D>A>CAFEFDDGFEFE @read_150_151/2 TCGCTGCGGTATCTAGTGTGGTGATACTATCTAGTGTGGTGTCTTGCAACAACACTGCTAGTCATAGGTCTGATTTGGGGGAGAAAATAGTTTTGAGATC + HHHHHHHHHHHHHFHGFHH?DGGHHHHHHHEHDGGHEHHFGBFGDGFFFHHHHFED.7CB<<G?F@HGHHHF?FFE@CEEEE*435:=A=?HHHHHH @read_150_152/2 TGAATCTAATTAAGCAAAGGAACAGAATAGAGTCTAGAAATAGACCCACACATAGAGACAACTGATTTTTGATAAAGGTGCAAAGACAATTCACTGGGAA + EBGFHHGGGFFGECHHHGGBEGHHHEEHFBFFGGHHHGHHFHHHEAFDBFHHHHHHGHFDHHE8BGEHHFHHGFHHHEIGHHHFECG6;88<<:1@4F<8 @read_150_153/2 TCGCTGCGATGTACAGAATTTTTTTTATTTTGGTGAAGTCTAGTGTATCTGTCTTTTTTCTTTTGGCTATGCTATTGGTGTCATATTCAAGAAGATTGCC + HHHHHGHHHHHHHHHHHHHHHHHHHHHHEDFGGHHHB6735AHHHHHHHHHHHHHHGHFHGHHFFG@CEHHHHHHGFFGDHHHH?5:A=BHHHHGBGFGG @read_150_154/2 ATAGTGATAAAAAAAAAAAAAAAAACATGTGGTAAGGGCATACAGTATTCAGAGAATGGTCAGGAAAGGCCTCTGAGCAACATTTAAGCACTGAGACGGC + HHHHEHHHHGGHHHHHGGEFHHHHHGGGGGG@<:.9DFFFF=EGGGGGGDFGHHHGDBDHHHHFGHFHHHHGHDFGHHGHHEBFHFGHHHEEDEA<< @read_150_155/2 TGAATCTCAACTGAAGGATGTCCTCTGCCCTTTTTTACTTTGCTCCAGCCCTGAGAACTGATTCAACCTTTTTTCCTCCTACTTGTGAGGAAAGAGTGCC + HHHHGHHHHHHHHHFGABEHHHHEGHHHHHGGHHHBEHHHHHGHHGBGGGHHHHHHHHHFHEHFHGDGHHHDHHHHHHFAGHFHHEFCCHFFHDEDFHF2 @read_150_156/2 ATAGTGATCTAGGCAAGCGAGAGAGAGAGAGTGAGAGAGAGAAAGACATAATTTCTTGAATTTAGATCAGAGTACCTTTGCCTGGAACCAATTAATTCTT + GFFHGHHHHHHHDBGFHEEEHHHHHHHDFHFHHHHHHHHHHHHHHHBHGHHHHHHGGFFE>DHHHHGGI@233BIDDHHHE@5053CBHHDEEHHHFB.8 @read_150_157/2 TCGCTGCAACAGGAAATCACTCACAAGAAGCAGTACTGTGTTTAGAAGACACTGCTGAAGATTTTGGGGGTCCAGAGATGGTGCCACTTAGTGATCCTCT + HHHHFEGEGHGGGHHHHGDCEBGHHHHE;GHHHHHHHHFFHFHHHHHHHHGGHHHHHHHHHHHDC:79CFDGFHHHHHHGGEEE>3-EEEB>>34&@9?? @read_150_158/2 ATAGTGAACCATCACAGGAAGCCGCCTGCTTTCTTCTTTAAACTTAATATAGGGCTGCTTCGGCCTAAGGGTCCCCATGATTTTCCTTCTTTCTTGGTGT + HHHHGHHHHHHHHHHEGFGGCCE;EHHHHGHHC?HHHHHHHHHGGHHHHBGGEFHHHHHHHHHHHHHHHH38GBHHEGHHEHHHHDHHGBC<9@::>@FF @read_150_159/2 ATAGTGAACCACCTAACAACAACCCACCATAAACCACCAAAGAAGGGAAGCTCCAAGCCGCCTCACCCACACAGCACTGCAGAAGCGTCACTAGTCACAA + GGHHHHHHHHHHHHHHHHHFHHHHHHFFGDDEHHFHHHHFDDDHHFE=BHHHHHHHHHHHGDGDDAD>?@FFGHHFI:)875?C?EHF>>@BHH?HHHGE @read_150_160/2 TGAATCTGCAGAGAGAGAGAGACAGTGAGAAATTGAGAGAGAGACAGTGAGAAAGTGAGAGAGAAGAAAACAACAATAACAATAATGGAATGAATTGGGT + FEHHHHHHHHHHHHHHHHHHFDEEHHHHHBHBFG>EFIGGDDHHHHFFFHHHHHHGHHHHFHB@@>.DHHHHHHHFHBFF@BAGHHHHHD9>DC?FDCEE @read_150_161/2 TCGCTGCTACAAAAATTAGCCGGGTGTGTTGGTGTGCCTGTGGTCCCAGCTACTCAGGTGGCTGAGGCGGGAGGATCGCTTGAGTCCAGGAGGTTGAGGC + HHHHHGEB@FHHHGFBACAHFHHHHFHHHHEHHHFFHHHHHCBBGB(18BE96;829:3FFEBE@>E?>;7387EHBHHG5?AGD<.:<1:AA>EBECGG @read_150_162/2 TCGCTGCCAGATTAAGCTTTCTAAAACAGAGCTCAGATATCACTCTCCCTCAAAGAAACCTGGAGACCCAATGACTTGTCCATTAATCCTAAACTTCTTT + GGGDDHHHHHHHFF=*27BEEGFHHHFDCHGFHGBEFHHGHHHHHA6?HHHHHHHHHHHHHHHHGFHHHHHHHHHHFHDEFC:AAFHDEHBFDEHFHGHH @read_150_163/2 TCGCTGCACACAAAGACGCACATGTACAAGCACACTGAAAGAGTCACAGAAACAAAACATATCAAAGCAATAGGACCCAACCTGAGCAATATAGCAAGAC + HHHHEGIHHHHDEEHHHFGGE7>HGGFA<@@/ @read_150_166/2 ATAGTGAGACTTTAAATTTTAGAAAGTGTAGATATACAGCAAAATTGTGAATAGTACAGAGTGTTCCCCTATATATTCTGTACCCAGTTTTCCCTATGGA + BGG66>?<9C..CCCBB,??EB;BA=BFHHHHHFHHHHHHHHHHHHHHHHGIIEE5GHHHHHHDDADDHGEEEFHGEBFFB@.AD>BB@CFECFCACH @read_150_170/2 ATAGTGAGTTGCCCAGGCTTGTTTCAAACTCCTGGGCTCAAGCAATCTTCCTGCCACAGCCTCCCAAAGTGCTGCAATTACAGACATGAGCTACTGCACC + HHHFDB@EHHHGEHF8:5?:DDEGGHGC?CA:=A@GEGGGHHECHFEHHHHHHHCC;DGEGHHFGB?HHHHE==EHHH7,73<4@:@GGHEEDDC.9.8< @read_150_171/2 TGAATCTAACAGAATGAGAAAAGAATAAGGATGAAGAGAGATTTGTATGATGCCATCAAGCATACCAACAAAGGCATAGTGGGGGTCCTAGAAGGAGAGA + HHHHHHHHHHHFDD62EE@@DHHHHFEGDHHFHHFHHHFC>,>5F2&468DFFHHHFGFFBEHHFHHHHFHHHHHHHHHFDEDEEHBD@FFGGHHHHHHH @read_150_172/2 TGAATCTGTATTTGTATAGTTTCCAAAATTCCTCTTGTTATTGATTTCTGGTTTTATTCCATTGTGATGAGAGAAGATGCTTAATATTATTTAATTTTTT + HHHHHHEFGGHHHHHHHHHHHHDDE=DDD?CHHHHHFHHFE>;BG@FFFHFGFFHHHHHHHGGCCAE@G@B<9A<>DHHGG8@B=BCEFEFFE>,>:?D8 @read_150_173/2 ATAGTGATGTTAAGCTGTATGGCTTTGGGCAAATAATGTAATCTCTTTAAGTCTCGGGATCCTCATCTGTAAAATGAACTGAATAATATCTACTTCCTAT + EEHHHE;GHHHHGHHHHHFDECFFHHHHHHHGEGGAEEDHFHFHHHEDHHFFHHFHHHHHFHEHHGHFHEEFHHFEEEF;A??DBGHHFEFF.A+656@@ @read_150_174/2 TGAATCTATCAGTTTTCAGGATCTTCTCTAGATGTCTCACCTACCGTGACCACATTAAGATAGAACTACACATTCCTTTTAAACTTCATAGTACTTTTTT + HHHHHFDGEFEGGGHHHHHHEBGG29>5BH@?@FHHHHH@DDB@.:1<;CEGEGEEEEGGEHHEDF?>BA@:?6A=6-30<=F? @read_150_176/2 ATAGTGAGTAGAAAAGGAAAACCCATTTTCTGAAGAGGAATTCAAGCTGGCTGCAGAAATTGATATAAGTAAAGAGGAGCAGAATCTTCATAGCCAGGAC + DE5-16?A@DFDGGEBEEACHHHHGHHHHHHHEDHHFHHHHHHGHHHBE?AE89;>>FEHHHHHHHHFBHGB9>>FFHHHHFFEIHHHFFFDBHFDFG9' @read_150_177/2 ATAGTGAGTCTGAGACTTAGGTCCCTTCTAGATTGTAAGCTCCTTAAGGGGAGAGCCTGAATCTGGATTGATTGATTGATTCATTCATTCAGGTCTTTAT + HHHHHHHHHHHHHHFHHHHHHHHHHHHHHHHHED;BFGFHHHHHHFHHHHHFGFGHHHHGC38BF4=GDDHHFHHHHH;B3,-?=EFHHEBGHGDED;>.:;CFFC? @read_150_179/2 TCGCTGCACTACAGGCTCAAGCCACCACACCCGGCAATTTGTTTTTTTTTTTTTTTGAGACAGTCTCACTCTGTTGCCCAAGCTGGAGTGTAATGGCACG + /@FHHHHHHHHHGHHHHEECDBFFFHHHHFHHHHHHHHHHHHBBHHFGGEFFGGGBBC@CEGGEEHDFEHEBEEEGGGGEHHHHHHHFF;=D:=CB69.7 @read_150_180/2 TGAATCTCTGATCTCAAAGAAATTCATTCATGCCTTGCATTACAACAGGGATACATTCTGAAAAAATCATCAGTGGGTGATTTCATCATTGTGCGGGTAT + HHHHHHHHHHHHHHHHHBGHHHHHHEEGGHHHFHFFHHHBFFHHHHHHHHBCFFFG=DGHHHHHFHHHHHHFHHHFDB<,4>:5@/*8:;EFB@=CDFHHFFFFFECGGHF?@>:EHHGGBFFHGHHHE;*3.;FBGDDD?FHHDEGEFHFH@= @read_150_182/2 TCGCTGCTCAGGGAAAACATGGAGTTCTATGGGATTCCAGAGGTGCCTCACTTCCTCCAGCTGGGTTGGAGAAGAGGCGGCATTTCTGGAGGAGGTGGCC + HHHHHHHHHHHHHFHHFDDEBGD.D=EDDABDA.5@?HHEA1-'.GBA.,&-46?EBBBEEBEE=A@AHHHHHHHHHHHHHHGEHEEDBC@CB@@9.623( @read_150_184/2 ATAGTGATCAGATTCACCAAAGTTGAAATGAAGGAAAAAATGTTAAGGGCAGCCAGAGAGAAAAGTTGGGTTACCCACAAAGGGAAGCCCATCAGACTAA + HHFFECEE<->>366GFHHDBEGGHHHHHHHHHHFHHHHFIGGB=AIGBFGGIFEHHHHHG?==E@@DDAGFFHHHHHHFGGDC=B@DFF?+7DFDF?02 @read_150_185/2 TGAATCTCAGTGAAATTATTTTAAGTGCTATGCTTATTTAACCTCCTGAACAGCCTTAAGAGATCCGCATAGATCGGAAGAGCGTCGTGTAGGGAAAGAG + HHFHHHHHHHF=DHEHHHHHGHHH=A=FC@;@A??FFD:ACBEDF=CEFFHHHHHFGDDHGF=FGGF.;.4?:<0+87@GHHHF7;@4DCDFHHGG:17A @read_150_186/2 ATAGTGAGAAAGGAACAACTGATACCAGCCACTGCAAAAACATGCCAAATTGTAAAGACCATCAAGGCTAGGAAGAAACTGCATCAACTAACGAGCAAAA + HHHHHHHHHHHE@?BCBGGHHEE?EHHHHGE5BFHHGHHHHHGG;D=CGB?FFECEHHHHHHHHEHHHHHFFFGDFFGG=>.5>;=GGHHHHHGDEHHEH @read_150_187/2 TCGCTGCCAAAGCTACATACGGCACATTTCCCAGAACATGCCAGGTGGAGCCTGGCCCTGTTGATTGTGTGTGGCTGTCACTTGCAGTTTTGAGATCGGA + HHHHHH><@GGGEE>GEGGGFGGEEBEHFGEEHHHHFBBDEHFHHHHFCGHHHHHHFBBDFFHHHGHHEEGHHHHHFGGGGHEAD008&0+.8:7.<@<<5959EEHHHGEGGG@HEB=GHFCDFDCE?94AEF.;FEEG:,;E;E @read_150_189/2 TCGCTGCTGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCAAGGCAGGTGTATCGTCTGAGGTCAGGAGTTCTAGACCAGCCTGGCCAACCT + HHHGE=@A.7=DF8/DD5:.:<),39DEBHHBGIGEBGGDHC?:=B@DEBGHHHHB7:<-7@>58@=FFGGDGGHDHHHEDHHHGHHB>CFCCH<+.5): @read_150_190/2 ATAGTGAGGTACAAGCTGAAACACAGGCAGCCTGGGGCATGCCCCAGCCCAGCCAAGGGCTGAGCCAGTGTGCAAGCCAGGCGTGGCCAGGTGGGCTAAG + DBFEEEDDGEEHHHHHHHHHHHHHHHHHHH9FHHEEHHHHFFGCFHHFGGGHHHHHHFFFGDAEEA@DGHHHHHHHHHFHHGFFD@BBE?EHHFHDCDCB @read_150_191/2 TGAATCTCTGGAGTGCAGTGGTGAGATCTTGGCTCACTGAAGCCTCCACCTCCTGGGTTCAAGCAATTCTCCTGCCTCAGTCACCTGAGTACCTGGGATT + HHHHHHHHHHGFFFGHHHHE.7=FHHGGFGHHHHFHHGHHHHHFHHBHHCGHG@?17BDHHGGGFGHHHHEEDDFHB;4827--6-*:->?;EHHHHGHHHHHHHHHHHHHHHHCFHHHE=HHHHDDBGGFHFBCEDH @read_150_193/2 TCGCTGCCTCACATACTGTTTCCTCTGTCTAGAATGTTTCTCCCACCTTCATTTCTTTTTCTGGCCAATTTATATTCAACCTTCCGTTTGCAGTCTTAAG + HHHGFHHHHHHHHHFGHHHHHHHHHHHGGFCEFEDFHHHHHHGHHHHHHFHFHHHHHHECEGDFFHHHE344>?HFBBHHHFBF8>:7;';C@BBEHHFH @read_150_194/2 ATAGTGAGGCATATGTGCAAAGTCTGGAGGAAACCAGATGCAAGCTTTCAAGAATCCCCTTCCAGTAGAGTCACATAAGATGTGCTTAATTTCCCATTCA + HHHHHHHHHHHHHHHHHHFEFHHHHHHHGEHFHHHFFEE@:?DEBHHHGFHHHHHHHHHDGHHHHGFHHHHFFHFFFHG@DFGEHHHGGBHHFGGGHEGC @read_150_195/2 TGAATCTATGAGTCCTGGCACATAAGAGTACAGTATTATTTTTTAAAGCTTTATTGAATCTCAAGAAGTCCTAGGACAACTATTTGAAACCAAGTAAGAA + HHHHHHHHHHHHHHHHHHHHHHHHHHGGBFFHHHHFBCBHHFFEGFHHHHHH@>4D@D=FHHHHAHGGGE=@=EDG*ECDEFFF@BEBEEACAC @read_150_196/2 ATAGTGAACACAATTTTCAAAAGAAAAGAAAGTTGGACTTACTATAAAGTTATAATAGAGTATGGTATTTGTGTAAGGATAGACATATAGATCAGTAAAA + E@@723@@E?DDFHHHHHHHGAGEHHHHHG==FGHFDGGHHFHHHHDEFHHHHHHGGGHHHHHHHHHHHF=;EGG:;?3?:?DFHFHHEEGGGFB>@DDG @read_150_197/2 TCGCTGCTAAGATATAACAGTAAACACAATTGAATAGAAACAATTTTTACTCATTTTTTAATGTAGTCTAGGTATGCAGCTCTCTAATGGTTGGACTCTG + HHDB=GHHE?EGGGHHHHHHHHHHHCHHHGHHHHHHHHHHHHDEB0>9>;GFDEGFHFHHHHHHHGGEF;9?CDFCD=EHHAD?@EBAA<>GGHHHHHHH @read_150_198/2 ATAGTGATGAAAGTTGCTGAATGTGATGGCAGCTCAGAAGTCAAACACTTGTACACTTAATCCATAGATCGGAAGAGCGTCGTGTAGGGAAAGCGTGTAG + HHHHFEEEEHHHHHHHHEEFHHDHHHHHFHHFHFFHHHHHHHHFHHHHHGD@@=9CGE@>DHFEHDDEGGHHHBHHGBG9<:154BF@C555%,;AEC88 @read_150_199/2 TCGCTGCCGTAGAGACTGGGTTTCATCGTGTTAGCCAGGATGGTCTCAATCTCCTGACCTCGTGCTCCGCCCGCCTTGGCCTCCCAACGTGCTGGGATTA + HHHHGHHHHHHHHHHHGHHFHHHHHHDDEEGEGFFFHHHHHCFFHHGFHFHHHHHHFE;:9<93'8.@6?HEEGFHGE@@DEDHHFFDC/3:ECHGHHHH @read_150_200/2 ATAGTGATTTTTTTCTAATTATGTGAAGAATGATAGTGGTGTTCTGATGGGGATTGCATTGAATTTGTAGATTGCTTTTAGCAGTATGGCTATTTTCACA + HHHHHHGGEGGGHHHHFEFF=BBFGGHHHFCGHHHHGECBFFFEBEEDDHHHHGDDDGFHHHHHHHGHHHHHC?@?EGG38%0D>@EEHFHHH @read_150_201/2 ATAGTGATTATACATTTGAGTAGTCTCTGTAATCTTTTACTGGTTAATTTTTTGTATTATACATTTATTTTTCATCTCATGAGTTCTTGCTTTTGTCTTT + HGFHEEFFHHHHHHHHHHHHHHHHHHF@EEHHHHHHHHHFHHHHHGDFB;DDEEFHHGEEDCA;@EHHHHHHHHFFFCEGFGFB?A5@F>/?477)--37 @read_150_202/2 TCGCTGCGAACTTAAAGTATAATTTTAAAAAAGAAAGATAAAAAAATGCATCAGCATACTGTTCAAGTATGCTGAATTCTGTATTTTTTTCCTTTTAATC + AAACGFGFHHHHHHHHHHHHE?EG?D>:<99).>;BGHHFEEHHHGGFHHHHFHEEHFGFBGFH@BA5DGCBA?FDDHF;EEGGI=>.7@DEC7 @read_150_203/2 TCGCTGCTCCCCTTCCCAATTAATTTTATAACAAAGTTAGTTAAGAGTTTGGCCAAAGAGAGAAAAAAAGTCTGAAAAGAAAAAGCCTCAGAAAAGGCTT + HFD;<5GEE6936BDEHHHHFCHHGHFEEG?DFADEGHHHHHA'<512.BDFHHHHHHHGHHHEF;3::>DCGGEFDBBFHGFGEHFGDFEGEFG@@.@= @read_150_204/2 ATAGTGAGCATATGCTCCAGTACATTTCTTCATGGGTACCTTCTAAAATATTCCTATATTTTAACTGTCTTAGCAACAACATCATCACTCCCAATTATAG + HHHHFHGHHHHHHHHHHD=.;>946;DBEGEHFFFGHHHHFHFHHFEFHHHHHGHHHHHEHEGHGEGGHHHHHBBFEE5:-6=FHD=D.>55.9DFDFFF @read_150_205/2 ATAGTGACCTGTTGGCTTTGACTTAGCTCAATCACCTTAACCCAGTGTCTTAAAATTCTTGATTTTGAGTTTCTTATCCATCCAGTTTATTTACACCTGA + DC@C8DEFGGHHHHHHHHHHHHBGBHHHHHHHHB@DGE=HHHHHHHHHFFGHHHEEDA?BEGGEEF=FCC?@GGGFHHHHG:@AEDFHHHCHGGHHD@79 @read_150_206/2 TCGCTGCAGAATCAATAGAGCATTTGTATTTATGCTGAAGGAGAGAATTGAATTTCAAGAAGTGAGTAGTTAACATCAAATGCTTCGGAGAGGTCCAAAA + HHHHHHEGHHHDHHHHEEGGDHGGGFFFHHEA698=BGHECHFGEHHHHDFFHGEB=@>.??81206@DD??HHAFFHF?HHGBGA<0 @read_150_207/2 ATAGTGAGGCCTCCCAAAGTGCTGGATTACAGGTGTACGAATTAAACAAATAAAATGTGTTTAGATGCATCGCCACTCCTAAAACTACATAAAACATAGA + FHHEFHHHHHHF==FHFFGHEDA@BGHHHHHHGHHHFHHHHHHHFFFFHHHEHHHHHHHHHHHHGHHHHHFE747E:FGBDDEF?EE: @read_150_209/2 TCGCTGCTGGACTAGAATTAGAGCTACAGATATCAACTCATGAATTTCAATGTATATAAACATAAATATGTAAATGTCTATACACAGAATACATATATTC + HHHHHHHHHHHHHHHEFHHHHHHHGHEEGA??EHHFEEFHHHHGGGGFFHF@FHHHHHHHG@7.>=GGHHC=CBCGGE6A557>:D?GD;44@.2,17(1 @read_150_210/2 ATAGTGAAGATGGCCTTGGCCAGTAACAATGTCATGCTTTCTATGGTGCTATGTAAAGTCAATGTCTCACTTTGAATCCAGCCACCAAAAACCAAGTCTC + HHHHHFHHHHHHHHHH@FHGCBEHHE>GFFEHHHFFFHGGHHHHHGHHHHHHE?==@==EHHFE77EFGFFFFHHHEHG?67'-52? @read_150_211/2 TGAATCTCTGGGCTCTCCAGAGTTGGGCCAAACACCTTACTTTACAGATAAAGGAAGTGGGGCACACCCAGGGGTAGAAACCAGCCTGAGGACTTCCAGT + HHHFEB.B<>DGGA9-<;HHHHHHFBGGHHHGE?<*4992@C4=1>9;.EGEBGEHHEEBB@ADHHHHHHE?>B6;ACEFGGGFHFHF./8(?B@CDDD>7D/@2:DDC?++++ADGFHHHFFE<4ACCHHFFFDGEDB6-;CE @read_150_213/2 ATAGTGAAGTAGCTGGGATTACAGGCGCGCGCCACCACGCCCAGCTAATTTTTTTTGTATTTTTACTAGCGACGGGGTTTCACCATGTTGGGCAGGCTCG + =DDEBFHHHHHHHHFHEC@7;GHFHGGHF?BFEEFHFBCD9,<6BF?EGEHHHHFFGHHHHHHHHGHEHHEDFHHFHFHHHHFFFHBFHB5>;EEF56,3 @read_150_214/2 ATAGTGAATATATCATAACTCCTTCCCATGCCAGTAGACTTGACTCCAATGTAATTGTTTTAAAGGTACATTATATCTCATACTGTGGTGCTCCATAATT + HHE@?=FFFHHHHHHHFBDDFFHGHHHGEFHHHEDHHE=8A<>DHHHHHHFHHHHHHHHHHHHHB>CC@568@98;;?FGFHFGFCE>FCDDBF8GIGGH @read_150_215/2 TGAATCTTCATCCATCTATACTTTTGTCCATCCATCTATCCATCCATTCATCTATATTTTTGTCCATCCATCTATCCATCCATTCATCTATATTTTTGTC + HHHHHEHFHHHGFGGGEDEFHHHHHHHHFFHHHHHEF@<>.>C=?CFFGGDCBDGHDHHHHHHGHGHGIFDDDEFDGDHEHFCGB94:FCEFFFCG5858 @read_150_216/2 ATAGTGATGAACATGATACAAACTCATCCCATGTTTTTGAAATGGATATATTTAAGACAAAAATGTTAATAGCACCTCCAGGATGCTGGTTTCCAGGATG + HHHHHHHHHHHHH@BGHHHHHGB@FHHGAC5;>;>E92>>-@GGG:5<-GFHFF @read_150_217/2 TCGCTGCTACCCTTTGACCATCACTGAATTTTTTTTTCTTTTTCTTTTTTTTTTTTTATGAGACAGTCTCACTCTGTCACCCAGCCTGGAATGCAGTGGT + HHHHFGHHHHHHHHHHHHHFHHHHHHHHDEHHHHHHHHDCCFB9:FEHHHHHHHHHG69.193915CFE;FHHFFHHHHFEF?CDDEEEFGHDDDAFGGH @read_150_218/2 TGAATCTGTCATAAGAAAGGAGAGGAAGGGACATAATCCTGTGTGTTTACCATTTATGTGGTCTCTTTTCATCTATTATCCATTTAATCCCTGGACAATC + HHHGD>???A>7;FFHHHEHGGGGGFHHHHHHFHHHHHHHHHHGHHEFFFHHHHFHGGGHHHHHHHCFHHHHHHFFED.EFIDHFF?G;@EFABBEHHHH @read_150_219/2 TCGCTGCCCTATGTGACAGAGCAAGACCTTGTCTCCAAAAATAAAAAAAGAAAAAAGAAATACTTTAGTTTTGAGATCGGAAGAGCGTCGTGTAGGGAAA + FHHHFEHHHHHHHHHHHBDGBHHGHHHHD@AHHHHHHGGGEH>><@EHFFHHHHFHHHHHHHHGHHHB@=C@DDHH@DHGFDHHHFHHHFHHFFCD>>9EFH=CEEDFE;,;EEEDFHHGHHFC;D5 @read_150_221/2 TCGCTGCTTGTAGTAATATTGTTACTGCTATAAGAGGGAAGGAACATGCTAGCTTTCCTCCTTGTTTATTGAATACAGCCTGCCATAAACGCAATTTTAT + HHHHGHHHHHBEE:=EHHHHHEGGCHHA:1<<@99575.8EDFFHHHHFF:8D@DGEHHEGGFFHHGHG@E=7862-28DCBHHHCE:E9(3HFHEC=/; @read_150_222/2 TCGCTGCAGTGAGAGGTTTAAGAGGTTAAGATGAACTTAAAGAAAAGAAAGAGACATCCAGAAGAGGTGACTGAGTGTAAGTAGAAGCAGGAAAGGGAAA + HHHHHHHHHHHHHHHHHHFHHHFHHHHHHHHHHHHHHHHHHHGGGFHHHHHHHHFHHHEE@EC'BBHHHHHGFFF?EEFFHFFDC6BDFE@ADB@EHHHHHHHHHFGAEHHHHHFHHFHHHHHHHHHHHFEHHGGHE=.A81107AGHGFHHHBEGHHBEFFEBGHHHHF>5--;=DBB/DGFGHHHGF;88@5&3EEGDBDD>,%,CEEEFB @read_150_226/2 TCGCTGCCAATTGAATCATGGGGGCAAGTCTTTCCCATGCTGTTCTCATGAGAGTGAGTAAGTAACACGAGATCTAATGATTTTATAAAGAGGAGTTCCC + HHHHHHHHHHHHHHHHHHHHHFHGHHHHHHHHHHHFDHHHFGGFHEFFHHHHHD@@7-396)))3@>>5<)7@EGG;EFFEB9-116('(,-3BEDCBD? @read_150_227/2 TGAATCTTGTCAGATGCTCACTCCGCATAGATCGGAAGAGCGTCGTGTAGAGACAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAACAAA + HHHHHHHHHHHHHHHHHHHHHHDGHHHHHGGDBFFEEGEHFHHHHHG?>@(-((:>C@EC@::GCGGFFHG57@?(4EGDD@;::CFHHHHFH@'%-+,6 @read_150_228/2 ATAGTGAAGGTGTTGCCAAAAGAGACTAACATTTGAGTTAGTGGGCTGGGGAAGGCAGAACCATCCTTAATCTGGTGGGCACAATCTAATCAGCTCCCAG + B@EDHDFIGCBEEEEHHHHGCCBEHHHGEGHHHHHHHHHHHB;5@,3/@DEBDCA<DFFHGGHHEFFDDHHFFHFFEEEHF @read_150_230/2 TGAATCTACTTGGATGGGAGATACTAGCGTAGGATAGAGTGGATGCAGATAAATTTATAAGTGGCAGAGGGGCAGAATTTGAAAAAAAAAATCCATTTCA + HHHHHGD@=FBCAGHHFCDFEHHHHHHHHFFCFADEGGFCBEBD;)=?AHHGGGGHHHHHHHGHHHHHHGHHFD7;A=5D@@E;9ABEBHDEFFDFFEBG @read_150_231/2 ATAGTGATGAAAAGTGTAATCTCTGTCTAAATTCACCTTGTCACCATGTAGAATTCTAGCTACTCCATCTTCATTTGTTGAAAAGACTGTCCTTTCTCCA + DGHHHF@DA>CAA@HHHEGFFGGGHHHHHHHHHHHFGGEGHFHHHHHHHHHHHHHHHHHHHHHHGGBBDGEDHHH?9:<>BFGHF;BGFGFBFGHHHHE= @read_150_232/2 TCGCTGCTTATATCTGTAGCTAAGCTGATATGTTTAATTTCCTAAGTCTCATATATAAAAATAAAGGTTATATGAAATTCTATGTTACTAGTGAGGTTCT + HHHHHEFHHHHHFD=C;*33):DA1.D?HHHFGGHEEDDDHFGGGFHHHDDDDEHHHHHHHHBEGHHHHHGBGGG@,CHB.?=<2%'%%?BGCDFHE@?9 @read_150_233/2 TCGCTGCCCAAGGCTCCCACGGGCACAGGCTCAAGCCAGCCTGCTAGAAGGTGAGATGCTGCCCGGGGGAGAACTGGGGAGCCCTGGCCGATGGTCTGCT + HHHHHHHHHHEHE8BEEHHHGHHHHGHGDAAFHHHHHHDEEEGHHHDHHHHHHGGEE(6-81'.CFFHHHHHHC.6AECCHHBEFHGGHGHHHGFGGGFB @read_150_234/2 ATAGTGAGAAAACAACCTGCAACCAAATTAGTGACTGAATTTTTTAGTTAACTCAAAATTCCAAATCAGAGGGTTTTGCAATGCCTGGAGGAACCTTGGA + HHHHHHHHHHHHHHHHHFGHDGGGFHHHHHEBAAEGHBEEFFHHHF:;FHHHHH@>C83@FHHHHHHHHHHHHHHFBHHHGGGCFEHEHHHFHBEC?>@1 @read_150_235/2 ATAGTGATTCATTTTAGATGTTTGCTGTCAAGTTTTGCTTTTCCACGAAACAAGCAGTTTTCAGCCCAGCAGGAAGTTAAAAACACTGGTAAATCAACAA + HHHFGHHHHHGE*=AFGGFGEB@>95>:,CHHHHHHHHHHHHHHHHFHHHGDEEGHHHHHHHHHEBHHHFEEDFHHHHGHBEDDDGHEFFHHH?;5A?D@ @read_150_236/2 TCGCTGCGGGGGAGGGAGTTTGGTGCTTGTCACTGACGCAGGAACAAGGTGCTTTCTGTAGCTCTGATTTGTTGCTGGCTGAGTGTGAATGATGTCAGGC + HFFGEHHHHHHHGA::@GGFFGGHHHFD@@DHHCCFGFEEFDHGGGFGHHHHHHHGC>7DFE<2):@C;@D@/,7>?AFEHFDFHHHHGA@?;A@9DFFD @read_150_237/2 ATAGTGATATATTTGCAGAGCAATATGAGAAAAAATGAGATTGCAATTTTAATTTTGAAAGTTTTCCTCTTTTTAAAATTCTTAGTCTCATTGAAACGCT + DDHHHHHHDHHHHFHHHHHHGHHHHHHHHHHHHDA:3>41<0:DAFEGG@GGGGHHGD@@66EHGHHF835.5*-(&61 @read_150_238/2 ATAGTGAAATGACATTTTGAAACAAAAATGTTTGCTTTTGTTGACATTCAATGACATTTTGTTGATTCTTTTCAAAAAAATCTTCTAAATATTGTATGTT + HHHFHHHHEHHHHGFHHGFHHHHHHHHEEEHHHHGHHHHHHHHHHHHFHFFFFHHFGHHHHHHFFB>1.:-=&99GCDGGHHHGGGGE80CB95=?HEE; @read_150_239/2 TCGCTGCGTTCTCGATCTCCTGATCTTGTGATCCGCCCACCTGGCCTCCCAAAGTCCTGGGATTACAGGCATGAGCCATCACGCCTAGCCTATGACTGCA + HHHHHHHHHHHHHGGHHHHHHGGGEEHHHHHFEHHEEFEDEBHHHFFHHHHHHHHGEGHFHHHHHHHHHHHHHHHHHHHHHHHBFFHHHDDCACHGEBCF @read_150_240/2 ATAGTGAAGTGCTATAAATTTTTCTCTAAACACTGCTTTAGCTGTGTCCCAGAGATTCTCATACATTATGACTTTGTTCTCACTGGTTTCAAATAACTTA + HHHHGDEEEFGHHHHHHHHHGFFFFFEHHHFFHHHHHHHHHHHHHHHHHHHHHHHGBGHHHEB?E:*:>>DA5;.@CCE:=;=>>D=<<;38>?CFFCBF @read_150_241/2 TGAATCTAACTAAGAGGTTGAGCATCATTAAACAGGGGATGGTGTGAACTTGGGAGCCTCTTGATGTGACACAATACAAAATGCACTGCAGCATCTATGA + HHHHHHHFHHE=CDDDDE4DGHHHHHHHGHHHHHHFFHHGD58(;BBDADBEHFEGGAB.BCBEDEFHHC'.><:5CC>>AEEFDGG@@AB;7/BGE=EGFGBBB=>>?HFHA@.1)&21;36<',<>.&:39FF @read_150_243/2 ATAGTGATTTTTTTTTTTTTTTGAGACGGAGTCTTGCTGTCACCCAGGCTGGAGTGCAGTGGCGAGATCTCAGCTCACTGCAAGCTCTGCCTCCCGGGTT + HHHHHDFGGHHHA@HHHE=BEGBD8EHHHHFBFG>DD@@HHHFFFEEBFHHHEE?;DFHEHEHHHHHHFEEHDGGDBABCBDBFFF?@GDFHHHBD@7;> @read_150_244/2 ATAGTGACAAGCCCTGATGCTTCCGTGATGTTGCCTCTCTGGGCATTTAAACTCATTCCCAGAACAATTTCTATGAAGCTTTTGAAAGTTGGAAATGGGC + HHHHHHHHHGHHHHHHHBGGG@IHHHHHHGGH=D;EGGHGGDHHHHHHHHHHHHHGGGG=FGEHHHHHHEGBFFHHHHFCFHFFGHHHHHHHHHFHHHHH @read_150_245/2 ATAGTGACTTTAAAAATCATTCTCTCATTGCCTTTAAAGGTATTTAATACTTTAAAACATAATTATTTTATAGTAAATCCATAGATAGGAAGAGCGTCGT + HHHHHHHHHHHHHGHHHHHHHHHHHHHHHHHHHHHHHHFC<>.@218?HFC8@<>@CEGHHHGG?@EGHHHHHFFDBHHHHFGGCE=BHHHHHEEFHGCGF @read_150_248/2 TGAATCTTTGGACACTCTGGGGAATTTTAAAGAAGGGAATAGGGATAGAAAGAATCCGCATAGATCGGAAGAGCGTCGTGTAGGGACAGAGTGTAGATCT + HHHHHHHHHHHHEDEGGGGHHHHHHHDGGFHHHHHFHHGFFHHE=>IEGFGEE=CGGDGGFFGGD+?37B@C@BFFFFHHGHA=4')>GEF@CHHHHHH9:..@3;3.8:FGFGCFHHHFFFGEFHHHG=9A@@GB@A*0:.>>4BD@F?*)02:>CBEC @read_150_252/2 TCGCTGCCATACTGGAAGGTTGCCTAACAAACCACCAAAGCTTTTTTTAACTCTCTAAGGGAAGGTACTTTTGTTTGACTTACTATTTCCTATTGATTAG + FEBHHHFGEEFFGHHEEGHHHCFFHHHHEFFEDDEFGHHHHHHBFFHHHHFEDGHHHHHGGFGFADGHHFHHHHHHHHHHDADBE?3:1FHHFFHFFCDA @read_150_253/2 TCGCTGCAACCTGAACTGACCCTGGCAGGACAGTTGCTGCTTAGAGCCCACTGAGAATACAGCCAATTAAATGGGGAAATATGGAAGAAGACCTCCACGG + HFGEFHHHHHHHHHHHBGGHHHFE@D>@:<>?CHE7651-2-DHFHFFHGHHHHHHHEFHFHHHHHHFIGD9:<>7/@GGD@BGEHFEED;EHCD24:G9 @read_150_254/2 TCGCTGCTGTGTGGACAATGGGAAGGAATATTGTGCTTGGGGTATGTCTAAGGCTTATAGGAAAAGGCTTGAGCTGCAGGTTAAGTATCTTATGATAAGC + HHHHFHHHFHHHHHHF=FGGCEIGADAEFEBEEEBBG@AA,&:HHHHHEHHFGGGFGGHHHHHHHGEGGGB@?=GHDEEBGGGDCHGHHHFFEE;:@893 @read_150_255/2 TCGCTGCGGATTTCCATGTTACAGTCTGAGTCTTGAGGCAGAATTACTTCTTCCTTTTTCCTTTTTTTTTTTTTTTTTTTTGAGATGGCGTCTTGTTCTG + HHHHHHHHCGFG=FFHHHEHHHHHFHHHHEGGHHHHFFHGHHHGBHHCHHHHHHHHHHHHEFCAHHFFFF8DEHFHHEFDGGGFFHGBG<05GHHFB@C? @read_150_256/2 TCGCTGCATATTTCTAAGTAGGTAGAAGAGCGGACTTGAAATGTTCCCAATACATATAAATGATAAATACTCGGCCTAGTGTAGTGGCTCACACCTGTAA + C>@A<:=E@;HHGGHHHHHHHHHHBGFEHHHGHHHHHHEHHHHDEEEFFFGEE0&<.FHHHHHHFGDDDDEFFEDGFG9>::-7568:5:8HADHHH @read_150_257/2 TGAATCTATAAGTGATTTTGGGATAACGATCTACCAGAATGGGGATATTTCACCCTTGGTTCTGAGATGCAAACCAAAGAATATCTCCGCATAGATCGGA + HHHHGG@=FF<=DGIF=EDDHEEEHFEHHHHHHFEEFHFGHHHHHHHFHGEHGHHHFHHHHGGHHHHHHHHHEHHHGEGGBF?E?0099?9@=8<<<5+B @read_150_258/2 TGAATCTCTATTCGGCCGTCTTGGCTCCTCCTCCCCCTACACACATTCTTAACCCTTTGGCAAACATATCCAAACACACAAAAGCTACTGAAATTGTTCC + B87..68BFG@9DFFGGBA=@GEEHA;A6:EGDEFGEF9E:63:;EGEEEHG@@EFGHHHH;5AFHHG? @read_150_263/2 ATAGTGAGGAGCATACACCAAACTCTTGGCATTATCCTTTTGATAGTCATAATAGTAGTCTCCCCGGTCTGCCGTATTCCCTCCAAACTTTTAGATATTT + HHHHHHHHHHGEFFGGDDDDEEBFE5@/7367AHHHHHHHHHHE>DEFHF>:=,%69@;/EBEDFHHEADD @read_150_264/2 TCGCTGCAGCTATAAGATGCTGTGCCCTCAGGGTGGGGTGGTGCAGGACAGTTGTTAAAAGCCTAGACTTGAGAGATGAAGGCTCAAGTCCTGGTTCTGC + HHHHHHHGHHHHHGEC.C=BCHHHFHHFGBHHFFFCCD9/>;B@EEEGHHDD<54;AAECCFHGHFHH<6)5A@DCCFGGE @read_150_269/2 TCGCTGCCATTTCTAAGAAACATAGCACAGCTTTTAAGGTGTTTAACACAGTGCCTCAAATAAAGCGACCTAAATCTAAATTTATTTTTATTATAAATTA + HHHHHHHHDHHEHHHHHHHHHHHHHHHHHHHHHHH>CEFEFFDDFGB6ACHHHHGHGGGEHHHHHHHHHEGFFEDEEEE>BFHHDHHHFCCFFAC.8>FB @read_150_270/2 TCGCTGCAAATGTGTTTGTATGCTTTTTTTTTTTTTTTTTTTTTTTTTAAAAAGGAAAAGTATGCAATGGGTTTGGGATAAGGCCAGAGGTTTTTCTTTC + HHHHHHHHGB?GHHHHHFDAAHEHBEHHHEHHHHHGFFFEECFCHHFFFD?FCBFHHGGEGGGHHHEDEE;GGGEFFF?@EEEEEFDA>DFHEHHHHHFF @read_150_271/2 ATAGTGATGTTCAGGTTTTGAATTTCTTCATGGTTCAATCTTGGTGTGTCTGGAATGTATCCACTTCTTCTAGATTTTCCAATTTATTGACACATAGTTG + HHHHHHHHHHHHHHHHHHHHGGGHHHHFEG134A.?BGGA?>;>;DGGFHHHHHGHHHHHHHHGGE?8DEDBGGGHHHCFFEEHFHHFEB @read_150_273/2 TCGCTGCATCTATGTACTCATAGAATGTCTCACCCACTATCATGGTATAGTACACAGAATTGCCTCTTCCCAAGGAATTCATTTCACAACAAAGGAAATG + HHHHHHHHHHHHHHHHHHHBEEFFGHHGGCHHHHHHHHHHDGBGHHHFFCACCGGHFHHHHECHHHHHHHGHHHHHHHGHHHHHGHHHCFFHDEHHHHB/ @read_150_274/2 ATAGTGAAGCCTCGACCCTTAGGGCTCTTCCATTCCGGAAAAACATTTCGGCACCAAGGAGACATCCCAAGGAAAGCACTAGTTTAAAAATGTTGCCTTC + HHFGBFHHHHHHHHHHHHFHHHFGHHHHHHHHHHHHHHHHHHHHHHFHHGGFBDHEE7>FCDEC??:@BHHHHHHHHHHHHEHHH=EHGHHCE@HHHHFE @read_150_275/2 ATAGTGACCTCATTGCTCCTTATATTCCCCTCTCAGACTCCTTGGAACCAACTCCAGTATGGCTTTCAGGCCAATCCATAGATCGGAAGAGCGTCGTGTA + HHHHHHHHHHHHHHHHHDGHHHFHHHHHHHHHGEDGFBEADDA40>/EHFGFFC?EHHACCAFE8AD?EFHHG;7)).?D:CBBCFHHHHHHHHFDAC.GGGGBFHHHEEEGBGHHFFFHHHHHHHHHHGG.<3DGHHHHHHFFGBFGFFHHHHF?DHHHHFBCEFFGEFE>2: @read_150_277/2 TCGCTGCTTTGACTTCAGTTTCTGAAATCTTAATCATGCACAGTTTAATCAATAGCTACATTTTTCTCACATTTTAAAATAGATTATTAAATGGTCAGTT + HHHHHHDHHHHHHHHHDD=@FHHHHHHHHHHHHHHHHHHHEHHHHHHHHHHHHHFFGHHGEGGFFHHHHE@CAA<:B9GG?4DD?:@FDBEFFE;CA@<0 @read_150_278/2 TCGATGCTCAATCTGTATGTTATCCCAGTACCCTTTGCCTTCCGTCAGGAAGAAGAGTCCATAGCCATGTTCCTCAGGCTGTGTTCTGGTTAGTTATGGC + HHHHHDCDGFEEBCDEDFHHHHHHHHHBEEAFHCDCEEFGHHHHFFEDEA>2%--?@EEBIEEFEGGHGGF@GGFDGHHHHHHHHHGHFFB7)-9BEHG/ @read_150_279/2 TCGCTGCGCTGAGGCGGGCAGATCACAAGGTCAGGAGTTCAAGACCAGCCTGGCCAACATGATGAAACCCCATCTCTACCAAAAATACACAAATTCGCTG + HHHHFHHHHHEE?DFHHHHHGGGGHGGHHEHHHHHEBFHGC@C3FGB/B.2:DFFFHGFCAFHHHHHHHHHHGHFBDA@;+3CDHHHEFHHHHDH@CDCHHFFDDE?HF/5C @read_150_281/2 ATAGTGATATTAAGTAAAACATGTAGTGTGTCAGATGGTGCTAAGTGCAGAAGGGAGAGCTGGGGCTGTGGCCAGGGCTGCAGTTGAATCCATAGATCGG + B.=GHHHHHHHGHHHHHGGHE87;=-5>ECA@EFF=D66EHEGBFGED:4BCDDDEDHHHGFGHHHGCGHHDFG@DD67DHHFCCEHBF>337:BHHFBC @read_150_282/2 TGAATCTGATTTAATCTGTTTCTGACATTAGAATATATATATATCTTTATTGGAGAATCTTTGGCCACATCAAAAGTATCAAAACATTTCAGCATTAAAG + HHHHHHHHHHHHHHHHHH?@EHHHHECGHEHHHGHH@FHH>:DGB=69AFHHHHHDIGDEECHHHHHHHFHHHHHHHHHFGEGHHHHFFC>6FHHHGA?5 @read_150_283/2 ATAGTGAAGCCATCAGTGCAGGCTAGGGGAGAGAAGGCAGGGTGGCAGGAGTGGAGACCATAGGCATTTGAGCCACTTCCTCATGTAACTTACTTGTGCC + DHHHHHHHHHHHHHEGEEGHGGHHHHHHGGDDBDBBGFFFFFHHHHHHHHHHHHHHEBFEDHHHHHHHHE:9EDDHHFFFFFHHE8BF@FHFFGEHHFGB @read_150_284/2 ATAGTGAACCCAGTCCTGCCCCCTGGGCTCCCTTCAAATCTTTTTTTTTTTTTTTTTTTGAGACAGAGTCCTGCTCTGTAATCCATAGATCGGAAGAGCG + HHEDC79??AEHHHHHGGGHHHHHHH=>CHHHHHHGHHHHFHHHHHHHGIDGBEGFDHHHGGECD.<,9977;@D7ADCDGHHFFDD=DDFCGEA;BEEB @read_150_285/2 ATAGTGACACTGCATTCCAGCCTGGGTGACAGAGTGAGACTCCATCTCAAAAAAAAATAAAAATCCATAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTG + HHHHHHEFHHHHFG@FFFFGEEHHHFBBEEF=>:>8CD/>4*A=EHFEFGGGGIGGFFHHGGDGDBEEFDEHHHHHHHHHHHHHFEC,<<@G @read_150_286/2 ATAGTGAATCTAAGACCTGAAACTATAAATATTTTAAAAGATAACATTGGAAAACCTTTCTATACATTAGCTTAGGCAAGGATTTCATGACCAAGAACCC + HHHHHHHGHHHHHHGHHHHHDEHHHHHHHHHHHHHHFFHHHDCDE@<@CCGFFGGHHHEDFHGHHFHHHGHHEEEBGF.(.7?B?@GADDCC@CEF=.>>ABHHHHFFHHHH @read_150_288/2 TGAATCTCCCCTCACCTGGCTGCTTCCACAGCTCTGTAGCAAGAGTTCTAACCTTTTTTCACCGTGAAGCCTGCTGAGAATAAGAGCTGTGGACTGTTTT + HHHHHHFHHHHCB<@-8@EFHGCGGHHHHHAE@@@;GEFD:.EBHFHH?>>AGHGEHBFDDHHHHDFHHHHHHHH;<89A?EEHHHHHGDDFHEEEEEGEEHHFFHFFFF<9988D@?CCD@CF??DGFF6 @read_150_293/2 TCGCTGCTAATTTTTTGTATTTTTAGTAGAGACAGGGTTTCACTATGTTGGCCAGGTTGGTCTCGAACTCCTGACCTCGTGATCCACCCACCTCGGCCTC + HHHHHHHHHHHBGFGHHHHHEHHHHHHHHHHHF@ACHHHHHHHHHFFFEEFGFDHHHHHHHHHHHCDGGGGHHHHHGEA=E<>HHFEBFFFHH?),5C?A @read_150_294/2 TGAATCTATTAATCATAAAGGGATGCTGGATTTTGTCAAATGCTTTTTCTGCATCTCTCGATATGATTATGTGATTTTTGTTTTTATCCGCATAGATCGG + HHHHHHHHHHHGHHHEHHHHDDDGDGHHHHHHHHHHHHFGHE7C>>5939B3+15EHEE=HHHHHG=@@>5.3;9CFBGHHGB7?DFFE?>EBDBD@@DGEDHHEHHHHFGGHHGDHEHHHHHHHHHBFHHHHFA@FFFFDD@ @read_150_296/2 TGAATCTGGTGTTCAGGAAAATTATCTATCGTCTGATTAATCTCCTCCACCTGAAAGCGTTCCTAGGAAAAATACTCTGTAAATTTGTATTTTCCGCATA + HHHHEFEGFEHHHHHHHGFFEA=CDGAB>@HGGFHHHHDD@=??DEFHHHHHHHHHFFDDGFGG@GDGHHHHHHHHGE?7D9GGE1CDFHHHHHEHHHE? @read_150_297/2 TCGCTGCCACTTTAAAGACTGTTCTGACACCCCCACAAGTCACCCCCTCACTTTGGTCAAGCATAAAATATTGAATACAAGGTAATGAATGCATGGAAAG + HHHHHHHHHHHHHHHHHHHHHHHHHFBECBGFEHHHHHHFA68EED2GEHHHHHHHHHHHHHHHG8ABE9.;CCCGFFHBBEGGGEF@;==76<9:9*3% @read_150_298/2 TGAATCTTGGGTGAACATCAAAACATGATATTTAAGACAGAAGCCAGACACAGAAGATTAAACTTTTGATTTCATTTACCTGAGCTTTGAAAACTGTAAA + HGGCCHHFEDDGFGGHHGFHHHHHHHHHHFHHHEFEHE75?GFHHHHHHFFHHHHHHHHHHHHHGFGHHBA:@:5:?EDDHEB/%.7.:0DFGDGFDCHF @read_150_299/2 ATAGTGAGCATCCCCGGGATAGATTCCATTTGGTCATGATGAATAAACTTTTTAATATGCTGTTGAATTTAGTTTGCTAGTACTTTGTTGAGGATTGTTG + HHHHHHHHGFHHHHHGHHHHGC=@@GFGGHHHHHHHHHHHHEHHHGFGFFHGFEHG?FDFHHDCBEHHHHHHDDDAA?FGHGGFFF?>.9B:5-3:*>55 @read_150_300/2 ATAGTGAATGTGCACAACGTGCAAATTTGTTACATATGTATACATGTGCCATGTTGGTGTGCTGCACCCCTTAACTTGTCATTTACATTCGGTATATCCC + HHFHHHHHHHHHHHHHE/8EHHHHHHHHHHHHHFFHFHHHHEDBH@D/3%03/7:<5* @read_150_301/2 TGAATCTCTTTGAATGTGGCCCAACACAAATTTGTAAACTTTCTTAAAACATTACAAGATTTTTTTTGCAACTTTTAAAGCCCATCAGCTACTATTAGTG + IGGHD?@DC@@AGHHHHHHHFHGGFHFGGHHHHHHEFFFHHFFHHHHGFBEGHEDHHHGGGF?EDGGFC;EEHFGHHB;2<..07/;-66)-5-)*-01:5=ABBBHGFHHHHHHGHHHHHHHFAC<),144?BE @read_150_303/2 ATAGTGATCCCCTTGTGCATCCCCCTAGAATTCTGCACTTACCTTTGTCACAGCCCTTGTCAGCTGGTACAAGCGTATCTCCCACACTGAACTGCAACTC + HHHHHHHHHHHBCGGHHGFGHHHGHFHHHF42.?9HHHHHHHHHHHHFFFFGHHGHHEGGHHHGEFHHHHEHHFHFGHGDFGHHHGFHFBFEABD7@=<> @read_150_304/2 TGAATCTAAAATAAATGAACTATGTGACTTTGGATAAATCATTTAACCCCATCACCTATAAAACAAAGGAAATCGACTAGATAATCTCTACAGTGCCCCC + 514BEGB@DEFEGA=:CBGHEGHDD@HHHHHFCBEFGEDD, @read_150_305/2 TGAATCTATTTTTAGGTATTTGTTATAGCAACAGCCCCACTGCTTGGTACCAATTTTGTGTCTTATTTCAATTTGTGCTGCTAAAACAGAATCCTACAGT + B:AEGBA=EHHHHHHHHHHHFFDF/DHHGBG9< @read_150_306/2 ATAGTGAGGATTATAGGCGTGAGCCTCCACTGGTTTGGTTATTATAGGTTCAATAACCCATAGCTAATGTTATATAAATTTTAAAAGCCTAGGTTAACAA + @@AEB==E@GHHHHHHHHGGEHHHHHHHHHHHHHHGGFFBBFHHHGHFHHHHHHHEDGHHHDF/CHGGGHFGGGHHGCDEEEE?FFGFFFHHHDFAA;:D @read_150_307/2 ATAGTGAATATACAGATATAATACATTTGACAATAATAGCACAAAGAGGGGTAGTGAAGAAAACTAAAATAGTACCCCCTTTTCTGCATGGGCTTTATTC + FGHHHHHHHGHEBEBHHFFGHEGGBGEEEHHHHHHHHHHHHHHD6=;BCDHHHHHHHHHHFHHFGHHHEHHHHHHEBDHHHHHE?D;:21<,,-297GFG @read_150_308/2 ATAGTGAAACTCCTGGGCTCAAGTGATCCTCTTGCCCCAGCCTCCCAAGCAGCTGGGACTACAGGAGCATGCCACCATGCCGCCCAGCTAATTTTATTTT + GHHHHHHHHHDDGHHHHGHHHHHHHHDGGGHHHHHHHHHF;>@C=>BDFB8=D88<>HDGG;/=D6*6BGECA>5CEDHHHHH.<+<48>>>:A@>?BDD @read_150_309/2 TGAATCTAGAGGTTGCAGTGAGCCGAGATCACGCCATTACACTCCAGCCTGGGCAACAAGAGTGAAACTCCTTCCCAAAAAAAAAAAAAAAAAATATTCA + HHHHHHHH?FHHHHHHECFDGHF@EBHHHHHHHHHHHHHHHHHHHHHE??FFHHHHHHHHGHHHEHHFHHH@)<.GHHGEF8-6C?DGG?<<=B,.<'<< @read_150_310/2 TCGCTGCTTAAATAAGAATTCTGCATTTTCTGTGTATATGTGCTTGTGTTTGTGTATCTGTGATGGGGTGGAGGATGGAAATTGTTGTGGCAATTTAATT + FEF@FHHHHEFHHHHHDHHHGGGB?EEFEGGG38FHHFFHDECF>GE@BCAB@<@GEEHHHFHHHHHHHHHHEGHB9>>(>=DGFEF?HHFFFHHHG?BA @read_150_311/2 TCGCTGCATTTATTATTTCAAATACATTATGATACCAGAAGTCAGCCAGTAACAGTTCTGAGTATAAAAACATTTGGTAAATCCCACCTGTACATAAAAC + HHHHHHHHHHFFDGGGHHHHGGGEFHHFFGHFEEHHHHHHFHHHHFHF=<.<<9?EGFGGGDBFHHHHHHHHHHGGDDFHHHHHH>,30;?@/'5?(->A @read_150_312/2 TGAATCTGAAGACTAGATTGTTGGGTGTGGTCCCGGAGTGCTGTCAATGGGGGGCTTCTCTGTGCACAGGGCAGGACCCTCTGGGCAGCCAGTGCCCACA + HHHFHHHHHHHGGGGB@=CHFDDBDHFHGHGF?EEFHHC7;CHHHHHFFHHFGEEG8EGFEEFBBGGEF;>5>>998FFFGFFEE5;DC88EEDHHHHH@:)8EGGGFFHB@):@7-@A5>DGE9CADFEDC.:@@BEDHHHHHHHHGHHHEEFHHHGEFFHHHHDD@/@4AAGF>9:6B@BB @read_150_316/2 TCGCTGCCACCAGCTCTCTCAGATAAGGAAAAATCAACACAAGAACTCCAACAATCAAGAAGAAGGAGTGTTTCCTTACCTCCAAATGGTTGCACTGGCT + FFFBHH@A6649;GHHGEFFFFHHHHHHFGB7CHHHHE*461:>;A.36,))13:8DCDGDHHHHHHHHHHHGGEDB?A?=EE7956B+: @read_150_317/2 TGAATCTAATTTTCAAGCACTGTACAGAAAATGATAATATATTTATAGACAAATGAACAAGGAATCTTTTTAAAAAATTATTTCAATCCGCATAGATCGG + HHHHHHHHEHGGGHFGDFFDHHHHHHHHHHHHHEGCDHHHHHHHFF3<@EFHHHHHHHHHHHHHH::66:DAGGHFFFGGHFHHHFHHFGBHHHHCDE5< @read_150_318/2 TGAATCTGTCAGGAGCCTGTCCTTTAGGGATGACCTCATTTTTGCAGGGTAATGGTAATGAAATGTACTAGGGGTAAAAAGTAATATCAAGGCTAACTTA + BDC<92@FHHHHHHHHHGFHHF.1>'+8EED>-79F8;DGFFFFHHDCDAA?7;?EFFHHHHGFHEDHH=GFFFFGFFH@HHHE27..D;3=DGCCHHFF:@GHHHHHHHFHHHHHHFHHHHGCE5BGEHE@CDGFHHHHHFFHFEGHGGHDHHHFFBEHHHHHHHHH @read_150_320/2 TGAATCTCAGGAACGACAGGAGTGCTGGGTGTGCAATCATTCATTTGCTACACATTTGTCCGCATAGATCGGAAGAGCGTCGTGGAGGGAAAGAGTGTAG + HHHHHHHFFGEEEHHHHHHHHHHHHHHHFFHDCDGDDGGBFHHHHHFEBHHHHHHHHHHHHH6EEEFG?HHHHDFFBC?;?:98&<:5CGHFHHGAHEBF @read_150_321/2 ATAGTGATTCTGACGATGCTGATAAGTATATAGAAGCTTTCCACATTTTTTTTTTTTTTTGAAACGGAGTCTTGCTCTCTCACCCAGGCTGGAGTGCAGT + GB@;>;/ABGGGFGHHGEHHHHHHHHDCGFFHHHHGDC5BC>>FCFHGDGGGGGHHHHDFGGFHHHGFHGHHHEEEEDEEHF@C;ACCEBE@D7)*=EC? @read_150_322/2 ATAGTGATGAAGAAGGTCAGTTTCTCTAAACACAAAAGCATGGGGGGAAAAACATAAAAGAGGGATTCCATATAAGATCTGGAACTTCTCTATTTAAATG + HHGGEHHHHHHGFHHHHDGEGHHGGGBGGFHEEGHD@<9=FGAFFHHHFDCEGHHHHHCEDD;81(7-7?@B@@4A7@BGHFFHFGGFED=ABBDFHF<8 @read_150_323/2 TGAATCTTGACCAATCATTTTCGCCCTATAAAAGACATTGGAGAAGCCAGTGAGGTGGGACTTGAAGAAGGGATTTATTTTCCGCATAGATCGGAAGAGC + HFFHHHHHHHHHHHHHHHHHHHHHHHHFFE?GBFEHHHHD@BEEEFFF>ECD>.:.B@@=6><863:6>>9:295DCBB=CDEDGHHBHFEGG@EEB==FGHGBFGFEHHFEHHHHHHB<&8DGDBF=FHHHHFF6...< @read_150_325/2 ATAGTGACTCCTGCTTCAGCGTCCTAAATTGCTGAGACTATAGGCATGAGCCACGATGCCCTGCCCCAAACACTTTTAAAGAGACATCATGCAATTTGAG + D@CBFDFEDDBEBGGHHHHHHHHH?;:DED;EEEEFEFHHHHHHEHHEHHHHEEEHHHHHDGCBCCAAFFCC7+>GEEDE65GECB@EDDBG;@>DDECH @read_150_326/2 TCGCTGCTGCTTCTTCCTTGAGACACAGCAATATTGAAATTAGGCCAACCCTACAATGGCCTGTAAGTGTTTAGGTGAAAGATAGAACCACATCTCTCAT + HHFEHHFCDGHHHHHGHHHFGHGGEDGHHHFFFFCCBA@:158.=?@FFHHFHGHHHHHHHHHFGFEGHDFFGDHHD=ABCFE8/;@EH;D=EF?AAEHH @read_150_327/2 TCGCTGCGAGGATATATTTTTTAAACTGTCATATGAGGAAACACTTTAGTATGTAATTTCCAAAAGTTACACAAAAATGTGGTCCTGAAAATGCATACCA + DGHHHHHHHHHHHHHHHHHHHHHHHHFHHEBGHBHHFFHHEBCFHGGHHHGEEHGGHHHHHHGHHHHFGBE@<-07>@:0>>',518EHGFHEEGHHHHHHHHHHFGGHHHFFGHHGHHHGGFHHHFFGEFHHF@D/46?BB@CD@?GGBEHHHHHHB;@CB/@GFFHH@CDEGGGGGHHHFGGEFDHFB>>ACDD@GHHFCDFDCDE?D@9;EEFE@FHHHHHHHHFFHGEDDBHFE=3 @read_150_331/2 ATAGTGATGGATTTTTCACTGTATGGGTGGATAAAATTGTCCAGGGCCCAAGTTGTTCTTTAAATCAGCTATTATAACGCTCTTTTGTGTGTGTACATGT + EHHHGD8CEFDHEGGEBDDE?CC@FHHHHHEFHHHGEHFHFEEGGDFFFEGGFFFHHHHHHGGFDCBEHHHHD<@*9.>@.;:1=EFFHHHHFFGGGA=+ @read_150_332/2 TCGCTGCACCAAAAAATGTTCTGTGCAGGAAACATGCAAAGGGGAAAGAAAAGACACACACAATACCTTTAAGGGTAAACAGCCTTTATCCCAAGTATAT + HFHHHHHHHHFFFHHGHD@+4=FGGHHH@<6>@>=BGG==BEGIFDDHHEHHHGGDEHGD@ADB=BCFHHHHHFFGGHHHHHGBFEBB@HGEEEEHD7EE @read_150_333/2 TCGCTGCTTTCTGAAGGTAATCTCGGGGTGGCGATGAGCAGGGTGGGCCTGAGGGGGCACTGCTCCCTAGTCTTATGTCACCCAGGGTTTACCTCCCCAC + HHHGHHHHHHDDCBEFHHHHDHHHHHHGFFCHHHHHHHHHHHFHHHHH@:BCEDBEEFFHHHFGGEEEGFHHHHGHGGEBFDEFFAADDCA>0+<94EEF @read_150_334/2 TGAATCTAAATAATTGGCAGTAGGGTGGGGTTGGGGAAGATTATACTACTCCTAAATCACAGGCTTTGTGCCCTTTTCATGTTAATATTCGTATGACTAT + 4<=GHHGHHHHHFHHHHHHHHFEDDBDGGHHHGHH?GH@>FFFHF9::3,;5<><<@<8/''*<>@EHEDEB:@>+=FHHHHDDF8;A@BFHEEEBFHGG @read_150_335/2 ATAGTGATTTCCTGACCTAAACTATTTGAATAGGTTGTTTATATATTAAGTTGTGCTAAGCCTAGTCTTCCCTCACAAAGGCTGTGCTTTGCTGGTCTTT + 8B=GHHHHHHFFGGAFGGI=DEHHFHHHHGGHHGGGAHHHHHHHHHHHHEGHHHHHHHHHHGHHIGHHHHHFHHHHFH@@HHHHHHGEEED97163 @read_150_336/2 TGAATCTCGACTGAATAGTTCCCAGATTCAGGTCAAACAAACAGAAAAAAATATGCATCCAAAGGGGAAAAAACCTGTTACTCCGCCTCCGCATAGATCG + HHHHHHHGG=67211CGHHHGGGEA67=;;EE998GGIE@<.EFDGGHHH;(4:()+?*4AEEEDAE@GFFFFB @read_150_337/2 ATAGTGACAGAGTTTTTTCCAACTTGGTTCCATTCTCCCCATCACTTTCAGGTACACCAATCAGACGTAGATTTGGAATCCATAGATCGGAAGAGCGTCG + GDCDEHHHHHHHHHBB=?7@GFHHHHGEEBE?FFHHHFEHHCEAFHHD406><4478>DEGFHGFFBFCFFGGFHHGHBBBEHHHGFBHFFCEEF1>CHH @read_150_338/2 TGAATCTAATTTGGGAAAACAACTTTTGTATACTTAAATTTTACATGTTTTTTTTTTTCCATTTCATTTCATTTGAAAGTCCTGAAGTAGATCATACTTC + HHEHHHHHHHHHHHHFEFDHFEHHEHHFFFHEGHHHFBE2@EHFBEEFHHGHHHHGFF=BFFGDGFHHHHHHGGGG@24,,;AEFE5>,-%;4GFDFHFF @read_150_339/2 TCGCTGCTCTTAAGTTTTGAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAACACAAAAAAAAAA + EEEEEEBGHGBGFHHHHFFEHHHGEE@<9GDC5FHHFHD=5@GEBE=CFGHHHHGEHHHGHHHHHHHHHGFHHHEHHHHGDDB?H>-)2.1<14FHHHHH @read_150_340/2 TGAATCTGATGTTGATAGATGAAGAGACAGGAAGAATTCGAATTTGTCTGGGACTCTGGAGTTCTCACCCTGCCCCTTACATTCTATATTTAACATCAAA + GHHHHHHDEFGHDHHHHEEGHHHHHHGFGGHHHHHHFGGFHHHHHHHGFGGGGHFHHHHHHHHHHHHHG4:@CCFHFFDHHHFHHHHBEHHEFBDHHFHH @read_150_341/2 TGAATCTGAAGTCCGTACATCAGTAGGCAGGTATGAAAGTGGCTTATGTATGTAAATATGTTGCTGTTATTTGCTTTGGAAATTTGTTGTCTAGCTTCAG + >=DGHHHHHFFFHHHHHHHHHHHGEHHHHGHHBHB'9<2+-=EFEHHB?BEGGE;EB?GHHHHHHFHHHHHEDEHFFBFGHHHFFD2<>D=C@<.:5?-68DACGGGHHFFF<=GGG@>?82-2,5=3*6AEGFGGEGFHFEHHHHFFEFHHH? @read_150_344/2 TCGCTGCGGCCATTTTCACGGTATTGATTGTTCCTACCCATGAGCATGGAATGTTCTTCCATTTGTTTGTATCCTCTTTTATTTCATTGAGCAGTGGTTT + HHHFDBEGFHHGFFFGGEEFHHFDHHHHHHHHHHGHHHHHHHHH9':?DB=CD=94?DHHGDEFFFHHHHEIEE@5>,7BEEEDEBDBCEGEEHFCCD170)4?CD@CFHE @read_150_347/2 TGAATCTGAGTAGCACGGGTAAAACTATACATTTTTTACTTAATGTAATATCCTAAACATATTTTATATAGCAATACAATCTTGAAAAATCATGCCTTCA + DHHHHHHHHHHHGHHHEGHHG@DDDHHHHHHHHHHHHHHHHCCDGGFBGEHHGGGHHHHGGHHHEDEEBEDD4983.< @read_150_349/2 TGAATCTATTCCTATTTGGCCATCTTGGAACTGCCCCTGCACTGATACATTCTGACCTGATAATTCTAAATTTGGGAATTTATCCCAAGGAATGAATCTT + 50-316:5/BGFGEEGHHHHHHHHHHHEDHHHHHHHHHHHHHHHHFFFFB??6DEHHFHHHHHHHHHHHHHHHEHHHHFF@673,888.8GBEFE>1779 @read_150_350/2 ATAGTGAGAGAGCGAGACCATCCTGGCTAACACAGTGAAACCACATCTCTACTAAAAATACAAGAAAAAAATTAGCCGGGCGTGGTGGCAGGAATCCATA + HHHHHGHHHHHHHHHHHHHHHFBC@>>3BFHHHHHHHHHHGFHHHHFABGADCEFHHHHHD@FGHGHFHHGFHHHHHHFHHEEE=;<4988.< @read_150_351/2 TCGCTGCTCCATCACTCCTCTCATTGAATCCTACATTTCTCAGCTGTTGCACAGGTACCTGCTTCAGCTACCCTATTGCATGGAGCAATCTATTGAATGG + HHHHHHHHFFHEHHHHHHHHHHHHHGGHHHC>DDDFFGEFF?A,2'38'/6?.DCGHHGFEFEGGECBGGHHFFEHHHGGEHEFEFEDDGFHHHDB@993 @read_150_352/2 ATAGTGAGGCTGTTAGCATTTAAGTTAATGCAACTTGAGAAAAACAAGGGGAGTTAAAATATCATGGAGGTGGGAATGTTCTGAGTCCTGATTCCATCAG + HHHHEHEEDHHHHHHHEGGEDGGEGGEE/FHFGHGHHHFHHHFEFHHHHHHHHHHHFDDFCABGGGHGGHHHFHHHHHHFGHHHFHE?AA>7ACD?FBFG @read_150_353/2 TGAATCTCTCGTCATTTACATTAGGTATTTCTCCTAATGCTATCTCTCCACCAACCCCCTGCCCTATAATAGACCCCGGTGTGTGATGTTCCCCACCCTG + HHHHHHHHGGDCGFBFHHHHHEFFFHHHHHDB2;FHFGFHHFHHH@>?CC@A@AA26BCHCBDFHHHHGHGG@>>:@EHHHEHH5CFFHFFFEEDEGF=@ @read_150_354/2 ATAGTGACAAGAACTTCAGTAAGAAGAGAATGAATTCAGGGCTTTGCACATGAAGCCAAGCAGATGCCTGTGTTTACAAATAATAAACATAATGAAAAAT + HHHD9.@>BEEFHHHFAEDHHHHHHHGFFB935BCBEGGHHHHHHHHHHHEGGGEFHDE>FHHHF=5;@:9;5CC;?97AEEEEHHHHEEGGGHBBGIFF @read_150_355/2 TGAATCTACCAACTTTATTAAAACAGGCTTGGAACATTTTTCTCCATAGAAGAATAGTAATAAGACATTCTACATTTCCTGGACATGGCCAGTTTAAAAT + BBCGGFGGGHHHGGHHHHHHGEGAGHHHFHGHHHHHHFHHHFHHHHHHHHG?A@DEF8EGGHHDGH?@C>FDEE@DCCA=A@BFHHHFDGHH?EHHFEGF @read_150_356/2 TGAATCTCAGAAGAATTGCTTGAACCCAGGAGGCAGAGGTTGCAGTGAGCCAAGATTGCGTAGCTGCACTCCAGCCTAGGTGACAGAATGAGACCCTGTC + HHHHHHHGHHHGDGFFGHEHHHHFGEBGHFGFAADHHHEHHHHHHGGHGEFEEEEGHHHHHHHHGEEHHHGC>8EHHHFEDBFEFE;,1,117:>DEE99 @read_150_357/2 ATAGTGACATGCACATAGTCACACACAGACCCACACACAAATGTACACACACACACGGACCCACACACAAATGGACACACTCACATATGTTTACTGCCAC + EDG8EB=.1-EE?./-266>9DDB=DDHHHHHHHHHHHFHFHFBFHHHHHD41'+/B?@<9= @read_150_358/2 ATAGTGATGAATCGGCTTGGCAAACATGCCCTCACCCACTCCTTTAGGGAGTGTAGCAATGTCTGCTTGTTACATAGGAGAGAGCGTCAGCTAGATTGCT + HHHHEFEHHGHHHHBGFGEEFDHHHGEBHHHHHFHGGHHHHHHEG52>4B @read_150_359/2 ATAGTGAGTTCATTCGGATGCAGGAAGTGAGGAGGAATAACATGAAGGGGATTGACCAGATGCCTCAATTCTAATCAGCTGAATGGAGATACTTATGATA + HHHHHGGGC.EHFHHHHHHFHHHFHGHH;FHEHHHHGEAFDA?AFHFFGFHHHH@DD.<9EHHFCDG@??88EEDFEHHGHHEBFCC=DFHHHHHGBGGD @read_150_360/2 ATAGTGAGTGAGGACCTGCACCGGCCCCGGTCTCTGAGTTCCCTCAGTATTTATTGATCACTATCTTTACCATCTTGGCAGGGGGAATGTGGTGTGACTA + HHHHHHGD?7.1DFFFGHHHFFBFHHHHHHHHHHHHHHHHGE<5DD:9.<<;HEHFHHHHHHHHHHHHHHHHCEEEHFIGGHHHEHHHFEB=EHHDEHEDD=6:7><95GFHFBFECHHBDEBCEHH @read_150_362/2 TCGCTGCCCTGGAATCCCTTCCCTTTATCCCCATCTTTTAATCCATCTTGTAAATCTTAACCATCCTTCAAGATCCAGGTCAAATTGCCAAGTTTTGAGA + CB@CAD>CD@<;6>>EDDDDFFHFGEEGBDGGFFBFFF4@CFBFFHHHHHHHCEDECDGIF?@AFHFFECB @read_150_363/2 TCGCTGCTAGAAATCTTTTAAAATAAAATGCCTTATCACTTAATGCAGTTTTGAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTC + DBHHHHHHHGHHHHHHHFGEEGHHGFHFHHHHHHHHHHGHEGGFDFFHHBEEHHHHHHHHHHE:53=DEEGGGEHFF=BE:F=B.=DBFF4>>>)<68<7 @read_150_364/2 TCGCTGCTAATATGTTAATGCCTTGTAGTACTTTATGAAAATACTCAGTGGTTGCTTACAAGGTGAAGCAAAACTTGGCCAGGACTTTGCAATACCCAAG + HHHHHHFHHHHHHHGDHHHDEFHHHHHHHHHHHHHHHHHEFB?:>A@@5CHHHHHGGGFFGGGGGFFHFHHHHFHHGGHF>.A=DHGHBHHDHFGHHHHH @read_150_365/2 ATAGTGAGAGGGGATTTGGGCCATGTCTTTAGCAGCTCCCAGGAATAGTGTCTATCAACTGTAGAGTGACTTCTCGTATATTGTTTTTGGCCATCAGGAC + GGEHHHHHHDDHFEHHFFHHHHHHE>66A=GBDGGFFEEEEG=?8EDBDHHEGFHFFDDFHB&&/%3'/B=<>6AC?>9BFF @read_150_367/2 ATAGTGAGATAGAAAATATAAATCCCCAGATATCCTCTTCCCCTGTCCAAGGGCAAAAGATGACCAGGCCTAGGGAGGAAAGACTCCTGTACAGTCTGGT + HHHHGEFGFEGGGHHHHHHHHFHHHHHHHHHHHEBEEDEHHHHGDE?D>8CEEGGFEB5>7=>BGHHHFFHHHHHHHHGHFHCC<>'9?;=3,+9<6D8D @read_150_368/2 TCGCTGCCGCGTGTCATTTTTAATAGATGTGATTACGGTTTGGAGTCTGATATTCTGGTAATTATCTTCCTGGGCTTAATCCCCATGCATTTTAGAGATC + HHHHHHGHHHHHHHHHHBGFEHFGHHBGFGDEB>>A7::HHHHHHHHHHHHHGGGHHFGHGGE8FFFHIFCGBC=DEHHHHD.70-64(*=>7'E@ABBD @read_150_369/2 TCGCTGCTCATTTGCTGTCCCAGTAAATGTCCTTTATAGCAAAAGGATCCAATCCAGAATCAGACAGTGCATTGAGTTGCCTTATCTCTTTCATCTCTTC + HHHHHHHHHHHHHHG=DDABGHHHHEC@=GHEGHHHFFFDHHEEEEGCBDCBIGEGGEEHHHHHHHHHGGGGHHHHFHHHHFHDAB9AEHEBGHDHHDHH @read_150_370/2 TGAATCTTTTTTTAATTTTTTTTATTTATTTGCGATGGAGTCTTCCTCTGTTGCCCAGGCTGGAGTGCAGTGGCACAACCTTGGCTCACTGCAAGATCTG + GFFHGEBGEFHHHHHHFGEEG;=+.<--4=DHHHFFHEEHHHHHGDFHHFHHHBHGFHHHHHHHFFFHH @read_150_372/2 TCGCTGCAAGCTGAAAACCATCATTCTCAGCAAACTAACACAGGAACAGAAAACCAAACACCCTATGTTCTCACACATAAATGGGAGTTGACTAATGAGA + HHHHFBC@;>@FFDA6-,.>317CCBFHHB@DGE:>A7<@>:?GDEHHHHCIG<>EGGD/:5.:+DHHGFHHHEGGD7DHHHHB5EFHHFFHHEDDDCE< @read_150_373/2 ATAGTGACACTGTTCACAAAACTTGGAACCCAAATGCCCATCAATGATAGACCGGATATAGAAAATGTGGCACATATACACCATGGAATACTATGCAGCC + HHHHHHHHHHGB@BDFHHHHHHHHGGGGFHHHHHHHHHHHFE<,%1@,:@HFFFEH @read_150_375/2 ATAGTGATTATTACCCTTCTTTTTTGCCAAATAGCCCTGAGGAAGGTAGTCATCAAATCGAGAATGGCTAAAATGAGGAATGAAGAAGATGGAAATTACA + HHHGEEGBED9659,+6@C8<=84/GDDDDBEGGFFHHHFDBBFHEEGHHFEE1::@GD@<.7.>@796.>5A:625?F?EHHHHFGGIBCEB,B8,77B @read_150_376/2 TGAATCTTTGACTACTGCATGTATGCAGTCAAGAGGAACTTATCCGCATAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCG + CDHHHHHHHHGHHHHHGGHHGEHHHHGEECE=BCBGHHHHHG?HE;=FHFHHHGEHHHHHFHIGHHHB-.4>4A?FCHHDHDD<9;/'.?FEHEHHD6=@ @read_150_377/2 TCGCTGCAGTTCAAGACCAGCCTGGCCAACATGGTGACACCCGGTGTCTACTAAAATACAAAAATTAGCCGGGCATGGTGGTTCATGCCTGTAATCCCAG + EFHHHHHHHHHEEFBFGHHGDGBGGHHHHHH@BHHHHHHEBD=;;GGG84,ABFHHGFGEEFDGHFHHHB;CDBCE?>:>:76E8A??GEEEFEDBCHHB @read_150_378/2 ATAGTGATGAGCAGTTTAGAACACAGACTGCTACTTCCTGAGACCTGTACCTGATTTTTCCATTATTGTAGCTGAATGCTGTGTTCTCAAGAAAGTGTTA + HHHHDDHHHHHGGHGCBBGHGHHHHHAB/BHEEHFHHHHHHFHHHHHHDDDEGGHHBDDFHHHEDEHHHC@FGHHHHHHHED>(1'&)/CHEFF7EEHEB @read_150_379/2 TCGCTGCGAACAATTGTATACTAACAAATTCGATAACATAGATGAAATGGGTAAATTTCTCAAAAGACAAACTGCCAAAACTGAATCAAAAAGAGAAAAA + HHHHHGFFHHHHEGHHEHHHHHHHHHFHHHHHHHHGFFE@FHHHEGGEHFHHHHGHBEFHHFEHHF?@;.9.BEGEFF?HHHFFHDEEEGEDF<@@E6DEFGE?7?@>9>F @read_150_381/2 ATAGTGATTTGGTTGGCCAGAATTTTCCCAATAAATAGATGTGAATATTTTCCCTGCAAAGTAAAAAAGTGATATAAAAAAGTTAATAAGTCATCTAAAG + IFFGGHHHHHHHHHHHHHHHHHGGGHHH>863:9EHHHHHHHHHHHDHHHHHHHEEGHHHHHHHGGFFEEHHHHHFGGHHHFHHBEBBBFC764%587<& @read_150_382/2 TCGCTGCGTGGAGCCCAAGACTTTACTACCTTCCACCTCTTCAATTCCATAGGTCCCTCAAAAAGTTGTGATTTGTGTAAGTGTAGGAAGTTTTGAGATC + GHHHFFEHG@EFHGGGHHGGHHHHHHEGHHHHHHHHHEHHHHHFHHHHDDGGEFGHHBGHHHHHHF/EEG8:.CHGB5,%781-(*A @read_150_384/2 TCGCTGCTTGCTGTCTCCTCCCCACAAATATTATTTTTGCTACCTTAAAAAGACTTTACTCTTGCAATTTAACAGTAAAAGGACACAAATAACAGTTTTG + HHHHHHFHHHHHHHHHHFGHHHFHHHHHHHHHHHHHHHHHHHHHEGHHFHCEFGHHHHHHHGFHHHHHHHHHGEFEFGHEG@ED@EF6ECEBEC@5<><9 @read_150_385/2 TGAAACTTTGCATGAAAACTCTACATTCACCCTTCTTTCTGAACTGCTTGACCCAATCTAATTAGAAAAAAACCAAACAGATCATCATAGTCAGAAAATG + F@>,+8865@AFGHHHHHAB>>:,1'6<:DEEB @read_150_386/2 TGAATCTCTAGCATAAATCCTCAGCATTCAGCTACAGTTCTTCCTTCCTCTATATTTTCAACAGTTACTATCAGTAGTTTTCATTAGCTCCTCAAAGCTA + FFFHHHHHHHHHEHHHHH@9@C2=DHEEEGHEEHHHHHHEFFEHHHHFEGGGGHHHGHH?EFEHHHE=BCE=GGEEEFDE*ED@FHHHHHHHHD8E?CEE @read_150_387/2 ATAGTGAAACTTGTCTAATTTTTAATCAGTCTTGCAACACAAATAACATCATCAGCCCCATTTTTACTGGTGAAGAAACTGAAGTACAGAGAGGTGAAGG + FHHHHHHHHHHHDFHHHHHGEEHHHBEGFHHHHHHHGFDFEEC5<6ECCAEEFFFHFECDFFBEDGEIEEE=BCD?;?GHHDHED>7CGD559:6903;( @read_150_388/2 ATAGTGATATCTGAGATTCCAATCCATAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGATCGCCGTATCATTAAAAAAAAAAAAAAA + HHHHHHHHHHHHHHHHHHEBEHHHHHE.EFHHHHHGHBDBBCHHHHHHFGGHHHHG@EEFDE?8@-7@ABA58BHGFFFFHHDEFFHH=3,?077>@@7@B@9DA5HHEDBHHHDFD @read_150_390/2 TGAAGCTGTGGCGGGCGCCTGTAATCCCAGCTACTCAGGAGGCTGAGGTAGGAGAATTGCTTGAACCCGAGAGGCGGAGGAAGCAGTGAGCTGAGATCAT + :910&7@EEHGGEEHHHGGFA=@FE@>247>DD=7EEFHHHHHFGGCH@HHHHHHHFFHHGCF@EGBFGHHHHDDC<@;,*=GFEHEEGBFCFB2=EGHH @read_150_391/2 ATAGTGAGTGAAACTCCAAGACAAGACTGGACTGGACAAGACCAAACCAAACTGGACCAGACCAAACTAGACAACACTGGTCAGGACCAGATAAGACCGG + HHHHHGHHHHHHHHHHHBCDFGHHHHHHHHFGGHHGEGG+/BGFF9329BGGFDDHHHHF@88>GHHHDACBEA8FDFHHHHEHGHFH@CHEFDHHBD51 @read_150_392/2 TGAATCTCCAGTTAGATGGCCCTGTTGCCTGTTTTAATGGAAAAAAAAAAAAAATCTTGTACAGATAGGGTCTCACTCCGCATAGATCGGAAGAGCGTCG + HHHHHGF@GEGEEHHHHHHHHGEFDCD?FHHG>>CHHE?FHHHHEDFFFC>.976=E=EE864G,078GGHHGHHGEFFGHEEGGGB<6=5,@=D?DEDH @read_150_393/2 ATAGTGACTACTGTGGATTCTTCCCTCGTACATGATTAACTTTCACCTTGTCAGAAAGACCTTCCCTGGCCATCCTATCCAAAATTTCAACCTTCTCCCA + HHHHHHHHHHHHHHGGFECBEGE5:@E@HHHEEEHHHEHHDDA9/BFFFHHHHHHEGEGA377-)66HHHHHGBEEA71,9;>5BEBBB;A;A@DDEGGH@6337FG@BFHHEBHHHHHGHHG@<<:+)+:D2<998 @read_150_395/2 TCGCTGCTGGCTGCGGGTGGGGGCTGCCTCCAGCAGAAGGCACAGGGAACAGGGCACGAGGACTGGTGATATTGGTGCTGTTTAGCAAACTATGACTGTC + HHHHHHHHHHHHGIGHHHHHHHGGIEEFDDBEDDEGGDDDFHGEE?@>?@<%.>4BEHHHHHHHFFHHB+)6)<;E?<;64(ECCCEEAHHHHF @read_150_396/2 TCGCTGCTTAGTATCTTTTTATTGGCCAGTAGTTAAGTGTTTTACACATGTTAATTTTACCCTATAAGGAAGGTTTCATTACCCTCATTTTACAGATAGA + HHHHHHFHHHGGHHHHFHHHHHGGGHHHGEGGHHHHHFFHHHHHFHFGGCEEE@HHHHFFF8(2())4>BEACCCFEBEDDFFFEBGGEH8%*)&9;C?D @read_150_397/2 ATAGTGAAATTGTAAAGTCATGGCTGCAGTTATGCCAGCAGGTGTGAGAATCTTGTGCTTCTTGCAAAATACCTTTGTATCTCCTATTAAAAATGCAGGT + HHHHHEGFHHHHHHHHHHHHHBDH9=GHHHGHHHHHHHBHHHG>FHFEEEEEHHHDEAA>BE @read_150_400/2 ATAGTGATGAAGGGTAAAATAGACAGCAAAACAATGAAATCCATAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCA + C@@EDHGGGEHHHHGHHH@@ABFF?HE?%)0085CGGGIDHHFGEGBBA?3;::.*<<>BGGGHHHHFEHHGFHHGGGFFGHECF?GFGGGFHHB>D>/@ @read_150_401/2 TGAATCTGGCGGGCGCTAGTAGTCCCAGCTGTTTGGGAGGCTGAGGCAGGAGAATCGCTTGAACCCGGGAGGCGGAGGTTGCAGTGAGCCAAGATCACGC + HHHHHHHHHHHHDEGE>:-,%.@FDGHGGFEHGHHHHHHFHHHCEGHHHFFGGHEHHHHHHHHHHHHHHHHHHFGDGB.8:DFE9358DEEG9.=;AHHH @read_150_402/2 TGAATCTACTAAAAGTACAAAAATTAGCTGGGCATGGTGGCGTGCGCCTGTAATCCCAGCTACTCGGTGGGCAAGGCAGGAGAATCGCTGGAAACCGGGA + HHHHEEEHHHHHHHFEGHHHHHHHHHHHHEHFEHHGHHHHE.=@@E?C@:=9<77@FDDFHGBB?FHHHHHB=FHHHHHGDDFFHHH<++.95,,9C@3< @read_150_403/2 TGAATCTAATGATACTGGAAAGCTGGGAAGGCTTTTAGGAGGTAGGGCAAGGAAGAAAGATGAATAAGCTGGAGGAATCCCAAGGTAAACTCACTTTAGA + IFHHHHEGFGHHHHHEGHHHHHHGIFEEFEGHHHHHFGHHGCHHEFBHHHFEHHHHHHHGDBFHHHHHHDGHHFEHEDFFEHEDFHGBHFEFFFDDD=>> @read_150_404/2 TGAATCTTCTGCTCCACCACCATGAACCTTCTCTCTCTCTCTCTCTCTTTCTCTGTCTGTCTCTGTCTCTCTCTCTCTGTCTCTCTCTCTCTCTCTCTCT + BCCBGHHHHEDEHHGHHHHHHHHHBBFHHH>26EEDHHHHHDEGHFD@@=@4:DEDGEGHHHHHHHHDDFEHEDGEGHHHHHHHFBG?CBFDBBDBBBFC @read_150_405/2 TGAATCTTCACCCAGAGGGCCTGACACGGTGGGACCTTCAACTCCGCATAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCG + B@@@AEACHHHHHHHD@?GC@GGBBGGGDFHEEGEFFHHHHHHHHGHGFFHFGGHHHHHEGGGEHEECBFGHFFGHHFHHHHHHFD>FFD=.?HEFFFEF @read_150_406/2 ATAGTGAGACAACCAAACATGCCCAGCAACTTTTCAAACATCTCCTGGGGGATAGTGCCACTCTCATTTTTTGCTGCCAGGAAATCAGATTGCTACAGAC + HFGDB>@C@EHHHHHE.?BBGHHHHHHHBHHHE<18ADD9;>/@'<CEC<.:8DD;*)35BBB>CCFFAFGGGFFFFGFFFGGGHHHHHF?GGF5(//?FHHEEGGGH?F89CCDFEHE?D @read_150_408/2 ATAGTGAATCATAGTTAATCTAATCCATAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGAATCATTAAAAAAAAAAAAAA + HFHHHHHHHHHFFHHHHHGHFGGHFGHFHHHHHHHHHHHHHHHHF==92'<>EFFEHHHHHHHHHHHGFHHBDEE@DGGFCDADDEF;CDDA@@=EC @read_150_412/2 ATAGTGATTTAAGGAATGAATTTGTTTGTTCGTTTGTTTTTGATAGAGACCAAGTCTCACTTTGTCACCCAGGCTATAATCCATAGATCGGAAGAGCGTC + FHHHHHHGGHHHHHHHHGEFHECEEBCCB<4>.33;6<>BDEEBEHHHHGHHHHGH=GGEHHHHG:@@;?@FGEFEHHHFFFHEGG>7 @read_150_413/2 ATAGTGAAAATTTTAAGACAGCTTTAAGAAGATTCTTTTTCTCTTTGCTTGCCTTTCCACATACATACTGCAAGTTGGTAACATTTTACATAAGATGATA + HHHHHHHHF8?FFGGE@CHHGGGFHFFHHHHHFBB@BHHHHHHHHHHFGGGDBDFHHHHG=8@A=DF?<>:6.;3>F=;:..3:EEHFFF@8A@A55::>1=;%--B @read_150_419/2 ATAGTGACTTTAATTTTAATTTGTATAGATACATCAAATTTGGGATTAAATACACATTGCTCCAATAACTAAATCTTTTTCAACGTATATTATTCTATAA + HGGGE@BHHHHFBEEEGFHHHHB.ADEFHHHB.EFFDBD>8<5;70,/EHHHHHHHFEHBGGE=0-4>: @read_150_420/2 ATAGTGATGTGACAATGTCCCCAGATGATTTTAGCCCTCAGCTGTCAAATTTTCCCAGCCGAGGCCCTGGGCATGGGGGAGCAAAGATAATCCACCTATG + 7@EBHHHHHHHHHFBHHHHHHFHFHHHDFFEHHHHHHHGHF>>=88*:>C<9<>?EHHHHHHHFFEFFFHHHHHHD?<8/A?=BEFHHH;GGHFFB7FFH @read_150_421/2 TCGCTGCTAAGCTTCATAAGGGAAGGACAAATATAATCCTTTACAGACAAGCAAATGCAAATGCTGAGGGATTTTCTCACCACCAGGCCTACCTCACAAG + HHHHHHHGGGHHHHHHGGHHHHHHHHEDD8F?>67B363DFFHHHDA=@/CCA48:>>@GGHHHHHHHHHFFGFFBD-8;@@CCE0-15<:B=39>B==D @read_150_422/2 ATAGTGAATATATAATTTTTAAATAAATTTATACATAATGTTTCAGGTAACAGTACAATAAAGGAAAATAAAACTGGATAAAAGGACAGAGTTTTAGGCC + GD86DFFGGEHHHHHHGGGHHGHHHB@EGHHHHHHGG@>FFFHHHFFBEHFHHFFHHHEHHHHHHHEFGGHFBEF@@BDEHHFFFGEGG;):.-3>.?%' @read_150_423/2 TCGCTGCATGATTGTGAGGCCTCCCCAGCCAAGTGAACTATGAGTCCAGTAAACCTCTTTTTCTTTATAAATTATCCAGTCTTGAGTATTTCTTCATAGC + DEE=8FHHFHFEHHHGGHFD>>FHHFD99?FGBDHEBFFHFHHHHGEEA:@EEHHHFHGFGEEFEFFHBEEGDA;EFHEEHGFFEEHF>BCAC;@AAEFB @read_150_424/2 TCGCTGCGGGCCACTGTGTCTAATCCCATAAGACCCAAGAATACCAGGAGTAAGTGAGTAGTAGAATTAATGCTGGCAGGAATCGGGAAAGAGTTTTGAG + <>@DBBCDDC4*06)>BHHHHHHHHGEFHHHHHHHHHHHD=??0C=GFEFHHHHHHHHHHHHHHHHHHHHHHFFEEEHF8@EGFE37)(.=+:-0BGECA @read_150_425/2 ATAGTGACAGAGAAAATAATATGCACCCAGTTCTCCAAGAGCTCTCTCCACCCCAGCACTGGGCCCCATCTTTCTACTTACCGCATTTTACCTTTGCTCC + HHHGHHHHHBEFHHHHGHHHHHHHHHHHHHHHHHHHHHHHHFBFHFHEHHHFFEEGHHGEEEHEHHFFGHFHG.*+.>@8>>2(3'33@8@EHDHGGGGH @read_150_426/2 TGAATCTTTTCCTGTCTTTCTGTCATAAGAGTGATTTGAAAATGATGAAACTTAAATGACTGTTTTAGTTGTATTATAATTCTAGAGTTCAGTCTTGGTG + HHFGGGEHHHHHHHHH@HHEFEBEDHHHHHHHGFHHEFE=BFHHCFFFHFHHFGGHHHEFHHFFHHHGG;?CDEBFFEEC:@,:.%-<@;6-7,,5:;>F @read_150_427/2 TCGCTGCCAGTCTCTAGAGCAATCCTGTCTCTTATTGCCACACACTGGTGAGGCCAGCATTGTCCTTGGAAGAAACAACTTCCCTAGACATTCCACATCC + HHHHHHHHHHHHE/CHHHHHHHHHGHHHHHDHFFEHHHHHHGHHHHHHHHHE=;:CFHHHHF@C@HHHHE.'6=<-)34;>4 @read_150_428/2 ATAGTGAAAATAGTCAACCGGAAGTACTTGTTGAATAAAAATATTGACTGAGTGAGAAAGGGAGGCTCTCTACCCTCATGGAGCTTATGTATGTAAAGGA + HHHHHHHHHHHHHHHHHHHHHHGGCDFGHHHFFHECFHHHHHFFGHHHDEEBIGGHGGGHGHEFHGHHHGGDFGHHFHHHHHHHGFHHHHCCDDHHEE?D @read_150_429/2 TCGCTGCAACACTTGGATACAAGTAGTTTTTTTGGAGATGATCCGTGGAAGCGCCAATGAGGAGTTTTGAGATCGGAAGAGCGTCGTGTAGGGAAAGAGT + GGHGHHHHHHHHHHHHHHHHH<66-AFCHB;B.B=26:5>DIB=GGGHH?GEEEFC>GDHHHHGHGHHHH=DEHHHHHHHFGAA?AGGEE=A;5968EEH @read_150_430/2 ATAGTGATACTTCCTGGGGTGCAGGAATGTCAGGTTTCTGTTCGGTGGAACATGCTCCTCATGGCACAGAATTGGCTACATGAAGTTAACCTACAGGCCA + HHHHHHFGECHHHHHFHHEFE@@EBGGHG89?;@;7-224(<,04@;;A;9826.)7GHHHHHHHHHHHHHDECBHHHHHGHHHGFFFGFEE<@HHHEEE @read_150_431/2 TGAATCTTGTGCCTGATAGAACTGCGACAGCCAAAAAATCTCTTTTCTTCTCTAGATTTCTAATCCGGGTCTCTCCAAGCCAGCCCTGAATGTCCAGGAT + HHHHHHHHHHHHHHHGHGDEGFHHEHHHHHFCHHFFHHFEGHHGGHHFGB@@?<@7*)2A>DBGIGF@HDD=G==EEHHHHFHHHHHHEGHF?FGB,3,: @read_150_432/2 TGAATCTCCCCTGGCTTTGTTATTTGTCTTTTTCTTATTGAAATTCTAGGACCTTAAATATATTTTTGGAAGATATGTTGACTTTTCATCAGAAACACAG + DEEHFDFHHHGHFHHHHHHHHHHHHHGEFGHHHHHHHFHFD9-DFFFGHG@DEFHHHHHHHF=<@DFEE>CFHHHHHHHHHFFEFGF;EECAEEEFHHDC @read_150_433/2 TCGCTGCAGTTTTCTTTTTATTTTAGTGGCATTGCTTTTAGTATTTTCTATTAAGCATGATGCTGGATTTGAAGGAAAAATATACAATTCTTATGTTAAG + HHHHHHHFEGAEEHHHEEEG>.5:.GHHHHHHEFDBEGBEGD=FHHHHGEFGFBB@EEG>BFFHHHHHHHHHHHHHD74459AB?ECDFHHHD@FB>5=. @read_150_434/2 ATAGTGATGCAGCCTTGACCTTCTGGGTTCAAGCAATACTCCCACCTCAGCCTCCCAAGTAACTGGGATTATAGATGTGCACCAACAGGCATTGCTTTAA + HHHHHFGHHHHHHHHHHHHHGHHHHHFHHHHHHHHFFHHHHHFBEHHHHHGGEHFFFHHHHHHHFGGFHHHHGHHHHHHHHDHHHHHHF@+6+<>>ACFH @read_150_435/2 ATAGTGATTCTGCCATGCTGCTCCCATGTCCCCCAACACAGAACTTGACCACAGAACTCATCACACTATACTTCTATTTTTATTTCTCAATCAATAGATC + <8:<@C89:6>=DGGHHHHHHHHHFHHFEFGHHHCHHHHCBE>77C?EHFGDGGGHHHHHHHHB@FGEGBFHHHE(;<>.<>ACGHE?>>.6'*5<(76: @read_150_436/2 TGAATCTGGCACAGTGGCTCATGCCTGTAATCCCAGCACTTTGGGAGGCTGAGGCAGATGGATCACCTGAGGTCAAGAGTTTGAGACCAGCGTGGCCAAC + DDCBFECC:@EEC@6HHHHGEHHG@3@EHHHGGFFC/BHHEBF7ACCDBA06<<==3-3/C;8DCFHHHHD?FGB@EEFFHFEEEBHHHHHHHHHHFHEHHHHHFB@E?D;E5AAD @read_150_438/2 TCGCTGCGCACATACTTTAAGAACCAGTCCCGAGTTCCAAGATGGCTGAATAGGAACAGCTCCGGTCTATGGTTCCAGTTTTGAGATCGGAAGAGCGTCG + GFFEE@<>:.-:>>FGEEGHGHHHFHHHHHHHHFCFFHHBFFFHHHGE/6BFGEEHFFGGCEDHGHGEGFHEG?HHHHHHFAEG<=DHHGHHGEE @read_150_439/2 TGAATCTATCACGCCACTGCATTCCAGCCTGGGCGACAGAGCCAGACTCCCTCTCAAAAAAAAAAAAAAAAAAAAAAAAATCCGCATAGATCGGAAGAGC + HHHHHHHHEEFEEBED8FHHHHHHE.7<> @read_150_441/2 TGAATCTCAATCCCACTAGGTAGGGATTATCACTGCAGTTATATAGACAAGGGACCTGTGGCTCAGGGAGGTTAAGCTACTTGCCAGATCTCATGGCTAA + HHHHHHHHHHHHHHHHHHDHHHGGGHHHGHHHHHFCDFHHHHEHHHHHDHHHHHGHHFGHHGB==DGA@<35=@EEHGDDHHH=FG0030-<@-56AC@CEFHHHHHFEEGGDFHHFHHGHFFHHFF23BDHHHHHHHHGHHHHHG=ADHHEHFC1==BFGE6);FDDDFEEEHFBDE+3(%'91 @read_150_444/2 ATAGTGAGTAAGTGTTTCTTGTGAAGGAGAAATATTAAGAAAAGTAAAATAAACTTAAAATGAGCCATTTCATCTTGGAAACAAAAATTGGAGGTGGAGA + GGGEHHHHHHHGGBEHHFGHHHHHBGFHHHE@FDFHHFFGGEEHHHHHHHHDDDDCC66@4<:D>0(-)05EFDEB4DDHHE?,/9ACEEHDCHH?DC>'/ @read_150_446/2 ATAGTGAAGAATATTTAAACCAGTAATTCTCATCCTTCAGCATATAACAGAATCACCTGGGAGGGCCTGTTAGGCTACCGACTGCTGGGCCCCGCCCCTA + HHHFGHHFIGGEHHHHHHHDDEGHHHHHHHFGFHHHHHHHHHHHHGGGEFGIGHHGHHHHHFHGHHHHD@FHFHHHEHHHHHHGHHHHHGFHD?HHFGEC @read_150_447/2 TCGCTGCCCATTTGCTGAATGCCTCCACGAATGGGCAGGAGATTGCTATGTTGTTGCATGTCACACTGAATTTGGCCAGCTTCAGAAATTCCCTACAGAA + HHDBEEEEEFHHHHHHFFHFHHHGD:ADEGHHBFGHEEEFB>CCGHHHHHHHHHHHHHHHHHHEE4=:><9>HEGD@GHHHFBBHHHFFFEHFHGHHGDE @read_150_448/2 TCGCTGCAGATTACTTTGGTTCATAAGTATTCTCTGGGAAACATAAATGTGAAAACAGAATTTAACTTTCTGGTGTACAAATAACTTTCTGCTTGTATGA + HHHHHHHHHGHHHHHHHEEEDEE8><CABGIGF?GGFBE;>GEHHHFHHEHFFHHGEGHHEEFB=GDEBEG*.@A9@@<9187BEHHHHGHHGHGDE9>EE @read_150_450/2 ATAGTGAACCCTCCATCTGCTCTTCTCTCAAATCCATAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAA + @GFHHGEEHHHHHHHHFE?DDC<>BFFHHHHHHHHHHHHGGHHHHHHFHHHHHHHHHHHHHHHHHHHEHHHFD7B85D=C6,<<('2,=EGGD;>:106( @read_150_451/2 TGAATCTCATTTGGAGCACTTTGTGGCCTTCGTTCGAAACAGGTATATCTTCACATAAAAGCTAGACAAAAGCCTTCTCAGAAACTTCTCTGTGATGATT + HHHHHHHHHHHHHHHHHHHHGDDB7618GGDFHHHG@B@A4?8>:>/-4=6@FCHHHHA9A?C><>3&4(120;EB@CC @read_150_452/2 ATAGTGAAAATGAACAAAAGAGAAAAGATAGGAGAAATATTATAGAGGTAGAAAGAATCCATAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATC + HFHGHGHHHEEFFFHHHHHHHHGGHHGGHHGGGHHHHHHEHHEHHHEAD+219--3-;7B;9>@EBGGGHHHFEGHHHHFB/6EFFHH51>>59;C,.?B @read_150_453/2 TGAATCTAAACTCGAGGTTTGTGTCGGGAAGGGGAGATAGAGGAGCAGGTGGAAAGTCTTGCAGGGCACATTGTCAAACAAAGCATCAGAGGCTGCAGGC + HHHHFHHHHHHGFHHHHG=5DFGHHGHHEHHHHHHHFHFF@6D=C@HHHHHHHHHFFBHDHHHHHHFHGBFHGGEEE?FEBFFFHHHHHHBA;1? @read_150_454/2 TCGCTGCAGGAGATACCCGGTTAAGAATCCGGTCGGGGAGGTAGGCTGGCCCTTGACATGGATAAGTCACAAATAAGTGGCTTAGGACTCCAGGAAGATA + =FHHHHHHHG<<<?@@EGGEFGFHHFCCFFF @read_150_455/2 TGAATCTGCCCTGCAACTACTTCAGGGAGAAACTAGCAGGTGCCCAGAAACTACTTTCTGCTTCCTCCCTGAAGTAATATGTAAAGTACCAACCACAATG + FD@/*3CBHHHHHHBGD=CCGEEEF@?BB@@EHHHHHHHHHH;<@>;-16/BDB@@16.5G9687D=GGHCCB>=G>.<<4>C@HFBDCHHHHB:+7:'6 @read_150_456/2 TCGCTGCATGTTAACAGAATAAATTTGAAAAACCACAAGATCATTCCAATAGATGCACAAAAACCATGAGAAAAACTTCAACAACACTTGACAATGAAAT + HHHHHGHHHHHFECHHHHHHFHHHHEEEHHEEHEHFBBFHHFHHGGEEFGHHHGHHFF>EGHHHEHHHHFGEDFCEBEEEE=D>:6EFGFEBEHHFFFEB @read_150_457/2 TGAATCTCATGCCAGACTTTGTTTCAAAAAATGAGTCAAATGAGAGACCGGCAGAGTGTGTGGCACCTGTTTTGTTGGCCTGAATCACAGCAGAGGTGAT + DDGEC:=@BBGDACCHHHHFGGF?DBEEED@@CDFHHHHHHHFHHFGGEEHHG@>@.@CFGGGHEGGGGG=>9968<;GFFHDDDA=DAA58FHHBEEHE @read_150_458/2 TCGCTGCTTATGCCCAGAAAAATCTACTTTAAAGTATGAATTGCTTCTTGTATCAAAGCACATACAAGTTGATTAGCAATTTATGTTCTATGTTTAGCAA + HHHHBGGGHHHHHHHHHHFHHGHHHHHHHHEFEBFHHHHHHHHEEEHHH?C>9705:7B=BADGGFHHGEGEGB;3&67(D?EBHFFGGDBDEHF?@DCE @read_150_459/2 TCGCTGCTTAAAATAGTAATCTCTTCCTAAAAATTCAACAGGTAATTATTGTTTGGTGAAAGAATATACTTACAAAACAAATTAATAAGATTACTTTGTC + HBHDD=EDGFHHHHHHHHFGGEHFGFA5=C>76HHGC7DFHHHFEHHFC-:5?@EGHHHEGFHEHHHHHHHHHHHHHHGEGD9>>E;:>?FFHHHFDA4D @read_150_461/2 ATAGTGATTTGTTAAATGAACGAATCTATGAGATGCTTCCCATGTGCAAAGTAAGGTTACAGGTGCTTTAAAGGTATTATTTGTTTTAATACTCACAATC + HHHHHHHHHGDDGGGFDGGEHHHHCDFFFHHHHHHHHHHHHF=C@.743-8DFEF@CCFHHHGDC=GGHHFFEEHHHHHHHHHHFGGHHHBCGHEGBHHF @read_150_462/2 TCGCTGCTGCTGAATTCCACCAAACATTTAGAGAACAAATATCAATCCTCCTCAAACCAGTGTGAAATATAGAGGAGGAGAGGATACTTCCAATGACATT + HHHHHHHHFHHHHHHHHHHHGHFGFHHFF65+1%EIG?<2,6.9(+)+33>>8DDHHHHHH@8DFHHEEA>6:ACC6GGG?0&>DEED:>@B>>DHE?B @read_150_464/2 TCGCTGCAGGCTACATCTTGGGGAACAAAAAAAAAAAAGAAAGTGATAACTAGTAATAATTTGAAAAAGTTATTTCAAATATACCTTAATGTTAAAACAG + =GGG@:=@BGFDHHHFEFHHGF?BB516=FFE=DDFFEEFHFHFHHFHHHHHHHHHHHED>@DDDHHHHHHHHHHHHHHHHHFGFF@=FFGEHDGFFGAE @read_150_465/2 TGAATCTACGTGACTCTCCTACATTTTCATCACATTTTAGTTATTTTCCATATCGATAGTTGAAACTGTCCTACAACTTCAGGGCTATAGCTATTTTTTT + GECDDEEHHHHHHHHHHHHHEEEHHHHGGGHFFFGBBGE@FHHFHHFFHHHHHHGHGHHHHEDDEFFHHHHHHHFHHHBHHH=DDEAGFEDB:;1><*,9 @read_150_466/2 TCGCTGCAGAAATAGCCACTTGTTAGGCCGAGGAAACCACCTGGGGTTCTGGCTGGTAATGAGCCTAGGGCATATGGAGAAATGTGGAGAGATTAGGAGG + @EHHHHHHHHGG?FHHBCCDHHFD5=EHB/><&'7,:=DHHHHHCCGDHHGGHHHHHHHHHHE8HHHHHHHHHHHHBDD@E7*1-.CF5FG@:635DHED @read_150_467/2 TGAATCTTATTAGCCCTTTGTCAGATGAGTAGATTGCAAAAATTTTCTCCCATTCTGTAGGTTGCCTGTTCACTCTGATGGTAGTTTCTTTTGCCGTACA + HHHHHHHHHHHHHEEFHCDEHHHFF@::;93.>@D @read_150_468/2 TCGCTGCCTGGCCCCAGGCCTGGCACCTGAGGTGTTCTGTCTGTCAACCTGAGCCTGGCTGGGAGCTGGGACGGCTCTTTCACCAGGCCTCTGGAGGAAA + >1-0+GGIHHGHHGEGC54=ECEHHCDC?HHGFHHHHDFAFC@GHHHHHHHHEFFHHHHHEEGGGGF>BA0CB@EGHHFAC8DAFHHFFA=FGFFEGFEE @read_150_469/2 ATAGTGACTTCTCATAACCATTAATGGAGAGAACTCCATGTGACACAGTAACTAGAGGGTAAGACTGGACCCACAGATGTTTTATATGCTATACAGATTA + HHHHHHGHHHGGEEDHHHHHHGHFFHDD8FHHFFEHFHHHDGHHHHHHHHHHHHB.55G8>C7FHHHHFHBFHHEGFFBHEAD=BHHGFHGBEC@@EBEG @read_150_470/2 ATAGTGATCTTTTTCCAACCAAGCAAGCACTAAGAAAATTCATTACCACCAAATGAGCTTTACAAGAGATCCTTAATAGAATTCTAAACATGGAAATTCC + DHHHHHHHDGGHHHHHHH=BDGEB??DEFHB<7;&>-:>;;9>@EGGHHHHHHEC=DE=B??C?BGGD4@DFEE:<1'-*)--5,DDF@,0*DCA:@('' @read_150_471/2 TCGCTGCATCATAAAAGAAAAATGATACATTCAACTTTATAAAAAGTAAAAACGGCCGGACACAGTGGCTCACGCCTGTAATCCCAACACTTCGGGAGGC + HHHHHHHHH71757@+-18BHGFFFHHC5AEFGHHHHHHHHHHHHHHHHGGHFGGHHHHHHHHH?DGGFFFC:.?:?DDCFGGGDC9;61)842:EHBBG @read_150_472/2 TCGCTGCGTAGCTGGAACTACAGGCACGTGCCACCATGCCCAGCTAATTTTTGTATGTAAAGTAGAGACGGGGTTTCACCATGTTGGCCAGGATGGTCTC + HHGGGHHHHHHHHHHHHFGGHHHHHFGHGEG@GF?HHHHFGEEHHFGGEEG@B;>)',*(.@6DEGGGEFGEHHHHHGEHHHHHHHGEGGGHHH?CEEC? @read_150_473/2 TGAATCTGTCCGCATAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAAA + =CFFFHHHHHHHFEEGDEECBGHHHHHHGGEHGDC:7>=>EHHHGFHHHHHHHGGFFHHH@:@EBE?9>8D=>A@>FFDHHHHHG?;<<<8-6@;EDDDE @read_150_474/2 TGAATCTATCTCGAGGCATCTGGAGCACCCACTCTCCTAGATTAGGAGCTTAGGCTCCCCTCCATCCCTAAGCAGATAATTTAGAACCGAGGAAGCTCTA + HHHHFEHHHFHHHEEGHHHDGCDEGHGHFF?DDFEHHHHFHHHHFGGGHHGFHHHHHHEEHHHEEGGEEFEFF:7@CF,+5<:>5=:89=DCHBFHHHHH @read_150_475/2 TGAATCTGTATTATATATAAATATGTAAATATATAATATAAATATATAAGTATACATATATGTATATTGAAATACATGTATGTGTGTGTATATATACATA + /33952-1@>DFGCDBBE,BEEDE@@8AEHHHHHHGCCHHFBHHHFCCB9=:=FDGHHHHHGGHGDDF@E3/5&2?>>FF?FGB?FEEEEBFHHEEHHHG @read_150_476/2 TGAATCTCCCTCCTACTCTTCACCAGTCTGTGTTGGGGCCATATCCGCATAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGGGGATCTCGGTGGTCGCC + HHHHHHHHHHHHHHHHHHGFCHHHHGHFFHEEHHFFHHHHHHHHHHHHHHHGHHHHHHHDHHHHHHHHDGDFCE@75C9<50'-5>@CDD@@GFFHHHFH @read_150_477/2 ATAGTGAGCACTCCAGCCTGGGTGACAGAGCAAGACTCTGTCTCAAAAAAAAAAAGAATTTATTCCGTCCCAGCTAATGCAATAACACAAGAAAAGTAAA + HHHHHGFHHHHHHHHHG>@A@GGHFHHHFHHHHGEEHC96<: @read_150_479/2 TCGCTGCAGCTAGTCTGGGATCCTTGAGGAACAGAAGTGGGATGCTGGGCTTTGTGCCTATGCAGGCAGCGATATCATCCATGTAGGCAATGTCGTCAAA + HHHHHHHHHHHHHHHHHHGFHGHHHHHHHHHHGGGFFBFHGGEHFHHEB/18:4A>;,,:AGEEH @read_150_480/2 TGAATCTTCCGCATAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAAAA + C=B8@<-CFHHHHG;DHHGFGGHHHHHHFDDD@GFHGGHH=DAE@B>ABBBDBCCHDEEIDGHHHHHHHF@7,)<@01;@?AD@@EEHHHFHCFFBHHDE @read_150_481/2 ATAGTGACCCAGCACCCAGTTTTCAGTGTCCTTGGAAACTTGGAGGAGTTCTGGGAAGGTGATAGGAAGATAGAAGAAGCCTTCTCCGAGCACCCAGAAT + GHHHHFHHHHHHHHHHHHHHGB<=?DBDGECE*9>BDFBCHHHD@37CEEFGHGGGEHHHHC83@EHHHEG?@;D==@:7CB;@@EFGHHHHHHHFADDE @read_150_482/2 ATAGTGACATTATTGTGGTATATTTGTTACAATTACTGGACTAATATGATACAGTATTATTAACTGACATCCACATTTTATTCAGATTTCTTTAGTTTTT + HHHHHHHHHHHHHHGBBHHHHHHHHHHHDEFGGDEHHHHHHFDGFFFFE6362()2//+=@;1<:BFGGEGB;BBE9<EFEFHHHHHHHFHHFECC;7FFGGHHHHFCDGHHGHHHHHHH@7(>>07@CFFFHB8@=<5:D?E?EGGG @read_150_484/2 ATAGTGAACAATACTGAACTGGGAGCCTCTTTAACCAAATAGATTAAGATGCTCTGATTGTCATGATTCAGATTGTCATGATTCTGATTGTCATGATTCA + >5-86@?88EE84485?FGGHHHHHE=EBA.<<0?@D@BCFHHEGFAD:BEEEHHHHHHH6/CCHGI?<>9AFFHHHDGDHHGFHBGB@FFGABBFFEGHHHHFHHHHCAGDECFHHDEDEEFHHFDEF??BDEE4:>6EGHHHHHBHHHHGGFFG?:>C>>@B=:=8ABBFGDGE/BFIGEFFEFFF@GEGEE?ADDC8:>GGGGCDC @read_150_488/2 TGAATCTCAAAAAATTCATTTAAAAATTCTTTATTTGATAAGTTCTGATATCCTCTCACTCAATAATCAAGGAACTATTTATTAGTAATTAACTATTGTA + /5<..CCFFGHHHHHHHHHHHGGEEEDD@HFGGHHHHFFGGFE6));DHGHHHHHHFE@?C5741&5BEGHHFFGABAEFHHEHGFBDF @read_150_490/2 TGAATCTGACCTCGTGATCCACCCGCCTTGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGCCTGATTTTTTTTTTAACTACCAGA + DGGHHFHHHFHHGHHHHFHHHHHHHHHHHHHHHHHEFGHHGEFFDDC@BHFHHHHGGHEFHHHHFHHHHHF8DEGEBBFEHGEGFHHBGHFGHHEGE:AD @read_150_491/2 TCGCTGCAATTCTCAGCCCATCTCAGGTCTAATTTAGCTCACTAAATTAGAAACTTTGTGGGTGGGACTAAGGGTATTTTATTGGTAGCCTTGAAACACA + BEHHHHHHHHHHHHHEEGFHHHHD9'3@;CHGGD6FAFHHHHHHHHHFEHHGGHEGG;BBDDDDC/07;725.;GGF @read_150_492/2 ATAGTGATAGAAGGTTCATGTTTTGAGCCTTTATGGTGATTGTGCAGCTCTCTTGAAAATTTACACTGTCATTTTATTTATAGCAGATGTCTCTTAAAGC + FFDEHHHHHHHHEEHHHHHHHGDCDFHBFGGBEEFHHHHHEE;HEDHHHHGBGGBDCDHHHGHFCHHFGHFFGGGD4><,::@5*DDEECBC=ACAGHHH @read_150_493/2 TCGCTGCAGTTTTGAAAAGTGAAGCTAAGAAATGATTTCTTTCACAATAATATCAAGATGAACAAAAACTTTTAGCAATGGCAATTCAATTTCTGCATAA + IGEFACCHHFF@GHHHHGHF59;A63@EEEGHHHHD(;3++583>DF,<:<>CCCCA?@BEHBDC/6 @read_150_495/2 TCGCTGCAGCCTGGGCAACAGAATGAGACTCTGTGTATAAATAAATAAAACTAAGAGAGTTCTCACATCGAGCTGTGAAGGTAGTTTGCTAATTTATCTG + FGG7GFHHHFEEDD=CHHHHHHHHHF@B=CABDC<::FHHHGHHFEHHHGGHHHHHHHHGFHHHEAB43-9FHHCHHHHHFHHFGHDGE@DFHHEF @read_150_496/2 TCGCTGCATTCCTGCCAGTTGGTGGATCCCAGAGGAAGGGCTGGCGTTTGTTCTGTTCATTCTTAGATTCTTAGCACCAAGCGCAGAGCTGGACACACAG + GGEEDEHHHHHHHHHBBHE:4GG?@E=ABCEHHHGHDHHHHGHHHHHHHHGGIGGFHFGHHHE?HHHHGHGHHHHHHHHH2/FGHHFHGGFGHGGHFHEGHGBBB-16>D<**11)))26*(5<;BE::1,);E9EDDE? @read_150_499/2 ATAGTGATGCAATAAGCTCACTACAGCCTCAACTTCCTGGGTTCAAGCAATCTTCCTGCCTCAATCTCCTGAGTGGTTGAGACTACAGGCACACCCCAAC + HHHHHHHHHHHFFIG?FGFFHHHHHFGGGFBBHHHHHHHFHHFGE;7>6:46?<:(>58;1-(,@<>>B50EGHFFBFHHF67?ACBHE?9%2 @read_150_500/2 ATAGTGATGGGTTACAGGGGGAGGAATAGACAACAGCCCAGAAAAATAAGTCAGGTAAAATGATAAGCGTTGGAAGAATAAAGCAAGGAAGAACAGGATA + HHHHHHHHHHF??B<)5514;A@FHGEFBHHHHHHHHHGHHHHHFHHHF>=EEG=EEDFFFHHGHGGHHHHCGF9&>;B@ adapterremoval-2.3.1/examples/interleaved.fq000066400000000000000000006552101350370616400212110ustar00rootroot00000000000000@read_150_1/1 CTTGGGTACTCAGCCTTAGGGTACCACATAGAGTTATCTTATATATTATAATTGCTCTTTTAACATAATTTTAAAAAATTTATATTAAACTTTCTCTGTT + HHHFFFFBBDGGGGGHHHHHGGFCDHGEE<@;+@C792A.CEEGGFFFFDEFGFHHHH@C2;@F;EDDHFDCCC@.DEEEG=BGEDC5>:=2@GFHHHFF @read_150_1/2 AGAAACCACAGTGACTTAAACAGAGAAAGTTTAATATAAATTTTTTAAAATTATGTTAAAAGAGCAATTATAATATATAAGTTAACTCTATGTGGTACCC + HHHFFHHHHHHGFBGHHEFBDG?B=GHHFGFHFHHHHHHHFBFHHHHHGGEEG=DGGGGCHHHHHHHGEA%5ADHHHH=G&&*>>099BEB@=?*59/''.CCFHFHHHHHH @read_150_2/2 TCTTTGGTTCTGTTTATATGCTGGATCACATTTATTGATTTGCATATATTGAACCAGCCTTGCATCCCAGGGATGAAGCCCACTCAGATCGGAAGAGAGT + HHHHHHHHHHGHHHHFGHGFGB<.36./AEFEEHGGBD9HHHHHGFE:A9:<.;<E6,735@GG @read_150_3/1 TATGTAATGACATAACTCTTATGGGCAACTTCACAAAAACACAGAAGAAAGCCCTCCTAAAGAATGAAATTCCAAAAAAAATCAGGTTACTGCTCACTGA + HHE=EE@DBBBGHGBFGGDDDDFFFHHHHHGHHHHHHGHHHE7BFHHHHHHG@4FEHHFHHHHFHHHHHHFFFE?EGCDE>CD:9=>+*;=37::ADDHF @read_150_3/2 GTCATTAACATTCACGAAGATAAATTTCTCCATTTTAAACAGAGACACTCAGTGAGCAGTAACCTGATTTTTTTTGGAATTTCATTCTTCAGGAGGGCTT + HHHHHHHHHHHHHHHHHH?GF5:@AFHHHGHFDDGGFFFHHFGHHHGGHHHHHHHHFGHFGEGC.18984>1BC=GFFAC<>E?..59&&-81:<<5EEB4DFHHEHFHHHHEGFFEEFCDHEFF:+1;?GFFCFHHHHHHHHHFHBB>>BEDGCDHHHHF @read_150_4/2 GAAGACTATCAGCCATTCTTTTCTGTTTAGAAGAATTCTTGCCTACTGGCAGGTTTTAAATTTGTTTCATTTCATGCCTTTATTCCTGGACAGTTTTTCC + HHHHHHHHFHHDEECEHBHHHHHHHHHHHHHHHEA?936>.@ABCDBCE>:>@CDGHHHGEBFE/38@EEFBFGHHHHHHEGH?DHHHH>'9DEC**'*6 @read_150_5/1 TACTCACGGACAAAGAATAAATATAGCTCCTCCAGGAGCTTAATAACTCAGTGCTGTCTAAACTCCTTACACCTGATGTTGATGCCATGGTTAGATAGTT + HHFFGGFDBHHEHHHHHHHHHHHHFHHHHFHHFEEDFD8=GHFFHHDHHHCHHFDHBHDDGFHHHHHHHHHHHHHHFD;>A5<(@<4:> @read_150_6/2 TCTGCGAAAGCTTCTGTTTAGTTAGGTGACGTTATCCCGTTTGCAACGAAATCCTCAGAGAGGTCCAAATATCCACCTGTGGAGTCGACATAAAGTGTGT + HHHHHHHHHHHGEEHHHHEHHHHHHHHHHHHHGGBG=<, @read_150_7/1 TAAGTAAGGTAGACAGCTAAGTCTAGTTTGTTCCCAGTGTTGTACCAGTCTCATCAGTGCCGTGTCTGGGTCTCACAGCCTCTGGTGTTCTATGCTGGAT + GFFEEDHHGHHHHHHHHB?GG77-/:>>@?6AC5GIB?BEBHHHHHHHHHHHHFGFHHHHHHEFEGF9?EHHHE@8BB12BEHHH @read_150_7/2 ACTTGCACCTCTTCATCAGAGGAGCAGATCCAGGAACAGAAGTCCTGCATTTACAGGCTCTTCATATCTTGTGCCGGGTTTGGCTGCCAGGTGGCCAGCT + HHHHG=BDEDFFGGHHHHHHHHHHHHFHHFHHHCGHHHHHEBHHHHHHHHHHHHHHGEEE??6BCFHE624@7=1AFGBDHHHFFE<<.>,1349EEHHHHHHHGFHFHHHHHEHHD=:>-7@BC2BHHHHHHHGBHEFFHHGGHFGFHHEEFHFBEBEFHHFFBCA?B @read_150_9/1 AGGGCATATATTTTGTCAAAACAAGTAGAGCCAGGCCTGCTGTCTGTATCAGCCCCACCTAGGCAGGTTTGGGATAAGGGAGGGAGTGAAGAGGGAAGGC + GFBDDGHHHHHHHHGGHHHGHHHCFFHHHHHHHHHFGGEA?FFFGEFBBA@;6BEA@EEEEEHHFEHFDDHHHHFEEGEB(:A:6C=>>CFFFCE?DEBD @read_150_9/2 GCCTTCCCTCTTCACTCCCTCCCTTATCCCAAACCTGCCTAGGTGGGGCTGATACAGACAGCAGGCCTGGCTCTACTTGTTTTGACAAAATATATGCCCT + GGGEBGHHHHHHHHHHHHHHHHHHHHFADHHHFHHHF?DEF@B>C;CDGEHGGHHHE@@DBFGHHHHGB>BBFEGEGHFHF8ADCFDEE4D?>H@:>DD= @read_150_10/1 TATAGATGAACTCTGATTTAGAATTTGTATAAGCTAAAGCATTATAGTAATAACTTTTAAAGTAGTATTTAAAATATCCTTATCTTACGTATATATGACT + <506@6?GHHHHGFHGFCFHHHHHHHHHHFGFF<3@C43F>AAEEFBFDFFHHHHHHHHED(0DAEBEFC?BFBEHHHHHC@85@GBGGFDCHEHHFCFB @read_150_10/2 TAGTCTTCTCTTTCCTGAGAATATTTTTATTGCAAATATGTAGTCATATATACGTAAGATAAGGATATTTTAAATACTACTTTAAAAGTTATTACTATAA + HHHHHHHHHHHHHHHHHHHHHHHHHHHHHFFFGHHHHHHHHHHHHEBDG>CCBB?FHFHHDEFHGDDGHHHHHH@BECHHEHGDHHHHHFHHHGEHHHHH @read_150_11/1 GCCCAAGCCATACTTCAATAAACGTACCATAGATGTGAAATACAGGATAGAGAGCAAGAGCTTTTGGCACGGTAATCTTAGATGTGGAAATTTACTCTAA + HHHGEGGHHGGFGGGFHHHECDDCCDDHHHHHHHHHHHHHFGGGHFHHFFHHHHHHHHHHHEHFFHFG?HHHFEE=EE8@8EEBEDHHHHHHHHBCDDHH @read_150_11/2 TCCTTCTTAATAATCGTATTAGAGTAAATTTCCACATCTAAGATTACCGTGCCAAAAGCTCTTGCTCTCTATCCTGTATTTTACATCTATGGTACGTTTA + HHHHHGEHHHHHHGHHHGGGHFGHHHHGGDHHGGHHHHHGHHFHHHFBD@FDFFHHHHHHHEHHHHHDDB=DA@@5DBC<.&9=AEHGFHGGD=1A;3CC @read_150_12/1 AAGGCCTTTGAAAAATAGTTTTTTTTTCTCTGACTACGTATTTGTTGTCATTGTCATCATATTTCCTCTTAATTCTCCAAGATAGTTTTACTTTGATTTT + HHHHHHHHGGGEGGGGGHHHHHHHHFCEBFGHHHEEHHHHHHHHHHBDGBHHHHHHHHHHHFFFFEHFFCDDDHHFGGHHHHHCCEHFBGHHFGHHEEHH @read_150_12/2 TTGCCTCAGATGTGGACCCAGTGTTAGATTTAGCATATAAGGATTTTAAACCAGATATTACAAATACGTTCAAAAATCAAAGTAAAACTATCTTGGAGAA + HFB<95>:5226A>>DDCB@--3;BFFH @read_150_13/1 CCTGAAGCAGCTGGCTAGTGGCTTATTACTTGTGACTGGACCTCTGGCCCTCAATCGAGTTCCTCTATGAAGAAAATACCAGAAATTTGTCATTGCGACT + HHHHGCC8EF@E8DB'/DDEFGCEHHHGGBHHHGGDD>>FHHHHHEE;EFHHGHHB@FD:<.?DDGHHGBDDEE=ACEGHHHHF=CC?DGBBHD@DF8 @read_150_14/1 TAAAGCCCTTGCTCCTTCATTTTAGTTATTTTGATCATGTCAGGTACGTTACAAACATTATTTATTTACTGCCATGCTACTATTGCTATATCAATGCTGA + HHHGHGGHHGGGGGHGGHHHHHHHHHHHHHHHHFFEHEEBBE>?DHHHHHHFGCGC@DHFDHHDDFFHFHFDEFHFFFGFHHBBGFFHHHHHHH=>:8BE @read_150_14/2 ATTATTGATTACTCTGGAAAATAATCAGCATTGATATAGCAATAGTAGCATGGCAGTCAATAAATAATGTTTGTAACGTACCTGACATAATCAAAATAAC + HHHHHEE=/?<*>FE;-53>>8=FEEFHHHHHHHFHHHHHHHHHEHHHHHHHHHEFEEHHHHFEBFEBC>FHEGE9?D @read_150_16/1 TATTGCTAATTTCCCAGATTTTTAAATACTGCCTGATGCTTATATCCTGCAAGTCCTGTCTAAAAATCAGTCAAGATCGGAAGAGCACACGTCTGAACTC + B@EHHHHHHHHFGHHGGBB@?CFFHHHHHHFEEHE@@CADAFFC>AHHFHFHHHHHHHGGFHFGE6.6HHHEEFFGGHHHHE@?=EGGFBFHHHHHEHHHHHHHHBEEFFGHG5CBCACDG @read_150_17/1 AGATGAGGAAATGGAGGCACAGAAGAGTCACTGTCTAAGGTCCCGCAGTTAGTAAACGGTGGAACCACGATCAGAAATCACAAGATCTGTGCTCTTCTCT + HHHHHHHHD?>A=@8.>HHHHD4*BFHHHB=BEHHHHFFFFEEDE77),BAA?>5%4:FGGDHFE@614A= @read_150_20/1 TGCCCTGCACAGGAGCTGGGGACAAAGACCAAGTATATTTTGTGTTATGCCACAGACCCCAACAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCA + HGGGFFHHHHHHHHHHHHHHHGHGFFCFEHHHHHHHHHFGHHHHHHHHFFCE:<*:6EDHFGFFGAHHHEBFHHF??CDCHB0DGHHHEGCFFCDBGFHH @read_150_20/2 TGTTGGGGTCTGTGGCATAACACAAAATATACTTGGTCTTTGTCCCCAGCTCCTGTGCAGGGCAAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTACA + HHHGGFHFHGHHHHHHHHHHHHHHFHFGHHHHHHHFHHHHHHHHHHHHGGFHHHHHHGGHE><.??D98EHEC:.B @read_150_21/1 TGAGATCAATTCCAGGTACATTTTTAACTTTTCCACAACACAGGTGGCCCCGTGGGCTGAGACTCAGGAACCCACCTCATCATCTGGTTCTGCTCACTGC + FEFFGDC/>=FFHHHHHHHCEHHEGEGFD-%%5CGCEHEHHFHHGFEH>>BDEEBDBFE.1%88 @read_150_22/1 CCACTCCTCCAGAGGATGGCACAGCATGGGAAATGAGGCTTTGGGCCTAGCAGATCTGGGTTCCAATCCTAGCTCAGCCTCTTTAATAGTTGTGTGACTG + HHHHHHHHFE@EEHDEEHHHHGHHHHHHHHHHHHHFFHGFHHGHHDHHHHHFHHHHHHHH@7:@E?DDDDFFEEDGGFFHHHHEHHH68><+(>4@EFDF @read_150_22/2 AAATGAGGCCTGAGTGAAGAATCTTGATACTCATAGGTCATTAGCTTCATGTAAAAAAAAAAAAAAAAAAAAATAAAAACCAAAAAAAAAAACCTTTGAT + HHHHEEFEGDHHFHHHHHHHHF8BCDEHHHHHHHHHHFFDEHHHHHBAADGFGGBFFFGCGGHHHHHHB.057(+2-9GGHFHHFHFA@@;>DEDEBEFG @read_150_23/1 CAAGGGATCTAGACTGCTCTGTCTATGAGAATCTAATGCCCTCCCCCTCCACCATGGAAAAATTGTCTTCCATGAAAATGATCCCTGGTGGGAGACCACT + HHHFHHHHHHHHHHHHHHHHHHFFH@EHHHF8@;@DD=EEHCFFAEFGFHHFHFGD<+(4EDFHHEFHHFFFFFHHHHHDFGGHFHHGB=CF?@>CD?CG @read_150_23/2 TCATAGTCTTCAGTGCACCTTAGATTGGGGTATTGTTTTGTTTTATTCCAAGTGAGCAGGGAACATGTTAATGTTGGACATGTTCTGAAACAGTTGATAA + GGFFGGGHHHHHHFHHHHHHGHHHHHHHGHHGFF=BDHB84DB@AC5(('97B?@E=6>@AHHHHFFEGEGHHHHFHFDGHHHHHGGHGHHGEDD?7>29 @read_150_24/1 GGTTTTGTTTTAGGGAAGAGGATGAGAGTCTTGGGCATCCGAGAGGACATGAAGAACAGGTTTCATTAAAGTAGGAACTCAAGTAAAAATAGTCATGCTG + HHHHHHHHHHGGGGFFFHHHHHHHHHHHFGGGGGHDBEHFEHEEGGHHFEDD?@>&7;>HHHHFHHHHCHFHHHDFFFHHFHGHHHHHHEHHHFHEHHHG @read_150_24/2 CAACTTAATGTGACTGAACTTAGAATTGGGAAGATTCACGTGCAGTTGACTCTCATGAGCCAATACAAATTGGCTCCAACACACCATCAGCATGACTATT + HHHHHHHHHHHHHHHHHHHHHEFHHHHHHHEHHGFDEFHHHHHHGHHHFDHHHHHHHFFDG@BCFFHGFHHHHGHEE@AD?2&5.544DE82EDHH=<45 @read_150_25/1 GCTGTTGGTGAAAATTCTTGTGATGTGTTTATTTATCTCACAGAATGAAACCTGTGTTTTTATTCACTGGGTTGGAAACACTGTTTTTGTAAGATCTAAG + HHHGGGD8/=B>:CCEGFHHFHCFDAFAEFHHHHHHHFDHHHHHHGGGDDECD@FFFGD8,;1 @read_150_25/2 AAATATCACTTGTTTCTAGTTTTATGCAGGATATTCAGTTGTTCACTATAGGTGAGAAAAGCTCAGAAATGTCTGTTCTTAGATCTTACAAAAACAGTGT + HHHHGDGGGGFGGHHBAB=??CCDDBGCDEGHHBHHHHHFCECBFGGDFFGHHHHHBB@.<3,+6<<9=DCBGGFHGED@GHC@GGEEFEGB?>DB>58E @read_150_26/1 TTGCAAGTAATTGCAGATGACTGTATTACCACAGGATAACATGAGCTGACATATTTTTTTGCTACATCTCCAATTGACTACTAGGCCAAAATCTTCATGG + HHHHHHHHHHHHHHHFGGHHHBGEEEGG=GDEFBEHHHHDHE?EHHHHHHHHFFBFHHHEHFFFHHHEED?BFB=DA?E?HHHEEHHHHH=>DHHFGHHH @read_150_26/2 AAAAATTATCCAGGCATGGTAATGGGCGCCTGTAGTCCCAGCTACTCAGGAGACTGAGGCAGGAGAATGGCGTAAATCTGGGAGGCAGAGTTTGCAGTGA + HHHG>:>98633131><>>??BFGHHEHHEHGC8=8@DDCHHHHHFD;7EHHHHHHHHHHGGHHHHHHHHHHHHHHHHHHHHHHHEEBEBGECDEEEE<8 @read_150_27/1 ACAACAATTTCTTCAGATAAGTCCTTTAATTTAACCACATGGACCCAGCCTGGGATCTCCGGGACATACAATCCTGTCTTAGGGCTCAGAAGTGCCCAGG + HHHHFGHHHHHHHHHHHHHHBGDFHHHHHFHHGFEE?/8<2>CEA?7CG?FDE3FCFFCFHD?@FHHHHF79573>EDDCGFHHHDFHD=EE;)--7:ADHBFFF @read_150_28/1 TATTGAGGCAAATTAAGTGTTTTAACAAGTGTGTATATTTGCCCTAATGCAGCTTAATTAACTATATCCTCACAAGATCGGAAGAGCACACGTCTGAACT + HHGHHHHHHHHGHHGHHHHHFFEEHHH?FFFGGGGGGGGGB=?>;FHEFFFGHHFHEHHHHHHFFHHHHHHDD3,>DDDDDEEEEGCEHFBFFHHHHGGH @read_150_28/2 TGTGAGGATATAGTTAATTAAGCTGCATTAGGGCAAATATACACACTTGTTAAAACACTTAATTTGCCTCAATAAGATCGGAAGAGCGTCGTGTAGGGAA + GDD??<9;:=EEG:?CCCC@FFGHHBGFFHFD=D@@>18>=<3=FHGGFHFFHGGHHCBHHHHFFFAFFFHHHHHHHDGHEFC9=DDBDDHHHHHHBGHH @read_150_29/1 AAGAGGTGTTTAGGTGAATGGGATTAGTGACGTTATAAAAGAGGCTGAAGAAATCTCCCTAGTCCCTTTCATCCTTTCGGCCATGTAAGGACATAGTGTT + HHEHGHHHBDDFHHHHGHHGGGHHHHHHHHHHHFFHHHHFHHHHHHFHHHFFHHHHHHFD@FF<.+->@.;?,4FFHHHHHHHHHFB @read_150_29/2 CTTGCCTTCTGCTTCCAAGATGGCATCTTGTTGTTGTGTCCTCTGGAGGGGTCCAACACTATGTCCTTACATGGCAGAAAGGATGAAAGGGACTAGTGAG + HHHHHHHGGDEDG;DHHHHHHHFBDAGD@EDEE@C:DBDEFHHFBDDHFFGGGFHHHHHHHH=:A+/BHHBBF==EFFFHGGEED;3/@7E=A>87)*.: @read_150_30/1 CTCTCCCTACAAGCACCCAGAGCAAGCTGTGCTGCAATCCCAGGGACTTGTACATGGCCCCTTTCCCTCCCTTACCGCCCAGTCAGCCCCTGCATACATC + EEDFGDBB@CGFHHHHHHHGHHHHHHHEEEGGDHHHHHHHHHHGB=@FCHHHFEHHEEDD=+E?FHHDA>>12+(D8?FDHHHFHHCFF9:>FF@CDBEE @read_150_30/2 CTCTCATCAGTCCCACTCTGGCTCTGGGTGTCTGTTAGGGCTGGATTCACAGAGTGAGGGGCCTCTGCTGACGAGGATGTATGCAGGGGCTGACTGGGCG + IGDDDHHHHHGHHHHHHHG=CBCB>&-+BEHHHHEGHHHHHHFBHHHFHD/5=60CFGHEEFGEHHBFC.2':.9?FBHHHHGFCFEEEHHHHB=A?@A4 @read_150_31/1 TCATTCAACCCTGTGGAACTCATCTCATCATTCTCTGTCTCCTGCTTCTGAATGCTTTAAGTCACTTATTTGTCTATCTTCCCCAGAGAGAAAGCCTGCT + HHHHHHHHHHHHHHHHHHHHHHHHHHHEEGHHHGGGGFFFEEDFCDHHFFHHEAD?FHFGEEE5<@;=>49GGHFHGHBEFB>ABBEFFFECEHFH @read_150_31/2 CTAAGCAGCAGGCTTTCTCTCTGGGGAAGATAGACAAATAAGTGACTTAAAGCATTCAGAAGCAGGAGACAGAGAATGATGAGATGAGTTCCACAGGGTT + HHHHFF?FGFHHHHHHHHHHHHHHHFFFHHG7D=CB<9>4;4>AFHA@>>EDCDBHHHHHHHHHHHHHGHHFHHHHHHFHHHD=5@DHG6CA58=DD>AE @read_150_32/1 CATGAACACCTTTATGAGTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCACCTAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAA + GGFGEEE9DC346GGHHHHEFEGGHHHHFHHHHEGGGHHHHHHHHHHHHFAC=E7ADFFFBEFEEFH@DHFCHHHFFGHHHHHHHHEHHHHHD@?>CBFB @read_150_32/2 ACTCATAAAGGTGTTCATGAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAA + HGGGGHHHHHGHHE8DHBGGGGGGEHHHHGGBHHHEFDCFEHBDEGGGHFFHBD555ADHHHHHHEGHHHHHFD43 @read_150_33/1 GCAACCTCTGCCTCCCAGGTTCAAATGATTCTCCTGTCTCAGCCTCCTGAGTAGCTGGGACTACAGGTATGCACCACCACGTCTGGCTAATTTTGTATTT + HHHHHHHHHH@@D?GD8GEHEB=EGH??:@GGGHFEFFFHHHHGFHHECFHHGHHHHHFEHHHHHFBFFHHHHHHHE<>@EFFC=9=GFDEEED65@BB@ @read_150_33/2 GTTCGAGACCACCTTGATTAACATGGTGAAACCCCATCTCTACTAAAAATACAAAATTAGCCAGACGTGGTGGTGCATACCTGTAGTCCCAGCTACTCAG + HHHHHHHHHHHHHEEHHHHHHHHHGHHHHGEEEHEHHHHHHHB6DHHFCDEDEGFHGGGHHHB8><)0-<9@;@HHGBFFHEEEGCFFEFFBFBCEDHFE @read_150_34/1 AAGAAAAGAAAAATGTAAACAAAGAACTGAATGCTGCTGAATAACAAAAGAGTCACTTACTTAAAAAAATAATAATTTCAGCTCATCTAAGAAATAGATA + HHHHHGGGGFFGGGGHHHHHDEGDGGGGGEFFGGFHHHHDB@FGGGHHHHHGHHHEFHHHFF@EFHHFAF>FDHEGHHHHHHHHEGGHHHHHHHHHHFED @read_150_34/2 GTTTCGGATCTTGATATTGCCCACTGTTGCTTGCTATCTATTTCTTAGATGAGCTGAAATTATTCTTTTTTTAAGTAAGTGACTCTTTTGTTATTCAGCA + FGGFDGGIBBEDB/9)/:HHHHDD=GGCEEFGBADA7EFEBC@DEGG?:C-/EDEDEG?BEGG4(4CCGFEE6EBFCCEE @read_150_35/1 TCAATACAGAATGATGCCAGCACAATGATACACAGGACAGCTGGGACCAAGAAATTTGAGAAGGTACAAATAAAAACTAAAAAAAAAAAAAAGTTTAATT + HHHGBBGGGGHHHHHHHHHHHHHHHHHHFHFFHFFHHHHHHHHHHHHHHFFHHHHHFHHEEHGHHFDFFHC?BFFFHHEHHHHHHGGBBEHHHFG86EFH @read_150_35/2 AGAAAGCACTGTGAACTTAGTCATTAAAAATGAATATTTAACAGTTCACTTTTGACATGCATTTTTAAAATTTAAATTAAACTTTTTTTTTTTTTTAGTT + HHHHHHHEEEEE/?636BGHDAEBDEBD@GEHHHHHHHHCD*1::CEDCCDB@GGEEFGFHHHHHGHHGHGHHHHHF8=FHHHHHHHBFHHHHHHFFHHH @read_150_36/1 GGGTTTGTAAAATAAATAAATAATGTGAACAATACCATCAGTGTTTGCATAGAAACAATATGATATCATTCTTAAAGAGATCGGAAGAGCACACGTCTGA + HHHHHHHGFHHHFHHHHHHHGGEHHHHHHHHEEHHHGGFHHHHHHHHHHHHHFEHHHGGE=EDEFHHGEEFD@?E::;24>6383;(.501>HHHHHHHH @read_150_36/2 CTTTAAGAATGATATCATATTGTTTCTATGCAAACACTGATGGTATTGTTCACATTATTTATTTATTTTACAAACCCAGATCGGAAGAGCGTCGTGTGGG + EF@@DEGHHHHHHHHHHHHEEEHHGHHHEFHGGCBHHHHHGHHHHHCCC>DDD;DHHHFIHHHHHHHHHGEFGFGHEHFGHHHH@*66G?1(03 @read_150_37/1 GGTCTATATGTGCCACATTTTCTTTATACAGTCTATCATTGATGGGCATTTGGGTTGGTTCCAAGTCTTTGCTATTGTGAATAGTGCTGCAATAAATATA + HHHHHHHGGFFEGFHHHHGBGD@??37=FFDAEFHHHHHHHHHHFEHHGGGHFEFFHHHHFFFHHHHEB-DHHEHHEEGFHHHGGHHFHECFGHHC@AFH @read_150_37/2 CCATTTGACCCAGCAATCCCATTACTGGGTATATACCCAAATGATTATAAATCATTCTACGATAAAGACGCATGCACACGTATATTTATTGCACCACTAT + BEED@FBFHHHHHHHHHHG;8CD=HHHHCB6>563<5?D432>..<6<>@923@CFGHHGEHCEEDEHHFHHHHHHHGHHHHFHHHHEHFCB:.<<2?@@69BDAHHHHHHEBHCH @read_150_38/2 GAAATACCTACACGCTAATGCAAAAAAGGTAGGGAAGCTGTCAGGTTTGCACCTTTTTTGTCTCATTGTTTAAGTGGAGCCAGTTTTTTTCCCAGGCTGG + EEDGGHHHHHHHHHHHHEEEFHHHHEGHFHHHHHHBGGHHHHHHHGFGBEGBDGGHEGHHHHHFEBB=HHHHHHHHHFHHADFDG@FFHDHFFFHFFBHD @read_150_39/1 TCTCCCAACCTTGTATGGTCCTAGGGGCTGTGATATGGTTTGGCTGTGTCCCCTCCCAAATCTCATCTTGAATTGTAGTTCTCATAAACCCCATGTGTCA + C?8><@CGGEDEECBEEHFFBE @read_150_40/1 CCAACATCTGTGGTTTTTGACTTTTTAATAATAGCCATTCTGATTGGTGTGAGATTATATCACATTGTAGTTTGATTTACATTTTTCTAATGATTAGTGA + HHHHHHHHHHHHHHHHHHHHHHFFHHFHHHHHHGHFFC/CEHDBDHFHHHHF<:DHHHGF<@*.>>?EFF?E@@C@6C.5EFEHHHHF>;::)04>?EFG @read_150_40/2 AAAACCAAATCACCTCATTAAAAAATGAGCAAAGGATGTGAACAGACACTTCTCCAAAGATGACATACAAATGGCCAACAAACATATGAAAAAAATCCCA + EGGHHHHFEHHEGHHHHHHHFFHHHHHGF=@E8CCHHHHFEHGGIGEEBD<47.5?GGGHHHC8CFHHHHHEG=CHHHHHHHFHHDEEGGFFFEEGEEF= @read_150_41/1 TTTTCCCATTGAGTGTTCTTAGCACCTTTGTTGAAAAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCACCTAATCTCGTATGCCGTCTTCTCCTT + HHHHHHHHGGGDA@BCDGGHHHHHHHHHGGEFFGBFHHHHHHHHHHFHHHCC??.AABC5DDHHHHEEEFFHHHHHD=FBHHHGGGGHHDD-%-&2 @read_150_41/2 TTTTCAACAAAGGTGCTAAGATCACTCAATGGGAAAAAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAA + HHEHHHHHHGEEEBEEHHHHBFEEEGGGC?EG6:;BGGEGEHHHHGFGDDHFEGGHHHHHGA>.?,47>6ADHHHHHHFGHHHEDDCDDFEFHHHHHHHH @read_150_42/1 ACGGAAACTAGCCAGAGTGGACTCTGTTGTCTACATGCAAGAAGATCGGAAGAGCACACGTCTGAACTCAAGTCACCACCTAATCTCGTATGCCGTCTTC + HHHHHHHHHHHHHHHHHHHHHHHHGGGGGGFCCHGHHHFBDDEFHHHDHBFHHHHGFBFHEDFFEHHC63@@<.119;C@B@BHDFGHHHHEE?CBCEFF @read_150_42/2 TCTTGCATGTAGACAACAGAGTCCACTCTGGCTATTTTCCGTAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + HHFFGE@.'8>>@DHFFDBHHFGED>13=699D=,>66EDEG669?CCCDE@44@6GHFHHGFGDA@>@?=HGECGG>@CFFCCBD?FFHEEFFC>.*/( @read_150_43/1 GCAGTGGTGACATGCATGACAGGCATTTGGGATCAGATGTTGCTGATCCAGAAGCCTAGGTGTGGCCATTTTGTCATGGCAACTGATAAGCAAGTAAATA + HHHHHHHHHHHHGGEB@C?HHHFCCGEFEEIEHHHHHEFF>4:>B:4C@9CAFHHHHHG.DEE@D77=BEHGGBA+,-(+7,7GC'5BDD;B?FDHGGGH @read_150_43/2 TTCAAAACAAACTGAACATCGCTGGAGATAAGTCAGATGACTACTCTACCCTATTTACTTGCTTAACAGTTGCCATGACAAAATGGCCACACCCAGGCTT + EHHHHHHFHHEIIEBE=@<-;AAFGHHC@>>BBGHHFHHHFHFE?EEHHDEGF7BHHHHHHFHHHHHHHHHHHHHHHHHHHG?@?DFFHE:.54HFH57@ @read_150_44/1 CCTCCTGTGCCCTGACCCTAATGACTTTTCTTCTCCGGGAATGAAGAAGCCAGAACCAACCAAGGTCTCACACCTTCACCTCTTCCCGAAAACTAACTCC + HHHHHHHHHHHHHHHHHHHEEGHECGGHHEDHF<7;BAHHCBFFFHHHHHHHHFFHHDCE928D@6<@@>>FHHHFBC+8 @read_150_45/2 TTTGCTCTCGTTGCCCAGGCTGGAGTGCAGTGGCACAATCTCGGCTCACCGCAACCTCCACCTCCCGGGTTCAAGAGATTCTCCTGCCTTAGCCTCCTGA + FHHHHHHHHHEHHHHHGGHHHHHEECDFFCHHHHHDHHFHHF@HHFGFHHHDDGGFGFB><>+923:7/DHHHHHHHHHHHGCDF@>76&>D;<;GGFHF @read_150_46/1 ATTGGTTTTTTTTTTTTTTTTTTTTGAGATGGAGTCTCGCTCTATCGCCCAGGCTGGAGTGCAGTGGTGCGATCTCAGTACACTGCAAGCTCCACCTCCC + HHHHHHHHHHHHHHHHHHCDD@EFCGHHHHHHHHHFHCDDFHHHHFDDDB>BHHHHHHHHHFEEFFGFDHHF/AF?CF8FBEFFFFFHFEBEEE @read_150_46/2 CCGGAGGCTGAGGCAGAATAGCGTGAACCCGGGAGGTGGAGCTTGCAGTGTACTGAGATCGCACCACTGCACTCCAGCCTGGGCGATAGAGCGAGACTCC + HHEGDEEFHHEGHHH9000;.252-DGFE9&7FFCBFFF*).>:,4 @read_150_47/1 CCTGTATATCTTAAGACTTCTTTCCCTTAAATTATTACCTTCTCCAAGAAGATTTCTATAACCCTCTAGGAGAAAAAAATGGGTGTTCCTCTCCCCCAGG + HHHHHHHHHHHGFHHHHHHHHHHFHEEEEEGGHFB6D?CD@@DDBGFHFHHFFAC>8CDHHE>)1 @read_150_48/1 AAGTTGCAGCAGGGGAAATACTCATTGAATTTGTCATCATTATTTTTGGCTTCTATCTTTATGAGAGCCATTTTAGTTTTCTAGTTTCAGTGATCTATTT + HHHFFFBGHHHHHHHHHHHHGGHFD=2=F??>973:9??A>+-:<7BF=DBE82@7>EHHGGHFHDDHHHHHHFHFHFBBGGHHHHHHHGGFEHHEFHHHHHHHFGEBDGEFHHHFDHEED=;46D7 @read_150_49/1 CTACATGTCATTAAGAACATTTGTGACTCATGGAAGCAGGTGAAAATATCAACATTAACAGGAGTTTGGAAGAATTTTATTCCAACCCTCATGAATGACT + GHHHHHHHHHHGGE@GBFDDGHHHHGHHHHHHH@CBHHFFGHHHHHHHFFHHHEHHFHHHFHHHHHHHHBD>@DDFFFGGHHFGCFFDGFGEEFFBFFFH @read_150_49/2 TTTAGGCTCCACTTCTAATTCTAGTTCTGTTGCTAATTCTATCACATCTGTAATTACTTCTTCCACTGAAGTCTTGAGCCCCCTCAGTCATTCATGAGGG + C@DHHHHHHHHHGEEFHHHEF;:47::2'-4.>CEIGGFFHHHHD=ADEEFFFG;@CCGHHHGGHFDEGE;8EHHHHHHHHGFF6BDFHEDFBHFFFHH? @read_150_50/1 ACTGATCCCAGGGAAGCTTTATCTATAGTGAATATTGTCTTAAATTATAGACTTTTTGCCAGTCTGTACTAGATCGGAAGAGCACACGTCTGAACTCCAG + FF;:?GGHHHHHHHHHHHHEHFFGHHHHHHGGHHHEEHEFFHHHHFHHHHHGGDDECBDDEBBCD74AABEFF;B@<@@@FEGHHEEE>,E=ACHHHHBE @read_150_50/2 AGTACAGACTGGCAAAAAGTCTATAATTTAAGACAATATTCACTATAGATAAAGCTTCCCTGGGATCAGTAGATCGGAAGAGCGTCGTGTAGGGAAAGAG + FFGHHHFGGGFDD@FFFHHHHHHHHH?BEGEEHHEHHHHFF?;A=::-*DGHHHHHHHHHGHHHHHHHHHHHHHHHFFGD699D69<<;ADF:99DD?.E @read_150_51/1 CAGAGGTGGCAAACCCTCCTTGCATAAAATATCACACTTGGGTAAGTGCAGTATGTTATGTGTCTTTAATAATGCCACATCAGCCCCAAGTATTAGATCG + HHHHHHHHHGD@3--5EFGHHHGHHHHHHEGHGEEDGGHHHHHHHHHHFHFFHHHHHHHHHHFD.CFCD4=E=DFHHHHEHHHFGHHHHHHHHBFF;;?> @read_150_51/2 AATACTTGGGGCTGATGTGGCATTATTAAAGACACATAACATACTGCACTTACCCAAGTGTGATATTTTATGCAAGGAGGGTTTGCCACCTCTGAGATCG + HHFHHHHHHHHHHHHHHHHFHHHB@',364.,& @read_150_52/1 GGCCAAAACAAGAGGCGGTAAAGAGAAAGGCAAGAATTGGTGGTCAAGTCCTGGCAGGGAAGGAGGACATCAGACATCCATAAATATCAAGAAGTGAGGG + HEEGGHHHHHHHHHGF?A;B57.+&1:/' @read_150_52/2 TGGGTCAAGACCTGCCCTTATTTCTCATCTGTTTACTCCCTCTATGTAGGAACACTGCCAATATTATTATTATTAGTCTGTATTCTGAGTCTACCTACTG + HHGEHHHHHHGHHHHHHHHHFHGHFEG@C@CD=9EGHHFHHHHHHHHE@CD<@>9.AFCCECFHHHHBEFEEEICC;<61)&5 @read_150_53/2 TTTGGCATCTTTCCTTCCTGGTATTCTCTGAGCTTCCTGAATAAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCAT + HHHHHHE..@CC/FG)6AHGHHHGHDHHF@D?D?CHHD@C>/1-BHGHEEEHHGEHHHHHHHEHHHHHHGGBHHFGGHGG@9.CCEBFDGHFFIA?7?<+ @read_150_54/1 AGTTAATAACACCTTCCTCTTCTCTGCTGTTGGATTCTAGCTTAGGTCTAATCTGTTCTAGGAAGACTTCCTAGGCCACCCCGTCAGATCGGAAGAGCAC + HHHHHHHHHHHGHGGEFDEHGHHHHHHFED>EHGHE?=?ECHHHHHHFHHHHHFHHFFH?=?BFHHEFEEFBGGHHHHHHHHHHHHGFFHHHHHGF;D<8 @read_150_54/2 GACGGGGTGGCCTAGGAAGTCTTCCTAGAACAGATTAGACCTAAGCTAGAATCCAACAGCAGAGAAGAGGAAGGTGTTATTAACTAGATCGGAAGAGCGT + GG8EAGHHHHHHHHHHHHHHGGCDEEHHHHHHHHHHHHFHHHHBB=EDHHHGIFFHHHHHHHHHHGHHH=DGFFGHHHHFFCGEHFBGFEADB?C9DCE? @read_150_55/1 TCCCTTCTTTTTCTTTTAATTTTATTTTTTACAGAGACAAGGTCACACTGGTCTCAAACTCCTGGCCTCAAGTTATCCTAAGGATTTTTATTATTTTTTA + HHHHHHHHHHHHEGGGGHHGEFGGGHGFEDDEGGEDGHHHHHHHHHHHHHFDHHGE?HHHHHEEEFFFHFFFHFDCEGHHHHHHEEEEFGGGGDGHFHHH @read_150_55/2 AAAAAGGAAAAAAGAAAAATAATAAAAAATAATAAAAATCCTTAGGATAACTTGAGGCCAGGAGTTTGAGACCAGTGTGACATTGGCTCTGTAAACAATA + GGEBGHHHHHHHHHHGGGHHHHHHGG<=8=:>>:+-,BEEHHHFHHFGGCGFFGGHHHFEE=@?DEGEHGB@9;=;DD1--*3.2%,:EG731)0%EEEFDFB>EEACABGGHHHHG@@EGGHHHEE>@ @read_150_56/2 ATGTGCAAATATAAAGATACCCAGGCTCCAACACAGAGATTCTGCTTAGTTGATTTGGGATGGGGCCCAGGCAGTTGGATTTGCTTAATAATGACTCCTT + HHHHHHHHHHHGHGHHHHHHHEHHHHHHHFE=?/CBEHHHHHHHHGBDGGGGEEHHHHHHGFCEDFDGHDGGDAE?@?9<>49'/4?@5@=FDBCF8:EH @read_150_57/1 GTCATTTAAATATAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCACCTAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAA + HHHHHHHHHHFE?GGHHHHHHEEB>?D7>*CB?FHHHHHFHEHHDFHGHHHHHHHEHHGFHFHHHFHHHHG>BCEFGE=;CFFHHHHHHGFHFGGHGG?F @read_150_57/2 ATATTTAAATGACAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAAAAA + HHHHHHHHHHHHGHHHHHHHH>ADEE/GGFD=:0(+://6-3>FA7;@DDAED?FDF< @read_150_59/2 TTCAAGATGGATTAAAGATTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCTAGGCATTACCATTCAGGACATAGGCGTGGGCAAGGAC + FFCDHF8=HHHHHF:>@AD@DFHHHHHHHHHHH@?EEEEHHEHHHEHHFFHHHHGGHFEA5847@HFHFHF@BEHHHHGGEFHFFEBEEFHFFHHHHF:> @read_150_60/1 CTCTGTCATCTGTTTCTTGGAGGCTTGCCCCACATCAGGTGGGTGGGACACACCCAGGAGGCTGTGCTCAGGATTTCTGGCCCGTGTCCCAGGTCACCAG + HHHGGCEHHHEEGGCDGGBDGGHGGHHHGHHEFGFHHHHHHHHHHHEHEBCDEHEEEBHHHHFEFHHHHHF;@8,BDDEB>:.EE@>??BB>AA=CC??DEGGECDEEGBBEEEEEEHHHHHHFHHHEEFBEGEGBGHHGGGG?GGHHHHHBEFDEDCEFACBBGGCFHHDEFCBG== @read_150_62/1 TTTAATATCAGAGACAAGGCAAGGATGTCCACTTTCACAGTCTTGCCCCTTTTCCTTAATATTGCACTGAAGGTCCTGGCAGCACAGTTACGACAGCAAC + HHHHHHGGGGGGGFGGHGDDEBDBD?3*7>?;E8GGFHHHHHBE @read_150_62/2 CTTGTTAAGGTCTTTTATTAATTCTACTATGCTATCTGTGGATTTTTAACTTCAATTTTATCATCTGCCATCACGACAGGTTGTTTTTTGCATTTCGATA + EFEEHHHEHHCGDBHHHGGH@/A=BFEEFFHHBEBHDG>1>GEDHHFHHHHGGG@><>>>DB814DEE6&3;<><).3FGEFGHFHHGFHFH< @read_150_63/2 TAATTTTTGTATTTTTAGTAAGACGGGGTTTCACCATGTTGTCCAGGCTGGTCTCGAACTCCTGACCTCAGATGGTCCACCCACCTTGGCCTCCTCAACT + DDGHHGGHHHHHFHHHHHHHHHHHHHHHFHDCFEBD63,:8EDHHCGGCFHHHHHHCDADB9,<@BGGE=+'.5,:>=BHHHE*2,)37?DDFFHGGGFGHHEFGHFEEGFE @read_150_66/2 TACCTGTCACTTACCTTCCTCTTGAAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCTCCGTATCATTAAAAAAAAAAAAAAAAA + HHHHHHHGGHHHHGGEEGHHHHHHHHHHHDD=ADHHHHHHHGGGHHHHHHHHHHHHHHHHHHFGGEHHHHF6.>@BECAAI=DEFCHHFHGHHHHHHHHH @read_150_67/1 ATTGATTATTGCCACAATTTCAGAGCCTGTTATTGGTCTATTCAGAGATTCAGCTTCTTCCTGGTTTAAGATCGGAAGAGCACACGTCTGAACTCCAGTC + HHHHHHHHHHHHHGGGHHHHHHHHHHHHEFGHHHFHHHHHFDCBFHHHHHFHHHFHHFHHFFEFHHBF>;><33273 @read_150_68/1 AAGTTCTCTGAAAGATAATTTGGAAAAAAGAGATTTTACTCCAATGAATACTTTGCAAACCGGGGAAACCCAAGATCGGAAGAGCACACGTCTGAACTCC + GGGGGEHHFD@BFDDGHHHHGGEEHHFFEGD:FFGHHHHHHHHHHHHHHHHHHGHFFHHHFFEHEFFEHHHHHHHHHHHHFBFFHHHHGFDDEHHHHHFD @read_150_68/2 TGGGTTTCCCCGGTTTGCAAAGTATTCATTGGAGTAAAATCTCTTTTTTCCAAATTATCATTCAGAGAACTTAGATCGGAAGAGCGTCGTGTAGGGAAAG + HHHGHHHHHHHHHHHHH@DGGGHHHHHFB=8C=@FEEFEBDDDDFAAFFEFGFCDB@211,<6(D;D@>@C=CCFHFFFBFHDEBBBCEGGEE?==?C;E @read_150_69/1 CCTGGCTTTGAAAACTCACACAATAATGCCTTCCTAATTATCTCTGATGACTAGTAGTAGGGACATTCCACCCCCCACAAATAGCAAAAGTGCTCCGATT + BFFFFFFHGHHHHHHHHHHHHHEF@FFCE:FDGGHFFBHHFFGFGGFHFFBDE:6>0?CHHHGD,92>>9;DE?FEEEEEDEHCHHHHHHHHHEFFFECC @read_150_69/2 AAATGAAACAACTTCTAAAACCTGTGTGATAATGATAATACAGATTGAGATGAAGAACTTTGAAAAGAGTTGGACAATCAGAATCAGATATTTGAATTCA + HHHDHHHHHGHDFEFDHHHHHHFHHHHHHBGGHHHHHHHHHHHHEHHHHHHHEEFFHHEHGB5*0GGFGAE=B2(;>=D>,@BB/5?>.A:991/+1%*) @read_150_70/1 TAGAAGAGGTGGCCGTAATTGCTGCTTGTCATTAATATTTTTACCAAATGGATTTCTCCATATGGCAGTTCCTTTCTGTCATGGGTTATTTATAATCCTT + EFGGGHHHHHHHHHHHHGGHHHHGGHHF?DEHHHHHHHHHHHFHHHHHHHHGGAA4=?BDCBDDF;DBHHHGGFHHHHHHHHEHHHHHFA.:.30DA6= @read_150_72/1 AGGGAGGGGTAGAGGCTGCACACATTGGCCTGGGGAGTCATATTTAAAGGGAAGAGCATGTGGGTCTTGTCTAAAGATCAAGTGTAGATAAGGACGGGAG + HGHHHHHFDFHEDHHHHGHHHHHHHHHHEHHHHHHFC=:)>EBEEHHHHHHFCCBDHEEDHH??EHFFEFDEDCCFHHHHHHHGGHHBC,DHHH@E4. @read_150_73/1 AACCTGGATTCCAGGTAAAAAGGTATTTGTACAGTCCAAGCTCAGCTAATTAGTTTGGGTAACCAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACC + HFFFHHHFHGBBF>;CEGHHGHDFGGEEC@@A?HHHHHHEBEBADFHHFFDCEFEHFHHHFBEEHHHGDDEG;48ECEHHHHHFBD=CFHHHHHHGFFEC @read_150_73/2 TGGTTACCCAAACTAATTAGCTGAGCTTGGACTGTACAAATACCTTTTTACCTGGAATCCAGGTTAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAG + GE8BEBGHHFECDIFFHHHHHHHGHDFHHHFHFDBDIGBE-.@4*BHHHHHHHHHHHHHFB=ECHHHHHHHHHHCEGEBEBEFE?EADDF=C>97<.@G@EHD>7@4DDGEFHHEGGHHHE?6/52'64AD<, @read_150_75/1 GTCCAGGATCCTGCTGTTGGCTGGGCTCTTCAATTATCCTCCAGGTATCCTCTCCCTTATCCCACATCCCCAGCTCCACCTTGTCTTTTCATGTGGTGTC + HHEA9<=DDEGFBGHHGEG@EGHHHHHHFE?:<<>FHGHHHHHHFGHHHHFFHHGHHHHHHHHHD==??=FFD=4?DIGED8EGGHHHGADD-FHEDBGHHHHHHFFHHHHHHEEB=EBEHHHHHHFHHHHHB@.@A6HFFF>@@5BHHHGGFFFDDFEFGGFFGHHEHHEDHHHFBHFFEGEHHGDHHHBFDD<6*/EEFGE86C2638 @read_150_78/1 CTCCTCTTTTTTCCCTGATAACTTTTCTTGCTCTGAGGTCTACTCTGTCTGAAATTAATATGACTACACCTGGTTTCTTTTGATTAGCATTAGCTGTTGT + DGGGHHHHEHFGEGGE@@>?=EGDDFAHHHHHHHBEGHHF6@HGFHHHHHHHHHHHHHHGFFHHHFEE?HCEFFFHHHHEHEFHHHHHHHHHHHHHFGFF @read_150_78/2 CTGAAAGTAGAAAAAGGAAAAATAAAAATAAGAACAATGAACTTGGGCAACACATAGAAAACAACAGCTAATGCTACTCAAAAGAAACCAGGTGTAGTCA + HHHHHHHHHHGHHHHHHHHEHHHHHHHF8;+ @read_150_79/1 GTGGCCGGGAGCAGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGCGTGTGGATCATGAGGTCAGGAGTTCAAGACCAGCCTGGCAGATCG + HHHHHHHHFEGGGGHHHEEE:>?HGEEE>><6'CCDBEHHH>6:5;7-2>< @read_150_81/1 GGTTTATAAAATTATATACAATAAACTAAATATACACATGTAGAATAGATCTTTGGAATACTTCCCCTGGCTTCTCTAAGTAAACACAGAATACTACACT + EBCBFGGHHHHHHHHHHHHHD66?FGHHHHHHHGHHHHHHHHFDGHHHFCDEHHHHFHEEHHHHHHHFEFHE??EDECC;03D8@CGGGEEFHHHHFGGF @read_150_81/2 AAGGCCCTTCTCTTTTGTTTCAGAAGTCTGCAGCTAGGTCAGCAGTGTAGTATTCTGTGTTTACTTAGAGAAGCCAGGGGAAGTATTCCAAAGATCTATT + HHHHHHHHHECGGGFFHHDDC5;G?:>@DB9EEDGFDCFHGHGHHHHHEGGDDDEHHHHHHFGHHHHHEEADBEA,(6HGDCD=>>C@BFBFHHBFDACE558:BEEF:>ADFDEHBEFHHHHG @read_150_83/1 AATTCATTTATTCCTTACTGATTAACTCATTGGTCATGTTTACTGTGTCAGGCAGTATGCAGTAAATATACAAACACCATTAGGTTTGCTCCTTGCTTTC + HHHHHHHHHHGHHHHHFG@DFFFHHHHHHEHHHHHHHHHFHHC@HGGHHHBFF@A45:FCFHFHHH@5EEDCEGEGGF@D?BEHHHHHHHHHHHHHHHHHEGDGEB@8?B?=>CHHHDHHHFHHHHHHHHH<-=FEGHHH=?@>EEDDDDHEB:?BEA561 @read_150_85/2 CTTTGTGTTCCTGGCTGTGAGCCGCCTCTGGATGGTGCCCCAAGGAGAGCTGCTGTGCAGCCTCAATAATTAACGCCTATGCAAATTGCCTTTTACACCT + HDHHHHGHFEBDGHHHHHHHHHHHFEHHFHHHHFFHFHGEHHFFGHEGEEGGGGA?6;/@BED@=6=B>9=*/DF?EF=BB::78C*57=D><<@EEHFF @read_150_86/1 TCCAGCCATGAGCCACCCCACCTGGCCTGATTTTTTTATTTTTAGTAGAAATGAGGTTTCGCCCTGTTGCCCAGGCTGGTCTTGGATTCCTGAACTCAAG + HHHHHE>DGFHHHGHHHHHHHHHGGHHHHHEGECHHHHHFHHHHHGFFDDD??@FHHHBFGBHGHEEBFFHFFFFEBHHEHHH=DHHEECG?DHGHGGHE @read_150_86/2 ACCACACTATGCCACAAGCTTGCCAGCTACCACTTCCATGTCAACGTATCAAGAAATACATCTGGGCCGGGCACAGTGGCTGACACCTGTAATCACAGCA + DBBFHHHHHHHHHHHHHHHHHHHHHEGHFFHEEGBDFEGEEDE@HFHEHFHHHHHHHGHFHHHHHHHHHHHHHHHFEFHHHB@*6CCCE;;.37+B79<: @read_150_87/1 TTCTGACACACAGGAGTTTACTTGAAGACCACTATTTAACCTTTTGATAGCCTTTTATGGCTACCCTGGTCCCTGAGAAAAATGAAAATGCATTTGCCTT + GHHHHHGGHHHHHHHHHFEHHFHDHGHHHGHHHHHHHHFGEHEHFHHHHHHEEBFHHBD>(6E96DFHFHHB90%%&913>FEG@EBDFGHHHHHHHHHG @read_150_87/2 CGTTGGTGGAGGCTGGCTTCTTGGTGCGAAATACAGACTCGGGCATTCTTGCTGAAGGCAAATGCATTTTCATTTTTCTAAGGGACCAGGGTAGCCATAA + DFHHHHFEHHHHHHHCHHHHHHGHHHHHADG@@BFHHHHFHHHHCCFFHHFGHHHFHH@DFHHHHEHHFGGGGGHHHHHHHGFDCEEDFGFBG?CB??B: @read_150_88/1 CCTGGTTCATTTACTAGCCACCTTATTGAGCACCTACTATACTGCTGCAAGCACCCCTTTTCTCGTGTCTCCCCTCTTTCTGCTGGAAGTTGCTTCCTAG + HHHHHHHHHHHHHHHHFEHHHHHHHGGGEE:?5CGHHHHEFHHHFD??B<=@=EDG@EDFHHHCGFHDFCFHHHEFFGHHHHHHHHHHHHHHHHHF?;-% @read_150_88/2 AAGAATTATAATTACCTTTGCAGAAAGATTTATCCTAACAATTAGGAAGCAACTTCCAGCAGAAAGAGGGGAGACACGAGAAAAGGGGTGCTTGCAGCAG + HHHHHHHHHGGFFDCDFFHHHG@;@6>>CEHE@GHHHHHHHHFD?HHHHBBFHHHDCCBBDEEEFEEEHGHHFFF@11;646=D=C?6@&/)6C@.:/-< @read_150_89/1 GCATTACGTTATGTGGCAATATTTACATCCTCTTTTAAATAAACTACATTCTGGATGCCACTGAAATTTATTTCTATTTAGTATTAAGTTTAGTAACACC + HHHHHHHHHHGGGGBBBAFHHGGGEDGDCEEBHHB297BCCBEEHEHHHHHHHHFFGFHHHFCDHHHFEEGHHHFGEHHHHEBG?HFDA9EFB@/;@?HF @read_150_89/2 TGATCTCAAGTTCGGAATGACTCAGAATTTCAAGACATTTATTTTGGCACCTAAAACTATTACAGACTTGAGTCAAGTGAATTATGGATTTACATGTGGG + HHHHHHHHHHHHHHEDGEBB236+:9<.<5EBEG9?.(;D8EHHHC=FGFHHHEGHHHHHHHHHHHHBB:EHHHHHFHHHFHGGHHHHHFBBD5=?DGBD @read_150_90/1 AATTATGAGCTAAATAAATACTTCCTTGAAATCACTAAGTTTTGGGGGAGGATAGAAGATAGGAGGATATACTGAAGAGGAAAATACTGAGGACTTATTT + HHHHHGGFGGGGFHHGGFHFG>>=6FFHHHHHHHHEFFFEHHHHHHFFFGFFHHHHHDC?BDDDEHHHGFA795,@?HDDEFGGGF<(52:1-6:FE.-& @read_150_90/2 TGAAATGTTTTTTCATTTGTTTGTGTCCTCTCTTATTTCCTTGATCAGTGTGTTGGTAGTTCTCCATATAATTTCTATCATTTTTTAGTTGAAGAAAAAT + HHH8A:6BCEFHHHHFEEGGHFHHHGGGHHGCGGHHHHHHHEHFC:EGGEDCC@@@FFBFDE8FGGHHHHHGDDCD296CFFDHHHFEHHBFC;ECA:+2 @read_150_91/1 TTGACCTTCTCTCCTGTTAAGTGCAGTAGGGCTTCCCCTCTTGACTTTCCTGGTTATAGCTTTCCATCACAGCTCCCCACATTCTCTCTTGATGTTGAAA + HHHHHG@4-256EEEEHHHHHHHHHGGGHGHHHHFGG20=CA>9C6427HHHFEFHHHHHGGHHHHHHED @read_150_91/2 TACTATCTGTGGTTTGCGAATCTACTAGGGGTCTTAGAACATATACTGCTCAGATAAGGGGAACTACTGTATTTTCTTGGGCAGGAGTATGATTTGCATA + HHHHHHGHHHHHHHHHGGHHHHHHGDCDD>.@>ABFHHHHHHHHHFFGEFFHHHHHHHHHHHFGGEEHHHHHHHHHHHEHHHH>C?D;EEFEHHHHHHHH @read_150_92/1 TAGTTTTAGATCTTAAACATTTTCAACCCTTTTGTGTGAATTACAAATTGTTTGACTAGTAGAAAATAAACAGGACAAAAACTGAGCAGTAGTCTTGTTT + HHHHHHHHEEBGHHF>>G>EGDHHHHHHHHHDDAFGEAD@<?GGFHHHHGHHHFCCCBEHDBGGGGGHHHHHHHHHHFCCEHHEHHHHHHHHHFHHHHGD88=@FEFE8=64 @read_150_93/1 TCGGCCTCCCAAATTGAGGGGATTACACACGTTAGTCTCTGCACCTGGCCTACTTATCCTTTAATATTGAAAATGAAAATCTCTATAAAAGGCAAAAATA + HHHHHGGHHFGHHHHHHGHFD==BDEEEEEHFHFFHHHHHFEEHHHHGH:AEHHHHHFHHHHHFE?;AFHHHHHHHHHECGB?HHHHFGD9EHHHFCCHF @read_150_93/2 AAAGCACTTTCTTATTTTTGCCTTTTATAGAGATTTTCATTTTCAATATTAAAGGATAAGTAGGCCAGGTGCAGAGACTAACGTGTGTAATCCCCTCAAT + C5@HHGHHHHHHHHHHHEGGBDGGHGGHHHEFFFGCFFHHH@CHHHG>@DDGGGFDCB76?ADEHHFFHCCGFHHEGB@EHHHHHFHHHHHFEG9AF6BH @read_150_94/1 TGAGCCACCATGCCTGGCCTAATTTTTTGTATTTTTAGTTGAGACAGGGTTTCACTATGATGGCCAGGCTGTTCTCGAATGCCTGACCTTGTGATCCACC + HHHHHHGHHHHHHHHHFHHHHHHHHGHHHHHHHGEHHHHHHHDHHDGHHHHFGHHFGFHCHFFB>GCFCGDEEEEFGEEEHHHH@?EA7<6&0(2BGGHD @read_150_94/2 TAATCCCAACACTTTGGGAGGCAGAGGCGGGTGGATCACAAGGTCAGGCATTCGAGAACAGCCTGGCCATCATAGTGAAACCCTGTCTCAACTAAAAATA + EDDC6-<56;CAHHHHHHHHHHHHFHHHHHHHHHHHHHHHHHHHHFHHHHHHHHHG8EGGHHHDCFHHHHHHFHHHHHHF=E=FFHHHHHE<76EDCHHH @read_150_95/1 AAAACCACAATGAGATATCATCTCACATCAGTTAGAATGGCGATCATTAAAAAGTCAGGAAACAACAGGTGCGGGAGAGGATGTGGAGAAACAGGAACAA + GGHEGGHHHHGHHHHHHHHHHHHHGGGHHHHHHHHHEHHHHHFHHHHHFCHFFFGGBB@EFHDHHHHHD;4A(2*3C?A@=6)>DGGEGHHHFHHEEH=B @read_150_95/2 TGTTCCTGTTTCTCCACATCCTCTCCAGCACCTGTTGTTTCCTGACTTTTTAATGATCGCCATTCTAACTGATGTGAGATGATATCTCATTGTGGTTTTA + HHG@EGIGHEHHHHHHHHHHHHHHHHFHHHHHHHHHHHHHHG?BHHHHFHFIGGHHHHGHHHEEF:;8GGHHGGHHFHEEDBEHHEF6655BDEGCEHDE @read_150_96/1 TGAGGAGGTTTAGGCTCAAGAGAAGGAGCAAAGTGTAACAAAAAGAGCACCAGGCAGTCAAGACCACTGACTTGCTAAGACCAAACCACTTTTTTATCTC + HHHHHHHHHHHHHHHHEEFGGGGHHGHHHHHHHGFHHHHFHHFF8@79@BDGFFFFHHHHFHFEFHB:BCFEFEFHHGGGFCACDBEA=GEEHHHHHHHG>EBGFHHHHHHHGGGGGFFHHHFHHFFEEDDHEFFEEHHHFGHGGFF0:+,-(+A @read_150_98/1 ACAAGTCCCAGTGAAAGACAGGATGAAGAGTGTTTGCTGACCAGTCTCCACTCTCCACCAGCCTTTCCTCTTCCAGCCACACCCTGCTCCTTCCCTCCCC + GGGHHHHHHHHHHHGFHGGFHHHHHHDCDEEHHHHHHHCFFHHFHGGGBCBGGGFHHFFF?FHHHB2@CCHHHFFEFCDD=>>CEAC=9.3*/7/,99@< @read_150_98/2 GGGGAGGGCAGGAGCAGGGTGTGGCTGGAAGAGGAAAGGCTGGTGGAGAGTGGAGACTGGTCAGCAAACACTCTTCATCCTGTCATTGGCTGGGACTTGT + GHHHHHHHHFGBGFGHHHHHHEFHHHGHHHHHHHDHACHHHHHHHFF9E?EGDCFDGHHHHDB=GBBBBBEEEHHHHHHE<6-7,:;))%4><;9CDFFC @read_150_99/1 TGACATTTACAAGGATGTTGATCTTGTTTTCCTTCATAATTTGGAGATGTAAATATTTCAAACTTTCCTATTGGTTCTGCTATTTGTAAATATACAGCTG + HHEGGGG?A>;EFHHHHGF?64>?FHGBHHHFCC>HHHHHHHFHHFFFFHFHHHHFEEDDEEHHHEHHHEBEFHFDHHHHHHHFGHHHHGGGHHHFFHHH @read_150_99/2 CTTATGTGTCCAAGGACAGCTGTATATTTACAAATAGCAGAACCAATAGGAAAGTTTGAAACATTTACATCTCCAAATTATGAAGGAAAACAAGATCAAC + HFFFGHEFHHHHHGDDFGHHHHBF>HHFHHGGFHFGGFHHFHGEDCFHHHHHHGEFB4,*2E @read_150_100/1 AATAAAAGTGAAAAAAGCAATCAACAGTTGAAATTGTTCATCACTAGCCCAACATCTTTCCTATCACATGCCCCTTCTTCTCTGCTAATAGAACCCCTAT + HHHHHHHHGGHHFCD=DCHHHHHHHE;@BGGCEGHHHHHFFGGGGHHHHCFGGEEEFCHCFF<;EFDBDCGGGGFDEGGEFHFFHHHFBFGGG;BD4>?E @read_150_100/2 TTTCTACCGATACCTAGCAAATAGGGGTTCTATTAGCAGAGAAGAAGGGGCATGTGATAGGAAAGATGTTGGGCTAGTGATGAACAATTTCAACTGTTGA + HHHHHGFHHHFEFEBEDEFFHGFHHHHDGGE=B@FHHHHHHHHHHGDE.ABGFDFFEF@FH @read_150_101/1 GATTACAGGTGTGAGCCACCTTGCCCAGCCTATTGTCTTATCAACAGGATTAACGGCATTTTCACAAGGAGTAGATTCCATCTCAAGAAACCATTTGTTT + HHHHHHHHHHHHHHHHHHHHHHHHBCEBFFGGGCGGEEFHHHFEEHE?B;6DA;DEDHHFHHHHBBBEDBFAEE@CEGBCDBGBEB@?=@@>GFHEFGEF @read_150_101/2 ATAACTAGACAACTGAAAATATGATTGAATTGCTGCAATCTCACGATCAAACTTGAATGGATGAGCAGCTATTCTTACGGGTGGGCAAACAAATGGTTTC + E@8<5<=D=DHHFDD>@.C>@BD== @read_150_103/1 CACACACACACACAATAGAATACTACTCAGCCATAAAAAAGGAAAGAATTAATGGCATTCACAGCAACCTGGATAGGATTGGAGACCATTATTCTAAGTG + HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGGEBGGGGHHHHHHHHEFHHHHHHEFHHHHHHHGEEDEGFHHHHHHHHHEEEEFE@);@;AADDEFADHH @read_150_103/2 GCCTTTGCATCCTCGTAGCCTAATTCCCACTTATGAGTGAGAACATACGATGTTCGGTTTTCCATTCCTGAGTTACTTCACTCAGAATAATGGTCTACAA + HHHGHHHHHHHFGBBDFGGHGD@HFDGEEHFHHFB.%3)331)%%-*'4()&*/ @read_150_104/1 ATACTTCAGGGGATGAGCCTGGGTCCTCCCCTCCTGGCTGACAGGAGCCTGGTGGGCAGTGGGTATGTGGGGCCCGTGTAGGGGGGTTGGGCAGCACTGG + HHGEEGGHHHHHHHHHHHHHHHHHFEG@>BFHHHHHHHHHHHHHHHHHHHHHHF=DEDGE,-AHHHHHHFEHFD9DEEGEHHHHHHHHFHGFFFACEFHH @read_150_104/2 ACCAGTCCCTGGCTCCCTGGCCAGGCCCAGTGCTGCCCAACCCCCCTACACGGGCCCCACATACCCACTGCCCACCAGGCTCCTGTCAGCCAGGAGGGGA + HHHHHHHHA?HGHHHFDBHHHHHGFHF9>ADD7828.?EEDD35:A<.A@><9ADE@@@C@7&%< @read_150_105/1 CATAGCCCTTCAGTGGATACGTTGGGGAATGGAAAATGAGTTATTCAATTGACTCATTCAAATGAGTCCTGGTTTTTCTTCCATAATATACAGATAAGCA + HFGGGFFFFFHHGGFGGHFFGGGDHHHFFBDEDGHHHG>10+8<@B5<+)6(8;EHEFF:AHDGGHFHF)85CD6: @read_150_106/1 CCCTCTTCATATGACTCAAGGCTGCCTCACATCCTGATGTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCACCTAATCTCGTATGCCGTCTTCTG + HHHHHGFFFGGHHHHECC@@BGHEEFGHGHHHHHEFFCFBHHHHGGHFHHFFHGGGHHHHHHHHHHHHFDDDA9BCBBFDDFFHHHHHHHGFHHHFBBB? @read_150_106/2 ACATCAGGATGTGAGGCAGCCTTGAGTCATATGAAGAGGGAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAA + HHFFHE>?<<@GGDDGD@EHHHHHFGHHHFHHHHHHHHHHHFFHHHHHHHGGGHHHHHFHFGGHHHHHHDHHFFHGHHHHFGFHH@@EBGE=GGGHHHHH @read_150_107/1 ACTAAGTCTTGTTTGCATTCCCTTTCGGAGCAAGAAATCAATCAGATTTGCATATAGGGAAAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCACC + HHHHHHHHHHHGEDDFGHHHHHHHHGGFHHHGGBGHHHHGGGGHHHHHHHFHHFFHHHHHHFAADCFFB?>;;?GHHHHHHHHHHHHHEHHHHHCFHHHH @read_150_107/2 TTTCCCTATATGCAAATCTGATTGATTTCTTGCTCCGAAAGGGAATGCAAACAAGACTTAGTAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATC + HHHHFFGGGGHHHHH@50)6C599;D?>HHHGGHHHHHGAEBFFFFBDHCHHHHHGGHHHHEHDHEGF@@EFHHHHHHHHHF><>BDDGBCE0<+>FCC; @read_150_108/1 TGATCTTTTCCTTTCTAGCTTAATGGCTTTCCTAGAAACAGAGCCTGAGGTAAGTATTGAATGCTAATGCTTTATTTAGGAGGTATGTTTTTATGGCTGC + HHHHGFBHHHHHHHHHG=2BGGHHHHFHGHHHHHE;>BBFDEF9BCC:,0FHHHHHHHHHEFHHHHBFFHHHHHFHHHHGGE=>>7DFHHHHCD.3>CDD @read_150_108/2 TGCTTCAAACTGCCTCGCTTCCCTTTTCGCTCAATTTTGCAGCCATAAAAACATACCTCCTAAATAAAGCATTAGCATTCAATACTTACCTCAGGCTCTG + HHHHHHHHHHHFFFHHHHHHHFGEEHHHHHHHHHHHHHHHHGGGFE;?CBFGIGGEHHHHHHHHHHHHEEEGHHHGFBGEHDHHHH?;DFBHHHHHH>9DABHHHHHHHHHHHFEEHFHHAGEFGGG @read_150_109/2 CAAGGTAACTCTCCCTGTGTGTCTTCCTGTAGTGCTGGCTCTCTGCCAGCTTGGCTCACTGCCCAGAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA + DDGGGFEEE@?7@CCGFHHHHHHHHHHHHHHHHHHHGGHFHHHFF;08DGHHHGGGHHHE@BE=D;>@?>6.:CGGGGFFGHHHDEFFHHHHFFFGD;AC.3CCFGGEHGFEFFD+/>3+2;29; @read_150_110/2 AGGCGCCCGCCACCACACCTGGCTAATTTTTGTATTTTTAGTAGAAATGAGGTTTTACCATGTTGGCCAGGCTGGACTCGAACTCCTGACCTCAGCTGAT + FHHHHBB=DC@ABFG=-11119=D9GGD.6.84?;DGFHHHHHHFEHHHHE??EE<*.::.@GGHHFH?HHE:.<4.:ABE?CDGEDFHDEEEHHHHHHFGFGF @read_150_111/2 CAGTCACCTCCAACAAATATTGCTACTGCTCATATCTTGGGAACTGCCTGCCATCAAGAGAAGCTGCAGTGGAAGAAGCATGAGATCTGCAGCCTTCATT + HHGHHHHFGEEE@6GGHHHHHHHHHEGGFGHGHHHHHHHDDBFHFFE/1@:>@GFHFHHHHEGFHHEHHHHHGGHHHHHCDGFFGHGFHHGFCHHHHHHH @read_150_112/1 TCACCATGTTGCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCACCTAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAA + HHHHHHHHHHHHHHHHHHHHHGGGGFGDFGFFHDDC?EACFFHHHHHHHHHHHHHFCGFFFHHHFEFDEFB@D@A4?7773,5*, @read_150_112/2 GCAACATGGTGAAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGCTCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA + GGFGBAEHHHGHHFHHHHEEA8CADD:.8DEDFHHHFGHEDCEBE>:*EFFDDBDGHGGFEBGF@>>B=336BDHHHHHHEBEE.659=AFHHFFBCA?E @read_150_113/1 TCACGCTTATTCATTGATGGGCTGCCTTCTTACCACATGTCCTTGACATGTTTTAATTCCTTAAGTCCTCATAGTAACCCTAGTACATGTACTCCTGTGA + HHHHGFFEB2GGHHHHHHHHHHHHGFGE8EAEFC97B<7DDEC@FHHFDFDGD=HHHHHDGHEE??CCEHH @read_150_113/2 CACAGGAGTACATGTACTAGGGTTACTATGAGGACTTAAGGAATTAAAACATGTCAAGGACATGTGGTAAGAAGGCAGCCCATCAATGAATACGCGTGAA + @><855@5D8BEE>DDDCBA1=58:<6;=B@GEEBFDC= @read_150_115/1 ATTTCAAACGGAGCCTCTTCCTTCACAGTTTTCCTTCAGAGCTCCTTTTTTTGTTTCCATTTTAAAGTTATTGTTTATTCTAGACAGGGAATCCTGCCAG + HHHGDCHHHHHHHHHHEAGHHHHHHHHHHHHAFGFHHHHHHHHHEB=EDEHEEBGHHHDFHE4DCFFFGFG@FHHFFGEFDFFHHHHHHHHHECCFFEFH @read_150_115/2 CAAAAAACAAAAAAAACTAGGTAGAATGTGATACATGTGAAAAGAGATCCAGCTCAAGTGCCTTGGGAGCTCAGGGGCGGGTGAGATTAATCTCTTTTTC + HHEHHHHHHHGF;9EE21,*60(2FFF@<<<:,A6,=D@@A@ @read_150_116/1 GATGGCAATGAGGCGCCACCAAGGTTTTTATTTTTCAACTTTTTACTTTGGAAAAAAACATTTTTTTTTTTTTTTGAGACAGAGTCTCACTCGGTCACCC + HHHEFFFFB=DA?CFEHHHHHHHHHHFHHHHHHHHHEHHHHHHHHHFHEDHHGGHHFBBHH?CBDDDB;:*3>HHGEE:61<<;+7?>?D@(%C5@@BHHHEGGECGG=@B8CDFFG;8EEIFFHHHHHHHHHHHFHHHHHGHHHHHHHHHHFHHHHFBE2?EFE.5,41-<5>AEFDCFBCFHFADG @read_150_117/1 TTGTCTATGGCTGCTTTTGTGCTTCATACAGCAGTGTTGACAAGTTATGACAGAGACAGTAGGTTTAAAAACCTAAAATAGTTACTTTCTGGCCCTTTAT + =;BGGGHHHHHHHHHHHHHHHHHHHHFFFB>HHHHHHHHGHHHGGHHFGFGGHFHGGHHHH>@<59>AFH8@EGGGGHHHHHFBEHHGIGHHHEGHFHGEGGGBHE=)4E7403A@D?DFBC @read_150_118/1 AAAAATCAACCGTGCCAATCCTCTGTCTCTTCAAGATTAGTTGTAGCTAATAGAGGGTGAACTATGGCTCAAATATAAAAAGATCGGAAGAGCACACGTC + HHHHHHHHHFGGHHEBGHHHHHHHHHHHHHHHHGBEFHHHHHHHGHHHHHHHHHHHHF6><FGHHEFHHEHHEEHHHHHFHHHHGDCC823*/%2/1DHHHG @read_150_119/2 TTGTAGTAACTCGAAGAATCAAGAGAAAAGCTAAATATTAACATCTAGATAGCAAGATTTAATGTGCAAAACTTTAGACTTCTTCAAGCTGAATCAGCCC + HHHHHHH@*?-5>9-><;=HHHHHHFHHHEDEEG/+86;2DDHEFHBEDCGBEFFB5CBE@FGGGDBFF?=;@<1')-/BGE@+6<5,@FBAE@AHHHFF @read_150_120/1 AGCAATTCTCCTGCTTCAGTCTCCTGAGTAGCTGGGATTACAGGCATGGGCCACCACGCCTGGCTAAATTTTGTATTTTTAATAGAGACGGGGTTTCTTC + GGGGHHHHHHHHHHHHHAHHGGHHHHHHHHHHF@?GFHHHHHHCFFFFHHHHHC?FFED=/BGHHHHHHHGEGHB=59ACA @read_150_120/2 ACTTTGGGGGGCCAAGGAGAGTGGATCACCTGAGGTCAGGAGTTCGAGAACAGTCTGGCCAACATGAAGAAACCCCGTCTCTATTAAAAATACAAAATTT + HHEEE?BGHHHHFHHHHHHGHHBH<@FFHHDDCDFHHHEGH?DDC>F?<3)+3*90>@;C@>DB3?ADGH@ACBC05ACDCEEGCFD=ADDDHH @read_150_121/1 CTCTATCTTTACCTCCAAAGTGCTTCCGCATCTCTTGTCCCATTTTCTTTTTTTTGCCCTATATTTTAAACCAGGATTCTGTTGCTGGCCATAACACATA + HHHHHHHHHHHHHHHHHHHHHGGHHFGE>>DDDDDEEEEHHHHHHHHFHFFHHHHHHHDDCEHCCFHHFHHFHHHHHHHHACC>?A?EFCHHHHHHHGFH @read_150_121/2 CAGAGATCTGGGTTCTAATCCCTGAGATGTTACTGATTTGGGGTATGTGTTATGGCCAGCAACAGAATCCTGGTTTAAAATATAGGGCAAAAAAAAGAAA + HHE=EHHHHEHHHHHHHHDDHHFEHHDDEEHHHHHHHHHGF>@@:FHHHHHEEGHHHHHHHDHHHBEEHGEHEDD72EEGHHHHEEEEHHHHHH;45,4C @read_150_122/1 TGTGTCCTCTCTGATTTCACTGAGCAGTGGTTTGTAGCTCTCCTTGAAGAGGTCCTTCACTTCCCTTGTTAGCTATATTCCTAGGTATTTTATTCTTTTT + FHHHHHHHHHHHHHHHHHHHHFHHHHHHHFGFGGHHDFEEGDBBBDDCFFHHF;>;B)')6GDAACE @read_150_123/2 ATATGACACCAGTGACTAATCCTGAAGTGCGGAAAATAGATGATCTCTCAGACAGGGAATTTAAAATTTCTGCCTAAAGGAACTCAACAAACCAAGATAG + HHGHHHHHHHHHHHHHHHHHHHHHDGGD5>CHHHHHHHGE/08ABBGBHHFIIGCDHHE@ADEEEHHGGBHHGFEHHHGBE@GFE7()9>,:FF@FG?>5 @read_150_124/1 CTTGTTCACCTAGCAACATTTAACAATGATACCTCTTTTAACAATTCAGGATGTGAACGACATAAATGAAGATGGTGAACATAGATCGGAAGAGCACACG + HHHHHHHHHHHHHHHHHGFBGGGGGFFFEGHHH;FFF@ABCCE;@EEEHHHHFHFHFEHHEFEEEHHHHGBFDHHHHCHHHHGHHHHHHHHH9CHGGHHE @read_150_124/2 ATGTTCACCATCTTCATTTATGTCGTTCACATCCTGAATTGTTAAAAGAGGTATCATTGTTAAATGTTGCTAGGTGAACAAGAGATCGGAAGAGCGTCGT + GBHHHHHHHHEBCC;<87CEHGHH@FEG>HHHHGFEHHEBEBGFHADCDFHHHHHE=B9CD(6EF @read_150_125/1 GACACCAGGTGGGCCTGAGCAGGGGGACCAAGCGCCTGATGGGCTGTGGGGCTAAGGGGGGAATCGGGTGGCTCCCGGGGGTACAGGCTGGGTGTTGGGT + FEEEDDDHHHFHHHHHHFHHHHHFEGGDFEGGHHHHHHFHHHHHHHHHHHEFHHHHHHHFHHHEHHHHHHFGB2?GDAAGHHHHBEHHHHHGCFHHGFFD @read_150_125/2 GGAAGGGAGCAGGGCCAGCAGGGGATAGGGGGCACTGCCAAGCTGTCAGGGAGGCCAAGGCACGGCTCATCCCTTCGGGGCCCCATTTGGTGCCTACTCT + HC?FFHHHHHEGHHHCBGHHEE.DHHHHHF<<7BGHHHHHGGFHHDCFHHHHHHDBEEGGGGEE;A<974<>:783:BAG=<>,86??GADB;57>@CB? @read_150_126/1 AAAGTAAGTGAACATAACATTAAAAAAATTCAAGGTGAAAATATCAAAGGAAACAATAGTGACTATTTCACTGTGATAAAAAGAAAATAATTGAAGGACA + HHHHHHHHHHHHHBGFDFHEBEBEEFHHHHHHHHGHG@CE829A-,>FHDEEFBHGHHHHHHFHHHHHHHHFEFFFBDHFBE756DFFDBE;BGHEHHEE @read_150_126/2 ATTTATTCTGACGGTGCATAAGTTTTAAATGTCCTTCAATTATTTTCTTTTTATCACAGTGAAATAGTCACTATTGTTTCCTTTGATATTTTCACATTGA + HHHHHHHHHHHHHHHHHHHCGGGGFFFHHFFGBBGGGHHHHHFFAEA>6=EEBDGHHHDD<><;8<.77DEHHHGHHHGC+797E.;>CAFDFFGGFFE:>EDHHHHHHHHHHHHHCHHHHHHHHHHHHGHHHGE/@=@BCDBB69B:ABEDEEHHHGGFHFHHHHHHFFHFDEHGHHHFFDDD>@DDA>FHEBFHFFDFFFHHHHHHHHHHHFFFFCGGFFGEFFGHHHHHHHFGEBFCBEH @read_150_128/2 CTTTCCTATCAAGCCAATCCAGAAGTAGGACTTACATTTGAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAA + @GEEEDDHHHGGG@DEEGHHFEEFFGHHHHHHGIGEHHHHHHFDBHHHHHHHHHHHHHHHHHHHFF=EGFAHHFHHHHHB@?D@CFGGG?AHHGFHHHHHHHGEE?EEHHHHDA=>EEEGHHHEEFHHHHHH?HHFFHHHHHHHHHHHHHHHHGGFHB8;E+'+8;CHHH @read_150_129/2 AGTCACTGAGGCCAGGAGAGGTTAGTGTAGGAAGAAGGATGCATAGCAAAGTGAAGGGAGCAGCACTAGGAGGTGATGAAGAGCATAGGTATTGAAATCC + HHHHGHEHHFDDFHHHHHHHHHHHHHF@?>,9)+(4B8EHHHHGGGFHHEDCDD45EGHHHHHHHHHHHGGHHHHFFHHHHHHHHHHHBGDCDB@87CC? @read_150_130/1 TGCAGATGAAGCTTGTCCGTGCCCAGTGCCTGAGTGTCTGGAGCTGTCTGCTGACTGGAGCTGGTGGCGGGATCCATGTCTTTCTCCTGCACTTGATCTT + HHHHGGGGHHHHHHHHGF?C=FGGDE=::2/&-6FFHHHHFFGHHFHFFFFFEEHHHFHH?D>FEHFFCDHFFDD4,04>DCFFHEE@CCDD4B-+)35D @read_150_130/2 GGCACTCTGCAGACAGCTCCAGAAAATCAGGCACTCGTCACACACAGAATTCCTCTAGTGGACAGGCTGCGTCATCCCATGAACAGGCAAGATCAAGTGC + DBBEG;<@@FDHHHHHGGHHHHHHFGGGHGHHHHHHFHHF=DHHEFGB/8:=785B9>@HHHHHHHHHHEC@@?@GHHHFHH@7EHEE@B55477&0:11 @read_150_131/1 GGTTACATCTTCACTTTGTAGAAGGCTAGAAGGCACAGTTTTCTGGCAGTTCAATGTAACTCAAATTGGTAACCTCCTTTTATCAGCTCCAATATTAAAC + GGGHGHHHHHHHHHGBEEHD;DHHGGDBGHGFFHCAFDEHHHHFFEHHGGFFHFGDEDGFFHFFHHHHHEHD@ADDDDDC>@8DHHGECCE@EHHHFGGB @read_150_131/2 TCACAGGAAGGTTTAATATTTGAGCTGATAAAAGGAGGCTACCAATTTGAGTTACATTGAACTGCCAGAAAACTGTGCCTTCTAGCCTTCTACAAAGTGA + HHHGFC@6?@@EFIIHD?FHHA@..45CDEE;BFFDHHHHFFFDFD?EEA4D @read_150_133/2 TTTCAGATTCCAGGAAGTTTAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAA + HHHHHHGHHHGGGG=C@=D@>@??=EE@GGFGGGHHHHGGEHHHHFDDDAFEEFF=>8DHHHHHHHHHGGFBDC>CBBGEEDB95.55;HHHHFEA=EE@ @read_150_134/1 CACAAACTTGTAAGAAACGTTTTAATTTGTCCTGTCAACTTCAACAAATTTACAAGAAAAAAACAAACAACCCTATTAGAAAGTGGGCAAAGGACATGAA + HHHHHHHGHFHGGGGGF8%9DBBHHHHHHFFFGGHFFHHHHHHH?E@:?BFHHBEHGGHHHGCEB,:0:))4;CD @read_150_135/1 CAGATTTTTGGTAGGTGCATTCTTCATGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCACCTACTCTCGTATGCCGTCTTCTGCTTGAAAAAAAA + HHHGHHHHFGFFEHHHHHHHGGHHHHHFHHGHFBHHBEDD@;DEDHHHHHHHHHHFHFGFHFCBAEEE)9EGFFHHHFFFEEGHHFFHFHGH512DFFED @read_150_135/2 CATGAAGAATGCACCTACCAAAAATCTGAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAA + HHHHHHGEGG=EHHHHHHHHFECBHEDF??FGFH;@GFD9@FIGGF@@>GGFEHHHHHHHHHHHHHHFHE8(<@)..:>CD,9 @read_150_137/1 CTACTAAATATACAAAAAAAAAAAAAATTAGCTGGGCATGGTGGCAGGCACCTGTAGTTTCAGCTACTCAGGAGAGATCGGAAGAGCAAACGTCTGAACT + HHHHHGFEDHHHHHHHHEE8GGHHHHGEGHHHHHHEFFFEHHHHHHHHHHHFDECE9D@DEHDDDEECAACCB:=9A=@BFHHAFFF0(+?DDEEGEEHE @read_150_137/2 CTCCTGAGTAGCTGAAACTACAGGTGCCTGCCACCATGCCCAGCTAATTTTTTTTTTTTTTGTATATTTAGTAGAGATCGGAAGAGCGTCGTGTAGGGAA + HHHEEBEHHHHHHHHFHHHHHHHHFGHHHHHHFGGGFHFGF?EGE566/)20?GCDEGDEHHHHHHFHHGFC=88BBCEEEDEFHHHE4G8:?;DFFHFE @read_150_138/1 AGATTTGTAACTTGGCACAAAAACTGCTTATGTTAGATATTCAATTTCCCTGTTCTTGTTCCAGGTTTTCAAAGAAATTCCCCTAGCATCCTTGTCACTT + HHHHHHHHHHHHHHHHHHHHGHHHHHHHF9?CEF@8:EHHHG@53ADEBEGFFC;=:<49AFFEFHGFFEF;2&%');6=AHHHHFFHHD@FHH?=EEEEHHHHHHGHHFCHHFEHGGGGG @read_150_139/2 GAATAATAAAAAAACCGGTCTCCTGCATAGCCATCTATGCCTGAATTACTCTTTCTCTATTGCAATCCCCTGTCTTGATATATCTACTCTGTCTAGGCAG + HHHHHHHHHHGGHHHGGGFBBGGFB<2)@BHED:73.66)+9DBB4;ACBHHHHHHHHHHHHHFFAGDBAB<9DHHHF?EHHHEE@EB>DDHHHHEE5<= @read_150_140/1 TCTAGAAGTTGTATTTCTTAAAAATAAATGTAATGTGGCTACTTGGAAGAAAGAAGAATGGGAAACGTTGATTTTTCTTGTAATCATTTATAGGCTATTG + BCDAADHHHHGFEHG=@;;>D@HHHHHHHHHHFHHED>AFHHHH @read_150_140/2 ACAGAGCGAGACTCCATCTCAAAAAAATAAAATAAAATAAAATAAAATAAAATAAAATAAAATAAAAATAGAGCCTCTGACATGAGTTCCACCAGAAAAC + :>>>:14D @read_150_141/1 TCTAAAAGTTTTAAGACCATTAGGTTTGATCGTCTTTCTTCTTTAATCTGGAAAGTTTGTCTTCAATTCCTGTATGAGACTTTAGGAGTTTCGAGAGCGG + HHHF=FHHHHHHFFGHHHHFFHHHHGGHHHHHHEE=6FGEFFHHHFGFHHHHHHFHHHHHHHHHHHEFHCEEHFHHGFBD:;2E8BGFE6EEE@C2%9;F @read_150_141/2 CGAAACTCCTAAAGTCTCATACAGGAATTGAAGACAAACTTTCCAGATTAAAGAAGAAAGACGATCAAACCTAATGGTCTTAAAACTTTTAGAAGATCGG + HHHHHHHHHHHHHHFFHHG@EGG8CHHBDCEEDCDHHHHHHFHFFHFFGGEECCA>DHHEGDB?C.:FHHHF??=DBFFEG=EHHHFFIGE?>2:(8>.1 @read_150_142/1 CTTTCAGGCAAAAATTTTGAAGTAAGATGTGATGCAAAATTTTTTATTGAATTCAGTATATTTGGCCCTATATTCTTGACTGTAGTAGTCAGAGGAGGCT + GGFFDBEACBDBBEEEHHHHHHHHHHHFEEHHHHGHHHHHHHGBDA:EGGHDB??GGGFFDHFHHHA9>EFEDCFGFEDDHEEBDEGGHHHHHHFGF:DF @read_150_142/2 TCACTCCCCACCTTTCACTGAACTAAATTATTATGGGCTTTTAGGTGAGTGGGAACCAAACTTTTTTTGTTGCCTCATTGTATGTTTGAGTCCATTTGTT + GGED=FGHHHHHHHHHHHHHHGGGDGGEDDDDEEEFHHHHHFHHFFHHHGHHHGFHHHABGHHHHHHHHFEEEGFHGHEHHHHHHEGCDFBB.CD @read_150_143/2 ACACTTGGAAGTTCTCGGGGAGCTCTAGATCCCTCTGTCTCCCCACTTCCCTCCTCCCTCCTCTCGTCACCTCCTTTCCTCTTGCCTTGACTCTCTGGCC + EFHHHHFD?=-9;:>CDEHHHHHH@0'-.6;@EFFFFGGHHHFED=CE/->99=FBB+3> @read_150_144/2 AGTTTGAATTGTACGAATGGTCCCATTTTCTAGCTCAAATCCTTTTTTTTTTTTTTTTTTTTTTTGAGACAGAGTCTCGCTCTGTGGCCAAGCTGGAGTG + HHHGGDGHHHHHHHHHFGGGHHFHGHHHHHGHHFHHHHHHHHHHHHFHHFHGDEFGHBB?DDGGGGEEB4<8=21:@CBF?1&6<(+9=CHHFDEDB9GF @read_150_145/1 ATATCAGTTAATAAATGTTAGATTCATTGGACAGTACCAGGCACATAGTTAAAGTGCAGTAAATAGTAGTTATTGTTGGTATTGGTGTTATTTTATGTTG + HHHHHHHHHHHHHFGHHHHHHHGHHFFEHHEHHFFHHHHEHHDDBCDFHHHHGGGEHHHHFDB9BFHHHHDEEHFFHHHHHHHDE;:BGDEHHHHFHD3( @read_150_145/2 AACCAGTGAACAATCCACAGGCTGCAAAGATGATGTTCCTATTTCCTCATGAAGGTTCCCAATCACTCATCCACTTTTGATTAAAGAAAAGTGAATGCAC + HHHHFHHHHHHHHHHHHHEHHHHHHFGDDGHHHHHHHHFHHGGEHG@ADFHHHHHHHDCBBDHGH<@=GGHHFHHHHHEDFFBCGGEDEHGFF9ABEFGG @read_150_146/1 GGGGATGATTTTCTTGTGGTATGCCAGTGACATTGCCTCCTCAAGAGACCTTTTTAATTTAGCTTTATGGAAAGTAATATAAGATCGGAAGAGCACACGT + HHEEEBCCGGGGHHHHHFFHHHHHHHHEGGEHHHHHHHHHHHFHEEFAAFHHHHGGGFEHHHHHFHHHC@CBEC:;::=D?HHHHFHFEDEDDFFHHHFF @read_150_146/2 TATATTACTTTCCATAAAGCTAAATTAAAAAGGTCTCTTGAGGAGGCAATGTCACTGGCATACCACAAGAAAATCATCCCCAGATCGGAAGAGCGTCGTG + HHHHGHHHHGHHHHHHHHHHHHHHHGG@?>.DHHFGHFHGDAFHHH@=AC<;CB/3(8D:EHHHHEEHHHHDEGGGHHHFHHHHHHHHHHDEFGFHFF;= @read_150_147/1 CAGGTTCTCCAAAGCAGATCGGTGCTCAAGTACCAGGAGTTTAGGAGTCATGAGGCTGAGAACCTCTTCACAGGGCCTGCTGCCCCACCCAGGGGGAAAC + GEEEGFFFHHHHHHHHHEHHHHHHHHHFFA9=CBHHHHHHHHHHFHECHFFFHHHHHHHHFHHHFFFHHFD349EDDDFHHHFEHHHFHHHHHFFEEHHH @read_150_147/2 TGAGATTCCCTGTCATACCAGTTATGGATAAATTTGCATTTTGGATGGGACATTACTGGACCAGCCCATTTTAGGCAGTTCCGTTTCCCCCTGGGTGGGG + HHHHHHHHHHHHHHHCE@GHHFGGFGGFCFHHHHHFGHHHHGGFHHHHA.GBCDDEGEC@GGHHEFGGGF@572(5-<ADFGHHEF=B:>F>BDHGFFGHF @read_150_148/2 TCTAACATTCCTGGCACGGAGGTGCATAGGGAAACATCATGTATTTCACAACTCCTTACTAAGAGGATAAAAATGACTAATTCCTTAGGAGAGACAAGGT + <56:<.5??EFGGF:EHHHHHHFGB:?DGHHHHHHHFFHHHHHHHHHHHHFGHHHHHGGEHHEF@EHHHHHHHHHHEFEFFFH>>?2?CBC::>CHHHEG @read_150_149/1 CAGGAGTTTGAGACCAGCCTGGCCAGCATGGTGAAACCCCGTCTCTACTAAAAATAGAAAAATTAGCCAGGCATCGTAGCGTGTGCCTGTAATCCCAGCT + HHHHHHDEEHHHHHHHHHHEGHHHGHGHHHGFA@HHHHC?GGHHHHHHHDBDB%395>@DEEFFAHFHEFHF@9EHHHHHHH@GGHHHHFFEFHHHFFGF @read_150_149/2 GTCTCGCTCTGTCGCTCAGGCTGGAGTGCAGTGGCACAATCTCGGCTCACTGCAACCTCTGCCTCCTGGGTTCAAGCGATTCTCCTGCCTCGGCCTCCCG + HHHHHGGE=DEFFBCEGHHHHGHHHHHHFHDGHCEB?17/.;EBEFGFDD6BGFFFBGHEB=:80.6607FHHDFBFGHGHEFC/3:+=6115DHGGG80 @read_150_150/1 ACTGTGCATAGGGCCAGTGCCCCAACTCCTGCATTGTTCAGAGGTCAACTCTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT + GGHHDHGGHHHHHHHHHHHHHHHHFGHHGGGEHHHHGGGGEADFHHHHH@FFGHFHHHHHHHHHFCHACFE=ADFFHHFHHHHHHHHHHHHHHGGHHHHH @read_150_150/2 GTATACAGGATTTAGTACTAATCTAGTTTTAGACATCCACTGGGGGTCGTGAAATGTAATCCTCATGAATAACGGCAGGGGGATTACTGCAGCTTTGTGT + GGGGFHHHHHHHBGGHHEHHHFHHHHHHBDFFHHCGHEFEFHHHHBFFGEHHHHHHHHHHHHFABEEDDHHHHHHFEHFDC?DBBDFFF49=7,6)%4>B @read_150_151/1 GAAAATGAGAAAGAGTATTTAGAGATTTTACTGTCTGTGGTGGGTGATTTTAACGTAGGTCTTGCAAAGTAGGTAATTAGATCGGAAGAGCACACGGCTT + HHHHHHHHHHHHHGGGHHGHGFGFGGGHHHHH@HEEFHEGHHGDFECDAA=A?FEHHHFFFGGHHFHHHHHHHHHE26@CEHHHHHGHHFHG?B8.*>>> @read_150_151/2 AATTACCTACTTTGCAAGACCTACGTTAAAATCACCCACCACAGACAGTAAAATCTCTAAATACTCTTTCTCATTTTCAGATCGGAAGAGCGTCGTGTAG + FEHHHHHFFBF=@DCGGHHHHGGHHHFFFEDA;>B@GHHHHHHBDEEFHHFHHHHHGGHHHHHHHHHHHHHHHHHHBDBFFHHHGHHHHE;@AHFH?DD, @read_150_152/1 AGTTTTATTATTGGTCTTCAATCAAAAGGCAACATGCCATTGATAGAAAAGGGTAACTTTACAAAATAAAATACACTGTTTCCCTAAAGGAATTAAAGAA + HHHHGGGFGFGHHD4FHEFHGGHHEFEEDFFHHHEFGHHHHHHHHHEHHFHFHCBDHHCHHHHHBAEDC8@EEEB=C=/1&;EDDHHHHHHHGFGFDDDC @read_150_152/2 GATTATATAAACAGATATTTTCTTTATCTATAAAAATCAGGTAATGAGTGCTCTGGGAATTTGAGTAGGATAGGATAGTTTCTTTAATTCCTTTAGGGAA + B@GDCEEEHGHHHHHHHHHHHGDGGHHHHHEHHF@A?@:=%1/D=8,?ABDHHEECFHEHHHGHGB@8<8CC>>.6>CHHHHHHHCC@CEA3;CFHGGEGHHHGFGHGB??DFBFBFEC @read_150_153/2 TCCCCCTCCCCTTCCTCTCCCCTTCCCTCCCCTTCCCCTTCCTTTCTTCCTTCTCCCTTTCCCTTCTCCTTCCTTCTTTCTCGCCTTCCCCTTCCCCTTC + FGEFHHHHHHHHHHHHHHHHGGDDEHHHHEH>=.:1*++<@:DEB>4@58@:FHHHHHHHEGGHHGGGGG46-,31,:FFHFFHHDABC< @read_150_154/1 TTTTTTAAAACCTTTGTCTAGTAACTCCAATTTCTGTCCTTCCTCCAGGATGGTTTCTGTCAATTAACCTTGGTCCTTTGAATTAGTCATATTTTTGTAA + FEGGHHHHHHHHHFBDHFHHHHFGHFFFHHHGHGHHGFHHFHHHHFHHHHHHHHEFDEHHHHGGGD?DCDFFFFEHHHHHHHC@7CGHHE:?EEHHE><> @read_150_154/2 TACAAAAATATGACTAATTCAAAGGACCAAGGTTAATTGACAGAAACCATCCTGGAGGAAGGACAGAAATTGGAGTTACTAGACAAAGGTTTTAAAAAAA + 95<<@@DDDEBEHHDGDHHHD?C@BBBHHHFHGB>FHHHHHHHFI8><<?GEFFEEFHHHHHHHHFFEDFDF?D?6/CCD;A:4??ABHHHHFF?@DF< @read_150_155/2 TTCCCATGAAGGTAACAGGCATATAAAGTAGGGGGCAACCTTTATTAGAAAAGAAAAATATCTAACTCATATGCAGAGAGGCAGACAATCTTATCAAACA + HHHHHHHHHHHHHGHHHHFHHHHGDEHBFFE>;A7C>>;:.@CEHHFFFHHBE<.60(''64B@D/;<<5ADGGFHHHHHHHHHGHHHGCBEAA?BCFHH @read_150_156/1 GGATAAGGCACACACAGAAGAGTGTCATGAAAGCCTCCCACCCACCAGTATTTTCTGAGCATGCACCACATGCAGGCCCCGCAGAGGGCCTTCCACACCT + GGGHHHHHHHHHHGGHHHHHHHHHHHHGHGHGBFFHHHHHFGFF?00,/EABFEG @read_150_157/1 TCCTCCCAACTCCCACGGCATTATGCTGCTGTCATTGAAACCTACCACCTTCACCAGCCCAGACAACATGGTGAAACCCCATCTCTACTAAAAATACAAA + HHHHHHHHHHHHHHHHHHHEHF?A>?EHHFGEEHHHHHHFHHFFFBFHHFGGGB:BFB?CAEHHHHHHFHEHHHHHHHGGHHHHHHGHHHHHHHHHHHEE @read_150_157/2 GTCCAATTTTTGTATTTTTAGTAGAGATGGGGTTTCACCATGTTGTCTGGGCTGGTGAAGGTGGTAGGTTTCAATGACAGCAGCATAATGCCGTGGGAGT + @ECDCD>6.>7CEGHHHHFHHHHHHFHHHHHBEGBHHHHHHHHHGCBEEEHHHHHGHFHHGGHHHHFHHHHHFHH9EFHHHHHHF@CCDFHHHFH:?AA? @read_150_158/1 ATGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCACCTAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAATAAAAAA + HHHHHHHHFGHHGGFHHDFF;CEEEEGC=@?19@A@5BBGBGEBDHHHHHHHHHHGGDDCDEHFHHFHHFFFGHHHHHHBG51?HDEEHHHBFHHHHFDEBEBGFH @read_150_159/1 GGATTCCTCCTGAGGCTATGAAAATGTTTTATCTCCCCTGCCCGACTTATCACCAAGTCAGTGGTGATTTCTCAGTCATCCAGGTCATTACTGTAGGCAC + FFFGHHFGHHFEE@EHBBE=EGCDD8DDE/485>C@BCCEHHHHDHHHHHHFFFFHHHHBBFDDBDGGGHBGFGCAFG?EEEHH;<><>BFHHHHHHHHGFFFHHHHHFHFHHFGGD.FGGEEBEFHHHDBGHHHHGGBCEDEEGHHHHEEEEEFCFHGDF5<:A;6FF @read_150_160/1 CAGGACAGGGTGGGTGGGCTATGTCCCTGTGGGTTCACAAAGCCTCATATTCACACTCTGACCCTTCAGGAAGCTGCTACAGATCGGAAGAGCACACGTC + HHHHHHEFF89:=EGHHHHGBEGHHHHHHHHHGHHHEFGCD-)>@1<7>C=BHHHHHHHFFGHFHHHE;-*.<09CC@8A?GEB@FBGB@9>2?91:./- @read_150_160/2 GTAGCAGCTTCCTGAAGGGTCAGAGTGTGAATATGAGTCTTTGTGAACCAACAGGGACATAGCCCACCCACCCTGTCCTGAGATCGGAAGAGCGTCGTGT + HHHHHHHHHHHHEE@EGEB/5<73BFHHGC1<:<>?HHF<8=A=<;-1<.2-,:22HHHHHHFHHHHHHHGHEGGDEFEHFD446GFHHE=+@AFHH @read_150_161/1 ACTAAAAATACAAAAAATTAGCCGGGTGTGGTAGCGGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCGTGAAACCGGGGGGCGG + HFFGHHHHHHHHHHHHHHHHGHHHHHHHHB-0:;6:EEHHEBFHFHHHHHHHHDFHFFHFFBBDFEDDEGHDBHEHHHHHHEHF5CD-5@;8;-&3DHFE @read_150_161/2 TATTGCCCAGGCTGGAGTGCAGTGGTGCCATCTCGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCCTGCCTCAGCCTCACGAGTAGCTGG + FBHHGEGHHHHHHHHHEEEFBHGEGHHGGHHHHHHHFHHHHHHHHFEHHHFHDDGHHHHEAB74/>=B=GBFFHFF?EDH@EHHE?=,2>9%1>FHHFC??FHHHHGGEGHHGHHHGHHHHHHHHHH @read_150_163/2 GATCTCAAACCTCTTAATTCACTCAGAGCACCAAGGAGCTTGAGTTTCTTGTATATTATATTAGGCTGTTTTTGCATTGTTATAAAGAAATATCTGAAGG + HHHHFGGHHHHHDEGGHHHHHHHHHFFDGFF48FHHGHBFECC:6>5C6?DE8CCC@@HHHHHHHHHHHHHGHH>EHHGGHHFEHHHHFHFCB5;<;ABE @read_150_164/1 TTAGGAAATAATACAGAGAGATCCTGCATGCCTGTTACCTGGTTTCTCCCAGTGATAACATCTTGTAAACTACAATACAATATCAAGATCGGAAGAGCAC + HHHHGEBGGFHGEGFHHGAAEEGHHHHHHHHGGHGHHHFFCBC.E>F9BHHHHHGEFHHHHHGD=FFDEEEC>EHHHHHHHGGEB<6=A>@>ADGFB>5* @read_150_164/2 TGATATTGTATTGTAGTTTACAAGATGTTATCACTGGGAGAAACCAGGTAACAGGCATGCAGGATCTCTCTGTATTATTTCCTAAAGATCGGAAGAGCGT + HHHHGGG@EEGFFHHHHEDDDHHGHB=@FHHHHEDHHHHH@;EFGFCGGADDHHHHCDDFHFED5DDDCAGFHHFHHHFHFG;EEB><>,;@6-&/3:6C @read_150_165/1 CCCCATGAGCTAAGAATGGTTTTTACTTTTTTGAATAGTTGATGAAAGTCAAAAGAGAGGGATAATATTTTGTGACATGAGAAAATGATATGAAATTCAG + HHHHHHHHHHHHHHHHHFEEHHHE=BEHHHHHHHHE@916FHHHHHHEEHFEFFFH?HHHHHHFEF=CCC?@6,:GCCDHHGGGHHHGG703:(5(33&( @read_150_165/2 GAGCAAGACTCCAACTCAAAAAAAAGGAAAAAAAAAAAAAGAAAAAAATATCCAGATGAAGAAACATGCCCGGGTTATAACAAAACTTTATTTATGGATG + >--;BGHGDGED7-9HHHHGHBBBB@FFCHHHHHHHHHHHEEHHEHHHHHE=EEFGBFGDBBEFFEHHGGGBFFHFGGGFHHHFHFEBB;GCFHHHHHFBDDDEHHHHHHGD=@?CFFF@BHHH@F @read_150_166/2 TATTCTAGAAGAGATTAATGAGCCATGGATAATGAATGACCAAGGACTATTCATCTTTAGATTTTTTTTTTAATTGAAATATCCACTGGGCTTTAAATAA + HHHHFGEHHE@FEHHHHHHHHHHHFFFHHHHHFEIHGGDBDDHHFE8EEEGFGGA774E,5?FGHHHGEGEGFHHHFFHHFEEE?.&<@EG;?FFFFBB- @read_150_167/1 TTGATTACTGTAGCATTATAGTAAGACTGGAAGTTGACAAGTGTCAGTACTTCACTTTGTTCTCCACCAATATTGTGTTGGCTATTCTGGGTCTTTTGCC + DBFGGGGFDFFHHHFEGCC>DFHHHHHEEBGGHDCCEBHHHHHEDBEFBEHHHCBCHHHH@FEHEHEDDD7:@C52>?ACGGGHF=GEGH@E@3DAE?HHGGFHHHHFHHFFHHHHHHGHHHHHHHHFIHHHG@=?DECAB@ABFHHHHGGEDHEFEHFCFF @read_150_168/1 GTATATAGTAAGTGCAATCAATAAATGTTAGCTATTATCATTAGCTATAATTACCATACATCCTTTCATGGAGCAGTTGGAATAATCTTTTAAAAACATA + HHHHGCEFFFEAEEGEDEB@EEEEGHHGGFFHHHHHEFFFBGGGGGEEHB&6FFFEGGDFHHHHFEDBCDEEHHHHHHHHDGGGHHHHCHHHHFD/*5)5 @read_150_168/2 GGAGTCAAGGGCTAGGAAATGTAGAGCCTTTAGCCATCGTAATCTGTTAGAATTCCATTGTAACTGAAATGGGAACTCACTGGAGAATCTTAAGCACAAG + GFGDGGHHHGDF?6:.2+===;;BHDHHE?=AD8CHFHHCDFHHHHHEEGFDG/A9.;CGGBBDCHBB5:8DCBBDEHHHHHHHGFG?BFHHEF? @read_150_169/1 GTAGAAATATCTAATGTAAACTAGAAAATAGAATGTAATTTGTAAAACAGTAACATAAACAGTCTAGATACAATATCGGTAATTAAAATTCAGCTGAGGA + BBDDDDFEEECEEHHHHHHHBDGGHHHHHHGFHHGBFHFHHHHHHGHHDDAB8=GBFG:HF?EHE77DDD48EEGHFB>6=CDDDEAB=6C@859@DGHHHHHDBCGHHFFFCBC=<<%)62-32=A(/@&(6D> @read_150_170/1 CCAAATGCCTATGATTCTGAAACTAACAACACTGTGGAACGACAGTGTGGAGAGGACACTGGATGGGATCAGAATTGATTCTAGTCCAAACTCTGCTATC + HHHHGHHGEFGFHHHHHHHHHHFBFDCHHHHHHHHHHHGGEHFHHHHHHHHHHHHGHB@?@BGFFHFFB=7FFEFGGGHHG?E?EDE23&@.15>?A>5) @read_150_170/2 GGAATTAAAGTAAACGGTTTTTGAGGTCACAAAACTGATGCAACCGTGCTCAGAGAAGTCTAATGTCTTTTCTAGGTCACAGCTATAGCAGAGCTTGGAC + HHHHFBFFHHHGFGHHHHHHGHHEBHFGGHHHBDGGHHHHHHHHH?DHHHHHHHHHHGHFGGGHHHHHFHHHHHHHEC2C=?=>DCA?H @read_150_172/1 AGGCTATCCCATGCCTGCCTGCCCCTACTAAATTCTCATCTCCCATACTTCCCTGCTAAATCTATGATTTCCCCCACCTTACTATTATAATCCCCCTTGA + HHHHHHHCCDHHHHHHDDDFFFHHHHEHHHHHHHHHHHHHFADFEHHDHHGHHHGCEFEHHDB5FFFD9AEFHHHHFDEEFHGHHHFHHFHHHGHHHHHG @read_150_172/2 GACATATATTAAGAAGGCAAAAGCTGGAAATTTAAATTCAAGGGGGATTATAATAGTAAGGTGGGGGAAATCATAGATTTAGCAGGGAAGTATGGGAGCT + HHHEFG8?FGHFABGG<7;EFHFF;EGGGEFH @read_150_173/2 TGTATGATGGGAATGGGCCACTGTGCCCAGCTTTTTGGCATTTTGAAAATGGAATTGTTTGTCTTTTTATTATTGAAATGTGTGAATTCTTTATATATTT + GFEHHHHHHHBDEEB;;8EEGGF@8?DFHHHF@9:>GIDDFFHHFDC7@>CBDGFB<488:.>.5?7:6:AB6<40..8=CD?AA*6EB?@EFGDGEEEH @read_150_174/1 CTCAAATGATATGAAGCAAAATCTGGCATTATAAGAAAGAGATAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCACCTAATCTCGTATGCCGTCTT + HHHHHHHHEFHHGBBGFHHHHFHHHHHHHHHHHF?FAGDFFHHHHHHHHHHHHHHE7>AC7:BFFFEEHHEEEFFFFFFHHHHHHFGHHGHHFHFHHHHH @read_150_174/2 ATCTCTTTCTTATAATGCCAGATTTTGCTTCATATCATTTGAGAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCAT + 8DDHHFHHHHHHFFGGHHHHHHHHHHHHFGHHG:HGGHHHHHGF?8'53CHHHHE@C2:67@FG;6>@CHHGGEFDHHHHHHHHD?CADE??FHHHHGHF @read_150_175/1 CTAATTTTTCTAGAAAAAAATAGAAAATTTGTCACTGTTATTTACTTGCACTTAAAAATAAAACAAAATATCACTCAAAAGCAATGACTTATGTTTCTTT + GHHHGGHFHHHHGB=DDGFGHHHHHHHHHHHB=4>@HHHHHHC?DGD11<9@HD;GA?;@CABHHHDFHHHHDFEHHHHEEE.8(5>H @read_150_175/2 GTCCAAGGGAGGAGGATTGCCTGAACACAGGAATTTGAAACCAGCCTAGGCATCATAGTGAAACCCTGTCTCTGTAAAATTAAATATATATAGTTTTAAA + EHHHFHHHHHHHHHHHB?CBGE7555<4@=GHHHHFFEHHHGHGHHHHHHHHHHHGHEGFHHHHHHHB<@6416@ADGEFHHDCHHHHHFHHE-5BB @read_150_176/1 AGGGAACACAGGGTATTTCAAAAAGCTCCATAAGCAACTAAATTGAGGAGTGAAGAAAAACGGACAAAAATAATGAGATTTTAAAAGGGTCTTTTGCAAA + HHHHHHHHHHHGFBCEHHHHHHHHHHHHHHHEEHHHEEFHHHHHHEHHHHFAHFFHE@A7-/11-A49.?<;.<<.7.>323=GHGGGHGHHHHHHE=GHHHH@DGFFF?=DEDHGFHHH @read_150_177/1 ATGGCTTTATAATTTTTTTTCCTTTATCTGATCATATGGTGTAGAACAGGAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCACCTAATCTCGTAT + HHHHHHHHGHHHGHHHHHH@BDFHDHHHHHHDGEGEEHHBFGFFFHHHHHHHHHHHHHEEF7(*(2/,@2++5=GHGEAA @read_150_177/2 TCCTGTTCTACACCATATGATCAGATAAAGGAAAAAAAATTATAAAGCCATAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGC + HFBHHHHHHHHHGGHHHHHHHHHHHGD.38:;;EGGGDHHGEFHHHHEECDDDFFHHFFD846==HHHGHHHHHG>.*63;;BEHHHFFC>,5?EHFGEFHHHHHFHHFBCFGEHHBDBA??@D=BHHHF/)?9>>AD=C4@ @read_150_179/2 GCTAGAAGTTCCAGGGACAGTGTGGAAACAGCAAACAGATTGAGAAAGATAATCGTGGGAGTGTGAGACGTGTCAAGCCTACATTGTGCAGTGCGGAGGT + HHHHHHHHHHHHHHHHHHHHHHGHHGEGGHFHHFABEHHHHHHHG>CHDHHHHHFHHGGFFDBGEEACB@FFBFFEE=BHHHFED;<@:-13<:;13(32 @read_150_180/1 AGGCACCTGCCACCACACCTGGCTAATTTTTGTATTTTTAGCAGAGACGGGGTTTCACCATGTTGGCCAGGCTGGTCTCGAACTCCTGACCTCAGGTAAT + HHHHHHHGGGHHHHHHHHHHHHHHHHHHHHEFEAA4FHHHEHHHHHHHHHHHHHFEHEFHHHEFFDDB?;>ACGGEFGDFHHFEHHHHEED67@;*28,B @read_150_180/2 AAGAAAAACAAACCCCAAATTCGAGAGGAGTTCTAGAAATATATAAGAAGAGGGCCAGGCGCAGTGGCTCATGCCTGTAATCCCCGAACTTTGGGAGGCC + EDHHGHHHHHHBEHHHHHHHB?;EGHFGEEDB8(<<@B.>FC;CA-1/)(9 @read_150_181/1 TTGTTTAACAAGCTTATTATGATACTGAAAAAGAATGGTTACCATTAGCAGAAGCAAGAAGAGATGAAGTTTTTATGTAAGTAAAACTTCACCTAACAGA + DGGEEDBGFGGHHHHHHHHHHHHGBEFHGHHFCDEHHFFGDHHFHHHFFFHHHHHFHHHHHHHHFHHEFEFFFC?7)/(187179><@@BFF@C893>3/ @read_150_181/2 TTCATTAAGGGTTGCAAAATGGAGATATCCTAATGCTATCATTTTTTCATCTGTTAGGTGAAGTTTTACTTACATAAAAACTTCATCTCTTCTTGCTTCT + GGHHHHHHHFEHHHHHHHHHHHHHHHHHHHGGHHEHHHHHHHHGFDFHHGFFDGEGGHHFHHFH?FFFFHHFH=6=@7<<3%0FFFFHHHBDE9>EGDA> @read_150_182/1 GTCTTGAACTCCTGGCCTTAAGTGATCCTCTCCCACCTCGGGCCTCCCATGTTACTGGGATTACAGGTGTGAGCTCGGAAGAGCACACGTCTGAACTCCA + HHHHHHHHHHHHHHHHGGHHHHHEGHHHHHF;=>FHFE @read_150_182/2 CACACCTGTAATCCCAGTAACATGGGAGGCCCGAGGTGGGAGAGGATCACTTAAGGCCAGGAGTTCAAGACAGATCGGAAGAGCGTCGTGTAGGGAAATA + HHHHHHHHHHHHEGBEGGGFAFF>@-8>>-,/EHEAHHHHHHGGDBBBEGFGHHHHHE=@CDB:.4@ED>FAAFHHHGFHFHFHFFFEFFE<@=DD@5,? @read_150_183/1 AGGTGACTGGTTGCTGAAGAAAGAGTACCAGGTGGAATAGGACAGCAAAGCTATGGTGACAGAATGAAGAGATTGACTTCTTTGCTGCCTTCAGAGAACA + HHHHGHHHHHHHHEBFEHHGGGHHHHHHGGHHEEHHHHDEEAFHHGDEFGEHHHHHHHHHFHEFFEFCFF?2D;DGDD@GGCBF?FEGGGEEGG@ADEGC @read_150_183/2 AGGAACTTGTTTAAATTGAATCAAAGGCTGACTTCCTGGCAGATTTTCTCTGTGTATTGGTTTTGTTCTCTGAAGGCAGCAAAGCAGTCAATCTCTTCAT + HHHGGGHHHHHHHFGDB4@@FEHHGHHHFGHHHF>GGGGBFEGGFGHHHHFEEHHHHHHHHHHHH@GEHGEHHHBGGFEEEEGG<;EBFECDDEFGGFA> @read_150_184/1 GTTCTGACTGATCAGAAGCAGCTTCCACTTACCATCAGTGTCACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCACCTAATCTCGTATGCCGTCT + HHHGHHHHGGGHHHGGEEEEGGGDCCFEFFHHHHHHHGG:EFFFHHHHDFHHHHHEDCEHHHDDABDFFGG?CEHHHHHHEFHHGHFHDGFEDBD9EHFC @read_150_184/2 GTGACACTGATGGTAAGTGGAAGCTGCTTCTGATCAGTCAGAACAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCA + DDEB@DBBFCDFHHHHHHHH@CAEEB3376EEE::?FHHC@@.3-5=99EGDCE @read_150_185/1 GCTATTGCACATGTGCCGAAGAAGATATTATAAGATTTGCAGAAAAAGCAGTTATGCTTTGGAGATAAGAAAGATCGGAAGAGCACACGTCTGAACTCCA + DDGGHHHHHHFFHHHHGHHHHHHHHEHEEEHGGHHHHHHHHHCDDGDB>CDDFHHEFF=9EGHHBFFDHFHHHFHHHHGFHHFFHHFFHFBEHHHHEFCA @read_150_185/2 TTCTTATCTCCAAAGCATAACTGCTTTTTCTGCAAATCTTATAATATCTTCTTCGGCACATGTGCAATAGCAGATCGGAAGAGCGTCGTGTAGGGAAAGA + HHHHHE=C2.67BEDIGCHHHHHHHHHHHHHHEFHHGEGCFE?BEHEIB?CDDFHHHHHHHHHHHHHHHHHHDDFDHHHGFDDC+?B@HHHGGB=BDA16 @read_150_186/1 GCTTGAGAGGCAGCAATATGATGTATTCTTTTCATAATAACAAATAGGGCATAAATAATAAATTTATTTATTATTTTGTTATGTTTAATAAATACACATT + HHHHHHHHHHHHHHGGBAADGHHHHHHHGHHDGHHHHHHHHHHHHHHHEEDEA305;ADB?FHHGFFFB?A=DDFFHHHHHHF>BEFHHHED097BDBEH @read_150_186/2 CTTTAGCTTTACAGAAAAACTGAGAACAAAATGCAGTGTTCTCATGAATTCCTTCTACCCTTTGCACAATTTCTCTATTATTACAACCTTGTATTAGTAT + HHHHHHHHHFHHHHHE@<>:5C;EGEGG?EHHGEE<))18EFHHEE>BBDFE<@HEGGHHHHHFEFHHHHD.=@? @read_150_187/2 TTCTGTCTAGCAGAATATGAAGAAATCCCGTTTCCAACGAAGGTCTCAAAGAGGTCTGAATATCCACTTGCAGACTTTACAAACAGAGTGTTTCCTAACT + HHHHHHHHHHFHHHHHHHHHHHHEEHGGDBEHHHHHHHHGHHHHGHHBGFHHHHB?FFGHHHEHHHGED5DDCCFHHFHHHGEGHHHHHHHHEEECDC69BGHH<66;+196FBE;EFFD81'CGFHCFHFFEFGHHHEEC8EHGHHHG@CFD8<-'7388GGBA?6?=A618)59DE@/DBDB @read_150_190/1 AAAAAAAAAAAAGACTGGGAATGGTGGCTCACACCCGTAATCCCAGCACTTTGGGAGGCCAAGGGATCACTTGAGGTCAGGAGTTCAAGACCAGCCTGGC + HHHHHHHHHHHHHHHHHGGGGHFH<9@@GFAAHHHHHFHHHHHFFFHHFF7=?>@A-B=<>36EFHFDG=FEEEC?@CEEHEDHHHHHFE?GGFEHHHFF @read_150_190/2 ATTATAGACGTGTACCACCATTCCCGGCTAATTTTTTGTACTCTTAGCAGAAGCAGGGTTTCACTATGTTGGCCAGGCTGGTCTTGAACTCCTGACCTCA + GGHHHHHHECDEHHHB8=FHHHHHHFHHHHHFEEEFHHHHHHHFFFFFBHGGGGGGGHBHHHHHHHHE8:BEFBEBDHHHGFHD=<5,59496/:5=C88 @read_150_191/1 TTTTGCGTTATCTGTTTTATATTTTAGAAGAGTATATTTCACTACATTATCCAGAGGGATTTTGCTCAGAATCTCATTAGTGTGTTTTGAGTCAGATCGG + GGGGGGGFFD=C?<6BBFHHHHHHHHHHHHHHHEGGFCCCHHHHHHHHDDGFHHHHHHHHHEEEHHHHFFHFFHFHHGGGFBHGGCDDB4>C@1817EDCFH@ @read_150_192/2 CCTGGGGAAATGAGGAAAGAGACCTAGACTTAATGTAGATAAAACAAATTGACATGGGACGTGAATGGGAGAGAAATGAGAAAACCATTCTAGACTAAAG + HHFHHHHHHHHGGGGHCBBHEHHHHHHGHHHHFFF=?>>:@77AHHFG/DEFHHFHFG8CCA>FHHHD@EFHF8B<396=>?@?>DDD;C;DCE=GFEAA @read_150_193/1 TTACATTTCCACCAGCAACACATGAGAGTTCCAGTTTCTCTGCATCATCAACACTTGTTATTATCTGCCTTTTTTATTAGAGCCACCCTAGTGGGTGTGA + HHHHHHGG@>CGHHHHEFF8@HHHEBFHGGB?<55BBFHGGFHHHHHFFHHHHHEDD3>CEF @read_150_193/2 TAAGCACAAAAAAATATGCTCAAAATAGTCATTTGGGAAATGCAAATCAAAAGTGTGACATACTTCACACCCACTAGGGTGGCTCTAATAAAAAAGGCAG + EEBDBFHHHHHGFFFHHHHHFHHHEGDDFFHHHHHHHHHFBEEFHEBEEEGHGGCEEED6-DHHHHHHHHHA6GFFDF78C95BEHFEDDB@@ABAFFHF @read_150_194/1 AGGGCCGTTCCATCTGAGGTGAAGACAGGCAGGCATTTGTTAGGTTTGCGGGACTGCTGGGTGACATGGTTCAGCTGTGTCCCCACCCAAATCTCATCTT + GGGHHHHHHHHFFGGHEEEEGFHHHH@GG>-79.EFBBGGGGHECFEFHFFFFHHHHHFH @read_150_194/2 CATGAGACTTTTTCACTACCATGAGAACAGTATGGGGGAAGCTGCCCCCATGATTAAGGTATCTCCCACTGGGTCCCTCCCACAACACTGGGGAATGATG + HHHHHHG=ECEHHHHHHHHDGEGGE;FEHGGHHHHHHHFFD>?CFHFHHHHHHHH@>4724:BBFFHHHHHHHHHHHHHHHHEGBEEB/DBACFEE;A@5 @read_150_195/1 TTTGTTTCCTTTGTTTCTTTTTCTGCTTTTCTTCCCCACTGCCTTCCTTTGGATTGTGTTTTTTTTTTTTCTGGTTCAATTAAAACATTTTTTAACCGAT + HHHHHHHHHHHGGGGHHHHHHHHHFDCHHHHHFHHHHHFFHFHHHHHHBDFEHHHDFFEEHHHFFFFFFBEGEHHHHHFFDEGHHHDDFHHHHEFFFFBC @read_150_195/2 ACGCATCGGTTAAAAAATGTTTTAATTGAACCAGAAAAAAAAAAAACACAATCCAAAGGAAGGCAGTGGGGAAGAAAAGCAGAAAAAGAAACAATGGAAA + )0+/AEHHHHHGFFHHHHHHHHC.BGHHHGHHEHHHHHHHHHFHHDE, @read_150_196/2 GTTGCCGTGACATGCATGCCGTTCTCCACGGACACTGTGCTTGCTCTGGTCTCCATGCCTGCACCTGTTGCCTCACTGTGGCTTTCTTCCCCGCCCCACC + HHHGGHHHHHHHFFHHHGFHFE@@CADBGGHHHHHHHHFFGE=FBDDA?9FHGGGDD>DC@HHHHHHHHHHHHHHHHHHHHHHHHHHHDC='EHHFBH @read_150_197/2 TGGGAGGCTGAGGTGGGAGGATTGCTTGAGTCCAGGAGTTCAAGACCAGCCTGGGCAACATAGCAAGACCCTGTCTCTACAAAAAATTTAAAAGTTAGCG + HGFBFFGFB;:7@6.@888038:@::CB89;.DHHEEHHGHHFHHGEEFFGFDFHGGHHHGHHHHHHGDCGGGHHHHHCGEBDGEHHHDHEEDEHFBBFE @read_150_198/1 CTGCCCAGCAGCAGCTAGGATACAATATTGGTCTCATAGGGTTGAGGGGTGAGCGTGTTATCCACGTGGAGGGTTATCCAACAGAGTGTTTGGCTGGCTG + HHHHHHHHHHHHHGGGHHHHA4E@CD;DDFHHB@BGGFFGHHBEFDDCFHFHHHHHHCB=BFHEEEGEHHHHHHHGECEE?GHHHHHHHHHHH@GE@EEHHHHHHHHGGGGFHHHHG=C@AFHHHHHHHHG@HHHA @read_150_199/1 GATGAGGCTACAGTTTGGCAGAAGGCAGTTTATAAAAGGCCTCACAGACAATGGAAAACATTTTATAATTATTCTAAAATAATGAAGAATAATTAAATGA + GHHHHHHHHHHHHHHHHHHHHHHHGHHHHHHHHHCBHEEE@DDD6BFFBD8:BE?FEGHH?@CCEECFHHHC;7B>>BDDHGDD@EHHHHFHHHFHHFHHHFABHHHHFHHHHHHHHHHHHHHHFHHHHHFF@EEDBHCFHB0&%-(78DD@.C @read_150_200/1 GTTTTATAACTTCAACATGTGAATTTTGAGGGGACCTAACTCAGTCCATAATAGTGTATTTAAAAAACTAAAAGACGTTTGAAGAGGGAGATATGATGCA + EFFGGCEB>@EEEEEBGHHGD?GHHHHHGEAHFECDDAFFFEFBB2<.CDFFGHHHHHHBHHHCDED=.6:2687?CEBDBGHHBHHHHHGEFHH @read_150_200/2 GCCAATGTCATATGTCTTGTCATCCTGCCAGTCTGCATGCCTGCTGGCCTATTCATAGCATAGATATTTTATGGTAAGGGGTGATATTTGAATTGATACT + HHHHHHHHHHGGGFHHHHHHHHHHFGGG8?-2>>=FDEEEDFHHHHHHHECFFFHGBGEHHHHDB8*::+31).>E6.0.3?>@.DGHFDEEHHHHEEA; @read_150_201/1 AATGAAAAATCAAGTAATGAAATTGTCAGCTGCATAGCCAGTAGAAAAGACAAAACCAAAAAGAAGAGAAGGAGGGAAAGAGGGTGGCAAAATGTAATGC + HGFACDEE@?BCGHHHHHHHHHFHHHHHHHGEFEGHFD48./6@FFFDEHHHHHHHFHHHHHHHEFFHHHHHHHHHHHHGHHHFHHHHGFFD/%7?5CBB @read_150_201/2 CCAACCCACCCCAGCCTCGCTCCTCTTCTGAGACTCCCACCTTCCCAGGGGAGAGTGTGCAGTAATTCACTGTCACTGTGCATTATATTTTGCCACCCTC + HHHHHG@A3EGEACDB@HHFEHHHHHCFFCFFDEFFF;?F;DGFFFHHHDFHEEEHFGFHFDB?B9C @read_150_203/2 CAATGAAACTATCCTTCAAACATGAAAGAGAAAGAAAGATATTCTCAAATAAAAATTTATTGAAAGGAGATCTACATTATAAAAAATGTTGAAAAAAAGT + HGGFD@@CBDHGHHHHFFGB@@DFHHHHHHHHHGGGGFHGEEFHHFHHHHGGFHHHEEGHHHHHHCHHFFG<>;?GHHHFHHHFGHHHEHF;?FDHGBHH @read_150_204/1 CTTTAGAGAAAAAATTGACTAACTTCAGAAAAGATTTTGTAGTTGAATTAAATCTCGTAAACATGAGTAACAGTTATGGCCAGAGAATAGAGTTTATGAG + GEHHHHHHHHHHHGGCGGHHFHHHHHD@FFHEFFGGGC??59>,>DFHHHHHGBHHHEBAB?DC>FHHEE?1772=>@BHHHHHFGGGGHHHEHFFHHHH @read_150_204/2 TTGCCTAGTCTTAGTGTCTCATAAACTCTATTCTCTGGCCATAACTGTTACTCATGTTTACGAGATTTAATTCAACTACAAAATCTTTTCTGAAGTTAGT + HEHHHHGGEHHHHHF?:;EFHF=>DGGBAC@>@@HF=FHHHHFEBFFHHHFGIFGGGDHDBDGGFEHHHHGDCBFFBEBCDHHHGHGEEHHED0&%%?BD @read_150_205/1 CTTCCTGGCTAGACCACGTCAGAGGCCACTGGCAAGCCTGTAGCTTCCTGCCGGTTGGCTTAGGTGTTCTGCTGTGGTCCCTCAGCTGGGGTCGCTATGG + EGGGBEHHHHHGHGHHHHGGDFFHHHHHHHGGFAHHHFD8:9EFFHFFFHHHHDDHAFHHEFHHHHDFHHHFFHHHHECEFADBE9+,1;3:8.924:'8 @read_150_205/2 ATCGGGTGCAAGATACTTCCCTGATCAGCCACCTCTACCTCAGTTCCTGGTAAGAAACGTGGTCACTGGGGACCACGTGAAGTCATTTAGCTGAGGACAG + HHFD=@9BFHHHHHHHEHHHHFHHBHHGB?GBGB096?EHHB65/%53355 @read_150_206/1 ATCTGTGTAGTTTTAGAACACTGGGAGTAGCCTTTAGAATCGAGAGGAAGAGGCTCCAGTGAGTTATGAAGACAGCATTTTCTTGAAGATCGGAAGAGCA + <=DBGGGGGFDHHHHHHHHFCGHHHHHEEFHHHHFDDEE@HHHHHHHHHHHHHHHE/36GHFBHEHEEFHFFFDADAEDED.EBGHEFEHEFHHFFHHHH @read_150_206/2 TCAAGAAAATGCTGTCTTCATAACTCACTGGAGCCTCTTCCTCTCGATTCTAAAGGCTACTCCCAGTGTTCTAAAACTACACAGATAGATCGGAAGAGCG + E8B<<74DD=EC663?GGGFHHHHFGFFHHHHHBEEHEFBFHFFHHF5EEEGHHHHFGB=GGHFGFFB8DB@HHHEFHFEEFHA@EGHHHFACBFFE-80 @read_150_207/1 AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCACCTAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA + GGFHHHHEHGHHHHHHFEEHHHHHECHHHHHGGFFHHHHHHHHHHDCDFHD?AAD673ADDFHHDFFFFFHHHHHHHHHHFDDBGD>CDCDCHEGHHHHF @read_150_207/2 AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA + HHFFHHFDDHHHHBDDEFHHHHHHHHHHHEFFAD8=FHHHHEHHHHHGHHHHHHGGGGHHGGGHHGGGGHGEEDEHHHHHGDFBDHCDHHHFB>BHHF?B @read_150_208/1 TAAGCATCTTAAAAGAGAGCAATATTTTAAGAATAAAATATGTTATTTTTAATCATTAGCCATTGTTAACTGCGATGTAATGCAGTTTTGTCAGCCAGGC + HHHHHHHHHGFHHHHHHHHFFGFFHHHHHHHDCBGFHHHFHHHHHHFHHHHHE<+A@FEFBDDFFHHHFHEBDFHHFEDHHHHFFDFHHHFEEHHFGFD? @read_150_208/2 CTCATTTTTACTCATTTTGATTCTTGTTTTCTGTAGATGAGACTTTCACTGTTCAGCCTTGCTTTACTGTGCCTGGCTGACAAAACTGCATTACATCGCA + HFHHHHHGEGHHHHHHHHHHHHHHHHFHHFFFGHFHHHHH1'''+6EEHHGGGIFHHHHEGGF@8666,DHHHFFDGGGFFA@EGHHFFGGHHHEHHHFF @read_150_209/1 GCTTGGGCTCAGAGGCCTGACACCAGGGAAGGCTTCTGATTGATCCAGCTTGAGTCTAGACTCAAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACC + HHHHHHHHHHHHHHEGGGEHHFFFFHHHHHHGEEFHHHHHHHGHHHHHHFF=5D@>?DFHHHHFFHHHHHGGHHHHHHDGFFHECFDEFGHHHFFHHGHG @read_150_209/2 TTGAGTCTAGACTCAAGCTGGATCAATCAGAAGCCTTCCCTGGTGTCAGGCCTCTGAGCCCAAGCAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAG + HHHHHHHFHHHGHHHHHEGBBGHHFEHHHGHHED83@>DFHHHFHD>)1CEGBBBGBEEGDFGGHHHHHHGHHHHHGHGHHHHHHCDBEGGGDEGHHHHH @read_150_210/1 ACAGTCAAGTCCATGGGACTTTTTTTAATAGCAACTCAGTAAATTTATTGACTTATTTTAAGACTGTAACAATAGAATTGTTTTCATTTTAGCACTTAGT + HHHHHHHHGGDFBFEHHGHHFGGGFGGGGHGGEEDD/EBFEHHHHHHHHHFB?DDFGFHEEHHFGHHE@E3)'9?GGEEDFHHHHHHGG@G=DDE5BBGG @read_150_210/2 TAAATGGATAAATAACAGTAGAGTGTTTACAACAGTAACTGGTACAGGGCTTGTTCAATAATCATTAACTGACATCATGTATGCTAATTAAGTTACATAG + GEFEGDB,2,*0EBEEE;6EFFEHHHHHHHHDGHHHHHHHGFGDBDA9<'<>DFGHDABFFHHHHABBHHHHEB?@43+AEFGG>9729+.7;.EIHHHHFHHHHHHHHHACDCEFFHHHEE@BFHHHHEFHHHGGH?@@BHHHHFECCABHHHHH @read_150_211/2 TTAAAACAGAAAGAAAAAATTGTCAACCAAAAATTCTATACTTATGAAAACCATAATTCAAAAAGTTCAAGAGGAACTCTAACTTCCCAGATAAACAAAA + HHHHHHD?=97DHHHHHHHHHHHGFHHHHHHEGHHHHHGFDADFHFFHEDCDGGFHHHEHFDCHHHHHHHDEFFBCCHHFDHHHHHHHHHHHHCFCA8DB @read_150_212/1 GTCTAAGACACAGACACTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCACCTAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAA + HHHHHHHHHHHHGGHHHHDFHHHHHGFFHGGA<6?GDDAFBGFHEHHFHEADCBHHFFFHFEEHHGHEGGFHFEEFFG@GHHGHGHHHDFHHHFHHHF@F @read_150_212/2 GAGTGTCTGTGTCTTAGACAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAA + HHHHHHHHHHECCBEHHHHHHHHHEHHHHHGFGGEGGFFHHHHHHHHHHHHHHHHHFGGEGFF@=BEEEEHFEGIGGBFFC55+CFFGGFFBFEEEFEAD @read_150_213/1 TATGGAAAGCTTCAGGCTCTCAGAATTTGCAGCAGCAGTTCCAACTTGCAGATGGCAATAATTTTAGTAACTGCTGCCACCACTTGGCCCCAGACAATCA + HHDGHHHHHHHHHHHHHHHHHE@<=BE@@>FGC54@DHHHHHHDAA:??9EHFD;7AF-C??+9A><<.A?7>*)12-EEEHFHHF;@6,EGGGDDD=?EGEECCEGHHHEGE@FHHDEFGFGGFEE@53,2<9AB=@;@ @read_150_214/1 TTTTTAATTCTCCAAAGGTAGGCATGCTTCATAAATCCAAGTAAGTGATCACATGCCCTCCTGTTCCCGGCCCCAGAAGCAGCCTAGAAAGCTTATTTGG + HHHHHHHHHHHHHHHGHHHHE@>>BE=DDDEHHHHHHHGGGFCEHFHHF<86CHFHHHFDBCBEHEHHHHHDDADGGBGGBEABDBDFHHHHHGE@C>DF @read_150_214/2 CTTGAGAAATGTGTTTCCTTTGTTCATCTGAGGAAATCTAAACTCTATTCCAAATAAGCTTTCTAGGCTGCTTCTGGGGCCGGGAACAGGAGGGCATGTG + HHHHHEGEEGGHHHHHHHHHGDB?GEHHFBFFFGEFGFHHHEFHHHHHHHFBCCEDEEG=EBGGGHHHGGHFCDDHHHHH?..AA@=E53)3*;<)/*6' @read_150_215/1 TGATACAGTCTCATATAATTTCCACAATAGTTCCATGGGACAGATTAAATTATTAGCCCAGCCAATGGATGGGAAGGGCAAGTAGGATTTTATTTGCCAA + HHHHDFBEGGHHHHHHHGHGHHHHHHHGHGFHGA5ACE @read_150_215/2 TGCAATATTATTCATAATAGCCAATATATGGAATCAACCCACCATCTCCTAGCTATGTGTTCTTGGCAAATAAAATCCTACTTGCCCTTCCCATCCATTG + HHHHHHHHHHHFDEEHHFEEGBBFGEEB@<2/C>?AFEGHGBC:2'..;2CCGHHHHHHHHHHHFGHHHHE@AHDDB.,;C;77/0-,@BFHFE?A=?>= @read_150_216/1 CATAGGTACATACCATCATGCCTGGCTATATTTATTTTATTTTATTAAATTTATTTTTTTTATTTTTGTAGAGAGGAGGTCTTGCTGTGTTGCCCAGGCT + HHHHHHHHE@:CHHHHHHHGHHHHHHHFGHHHHFFFBDFEHHHHHHDHEEEHHHHGGDGHFGD>@HHHHDFC9*>,(, @read_150_217/2 CTTTTGAATGAATATTACAATTGATCCTTATTTAGGTCATTTCTCTTAAGCATACTACATCAGCAATGTTAAAAAGTGCCCAGAAATCAAAATTACCAAA + GG?.;GEHHHHGGEHHHGHHHHHHHF.>=FFGHHHDDEGHHHFF>FHHC?<<>>>;7;CHEEDDD=DBEFBFGHC@BHHEGHHHHHHHHGHHFDE@AGBF @read_150_218/1 CAAGATTTTTGTCTACTTTGTTAACTGATGTAGCCCCAGAGTCACAGTAGACACTAGAAAAATAATCATTAAATGAAGGGAAAAAAACTCAGTGGTTTAC + CDEECBFFFGHHHHHHHGGDEGHHHGGGHGE?86ADEEEHHHHHCGEB@HHEGHGFHHGDD;;@GE?;<)/-8*11 @read_150_218/2 TGAGAAGGCCATGGAGCAGGGATGCCTCCAATCCTTGAAAGGCATGTGACATGAGTAGGGAAAATATTTGCTATTGTAAACCACGGAGTTTTTTTCCCTT + HHHHHHHHFFEGFHFHHHHHFDEBHE:2<38:GGHHHHHHEGGFHFFHHHHHHHHHHHHHHHHGHFFFBEFHHHFHGG6?G?>D%7;@DFFGEED<,5F;=D6--B?EADADBC<<FGGFEFGGHHHHHBEEGGHHFBHHHHHFFDFFHHEF9*.@@GDFEFFFCFEE;82 @read_150_221/1 AAAACCGTTTCCAACGAAGGCCTCTAAGTGGTCAAATTATGCAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCACCTAATCTCGTATGCCGTCTT + GGHHHHHHHFEHHHHHHHHGGFGGHHHHGFBCFGGHHHHHHHHHHHHHHHHHFDFDBCEFHHHHH@CHHHEHHFBFFE8GBFHHHHHF<<;+*4+)1;;H @read_150_221/2 TGCATAATTTGACCACTTAGAGGCCTTCGTTGGAAACGGTTTTAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCAT + GGGGGHHHHHHHGGGGFHHHHHHHGHHHHHHHHHFHHHHHHHGFFFHHHHGGFHHGFE@:;3<:=E=EEEHHHHHDDHHHHFHBE=<<<>FHHGHGGDGE=EGECEHHHHHHHHEEHHBBEEEHF9';EEA41566.;82>>=DEFD @read_150_223/1 GGGGAGAATCTCTGAGTTTAAGCCATATGGTATTCTGGAAGTAAGGGGTTCTGATTAATATGGGCATGTGAAAAGGGCTCTGTATCTGGGTCATCATAAA + HHHHGHHHHHHHHFGHHHHHHHHHHHHHHHEGGHHGGGEEFHDCHGHHHHECB;?CEFGGGGHFE6<6,2?@8-ADDBDEE8GGFGHHHHFF<7,,958? @read_150_223/2 TGCATATTTTGACATGTGCCCCTCAATACACACACACAAGACACTCTGATTCTCACTAATCATATTTCTGGGGTTTTTTTCTGACATGAACACACAGATT + HHHHHFFIBHGGFFHHHHHHHHHHCGEHHHHHGGGGGHFGEEF?EHFFBAFFDCBD=-+9:34EF?GGHHHHHHHHHHFGHEB363+>A<>>@=>FFHHH;?HBGDGHFHE;'/07. @read_150_224/2 CCAATTATGTAGCAGATCCTTCCCTACTTCTGCACACTCAAGTTTTTTGTATTTCTACAATTACTATATTTTTAGGTTGTTTGTAATCTAGTAATGCTCA + A@=ADHHHHHHHHFEEEEEHHHHHHHHHGE>@@.>CFB>FEIEHHHHFFFEFEEEEEE=;:<<@HHH>=.ADEHHHEGGFHHHE<;<127(=DEBFEE/; @read_150_225/1 CTAAAGGTAATAAGAGCCATCTATGACAAATCCACAGCCAACATTATACTGAACACAGAAATGTTGAAAGCATTACCCTTGAGAGATCGGAAGAGCACAC + HHHHHHHHHHHHHHHHHDFHHHHHHHGGEFFE5?BEHHHHHHHHHHHFHFHHFDDFFHF>GFHHF@DHFH?EFFFE9ECFHHHHHHHBHHF9*,>CHFGC @read_150_225/2 CTCAAGGGTAATGCTTTCAACATTTCTGTGTTCAGTATAATGTTGGCTGTGGATTTGTCATAGATGGCTCTTATTACCTTTAGAGATCGGAAGAGCGTCG + HHG=CCFHHGFHHHHHHHHHHHHHHFFFFBGBGHHHHHFHHHHHHHHHFHHHHHHHHHFHHHFHHHHHHGGHHHEFHHHEGHHHHGE,>;DHHHHFB1=> @read_150_226/1 CCTGAGAGTGGGAGGGAAACTACCGTCATTCTGCTCATGTTTCTTCTTGACCTCTTGCATAATCTTTTTGTTTTCTAGACAGTTCACTAATTGTTGAATT + HHHHHHHHH<=DDFHHHDE?DFDGEDHHHHEDDBBHH:DCFFFHHEFFGDGGHHHHHHHHHFHHDC9@BED??:CFEEEFEEHFDDFFFCC@CFIGFFGH @read_150_226/2 TATACAGTAAAATTCAACAATTAGTGAACTGTCTAGAAAACAAAAAGATTATGCAAGAGGTCAAGAAGAAACATGAGCAGAATGACGGTAGTTTCCCTCC + HHHHHHHHHHB74BBHDGGFFGEEHHHHHHHHHHFHHDEEGE=FHE?FFFHGGGGHHHHHHHHHEGG@GFHHBE;68; @read_150_227/2 ATATAAAGTGACAGATGAACATATATTTTTCCTCTCAGATGGAAACATAAATGGTTCTGAAGACTCAAAGGCCTATTTTGCTTCCAGGGACATAAATTTC + @DHHHHHHHHHFHHHHHEB7435F@@EEFHF>;>BHGGGG666::166568EEB@DE8@DGFHFFEFFHHFCABEGHHHFE8BHHHHHHHGHGEDB;>A? @read_150_228/1 AAACGGGAGTTCCTCTGCACATGCGCTCTTGCCTGCTGCCATGTAAGATGTGTCTTGCTTCTCCTTCACCTTCTGCTATGATTGTGAGGCCTCCTCAGCC + GGGFFFGGHHEEHFGGGFFBHHHHHHHFHFGFGHHHHHHHHGHHHHHHFFGHEHHFCCF=>7,5>;4DDEHHFCDDDFFHEHGFGGHHHGHA5.*.(-(A @read_150_228/2 CAGGGTAATTTATAAAGAAAAAGAGGTTTAATGGACTCACAGTTCCATGTGGCTGGGGAGGCCTCACAATCATAGCAGAAGGTGAAGGAGAAGCAAGACA + HHHFFG;CBDHHGEGHHHHHHHHHHHGEBEGFGG?HFFBGHHHFFGD?EEGGHHHHHHBHHHHHHHHHHHEGD:>@BBA@AEHHHEAEEEHHHHEDCDBE @read_150_229/1 AACTTATGGTAGTTATTTTATTTTTTTGAGACAGGGTCTTCCTCTGTTGCCCAGGCCGGAGTATACTGGTAGGGTCATAGTTCGCTGCAGCTTTATCTCC + GHHHHHHHHHHHHHHHHEFHGGHHF=GGEEHHFGHHHHGHHCEHHEBEFHHHHHG5*;AB479>FFHHHDA;3DDGHHHHHHHHEHDEGHHHHFHHHH?F @read_150_229/2 AAGAATTGCCTGAGACAGGGAGATAAAGCTGCAGCGAACTATGACCCTACCAGTATACTCCAGCCTGGGCAACAGAGGAAGACCCTGTCTCAAAAAAATA + HHHHHHHHHHFFFHHHHHHHCF8?EEGFDDGHHFFHHHHHHGGEFHHHHHFHHHFGHDB=1,8FHHHEEEB?DDDFGDBFHGDDC&&45BEFFDD @read_150_230/1 CAAGAATGGAAACAAGGCCAGAGGATTGAAGTAGCCTGGTGTGTAACAAAGTGATCCTTGAGTTAAGGTCAGTTTCTTGGGAAGACTTGGAGGCTTAAGA + HHHHGEEEFHHHGGHHHHHHGHFGGHHHEBGGGGHHHHHHGHHGCEHHHFFCF<>ADFHFHGGF;FFG?BEEEFGHHHHHHFFFE @read_150_230/2 TGTTTGCATCTTCCCAAGACAGAGTTTTCCCTGTGACCACTTGTGCCTACGGATGAGTCTTAAGCCTCCAAGTCTTCCCAAGAAACTGACCTTAACTCAA + BHHFGHHHHHHHHHHHHCA:DCEHHHHHHHHGGHHHFDGEHHGIEFFHHHDDEHHHHHHHHHHED?DD=FGE>CE;<2:0--;5.<>CGGHH@B/<((7A @read_150_231/1 ATTACCCTATGAGAGAACGAGTAAAAAATATGCATGATGGATAGGGTTCAATTAACTATAGCAACAGACAGAGTTCCTAGTATGAATCAAGATGTTCTAA + GGHHHHHHFHHHHHHHHHHHHHHHFHHHHHHFHGGGGHHEHGHHFGGFFHHHFHFDFHHFHHHHHHHEFEFHHHHHHHHHFHHHHHGGGHEC=DDDHF?B @read_150_231/2 ACCTATGTGTGTTCATAGGCCTAAGGGTAGGAAGTGTGTTTGTTTCCTACTCTTAGAACATCTTGATTCATACTAGGAACTCTGTCTGTTGCTATAGTTA + G@@EHFFHHHHHHHHHGGFFHHHHHHHEFFHCHHHHHHHHHHHHHHHHFFFFHHHGFFFHFFEGGFFG5.*<-84F=EEGHFHHHHHFHFFEEGGEFFDD @read_150_232/1 AGTAGCTGAGACTATAGGTGCTTGCCACTATGCCCAGCTAATTTTTGTATTTTTAGTAGAGGCCAGGTTTCACCATGTTGGCCAGAGATCGGAAGAGCAC + HHHHHHHHHHHHHGGGGDGD@AD>;2.5@>EBGGHHEFBGCBBGH@CEEHEHDFEEEECEDFHFHFHHHHEB7:FGGDDDD8E6<><<:>GGB:;@BFHHHHHFFCFFHHGBGGIFBBFFCG; @read_150_233/1 TTTGTGTTTTTTGTTTACTTTTGTGGTAGGAACACTTACCAAGAGATGTCCTCTCTCATTTTTTTTTTTTTTTTTTTTTTTGAGACAGGATCTAACTCTG + EDA?BBFGGGF3DFG=30)),6EHHHH?4GHFCEFFFGBCCGEFGHHHH@5--,G?GHHGHF.8-2>D:7:<:<>CFBFBH8-7=<< @read_150_235/1 TGGCCAGCAGGATATTCAGGAGTGTCCAGAATAGAGTTTGCTAATCAGTGGCTTGTGGACCTAATATGGCTTGAGTACCTAATTTTTTTTGACAGCACGT + HHHHHHHHGGHHHHHHHGHGHHHHHGFBHGGFFGHHFFCD9>@BBFFHHHFFGHHHEHHDHHHEGGA;?ACCHFFGDFEHEHHHGHFFGG@C:FFEEFFH @read_150_235/2 TGAGTCGGTAATTGTTGAAGCTAGGTATTAGATAATGGGGATATTAATACTATACTGTGTAAATATGTATACGTTTTAAAATTTCCACAAAACTTTTAAA + HHHHHHHHGEGEHGG=FHHHHHHHHHHGFHHHHHHHGHGFHHFF@57>=CCB@=FHHHHHEGHFFHHFF3EHHHGHHHDBE><>?FFHFGHHFEEHHE@F @read_150_236/1 TCAGTCGAGTTAACTTCAATGAGTGTTTCTCAGTGTTGCACTAGGTGCTATAAGAAACATAGAGAAGTACAATAACATCTCAGCTCTCCAAAGATCGGAA + GHHHGGGGGGCGGDEGGGHHHHHHHHG@DHHDBGFHHHFFHHFF?314?AC>.8F@@BEEGGFGHHFDGEHHHFHHHHHGGDE7@7FGEB44228B?FF @read_150_237/2 CTGGCCTTGATTTTTAGTTGAGATGGGGTCTCTCTATGTTGCCCAGACTGGTCTCCAACTCCTGGGCTCAAGAGATCCTCCTGCCTAGGCCTCCCAAAGT + HHHGDFFHHHHHHHHHHHHHFHHCCHHHHEHBG.;DHE===>>5BGE>?;DEEFHDBABEGBBGEHHHHHGFB=3DAB>==<.:4C8F5BGGGGFDC59, @read_150_238/1 CGTTGCTCCAGCTGAACTGCTCTATGCTGAAGCCCTGCAGGTCTCAAGTGTTTGGTTCAGAGTAATTTCAGGCCATATGAATGCTTTCTTAAGTATCATT + >>CC@BEEFCCEDGGGFFHEDHGEGBBFHHHHGFGFGGGFHHHHHFFFHHC:;?A:=@@ED:ACCEFBBHHHHHFHHHGGGBFEHHHHHHHH?@HHHHEE @read_150_238/2 CTAAATATGGTAATAGCTGGCAGACAGCCAGCCCAGTAAATTCCAATGATACTTAAGAAAGCATTCATATGGCCTGAAATTACTCTGAACCAAACACTTG + GFFHFFHE=87;GGA8E8:=83EHHCHHHB@GGGGEHHHHHHHHFGGFF?GHHHHHHHHGCEEG@8.?FA@HHG=CAEEFFFHGHHHFC>FE=GGBCDHA @read_150_239/1 TGCACTCCCACCTGGAGGACAGAATAAGACCGTGTCTCAAAAAAAAATTAGGCAAACAAATTCACTAATAATTGCCATGTGATCAGTTGAAAAATCCAAA + HHHHHHFHHHHHEDGFCFHGGGDECHHHHGHHGBGFHHHHHF=DEFFE:AD4D>7D6< @read_150_239/2 GTTCAACATGCCAAAATTCTCATGCTTTCTTTTTTTGGATTTTTCAACTGATCACATGGCAATTATTAGTGAATTTGTTTGCCTAATTTTTTTTTGAGAC + HFD?GHHHHHHHHHHHHHHHHGHHHHFHHGE/2HFDAEED869EEHHFFGFGDD=DC@G=:GHHHHGFHHHEBFFFHHHAGHHHHHHHHHHGGGHHHHHHHHGDDFHHGHHHHHHFF<>+17<HHFH@BC@<=AEBCHHHHHH @read_150_241/1 TATTATCCCTTATATGACATTCTGAACAAAAGGCAAAACTATGACAGAAAACAGATCAGCAGTTGCCAGGGGCTGAGGCTCAGGACTGATTACAAAAACG + GGHHHHHHHHGHHHHHHHHHHGGGHHGBGG@BFFEHHHHHHHHHEDBHHFHHHHHHHBECEFEFHBFEDF>BEECGGGHHFGGFGEEEFEHHFHHHHHHH @read_150_241/2 CATCTACCACAATCAAGACATAGAATAGTTCCGTTACTCTAAAAAATTCCCTTATACGTTTTTGTAATCAGTCCTGAGCCTCAGCCCCTGGCAACTGCTG + ..*65;EEFFHHHFHHFFDGBEFDHHHHHEHEGHHHHHHHFFHHEEDFHHHH@EDFGDBCHHHGHHFGDHHHHHG@EEEEGEHA=><;CDHF7).8?-7; @read_150_242/1 TAGTCTTAAAACCTTGCAGTTTTGTGGGGTTTTTTTTTTGTTTGTTTTGCTTTACTCTGTCATTTACTTGCAACATGCTGCCTATTATCAAGTTGTGATG + HHHHHHHHHHHHHHHHHGEEHHHHHHHHHHHHHHHGBDCC/BHHHHHHHHFHEBHHHHHFDEGGHHHFEHBBFHFHHEBBA9&+DFFFHHHHHFD+1)3< @read_150_242/2 AGTGATATTTAGGAAAAATAAACATCACAACTTGATAATAGGCAGCATGTTGCAAGTAAATGACAGAGTAAAGCAAAACAAACAAAAAAAAAACCCCACA + HHHHHHHHGGHHHHHHHFFHHFHHHFGGHHG?GGHGGFDHHHBD=GFC>?@A7*43-->GHHHHGHHHHCB-*6BHHHHHHG:;EDFGFHHHBEBEFHHD @read_150_243/1 CTAGCATAGGGGTCAGGACTTTGGGTTCAGTAGTCCAGATGTGTGTTTGAGCTCTTGTCTCCTCCACATGACTGTAGCAAATCACTTAACCTCTTCAAAT + HHHFHHHHHHHHHHHHHHHEHHEGGHHHHHFHHHHHHHHHHFHHHHHHHHHHFEGHEAGEEB7>DH?DHB@ADBEEEE?DHHGE.E=B/955;=F9.>EFCH?9;EFFFACCADD@>@GFGHHHHHBC>>DD:A>?@GE?A@D4A?CDEFFHEFFGEEDBCBBD;=EEGFE<;BGHHE6C8;01,60A9EFHHFEFEEEHG6;D?B>=5CCEF?GEEFDD?7>7FBE?G..* @read_150_249/1 CTGGCCTATTGATCTTAACCATGTGGAGACCGTAGGACCCACTGTGGGCTTAGAGTCCCATTCCAGCCCAAGTGAGACCCATCTAGGAAATGGATGTTGA + GGGHFFHHHHHHHHHGGHHHHHHHHFE@D=350*>HHHHHHHHHC<@BEFFFHHHHHHHHEFEDEHHHFFGEECEG>>;2>,15ABB>?06):BBAFE>,,,+)*? @read_150_250/1 TCAGAAAACTGAAACTGAACCCCTTCCTTACAACTTACACAAAAATTAACTCAAGATGGATTAAAGACTTAAATGTAAAACCCCAAACCATAAAAACTCT + @EGFHHHHHHHHHHHHHHHHHGGHFEEHHDHHHFHHDBA@DHFB9BE@CDEHHHHHHHHHADDDHHHHHHHFFF=FCD>@89+3)/*:BHHHEFFDFGHH @read_150_250/2 TTTTGCCATTTTTGTCATGAAGTCTTTGCCCATGCCTATGTTCTGAATGGTAATGCCTAGGTTTTCTTCTAGAGTTTTTATGGTTTGGGGTTTTCCATTT + HHHHHHHHHHHHGHHHHHHHHD.DA8CCEHHHHGGE@@BHHFB=FBFFFHDDC@=C=65()9<5AGHHHHHHFHHHHHHHHHHHHHEEEFHHHF(@;4:3 @read_150_251/1 TGGTCTCGAACTCCTGACCTCAGGTGATCCACTCACCTCAGCCTCCCAAAGTGATGAGATTACAGCCGTGAGCCACTGAGCCCAGCCAAGTTGTAAATAT + FFFHHHHHHHHHEEFGGGGGGHHHHHHHFEHHC?@EDGHHFEHEFHFHBFFBHHFBDFHHF:5.7>,48CGHHHHHBFFHHHB9;:=A=:AE<5'-)-,>+ @read_150_252/1 AGGTACTGAATTTAGTTGCATGTGTTTTAGTGTCCTGTTATCTGGAACGTGTCTACAACTCGTCTTTGTCTTTTACAGCATTGACATTTTTCTAAGATTG + HHHEBEEBFBGHHHHF6FGHHGEEE@HHHBEEDCAEGGHHHHHHEDHEGCEFFFEFCFFHHFFHHFFGED?0)15:5AHGCCBEBB@ED;GHHHHHHHHHGFHGBGFGFFG=@&'+CGHHHHFHEE@* @read_150_253/1 TGTTAACTACATGGCCACTGTAGGCATTTGAGTTGATACTACCTGGTATACCCTTGCTGAGTCTTGTCTGCTCATCCATAAAATGGAGACATTAAAAATT + HHGGEFGGFFFHHHHHHGHHAHHGHHHHHFHHHHHGHEFHHHEHHEEAHHHHHHHHFHHHHHHEFHEEBBGHHFFHBGGHHH?B;;<(&-1+;CHHF?FE @read_150_253/2 CTTGAGCCCTGGAGGTCAAGGCTGTAGTGAGCCATGATTGTGCCTGCCTCTGCACTCCAGCCTGGGCAACAGAGTGAAACTTTATCTCAAAAAAAAAAAA + HHHHHHHHHHHHGGGHHHHHHHHHHHHHFGFEBGDFHHHHHHHHHFGGGGGGGAEHHHHCBGGBBEGGHHCD@E/<@<@AHHE>>CDHHHHHHHFD9DGA>CGGFFHFBCFFG=< @read_150_255/1 CTGACCCTTGCTGAACTGGGGTCCCTTTGTGAGTGTCTCAGTCTAGAGGTACCTCCCTCCCTGGGGGGTCTCAGCTCCTGGAGTCGCAGGCCCTTGGGGC + HHHHHHHHHFDFGFGHHHEFGFBDCFGGEHHHHHHGDEEBD334FEHFE?4:,>>>?AEEGB9F>894??HHFGHHFH @read_150_255/2 GACATTGGAAGGTTAGATGAGACTGAACAGGTGAGAAAACTCTTAGGGTCCCCAGACAGCATTGAGATCTCACAGAGGGGCCCCAAGGGCGTGCGACCCC + EHHHHHHHHHHHHHHHFFHHHHHHHGHGAFGDCEHEBEHHHHHHHHGIGFHHHHFHHGGFGHHHHHHHHHHHHHHHHGGCE8:<>=FHFHHHHHHFGGHHFHHHHFEGGHHH @read_150_256/2 GTAAAACAGACCTGACCAATTTTAGGGTTTTAATCCTTCAAATAAACTAATGTCCATGAAAACAGATGCAAAGTGTTTAAGCTAGCCTCATGATGAAGAA + GHCD@@=C:>>D?EGHHHHHHHEEEFFHE?HHGFFHHHHHEDDHHHHEFFHFGGHHHHGHHGGEGFCC@;C<7<&(3;??EE@B@CFECDADH07A4008 @read_150_257/1 GCTCCTGAAGGAAGCACTAAACATGGAAAGGAACAACAGTACCAGCCACTACAAAAACATGCCAAATTGTAAAGATCATTGATGCTATGAAGAAACTGCA + HHHHHHHHHHHHHHEGGFFEHHHGFHHHHHGFCA,1-(:<6:CFCFE6;>)5A3:@EFEHFGFFHHFD8:,639@:++6CBB66?EGGFFHFC=FBFHHHHGHHEEDF<6& @read_150_259/1 TTTTGTGGACATATATGTTTTTCATTTCTCCACGATAAATATATTTAGGAGTGGAATTGTCTAATCAGAGGTATGTTTAACTCAGATCGGAAGAGCACAC + DDDHHHHGBDFHHHFHG>ADEHHGHGGGG?3;8ADDAC>GFHGDHE@<:/DGGGAEGFHHHHHCFFFHHHHCEF@DHHHHHHHGGHFFDDB1.:5>A=B? @read_150_259/2 GAGTTAAACATACCTCTGATTAGACAATTCCTCTCCTAAATATATTTATCGTGGAGAAATGAAAAACATATATGTCCACAAAAAGATCGGAAGAGCGTCG + G7;<;G:FGHHHHHHHHHHEHF8,:<972/22589EEHE;DCDHHGHHGGHHHHHHF:8=I@@><6<:9BFHHHHGGGFHHBGGFHHHHHGHFDAC-5&( @read_150_260/1 GTCAATAAGGGTGCCACTGGCAAATTCGTCATTTAGGATGCTGTATTTTTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCACCTAATCTCGTAT + HHHHHEEHHHHHHHHHHHHHHHHHHHHHHHEEEGGHHHHHHHHHHHHHHBH@EBB1AFHHEFF>CFHHHFGBHBEHHHHHHGGGHGHGFGHHFEFHHDHH @read_150_260/2 GAAAAATACAGCATCCTAAATGACGAATTTGCCAGTGGCACCCTTATTGACAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGC + DEE89;<=>ACCBB/7BBHHDDE5@GEDHHHECCEDFCDAGFFHFCGHHFGIBDBGHHBDFHHHHHHHHH?.FIDA41<6??A=?2<57?DA8<9DEGD@ @read_150_261/1 TTTCTGAGACTGTGCGTGGATTTAATACGTCACATTTCGATGATTTGAGGGAGATGGTGATGGGTTGGGGAACTGAGGAAAGATCGGAAGAGCACACGTC + D?DDGHHHHGHHGEGGFHHHHFHHFHFAC=HHHHHHHHHHHHFDGB<38+4A @read_150_262/1 TAGGTTTTTAAGAATTGTCTAGTTGTTACAGTGAGTATGATTATTGAAATGTGATCTGCTTACCACAGAAGAAATATTTAGAATTGTGGCACTGTTTCAA + HHHHHHHHHEGHHHHHHHHHHHGHHHFHBGB@EDDFHHHHHHHEDHFCF3??FFFHHHEHHHHHFHFEFFBHFHEHHHFDEBFHHHACB8GFC5CDDF @read_150_263/1 CAAAACTGGCAGCATAGGTTTCAACCAAACATCGTAATGCAAGATCTGCAAACACAATTATGTGGCCCCCCCAAACCACATCATCTTTAAAAATAAATAC + HHHHHHHHHFFFEEEF?+97GHHEHHGDD>FEEEDCE?DFEHHHHHHGFEDGGEHHHHHHBGFHHHH@<@==9+)8>>?5?CGGHGFHHHGGGDDFHHHH @read_150_263/2 AAATCATTAAAGAAATTGAGAAGATAGAAGAGCAAATTTGAATGAAGTTGATAATTCATGATAGTATTCTTACAAATATAAAGCTGAGTAGGTTTTTGCT + HHHHHHHHHHHHHHHFHHHHHHHHHHHHEEHHHHBFHFHHHHHFFE/BGBDE:@@EGFFHH??=C;3-5BFBGGHBFHHHGEDEEG?@=8@FDDDDBC>= @read_150_264/1 TTCTTTTCTTTTTTTTTTTTGAGACGGAGTTTTGCTCTGTTGCCCAGGCTGGAGTGCAGTGGCGCAATCTCGGCTCACTGCAAGCTCCGCCTCCCGCGTT + F6939DFFGEGHHHEF?=CB@@F@AHHHHGGHHCDHHHDHHHHHHFFHHHEEG><9E9=07FFGFFHFGEAE@CCEHHFEGCEHHGGGBB;>5;BGFHFE @read_150_264/2 AATACAAAAAATTAGCCGGGCGTGGTGGCGGGCACCTGTAGTCCCAGCTACTCCGGAGGCTGAGGCAGGAGAATGGCCTGAACGCGGGAGGCGGAGCTTG + DCEFFGHHHGHHHHFHG:5@C=<.BB?FHGGC=DFHHHHHHHFHEHDCABEEEBB3CFFEGBBHHHHFGGHHCFEHHHHF@EEC@%25:12>11/9645' @read_150_265/1 AGGCTTGGGCCTTCTCACTCCTTCACCATCTCTTGTGCTGGAATACAGAATTTTGTTCATTATTACTATTATTTTATAGACATGGGGTCTTGTTCTGCTG + HHGHHHGHCDHHHGAAA?GHHHHHHHHHHHHHHHBEFFC?CEFDEEHHHGHHEHHD5:BEEHHBBHHHHFHH?AF@EFGG@=>4=FHEBDEEEDGBGHG6 @read_150_265/2 AGGAGTTCATAGTTACAGCGAGCTATGATTGCACTTCTGCATTCCAGCCTGGGCAGCAGAACAAGACCCCATGTCTATAAAATAATGGTAATAATGAACA + HHHDHB5EFGGFBDDDD>9FHHHFHHHHFHHHE4;?GHHGHFFGH6AAEBEEGGEEFHFFHHHHHHHGGHHHHFHHFHEEDCF@@='.8/1/%,4>;?DD @read_150_266/1 CCTCCATTTTCTCATCTGTAAATCAAGATAATAGTATTATACTTTCAAGAGCTATTGTGAGCACAAAATGAGTTAATATGAGGATTACATGTATACATAA + D8EEHHHHHHHHHHHHHHHHHHHHEHHFFGHHHGHHHHHHHHHHHHHHHHHHFDDC>HHHHHHDDEFFBEEBHFFGFHHFFFHHHHHHHFGFHHGHHH@B @read_150_266/2 GTATATTGTATGTATATATGTATGTAGGTATGTATTTTTCATAAACATTTATTATATATTTATTATGTATACATGTAATCCTCATATTAACTCATTTTGT + @EBFGGG8=2@BHHHHHHHHHHHEEHHHHHHHHHHHFFFHHHED/GGG.:BCDEDGFB;HHEEGHDHHHHHHHFHHEEEFEGEG@<:6EFFHHHFDBGDB @read_150_267/1 ACTATTGATGGTGGACAAGAATGTTTTCTTGTCAAGAACATACGATTTAGAATGAAAAGATGAGGGTTTGACTTTTATAGCATTGAACAGGTTAACCTCT + GDC>>FGGGEEFFEGBEHHGGGGGHGDDHHHHHCHHFHGGGEFB?@A=??AEHHHFFFEHHHEDFDCBDEHHHHHHA<5>47;@EHHCE @read_150_267/2 CAACTGAAACCATTTAAAAATGTATAAAACTGAAGCTCAGAGGTTAACCTGTTCAATGCTATAAAAGTCAAACCCTCATCTTTTCATTCTAAAACGTATG + HHEEGHHDCCFHHHHHHHHHGHHFGHHHHHFHHHHGHC?>E4?:38GBC@HHHHHHHHHHHHHHHHHHHHHHHHFHHHHHGD@F/<99.BF@<+/7AFFF @read_150_268/1 GTGCAGAGTCTAAGACAAATAGGGAGGATCAATGACCCTTGGAAGTTCCTTCTAACAAGACAGTAAATATGGTCAAACAGTAGAGCGAAAGAGCAAACCT + HFFEGFHGHHHHHHHGHHHEHDEF<(9>@CFEHHCEDEDBBCFB5BED;*DBBED>6774),%'7 @read_150_268/2 ACTGTTTGACCATATTTACTGTCTTGTTAGAAGGAACTTCCAAGGGGCATTGATCCTCCCTATTTGTCTTAGACTCTGCACAGATCGGAAGAGCGTCGTG + FHHHHHHHHGF8FD>=DGFEBGFBI<@ADA?FFHHHHHHDCB@C,6::==408E@CEBEFGHHHHFAFFEGHHCHHHHBCFHHHHH @read_150_269/1 CTCACTGCAACCTCCAGACATGTGTCTGTTCGTGTCGTTTGCCCACTTTCTAATGGAGTCATGTTTTACTTGTTGATTTGAGTTCCTTATAGATGCTGGA + HHHHHHHHHHHHHHHHHHHHHHHHHGHFBFBED9AEEHHHE;@ABFBADACHGF502DBDD@@EFFHHFDHFFHHHHHHHFGGHHBBEEEHHHHHHHHHG @read_150_269/2 AATATCTGCAAACTAAGCATCTGACAAAGGTCTAATATCCAGCATCTATAAGGAACTCAAATCAACAAGTAAAACATGACTCCATTAGAAAGTGGGCAAA + HHHHHHHHHHHFHHB@GBCHHHHHHHHFFBHHHHHHHBGHG>;DE<5;B>DGHFFFFBDDGGFFEBEE??BIHH?DEGF?EEEHHHHD(.AD?AC>BEGG @read_150_270/1 CACACTCCTTACCCTCTTTAATAAACTGATGGTTATCTCAACTGGTACAATCTTTCCTTCTTTAATGTACTTTTCAATAAGTTCACCATACTGTGAATCT + HHHHHHHHHHHHEEDGHHHGHHHHHHGHGFHHHGGFFFFHHFFHFBEFCC9?DBBBDFFF9=3=DFFBB>AADFHHHHFEBD?HHHHHHGGGAB?FGBHF @read_150_270/2 TCTTAAATTTTTCTTTATTATTTAATATACAAGCAAAACTTCTTTATTGTAGAAAAATTAGAATATAGAAATTAACACAAAGGAAAAAAAGTATAGTCCT + C@EGHFHHHFEDDGGEE=@BEGEEHHHHHHHHHFEEBABDHHHHG?GB@DHHFFHHHDHHHHHHHE@CEH@A?HHHHHEH9511GGHFFF>.?GGGGHHH @read_150_271/1 GCCACATAACACTTGGCATTTCCAGACTGCTTGACATGTGCTAAGCACGGTGCTGGGGGTAAGGGGATGAGCAACACTGGCAAGGCTCCTGCCTAACCTT + HHHHHHHHHHHHHHHHHGHHHFFFGHFFGFFB<*2CHFHHHHHFHBEDBFHHGDBCC?AFHHHHFHBF< @read_150_272/1 AGAAGTGAAGAAGACTCATACAAACATAAAAGCAGTAGAGAAGCTGAAAAATAGACTGGTTCTAAATATATTTTGGCGGTAGAGAGATCGGAAGAGCACA + HHHHHHHHDCDFHHHHHHHHGG?>:F;5=6>DD?D=BDGFEF @read_150_272/2 CTCTACCGCCAAAATATATTTAGAACCAGTCTATTTTTCAGCTTCTCTACTGCTTTTATGTTTGTATGAGTCTTCTTCACTTCTAGATCGGAAGAGCGTC + HHHHEBBFEHHHHFGHHHHHHHE.C+)7CHHHHHHHHHHGDFHHHEE@EHHHHHHHHFFHGGE/GFIGHHHHGGEA:1)<3CFBEDDHHHHDHEEBFEHHHFFHHFF??GGHHH @read_150_273/2 TTAAAAGTAATAAATACAAAAAAGAAAGCTTCTGTCCATTTTTTTCACCCTTTCTTTTATTCAAATGATATCCTGGGTTTAAAAAGAGAAAAAGATCGGA + GGGHHHFFEHHHHHHHGGBHHHHGGHHHHHHGHHHHFFE?DHHHHHFHH@CCCDDFFFHHHFHHIDHFFCDHFDD=EA.6,7.8;>8CEE>CFFFHHHE@ @read_150_274/1 GTCTTCCTCCAGGGAACACAAGATGGTGGGGAAACTGTCCACCCTGATCTCACTTTTTCTAGTGTAAAAACTGTGAGATGAGTACGAGAACATTGTCCAC + FGGHHHHHHGHHHGGHHHHHHHHHHBCFFBHHHFFHHFDEFFFHHHHHHHEFGHHHFGGFFFHHHDFFF?H??E=EFFCDEHHHHFCHHHEC@;0.7BD= @read_150_274/2 CAGCGCCAAGGTTAGCACCAGCAATATCCCAGTACTCGAATATAAGGATAAGACAACTCTTGGGGCCACAGAGAAGTGAAGAAACTGTGAGTACATGGTA + 2-24@<:?>DG@??>2;>:=;55.CHFHHGHHHHCHFHHHHHHHHBGGFBGGIGFHGBCHEDEEEGF@GEGF=HHHHHHHHEEEEGGAA6(,,55@CGHHHGFFHGHHHGHGFHHGGHHHHGCDDG;=GGHHFFEHHHHHB5::@DE@99D71ABE?>BHHFHHHHHHEEBC>DBHFFHHHFHFHGHECDDEEFFFEFHHHFHH@DEHHFBFFGGFHFHHB>F @read_150_276/2 TTGAGCTTGCTTAGTTCTACCAGGAAACAGCAAGGGCAGGAGGTCTGGCCCTACCACCCGTGTGCACCCTTGGTTAATACTCTCTAGAGCAGAACCCAGA + HHHHHHHHHHHHHHHHHDBDGEEFHHHHHFHGG5B?EEHHHHHHFHFFBD57EGIHHHHHHHHHHHHHFFHHHHHHHFFHHGGEDHHEEEHHHHHHHHHG @read_150_277/1 TAGTCATGTAGATTTTAAGTGGTCTGCTTATAACCCTATATTCTCATAACCCTTTTTTTAGTGCATGTTTTTATAGAATATGAGGTTTTTCAGGAACAAA + <=DB>9-7GHHHHHHGFFGGGGD??B/:CBGHHHGDGDGGGFHHHHHHGD>=8EGDHHHHHHHHHHHHHHHHFFHHHHHH>96BGCEEHHGFDGHHHFE?4FHHHHHH @read_150_278/1 AAGTCCATTCGTTTTGGAAAGAAAATTCTCATTGTTCTCCCCTGCCTGCATGTTTGTAGCTTAATAGTATAGGTTTGGGACAGCTAATCCCTGAGACATA + FF=2-14>8D=BGGFGE=FFD<:8CB=FEEEHFGHHHHHBFHBFEG?9>3?DHHHHB@DBFFFHFF9FCDDEDDDHHGHGE<>4>EBEBDG@CFEFFFGH @read_150_278/2 ACAATATGTCTCAGGGATTAGCTGTCCCAAACCTATACTATTAAGCTACAAACATGCAGGCAGGGGAGAACAATGAGAATTTTCTTTCCAAAACGAATGG + HHD?:DGGEHHHHHHHHHHH<466HDG=D@DFFCDEHHHHHHHHHHHHFEGFFHHHHHHHHGGGHHHHHHHEFFHHHHHFGDEHHADIDFHDCHF=FHFH @read_150_279/1 TAGAGTTCTCCAGGGAAACAGAACCAATAAGAGAGATTGGTAAATATTATAAGTAAAAGATATATAGAAATAAACATATAGGGAGATATAGATATATAAA + HHHHHHHHHHHHHHHHHGGHHHHHHHHFFGHFA@<:BEFBHF@75791<9DDDDE2=09EEGGGD@;=CE @read_150_279/2 AATAAATACACATATATTTATATATCTATATCTCCCTATATGTTTATTTCTATATATCTTTTACTTATAATATTTACCAATCTCTCGTATTAGTTCTGTT + HHFE8CA@@;.:-@GHHHHGFA=@BHHHHHHHGE>A:EHHHC>>@EEGGGFIGHHDCDHHHHHHHHHHHBEFBB=CHHHFHHG=49.;52)->;EED>:; @read_150_280/1 AGACTCCTATACACTTCAATTTTCCAGCAATCCATAAAATTGAAACATAAAAATAGGATTCTATTTCCCTTGTTCATTCTATATCTTACCAAGATCGGAA + HHDDDA-?HF979>(DB=0>FACDFFHHHHHHHHGB?6>BGHHGFHHFFHF @read_150_280/2 TGGTAAGATATAGAATGAACAAGGGAAATAGAATCCTATTTTTATGTTTCAATTTTATGGATTGCTGGAAAATTGAAGTGTATAGGAGTCTAGATCGGAA + 9--8;7-0,BGF8GHHHHHHHHHHHHHHHGHHHHHBFHHHHFF?<..:5FGCEEFGFGC5C@EGHHHHHHHFDFFGHFGGHHHDD@8-)4:>.EHHHDB? @read_150_281/1 GGTAACAGGGAAGGTGGTGGGAAGTGGTTGGATCCTGAATGTATCTTGAAGGTAGAGCCGATGAGGTTTGCTGATGAGTTGGATGTGGGTGTGAGAGAGA + FBGGHHHHHHHHH9GE@BBD<9::8BHHHGGHHHHDDD?EGG@@EFHHHFAAAABGFHHFGDFF8::,>1FHFHHHHHHHHHFFFHFDGFGGEAGHFEFF?=EEDEHB?=CC @read_150_282/1 AGACCTCTGAATAATTGTTTCATGTGATCTACATGAATAGTGTATTATTACTCATTACCAAGTAATTACCAAGATAGTCAACAAGATATAGCCCAAAGGG + @>>=DHHHHHHGGGHHGHHHHHGHHHGHHHHGFECDHHHFEFHHFHF?FFHEAEEHFB@@CFHE?FFFGFEGHHADHFCDGBBGB=DHHHHHHFHHHHHH @read_150_282/2 CTCCCAACTCTTCCTTCCTCCCCACCCCCCTCCACCACCCAAATTATTGTGTATAATTCCCTTTGGGCTATATCTTGTTGACTATCTTGGTAATTACTTG + I?EEEHHHHHHFFGGHHHHHHHHHHHHHHHHHE@,9EEEGEFFHHHFEHHHHHHHHHHHHEEGG6;CGHHHHHHHGHHHHHHHFFGD=C5.=65FHHFFA @read_150_283/1 GAAGGACAGCCAGCCAAGAGAGGAACAGGCCAACTATGTTCAGTCTCTACAGCAAGAAGCACAGGATCTTCCACAGCCAGACTCAACGATTTCATGATGC + GDFBBGEEHEGHHHHHHHHHHHFHHHGGCF@FFGD=FEHHHHHHHHEFHHF9EHFFHHHC@6DFHHHFHHCFFCBHHHHGHHHHFEE7??@A=CFFGDDD @read_150_283/2 TTTGCATCATGAAATCGTTGAGTCTGGCTGTGGAAGATCCTGTGCTTCTTGCTGTAGAGACTGAACATAGTTGGCCTGTTCCTCTCTTGGCTGGCTGTCC + HHHFIFGGFHHHHHHHDDDDGHEC;@<=G?EFFFFCGHHHHHHHHFHCGGFGGEEGFEB8),+;EFFFHHFFADFC,4DAE6E=8DADFFBA==FHFFFH @read_150_284/1 TTCCTGGTGCTTCAATTTCCTGTTTGTAAAATGAAGAAGTTGGACAAGATGATATCCAAACATTCTTCTAACTTTCACCTTCTGTGATTGTCTGTGTGGG + GHHHHHHHEGHHHHHHEEFHHHHEBBDDFCFBEF=HHFFHHHHHHHHHHHHHEFGEHHCCHHDDFDEDHFFDC9<@A?DBFGHEHHHHHHEE=<>;DDFG @read_150_284/2 TCTTCAGAGTGCTTATAAAATACAAACCCACACAGACAATCACAGAAGGTGAAAGTTAGAAGAATGTTTGGATATCATCTTGTCCAACTTCTTCATTTTA + C5FGGHHHHHD=DGFCFGHHHC26DBEHHHEG<@BE>FFHHH03<*1:BGHHEEHHHGFFHHHHHFFEHHHHHHEEHGCB8D,>@B@BDDHHCC@EC @read_150_285/1 ATGCTAATTAACCAAATTCTGCAAAACAGAGGGTTCAGGAACTAAGCTGATAAAGACTGAATTCTCCTGGAAAGGATATGTGACAGAGGGAGAGAGTATG + HHHHHHGHHHHHHHHHHHHHHHHHFDFFGHHHHHHHHHFFHHDDDADHHGHHHHHHHHFFHHHHGGGHHHD@CEEGHHGEEGHFFEHHHHGB?GHHHBAB @read_150_285/2 TCTAAAACTGACAGGGAAAAAGTTAATGTAAATATTCACAGTCCCTTTGCTTCAGTCATACTCTCTCCCTCTGTCACATATCCTTTCCAGGAGAATTCAG + GBBFGHHDDD;17(.:=DHH@D?E?FFED?FFFGHHHHHHHHHFFGHGFH @read_150_286/2 CAGCACCACACCACACCTATTCCAAAATTGGCCACATAGTTGGAAGTAAAGCACTCCTCAGCAAATGTAAAAGAACAGAAATTATAACAAACTGTCTCTC + HHHHHHDGHGGFHHHHHHHHHGBD7+2;(1):?AFDDGEEHHHHHHHBE?DGGGB=B@@:@?:FHHHHHHHHHHHGFHHHHDGA:CDAEBE@7:EGG@;9 @read_150_287/1 CAGACATTGTATTTTTCATCTCTAGAAGTTCAGGCTGGGTCTTCCATGTCTCTGCTTCCATGTTCAAGCTTCCCTTTACCTTCTTGTTGTGGAATGTTAT + HHHHHHHGEHHHHHHGGHHHHHDHHHHHGGHHHHHHFGDBEHFFFHHHHHFDEEEHFFHHEHHHHHHFFHFFFHFHHGGGHFCFBEE6:48*2AEHHFFH @read_150_287/2 TAATGATAACATTCCACAACAAGAAGGTAAAGGGAAGCTTGAACATGGAAGCAGAGACATGGAAGACCCAGCCTGAACTTCTAGAGATGAAAAATACAAT + HHHFCHHHHHHHHHHHHHFF;BBGEGGHHHFH>B><<:=><;<-.CCHHHHHHEFCBGGGEBHHHB@4BABDFFD:7DC>8'01->EEF6GBBEHHHHBF @read_150_288/1 CAGCTACTCCGGAGGCTGAGGCAGGAGAACCGCTGGAACCCAAGAGGCGAAAGTTGCAGTGAGCCGAGCTCGCACCACTGCACTCCAGCCTGGGTTACAG + HHHHHHHHHGBBEHFHHHHHHHHHHHHHHHHHHHEHHHHHHHHADCHFHHFHHFBCF;>,;0A3,/6A+E8EED2DEC:,'/.?;;'%*0>E=GEDBH.>*:,*<;?=>:BB @read_150_289/1 TTCCCATTTTTCAGATGAGGAAACTGAGGCTCAGAGAAGTTATGTGATTTGTTCAAAGTCACACCACTAAGTAGAAAAGCTAGGACTGTAGGCAGATCTG + HHHHHHHHGFFHHHHHFGHHHHHHHHC>?A:@@@ECC<19ADDFCFGFHFHHHFCDHFHHE5;C=BA88>.*'01;C>DDGHHHGHHHEDEGFGGE452( @read_150_289/2 TGAATAACATGATGCCCTTTGAAAAATATGATAACATAAGGGTATAATGATCAACAAAGTATCTTTGTGGTTAAGAGTCTCAGAATAAAAATTAGACAGA + HHHHHHHHHHHHHHHHHHHHHH<41AFEGFDHB?AGHEEEFFHHHHHHHHHHG@94:GD?.AB2?*; @read_150_290/1 GATGATCTGTGCAGCAAACCACCATGGCACACGTTTACTTGTGTAACAAACCTGCTCATCCTCCACATGTACCCATGAACTTAAAATAAAAGTTGAAGAA + HHFFGHHHHFGACAFHFHHHHHHHFGGFEFHHH?<5<>@>,32=:>>FHHHHHFHHFFGGEGEEFFDDDFDDDF@GGHHHHHHHHHFE?FGFFEHHFGHF @read_150_290/2 TCCAGATTTGTTCTTTTTGCTCAGGATTACTTTGGCTGTCTGTGCTCTTTTTTTGGTTCTATATGAATTTTAGGATTGTTCGTTCTTTCTTTTTCTTTTC + BB?HHHHHHHHHHHHC@@8B@>CG<5.<-====FHHHFFF?EFFEDFHHHHHHHFHFFHHEHHHHHEHHHD?4FH @read_150_291/2 GCAACAATTAGGTACATATCAGAATCTCCATGTTAGTTTGAGTCGTGTGAGAAGCACACACCAAGATGAGAGTAGATGTGCAAGAGATGCACTGGGAGGA + EEGHHHHHHHHHHHHFDC@BEEHHHGGECE@@=; @read_150_292/1 TGAGTCTGATTTTGCTGTGGACAATGTTGGGAATAGAACTCTGCGCAGGAGGAGAAAGGTAAAACGCATGGCAGTAGATCTCCCACAGGACATCGCTAAC + FEHHHHHHHHHFFHHGG@DFHHHHHHHG>@73ACA>>FHHHHHFHHHHHGHHB/A9CFDGG=)5,*087.4*19ADCDDB?A @read_150_294/1 ATCCCACAGCATTTCTTTTTAATAACTGTTCAGCTACAAAATTTTATTGGTATCTTTTTATGTTCCCTCTAGAGGATGTAAGATCGGAAGAGCACACGTC + HGHGFEDBGGE=DDGGGGGHHHHHHHHHHHHHHHHFGFHHHHHFHGEHHHHFHHHHF?EFBCDDB/34==ECDHHHHHHHGHHD9).@C>=CCFHHHHHG @read_150_294/2 TACATCCTCTAGAGGGAACATAAAAAGATACCAATAAAATTTTGTAGCTGAACAGTTATGAAAAAGAAATGCTGTGGGATAGATCGGAAGAGCGTCGTGT + FHHHHHHHHGHHHHHHHHHHHHHFHFEBCFHHGGFG4<>>E><,)45:>526?6>E;@2,5.<8@<):D@BBFHHHHHHHHHHHHEEEDHFBGB???>?> @read_150_295/1 TGACTTTCTTTTTTCCTCCTAAATAAGGACAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCACCTAATCTCGTATGCCGTCTTCTGCTTGAAGAA + HHHHBD=EEHFHHHHHGF@DHHHFGHHHHHHHBGEADA<339CBEEFFEFHHHHHHHDFFCB9;9BFFHHHHFFBEGHHGGHHHHGHHHGEDC:>A0'7: @read_150_295/2 TGTCCTTATTTAGGAGGAAAAAAGAAAGTCAAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAA + HHHEDHDFFEHHFHHEEEFEGFFBFHHHHHEHHHHHHG@>BCGGGA@::B@BEHFGFDGHGHHHGGHHHHHHHHHHEDHHHHD6(BA=>.<79=?E=?HHHHHG@A=CDGGBGHHHHHCDGHHHHHHHHHHHHFHDEEHFFFHCBEEEDC@B8CHHHHHFDCG>>6@@BFBH>DAE @read_150_297/1 GGCTAGGCCAGTCTGTTTCCACCACATGAACAGGCAGATAGGTTCAAGGGTGCTTGGCAGTATTGTGGGGAATGTAGATTAGAGTCCAGGGGACCTGAGT + DGHHHGHHHHHHHHGHHHEGEGGEGHHHHHHHHHHHF>,4BFFHHHHBCGHHHHFFHFHHHHHHHHFFHHHHHC7:<<-),6EFHHHHHGDBBGB@':>A @read_150_297/2 GGCCCAGAGAGCCTGCAGGGTGCCCAGCACCAGGCTTGAAACAGCCCTGAAGCAGCTACGTCCCATTTCCCGGTGAGTGGCACAGCCCACCTTTGAACTC + HHHHHHHHHHF@G@@56<55F@E/?83:.=BE401<:?HHHHHHHGAC=;29:;.FHHHHHHHHHHHHHB:6GFHHHHHHGGHHFHHFHGGFDGBD8<<9 @read_150_298/1 ACTTCTTGTGCATCCCTTGTTTCCCTGGCTAAGGCTTTCCAAGACTGAAGGCAACACTGTCTTGAGGCACAAGAATCCAATGTTTCTTGGTAGGAGCGGG + HHHHHFGGGHHHHHHHHHEDHHHHHEED@>76D4=FFBGFHHHHFGGFFFHHFDDEBFFDDGFFGH?@CB>>+BEHHHHEEHHHHHHFE<7@DBBA:*0; @read_150_298/2 TTGTCTGATAGTAGTGCAGTTTGCATTCCAGCTCCTACCAAGAAACATTGGATTCTTGTGCCTCAAGACAGTGTTGCCTTCAGTCTTGGAAAGCCTGAGC + HEGHHHHHHHHHHHDCEHHHHHHH@FFGGFFBGFHHHHHHFDEGHHHHHHHHDFFHHHHHD>@:4B@DC?GFCBEHDBD491);:2,'),22,,)*%',5 @read_150_299/1 GGATCACCTGAGGTCAGGAGTTCGAGACCAGCCTGACCAACATGGAGAAACCCGTCTCTACTAAAAATACAAAATTAGCTGGGCGTGGTGGCGCATGCCT + EEE?@BGGGGGGGEBDGHH@AEGHHCC>?4@FEFGHECFBDB>5??DB?@EHHHGHHHHB@;B?;?39:ADFGGGGHHHHHC>E?DEHHHFH5(*:BHHGGHHHHHH @read_150_301/2 ATCTGACCCCAGGCTAGGCCAAGGCCAGAACATTTATCGAATCCCTACTGCATATCAGGCATTGTGCCATATTTGGTCTCATTTAACCCTCACCACAACC + HHGHHFGGHFHHHHHGFHHHGHHHHFFFFHGGIGHHHHE8EGEEFHHEHFHHFHFGEGGGHHHHHGHHGGGGE?G/><*4 @read_150_302/2 TTCTATGGAAAGACTATTTCTGAAAACAATATAATAAAATATCTAAAATAATTTTAAAAGTGCTGGAGTAACTTTTCTAAAATGAAGGATGTTGTATAAA + HHHHHHHHHHHHHHHHHHFHHACBHHHFFDBHHHHHGFF77BDDCGEEHHGFFBBG@DDCGFHEHHHHHHHHHFEHHHHHH@C>.@BCBC2<>4875CF@ @read_150_303/1 GGGCCCATCATTCTCCAGGGGAGATGGCTCTTCCTATACAGAGTCAAGGACCTCTGGAAACACAATATTCAGAGTTAATATATTCCACAAATACTTATCA + HHHHHHEEEFEF982<@G?CBGFGH?DCFEGFDBFEFEEFC??=GHBHFFHHHFHHHHHHCCBBC@:>DHGFHGFGFGEHHHEEHHHFHFFHHFFDBF=< @read_150_303/2 TAGCTTATGCAATTGGCCACTACTGTACCACTGAAACCTGGTACATTGTAGGGACATGATAAGTATTTGTGGAATATATTAACTCTGAATATTGTGTTTC + HHHHHHHHHHHG@>:GEEFFEHHFFFEHHHHHHHFGEBCDDGFHHHHHGBBEHHGDB;?C;CDFEBCHHH@@CHHHHFFDFBA?FHHEGFFHFGHFDEFF @read_150_304/1 TCCATGGGGGATTGGTTCTAGGGTCTTCTATGAATACCAAAATTCATGGATGCTCATGCTACTTATATAAAATGGCAGAGTATTTTATATGGCTTCTGTA + HHHHHGGGEGHHHHHHHHFFGGFHHHBHEHEDEBEDHHHHFHHHHHHHHHEBDBGFFCA@BEEFGB6CCDFDBD?C88GGFFHHHHHG=6>BD70)&8C> @read_150_304/2 TGGTCATTATTCAATAAAGAATAGAGTATAATAACTATTTACATGGCATTTACATTGTATTAGGTATTACAAGCAATCTAGAGATGATTTGATGTATATA + 8@@GFGGGGGD@<173=((2GGFGGFHHHHHHHHHEHHHEHEHHFFFFBDHHC:>EFFHHEEGEHHGG.?EEEGGFHDGF.:22:EFGBD738?D@6AFF @read_150_305/1 CAAGAATAATGTGCCCAGCAAAGCTATTAAAACAAGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCACCTAATCTCGTATGCCGTCTTCTGCTTG + FHHHGGBEGBDEHHHHHHEHGGGFFHFGEGHHHHD,::=AFHHHHHBHFHHHGGEFFHHFFHED?DHFHHHDFEFHHHHHHEEHFED65@:FGGGGHEHG8DE<<8DDBC?CCCFBECEBHF @read_150_306/1 AGAACGTAATTTTCAGGTCATGGACAAATTTTTTACTGTAGAATATGAAGGGGTATATACAAAATGTCATGACTATGACAGCAATAAGTGTATAAATTAA + HHHHHHHHHHEEEHHHHHHHHHHHHHHHHGGHHDCDDEFHHFHHHHHHHHHHEBCEFHCB<@CC;:ADHFC?D;:;>?FEHFF @read_150_306/2 TGGCCTTTTTTCACATCAAGTTGTGCTACAGTCAGTTTAGAAAATGACACTTGCATTGTGGAGTGGAAGTTGAGGAGCCAGTGAGTTACATTAATTTATA + HFDHHHHHHHGEHDFD@BCD@GHHHHHHGBEEEHH@CBC8E@6?HE2-33;>;=FFGGGHBGGG?,+<<2FBGEHHH?B;918FEEEHFGFDGGGH;>/B @read_150_307/1 GGCCCTGACGTCACGCACGGTCACGTGGCCCCGCCTCCCGCTGGATCTTTAAGTAGAAAGTAATCTATCAGGCCAGTCCTTAAAACGGGACTTTCGACTA + HHHHHGHHHHFGGHHHFHHHHFHHHHEDGD0==GD7;?FFHHHHFHHFDFHFHHHEDDHHHFFFF7DDGG<:>EDDHHHHHG=7.EEF?>::<>AFHHHHHHHHFEGHGFBCFA@@>:EEEEHHHBFC5?FDGEFHHFHHFHEFD @read_150_310/1 GAGCTTTTTTTCTTATGCTTGTTGACTGCATGTATGTCGTCTTTTGAAAGGTGTCTGCTCATGTCCTTTGCCCACATAATGAGGTTTTGCTACATGTGAT + HHHHHHFFFFHHHHHHHHHHHHHHHGGEEFHHHFCEHEEEFFEEFEFHHHHHHHFEGHEEHDFDHHFHHHHHGGFFGEDDDFBGFHGHHEGGGHFHGCA> @read_150_310/2 GTCCCCAACATAAAGAAATTATAAATGTGTCAGATGATTGATATGCTGATTGCCTGGATCCGTTCTGATCACTATATATCACATGTAGCAAAACCTCATT + GGEDC:><=GGEFFFGGGHHHEFHHHHBD=FGGEFHHFCDEHHHGGHHEAFEEHFFHHGHHHHHHGHDEGFEDAFHHHGFDDHEEDHEEFEEFFD359.) @read_150_311/1 GAAGGGTGATTATTAAAAAGTCAAATAAGGCCAAGTGCAGTGGCTCATATCTCTAATCCCAGCACTTTGGGAGGCCGGGGCAGGCGGATCACCTGAGGTC + HHHHHHFF=CEGHHHHGGFDHHHHHGGFHGAEBFGHHHHHHHBHHDE?GBFDBGHHHFFFEEEECHFEHHHHAAHHHEFE,>7BAE5@38,/@CFFHDDA @read_150_311/2 GCCGGGCTGGTCTCAAACTCCTGACCTCAGGTGATCCGCCTGCCCCGGCCTCCCAAAGTGCTGGGATTAGAGATATGAGCCACTGCACTTGGCCTTATTT + HHHHHHHHHHHHHHHHHHDGHHHHHHHFHHGGHHBDGGEEF?AHFHHHH+8>-*9GHEBEDGDHHHHHHHFFGAB<6:>9;9%',;96=D4DFGHHHEFC @read_150_312/1 CGTGTGTCACCAGGCCCAGCTAATTTTTGTATTTTTAATAAAGACGGGGTTTCATCATGTTGGCCAGGGTGGTCTCGATCTCTTAGATCGGAAGAGCACA + HHHHHHHHHHHHHHGEGFGGHCGGECBEEEE@/D?HHHHHHHHHHHGFHHHEHFFHHGEDDEDHFCFFDCDBA>;EEEEF@>5:?GHFHHHHHHHHHFH< @read_150_312/2 AAGAGATCGAGACCACCCTGGCCAACATGATGAAACCCCGTCTTTATTAAAAATACAAAAATTAGCTGGGCCTGGTGACACACGAGATCGGAAGAGCGTC + HHHHHHFGEHC8@=HHGHHHHHHHHHEEGHHFFFHHHHHHHHHFF+C=IGDDDDGGFBECD>;BFCFFF?/A?=9DE?:7:@/5FHHHHB<7@D?FFHHC @read_150_313/1 TCAGGCTATGCTAATTACTGTCATAGATTCTGCAGCAGCCCATTAAATATACAAATTACAGAATTAAAGAGCCAGAGCTCTTCATGATTAATCTCTAAAT + HHHHHHHHHHHHFBCCB@7=DDDHHFGHHHHHHHHHHHHHHHHHHHHFGGG@EHHFHHHFHHFHHFGFHHHHHEDHGH=8@9ADHHHGGGHHHHHHHHGB @read_150_313/2 GTTCATTGGGCTCACTCAGCCAAAAGTAGAGGGAAACTTTGTACAGACATCATTAGTTTTTCTCCATTTAGAGATTAATCATGAAGAGCTCTGGCCCTTT + HHHHHHHHHHHHHEBHGFDDA@DFHFHHHHHHHHHHBHHHDGEHA78A@BHFHHHHHHHGECGG<:-CCD=DGHHHHHHH=DA,2>>@D@EFHFFFFFGHHHDGEDDDDEFHHHHFGADDGHHHHHHHFFFHF@DDBG @read_150_314/2 ACCATCGGGTTTGTTTTTATTTTAATTAGACTTCTATTTTTGAGATAATTGTAGATATGCATGCAGTTATGAAGATAATGCAGAGATCTGGTATACCCAT + HFD8EIGHHHHHEGDC>78HG=C;97GHHHHG?@BEEGEGEABBC@?AEGECDDEFFEEFD@?GGGHHHHGBEEHHHHHF?EEFA71=BFCCD==9,1,2 @read_150_315/1 CCATGACTCCAGACTTGCTTTGACACCTTGCACACCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCACCTAATCTCGTATGCCGTCTTCTGCTTG + HHHHHHHHHHHHHHHHHHHHGGGGGFCGHHHHDE6B@9<8C?AA8<1B>B247EDD>5= @read_150_318/1 CGCACTGTGCCTTACACGTAGTCAGGACTCAATAAATATTTGATAAGGCAAGAAGGAGGGGGAAAAAGCAAGATGACTTACTAGATCCATTGATCCGAAT + HHHHHEFCC@DDDDFFEEDD>>@A>CFFFFDDH?:FHHHHHHHHHHHHHHHHEDHHHHHHFCHHHHFEDBA.;@ACFGHGHHHHFF00>BE16.%)3((5 @read_150_318/2 GAAGCTGAGACAAGTGAAGCAACTTATCTATGTCCATACAGTTCTTATAACTAGAGGAGGCAAATTCTGATCAATGGATCTAGTAAGTCATCTTGCTTTT + HHHHHHEGFDB@GFHHHHHHB@FHHHHHHHHEFEAB@;<5@**)8?GFGCEG=DGHHHGGHHHHHHHHHHGDC@HHHHHGEEHFFFFFCBCFHD@*5BCB @read_150_319/1 GTGTGTGTGTCTGTGAATCTTTAATTAATCTCTTGAGTCCTTTTTGAGAAAGAAACCCTGTCTCATTCAAGTTTGTTCCCCAGGGCCTGACATAAAACTG + HHHHHHHEEGGFHHHHHHHHHGHHHGGHHCHHHHHHHHHHHHHFGBDDFHHHHHHHFFFEHHCHGFFHHHF:CHEDDADDGEEBADD?489.159HHHFF @read_150_319/2 CTGCATCATTCATTTGTTCATTTTGTCATTCATTTGCTTGTTTATTTAGGCATTCATTTACCAAACACTGTGCTTACAGTTTTATGTCAGGCCCTGGGGA + HFHHHHHHHHGHHHEFHHHHHHHDEEEGGEGFECB=DDBDBD:B;>BDHC>=4<=9+3:@<>.DGFCEHHHGEGHHHBEHHFBBBBDEBFA;,A;EB@FD @read_150_320/1 GCTGAACTCGTACTCTCTAGCTGAGCACATAACTTGGGTGAGCCTCAGTTTAGATCGGGAGAGCACACGTCTGAACTCCAGTCACCACCCAATCTCGTAT + GGGGHHHHHHGGGGGHHHHBEEHHHHHHHHHHHHFEGGGFHHHHHHHHBDFHHADE72)0??DDEHHHEF?@6:>CA@FHHHD;.DCGIGGGHHHHHHHHHGHHF@GGHFF7EHHHHHEG@HHHHFF@BDA@DHHBE @read_150_321/1 CTCTGAACGTACCAGAACGTTCATGTGGACAGGAGGGAACTGAACTTGCTCCGTGGCAGAAGAGCGTACCCACACCTGAACTAGGATGGCGGCACAGGTT + HHHHHHHHHFFFEB>FFFBBHHFD>>D;GFHFBFGHHHDE@DDGHHFHEEFEFEHHHHFHHHHF?DFHHE=DC@?EC9>CHGEA@FDBB?ADGGB@EFFB @read_150_321/2 TGTTCGCTGGAGTCCGGACAGTTTGGGCTCGGAAATGGCTCTGCTGCCATTCGGAGCTAAGAGCACAGCCCGTTCGCCCTTTCACTGTCGCCTTCCGGGT + DCDHFGHFDB65CGHHBBCDDHHHHHHHEHHHG@AHHBGHHEGHHHFHHHHHHHE@,07EEFHFEGHHFHHHHHHEEDCD@.5.> @read_150_322/1 AGAAGAACCTATGTGAGCAGCCCTCTCGCCTGTTCTTGAACGCCTGTGCTTGGTTACATAACATTGGCAAGGATTGCTCAAACTGGCAAGAGGCAGGATG + GFDDFGGHEHHHHHGHHHHBFFHHHHHGF9GHHHHHFHHHHHFHFHHHHGHEEHF?7;@E9DD>HGHHFHFFFFDHGHHHHGFHH><8;-0?E@DEEEFF @read_150_322/2 TCTCTCACTCTGAGTCATGGCTGGCTTCAAGTTCCCCAGCCTGGCAGGCAGGGCCAGGAGCCATTTCCCAGCCTGTGAGAGTATCTTCCCACACCCCACA + HHF<93*+=GHHHHHHHHHGBHHHHHHHHHGGGGGH?EHHHHHFFHHHEDGFD@A@<:DDD=F.>AC:?EHEGDH3;AEEHHHFDGHFEBHHFEHHHHHE @read_150_323/1 TACCTATTTACATTTTGATATCTGCATTTTACCAATAATTTTTAAGGCTGTTTTTATTTCTCAAAGATTAAAGTCATGTGAACTAAAAGGGACCGCAGCT + HHHHHHHHHHHHHHHHHHHHGGGHHGFFHHHHHFBHHFGE?EFEFHHFFFBFHFHHHFFHFHDFEHFHHFFDHHHFBFHHHHGHHDGGGA'2,-%,27:: @read_150_323/2 TGGCCTAAAGGAATACAAGTGCTTGGATCAAATATTTTTTAAAGGGAAGATAAAAGCTGTGGTACCTTTTAGTTCACATGACTTTAATCTTTGAGAAATA + HHHHHHHHFHHHHHHHHHHHHHEGIDE9/@>DEGHHHHHHHHHHEGDHHFHHHHHGHFFGDGHEE?GFFEHHFE>G?CCBHHHFEAFHHHHHFH?BEFEE @read_150_324/1 CATTTTTCTCCTATGTTTTCTTAGGAAAATTGCCAAATTATCTAATCTGCCTTTTGTTTGTAGGTAGGGAAAATTACATGACTTTTTTTCACTTTCAAAA + HHGHHGFCBCBEH?FGDCBFGHHHHHHHHHHHHHEHHHHFHHHHHHHFEGHHHC.1;BBCFDBGFHFHFFHHHHHHG@>DEDCDFHHHHEFFHFEHHHFF @read_150_324/2 GTTTTTATTTAATACGGCACTGCAGAACAAAGAGGAAATAATAGTTTTTAGAGACAGCTACTGTGGCAACTTCTGGAAGTGAAAAAAAGTCATGTAATTT + 7<:?@EGHHHBGHHHEHHHHHHHF@FFHCCHHGBEFHHFFHGHHHGECHHHHGGGGFBEDCDG>43<<>8<)*(6(:;<91BFHHFHHHHFHHHHHHE*8 @read_150_325/1 GAGGCTACTCTCATATGGCAGCAAAAACCCTGGGGTTCTCATCCAGGCCTCTCAACACACTGGTGGTTGGGAAACTGCTATATAGTATGATTCTTTGTCT + HHHHHHHHHHHHHHHHHHHHHDF;>FFFHHHHEEECDEEDC89FEEEEBFFCA, @read_150_326/1 AGAGAAGTGAGATTGCAGGGCAAATTGCTGACCCTAAAACTGAAAAGACAAACAACGGATACAGAGACTGACAATTTACCAAATCAAAAGCTCATGGGCA + HHDACEEDDDBDGEHHFFGHHHHHHHFFGEEGFFFCFGBFHHHHHHHHHHHHHHHHDFEDBDECB:9(165AFCHHHHHHHHHDEHHFEEGGGFFFCEC: @read_150_326/2 TCCCAGTGACTGGTCCCCTTGGTTTTAAACTCAGAATCAACCTCGCCGAGCCTCCAGCACATCATAAATGACAGGTTATGTTTTGCTAACCCAATACTGG + FHHHHHHHHHHHHHHHHHFGBCDDDGHHGGFHHHGHHHHFDA(,82)=DGHHHHHHHHE@DCB5@4:DDHHGHHHHHHHHHFHHHB:9'6AAD@FFHHE?ABHFHHHEBGE??CA9A=DHHHA?HBA@EGFGGDDDEEEEEGEGFDFG=EFHHHHHHHHGDHFA>B)>*4.CGEE? @read_150_328/1 AAGCAAAATGAAGTTCTTTCTGTTGCTTTTCACCATTGGGTTCTGCTGGGCTCAGTATTCCCCAAATACACAACAAGGACGGACATCTATTGTTCATCTG + HHHHHHHFGGHFHHHHHHHHHHHHHHFGHHHHHHHHFFHHHHFGHHHFDHHHHFHHHHHHHFDCCGA;<7%+:EFHHGGGHHHHHFFGGG?CEHFEFG45 @read_150_328/2 GATACTATGAATCATACCCGCCTGAACCCCTCCAAATCCCTTCGGAGCTAAATATCGCTCACATTCAAGAGCAATATCAACCCATCGCCATTCAAACAGA + HHFGHHHHHHHHHHHEB?*(9E86@?FHHHCHECCCGEHE>;CEDEFFHFDBHEGHFHFCCHH @read_150_329/1 TTGAAACACTCGTTTTGTGGAATTTGCAAGTGGAGATTTCAGCCGTGTTGAGGTAAATAGTAGAAAAGGAAATATCTTCGTATAAATACTAGATCGGAAG + HFHHHHHGGEGHEEFHHHHHHHHHHHHFHFFHHHHHHHHFHHHHHHHHHHHFEGHHHGGBH@EFFA0BCHHHHDFHHGD?@EEFF.'A>?=FHHBEGGD4 @read_150_329/2 AGTTTTTATACGAAGATATTTCCTTTTCTACTATTTACCTCAACACGGATGCAATCTCCACTTGCAAATTCCACAAAACGAGTGTTTCAAAGATCGGAAG + HHDHHHHHHHHHHHHHEG@@93@@6BHHDBFGEGHHHHHHBFEE/1-1*8.'*2*<0'>?6;?DHHHHHHHHFB>.:<=EFFH@B.:,3AC=..3?DFHHFA?%+ @read_150_331/1 GTGGTACCAAACACAGCAACAGCCTCCACATCTTTTAAGGCATTACACACTTGAACTCCACAAGTCTAGGAGACAATCAATAATAGATAATTATTATCCT + HGGFEHHHHHHHHHGGHHHHHGGHHGHHHHGCGGFHHF>FHDFEEFEHFHHHHHHHHHHHH@???FHFF?=?<649781)<9?FEDDCHHHHFHHHHHHH @read_150_331/2 GTGAGGTGAACCAGCAAGTGCACTGGCTGAGGGGACTGGAGTTCTAGCCTCTGAACCAGTTTCCTCCTGTGCCAAAGGAGGATAATAATTATCTATTATT + HHHHHHHHHHHHHFHHHHHHHHHHHHEGHHHHHHHHHHHHHFHHHHHHEHEECEE/32'38EA3AEFFEHHHEHHHHHHHHGGEHHFEEDFGGABBE??< @read_150_332/1 AGGCCTCAAAGAGGTCTGAATATCCACTTGCAGACTTTACAAACAGAGTGTTTCCTAACTGCTCTATGAAAAGAAAGGTTAAACTCTGTGAGTTGAACGC + GGGEDCFFFFB;GGHGGHHHHHHHHHHHHHHHGHHEHHGCCFFF<.BDEBHHHEEGHHHHEAB>CCCCFHHE9FHGGHHHHGEGECEFHHHHA5.>F @read_150_333/1 TGACCAGATTTAGAATTATAAACCAATTCATGGGCTGGAGCCAATGGTTTGATGGATAATTAGGGTCTTTGAAGGAGCACAGTTGAAAAATAGGTGACAA + HHHHHHHHHHHHFFFHHHHHHHHGG@GF@E@@5GGGFFGHHHHFFHFCC9FHHFAEHHHHHHHHEDDBE@B6CEB<73@@6)<.@5C??AD @read_150_334/1 ATGAAAAGGAAGACAAGCAAGAATCTAAGAAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCACCTAATCTCGTATGCCGTCTTCTGCTTGAAAAC + HHHGGGHHHGGHFFED@CC;FAA@C6+>>>DDDHH;<9DBHHFHHFCHHHHHHHHHFEFHHFHHBFCHHHHFHEFHHHB8?FC@@DFHHGHHHHHHF46( @read_150_334/2 TTCTTAGATTCTTGCTTGTCTTCCTTTTCATAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAA + HHHHHGB=/@<9@GGBE/@FBBGHHHHHHHHHHBECFHHHHHGFDD8AE-%3B933DEEBFDGEEEGG@DDGDHHHGFFHHH @read_150_335/2 GGCAGAGGAAAGACATTATAGACAGGACTGAGTGGCCTGACATGAGGTGGGAGGAGGTCATTCAACTTAGTCATTCAGCAGTTCACTTAGTCATTCAGCA + FBEEHHHHHHHFGGGHHHHHHHHHGEEEE?EEGHHFGFFFHHFHHHHHHHHHHHHHHHFEHFGDHHGFEEDEEE9:8?CGHHHGGE?EGEHHFC<<:.66 @read_150_336/1 GAAAGACTTTACCATCTAGGTTCGATAGCTGGGTCTAGGAAATACACTGACAATACACAGATTTAACAGGAAAAAGGGTAAACAAATTTATTAATTTTTA + F@@GGEGGHHHHHHGHHHHHHHHHHHGHHHHHHGDHHHEHHHFFD;=-*B?DEEFEGECHEEEFHHHHHHHHHFFFD40?ADFGGFHHHHHHHHHHHHH? @read_150_336/2 CACGGTAGCCCACATCTCCTCTCCCTTTTCTCTGTTAAGATGGCATCACTTTTTTGTGATATTGTTTTTTTCTTCCTATGATGGCCCCTGTGCACATCCT + BC@CHHHEDHFFHHHHHHHHHHHHHHD293>6.:8D;GEHE@BHHHHHHHHHHHHHHHHDCC@>5CHHFGGGHHGGEGBDGDFHHGG4FEEFHFFD/)1: @read_150_337/1 CCTCTGATCAGACAGGTGTGGCATCAAATCCTGGCCCAGACACAAAAGCTGTTTGACTTTGGACAACATACTTAATCTCCCTGAGCCTGGGACTCTTCTA + GGGHHHHHHHHHHHFFFHHHHHGHHHHHHHGG9;47DDGHHHHHFBFBBBEFEHHHHHHFBGFFHHHHFF@>CDAAGHHHHFEHHFHHFEEHH@7=E@GFFB=?328HHFF+78*;>. @read_150_340/1 TAAAAGGCAAAGATATTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCACCTAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAA + CEEDGGFG?FHHHHGGHHHHHHDF;FFEA;:=FGFHHHHHHHHHHHFBEE?BEGGFF@EEEEEFAF?6E9?DBBCFFFFBGG;?BDGHHGHBFFEEC9@; @read_150_340/2 AATATCTTTGCCTTTTAAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAA + DBGEDHHHH89=BGFFGGGBBHHHGHHHFGHHHHGHHD@E>BGFFF??FFHHHHGHHHD?GFHHHHHDHFDBBGEGFBE7;A:>FACEHFFFHE0>(0)) @read_150_341/1 AATTATACTATTATGTATTATGTTTAATTTTGAAAAAGTATGAAATAATAATAAAGTTAAAAACCTAAAAGTTTTTAAGAGAAATATATATTACAAAATA + HHHGEGHFGGHHHHHHHHGGF;E@>BB@CGHEFHHCDHEGGG=ACEHFHHGBCHEGHFHHHHHFHHHHEEFFEEEFD8EEG@CEHHHCCFGFDEEHHHHH @read_150_341/2 GGTAGCAGAGATTGCAGTGAACCAAGATTGCACCACTGCACTCCAGCCTGGGTAACAGAACAAGACCTTGTCTCACCAAAAAAAAAAAAAAAAAAAAGAG + HHHHHHHHHHFFEBGHHHHHGHHHHHHHHHHH=AFHHGFHHFDDF=GFHHEGDEHE @read_150_342/1 CGCCCGGAGGCTGGCCTGGGGTCTGACATCAACGACACAGGCGGGGAGTGGAAGTCCTTCCGCACAACATGGTGTGGGGCTGCGGGGGTGTGGACGCGCC + HHHHHHHHHHHHHGGGFFHHHHHHHHDFFGHHHHHHHHHHGBHHHFGGHFHHHHHHHHHEEEBC;E?HHBAEBFFGEFHHHHHHECHHHHHHHGGHBGEH @read_150_342/2 TTTGATTTGCAGCATCTTTGAGCCTCTACGACAAAAAAACCGCGAAGCACGCCCAGCCCTCCCCCGGCACCCCGAAAAGCACCCACTCCCTCCCGGGGAC + HHHHHHHGHFEHHHHHHFHHEHHHHFGCFGHFEHHHHHHHA=CEGHHHGHHHHHHHHHGGGFFFGHEHHHHHHHHHHGHHHHHHHGGGDC08==?EEBBH @read_150_343/1 AAAGAGCAAGAGAACTAGAATGAGAAGCAGAGCCTAGGCCAGGCATGATGGCTCATGCCTGTAATCCCAGTACTTTTGGAGGCCAAGGTGGGGGGATCAC + HHHHHHHHHHHHHHFFF<?<<>@9->>:A:((6.DCBCGHHHHHHHFHHHHHDGEF<58EHHHHEHHHHHHDFGDHHEC?BEC--->.8>4>AFHF>>@?;CH @read_150_344/1 AATGCTACCAGAATAGAGGCACCATATAGTACATTGAGTGCTGCCATAGAGCTATAGGATGAAAGATAAAGAAATAATTCATTTGACTTGGAGGAGTATA + HHHHHFHHHHHHHHHHGGFHHH=DD6BHHHHFGHHFFHHHHGHHHHHHHFHHHHHHHHHDHHHFHFFBFFHFEFHHHHHHEDD=<627?B%*%-70<9DC @read_150_344/2 GCATCGCTATACTCCTTCAAGTCAAATGAATTATTTCTTTATCTTTCATCCTATAGCTCTATGGCAGCGCTCAATGTACTATATGGTGCCTCTATTCTGG + HHGGHHHHHHHHHHHHHHHHGDGHHHH?BFHHHFHHHFEHHHHHHHHHHHHHHHHHG@CBCABEEG=:-0;+(:;DHEHHDBFGFFCGGHHHHEF/+ADE @read_150_345/1 TATTCTGCAACATGGATGAACCTGGAAAGCATTATGCTAGGTGAAAAATGTCAGTCACTAGAGACCATATGTTATATTATTTCACTTATATGAAAGTCCA + FFFGEGGGDDHHHHHHHGFGHHHHHHHHHHHHHHDFFFFBEEHFFHHHHHHHHEEEEEFFDHHHEGEFEFHHHHFFFFHHHHHHEDBBF=FFFFFGHFHH @read_150_345/2 TATCCCTCTAGGCAACCACTAGTAGATCTTTCTGTTTCTAGAGATTTCCCTGTTCTGGACTTTCATATAAGTGAAATAATATAACATATGGTCTCTAGTG + GHDDHHHHHHHFHHHHHHHHEEF@BEABHHHHHHHHHHHHHHHHHHHHHBEHGHHHHHHHHHHHHHHHHHHHHHHB?=EE3C*8.5CC3.:7EBFHG=@5 @read_150_346/1 TACCTCATCTCCACCACTCTCTCCTCCAGCTACAAGGGCCTCCTGCTCTTCCTCAAACTCAGCAAGCACCATCCTGCTGCAGGGCCTTTGCACTGCTGTC + HHHHHHHHHEDF8EEC-279DADFFHFDBGHHHHCBA9BCBEB39FCAEACDHHHHFBEFHHHHH @read_150_346/2 CAGAACACGACAGCAGTGCAAAGGCCCTGCAGCAGGATGGTGCTTGCTGAGTTTGAGGAAGAGCAGGAGGCCCTTGTAGCTGGAGGAGAGAGTGGTGGAG + B@GFHHHHHHGEHHHHHHHHHHHHHGFHEGHHHEEFEEHHHHHHHGFFFHHHHHHHHHHC:<<>:EGFHHHHB@HHHHHFHHHGD?ICFHHHECE6;B,/ @read_150_347/1 TAATTAGTGGAGACAGCTACCAGGGATCAGATGCTAACTACTGATTCAGTAGACTATTGAAAGTAAATTAATACAAGTATCTACCATTCACAGAAGAAAG + HHHHHHHHHD=@FHHHHGFHGGHHHDBFF?HHFFEEFHHHHHFHHHHHHHFFHFGGHCHHHHHHHHHHHH??DFEFEECDHFFHHHHHHD9FFFHHFBGF @read_150_347/2 ATTCAATACTTATGAGATATTTAATCAGGTCATTAACTCTAACTTGTGATAAAATTAGTAGCCCTGATGAATTTCTACTTGCAGTTTAAATCAGTGTCAC + HHHHHHHHHHHHHHHFGHHGGHHHFEAG<.BDGGHHHF?CEIGEFHHHHD=BCACFHHHHHHHDGGHHHHHHE63>DCDEEB=CEDGHEFFHHHHHHGGF @read_150_348/1 ACCAAGAAAATATCTTCATTTTTTTTCCTTTCTCCTTTATCATGTGACATAAGATTTATTGACTTCACATTAGCATTTAAGTATCGTTAACTTTATGTAT + @C@DDEE>>?ECD:;GHHHHHHHHFHFFFFFEGGGHHHHHHHECHHHHHFFFHH@FFHHDFB?FHHFFCAACA?DGHHHHHHFHHHFGGGEFHEHCED;4 @read_150_348/2 CAACTATCCTTCATACAACCAAAATGCACCAGTCCCCAACCCAAATACATAAAGTTAACGATACTTAAATGCTAATGTGAAGTCAATAAATCTTATGTCA + FFHHHHHHHEDGHHHHHHHHGHHFFEDEC@B<>>GHHHHHEFEEGHHHFF;7.:EHHHHHHHHFHHHHHHGHFHFFEHEACEEEHFG@?EHGEHFDFE=C @read_150_349/1 AATTACTACCCAACTATTTCAGCCTTGATTTCACCTTTGTGGTTTGCATTCAGGTTGCACCCACTGGCCACTTTGTCTCCATAGAATCCTTGACCATCCA + HHHHHHHHE=@HHHHHHHHHE=BHHGFGBGHHH@AFFGGEGGGHHHCFEHF3?E>EDDFDHHHHFFDBBBEEDCEBEFFG=4:6:6@:'DHGHHFH @read_150_349/2 ACCAGATGTGGAAACAAGGAAGTGAAGGTACATCTTAGCATTAGAAATTTCCGTGGCCAGAATGGTGGATGGTCAAGGATTCTATGGAGACAAAGTGGCC + HHHHHGGHHHHGHGFG?FHHHGHHHE;DCCEBHHE93EFFHHHHHHHHFC..14;.7 @read_150_350/1 AAGTTTGAGGTGGCAATGAATACTGAGGTAGGAATTTCCAGTAAGTAGAATAGAAATGTCTGGAGTTTTTTTTAGCTAAGAGTGGAATTGAGATAACTAT + HHHHHHHHHHHHHHHHHHHHHHCHHHHGFFHHEHHHBFGE@=HDHHG?A9DDEGHHHHGHHFEECCBF9FFHHHHEDDDBBFFFHHDEFFFHHFDHE?.E @read_150_350/2 AGTTGTCTTTTCTTTGAAATGTTGGTATTCTTTGATACTCTGTTCTCTTGTCACTCTCTAAATTCCCCATGGGTTATTTTATCCATTTAGTTATTGTGTT + HHHHHHHHHHHHHHGHHEEEFBD6-/@A@@HHHHFHHHHEHHD/CGGEHHHHHHHHHHHHHHHHHHHHHHHGHEHHHEFFGG=ACGA7<5><52DGFHF? @read_150_351/1 AATGATGGGATAGTAGAATTTTCTAAGAGATTAATAAAACACAAAAACAGCCTTTGAAACTTAGCTGTGACCCCAATTGCATCCCTTTATGAATCACAAA + HGFEGHHHHHGHHHHGHHFGFGGGDGE>@@GGGHHHHHHHHHHHHHHHHHHHHHHHHHHHFHFHHHHCD=AGGAFFGHHHGGHHGHHFFFCEH>9FGGD: @read_150_351/2 TCGCTGAGCAATTTGTTCTTTATTTTTTACACTAAGTTTGTGATTCATAAAGGGATGCAATTGGGGTCACAGCTAAGTTTCAAAGGCTGTTTTTGGGTTT + HHHHHHGHHHHHHHHHHHHHHEF=A@@@EHFEGGGHHHHHHBC>>57>=@BB?46A42*5:6-9-36:??HHHHHHHEFCHGFA?;??-/>:=.0&79EBHH?><:DEFHHHHGGEHHE=B@6>>.>:C@.CHHHHEEEGFFGHFHHD@?BEDGHHFFFDHHHHHHHH @read_150_353/1 CCATCAGCAAGTTTTGTTGATTATAGCTTCAAAATGCATCCCAGATGCAACCACTTCACATCATCTCTAGTGCTGGCAGAGATCGGAAGAGCACACGTCT + HHHHHHHHHHHHHHHHHHGGGGEEEFD@HHHHFCEACD65E?DDHHDDFFEEHHHHHHHHHDEHEFGCFFDCBD@DGGBEFFEGFHFB?BFCCHHHHHHF @read_150_353/2 CTGCCAGCACTAGAGATGATGTGAAGTGGTTGCATCTGGGATGCATTTTGAAGCTATAATCAACAAAACTTGCTGATGGAGATCGGAAGAGCGTCGTGTA + HHGFGGHHHHHHHHHHHHHHIDBGGAE?>CHEB31>EGEDA>CEEEAGHHF @read_150_354/1 ACCATCTGTATTAGTCTGTTCTCACACTGCTGTAAGGGTACTACCCAAGATTGGGTAATTTATAAACAAAGGAGGTTTAATTGACTCACAGTTTTGCATG + HHHHGFFHHHHHHBDGGDDGBEEEHHHHHFFA>CHHHHHHHGFHHHHHHHBFGG>EEFHHHHCDGHGFHEEDHHHHHHHHHGBHBF68*?EBDDECFCBF @read_150_354/2 CACTCTCTCTCCTGCCGCCTTGTGAAGAAAGTACCTGCTTCCCTTTCCGCCATGATTGTAAATTTCCTGAGGCCTCCCCAGCCATGCAAAACTGTGAGTC + CCC;<89>?DEEEDGCCHFF3:6.?6@BB4BH?:FHHHHHFHE@+56FEEGEEEGHHHHHHHHHH@FBEDE?<58:EEHHHHFHGGFEA52 @read_150_355/1 CTACAATTGTGGTTTTGTAAGAAAAACAGTCTTAAAGATTTCCAATAATTCCCACAATGGCCATAAATTATCCTGGGTGTCATTTTCCCATCAATTTAAA + HHHHHHEDFHGGHHHHHHHHGEFGHHHHHGFGEDDBEFGFGF@DGGGGHHHHHFF=D?GDFHHHGHHEGE.4=A@AA79>FHHGE?FHD/,23;7@GGFF @read_150_355/2 TGTGCCTTTTTAAATTGATGGGAAAATGACACCCAGGATAATTTATGGCCATTGTGGGAATTATTGGAAATCTTTAAGACTGTTTTTCTTAGCGAAGCAC + HHHHHHHGGGFHHGHHHHHGFEHFCCDF@<@.6EBBHEGFHHFFHBDCFEEEIEEGGGHHHHHHHHHHHFFDEEEHFHHHHHFDHHEAA.@+-%-5&3EG @read_150_356/1 ACCCCTAAGGTAGAAATAAGCTTAGTGTGTTTGAGGAAGAAAATGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCACCTAATCTCGTATGCCGTC + HHHHHHHHHHHC><);,:4??FHHHEHFDBD<8DEHCFHEEHFFEFD8GGDDHHHHFB@DHCEEHFEAHEBCGGGGGGGGCCFHHGGE,705BDFGH @read_150_356/2 CATTTTCTTCCTCAAACACACTAAGCTTATTTCTACCTTAGGGGTAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATC + HHHHHHHHHHHHHB?@=@>CDDEGGFGGHHHHHHHHFFHHHF?GF?FHHHHHHGHHHHHHD@06FHHBFEHBGGHHGHHHHFHHGBFDEHHHC>>@E=E@ @read_150_357/1 TTCTAGGGCTTAATTTACTGTTTTAAATAAAATAAACATAAATAGAAGCTTCACTATTTTCCTTTCACATGCCAACAGATCACCTTGTGCAGTCACTGGG + HHGGGGGE@:BHHHHHHHHHHHHHHGGGHHHHHHHHHHHFHHHHHHHHHHHHHFHFHHBE>AGEFHHHDGADHHFHHEFGHHHHHHHHGGB78>=@DFDA @read_150_357/2 CTTTACCTTTTATTACCTAGCTTCCCTTTTAGGTCTTTAAGACAAAGGTCAAGATCTCATTCCATTACCTAATCTATACCTACAGGACAACTATTTGATA + HHHHGHHHHGHHHHHHGBA.38@EEHHHHC@>A@=>.5,(@C=@=?@EHHHHGDHHHFFHHBGFHHHHHHEEG=HHFBDGHHH?DFEGFDFEEHHFF??AGEEGGFHCDFFB/BCCDBEBEHHHHHHHDHHHHHHGDE@AHHHFEHHHGGHGEEDHHHHHHG52?9AA=; @read_150_358/2 GAAAAGGACAACAGAGGGTTACAGGATCACCTTCATTCTCATATCAGAGAAATCTTTCCTGGATTCTCTTTGGCTCTGGTCACCATGTCAGGGTCCTCAC + HHHGHHHHHHHHHHHHHHHHHHHFHHHHHFHHHGGHHHHHHHHHHHHHFEAAAFGHH@HHHHHHHHGGDFBGHHHGDAEHHHHHFHHHHHFH?BHD>BEG @read_150_359/1 ACCAGTTAAACGTAAGTGTTTCTCTGAGTTCCTTGCGCCACTCTAGCAAATCAATGGACTTCAAAGAGAGGATCGTAGGAATCCCAACTTGAAGTCAGTT + HHHHHHHHHHHGDHHHHGGGHHHHHHHHHHHHB4)'&*7110) @read_150_359/2 CACAGCAAGCAAGCGAGCAGTTCTGCAGTGGATACCAGCTGGGCTCCCTCCAATTCTGTTCCAACACTATCTACCTGGCGATAGCAGTAGAAACCACAGG + GHHHHHHHHHHDCGEDHHHHHHHCDHGHHHHHHHGECCFF=:5?FFHEDHHHHHHHHHHF@FEHHF@AGGD@AEEFFEEEHHGFEHHHHGH@=,6;EEDD @read_150_360/1 CAGGCTGCCAGGCCAACCGGGGAGAGGGAGGCTAAACCTGGAGCATCTCATGAATAGGCCTAGGATATCCCTGCTGCCTGGGCCCCTCCCGGGATGACCA + HHHHHHHFHHHGFGHHHHEEHHHHHEFGE>>BGF;FFHHHHFDFHHHHGDFEDEEGGGGHGGFCEHFFDEFFCFFFCFFBBEB3E8*8>FDB=EAFHHFF @read_150_360/2 AATGTTGTGTTTTCTCCTAAACTGGTTTTCATCCAAATCTTGTGTTGCTCAGAAAAACATGGAGCCAGAAAGCCAAATTCCAGAGTCCTCTCTGTGGTCA + HHHHHHFFFHFHHHHHHHHHFHHHHHHHHHHHHHHHHHHHEBDEEFHBGECD@757631:6B9DD:GGB*09A?EGGDDDBDCCEHHHHHHEHEDBA.@. @read_150_361/1 AGAAGACTATGAGACACTAAGAGAAAAATTAAGGTAAAAAAGACACACACTTAGAAAAACACACATAAGGAGGAGGGAGGAGGTTAAGACATTTTACTAT + HHHGBBHHHHHHEEHHAFHHHHHHHHFGHHHHHHHHGHHHHHHHEHHEHFC?HHFHBEBHHFC<6))60AEA5AEFFC59>>AC/--7DDHGGHHHHHGE @read_150_361/2 GTTTCCATTCACAGCACATAGGAAAATGTCTTAACCTCCTCCCTCCTCCTTATGTGTGTTTTTCTAAGTGTGTGTCTTTTTTACCTTAATTTTTATCTTA + HHHHGFHHGEEHHHHG@=9965;=DDFHHH<>:B@D5:;5=.>59@DDGFGGHHHHHHHHHFFEGFHHHHHHHHHHHHGGGBHHHGHHHH28EC,+)6); @read_150_362/1 TTGCAGCAAATATGGAAAACTGTTGTCCTCTTATAACATAAAATTTATCTTATAACAAGAAAAAAAACACCAATGCACCAAAAAATAAGCAGAGGACAAG + FFD@GGEF@GGGGHHHHHHHHHHHHGHGDBE=@DHHHHHGGHEGHHHHFHHHHFFHHHHD+)4,;DHHFFEEA5FGHHHEBFHHHHHF@@@*39BCC4>= @read_150_362/2 TGTCCTCTGCTTATTTTTTGGTGCATTGGTGTTTTTTTTCTTGTTATAAGATAAATTTTATGTTATAAGAGGACAACAGTTTTCCATATTTGCTGCAAAG + HHHHHHHHHHHHEE9*CFHHHHHHBEEHHFE?BDCGB@BEFE@;=FFHHFGHHHFHHHHHHHFB=64E=EEFDGGFEECBGHHHHHD=?@,,.<7CC@AC @read_150_363/1 GAGAGGTGTTTGGGACATGGGGTAGACCCCTCATGAGTGGCTTGGTGCCCTCTCGTGATAATGAGAGAGTTCCTGTTATGGTAGTTCATATGAGAGCTAG + GGHHHHHGHHHHHHHHA5.E? @read_150_363/2 AAACAACTAGCTCACATATGAACTACCATAAAAGGAACTCTCTCATTATCACGAGAGGGCACCAAGCCACTCATGAGGGGTCTACCCCATGTCCCAAACA + HFE;;??CBDFB8.@DHHHHG8DDEHCGE?011/%+:DGGBEFDBGHHHFFGGFGHHHHHHHHHHHHHHHHHHEEHHFCEFADFFHHFFFCDFDDCBF?@ @read_150_364/1 ATTCTGAGCTCCTGGGGTTAGGGCTTCGCCTGTGAATTTGAGGGGACCCAGTGCCCTTCCTCGAAATGTCGTGTTGACTGGCAGTGGCTCTTTGTTCCGG + HHHHHHHECCGEGHGHHHHHHHHHHHHHGFHFFFFHHHHHHHHGFHHHHHHHHDFHHHFHHHHHHHFFDHEFEBFFFHHA5>CEDFGHHHGEDHFHHHHHHHHHFCGHHGHGFHHE3);<,4(D>ECCEG? @read_150_365/1 AGGTGGTTTGTTGATTAAAACATCAATGGCTTTAGTTGTCTAGTCATTCTGTCCAAGAATTATAACCAAGTACTTGTAGGCAGGCAGTGATGCTATAGCA + FHHHHHHHHHHHHHHHHHHFFFD>=@8DC3::B@BFHHHHDDCFHHHFHHHHHFHCHDFHHHHHEHHDCC@8FGGHEDF??(HHHHEHDHHHFEBA6)8=53-21(A @read_150_366/2 CTCCTAGATGGGAATTGAACAATGAGAACACATGGACACAGGAAGGGGAACATCATACTCTGGGGACTGTTGTGGGGTGGGGGGAGGGGGGAGGGATAGC + HEBDFHHHGDFFGGHHHFHC864BGHHHHHGHHHHC53;?->9605DHECF=BGFHHHHHHHHHHHHHEEDEHHHBFBHHHHFHHHHHFFEGB+.=AA@D @read_150_369/1 CTGAAGATTCTTGGAAAATTATTGATCCTCTCTGAGAAAGAAAGAGCTCTCTCCACTCTTAGAAGTTCTGTAAGATCCCACCAAAAAATATCACCTTCTT + HHHHHHHGGFEEHHHHHHHHFFGEGHHHHHFFEEEFFFECHHHHHE?<:9C?@ @read_150_370/1 TGTCCAGAATATTATCCTTCAATCTGCCACCTGCTTAATAATCATAACAAAAAGAAATTTTACAATTATGAGCATATTTGCAACATTTCTATTTACATAT + DDBGGGGHHHF;@F;EGHHHHFGGHHFHHHHFHHHHEEHHHHHCHHHFHFFFCADFFFGBDBFFHHHHHHEE2DCDGGHHHF;B>::)6'%1;ABD=6;F @read_150_370/2 CATGTTGGAATGATACAAAGTTTGTTAACTGAGGGAATGAGTTAAAATATGTAAATTGAAATGTTGCAAATATGCTCATAATTGTAAAATTTCTTTTTGT + HFHHFGG;?9BD@59:6DDGGGGGFDBHG@HHHHHHHHFCFFHGEGGFHHHHHHHHHHHHHGHHHHHHHFFDBGBGBEFHHHFHEEAEFEBA58(>FBBA @read_150_371/1 CCACATTCCCTTGGTGGCAAGTCAATTGCGGGGACGCCTGCTTTGGCTGCTCACTCACATTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCACCT + DCDDDBDECHHHHHHHHHEHHHHHFHHHGGDGGHHHHHHGGEDDDGBCFF:9?ADHHEEBEEFFHAEFEEFHHCDGFHHFFFFFEFFDDHHHHHHHHHFH @read_150_371/2 AATGTGAGTGAGCAGCCAAAGCAGGCGTCCCCGCAATTGACTTGCCACCAAGGGAATGTGGAGATCGGAATAGCGTCGTGTAGGGAAAGAGTGTAGATCT + HHFHDGGEEEEFFGHG9129DHHHHHHHHHG?@?<6:72GE?7)+>=DHHHGHHHHHGGFHEG4>ED><.+6(5D:CHHHHGDH:GHHFFHHHFHDG@DF @read_150_372/1 AAAAAAAAAATAGGTATGGGCAAGATGACTCTAGGAGATTAGAAAAAATATTTTTGGCTGGGTTCAGTGGCTCACACCTGTAGATCGGAAGAGCACACGT + GGGGGEECCHHHHHHHFHHHHHF=DFFHHHHHHHHHHHHHHHHHHBFCBFHHHHHHHFFFGDAA9CEHDDEEBEFHHHED8EEE9FHHDFFC4@C@-1D9 @read_150_372/2 ACAGGTGTGAGCCACTGAACCCAGCCAAAAATATTTTTTCTAATCTCCTAGAGTCATCTTGCCCATACCTATTTTTTTTACAGATCGGAAGAGCGGCGTG + HHHHHHH?;1@BDDGGGDDDFB@CGE(5?.:EFHE?::7@EHHFGHHEHHHHHHD<=?@CE?=EC;?:CHHHEEEHEGHEFHHHEECEEBFHHHFCCEBBGGGFFHHHHGFEEBF4*..>FFHHH @read_150_373/2 AAAGGAGGGTTGTTTTTGAGTCTCTTAAGTGTGATTTAAGAAAATAATCTGTTTGGTTTGAGAGCTTAACCACATTCATTCAATTTCTTTGTTCACGTTT + HHB@FHHHHHHHHHHHHHHHD;..:ACFHHHFHHEGGGFEHHDFGC?;:=68EEFCEB48@CHHHHHHGHHHHHHFGHHHAHHFGHHHHFHHFB,-5=DB @read_150_374/1 CTCTTAACATAGACTAATTTATCAATGATCCTATTAAATATTAATAGGTACTAATTTTAGATCCATGTTTACAGACGAGAAAATGGTACTAATTTAGATC + 98DDBGHHHHHHHHHGHHHHHHHHHHH30CBGGHHFHHHFEHHHHFFEFHF;5<:(?49AA@BEBCE @read_150_374/2 TTCATTTTCTCATCAGTAAAAATGGATCTAAATTAGTACCATTTTCTCGTCTGTAACCATGGATCTAAAATTAGTACCTATTAATATTTAATAGGATCAT + HHHHHHDHHHHHHHHHH@GGGFFFHHEGGCHHHDCGHHHHHHHHHHFFGGEHHGE729=C@;EEEFFGHHHHHHF@CFHFDFDE6,5:@4DA@95>-,;9 @read_150_375/1 TCATTGTACACCTTAACTGTATACATTTTTTATTAAAAAATAACAGAACAGTAACATGTGAGGTTGTGGCTGTTATTATCATTAGTTGTAGTAATAGCAG + GEGGGHGGB>HGHHHHHHHFGHHG9DBEHHFHHHFHHHHHHHHFGBHHHHHHHHHFDEB::4>CEHGFEGFHHH @read_150_376/1 CCCAGAACACCTTTTTCATCCTGTGATTCTCTCTGAAATGTTAAGTGAGGAATTGAGTCAACTGAAATGTTGAATTAGCTTGAAAAGATTCATGACCCTA + HGFFGHHHHHHHHHHHHHHHHFDC7DEBGGFHHHEEHFDGHHHHHHFFDEHHHHFHFGGDCEHGGEHFHHGD791<4B@HGGFFHFHHFFHHEHHFDACE @read_150_376/2 AGCCAATGGCTCATAATAAATGTCTTTCTACATATCTATACCTATCCTGTGGGTTCTGTTTCCCTAGAGAACCTTGAGTAATAGAAATATAGTCCCTATT + HHHHHHHHHHHHHHHFHHHHHEHHHGG8/>,709@EE645EE>*;?GFFDDABGCHHHHHHHHHDHHHHD459;,';??42:.5*HGEDHHHHAFHHHEHHHHHHHFGFCHHHHHHHHHHHD6CEFFFEHHHF @read_150_378/2 CAAAAATACAAAAATTAGCCGGGCGAGGTGGTGGGTGCCTGTAGTCCCAGCTACTTGGGAGGCTGAGGCAGGAGAATCGCTTGAACCTGGGAGGTGGAGG + HHHHGHHHHHHHHHHHHHHHHHHHHHHHHHHHHGGHHHHHHHHHHHHFHHEFHFFB@EGHHHE2>?CFFHHHHFHFHHHDEFGGDHB<:9-3E9>?CAAA @read_150_379/1 AGACCTAAAGTGTATGGGGTTCTATGTGAGCTGATAAAAATGCTCTAAATTTGACTTTGTTGATGGTGGCATAGATCGGAAGAGCACACGTCTGAACTCC + HHHHHHHHHHHHHEBEGHHHHHHHHBGHHHHHHFDFHHHHHHFFEEGG?=@CCF??GEDFHEHHHFHC?4/>71?HGGGD5C5BFFCHHHE>DDEGGFFH @read_150_379/2 ATGCCACCATCAACAAAGTCAAATTTAGAGCATTTTTATCAGCTCACATAGAACCCCATACACTTTAGGTCTAGATCGGAAGAGCGTCGTGTAGGGAAAG + =8EFEGCDCDEFHEDEEEGGEBHHHF@BFDFDCACG:2<64A*+CE6;;8@B/>8:.=BGCFDDABFFHHHHHHHHE@HHGHFHG@5EEEFFGHEGHHB= @read_150_380/1 CGAGAGCAGCCCTTTTAAGTGTAAGGCAGTGCACATCCACAATCTAAGGTTCGTTCTTTCTGTAAGCATTAAACAAGACCATCTGTGTACCAGGCCAGTG + 8FFGGGGGGGHHHHHHHHHHHHHHHHHHHHHHGFHHHHHHHHHHHHHHGGHHHEFFGHHEE=E?FEFCHFDDE;.0.+%'::GGHHHHGHBGDB?HHGHH @read_150_380/2 CTTACCCATCCTGTACTGTAATTGTTTGTATCTTGTGAGGGCGGGGGTTGTGTCTCACATCCTGGCATTCCCTGGGCACAGCACTGGCCTGGTACACAGA + HHHHHHHHHHHHHHGHH=GGHHHHHHHHDDHHHHHHHHEEBHD?DABC@5AC?GHHHHGGFE?DHHHGCGF=EEFHHHHGD6=<B>47BFHHHHHGHHHHHHEHHGG:<=65937BDH @read_150_382/1 ATTTCTTAGCATTTTTCTTGAGTCTATATCTAATCTTAATTCAAATATGTTTCATTTATTTTTATCAAAAGAATAAATTAAGAACCAAAAATGTTAACAA + <7-??9>><>><=A@DD;;>EBDADFGCHB=BDGFDEEGGFFEBGFHHHHGGBHHF??HHHHHHFHHHHH?DEDBEEBA?DHHHHHHHFFHHEEHHHA>: @read_150_382/2 AGGATTATACTTTCACTCAAGCCTTTTCAAAAGATTAATGCTCTATTTATGAAATAGCATTGTTAACATTTTTGGTTCTTAATTTATTCTTTTGATAAAA + HHG=EHHHHFEBGFHEEEEHEFHHHEEDDC@@886BEBCBE9DC?AA@FFHGGGGFFFF=:D>9DEFF?BEB;52 @read_150_383/2 TCTGTAAAATGGGAATTTTATGTCTCATAAACCCAGCCTTGGCTGGGCTTGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCAAGATGAGCGGA + FG?>BHHHC/DBEFHEDBDEGGCBDFHHFFHFBBHHHHHHHH?;42E=DEDBF@>FHHHHFHHGEHH=:@DB<75:9E @read_150_384/1 AGGTTAACTGTTATCTGAACTCCGAGTTACAAAATGATGAAGATTAGTTTTGTTAAAGATTCTGACTGTGAAATCATCAGGAAATATATTTGTAATAGGC + GEFHHHHGHHHHHECFHHHHHHHHHHHECGDFFGGHHHHHHFFECGGFHHHDFHHHHHHHHH>@F9?/=EFF@BD @read_150_385/1 AGAGTAAAAAGAGATCTTCAAGTTTTCCTACTACAGCACAACAGTTTGAGAAGTCAGAGGCTTCTACAGTTTGTAACTCAGTCAGTTAAATTGCTAGATA + HHHHGGEGHHH@GHHHHFDGEGGFBDDHHHHFGGHHHFEHHEFHHFHHHF@GHFFEEED<->GGGHHHGEGFEEHHBDEG @read_150_385/2 AATACAGTCAGTTTTAAATTGAGGACTACAAATATCTAGCAATTTAACTGACTGAGTTACAAACTGTAGAAGCCTCTGACTTCTGAAACTGTTGTGCTGG + :88DBHGHHHHHHHHGHHHHHFBEE?HFF=DBGGGHHHHHHGEHHHEHHHHHHDDFFHGFFFFE=.*&/;CHHHHCD@FFD(>>,,@GHHEHFHHEF@:' @read_150_386/1 CTTTCTTTAAAATGTATATAGATATTACTTTTAAATAGCATGCCGTTTTGTTTAGTGGATGCTTTCTCTGGCCAGAAGCAAAAGAAAAGAAAAGAAAAGC + HGHHHHHHHHHHHHHHFHGFHHHHHHHGGHHHHHHHHHHHHEEA646BCDFGGG=CDA??HHHHHHHHHEHHFEAG @read_150_386/2 GGAACCATGATCCCTCTACTTGTTCCTCATCTTTCCCCTCTTCCTTGAGAAACCCTCTCCTCTGCTTTTCTTTTCTTTTCTTTTGCTTCTGGCCAGAGAA + BBGCCCBDDGGHHGGHHHHHHHHE=DB<<79E@@@?>:??946+8ECFFHHFF@CFEB=@BD.EEDF;@GFAA?@;DDHGDDGHHHHHEEEEEAAEHHHF @read_150_387/1 CCCAAAACTAAGTTCGCTTCATGTCTCTCATGACAGGGAGGAAACTTAGTGTTCCTTGGAGACCTGAAGGGATGCAGTGAGCTTAAGAATTTTCAAGAGC + HHHHHHHHHHHHHH@:@EGGGHHBGF@*>CBCGBEHHHFFD@DGHEE<>EFHHHEEDDFEHHHHHE1AAEDHHFDFEE77@ @read_150_388/1 TCTCCCACCTCAGCCTCCCCAGTAGCTGGGACTACAGGCACCAACCAGTGTGGGCCCAGCTAATTTTGTATTTTTTGGTAGAGTCAGGGGTTTCACGATG + GF8FEGHHHHFFGGGGGE8D?CGHHHHHHHHHAHHHHHHE>6,::1)2%&85 @read_150_388/2 GAGGTCAGGAGTTTGAAACCAGCCTGGCCAACATGGTGAAACCCCTGACTCTACCAAAAAATACAAAATTAGCTGGGCCCACACTGGTGGGTGCCTGTAG + HHHHHHHHHHHHHHHHGF75>2-<@C7@GE9EECDEECCB??GHFE@A@D93;GGGBFHHHGFFEGFHFF@.<354,2*'>AABB8EEHHHHHEG?F??F @read_150_389/1 ACCAGTCCCAAAAATGTTTTTTAGGAATAAAGTACCCAGTTTCCAGTGATGTTGTAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCACCTAATCT + HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHFFEEBDDD>GHHHHHDFHHHHHHHHHFHEACEEHHHHHDEEBFFHHHHHHHFFHHEFHFFBFFDHGEEE9 @read_150_389/2 TACAACATCACTGGAAACTGGGTACTTTATTCCTAAAAAACATTTTTGGGACTGGTAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTG + DDDDHHHHHHHGG==:641265>DDBE?6GDFHFGDEDFHHHHHHHHHHFCFHHHHHHHHHHHHHHGFFFHHHHH8>@=FHHGBHGGF5&0EDDGEE5;< @read_150_390/1 AGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAAAAGAAAATGGCTGTAGCAGTTCTAGGTCTCACATCTATGTACCACACCATTCA + HFHHHHHHHHHGGGHHHHHHHHHHGHHFG@@5;4;BGGEAB?FEHBHHHED?BFHHHHF=?<= @read_150_391/1 CGTCTCCAAAAAAAAAAAAAAAAAAAAAAGCACGGAAACACACACACACACCTCTATCACAATGTGTATTCATTAATATAACTCATCCGCAAACTACACT + GGD@FHGHHHHHHHHHGGGGHHHHHHGBFHHHHHHGHHFFHHE;.6>=EBGEHHFHHHHHHB>D?DD; @read_150_392/1 ACAGACTAATACAGGCGGATAACCAGAAAAAAAATGAAAAAGAAAGATAGCTAGTAAAATAAGTGCGTTGCTTTTTTATTCCATGTAGACTCTATGTCTT + HHHGHHGFEEGEEEGHHHHHHFEBFHHHHHBCBBBEFHHHHEHHGHHHFHHHHHHHHHHHHHHHG=1AFHEEEFFHHHFHHHHHBFHFFHHHGGEHHHGG @read_150_392/2 AGAGACAGATCATGAAAAGATTCTGGTAAATGGTTGGAGTTTCAGTGATTCAAAGCTGAGCACCACACTCAGTACTTTTTATTCTCTTAACCCTAAAGAC + HHHHHHHHHHHHGGGHHHGG7C?GGHHHHHHHHHEHEHHEB?B6.:DFFHEFBBAECC=B9+CEE5BD@HGHGB-8:.9EDAC=B?C@B@GGFHHHHEF4 @read_150_393/1 GTTCGAGATCACCCTGGTCAACATGGTGAAACCCCGTCTCTATTAATAATACAAAAATTATCCAGGTATGGTGGCGCATGCCTGTAGTCCCAGCTACTTG + GHHHHGGHHHHHHGGGEGHHHHHHHGGBGFHFF=9=260&<5AEEHHFHHFBEFGFHHHHHHHHHHHFE6;;09AHHHHHHHHHHHHFBC?.;><(.A@.GHBCEC= @read_150_394/1 CTTTCGAGGTCCTTCTTTATTGGCCATGCTGAATCATCTCTATTCCCAAGTTTTACTTGATAATAAATGTTCAGACAGATATTGCATGCTCACTGCTTTC + HHHHHGGGFHHHHHHHHHHHHBEFGEEEHHHCDFFGDC?BDCEEGHHHHHHEHHFHHHHEDFHHF?GEEHFEFGG/8BHHGGH?DHHD?FGHHHFHHHHH @read_150_394/2 AGGTGTTCACAGCCCCCGAGGCTTTGAAAATGGGAGGGCTTTTGAGGTCAAGTAGGATGAGCTGCAGGTCTAATTTGAAAGCAGTGAGCATGCAATATCT + HHHHHHHHHHHHHHHHHHHHHHHHHCDCFCEHGGFHHFEHHGFGGHFD>CD@>CGHHHHHFEHHGGEFHCA@CAC6DHHHCCFHHHHH8.BBDEHEFDFD @read_150_395/1 CATTTAAGTCTTTAATCCATCTTGAATTAATTTTTGTATAAGGTGTAAGGAAGGGATCCAGTTTCAGCTTTCTACATATGGCTAGCTAGTTTTCCCAGAA + HGGGB9@@@EA20?FF===<@DEEBHHHHHFFCFFDBEECCEEHHHHHHHHHHHFE?FF95:;0+5 @read_150_395/2 GAGCCCTCAGAAATAATGCCACACATCTACAACTAACTGATCTTTGACAAAGCTGACAAAAACAAGAAATGGGGAAAGCATTCCCTATTTAAAAAATGGT + DBBEGDFGHHHHHHHHHEECEHHHHGGFHDBD6629C8BB5CCEBEB9;@GGGHHHHHHFHHHFHHHGGFDABGG@BCE@>+>=>CFEEE=B)6;29,4A @read_150_396/1 TCCTTCAGACTTCTGAACTTTTGCATTTGCCGTGTCCTGTGCTGGAAATGCCCTTTTTACCTCTTGACTGGGGGTGGGGGAGGTCTTGTTCATTTAAGTT + HHHHHHBDFF@DGGGHHHHHHHHHHHHHHHGFHDGGGFFD>7@EDHHHHHHHHFFHHBFDDDAD=B=3GDEHHFGFFGGGHHGHHHHEFHHHHHHHHHHG @read_150_396/2 TAAATGAACTAGAACTTAAATGAACAAGACCTCCCCCACCCCCAGTCAAGAGGTAAAAAGGGCATTTCCAGCACACGACACGGCAAATGCAAAAGTTCAG + HFHGGB?C/;97<68FHHGBF@EHHHHHHGFB>@@HHHHHHHHHFFEFEFHHHHFGGHHH=@ACB@GDC853F98DCDHHEFFFFHFF @read_150_397/1 TACCTGGGTTACACAGTTTCCTGCTCTTGGATTCACCAAAATTCATTTAATGCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGACCTAATCTCGT + GGHHHHHHHHHHHE=DFEEE@DFHHHGDDGHHHEEGFFDFHHFGB8EFHHEHHHHHHBAC=;=BCC>EEBDBFEHGGEDHHDEEC>1(8GEFHHHHHHHH @read_150_397/2 GCATTAAATGAATTTTGGTAAATCCAAGAGCAGGAAACTGTGTAACCCAGGTAAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCACGGTGGTC + HHFHGGHH@EHHHHHHFHHHGGGHHHFFHEGF*BF@<-=<@@EHHHHHHHGEC<.>>5>EHHEC?EEG@D@CB:AFHHHHGFAB?<>39-,.GHD366BF @read_150_398/1 GGACACTTCTATCAATCAGGTTTCCATCAGGTTTCTTGCAAATGGCCGCTGCTCTCTGTCCACCTTTAACTGTGAACTTTTCCAGGACAGGGACTGTATC + HHHHHHHHHHHHHGHHHHHHGGGGHHHHHHHHGHEHHHFFHHHHHHFGHGGDDFFFFHHHHFBGCGEHDAEHHE6*3?:>EBHHHFEEFEEEFB:FHHHHBGC?GGHHH::F@F @read_150_399/2 TTTGGGGCTATTTTTCTAGATCTCATAGGTGTGCTTCATTCTTTTTTATTCTTTTTCTTTTTGTTTCCTCTGACTAGATCGGAAGAGCGTCGTGTAGGGA + E?DEDGBEGGGGGB@CDEEDGHHHHHGEHHGGGEDFFHHHHFHHHHHHHHHHHHHEDBD8<5535AB=A@DDEDE@),836BE.3.777(70-2BFFEFCD/HHHE9DFADHHGGHHGFHHHHHHHHHHHFHHHGFFE@AFH=FGEFC?E4DDDEBFGGBHEE6E @read_150_402/1 AGGGTGGGAGCTAAAGCAAAGATCTCATCAATCTACAGAATGAAGGGACAGCATGGGAGATATCTATGGCCCACCCAGGTCTAAAATTCAATGAGTTTCT + HHHHHGFEHHHHHHGHHHGGCFHHHHHHHFHGGGFGGGBGHHFHHHHHHCBADHBEE>086848:>E7%(5.BF @read_150_403/2 AAAACTGTTCATCTGTCTCCTTGTGAATACCTTAGAGTAGGGGAGGGCCATGATTGACACATCTGTTGTTTGAGAAATGTCTGATGCCCTCATTAGGTTT + B=FHHHHHEHHHHHHHHHHHHHHH>EFGFEHHHHHHHHHHHHHHHCDC>>DDEEEFDFGFHHHHHHHGG>;@E-0:>190<68.EHHHHH@5BHHEA9FF @read_150_404/1 ACAATAAACTCAAACAAATTTACAAGAAAAAAACAACCCCATCAAAAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCACCTAATCTCGTATGCCG + GHHHHHHEHHEEDD8FFHHHGHGGHHHHFHHHHHGDHHHFGGFFCEHFEFEHHGHFHHFHHHCCBFFHHHFCHHFGGHCGEHF?DDFF/&9? @read_150_405/1 CAACTTCATCTAGAACCCAGTATAGTTCCAGTGGCTTTTTAGGGCCTCTCCTGGGCACCGGATCCAGAGCCACTCAGAAGGACGTTGCTGAGTTCCTGTC + HHGGHHHHHHHHHHGGHHHHHHHHHHGGGHHHGGGHHHHEHHHHHHHFFFHFFHHEEHHFH@FFHHFFHHFFE8FHHHHFHHFGFHBFCCHBFGECCFHH @read_150_405/2 TCCCTGAGGCCCACCTGCTGTCCTAGAGAGCTGTCCCCAAGCCTAAGCCCCTGTCACTGCTGGGAGCCGGATGCCCGGGCCCTCTGCTGGGTAACTGGGG + HHHGGGGFCHHHDGGHHEGCFGFHHHHHDFEGGCHHHHHHGBFHHFDBFCFEFHH@>F,,'0-32257(6;GGHHHHGHEDCHHHFHEBBE@D @read_150_406/1 AAACCCCATCTCTACTGAAAACACAAAAAAGTAGATGGGAAGAGCACACGTCTGAACTCCAGTCACCACCTAATCTCGTATGCCGTCTTCTGCTTGAAAA + GEEFEHHHHHHHHHHHHHHHEHHHHHHHHHHHHHC;03,1>4CFHHHHGFHHHHHFHHHHE;+/-9EHHHFHFBDGGBEFHHFBDF?==BHHHHHDFDEE @read_150_406/2 ACTTTTTTGTGTTTTCAGTAGAGATGGGGTTTAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGTCGTATCATTAAAAAAAAAA + GHHHHHHHHHBGGGGFFBD?;>5@D<8629 @read_150_407/1 AGTTGAGATAAAAGCCTTTCTGGTGACCTCTAACCCCCTGGTCTGGCAGCTGGTTTCAGCTTATAATTGCTGAGAAGGTAAAGGTGTTCTAGGATAGTAT + DCDDDHHHHHHHHFGGBEHHHHGBGEEEEEHHHHGHHHHHHHHHGGCAAFFECDF:EGGHEHHH@@EBGHHFHHHHHHG4DHHBDFFFHHHHFCDAAFC4CBEEEFFC@HHHHHHHHHHHGFHFHHHHHECCBEB @read_150_408/2 GGAAGGATTGCTTGAGCTTGGAAAATTGAGGCTGCAGTGAGCCATGATTGCACCACTGCATTCTAGCCTGCATGATGGGAATGAGTCCCTGCCTAATTTA + HFCDHHHHHHHHEBCEGEEDBGGFGAGF>>FGGGGFFHFFG@A?HHHHHHHHHHHHHHHHHHHHHHHHHC@@HHHHHDG6EACFEHHFHFD4*7BD29>2 @read_150_409/1 GCATGAGATGTCCTGGTGTTCAGGGAACACAGTTAAACAAAAGTGTGATGCTGCTGTGGGAAAGCCTGCCCCAGGACACCACCATACCATGCTGTCTTCA + FGFBEGHHHHHGHHHGGHHHGFFGHHFBFHHH?;;DDB.EFHHHHHHHHHHFGHEFFDEFECEBEHHCDB?HHFHHHHHHHHHHHHHDFHHFB596 @read_150_409/2 AGGAGAAAGCATTGCCTGGGAATAAAACTTCAGCTGGCAGGAACTGAAGACAGCATGGTATGGTGGTGTCCTGGGGCAGGCTTTCCGACAGCAGCATCAC + HHHHHHHHHHHHHHHHHHHHHGGGB@CFB=FHHHHGEB:BE//8=HHHHFHHHHHHHHHHHHHFHHHHHHHHHCDDHHF@HHHGBD,.4743=FF.91/A @read_150_410/1 TGCCCAGCCCTTGGTACACCACTGAGCCCTGGCACCTAAAATAGTGGCTACTCATAGCAAGCACTCAGTATCTGCAGAATGAACCAATAGATCAGATGGG + HHGFBDEDHHGHHHHHHHHGE=AADBEDDGIGHHHHHHHHHHFF?;=>EFHFCDFHHHHFHHFFHHHFFFAAEEFHGHCDD5A9DEADHF24/;@GE8.2 @read_150_410/2 GATCTATTGGTTCATTCTGCAGATACTGAGTGCTTGCTATGAGTAGCCACTATTTTAGGTGCCAGGGCTCAGTGGTGTACCAAGGGCTGGGCAAGATCGG + HHHHHHHHHHHHHEHHHHEHFGGHGHHFF?DB@EHDDDAEFFEHHDDGFHHHHHGED84+;*3?BBFHHFEEHHHHEEHHDDEBHGGGFGG9;37@>>>: @read_150_411/1 GCATCTAAAATTTCTGAAGAACAGCAGTGTGTTATGTCTCTGAGTTCTAACAACAGACCATTAACCTACTCCGTACCGAGGGAGATCGGAAGAGCACACG + HHHHGGEFFFFGGHHHHHHHHHHHHHHEBFGGHG?HHHHHHDHHEGGGGGFDDGHFDA???FECBFFD4@A9%3/:A@F?DGGEBDFCFHHHHHHDD@,; @read_150_411/2 CCCTCGGTAAGGAGTAGGTTAATGGTCTGTTGTTAGAACTCAGAGACATAACACACTGCTGTTCGTCAGAAATTTTAGATGCAGATCGGAAGAGCGTCGT + GGGHHHHHHHHHHHFG:;/422>EEDD;EEEBFFEE @read_150_412/1 GATGTAAAGTGAAAAATTAGAAGTACATTTAAGAGTGACATATGAGAAAATCATTAAATAATGCAGAAAGGGGTAATTAAGATTCATACCAAGATGAACG + D7036@DBEGGGGFHHHHHHGFFDD-*:5B@FHGHHHHHFHFHHHHFFEFEHHHHHHHFE=AD@?.4CDD<-/539BCDDEEEHH=5A5''0,8=DFHHH @read_150_412/2 TTTGTAACCAACTTTTGTCATTAACAATTTACTGGACTTGTCAACAAACCTAAATCTGTATCGTCTATAATGGCTACGTTCATTTTGGTATGAATCTTAA + CEEGBGB@@5EHHEGGHB@GFF@DDCC=:?EFGHHEE93ABHHFEEHHHHFGC@?FFGHHHFHCGH@CGEHHHHB41<@DCDDDGGHHHHFDGG?2>8BFHHGHHHHHHGFHHHHHHHHHHHHHHHHHHHHHHFFHHGHHG@EEDDHHHFFFHHGGHHFHFHFHGGA9=<=@E@?EE.CCCEFDEGFF @read_150_413/2 TGAATATCCTTTATTTCTTTCTCCTGTCTGATTGCCCTGGCCAGAACTTCCAACACTATGTTGAATAAGAGTGGTGAGAGAGGGCATCCCTGTCTTGTGC + HHHHHFBDDHE;AFDD@@EDCHHHHBHHHHHHHHHHHHHE<>3 @read_150_414/1 ACGTGTATGTGTAAGGGCTATCACGTAGATTGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCACCTAATCTCGTATGCCGTCTTCTGCTTGAAAA + CDEEFB27DD@CDFGHHHHHHHHHHHHHHHHHGHHHHHGDDHHHEBFEFGGHHHHHFFHHHHHHHFHHHHHHEE@FGGFHHHHHHHHHHHHHHDC/,7/< @read_150_414/2 CAATCTACGTGATAGCCCTTACACATACACGTAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAA + GDC@A@EHF@*3@?,6CEG@FFEFDBGA?CDEFFHCA @read_150_415/1 CAAATGAGACCAGACTGCAAAATGAGTTTATGTTCCAAGACTCATTCATTTATTTTTGGGTTTCAATCAAGATCGGAAGAGCACACGTCTGAACTCCAGT + HHHHHHHHHHHHHHHFHHHEEFC;D65666FDHHHE?<'@>?CFHHGGGGFHHHFBEHEFGG?GFHHFHEBBFFFHHFFFHHHHHHGGHHHHFFBHFHBG @read_150_415/2 TGATTGAAACCCAAAAATAAATGAATGAGTCTTGGAACATAAACTCATTTTGCAGTCTGGTCTCATTTGAGATCGGAAGAGCGTCGTGTAGGGAAAAAGT + HED@:BGHHHHHHHHHHHHHHHHHHHC=EDBGGEHHHEFGHHHHHHHHHHHGHHHHHHHHHHHHHHHFHHEHHEEGFEBE>CEFHHHHGHEFC@D>)5D@ @read_150_416/1 TTTTTTTTCCATTTAGCATAATTACTTTGAAATCTGCCCATACTGTTGTCTGTATCAATAGTGTATTCCTTTCATCTCTGAGTGTCATTCCATTTTGTGG + HGGGFGBBDGBEGGGFGHGGGHHGGHHHHHGGHHEDGDHHHHHHHHHHHFFGEHHHHFHGFHFHHFFBEHHHHFFGGHE?GGE8A?AD.DEFFHGEBEFD @read_150_416/2 GCAAATGAATAAGCAAATTATGGCATTTCCACAAAATGGAATGACACTCAGAGATGAAAGGAATACACTATTGATACAGACAACAGTATGGGCAGATTTC + HHHGEBCEEGGHHHHDHHF8>3(8?HHHGHHHHHGDHHFFHHECBC5DEEFFHHFHHHHHBDDGDGHHEHHHHHHEEE?GFHHF:-388861,=FFEFBA @read_150_417/1 AGAGTGGTATTAGAAGCCAACACGTGGATGCCATGTATGCTCATTGTTACTGAGGCATCATTGTTTCTATGGGCTCCTAGCTGACAGAACCTGGAAATAT + GHHHHHHHHGHHFHHHHHHHHHHHHFHHBHGGHHHHHHFEGHFFFHHCHHHHHHGB=A996)AAHHEEH9CA.DDGDEFAHHFGFFGGFHHHDHHGGFG( @read_150_417/2 ATTATAGATAGGTGTATACACACAGGTCAGCATATTTCCAGGTTCTGTCAGCTAGGAGCCCATAGAAACAATGATGCCTCAGTAACAATGAGCATACATG + HHDA@=B/66*A.>>C;A?@FGGHHHHHHHHHHCFDEB?E?>7A*16DDEEDDBFFHHHHG=DEHHHGD @read_150_418/2 TCTTTCAACAAATTGAAATTGAATTGCTTTTGCATCTTTGTCAAAAATTGTACATGTTGGGCATACATGTGTGGGGCTATTTCCAGGTTCTATATTCAGT + HHHHHHHHHHHHHHHHHHHHHHHHFGHHHHHHHEEHFAAA;:DFHHHHHHHFGFHHHFHHHFHHEEBFGHHHHHHFHHHHFEHF?5>+:<-8)11?EHEA @read_150_419/1 TAGATTGGGAAAGTAAAATGAACTTTGTCTGTAACTGAAAGTCATCAGTGACCACATTGTAGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCACC + FHHHHHFFGGHHHHHHHHGGHHDDHHHHGFE=FHHHHEHHHHHHBHHHHGHHFEEHHHFE?C=EFFHHF?ED6?>D>CA;.39>CD=*BHG=:BEEG@D5>=CA@<7EDCFFFGFFFHHHBAGGH=D@FHHB=DD?EGGHF=:>.39=ECCFHHHHGHHH;@ @read_150_420/1 CAAAGGAGTTTCTGAGAATCATTCTGTCTAGTCTTTATACGAAGATATTTCCTTTTCTACCATTGAGCCCAAAGCGGCTGAAATCTCCACTTGCAAAGAT + HHHHHHGHHHEEEHHHHHEEG?FFGHEGHHFFFHHHHHHHFGGGHHHHHHHHHHC5BDHHFHE8-'%&'%)/87ADB;>FEFEBCFFBHHHE @read_150_420/2 TTGCAAGTGGAGATTTCAGCCGCTTTGGGGGCAATGGTAGAAAAGGAAATATCTTCGTATAAAGACTAGACAGAATGATTCTCAGAAACTCCTTTGAGAT + FFBGGGGF==.75,98@BHEHHHHHHHHHC',DB@@FFEEFHGGFFHHHHHHHHFHGHHHHHHHHFFGEHEHEGEEC9>=:@BFF@>EFFHFHE<.0%)1 @read_150_421/1 CTCTCTAGTAGCTGGGACTACAGGCGCCCGCCACCACGCCCGGCTAGTTTTTTTTTGTATTTTTAGTAGAGATGGGGTTTCTCCGTGTTAGTCAGGATGG + HEFHHHHHHHHHHHHHHHHAGHHHHFFFEEGGHHGGGGFHHHHHHHEGFFHHHB?FGGGFHHHHHHHHFEB:352FGGGHHHDHHFHHHFFFFEHHHHHFFGHCGGEE@FHHEFF @read_150_422/1 AGACCAAGAAGAGCTCCCAAACTGCACAAATACATGGAAATTAAACAATTTACTCCTGAATAACTCCTGGATGAACATCAAAATTAGGACATACATAAAA + HHHHEEDGHHHFGGGC@E?FGFGEGHHFHHHHHHHHHHHHFHHHHHHH?D@FHH>5@9&);?EFFFEFDEEEFB>@59DDEBCFBGFGGH;A:DBEEEEE @read_150_422/2 TTTGGTAAGTAGTGTTCTTATTTTCATTAACTTCAAATTTTTTTTATGTATGTCCTAATTTTGATGTTCATCCAGGAGTTATTCAGGAGTAAATTGTTTA + HHHGG?>@FGHHHFFHHGHHHFB=>07;/A,9ADD@C:<66@514ADAGG @read_150_423/2 CTGCTACTTGACTGAATTCATTTATTCTAGTAACTGTGGAATTTTTAGGGGTTTCTACATACAGGGTCATGTCATCTGCACACAGGGATAATTTTTCAGA + HHHHHHHFE;GFE;<67HHHHHHHHFFDDBGGFFFGDEGHHGEFBBB7:;0,:.6@+,-:>6GFGFHHHFHFGD@9,7<>)>?CF @read_150_424/1 CGTCTTCGTCCTCTCTCCAGTCCTCCTCTTCTGAGGTTCAGGGAGTGGCCGCAGCGGAGGGGAAAAGCGAGACAGGTTAGTCTGGGAGCAGAGAGCACCC + HHHHHHHHHHHHHHHHHGHHHHE=BBCCF=BFGHHHHHFHHHHD@HHHHHHHGFEHFGHHHHFEHHHGHFHHFEC@A8BHFHEFDCFBED@1/+. @read_150_424/2 GTGGCTTGGGAATTGGAATGCCGGCCTAACTCCAAAGCCCACACTCTTAAAACCACTGCGCTGGGTGGCTGCTCCTGCCGAGCGCTCTCTGCTCCCAGAC + HDE@BHHHHHGGEEHHGHHHG@BEHHHHHHHHHFD-@=CFEGHHHFFFEH?7BAGHHHEEEFFGGGFFDBFFHHD.?AFEHG51739: @read_150_426/2 GTATACTGAGGAAGGGACCTGGTGGGAGGTGATTGGATCATGGGGGTGGTTTCTCCTATGCTGTTCTCATGAAAGTGAGAATTCTCATGAGATCTGAAGG + HHHHHHHHHHHHHHHHHHG=BB83>DDA.:-49<-ABB=FBFHEGECFHFHHHHGGFHHBBD85>EEHBABDFHEECHFDEEDGDEGFEBBFFHHHEEEG @read_150_427/1 TGGCATTTTACTGGTTAGAATCTCATTTACTGCATACAATAAAAAACTCAAAGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCACCTAATCTCGT + GHHHHHHHHHHHHEGHFHHHHHHHHHFHHHHH=>+BDHHFGFFHHHHHHHHHHHDFFD8,47EBCAHHEEEFB@9GGFB<@FHHHFHGGGEBBEGGHHFADGEBF@;:?>E @read_150_429/2 GCATGGCATGCCATGTTGGAGGTGGAAGGGGGCACTCTCTTCTCATCCTGTCTTCTAAAAAACAAAACCAAAACTCATCTATTGACCCACTGGCTAAGAA + HHHHHHHHHF@2<=@@DD?:6GGG;<.83CDEEHHHHHHFHD0CACA7B@:EECBGHHH..6BBDB@>:>@AEHHHFGHF@EECFEHHHHHHHHHHHHHFGG<><@CBE;B=.DEHHHHB:--+2EHHHHHHFGFDDBFEFEECFFEFD/C@A @read_150_431/1 AGAGAAGAGGTAGAAGATGACTCCTTTGGTAGAGGTAGAAGATGACTCCTTTGGTAACTGGATCAACTGGCACTGGAAATCAAGGAGGAGGAATAGCCTT + HHHHHHHHHHHHFFGGGHHHGHHHHHHHHHHHEEGHHHHHHHHFFE?7EFHHFHHHHHHHHHHD@A=++EABFFEGHEGGHHHHHHHHHHEHFHB%*ADH @read_150_431/2 CCTCTGAGACATGTCTCCTGGATGTCCCACTGTACCTCCAACTCAACACGTCCAAGACAGAATCTGCTATCTTCCCCCAAGTGTGTTCCTCCTCCTTGAT + HHHHEFHHH=B@FHHGFHHHHHHECHEFDEEHHHEHHHHHHHHHHHHHFEHHHHHHHHHHDGG=>GFHHHHHEEHFHHGHFGFGACAC>@EBFHHHHHHH @read_150_432/1 TATTTTGAGAGAGAGAATATATTCACATAAATTTTATTATAGGATATTATTATATTTGTTCTATTTTACTATTAGTTCTTGTTAATATCTCTCTGTGCCT + HHHHHHHHDFF@BBBDGGGHHHHHFHHHHFHHGHHHHHHHHEF?2/:BBE;@GHHEEHBAHHFFC9;DCFDHHHHB86=DF???B0>:CFFDFHFEBFDB @read_150_432/2 TGATTTACCGAAGCCTAAGCGTCTAGATTGAATGGGGAGAAGCAGATCAGAGGATATCATTCCACTACAGTAGACACCCTTATCTATGGGGATATGCTCC + DDDGGHHHHHDDCGFEEEEHHFFEEEHHHHHHHHHHFDGFFFFEEFHHHHGGGHHHHHHHHHHBHHHHDEHHHHHFHHHFFHHH@;:;C/*8>:?7,4:A @read_150_433/1 TGCCCTGGATGGTCAGGGACTTGGAAGAAACATGATTGGAAAACTGGTGATGAAAAAATTTGGGCAAGAGGAATGTGGATGGACCTGTCTGAGTGATCAA + HHHHHHHGEHHHHHHGHHHHHGHHHHHHHHHHGFFDBFFHFEFFHHFHHFFGGGHFHHFFHH@<ECDHHDDDDEGAAFFCBGFEGBB@>FGGGHHGHHHHHHHHHFDDDDBCFE @read_150_434/2 TTCAAATAGGCATTTCTCTGATTATATATAATGTGGAGCATCTTTTTATATGATTACGTGCCTTCTGTATATCTTCTTTGATGAGGTGTTTGTTAAGGTC + GFDEHHHGGDHGFFHHHHHHHHHFGHHHHHH?CDDBHHFDHHHHFHGIGGGHGHHEHHHHGGHHDF86@@??EGIHFHHHBDGDHFHHHHFGIFFFGFHF @read_150_435/1 CCATGATGGATGAGGAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCACCTAATCTCGTATGCCGTCTTCTGCTTGAAAAAGAAAAAAAAAAAAAA + HHHHHHHHHHHHHHHHHHHFHHHH?HD@HGFHHHHHHFGHHE==FHHFGF5;(7>;;6;=EEE>:A@CCHHGFBHGGBB/:AC@A(.>EFEFFHHHGBEH @read_150_435/2 TCCTCATCCATCATGGAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAA + HEEFHHHHHHHHHHHCAGHHHHHHHHHHHHHHHHDBFH@B9CEEFEA4:ADDFFHHHHHFEGEEB?:DFHHHHGI?DEEE@@>:6.GHHA@:31 @read_150_436/2 TTCCAGGTCAGTCTCTTTTAACTGCTCTCCTGAGTTCAACTCGCAGTTGCTCTTAGCTGTTCACCTCTTTTCTCACTTTGGGTGTGTTGGCTTTATTACA + EE6DDFDGGHHHHHHHGFHHHHHHHHHHHHHHHFD5;BFGFEAGFHGEEFGGGGGGFBE=DDDHFEEDFFIGGHHHHFFDFB?;67<>BD@EFF?GEGFE @read_150_437/1 ATCTATGTTCATCAGGGATATTGGCCTGTAGTTTTCTTTTCTTGTAGTGTCTTTGTCTGGCTTTAGTATCAGGGTAATGCTGGCCTTGCAAAAGGAATTG + HHHHHHHHHHHHHHHHHFGHHHHHHHHFFHHHHHHHHHHHHHDBHHGGHHFFFFHFDACFFHHFHHFF?EACFFDHHHGGHFHHHHGDBE<1(503BEBG @read_150_437/2 TCTCACAGGACTTAATGGCTTCACTGGTGAAGTCTACCGAACAATTAAAGAAGAATTAATGCTAACCCTTTTCAAACTCTTCCAAAAAGCTGAAGAGGAG + HHHHHHHHHGDD8GE=CBDDEEEHEGGEBG;EFFEHEHHHHHD?:>DFFFHHHHHHHHFHHHHFF?FFHHHHHHEHEFF??7>A;DEFFHFFHEHECCFF @read_150_438/1 TGGGTGAGGGGAGGGGGCAGGACTGCAAGCATCTAGAGGGTAGAAGTCAGTGGGCTGTTAAACATGTTCTAATGCACAGGACAGCCCCCAACACAAAGAA + HHHHHHHEE2DGHHHHHHHHHHHGGHHGFFHHHHHGF'(,.6.=B;-:.(0H7:=D@8CHFFFFFGHHFHEFGGDGEGGHHHGHHHHHEGGFHHHHEBAEEEBHHHGGFEFEE@@BECC:CDFHBHHGG @read_150_439/2 GCAATTGTTTGTTAAAGAAGGATTAGAAACGGCTAGGAGAGAGTGAATTTGATAGTGTGGTGGAGATAGCTGCGGAGAGGTAGAAGGTGGCATAAGAACG + 226:?6DEHHHFDED3-<@8AB4<4C<>@=<5>5<:BFFFDEB@:6@DBE?FHHHHHHHHEG=@@HBBDFBEDADHHHFGDHHHFEGHBEHHEEE @read_150_440/1 CTACTAGATGGTGCTATGATTGAGGGACCCAAGACCAGCTGAATCCCATTATGATGAAGCCTCCTTTTCTTCCCTTTCTCCTGTCAATGTTTCTAAGGAT + HHHHHHHHGEHHHHHHFFEFHFHHHHHHGG@BAHHGECDFEHFHHFFGFHD+80@>@FHDHHHHDFHFHHFFGFDHHHHEHHHHGHHHFGFFEHHHHHFE @read_150_440/2 TTGGAATGAAAACCTCAGTTTAGAGTAAAGCATGTCTGCGCGCTCCAGTTGATTTGCTAGTCCCCACCCTGTGCAGTAATATCCTTAGAAACATTGACAG + HFHHHHHHHHHHHHHHHHHHHHHFHHHHHGGHHHBFF@?@DDDFHHHHEHHHHHFEHDGGHHGF<8HHFFDEHHHHHHHFHHHHHHFHHHHFFED5DEGHHHHFBFHHHHFEHHHHHHGHHGG @read_150_443/2 ATGGGAAAGGTAACAGGATAATAGTATATTTGTGAGATATCTGTTTTTCCAGTTTAGTTAAAAGATTAAGTTTACTGTAAACATATACTGTACAAAGCAT + HHHHHHHHHGHHHHHHHHHEEEHHHHHHHHHGBEGDFFCGFHHHHF:@:GHHHFHHHDFGHHFHHFHHHHHHHHHHFBGGGDFHHHGHHGDHHHHDGHHH @read_150_444/1 AGTTAGTGATGTTGACACCTCTGCATTTTAACACTGGGATTTCTTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCACCTAATCTCGTATGCCGTC + HHHHHHHHHHHHHHHHHHHHHHHHHHHHFHHHHFGGHHHHHHHF?C=9CEEDBFC@<79>578-9DBCCFFFE/&(/6<, @read_150_445/1 TAAAGGAAAATATGTGCTATCAATGAGGTACCCACAGAGGACAGGCACAAAGGAGCAGTAGAGCCTGCAGAGCTAGACTAAAGTTGTATTTATTTTTTCT + HHHHHHFEDEFEECHHHHHHHHHEEFFFHHHHHHC>FHHHHHHHHFFD?F>478-1>DDBD;6>;?A?DFHFDFHGGBDGB9C>G@39<'178<:BFHEH @read_150_445/2 CCTGGAAGTCACGCTGATTTAAAGAAAAAATAAATACAACTTTAGTCTAGCTCTGCAGGCTCTACTGCTCCTTTGTGCCTGTCCTCTGTAGGTACCTCAT + HHHHEEEEGHHHHHDEHHDBDEFHGE?HHHHHHHHHHHHHFEDE@EFEHHFFCHHGEEGGEFGBHHHHHHGHH:GFG>CD>CEGFBEB/,;5;><.9:;@ @read_150_446/1 AGTAGATAGATCCATGATATATTCATAAAGTAGCTCTCCTAAGTATTTCTTTCTAAGTATTAGATTAAAAACATTTGGTAGCCAGGTGCAGTAGCTCGCA + GGHHHHHHHHFHCB@FGEDD:EHHGGHHDHHHHHGDEFGFHHHHHEB3:6EHH?AHHGGHHFHGGHHHHF=DGBGFEDBFGG @read_150_446/2 TGCTGGGATTACAGGTGCGAGCTACTGCACCTGGCTACCAAATGTTTTTAATCTAATCCTTAGAAAGAAATACTTAGGAGAGCTACTTTATGAATATATC + HHHHHHHEEHHHHHHEEEEHHHHHHHHHHFHHHFHHHCHHHHHDGHHHHHHHHHG8A4;HHHHDGD??EGGGEBFE5@@/3;A@;;BHHHFEBF6ECFHHFHHGHHHHHFHHHHHFDBEHHHHBFIGHHHEEC;HHHHGDFEHDFHHHHHE@/...<;?FDHB7BFHHHFEDFF?C9 @read_150_448/1 GAGGCTCGAGGATCACTTGAGCCAAGGAATTCAAGGCCAGACCAGCAACACAGTGAGACCTTGTCTCTAAAAACAACCAAAATCCCTCTGCTGGGGGCAG + HHHHHHHHHHHHHHHBEFFGHHHGHHGEHEEEGHHHHHHHHHHHFHHHFFHHHFCHHF>;DA>AED4??E @read_150_448/2 CTCAATATTAATTCTCACTCTGCCCCCAGCAGAGGGATTTTGTTTGTTTTTAGAGACAAGGTCTCACTGTGTTGCTGGTCTGGCCTTGAATTCCTTGGCT + >><<<;<3@@@=D<:;FDDEHHHFHHGHHHHHHHHHGFIGDHHEG?DA+>7EFAEE>6&0A?GHHHF@CDGEBCG= @read_150_450/1 AGGAGAATCTCATACTGGCTTCAGAAGATAAGGGAAGTCTTCCCAGACACAGAGTCCCCTCCAGCCTATACACAGCCAGTCCAGGCACTGGTATGGTCAC + HHHHHGGGHHHHGHHHHHHHHHHHHBBGEGCAGHHHHHHHGHHHHHED/?ECHHEHEGGBHHHDDCFGEC9@-:CHHHHHHHHGG@DG@@AD5%1,4BEF @read_150_450/2 AGCAGCTGGATGACCTTCATGGGTGTCCATTGCCCTAGCTTAGTGACCCTACCAGTGCCTGGACTGGTTGTGTATAGGCTGGAGGGGACTCTGTGTCTGG + HHHFFFHHHHHHHHHHFHHHHDCGGFFGG;DFFFEGFGFHHHHHHFGEEEHGGHE;DDB8.86A<33,B9BHHHD6.A5EHFECB?@DDDCEHHFDGFHH @read_150_451/1 GTCCTAAAATAGCACTATCATTTGATTAACATTGCACAATTTATAGAAGAGTTCCATATACAAGTCAATTAGCAATTTAACAAATACTCTATTAAACACC + FGFHHHHHHHHFFFFGBGGFGHHHHHHHHHHHHGHHHGFFHHHHHEEFHFD?EF=4DFCCHHBCFF??*>FFECHGEBE=HGFHHHHGG?;7CDFHFHHH @read_150_451/2 AAGGAGTATGTTTGTACTTTTCTCAGCTCCTACTACAGGATTTGCCACATGGTGTTTAATAGAGTATTTGTTAAATTGCTAATTGACTTGTATATGGAAC + BCB=?;=EHHHHHHHHFFHHHHHHHHHHHHHHHHHHHHHHFHHFFBFCDIEGDEHHHHBGHHHHFBBCDD@C7<>=@DDAD2.59::@BEGFEBFEFDFH @read_150_452/1 TTAATGTACATGATATGAATGTGAAGCATAAAATTAAATAAAATTTTTCCCCATTGGCTTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCACCTA + GEEG@FDE=CCB@CCC6CDDFHHGEHHHHHGFHHHHHHHHHHHHHHHGHHHHHDD<&*&)3@1:EBHHHHFEAEGHHHHHHHHHHHDBCGD=EHFD9?EEGHDICEGHHHHDFDHHHHHFFBEEFH @read_150_453/1 CAAAAAATGCATTGCAGGTGTTTTACATATCCCATCCTCTACTCCGGACAGGATTCACCTGATTGAAAATCTCATATTAGAACAAAAGGAGGGGAGGCCA + HHHHHHHHHHHHHHHGGGHHHHHHHHHHHHHHFFBHGDE6553<@10/349ECCCHHHFFFHHHFFEBBBFBCDDCCCEDFGHHHHHHHHGHHHHHHHHH @read_150_453/2 GGGCTTCCTGGCCTCCCCTCCTTTTGTTCTAATATGAGATTTTCAATCAGGTGAATCCTGTCTGGAGTAGAGGATGGGATATGTAAAACACCTGCAATGC + HHHEFEGGFHHFFDDFHHG/(01)2=<>DHHHHHGEGHHHHHHHHHHHHCEE@@76>BGBGDDBDFGB>>D9;;7DHHHHGHHHHHHHHHHEFHD>;:,6 @read_150_454/1 AGAATGAAAAGAAGGCACAGAAAAGTGAAAATACTTGCAAAACATATAACTGATAAACAACTTGTATCCAAATACAGGAAGAACTCTCAAAAGTAGATCG + EEBFE=BEA6CGHGHHHHHHHFF@=GEE@AFGFDHHHFHHGHFFF9:@CA===+8,>HHD,:AHHHGA?EEDE@CHHHHGCFHDHHHHHHHHHFGHGDDC @read_150_454/2 ACTTTTGAGAGTTCTTCCTGTATTTGGATACAAGTTGTTTATCAGTTATATGTTTTGCAAGTATTTTCACTTTTCTGTGCCTTCTTTTTATTCTAGATCG + .,.@B/<@B8<=@CBDFFHEBB:6+))6<=@HHHEDGHHGGAGFEEGGGCD=.5--%,,5:--1 @read_150_455/1 AATGATTAAAACTATAAACATACATCTGTAACATTTCTTTCTAAACTATTCTAGCACTTCAAAGCCTGAAGCCTATTACTGTTATATGGAGAAATGTATA + EEEEGHHHHHHHHHHHHHHGGHHHGGEE8HHHHHECFHHHEFFHGHHHHCFGFGFFEF>:<;BDFGG;AEHHFHHHGGGGHHGFFHGFGGFFHHHHHHHE @read_150_455/2 GTTTCACCAAATAACTCATTATAGCCAGAAGAGGGTATTGCTTCTTTCATTTGTGGCACTAGATAGGGCCCTATGTTTTTCACTATTTAGTATGTATACA + HHHHGFFDCEFHHHGHHHGGHHHHHHHHFHHFEFHHHHHHHB>E<@DEGEB/1419:<7DCD:CBC.:2E@@878BEGGGHHFAHHHHB:52(4:>E>GF @read_150_456/1 GGAGGGAGAGAGAAATAGAATATGAATAGAGAAAAGAGAACCCACAAACCTAACTATAACAGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCACC + HHHHHHEFEEBEGGGGHHHHFHHHHHHHGGGHHEFGGGGEFFHHHHHGHBFBGFD:061:=DFEB,>(C@FGGGDGGGEHFD,:>*&+BEEFFEHHDHG6 @read_150_456/2 CTGTTATAGTTAGGTTTGTGGGTTCTCTTTTCTCTATTCATCTTCTATTTCTCTCTCCCTCCAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATC + HHHHHHH=E@BEBEABEHHHHFHHHHHHEHHHFHHHC+>,:*346@D9AAEEGGGHHFC@EDAA6+?@FD<@D@<86:DCFGHHHFFEF?GHHHFHHHHE @read_150_457/1 TAATAACAGCATTTACAGTATTGTGACTATGTAAACGTTAATTCATGGAGGAGCCAAGTAGTATTCTATGAGTATAATTTCTTTCCTACACGTTTTTATT + HFEHHHHHHHHG@FEGGGFEEHHHHHHFFGEEHHHHHHHHFFHHHHHHBGGAFHHHHFFBEF6EGFBAEEEBEBEHGGFD9:+'21)0?CHHHFEBHHFH @read_150_457/2 CTATGACACGTACAGAACAAAACATCCAGGTCAAAGCGGAGGGATGTAGAGCCTGGGGAAAGAGGTCTCCTGGGCAAAAGGGGGACTTCCTAGAAAACTT + HHHHHHHHHHHHHHHHHHHHHEEEHFGGFGHHF8FHHHHHBFFFHHHHFGEFGEEHHHHHHHHHHHHEFGGFABGFDFC?A5675DDACB@EF6CA98;: @read_150_458/1 TGCAGCGCTCTTTACTTCTGGGTTTGGCCCAGATCTTAAGTCATCCACATATCTTCTGGTTTTCAAAATTTATTCATTCAATCAATATTTATTAATATTT + HHGHHHHHEFGEFHHHHHHHHHHGGHHFGGHHHHD@GFFFECBECFFHGHHHHHHHHHHHGGE@HHFDEEDFFHHHGHHHDBAFFHHHFFFBB=GGGDDF @read_150_458/2 TATTTTTGTACTTACCACATTGTATAAGTTTTGCTTCTACCTCTGAACTCTAAGCATGTATTTTGTCTTATTTTGTACTTCCTATACCTTGTACAGTATT + HHHDEGGHHHHHHHHHHHHHHFFBFHHGFHBGFFHHHHHHHEE5%,4(DEGEEGFHFIHHHHHEEGBEFGFHHEHHHHHEGBEB=.D/?CFA56'>87@/ @read_150_459/1 GAGTTGGAGACCAGCCTGGGCTACACAACAAGACCCTGACTCTACCAAAAAAAAAAGTTCTTTAATTAGCCAGGCATAATGGTGCACGCCTGTGGTCCCA + F@BEB<:8:9CC@BGDHGDGGHHHHGDBAGGEBGHHHHHHHHFGGFFGHHHHHHHHHHHHHHHHGFFFFHHHHHHHEEHHHHHEHHHGHHDDFHHHHHGF @read_150_459/2 TGGCCTCAGCCTTTAGAGTAGCTGGGACCACAGGCGGGCACCATTATGCCTGGCTAATTAAAGAACTTTTTTTTTTGGTAGAGTCAGGGTCTTGTTGTGT + HHHHHHHHHHHHEGGHDEEHHHFHHHGFHHGA?=)5'2AAG>FEE?EGFHHF?AED5)26+4 @read_150_460/1 TGAATAAGTGAAGGATGATGAAAAGAAAGGGACATGATTATATTTATGAATTCATCCCCAATCTTCCCTTGGGAATTATTTTCTGGACAAATCCTAAGTA + HHHHGFFFHHHHGGGHFDEEBC896EEEEG;B>HHHFCD?GEBHHHHHHEHHHFFHFGG63:@FFHFFHHHHHHHHHHGEC9FHHFDHHHHFFFGEFFHH @read_150_460/2 GCTGAAGTACTTAGGATTTGTCCAGAAAATAATTCCCAAGGGAAGATGGAGGATGAATTCATAAATATAATCATGTCCCTTTCTTTTCATCATCCTTCAC + HHHHHHHHHHHHHGGDDAAGHGEEHHGIGHHHHIHHHHHFFHFD9=;.*1FGGHHHHHHHHHHFFHHHHFHFDDD;GEHFHHEDCHFHH>EEEEADDB58 @read_150_461/1 AGAAATAGACCCAGGCATATCTGGTCAGTTGCTTTTCAACAAACTACCAAGATAATTCAATGGGGGAAAATAATCTTTTCAACAAATAGTAGATCGGAAG + GGGGHHHHHHHHHHHHHHHHGEEGC+BF@GGHHHHHHHEADGHHHHHHHGBEHHHEGHHHH@DDGHHHHHHHHF8EGGHHHHGIHBBBHHDCFB46A7BGGGFHGEEAC.5851 @read_150_462/1 GCAAATAGTGGCAGAGTGATTGTTTCCAAACTTCTTACTGATCAGCAGGAATACTGCTGTTTTCATAAATCAAAGCATTATTTTCTCGTTTAAAATCAAT + A>B>@>CFDAHHHHHHHHHGHHHHHHHHHHHHHHHECGFHHHHHHHHHHHHGE78.3>DDH>FEDFB=HHDDFFFGHHHHHFHHHGGHHEGB,5;EHHFH @read_150_462/2 TTTTAAAAAATCAAACCTAATTGCCAAAATCTGATGTTTACACATAGTTAAGAAAAGAAAGAGCTAAATTGATTTTAAACGAGAAAATAATGCTTTGATT + HGGGGC<4>DEEGGHHHHHHHHHHHHHHHHGE6+;GCEFFHHHEBDC;=HGFGGFEHHHDD<4GEGHHHHHHGHGFFDE@:8DFF=C??D1+7DD=EGFF @read_150_463/1 AGGCTGCCGGGCTGAGAGCGCGGAGACTCCTGCTAGGCTGTAGTCTGGCAGGCCGGGGGACTGGGTTTACTGGAAGAGTGTGAGGTGGGGATGCAGAGGG + HHHEGFFDDDHHHHFGGBAHHGHHHHHHHHE@DFEHHFEGGGHFBHHHFHGFFHCEFFFHCF72)77::>><9FFGGEHHHHFFB:D @read_150_463/2 GGGGATTTCAAGGACCTCCCTCTGCATCCCCACCTCACACTCTTCCAGTAAACCCAGTCCCCCGGACTGCCAGACTACAGCCTACCAGGAGTCTCCGCGC + HHHHHHHHHHHHHHFHHHHHHE8FHHF6:?D@FGGHHHHHHHHFHHHD8=FGHGFC=DGGHHHC?18=7FFEE@EFFEGGH<6,*;.DHHHEEBFDBADG @read_150_464/1 GGCCACCAGTTCAATTCAACAAAAAACTCTCTGGGAGTTCCAAATGTGCCAGGCACATTGCAGGGCACTGAGATCGGAAGAGCACACGTCTGAACTCCAG + GGGGEEGGFGFHGGHHHHHHHHGHHHHHFGHFFHHHHHHHHHHHHHHHHHHFFFHHFEFHHFGDFHHBCBHHC?FDEEEHFHHEBEDC5FFDCDHHF.79 @read_150_464/2 CAGTGCCCTGCAATGTGCCTGGCACATTTGGAACTCCCAGAGAGTTTTTTGTTGAATTGAACTGGTGGCCAGATCGGAAGAGCGTCGTGTAGGGAAAGAG + HHHFHHGFHHHHHHE;?>GBDFHHHHHHHHHEFGGDHHHHHFGGBECAHHHHHGIFGBED@6:60,/+2,A;CE7(9<<:EGFGB9- @read_150_465/1 TCTTTCAACAACTCTAGTAAGGAGGCGTGTTCCAAGATGGCTGAATAGGAACAGCTCTGGTCTGCTGCTCCCAGCGTGATCGACGCAGAAGACGGGTGAT + GGGCEE56CDEEGGHHHHHHHGDHHHHHH@/8BBGECHHFFHHHHFFCE=FHHHHHFBHGHHBB?5<0;9+02>D>>EEBEF@HFHFFGGC@B:9AADHF @read_150_465/2 CTCAGTGAGATGAACCAGGTACCTCAGTTGGAAATGCAGAAATCACCCGTCTTCTGCGTCGATCACGCTGGGAGCTGCAGACCAGAGCTGTTCCTATTCA + .66:@B>>BEHHHHHHFHHHHHHHHHHHGFGEHEBGFFD@FD9EEHFFAA:DDC?=6GEEBEEEHHHHEGD@@@45.;1*7CDF5EEECCEEGE4C@/'3 @read_150_466/1 AAAATGTAGGTAGGTCCTAGGTATATCAGGATGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCACCTAATCTCGTATGCCGTCTTCTGCTTGAAA + HHHHHFDGGFDDDA?GBDDEHHHHHHGD-D,1-98;??==;FFHHHHHHFHHGHHHHHHHE?863:FADE>CDCCGHGFGHHHFFHHHHHBHF=B(9:CF @read_150_466/2 CATCCTGATATACCTAGGACCTACCTACATTTTAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAA + HHH=GHHHHHHHE+EACGGGGE;>79?@CEB/BGHHHHHHFHEGGECDAHHGEGGEHHHHHHHHHHHHHHHHHHFDC?DB?GFDGHHHHHHHDFD?E<@) @read_150_467/1 TCATCAATTAAGGAAGGAAAAAACTCTGAAGTTAGTTGTTTTGCATCAAGGAGACAGAACAACTGGTTGATTGTTAGATGTTTCTGCTTCTCCATTAGTC + HHHHHHHHHHFFFHEFEFHHHHHHGGHGGGEHHGEAEA(;-208@>4.AFHHHDEHHHHHE=:BDGGBDAFFFHHHHHHHGGDBFGGGHFBGACBGHGHH @read_150_467/2 CTCCAGAGAGCCCCTCAGATTCTTTATTGATTCATCATCTTCAAACACCAGAAGGACTAATGGAGAAGCAGAAACATCTAACAATCAACCAGTTGTTCTG + @@EGFHHHHHGEEB@HGHHHHEHHDHHHHGEIGEEEHHHHHHHFFDD<.@*3689E65DAEBD>>4GFHHGFF4&:>=CGGBDGHHHHHHHHHC?E=@F@CBE7>C/=DEEE@FBFFHHHHHHHHFFDDD;7(6CHFFFCHHHHHHHHFEFFHHHHGFABDGGFFFHF@@+C @read_150_468/2 GTAGCTGGGACCACAGGCGCCCGCCTCCATGCCGGGCTAATTTTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTGTCAGGCAGGCTGGTCTCGATCTC + HHHHHHHHHHHHHFGEDGGGHHHHEHHFFFE83.-74586AB?AEEDDA/8(458?FEEEEEE98CDD59:>DBEGGGHHHHHHED5@FDFFHFHHHHFE @read_150_469/1 GTCAGGAGATCGAGACCATCCTGGCTAACACAGTGAAACCCCGCCTCTACTAAAAATACAAAAAATTAGCCGGGCGTCGTGGCGGGCGCCTGTAGTCCCA + F6DB8;EDBBFHHHHHFFDHHHGGGFHHHHHHGFHHHHHHHHHFF@BBFHHHHHHHFBC?HHDDC2BHHHHFHHHHHHHHHHFGGGHCCFFF @read_150_469/2 CTCCTGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACGACGCCCGGCTAATTTTTTGTATTTTTAGTAGAGGCGGGGTTTCACTGTGTTA + HHFC@=EBDEGHH@A@CCDDHHHEEEE*:<@@BGFAFCGFHFHHFHFHHHHHHG8<4(34362-EFBE;A.@ @read_150_470/1 CAACAAAAACAAAACCAAAAAAAGTGGGCTGTGGAACACTGAGAGGGGCTGGCCTACCCTTGGGGCATGGATCCCCTCCCCGCTACATCTCCCACCATTG + GEGGGGHHHHHHHHHHHHHHHHHHHGFHHHHHGGGGGHCDEFFHFBHHHHHHF6=EBFGB;EHFFFCH?BDDDCFHHEBGFFDFEGFEFHDDDAE<>=DG @read_150_470/2 TGGCAACTTCCTCACTCGCCGCTGGGCCAGGATGGATGACTCGATGGGCTTCAGCTGGGGGGTGGGCTTGGAGCTGTTGAGTGCGGAGTACGTGGCAGCC + HHHHHHGGHGHHHFEEFF:BCB=36>?FHDGHHEHB9EEHFE @read_150_471/2 ACTTGGCACTGACATAATTAAGCCAAACCAACCTTTGGAACCTCCAGTCCAATCTCATTCTGTTCTACATTCCAGCACCCCTCTCAGAGATCGGAAGAGC + HEDGEEFFGDFGHHHHED??CHHHHHHHHHDGHHEEEFHHECDD9DA>B587<=>-63-4-0><36?=EGCC,@@>?FB>BFFHHFDFEEHFE<9AECCA @read_150_472/1 TTTGAATTCCTTGTCTTATAGATCACACATCTTCTCTTTAGGATCTGTCACTGATGCCTTATTCTGTACATTTGGTGAGGTTATAAATCCCTGATTGTTC + HHHHHHHFFHHHHHHFFGGGGGHHHHHHHHFHHHHECHHHHEHEEFDFFHHHHHFHHHHHFEE@DDHHEGFHEEBGGGBFHGGEEHHHHHHHHFFHGBFF @read_150_472/2 AAAGAGGAATGGGCAGAGATCAACCCAGACTATGAATATTAGATTAAATACATAATTATTTAACGTGCAGACATCAACATGCATCCACATCCATCAAGAA + G=CBDEGGBGHHHHHHGFGGFBEHHGCHB59@74>A*,,1:9><-@GHHHHHHHHHHHHHHG=EC24.-BEHHH86A@BEEHDHHHEDCAD8&-11399A @read_150_473/1 TGCACACCCACCCTCCCTCCACCCCACCCCCCTTTCCCTTTTGCACCCCCACCACGGCCGCAGGCATCTCAGCACCATGCACCTCCCCCCCATGCCCTTG + HHHHHHHHHHHHHGGHFHHHHHHHHHFEFHHHHH?DFEDHHGHHHHFHHHHHHF9FFBEFFGEFHBBFF?8:1@@HHHG.,3;;+::AD?:DFF@FFFFF @read_150_473/2 CAGCTCTGGGGTGGGGGGCCTGGCCCACCTAACTGCTTCCATGGTTGAGGCAGGAATGGGAGCATTGCTTAGAGTGCAGCAAGAGGCTGTGTCCATGGTT + GGFDHHHHHGDEE@72:/.09496<+36@@845FFGGDFGHHGHHHHB@@5>>=>BFEHHHEFD<@BFEEDFF@/2<<;75=6EE4+ADE7----(,3': @read_150_474/1 TCACCTTGTTAGCCAGGATTGTCTCGATCTCCTGACTTCGTGATCTACCCGCCTCGGCCTCCCAAAGTGCTGGGATTACGGGCGTGAGCCACTGTGCCCG + EFFFEFFHHHHHHHHHHHHHHHHHHGEEDHHHHHFHHHHHDHHHHHHHHFHFEEDCDDBEEEGGGBEFEBHHHFHHGHHHH; @read_150_474/2 TCATATACTATGAAAAGTAGTTTTGTTTTTTTTTTTTTTAGCAGGGCATGGGGAACCAATGAAGAATTTAAAATAATAGGCCGGGCACAGTGGCTCACGC + HHGEHHGHHHHHHHHHFDEBCFFGGHFHGHHHB@;4*&67=FHD7@DHFFHHHDDEEEHHHHHHFHHHHHHHGGGC22)>CGF=@FFEGHHHFDCD.=A@ @read_150_475/1 TTGTGTGCTCTTGGTTCCCTAGTTCTTTTAGTTGTGATGTTAGGGTGTTGATTTAATATCTTTCTAGCTTTTCGATGTGGGCATTTAGTGCTATAAATTT + EDEEHHHHEEAGFHHHHHHHHHHHHA7,;:CBC@BGFEBGHCFC7HHHHHHDHHE??EB@9EEEGGA@HDBHFFFHHGFE@AD@DFFFECGEE<5C=?67 @read_150_475/2 GCTAAGTGGAAATTTATAGCACTAAATGCCCACATCGAAAAGCTAGAAAGATATTAAATCAACACCCTAACATCACAACTAAAAGAACTAGGGAACCAAG + HHHFGHHGGGGCDD?BGFHHHHHHHHFHHHHHCCD6B<<15@EBHHFFHHGGGGGHGFHHHHHHGEDEHFDHHHHHFHHHGD9;4*.>;5'73/9>57;1 @read_150_476/1 GTGCACAATTATATAAATTGCAAATAAAGATCATTTTACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCACCTAATCTCGTATGCCGTCTTCTGC + GFGFGEGFGHHHHHFHHHHHGGHHHHHHHHHHHHHFHHHFGFHEFHHHHHHHHFEHEHHHHHHHHFFDCCFFEHFHHHHGFGGEDFHHHB=E;A>><=,? @read_150_476/2 GTAAAATGATCTTTATTTGCAATTTATATAATTGTGCACAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTACA + GFGFDGFHHHHHHHGHFGFHHHHE@CFFHGHHHHEEECDEHGFHHGHFHHHHHHHHGG<-5,)8CGEEHHEFFIGDCDDCFEECEHE@FA9GF8E*4<.- @read_150_477/1 TCAAACGAGGCAAGTAAGAACATAACTGGAAATGTTTTGAAGACCCCCTACACAAACACACCTGCAGAGGCTCAGGCCATTTTAGTGTTGCACTCAAAGG + HHHHHHHHHHHHHHHHHHHHHHHHHHHHGGGGFHHHHHHHHHHHHFFFB@DBEHHHHBDDCFE9:6>EEF @read_150_478/1 CAAAATGAGAAGGTACAACCTCTTCCAATGTGTATTCTGTAAAATCTAACCTAGTAGTCCCCTGTCTATACAATGTGTTACTGAATCTCTGAATTAACCC + GE6<:6:2@@=FGGGHHHHGD9@DA;8>GHGFHHHHHFHHHHEFGGFHHHHHHHHHHHHHHHHFBHHFF@FDFFFEHHHFHHHHHHE?EE>>55<8;5-? @read_150_478/2 TACTTACAATAATGACTAATAAAGATAATAGGACATACCTCACCAACTAGGGGGTTAATTCAGAGATTCAGTAACACATTGTATAGACAGGGGACTACTA + HHGHHGHHHHHHHHGGHHHHEFHFHHHHHFHHDFFFHHHHHHHHHHGHE@4*2(((08EE@@DFHHHHHHFGEHHHHF7EGGGGGGHHHGGHHF@<;BHH @read_150_479/1 AACACTGGAGCTCCCAAATTTATAAACTAATTACTACTAGACCTAAGAAATGAGATAAATGGCCACAAATCCATTTGCTAATGGACTTAACATTTGTTAA + HHHHHHHFFHHHHHHHHHHDCDGGEB>7EEEGHHHFFGFFGGHHFC0@-5GE??DAEGGHHHHFHHHHHEEHFDBHC?<>@ @read_150_479/2 ACCTGTCTAGTGCTGTCAGTGGAGTATTAAAGTCCCCCCACAAATGGACTTAACATTTGTTAAGTGATTTATTGTTAACAAATGTTAAGTCCCTTAGCAA + HHHHHHHGGHHHHHHHHHHHHHHHHHGHHHHHHFB=?;ADFFGGHGGFHHHHFFFDCEHHHE@D@GDGGIHHHDFFFB485EHHHFHHGB8>,DEBFE2- @read_150_480/1 GGTACAGGTTTATGTACATATTGAACTACACTTTTTGTCATTATCTTAGAGTGTACTCCTTCTACTTACAAAAAAAAAAATACAACTGTAAAACAGACTC + HHHED=BDGBDECDEDGHFHHHHHHDDDEHHGHHHHHHFHHEEED@BDDDBBFFFHFA5AFBBGHHC<9?FHHHHGFGGEHHHHHHGFFABCECD98399 @read_150_480/2 TATTTTTTAAACTTTTTGTTAAAAGTGAAGACACAAACACTCACATTAGGCTAGGCTTACAGAGGGTCAAGATAATCAGTATTACCACTGGAAGGTCTCG + IFHHHHHHHHHHHHHHHHHHHHBEEEEEEGGEHFDHEFDHHFFEFED8?BEGGGGGGG=EEEB8*/:6,2)749EG @read_150_481/2 CCCCAAGTGTTAAAAGCTGGACACACTCTTAGACAAAATGAAATAATATTAGCAATGTTATTACAAACTTCAGTTATAACCAAAAGCAAATCATGAACAT + HHHHHHGGGBHHEFC@D9523',::@BEGGHHHHHHHHHHHE?GHH@EBHHGGGHHHGGGGHHHHHHHHHHEFHHHHFDDFCEEBCFEFGHHHBDCC%,. @read_150_482/1 AAAGTCTGAGGCCCTGAACAACAATTCCCAGGATGTCTTAAGTCCTGGTTTCCCATACTGATTCACGTTGTGCCCCAGTATTGGGAGTCATTGGATCCAC + HFFEFGGFGGGGGHHGFGGHHGEHGGGGGHHGCDFHHHFFDHHHHHHHDDAC?GE;A? @read_150_482/2 CCTCCACTTTGGGCATCTGAATATCTGACTGAATGATTGTTTGGGGTGTCAAAACAGGCCTGGAAAGAGACTTAACTTCAGAGTTCAAGGTGCTCTATTC + HHHHHHHHE=@BC=DECBCCDFB@BBBH@EFHHHHHHHFHHHHGGGDGGE@CEEGHHHHFHHFEEGHEHHHHHFFHBEHHGGGHFFHHHHEF??GEEEF> @read_150_483/1 AAAGTTTTACTACAATGTCATTTTAAAGTCATAGATAAAAGTCAAGACAGTGGTTATTAATTTGAGAAAAAAATATTTTACAAAGAGGAAGTGTAGTCAC + GGGHHHHHHHHHHHHHHHHGHHFHHHHHGF.6AFHHHHHHHHHFDHEHHHHHHFFFE>9BBHHBCFF@@70:CC @read_150_484/2 CTGGTGTTACTGAGAACTTTAAGGCACTGGCCTGTTCCTCCACTCCTATACATCCCCCAGTTGGGCCTCTTGGCATCGCCTTAATATCAAGATAAGATCG + <;DHHHHHHHHHHHHHGGGGGBGCHHHF@=EGHHHHHHHHHHHHHFFDDDEFFFFFH=7>:GHHHHHHFHHHHHE>7,/;@95CDGHFHHFEFFFFB77@ @read_150_485/1 TCCTGCCAAATGGTCCCCATTGCCAGTCTTAGAATGAAATCCACCTCGTAACAGCTACCAACTGATCTGCCCCCAGGGAGAGCTGTTATTCCATATTTTC + EEEGGEGGHHHHHGEFFFFHHHHHHHHHHHHHHHHGGGEEGFEHHHHHHEFHFHHHHHEEECGHHHFDDFEEHHHHHBDHHHHHHHHDBBFCED694?EC @read_150_485/2 CTTATGGGGACGCTTTCAAGATGAATAGGATAATGCATGTATCTCCCATAGCCCTGCAGCCTTATGCTTCATCCTGTCAGTGCAATCTTTTTAGGCAGGG + HHHFGHHHHDECBFDFGFEEHHHHHGFHHHHHHHHHGEEEDCEHHHFFF @read_150_486/1 ACTGTTGCTTTTCTCTCCTCCTTACCCATTTTCCAAGCCTGATGCACTTCTCAAGATCCAATCTGAATAGGTGAATTTACCCTTGACATACACTGCCTTG + HHHHHHHGGHHHHHGEB@B<@C@EDGEEHHHEE?FF?@BEGHHHHHGG9AFHH?B?9EEHHHHHFDCHHHHHHHFHFFFHHHHFGHHHHHD=FGGHHHFH @read_150_486/2 GCGGGGCTGGGGGGAGACTCAGGCAGAATTGTGAAGATATTCAATTGCTCCTGACTTTATCAATAATCTAACATTTCAACCTAACATTGATATCTATTTT + HHHHHHHHHHHHHHHHHHHHHHHHHHHH?AGEGHHFHGHHGHHHGD??B=EEHHGEGGEFCCB>,15793<*15:5@BEFFFEFH9@@DBD9->@BCEGFHHHHHHHHFDBHHHHD@:9?/;A2:@.=@;D=D>8@555=BHE @read_150_489/1 TTTCATGTTTATTTCTCAGTTCCCCGTATTATATATCTGCACAGTGTGGAAGGGAAATATGCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAC + HHHHHHHDGHG@BEFHHHGGHHHHHHHHHHHHFFHEEEGFHHHEHHHF@GHHHECHHHHCDEFHHHHFFDFFHHHGG@CGHGBCHEGHB?AA@@=6<2FD @read_150_489/2 AGCATATTTCCCTTCCACACTGTGTAGATATATAATACGGGGAACTGAGAAATAAACATGAAAAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGAAGAT + DEHHHHFHHHHHBHEHHFCC<.@C8CDGGGHHHHHHHHHHHA9<>?CFEFEEFGGHHHHHHGGFHHGFHHHHHHH8GHEBADDB?@C9EGHH:6A%'1>B @read_150_490/1 CACTGAGGAGAGTTTTATTGATGTGCCTGGCTTTACATAGGAAAAAAAAAAACCTTCTATGTTGAGTATTAAAGACACTTGAAAAGATCGGAAGAGCACA + DDEGBEFFHHHHHDDEGFGHHHHHHHHHHHHHHFHGEDAA4--2::GBHHDFFADFHHHHHFDDE??FFFEHHFABDBHHHFHHHHHHCHFHHGGFEEEE @read_150_490/2 TTTCAAGTGTCTTTAATACTCAACATAGAAGGTTTTTTTTTTTCCTATGTAAAGCCAGGCACATCAATAAAACTCTCCTCAGTGAGATCGGAAGAGCGTC + HHHHHHHGGHHGHDDHHHEHFHHHHHHE8EFFFEGHFBEFHHHHFHGGGDCBEHHFGHFEHHHHHHED@GHHD=CDDEADEGHHF85.=ACFFFHGFD@? @read_150_491/1 GAATAGGAACAGCTCCAGTCTACAGCTCCCAGCGTGAGTGACGCAGAAGACGGGTGATTTCTGCATTTCCATCTGAGGTACCGGGTTCATCTCACTAGCG + CBEEE@ADDGGGGGDBCGHHHHHHHHHGEHHHHFGHAC@?C9DDFEFHHBHHHHHHFHHHHFHHHFGGFHB7%%CEB:;@FD;ADFHHHH2.;2,4>EFHHHHHHHHEGDGFFHHHHHG@AGE?B7GHHFE3< @read_150_492/1 CGAGTATCTGGGATTACAGGCACGAGCTACCACGCCTGGTGAACTTGGACACCTTGATGAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCATCTA + HHHHHHHHHHGGFEE=CFFECDDHHHHGFEGHHGHFGBDEEFBB?6?GGFHHFDDEEEGHFGHFHC;B?FFFFFHFFHHEGGGB@CBHDHHHHH;<.738 @read_150_492/2 TCATCAAGGTGTCCAAGTTCACCAGGCGTGGTAGCTCGTGCCTGTAATCCCAGATACTCGAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGAAGTTATC + HHGGHGHGHHCD@FHHHGGHHHHHHHHDE9:>6=AEEHHFHFFHFDFFFFGGGBHHGHHHHHHFHHHHEE@D=EDEG9:.@=@.*8.8F8:&-2-&158: @read_150_493/1 GGCTGGAAATGTCATATGCCCCAATAACATAGAAATAATAAACTTTACCATGTCAAAGGTGAAGAAAGATAGTGAAGGTAAGGAAGCCTCATTAATTACC + HHHHHHHHFHHHHHHHHHGEHHHHHHHHHHEFHGHHHGHHHHCHGADFHFEEFH>DFA@CFHFHHHFHHFEE9CDHHHHHHHGGFFHHHFHHHHH@7CHF @read_150_493/2 TCCTCCTTACTCTACCATTGCACTGCTAAGTAGGCTTTTATTTTGCTGTATTTGCCACCTTTAAAATTTATCCTTCGCATCGTAGTCATAACAAGTGAGG + FHHHGEBEHHHHHHHGHHHHHHHHHHGGGHHHFFDHHHBFFHHHHHHHEFHHGHHHHGCECAGGHHHHHHFHHCEEEFFFBFGE2:?C@@?FFBEC==?? @read_150_494/1 TGGGGATAAAATATGGTAGGGAATATTTCAAACAGAGCATTCCAAGTAAATGCAAAGGCCCAGAGGAGAGAGAAAAACGGGGCATCTTCCAGGCAGTGAG + EGGGGHHHHHHHHHHHHHHHHHGHHHHHDEEFEFFC:29,;84+790AHEHDBHHGHHHHGHHHFC8>9DD?@A<@CDCAHHHHHHFBDHHCABHCA*4ACDBD @read_150_495/1 TCAGGAGGCCAAGGTGGGAGGATCACTGGAGCTCAAGAGGTCAAGGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCACCTAATCTCGTATGCCGT + FFFEFFHHHHHHHHHHHHHHHHFGEDFEDDEHHHHHHFGGHHHFEF@EFD@DFHHFEA?7A5/.E3ABDHHHH?EGGBDDFFE,2<2AC7FGEEHFFHHH @read_150_495/2 CCTTGACCTCTTGAGCTCCAGTGATCCTCCCACCTTGGCCTCCTGAAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTAT + HHFIGHHHHHHHHHHHHHHHHHHHHHEBBCHHHGFFHHHHEED=6C@FGGGBEGBCCDEEFHHFFHHHGGGGEBECHDGHHHHHHHHEHFHHHBHHHHBHHHFFDC0CEFHHHHHHAA @read_150_497/1 GAGTGGCAGCAATAGTTTCCCAAATTTCCTTTTCCTTTTTTTTTTTTTAACAATCATCCTCACACTGGATTCATTTATCTTGAGGTGGTTACCAACCACA + HHHHHHHHHHHHHGBFFHHHGFHHHHHHHHHGGD-CGGGFEDHHFFHFHHEGHHH@GHHHFFHF=B<;@FA:<;CFGEGGDHHEE?CFHHHHHHHHD @read_150_498/2 ATTCTGAGATTTTAGTGCTCCTGTCACCCAAGTAGTGTACATTGTACCTAATATGTAGTTTTTTTATCCGACACCCCTTCCACCTTCCCACTTCTGGCTC + HFGHHHHHHHHHHEFGGF@FHHHDCA>GGGCDEHFHHGFHHHHHHHHFHF?.EEE=CCDGHHHHHGGGFHHHHHEHHH@HFHHFBE<=@>08><.::*4; @read_150_499/1 AAAATTTAATAGGAAGTACTCATGTCCATTTATATCAAATCATAGAAGAATTTCAAAATAAGTAGCGCCATATAGAAAATGAATGTGAACACATTCTCCA + HHHHHHHHHHGGGHHHHHHHHHFEHHGDGFFHHHEGGFFHHHHFBFFHHHHHHHHECFBFFHHFFHHD9:@FFHHHHGHEFFHHHHFHHGEDEGHHHH=@ @read_150_499/2 TTCTTTTAGGGTGTGTCTCTCCTTGGAGAATGTGTTCACATTCATTTTCTATATGGCGCTACTTATTTTGAAATTCTTCTATGATTTGATATAAATGGAC + HHHHHHHHEHGFEFHHHHH>GFHA6CDBHDHHE88CAHHHHDGD=@..7ECGGGHGB8>?BEEFHHGGFCCGGFDE62@>=DBBAFHFHFFGHHHHEFF6 @read_150_500/1 ATGTCTGTTCATGTTCTTTGCCCACTTTTTAATGGGGTTGTTTGGTTTTTCCTTGTAAATTTGTTCAAGTTCCTTATAGATTCTGGACATTAAGTCTTTG + HGFFFHHHHHHHHHDFDBDFGGGFFDA9DDBFHHHHHHHHHHGHHHHHHHHHHHHFHDHE5EEFFHFBHGFHHHHHHFGHHHHFHC<>EBEEGHGGGFHH @read_150_500/2 ACAGAATGGGAGAAAATATTTGCAAACTAGGAGGGGAACAACAGACAAAGACTTAATGTCCAGAATCTATAAGGAACTTGAACAAATTTACAAGGAAAAA + EHHHHGDGEEGHHHHHHHHHH@@BEAHHHHEBFHHHHHHHHHHHEHHHHFHHHHHHHFHHHGFDHHGGE>B@?GHFE?ACEHHHHFDHHH<59FFEFEEGGGGCCCGHHGGGEFFFFHHHHHHGECE@@B9FHHEFHHFFB=BEHHHFAADDFEFDCEEF95DGFBCGGGGFHHHHH @read_150_2/1 ATCGCCTGCAGGCAGGGAAGTTACTCCGTCGTAGTTGGTTCTCGGGGCCCACACTTTATCAGGCTCGTGCTGGAGCCTGTGTGTCCCATAGTCCCCTCCT + HHHHHHHHHHHHHHHGGFHHHHHFFHHHHHHFGGFEEHFFAED8@<6ADA?82D?GGHFHHFFEAFHHHGDBHHE>@<1B6;C>2.7?FF??ECF=:4>CDFCA?CEE=A.+6:5//2.9 @read_150_5/1 AAATTATGTGGAGAAACACCAAGGAATCAGACATGTGAGTAAAACCATCTTGGATATTCCAGCCCAGCTAGCCACCAGGTGAATGCAGCTGAGTTATCCC + HHHHHHFFFHHHHHHHHHHHHEBBHHHHHHHHHHFHHHHHHHHAD6':FDFFHFFFBECFEDGB>EC@CBFFBEFDA?@DFFHHHHHHGFEHHHHHHHHE @read_150_6/1 CATTAACACTGGAGCCAGATTGTCTGGGTTGGAACCCCAGCTTTTCCACTTACTAGCTGTGTGATCTCAAGCAAACTGGGCCTCAGATATCTTGTCACTA + F=?7<>>EFGG?9:>FFHGGEB@=GHHHHHFGFFE?9EBHHHH>4->D9<9@DDEHHHHEDHHEHEHHFEEEFHD9/4F4=FFHHHHHHHHHFGFDG@DCBDDHHHHFDEECFFDDEEFHCCFBCDCFHHBFBDAFFHHGGHHE=BGG@DDDG<.D @read_150_8/1 TGAATAAATGTACAAATGTCTCCCGTTACAGCTGCCACATTCAGTGGGGTAGGTCTTATGATCATTTCTCTGAGGAAGGGTGCTGTGCTAATGGTCTCAG + GGGGGFEHHHHHHEGGBGHHHHH<>EEHC@BFHG@AFGFAEF8DAFG/EHFD9ACHHHHHHHHHHHHHHEBBECFGDHHHFCGHHH9<4%0:9:5+?>:6 @read_150_9/1 GTGGCTCACGCCTGTAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCACCTAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAA + @GGGGHHHHGFFHHHHGEFFFHGGGEGEHHHHHFFGGGECED:EBD?CBHHHD5.CEHHHHHHHHHE,@@>?>@@EHHEE62A>:ADDEG?:;AB>9?DF @read_150_10/1 TATATCTTTTTTTTTTTTTTTTTTTTTTTGAGGCAGAGTCTCGCTCTGTCGCCCAGGCTAGAGTGCAGTGGTGAGACCTTGGCTCACTGCCAGCTCCACC + GGHGGF?@DEEDGHGEDGD7*009DGHHHHGBCDGEGHHHHHHHHHHEGGHHFGGGGFHHHHFHHHFECC<*0.87'.+-91931BDBBGDFDDBHGGF? @read_150_11/1 ATTTCTTTCTTTCTTTTTTTTTTTGTTCCTTTGGCTAAGTAGCATTCGTAGTTTGTTTAGCCTTTTATCTGTTAATGGAACTTTAGGTTTTTTCCAGGTT + HHHHHHHHHHHHHHHHHHHGHHHHHHHGGGGGGHFDCHHHFFFFHHHFHHFHFHHHHHHHEHDFDFFHFHB>A@?GGFHHFFAAFFHHHHHGEFFCHFGF @read_150_12/1 TGCCTTCCGCCGTGTCCCTTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCACCTAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAA + HHHHHHHHHHHHHGGGHHHHHHHHHHGGDDGHHEEHFHHE14CB@DEFGGDFGEHE@;9D??DEFDF58DDBDDG=ADBDFGGGHGGHEEHEHHFHHFCD @read_150_13/1 TGTATATTATGCTAATAATCAATGTTTTATGCTTGGCAGTCTTCCATGCCCCGAAGATTCCTATACCCTTAAGGTCGCAATTGTTCGAGTAAGCTGTACG + HHHHHHHHHGHHHHHHHHHHGGHHHHHHHHGGHGGHHHFHHBFFGEHHHHEEHHHHHHHHHFGFHAEHHHHGFFHHHHHHHHDBHFHBEHFCHHFA3@DHFHHHHHHFHEEHHH@DFHHHHHFHHHHHHHHHHEAFFDBHHHHFFHHHHF @read_150_15/1 TAATATTTATGTTGGACTTTTATTTTAAAGAGTGGAAAGGAGCTTAAGGGTATCTACTCTGCCTAAAACAAACTATTAATCCTAAAATTATTTATTGGGT + HHHGHHGGHHHGDF:>7DBFEHHHHHHHHHHHGEEFHFHHHHHHHHEHHHFHHH>D?FFFFEHHHHFHFHHBEGFC>:=>4<7FHHFGHHHFDHGHEGHH @read_150_16/1 GTTGCTGGCATATAGACCCCATCACAGTATAGCACATTGCCTGGCACATGGGAAACACTAAGTATTTTTTAAGTAAATGAACAAACACATAATTTGACTT + ><@FFHHHHHHHHHGGGEHHHHEBFHGGHHEBFGFDBDHHHHHHHHHFB>?BGHFEA@CFE43;)9EHHHHFFHHHHFFFFHGHHFD@5@DGFGGFEB;A @read_150_17/1 CATGCAACTAAGAGTGAGCAGATATAGAATTGGGCCCAACATCTCCCGTGAACTTGGCATTGTAGCCTCTACCCCACACTTTCTCATATCTTATTACAAA + HHHHHHHHHHGGHHHHHHHHHHHHHHHGEGFHGGFFEEGFHHHHHHHHHHHHEFHHD<18;8EEEBFEFFGEDDEFFFCFGFG?B@DHHGFGDADGHHHF @read_150_18/1 GGTGCGTGACTGCAGTCCCAGCTACTCAGGAGGCTGACGTAGGAGGAGCCTTTGAGGCCAGGAGGCAGAGGCTGCAGTGAGCCATGATTGTGCCACTGCA + HHHHHHHDHHF?GFFFGEEHBBG9=EGHHGHHHDC:7-00@BHFGFFFFHHFEHHHHHHDGGC<@FBHH @read_150_19/1 ATATATTTTTCCTGTTTGCAGAGTCAACATTTTTGGGAATGTCTCTGAGAATATTATTTTGAGGGTTTCAAAAGCACTCTGTTCATACGACGACGACCAA + HHFDCGGHHHHHHHGHHHHGFFFACFFGGGHHHEGHHHHHHHHHHHHCEEEEFDHHHHHHHHFHHFFFHHHEDFDGFEFF99<@DC>EFHF@B;2>;@.3 @read_150_20/1 GCTTGGTAGATCTTACTCCATCCCTTTATTTTGAGCCTATGTGTGTCTCTGCACATGAGATGGGTTTCCTGAATACAGCACACTGATGGGTCTTGACTCT + FHHHHFFHHHHHHHFFEFFHHHHHHHHHHHHHCEFBDHHHGE@ABDGFHFG=D?>DCHHFFFHB9::<;@DHCCAHGGGHHFFFC?:@.FHHHHGGHHF7 @read_150_21/1 ACCTGGACTGTTTTACCCCAAGGGTTCAGGGATAGCCCCCATCTATTTGGCCAGGCATTAGCCCAAGACTTGAGCCAGTTCTCATACCTGGACCCTCTTG + HHHGCDGFHHHHHHHHHGGHHHHGGFBFG>=GGEDFDDBFHHFHHHCHHHHHHFHHHHDEHHHFFFFFFDEBDCFEEEDFGEEEEFFFEEHHGGFEFHGD @read_150_22/1 CTACTGCAATGAAAACCAACAGCAATGACAGTAGGAGTAATTCAGCCTTCGTTGAAAACATGACATCAAACACACTCTGGTTTCCCTGAATCTGTTGCCT + HHHHHHHHHHHHHHEBDEGGDAHHH5CCGAEEFGC:BEBEAAEHHH?CFHFFFB:D=DCEE8378DDD=BBBECEHFHHGFFDGGFHFGF @read_150_23/1 GAAGAATTAATATTGTAAAATGAACATACTACCCAAAGCAATCTACAAACCCAATACAATCTGTTTCAAAATACCAATGACATTCTTAACTGAAATAGAA + 5=@EEGGGHHHHHHHHHHHFGFHHHHHHHFHHHHHHHGEEHHHHHHHHHHHHEGHEHHHHHH?DHHHHHHHCBCBGGGFHHHHHHHHCBHHHHF?678:6 @read_150_24/1 TGCCATTGCATTCCAGCCTGGGCAACAGAGTGAGACTCCATCTCAAAAAAAAACAAAAAACCTAAATAAATATAATACCAACCTTGAAGAGTTATGATCA + GGHHHHHHEGHHHGHHHHHHHHGGHHHHHHHH??5(D@78@DF=FECCHBDEEFDEFHHHHHHEFFCCEBFFGHHGFFD9DGFGFHHHHGHFFFFFHGHH @read_150_25/1 CTATTAAAAATACAAAAAACTAGCTGGGCATGGTGGAGGGAGAGGAATTGCTTAAACCTGGGAGGCGGAGGTTGCAGTGAGCCAAAACCGTGCCACTGTA + HHHHFFGGFFGHFHHHHHHHHHHHHHHHHHHHFGHFFHHHE/11,3@B631?EGEC @read_150_26/1 ATTAGTTCTTTAAAATTTGGTAGAATTGACCAGTGAAACTATCAGGTCCACAGCTTTTTTTTCGTTAGGAGATAATGATTACTGATTCAGTCTCATTAGT + HHHGDBHHHGFFFDDDFDDGHHHHHHHDADHHHHEFGHBHHHHHHF?HHHHHHHHHHHHHGGB;AFB@>FDFEEFGGGHHHHGBDDGHHFHHHHD/:++7 @read_150_27/1 GACTACAGGCACGTGCCACCACACTTGGCTAATTTTTTTTTTTTTTTTTTTGAGATGGAGTCTCACTGTCGCCCAGGCTGTAGTGCAGTGGCACGATCTC + GGGFHHHEHHHHHHHHHHHHHGGGGGGGGHHBEBFEGGGGGHHFFFFHFFHEHHHFFHHHDAAB@BCC6;?>GHHHGHHHEHEBFFHEHFAF @read_150_28/1 CCATTTTCTACAGCTTAGTTTTAGAACTTAAAGAGGAGTTCCCATATACAGTAGATTGGGAGCCACTGTTCTAGATCAAGTCATCATTTTTACTTATTGG + HHHHHGGEEEGGF??FHHGHHHHHHHHEEEFGGFHHFCHDEDDDDFE@;9@*FHHFFBGGFBEEEHHHHFF8)>@6(976DHDDBFFHHGGGGEFHHHGH @read_150_29/1 ACCACGAAGAAAGTTTAAAATGTTGGCTTTGCAGTGAAGTTTCCTGACGCCTGATTATCTTTGTCTGGTTTAAGAACATAATTGTTTTTCTCTTGTTAAT + ><<<;CDFGGG?DD<><D9BBFFEDEFHHHHHEDDFADFFGFCFF@9@D @read_150_30/1 ACCTGATCCTTGTTTACCAGGAGAAGCTCTCTGTTGCCTCAGACAATGGGTTAAGCCATGAAGTGCAAAGTGACCTGAGCTGTGTGCTCAGACACTGAGT + HHHHFFFHHHHHFFGGGFHHHHHGHHHHHHHHHCHB93(DAD=CDHFHEFCCBHHFEGGHHFHHHHHFHGHHGFFGGGGEEGGFBGEBFHEHHHHFHHBE @read_150_31/1 AAATACCCTTCTTAGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCACCTAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAA + HHHHHGFHHHHHHGGHHHHHGFD?EGHHHHHHHHHGHFFHFFFHHHHFEGEFFHHHHFFHE>9010>>>EBEDDEGGGHHHHGDD?FEEHFHFGGEE5BD @read_150_32/1 AAAGCAAAATGGTAGGAGTAAGCCCCTCTTTATCAGTAATCCATGCCCCGAAGATTCCTATACCCTTAAGGTCGCAATTGTTCGAGTAAGCTGTACGCGC + GEABFADB<>FHHHA639CGHFGHHHHHHHHHDEFFEGGFCHHEBFHHHHHHHHDEHHHGGFHEFHHHHFEBBFFFDDGGGHGFGEDC?EDFFFHA757; @read_150_33/1 AAATAGAGTCTCACTTTGTCGCCCAAGCTGGAGTGCAGTGGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCACCTAATCTCGTATGCCGTCTTCT + GHHHHHGGFDBEGFFG=EEEGEEGFHHACE=@B?>:>FEECHBEBFFEFFEFFFFHGFEEFHHEHHH=CCDFD6AFG @read_150_36/1 AGATGTTTAGGTTTCCATTTCTTCCTCCCCTTATCATTTCCTAACGTACCATAGGTTGACCATACTTCAAAAGCTGTACTTTCATGGCCACTGCATCGAA + HHHHHHHGHHGHHHHBDDFGHHHHHHCGG@EEDBFF@<9,3+BFHHHHHHHEFEFHHFHFHHFFHHHFC=FHHHHHHGHHGE@@4+4AG>;?AAA,%0=> @read_150_37/1 ATTAAACTAAAGAGCTTTTGCACAGCAAAAGGAACAGTCAGCAGAGTAAACAGACAACCCACAGAGTGGGAGAAAATCTTCACAATCTCTACACCTGAGA + HHHHHHHHHHHHEC@GHHHHHHHHHHGCD=EGGGHHHHBDGGGCHHFFHHHHBFHHHHCFHHFHDHG@89%028ADFGFDBGGHHHHHHHGHHEHBCEHH @read_150_38/1 TAAGTTCACAGTTTCTCTTGCGAGGTGTGGCAGCGCTTCCTGTTGTACAAGACAGATGTTGCCCTGGTGTTACATGAATCATCGTATCTCCCTCATTTAA + GHHHHHHHHHHHHHEGDFFHHHHHHHEDCHHHFFGEGGHGGE?A?EHHHHHHHHBGGEEHHHHHHHE:EEEEEFEGFHHHFGHEEGHB<45>>?@@FGGG @read_150_39/1 ATATTGACCTGAAGTTTTCTTTTTTTGTTGTGTCTCTGACAGGTTTTGGTATCAAGATGATGCTGGCCTCATAGATTAAGTTGGGGAGGAGCCTCTCTCA + EEEFHHHHHHGHHHHHHHHHHFHHHHHHEGGHHFDFHHHHHHHHHHHFFBHHHHFGF==F=>CF*:@>1>/30EHGGEHHHHHHEFGFEC @read_150_41/1 AACTTTCCATAGTTCCAACATTAGTTGCTACTTGAAACAAACAAAAACACACACGCACATACAACGAAACAATAATCTTTGGTGAGGTCTTGCTGATACC + HHHHHHHGGEGGGGEF=EEEDHHGHHHHHHGGGEEHHHHHHHHHHHHHHHHHHHHHFFFG;>E?HHE??EEBA.CEGHHFB @read_150_42/1 CACTAAAATGGCCATACTGCCCAAGGTAATTTATAGATTCAGTGCTATCCCCATCAAGCTTCCACTGGGTTCATACGACGACGACCAATGGCACACTTAT + GD?CDFHHHHFHHHHHHHHHHEFFHEHCEHEC==6.;>A;)'+>@::@3/:(2247@@AEGGFGFFDHHHHHHHF @read_150_44/1 AGCTAGAATGAACATTCTAATGTTTGAGTTTTGGTGACCGTATGCGGGAAACTTGCTCTGTGCCCGCTCCGTATGTCACAACAGTGCGTGTATCACCTCA + HHHHHHGGFDGHHHHHHHHHHHFGHHHHHHG=HHHGGHHFEGGHHHHHHHEB@CD<*+:?DC;<@@BCDFFHHFHHFFHHFHHGE7'*:+-+9=?HA711 @read_150_45/1 GGGCTAGTTCTTGGATTCATGTCTGGCATGTTATAGGTGGTTAATGAATGATTGTTATAATATTTACCAAATAGTGCGTTTGGGATAAAACATGTTTTAT + GGHHHHGGEEGGGHHHGGGGGEHHHHDD;;C@BFGGEED8:AEHHGGGECDFFGGHFEFHB,6B=AD<;CCHBECFFHHHHHDDFEFHHFHCDHHFDEBE @read_150_46/1 TGTGGAGGTTTGAATCTGGGCTTGGTGTTCTATCTTTTCTAAATATATTTTGATCAACTAAATCACTTTGAAGGCATCTGTGGCAAATAATATAGATAAT + EE=4?GGHGGHHHHHHHHHHHHHHHHGGFFDDFBHHHHHHHHFFB?CCFHHHFHEHHEB939CFFHHFHHHHBGHHGGHHGEHHHHHHHHFFEDFEGHHG @read_150_47/1 CACAGGGCCTGGCACAGATCAGTGCCCTGTGAAGGGCTATGAGTTGAAAAAATAGTGACCTAGAGTGTACTGGGTGTCTCACCCAAACTTCCCTGACACG + EGGBGHHHHHHHHHHGEHHHHGHHGGGBC9D@<@GHHEEGHFDEFDHHHHHHFHHFHFFFFF==EFC;9);?BFFDGEEEDFFHHHHGHHFHFAB45.76 @read_150_48/1 TATTTGTTTTAAAGTCTTTAACTGCTAAAATTAAAAGTTATTAACTCTGTATTCAACTTTTCTACCCAACCAATGTTAGTTTTGTTGTTTATTTTTTTCC + FEEEHGHHHHHHHHHHHHHHGGGEBDDDFFEB=BHD80//'+-1AFFGF@A@@@()>HHCE@+6DECDFHFEBBFHGFGHEFDHGHHHHGG@EHC>CD.E?B<<6@@B?EGDFFFBGGFGGGGFE @read_150_54/1 CCAGCAGGCCCTGATTGTGGGTTAAAAAGAGAGGTTGGGGAGGTAGGGGAAGAAAGAGGGAAGGTACTTAGTTCATACGACGACGACCAATGGCACACTT + HHHHHHHHHHGHHHHHHHHHGG@BHHHHHHHHHGGBFHGFEBDA?FEFGHHHHHHHFHFHHHFHHHHHEFHHFFE9DGGHHEFGGGHHHHHEFFHHHFFH @read_150_55/1 AACCCAAGGTATCAGAAGCTATAAAATGGAAACAATCATGCTGTGAAGCCTCAGTAGCAAAATGCTGACCAATTAATTCTGTGTATGAAAGCTTCCTACC + GHHFFGCGFGFFHHHFGGGHFGGGGEHHHHGGG?>FHHHFHHHHHGFGGHHHDFC>6>@BHHHF@CE?EFFHHHHGDDDBGFDB@FHHDEHH;<7*07?C @read_150_56/1 TATTCAATAGGTATGTAATCTATGCCTAAGGCTGCTAAGGTAACTGATGCTGATAAAAAAGAAATCTATGTTACTGTCCTCAAGGATTTATAAAATTCAA + EGFFHHHHHHHHHHHHDHHHHHFFFHHHHHGGFFHHHHHFFFFFCHEFHFEHHHHHBFFHHHB34/=D8?DDDDHHHGGGHHHFHHHHFHHHGG @read_150_57/1 TACTATTTGTCTGCTCATAACTGTTTTACCCATGTGACTGCATTAGTATACATGAGAGTATGTGTTAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC + HHHHHHHHHHHHHHHHHHHHHHHFHFHHHHEGGFFHHHHHHGGHBHHFF79DEHHHFBC9EEFHHHHFDHHHFFGHHHHH?FD>8=ADGEFEEBFHHHHG @read_150_58/1 TTGTTTTGTCAGTACTAATAGGTAAAACTTGTGTGACCAACATATCCTTTTAGCATGGAGAAAATAAATTTGCTTTTGTTTGTTCATACGACGACGACCA + GGHHHHHHHHHFHHHHHHHGHHHHHHHHHHHED@4?;=AAFGHHHHHHHFECFEHHHHH@CCGGFFFA?EHHHHFHHHHHHHHCHHHHHHHHHDCA=FFF @read_150_59/1 ACCTTAATGTGAGCAATGTCAGTGGAGAGGTGGGGAATGGAGGTACTCGGTATAACTGAATGATCTAATTTGCCGTAGCGACGTACTTCAGCCTCCAGGA + HHHHHHHHHHHHHHHGFHHHGEGGFCBB@=EFBHHHHHHHFHHHHFFE?;=>904CEHHHD;>/702=@?CAB;-BBEECHHHHDHHHGGEEECFFGHHH @read_150_60/1 TAGCATTTCTGTGCCCTTGGACATATTGGAGGACAGAGAAGACTTAGTCTCTGACCTTGAGAAGTTTAAAATCTAGAGGAAAAGACTATTCTGCAAAATA + HHHHFFGHHHHFF=DE=@FHHHHHHHHDGHHHHHHHHHHHHHHHHHHHHHEFEEEHHGGGFHHHHECFFEHFHHHHHFGEA>7EBFFHHHFBFGBHFFD: @read_150_61/1 TTCTTATAGTTCTGGAGATTAGGAAGTCCAAGATCAAGCCACCAGCAACATCCAGTATCTGGTGAAGGTGTGCTTTCTGGTTCACAGATGGTGCCTTCTA + HHHHHHHHHHHHHHEEGGFDHHHHHHHHHHHHHGGGHGFHHFHHHHHFFEGFF?DEEBBFFHHFEFBFFHHF>EBBEFHGGFG?DBD,)9>EHHHFHHHH @read_150_62/1 GTAACCCACCTTAACTTGTCATCATGACTGCTGGAAATGATAAGTAGTCCTTTCACTTATTTTTGTTTGTTTTTGATTTTTTTGTTTCTTTTTTTTTTTT + HHHHGGFGGFFGHHHHHHFGHHHHHHHFBFFG9EFEEDDAHHGHGHHHHHHHHGHBCC@FHHHDDGGEEHHGFHEBEEDDBFHFFHDFHGFHHDDCFGBG @read_150_63/1 ATTATATACAGTGATTATATGAGAATAGCCTTATTTTATGAGATACATACTGAAGTATTTAGTAGTTAATAGGCATTACATCTGTAACTTACTCTCAAAA + CBED6@FHHHHGFFFGHFGGGDDDGHHF@CDFDGAD@CC@HH8:,8'9)EHHBD*=CDFGGEDHHGECFHEFGFBEBDEFFHHBEFEFHHDFGGGGFGFH @read_150_64/1 GATACAAAATTCTTGGCTGATAATTGTTTTGTTAGAGGAGGCTAAAAATAGGACCCCAATCCCTTCTAACTTGTAGGGTTTCTGCTAAGAAATCTGGGGT + HHHHHHHHEGGDDDD@EE@BDFGFHHHHHHHHHFHHFHHFDDFHHHFFHHFHHHHABFA>0766=DFHFFFB:9>DCFHHHFHHH<*1&)+)7.*'&/)7 @read_150_65/1 GCCGAGGTGGGCGGATCACCTTAGGTCTGGAGTTCGAGACCAGCCTGACCCGCATGGAGAAACCCCGTCTCTACTAAAAATACAAAATTAGCCGGGTGTG + HGHHHHHHHHHHHHHHHDDFEC:=FFCHHHHHHHHHFBFFHHHGHFFGHHFGHHFD8?C4EHHHHHHHFHHGFHFE?FGGGGHH @read_150_67/1 TGTAGAACGTGCAGGTGTGTTACATAGGTATACATGTACCATGGTGGTTTGCTGCACCTATCAACCCATCATCTAGGTTTTAAGCCCCATATGCATTAGG + HHHGGGGHHHHHHHHHGHHHHHHHHHHHHHHHHHHHGHHHHHHHHHHHHHEGGEHHEHGGHHHHHFGHHHDEBECDFFDE87B;9CFF?ADADFEFE9*2 @read_150_68/1 AGAATAAAATATTCATACATGCAACAACCTGGATCATCCCTCTCCAGAAATTATACTGAGTGAAAAAAGCTAATCTCAAAAGGTTATACACTTTATGATT + EEGGGGHHHHHHHHHHHHG8BD8FHHHFDA=EEFGFHHHFFHHHFEDB5GFH??EDHHHHFEFHHFD@<786EEDEEEEFEFBHFHHHCCGFEHHEBF9C @read_150_70/1 TGTATTAAAAATGTGGACCACAGTCTGTAGGACTGTAAGAAAACTTGCTCTGTGCCCGCTCCGTATGTCACAACAGTGCGTGTATCACCTCAATGCAGGA + HHHHHGGEGGEEFHHHHHHHHHHHHHHCBD@F@77AEEHGHHHHHHHHEFHHHHED;=42BG?EEEFHHFEFGHCGGGGHHHHHHHGGGHHHBBB5>>0) @read_150_71/1 TATGTTTCATTTAAAACACCAAATTTTAGGAAAAGTCAATAAAATGTTAAGTGATGTTAATGCTGATGACTATCCTGCAAAATAGAGGTACTTATTCTGC + EECDFGHHHFFFEHHHHHHHHHHHHHHHHHE*;@BDFGGEHDCF?;FHEG181AA*9,CDAA@GFDEE8;(/>DBFCFGGHCFEFHHHHHHHHHHHBBHH @read_150_74/1 TATCCCCAAGGGGCATCACTCAGCACAAACTGAGAAGCAGCAGTCCTACCGCTGGGTTGTAAGTATGTGGCTTTATTCCGGGGTTCTCTATTCCATTCCA + HHHHHHHHHHHHHHHHHHHHHHHFFHHGGDHHFFHHHHHHHHHGHHHHEGEEE92@CHHHHHHHEGDEEC=25C;GGGEGHHHHBFGHHHHHHHFHH>.@ @read_150_75/1 GTTCCATTGATCTATATCTCTGTTTTGGCACCAGTACCATGCTGTTTTGGTTACTGTAGCCTTGTAGTATACTAATTTGCCGTAGCGACGTACTTCAGCC + HHHHHHHHHHHHHHHHHHHHHHHHHHFHHHHHHHHHHHHFHHHFC@@DA=:DBHHHHGGFFBEB6,%5/6 @read_150_76/1 ACACAGAAATATTAATAATATGGCTTGATTCCCTTAAACTTTTCTATATTACGTTATAAAACTTTCCAGAGTTTCAAGATGTAGACTAGAAAAGGAAACA + HHHHHHHHHHBBDCGG?><9FHBEFHHHGHHHHHHHHHHHFHFE<>5@?HHHFHHHEGGF=GGGEGEBF@FC>9DEE>FHFDFHGHHFHHEGDFFEEHHH @read_150_77/1 AATCAAGGTGTGGCATATCTCAGCACTCTGCCATGCCCCGAAGATTCCTATACCCTTAAGGTCGCAATTGTTCGAGTGAGCTGTACGCGCCCATAAAAAA + HHHEGGHHHHADCFHHHHHHHHHHHHHHHHHHHHHHHDECFHHHHHHHDDFDFFHHHFHFHFHHFGGHHHC>AD<<0'.@DECFHHHHHHHHHH=DFHHF @read_150_78/1 AGGAAAGCGCAGTGTCCTTGAAGCCAAGTGAAGAAAATGTTTCAGGAAGAAGGGCATGATCAACTGCATCAAATGTTGATAGGTCCTGATCAACTGTATC + GHHHHHHHHHHHHHHHHHHFEDFFFCHHHHGEFFHHHGGFFFGGGCFGDDDGGHHHHGHHFFHHHHFFFBEB>BBGGGD<*10.4(72>7(-87DD @read_150_80/1 GCCTCCCAAAGTGCTGGGATTACAGGCATGAGCCACTGCACCCAGCCTAATTTTGTATTTTTAGTAGAGACGGGGTTTCACCATGTTGGCCAGGCTGGTC + HHHHHHHHHHHHHHGGEEBHHHEHHGGGGFEFGGFHFEHEHFHHEEHHFFGFHHHF@548GGGFFDGFDEAAA6:EBBEEGHHHHHEBD7@@=BEHHHFF @read_150_81/1 AGAAAAACAGACACACAAAACAACAGAACAGAATAGAGAGACCAAGAATAAATCTATGCTCTTACAGCCAACTGATTTCCAACAAAGGCATCAAGAACAC + HHHHHHHHHGFFHHHHHHHHHHHHHFFFEHGGGGEHHHHHHHHHHHHHHG=A@5?DHFGEHHHHHHF?EF@B@BBEBEGFHHHHHHHHHHE@EBBABF@: @read_150_82/1 CAAAGCACCTCTGGGCATTTTCATAACGACTCTTCTTACTGTTTGGGCTATAAATAGCCAGTGACTCTGCTCCACACAGCGTCCCCAGCCTAAGCCATGC + HHHHHHHHHHGEEEGEFHHHABEEEFFFF@FGIGHEE=@GF??DDHHHHHHHFFHGH??BCHHCHHHGEHHEGEF@EFFHF8>4C<2CDFHBFGDDAGHHEFHHHGG@GGFFGFF??DC=;@ @read_150_85/1 GCACCTTTTGATGTGTGGCAGGTAGCTCCGGAAATGATTCTGAGTATAGAAAAAAAGAATGGATCCACAAAAGCAACTGGGGTGGGGGGAGTAAGCTAAA + HHGGGFHHHHHGGBFFHHFGDBFHFBHHHHHHHHHHFHHHHFHHEHHHHHHHHFBEEGGHHHHH;7FHFHHHHHHHHHHEB=8DHHHBBB,*2-FHHFHE @read_150_86/1 TCCTCAAATAAAAATTGAGAACTTTTACAATATTTATCTTGGAAAAAAACTGAGTTTAACTGAAATTTTCTTCAATGAGGAAGTCATTCTGGTGATGGCG + HHHHHHHHGDFGHHHHHEHHHHHHHHGFHHHHGGGGFHHHHHHFGHHFHHEGFECDHHBD-@EHHHHFHDD?CB<;DHGEDFFFFGBDGEF?B8GGCBB6 @read_150_87/1 GGAGTTGTTAAAATCTCCTAACACCTGAAACCCACCTAAGGCCTGGATCATAGAGGAGGCACAATAAACATTGAATGAGTGAAACTTGCTCTGTGCCCGC + HHHHGHHHHHHHHHHHHFFFBCEHGGGGF=DHHHHHHHHHHHBHHHHHHHHHHCHHHHHGFFEGHHHEEBHHHHCDDDF?FHHHHHFHGEHHEBCFHHHH @read_150_88/1 AGTTTAGTTGGCAATCCAGGGCAGTCTTCATCAAGAAGAAAGATGGAAAGGTAGCCCTCTGTAATAACCACTAGCTGTTAAATTTGACCACCATCTGAAA + HHHHHHHHHHHHHHHBGFFHHHHHHHHGGDGGHHHHHHHHHHHHHHHHHHFHHFDD>>HHHHHHHEFHHGHHHHHGGGGHHHHGGHHHHFFHHHHHHHE? @read_150_89/1 GTGGAGAGTTACTGCAACAGGAAAGGCTTAGTGGGTAGAGACTAGAAATGGCAAGTATAAATGACAAATCTAAAAGTGACTGGACAGTACTAGATTGGGT + HHGGDEHGGBDGHHF9::>@9;=@DEDHB@GHHHHHHHHHHHHBFFFHHHHHGEFFHBBECDDEHHBB??9EE=+<@EEBEDDFHGG=,?@DFHHHHHHGGHDDDCFFGGHDDCA? @read_150_91/1 CAAAAAAAAAAAAAAAAAAAAATACACACACACACACACACACACACTCATGCACGATATAATGACATTTCAGTCAATGACAGATCAGTAAGATTATAAT + HHHHHHHHHHHHHHFHHHHHGDDHFHHHGFHHEECDFHHHHHE?DEFB?>CEHHHH@AHGHDCHHHHHHHHHE6:DADGHHHFDDFFFEHHFEEEGDGC@ @read_150_92/1 CCAGTCTTCTTTACTCTTCATTATGGACTTCATCTTTGCTGCATTCATATTCCCCAGGACTATCAAGTCCCATGTTGGCACTGTTCATACGACGACGACC + HHHHHHHHHGGEFGG@EHHHGGFEFEHHHHHHHHFHHHHHHGFFFHHFEGFGEFFBEHHHHBC:B079?BC9EHEHHHGGGHCDCDEFFECC=?EB>.:A @read_150_93/1 CAAAGGTGAACTAGTGTCTTCCTCCAGGGCAGCGTTTCTCAAACACAGCCCTACTGACATTTGGGGCCCTAATTTGCCGTGGCGACGTACTTCAGCCTCC + HHHHGGHGDHHHHHF?=26>D>:>>BGHHHHHHHHEHHHHHHHHFHHHHEA??@;>BCFFADHE:;<=ADDEGFGDE,07FDGHHFBHHHHFHFFHH @read_150_94/1 CTTATGTACATGGTAAGACCAGTGCCTACCATGAACCTATCTTTTTTACCTTTTTAATCATTGTTTTTTTCTGATTTGTTTAAAATTATAGGAATATCAA + HHHHHHHHHHHHFHHHHHHHHEFDA3CHBD+<@GGHHGGGGGGFCEHHHHHHHHHFHHHFHFHHBC@DCB>@+82&-1159DEEFECFB@HFFFG?HHHH @read_150_95/1 CTGTCTCAAAAAAAAAAAAAAAAGAAGCTGCAGTTTAGAAGATGGCTGAAATTTTACAGAATTAAAAATCAAAGACTTTCACAAATTTTACTAAGAGCAG + HHHHGGGHHGHHHHHHHEGHGCCC7FFHHHHHHHFFFHHHHFGFFEEEEHHGHH@HGHHHB<:5A;FGG?5@CHHBE @read_150_96/1 AGAAACATTTAAAAACAGACTAGACCAGGCAGAAGAAAGACTCTCACAACTTGAAGATAGGTCTTTTGAAATAATGCAGTCAGACAAAAATTAAAAAATA + <=F@CEEEBGHHHHHHHGGGHHHHHHHHGDEDFCDGHHHHDDHHHHFHHHHCEFDHFGFCGGGHFHFDB?-667;DCCFD>DHHHHHFGG@BEEDCEHGH @read_150_97/1 TTTTTTTTTTTTTCTAGAGACGGAGTCTCCCTCTGTCGCCCAGGCTGGAGAGCCGTGGCATGATCTCGGCTCACTGCAACCTCTGCCTCCCGGCTTCAAG + GHHHEFFFFHHHHHHHGEEE@GGG@GGGE?GGGHHEEHHHHHEA<28.>>87<9>C;>14BBBHFHHHFEFHHHHFGGGGHGGHEE@CFHHHHHHDFFFC @read_150_98/1 TGCAACCTCCGTCTCTTGGGTTCAACAGATTCTTCTGCCTCAGCCTCCCAAGTAGCTGGGATTACAGGTGCCTGCCACCACGCCTGGCTAATCTTTATAT + GGGGHHHHHHHGGFFHHHHHGGGGHHGEEFGGHHHHHHHHHHHHEHHFHFGGFF>CC?GGDEGGHFHFFHEEEEEGGGBFFFHHEHHHHHFCCHFEGGEB @read_150_99/1 CACTCCATGGGTCAGATACTATTGCGGTACAGGAGTGAAGCATGGTGAGAGATCACTCCACCTGAGGTGGGTTCTGTTAGGCTTGGGGATATTTGAGACT + HHHHHHGGGGGHHHGHHHHHHFGEC@@1><6>72=D:;9<74>@.9DEGGBFHHHHHFHHHHFFECBD?=FGGGGD;FFFHHHHBC;;8DB=8>FGEEHHHH?;8DHHHHHHFBE:,3--3?8= @read_150_101/1 CTTTCTGAGAAGTTTATTCTTCTCCTTATTCTTAGTGCCTTCATCACTCTGTGTTTTGGGGCATTCTTTTTCCTTCCAGACTCTTCAAAACACAAACGCT + HGGEFFE@BB@EAACHHHHHHHHGHFFHHHH@FHHHEGBHHEHHBC877BGGHHHHHHHHHFGHHFHFCEEBEEDCFB,4:12CC5/DG@56@@<>=FHG @read_150_102/1 GGGGGTGGCAGACACAGCTAGGCCCTGTGGTTCTGCCCATGGCCTCCCTCTGGGGGAAGCCCTCCTTGACTACAACCTAGAGAGAGCTCCTGCACATACC + GEHHHHHHHHHHHG?<>B<<8:3BGHHHHHHGHHHHHHHHHHHHH?DHFFEB:9:ABBEDAFGHHHFEDDE4 @read_150_104/1 GGTGGAGTAGGAAGGAGGTAGAGGATGTTAGGCTGAGAAATGTCCTGTCAGCTTGGACATGGTGTTGGCCAAATTTTTTTAAGTGAAGAATTTTCATTTT + EEDHHHHHHHHHHHHHHHHHGGHHGHHHHE88DGBDBC4@E=>BCFHHFFFHGHHHHHHHHHHHH @read_150_105/1 ACTATAGGCACCCACCACCATGCTTGGGTAATTTTGTTGTATTTGTAGTAGAAATGTGTTTTCACCATGTTGGTCAGGTGGGTCTTGAATCTCTGACCTC + AAD76:BGEGGGHHHHHFHHHDGGHHHHHGEHFB>FHHHHHFHHHHHHHHHHHHHHFHHCEFCBCDDEFHEEEEFHFGHHHHGFHGHHHHG?EFG@4.1/ @read_150_106/1 TGAGTTGCATGGCCCAAAACCATACAGCTGGTAGAAATCCGAATTGAAAAGGAAGCAAGGGGTCATCTCAGTTAAGCCTCTCGCTTTACAGACAAAATGA + FHHHHHHHHHHHHHHHHHGHEEHHHHHHHHHCD-=3,8FFAD=B;AHHHEFHHHHGGD8CFHHEB:::;<8>?CDGGHB;9D@A>BDB?D>EGDF::>5- @read_150_107/1 AAGAAATACTCTGCTTAGCATTTGATCTGAACAAAGATATATTCCCTAATGGAGAAGATAGGGCCTTTCAGACACCAGAAACTAACTTCTAATTTAACTG + HGHHHEFFGHHHHHHHHHFGGHHHHGGFGGHHHHFECCDAGHFHHEHHHHHHHHE5@AC @read_150_108/1 ATCACCTGAGGTTGGGAGTTCGAGACCAGCCTAGCCAACATGGTGAAACCCCTTCTCTATTAAAAATACAAAAATTAGCTGGGTGTGGTGGTGTGCGCCT + GGGHHHHHHGGGF@BGFGGFFGGEDFFFHHFHHFHHHHHHHHHHHHHHHFFFEFGFEGGGHFEHHFHEEHHHFGHHHHHHHEEFHB8D@HB//.DHHHEG @read_150_109/1 CCTACTTCTACCCCTCCGCAGGTAAAGCAATCTGTGGCAGAGGAAGCACTCACTTTTTAATTTGTCTGTACAAGTCCATTAGACCTCAAGAGTAGTGTGA + HHHHHHHHHEEHHHHHFFHHHHHHHHFHHHHD@FHHHHHHHEABFDDFHHHHGGE;@EHFE?GHHHFDHHHFHEFHHHHHHFGHGHHHHFFD<@?55?BECEF @read_150_112/1 AACCTCCCAGACTCAAGTGATCCTCCCACCTCAGCCTTTCACACAGCTGGGACTACAGGTGCGTGCCACCATGCCCAGCTAATTTTTTTTTTCTATTTTT + HHHHHHHHHHHHHHHHHHHHGEHGGHHHHHHHHH@DHHHFB@DHBBFHH?@:1CHHF:5DFHFH>27:@5>?ADCDFE>(/;CHFFFC @read_150_115/1 TGGCCTGATCTCGGCTCACTGCAACCTCTGCCTCCTGCGTTCAAGTGATTCTCCTGCCTCAGCCTCCCAAGTAGCTGGGATTACAGGCACGTGCCACCAT + HHFFDGGHHHHHFFG=EHHHHEGFHBHHHHFGHHEFD(55@BFFFEFEEFHHHHHHHHHHFFHFFHHHHHHHEEBGGDFGFD?5>AFGCEEFHHHGHHE+9FA78;/*((? @read_150_120/1 TCAAGACCTCACATTCTCTGATTTTCAGGTTAAAATGAATAATGAAAGGAAAGGGAGAGCGTCTCTCTTTACAATGCTGGAACAGATGTCTTGAGTCTGC + HHHHHHHHGHHDDFDEFGFHHHHHHEEHGHHCDFDBFEBFEEHHFFHHEAFCCEBD@;6/1>EEFEHHHHHFHCBDEEEEFFBEGHGGGCFFFHBGDGGB @read_150_121/1 GTATTTCTCCTAATGCTATCCCTCCTCCATTCCGCCACCCCACAACAGGCCCCAGTGTGTGATGTTCCCCGCCCTGTGTCCAAGTGTTCCCATTGTTCAA + HHHHEDC@=GHHHHHHHHHHHHHHHGHHHGHHHHFHHHHEFHHDDHHHHHHHEHGD@HHHFFHHAE@FDHHFDFCGGGGHHHFGGHHFA>>@7>:E?27; @read_150_122/1 GGAGAATCACTTGAACTCGGGAGGCAGAGCTTGCAGTGAGCCTAGATCACACCACTGCACTCCAGCCTGGGCGACAGAGCAAGACTCCATCTCAAAAAAA + HHHHHHGGFGHHHHHHHHHGFHHGGHHHHHE7(2:-E?>EHHHHHDFHHHHC>FEBEEFHHEHHEB576;,<8@@EDBGEBBGGHGGFF @read_150_123/1 GTTTCCAACGAAGGCCACAAGATGTCAGAATATCCACTTACAGAATTTACCAACAGAGCTAATTTGCCGTAGCGACGTACTTCAGCCTCCAGGAATTGGA + HHHHHHHHHHHHHHHFHHGEHHHHHBCHHHHHHHEHEFHHHHFFGFFFFDCDBGHHHFHCDHHFFEE@EE=BA778<@@DCEGFHFEDEEFHHEE;FEE? @read_150_124/1 CCACATGCCTGCCCTACTGGCTCATCTCTGACCTCACTCTCACCATGCTCCTCTTCCTTCTAGCACCATCGGCCTCCTGGCACTCCCGGGAACTGCCTCA + HHHCGHGHHHHHHHHHHHHHHHHFG@>2HHF?E>B8-9<77=FFEGGHHHHEFGFHHHHHFFHHHFHHCHHFCD3.=:591*'.%1,>A>AHEHHD- @read_150_125/1 CCTCAAAATCCCATTTCTAAAACAAGATCAATGTGGACAGCACTGTCATGCTAATTTGCCGTAGCGACGTACTTCAGCCTCCAGGAATTGGACCCTTACG + HHHHHHHHHHHHHGBDHGFHHHGHHHGHDDGGHHHHHFHHHHF@B@;5AGG?GEHHHEGHHHHHHHFHHEEB=DD:<>7BGG??=A;BHE96>FCHFHHB @read_150_126/1 GGGCACGGTGGCTCACACCTGTAATCCCAGCTTTTTGGGAGAATGAGGCAGGAGTTTCGCTTGAGTCCAGGAGTTCAAGACCAGCCTAGGCAATATAGCA + =BDEHHHHHHHHHHHHHGGGFHHHHHHHHHHFFFHHHHFHHHHHHHHHHHGFHHHEDA@E?8CBBD9CEHHHHCFEEGFFHHHHHHHHF=EHHHHECFHH @read_150_127/1 TCCGTGTGTGCATCTCCCCTCTCCTACCAGGGGGACCTGGACCTGGAGCTGTGAGTCTTTCAGTGACATGGGGTGGCTGGAGTCTGTAGGGGCAGTGGAA + HHHHHGGHDHHHHHHHHHHHHHHHHHHHHHHHHGHHHHHHHHHHHHF>A?GGFFHBGGGGFGD:EEHDDFHHHHHHHHHHF?FFGGDBGGGHGHHHFGBC @read_150_128/1 TATCCCAGCGTTTCCCAAACATGTTGGCTTGTTTCTCAAGCACTATTCTATTTCACATGATTAATGTTCTGAGCAACATACTTGGGGAAATAATGTATCA + HHHHHHHHHHHFD?GFHHHHHHHCDABFFEDFFHHHBB7@EEBEHHHFHHCCEHHFFFHFHHHHCFFCFHG8DBDDEHHHHHE>BA@-, @read_150_129/1 CATTGAAAAAAATTAAATAATGTAGAAACATGGAAAATAAAAATGAAAAATTGTATTGTCCTCTTCTTCTCAGTGGCACACACACAGACACAGATGGACA + GFGGHHHHHHHGGFFDF.CDDGFGGHGHHHEFFD2AFHHHHHHHFHHHHHHHHHHHHHHHHHFGGDEHHC>EFEHBEHHHHGGBHHHF5EF @read_150_130/1 GGCCTGCCTTAGTCTGAAAAAATTTTTTACTTTCCTATGGACAGTACCTCAGCTTGGTCCAAAATATTTCCCCCATTACTGTTTCTGAAAAAGGATGTCA + HHHHHHHHHHHEFAAF>BGDEDCDA5@GGFGHHHBDDDDCBAB7*?@-)+;AHHCHG?:@@DHHHE?FHHG58:1>>5EEDCBCFHF?FHHHHHEBFFHH @read_150_131/1 TGCACGTGGATAATTTGACCACTTAGAGGCCTTCGTTGGAAACGGGTTTTTTTCATGTAAGGCTAGACAGAAGAATTCTCAGTAACTTCCTTCTGTTGTG + FFFFBCBDDBFGDHHHHHHHHHGHHHE@@?AFFGGHHHHEHHHFHHHHHHHHHHHFHHHHEHFEFB<6EHHFCDDGFGFEBBDEHHHH?FHGEE7DHFGEFFGHHFGGFFFFCBHHHHHBEFHHHDEGGGFHHHHHHHFHHHHFCD5GEE?8 @read_150_135/1 TGCAGTGAAAAACAAAAGGGGCTAAACAACTAGGATATAGCCTGTGGTTCATACGACGACGACCAATGGCACACTTATCCGGTACTTGAGTTTCAATGCG + GGGGGGECBA@FHEGHH?EDHHHHHHFHFHGHHHFHHHHHDHHHHHHHHHHHFEFEGGCFGHHADFFHHHHHDBHFHHHHGGGDD=AE%413DC>EFHHH @read_150_136/1 ATGCATTTTCAAAGTGGCCTAACATATTTCTAAATGTTTTATGCTGTTTTGTTTTTCAAATATTATTGTATAGACCACAAAACAATTGGAAAACAATATT + ><>@DEBEB7B?>CC@EGHHHHHHHHHFDFGCEGBH@:B:DCGFFGHHHHGGECEDFHBEHFHFGHHEHDEFHHHHHGEEEFF?@?:FHA @read_150_137/1 TCATCCTGTATTCAATCTAAAATCAAATTGTGTGACAAGAACTTTACTAAAATATATCTTAAATCTATCCACAAACTTGCTCTGTGCCCGCTCCGTATGT + HHHHHHHHHHHHHHHHHHHHHHHHHHHHFDGGGGIC<*DC>9>FEFHHHFGHHFGGGGFFHHFFCCFEEFBEHHHFFGGGHHHHHHGEFFD5?A+'&-.. @read_150_138/1 AAAAATAAAAGTGATGGAATCTAAGTACGGAACCCTGTTTCTGTTCCACACCTGCACACTCATCAGCTGTGCAACTCTAGTCAAGACACTTCTTGAAACC + 75GGGG=>EHHHGHHGHHHEHHFHHHHFEBFHHFB7>FHHHHEHHHH?DHHHHHHHHHFBDFHHHHHFEHDDDFD566;:AEHGH?BGFHHFHHHHHFHH @read_150_139/1 TGGCTATTAAAATGTCAAAAAAACCAGATACTGGTGAGGTTGTGGAGAAAGGGGGATGCTTTTATACTGTTGGTAGGAGTGTAAATTAGTTTAACCATTG + FFFEGGGFHFFEHDB@BBDGEHFHHGFDDHHHHEGFDDD;?BFHHHHF:>/906??DEDD02C?EFFHHDFHBFHHHHE@CDHHHHHFHGCD@CHCCB@E @read_150_140/1 ATTCATTCATTTGTTCATCCGTGTAGCGAATATTTCTTAAGTGCCTTACTTTGCGTAGCTGTGTGCTTGGCAGTGGGATGATACCAAAGATGCACAAGCA + GCAEECGGHHHHHHHHHHHHHHHHHHBHDB::GFHHHEGFGGGFBFBFHHHHHHHFHHGBEEFHFBDDABHHHFEEBEHGHG<7<=@@9B;?DHHHHHHH @read_150_141/1 TAGTTGGAAGTAAAGCACTCCTCAGCAAATGTAAAAGAACAGAAATTGTAACAAACTGTTTCTTATACCACAGTGCAATCAAACTAGAGCTCATGATTAA + HHHEEHHHFGGGGGHHHHHHHHHFF?HHHHHD63@>BG@CFEEEFHFHHBD=CE.FHHHHFHHHHAD93D);54.<:=FDDDCA?D<8BBB@9:?DF>AB @read_150_142/1 CACTGGGACAATAAATGTAAACCAACACTGGACCTGGAAAACTGGGACGTGTGTTTGCCCTATACCAAGGTAAGCTAGACACAGCCACTGCCTTCATGGA + HHHHHHFEBHHHHHFHHHHHHHHHFHHHHHHHFFHHHHB?:@DDEHHGHHHBC55<999*,CHHHHHHFBGGFHHHHHHHHFFHHHHHHHGFDGHHFFG? @read_150_143/1 AATTGAACAACATGCTCCTGAATGACTCCTGAGTAACTAATGAAATTAAGGCAGAAATCAGTGTTATTTGAAACCAGTGAGAACAAAGACACAACATACC + HHHHHHHHHEHHHHFGHHHGHFDHHCB@DDBFFGFFFCEFBCA=?EEFFFH@7DAE>A@;;8*2EED@B9@HHHFGGFFFEDBHHHHHE?D;:4EAADHH @read_150_144/1 GCCTCACACACTCACGCACAGAAGCAAGACACCCCACCCGGTGTGATATGGCCAAGCTTCTGCCCTTTAGCACAAACTAAAAGTGTATTTCGTATTTTTC + GE=CFEBCHHHHHHHHHHHHHHHHHGHHGEBGGGGFHHHHDD6+?9GGF?:@><5BA+@A>>>DAD??:=EEC=@E@FBBEFHEEEGEBDCHHHACC@: @read_150_146/1 TGACTGGAGAAGTGTCCACATGAGTCTGTGGGAGGCAAGAGTTGGGGGTTGGGAGGAGGAGAGGGAGAGCTCAGTTCATACGACGACGACCAATGGCAGA + HHHHHHHHHHHHHHHHDFHHHHH=EDDFFFDEE69@BGGDCEHHHEDF?HFFFFEHHFHFD4ECDCEECHFHHFFHHHHHHHHHEEEGGFE@&.);CC.4 @read_150_147/1 AGAAAAACAGAACTGGAGAGAAGAAGGGAAAGACAGGTAGATCAAACATTAGAGGGAAATACTTTGAACCTAATTTGCCGTAGCGACGTACTTCAGCCTC + GGEEDCEGGGHHEFD>EFGHHFHHHFHHCBGGHHGFFFEHHHHHHHHHFHHHHHHFFEHDCADBEA4'&)>EHHGFFGEHHHHHGFHGGGEFFHEEHHHH @read_150_148/1 AGTTATACTGTCATTATAAGCCACTTATCCATCCTGGCGGGGAACAGGCTCTCTCTCACCTCTGCCCCATGCACGTGCTATGGTTGTACCTGGAGCAGCA + HHHHGGGB/?GGHHHHHHHFHHHHHFDDEEFHHHHEGHHFHHHF;@3==FF5CEFG@CFFEDBHHHHHHCGGGHHGFFF59CDFFFFEEFFGGEGGHFHH @read_150_149/1 TCAGCTTAAGCTTGCCGGTCATTACATGGGCCGTATTTACATATGAAAAAAATTACTTGTTTATTTGAAATCCAAATAGCGCTAGCTGTCCTGTATTTTA + EDDCA@EFFHHHHHHHHHHHHHHGGGGGHFHEHHHHHHHHHHGFEFFEHHHHFFFHHH9EFE;:9EEBDEG @read_150_150/1 CCATGTCCCTACAAAGGACATGAACTCATCATTTTTTATGGCTGCATAGTATTCCATGGTGTATATGTGCCACATTTTAGATCGGAAGAGCACACGTCTG + GBA@;=EBDBBGHHHHHH@?CGFHHHHHHHGGDFFEFHEEHFDCBGHHFB3/68DD/7><;DCFEHECFHBFFFHHHHHHHHFHFEEGGFHEFHGFGFFGH @read_150_152/1 TCTTGGGTTGCCAAGTATTCTTTTCTTTTTTATAATATCATTTTTGTTTCAATGGAATACTGTATTTCCACTGATCATATAACATAGGAAATAAAATACA + HHGEEHHHHHHHHCDEHFHHHHFHHHHGGGGFHHHFHHHHHHFEHCFHHHFEFCHHHHHHHA6EEGHHFDFHHHHHCCEGHHHHFHHHGGFHEEF?EHF< @read_150_153/1 TGAACAACGTCTAAAGACCCAGAAAAGTTCACAAAATGCAATACTGATGTAATTTCTACATTTTAGAGTTTTAAACTTGATAATATACTTTTTTGAATTT + HHHHHHHHGBED4C>FFHHHHHFGHHHFHHHHHHHHHFFFGHFEHHEECHHHHFHGFFEE>BHFHGHHHFFHHHFFGGHHHHHFGHE>9*.=3>DF>9+= @read_150_154/1 TTTAGAATTTAATCCCCTCTGTGCTGCAAAACTATGCATCAAAAACATGGCATTCTAGCTGCTTGCTCTTTAGAGTGGGAATATCATTTATCAGACTTCA + HHHHHHHHHHFGEBAEGHHHHHHHHHHHCCB+DD4CHHHHHHHHD9A?FHHHFB:EFHHHD?BBHEHHEHBFHFAEHHFGGHHGHHHHGGGGBGGFE?CB @read_150_155/1 GCAAATTTTGTATAATCCAAATTTTCTTTTCTTTTTCTGGAGACAGGGTCTCCCTCTGTCACCCAGGCTGGAGTGCAGGGGTGCAGTTATGGCTCACTGC + HHHHHHHEFE?:GFHHHHHHHHHHFHHHGGGFBCHHHHHHE;>@4?CDFFHFHHHHFHHFECEEEHHHHHHGGFEHHHHHHHHHHFEEGEHHFE?AEHD. @read_150_156/1 GACTTCAAACTATACTACAAGGCTACAGTAACCAAACCAGCATGGTACTGGTACCAAAACAGAGATATCGACCAATGGAACAGAACAGAGCCCTCAGAAA + G=EFHHHHHHHHHHHHGFEHHHHHHHHHHHHHHHHHHHEDGFEEBDFHHHHFFHHHDHHHHHFDEHC@+BFHBAB@DFHHHHHH@HGFGFHHGGFHFDCDBCEEEGGHEBABGGFGG@DFFFHDF @read_150_158/1 GGGCTTAAAACTATGCAAGTTTATTATCTTATAATTCTAGGGATCAGAAGCGGAAAACGGGCCTCAGTAGGCTAAAATCAAGGTGTTGGCAGAGCTGTGT + HHHHHHHHHGHHGGG?DBCGHHEHHHFFGFGGD?CD?>:-%6%,AHHHHHHFFHHHHHHHHHEEABFGH?DFDD@HHHEDD6356>69A3EEFEH?:8?C @read_150_159/1 CAGGCATAAGAAATTATAAAAGTATTAATTTGGGGAACTAATAAATGTCCATGAAATCTTCACAGTCCATGTTCTTCTGCCATGGCTTCAGCCGGTCCCT + EFHHHHHHHHHFB@@CFGDHHHGGFGE8E:EFHHHFHHHBDDDFHGEDBHHGC@<95ADEHHF=DFDGGGHD@HHHHFFHFFFGEHFGGEHGFCFEHHGGHHHHHFFCHHHH @read_150_163/1 AGAAAAAATACTATCATCCAAGGAGGATCATAAGCTGATCCAATGAGATGCCTCGGACTGCTTGATCTTCATCTTTCAGTTTCGCTGGGCTAACGTAGTC + GGGGHHHHHHHHHHBHHHHHHGGHGGHHHBDDEHHHHHHCHHHFHFDHHEFHHHHHGHGHF6?E @read_150_164/1 TGGCAAAACCCCGTCTCTACTAAAAATATAAAAAATTAGCTGGGTGTGATGGTGCCCACCTGTAGTCCCAGCTACTCGGGAGTCTGATGCAAAAGAATTG + HHHHHHHHHHHHHHHHHGHHFHEA<=B@FFHHHHHHHHHFHEFGHHHHHHHHHHHHD??7BFHHHHHEC>4@7BEGGHHHHH@BCBFG=::):?AC-D1. @read_150_165/1 GACCGGGGAGCCCGGGGTGGGGCAGGGGCACCAGCTACATGTATGAGGTAGGAGGAAGATTTTATTTTCTACTGGTCAAATCACTTAATCTCTCTGTGCC + GGGGGDGGHHFFEEEHHHHGHHHHHHCG@EGEHHHGHHHFHHHCFBDGAF@CFFEFHHH?DEDDFECFHHHCAGF?.57FCEEFB=FFEDFB/ @read_150_168/1 GATGCAAATAAAGAGAAATTATGAGATAGAGAGGAGGTAAACTGAAAATCCAGTAGGATTGCTTTGGTTTCTGTAAAGTGACGAGAAAAAAGAAAAGGTT + HHHHHHHHHHHHHHFGGFHHHGDDFGEHHHA@@+6--59A>7DDDFHFFFHHHDGB::8199DDD=BH7;CFHHHHHHHHFAD8EFBBE9BFHHHHHFFH @read_150_169/1 ATGGTGTTACCTCTTCCTACTTCCTAAGCCTCTGATTTCTATTATATTTATTACATTAGCTAGAAATGCCCATCAAATTTTGAATAAAGGGCATTCATAT + HHHHHHFFFDHHHHHHHHHHHBB@@CDHFHHHHHHHHFEBEHHHHHEHHHHHEFHHGFFEHFHHFFD?@CCB::A277;?,?HHHHHHGHHHGGHHGDEF @read_150_170/1 ATGAAGAAATCCCGTTTCCAACGAAGGCCTCAAGGAGTTCTGAATATCCACTTGCAGACTTTACAATCACTAATTTGCCGTAGCGACGTACTTCAGCCTC + HHHHHHHHHHHHGEGFGGGGGDGBEFGGEFGGGHHHHHHGE@)7<2'BGHHHHHHFFHHHHHHEAFEHFHFHFFHHFGGHHHHHHBHGFF<99CEDDDCD @read_150_171/1 TTCAAGCAATTCTGGTGCATCAGCCTCCTGAGTAGCTGGGACTACAGGTGTGCACCACCACGCCCAGCTAATTTTTGAAACTTGCTCTGTGCCCGCTCCG + FFGGGGEEEDHHHHHGGHCGGHHHHHG6FFHCHHEEGHHHBA?EHHHHHFHHHEFC?FFFFHHFCCHHHBBBDFFFFGHHHHHDHEDEEFGHEHHE@6:0 @read_150_172/1 ACAATAATACAACAAAGAAAACCAACAAAGTGAAAAAATAAAAATAAAAACAAGTCTTTAAAAAAGACAAATACAGGGACAGGTGCTGTGGCTCATGCCT + GGGHHHGHHHHHHHHHHHGEHHHHHFAHHHHHFHFFGHHFFF@CDEGEHFHHHHFBAHHFHHHFGGHHHEFFGHB:B=>:,@EHCHFHHEADFHHHHFFF @read_150_174/1 AGTTCCACATGGCTGGGGAGGCCTCACAATCATGGTGGAAGGTGAAAGGCATATCTCACATGCCATGCCCCGAAGATTCCTATACCCTTAAGGTCGCAAT + HHHHHHHGHHHHFFHHHDCDFHHHHHGEGHHHHHHHFECHGHHHHHEHHHFFHHHHHHGEHFFF5BEFHHGGEFCFFE62<919FBEEEE?FHHHHHHEG @read_150_175/1 CTATTAGAAAGTTCAAGATTCTCTGGGGTTCTTAGGATTTACTGTTCCCAAAACTCTGTCAAGAACAAGAAAATGACCTGTATACTTAACTGGTCTAGGC + HHHHHHHGFGE=BCFFFFHHHHHHHHHHHGFGHEHHHFFFDHB?HHHHHHHDC@G=E8CCDHHDEEEBEFHHHHHGFGHGDFDDCCE?DHHHHCFHHHEEBADFD@EGEGGGBHFFA5HHHHHFEFFFFFGGGFGGGFFGFFC:9,7=BFHFHHE?<;DFBADEBDF=?DFHHFHBGGGCBHHE5< @read_150_178/1 GAGACCAGTGTGTGGGAACCATGTTGAGTGGGAGTGGGGGGCGTCCAGGCACTCTGGTCTGGGTGGTGGGACAGGTCTAGGGTCTCAGAGGCCCATGGTG + GGHHHHHHHHHFFFDHHHHHHHHHHHHHHHHHHHFBHHHHHFHHFGHEHCE9*CGEEGFHHHFFFHHHHHEHHHEGGGHHHHHFGGFFC>C@FFC<::D5 @read_150_179/1 AGATTTTCATGCTAAATCAGCTCTAATTTGCCGTAGCGACGTACTTCAGCCTCCAGGAATTGGACCCTTACGCACACGCATTCATGAAAAAAAAAAAAAA + FFFDDGGHHHHHHEEEFD=D7BDEFFFBFHHHHHHHHHHHHHHEFCDBEFHFFGGFHHFHHHGFGGHHEE @read_150_183/1 TTCTCCAATCAAAAGACAGTGGCAGAATGCGTTTAAAAAGTAGAATTACATGCTACCTACAAGAGACTCACTTAAGATTTAAGGACACACAGATTGAAAG + HHHHHHHHHHHHHHHHHHHHFFFHHHHHHGHHHHGHHHHHHHHHFHHHFFFHHHGGHHFFHHHBBEEEHHHFBADFHHEHHHHHFHHHHGGFHFD>BED= @read_150_184/1 AACCTGCCCCAGGACGTCCTGATCACTATTTTCTCCTGGCACACTGCACTCCACTGTCCCTTCCTCCGTCACTCCAACCCTGCCACTCTAGGGGCTGGCT + GGGHHHFBD87?EEHHHHHHHDGGHGGGDGGEHHHHHHHHHFFFFHHHHHEFHEHHHFDDHHHGCFEHFHHFHHEGGDDEBFGHHHHHHHHHHEEF?,*3 @read_150_185/1 TTTTCCTATTTTGTAAAATGAGGGTTTTATAACTCATTTCAGGGACAGTTACCCTTTATCCATTTAGGGTACTAAATTGCCGTAGCGACGTACTTCAGCC + 8D?:CCDDGFD=EGHHHHFGGHHHHHHHHHHHHHHHHGEFGFE?E<69CHHHHHHHHEFGHHH;<@FFDFDC @read_150_186/1 TCTTTTTTCTCTTTGCTCCCTTAAGTACAATTTTTTTCTGTCTTTCCTTACCTGTCTTATTCTTTCAACCATTTGTATTTACCTCTTGTTTCATTACCTC + ?=CCBGFGEGHHHHFGHEC@DDBGDHHHHHFGHGCEEEHEGHHHEFHEFHHHGHHFBGHHHFFDEHHHHHHEHHGHHHHGGFFFGHFHCHHG=B5:EEHH @read_150_187/1 TTGCAAAAGAGGGACTAATTGAGAGGTGATATTACTGGTTTAAATGAGAAGAATTAAGAGTATAAATTAGGACTCGGGCATAAGTATGGATGTGGCACAA + HHHHHHHHHHHHGGHHHHHHHFGHHHHHHHHFBDDFFEHHEFD(/E?CFHHHFCFEFHHGEHGGDCGGEHGHHHGHHFIGEHHCC?=FGHHHHHHHHHEE @read_150_188/1 ATAATTTAACATTTATATTACCACCAAAAAACACATTTAGGTATAATCTAAAAAAATATGTACAAGATCTACAGGAGGAAAACTATAAAACTCTGAAGGT + HHHHFEDHHHHHHHHHFHHHHHHB?FHHHHHEDFGDDFHGAAAFHHHHHHHHHFCHHFFHHFDEEA2369EFFBHHHHHHHHHHHHHHGF?HDB'-6*57 @read_150_189/1 TTCTAGTTCTGTTCACCCAGGGACACTTCTTCACATTTGCCTCACTCCTGCGAAGTTAGGATGTCATGAGCTGTGTTGTAGAAGAAGGTAGTTGGGTGAG + HHHHHHHHHHHHHHHHGGGHHFFFHHGHHGC4E=DAEFHHHHA6EHHFEEHDFHHHHHHHHHHHHHHHF@E@0:9C=;@@?EC@BD8@CGFHF;EHHHHGHHFEHHEHHHFFHF=FHHDE?;BCFFFFEHHEFHHHHEHHHHHHHHHHHGDFGFE<.3=EB=D @read_150_192/1 GCTCGAGCCACAGCCTGATATGAATATTGATTGGAAAAAATGTCTCTCCCCTCGTCCCCCAGGCCCGGGGCTGCCAGGGAGCTCTCCGAGCAGTCTGGGA + HHHHHHHHHHHHGGGHHHHFDBFHHHA>@GGEHHHHHHHHHHHHFEBFFEGGHFFFFHCDEFDFFHHFFHFFHHHB;B.&372,(6/+2@AHHHHHHHFF @read_150_193/1 ACAAGTTTCAAGTATGTGGTAATGTAAGAGTCCAACTTCCTACAAGTCAATTTCTACTTGGAATCTAGTTCATACGACGACGACCAATGGCACACTTATC + EEHHHHHHGGHHFGBGGGGEGFEEHHHHHHHHHHHHHHHEGGCFCC=>>*>=B>DHDEEHHHFHHHHHHHEB?@676=DA@6DF8<476F.1DGGDFFEE @read_150_194/1 ACTAAAAATGCAAAAAATTAGCCAAGCGTGGTGGCAGGCGCCTGTAGTCCCAGCTACTCGGGAGGCCGAGACAGGAGAATCGCTTGAACCCGGGAGGCGG + HHHHHHHHHHHHGGGHHHHDEBGFFGHHHHHHHHHFGGGFFFHHHEHHHFEBEEEFGCBHHH@C;@942DA?A>EHGBA*3:--/ABCDEHBHFGGGGHC @read_150_195/1 ACCATTTATATGTTCTCTTTCTTTAAACATCAGATCATATTCCTTGGCCACTTATCTATTGGAATTATAGGATTTTTTGATTCATTTCTGAAGTCTCCAT + HHHHFHHHHHHHHHHHHGGHHHHHHHHHHHHHHHFEFEEBFHHHCEEGFGFH>=HDBHHHFF?DHHDCHHEEEFAEE@BHHBF?7@3;BDFBBFHHHHHE @read_150_196/1 AACACTCTTTTTGTGGAATTTGCAAGTGGAGATTTCAAGCGCTTTGAGGCCAAAGGCAGAAATGGAAATATCTTCGTATAAAAACTAGACAGAATCATTC + HHHHGGB@DBGBED;=BDBHHHHHHHHHGGHHHHFFHHHFBBBFFHHHHHHHHFFE@8BFHHHHHFHHHC?DFFFHHFEHHHEB;FFGFBECHHHHHHHH @read_150_197/1 TGAGCCAACATGGCCCATTATACTTAATGAATATGAACAAGACAAACTCAGTTCACATATTTCCAGATGATGAAATGAAGGTTCAGAACCATTGCTTCCA + GGGHHHFBBEFB>BCE8BCFHHHHHHFF?CEHHHBFHHHHDFHHHHHHHEHHFEHHHFFFFHEFFHHFC?:32:DGHHHHGGHHHFFFGGAFHHBGEHGD @read_150_198/1 ACTCCAGCCTGGGTGACAGAGCGAGACTCCACCTCAAAAAAAAAAAAAAAAAAGGAAATGAGCTCTAAAGCCTGTCCCAGACCCAGATTTCGATACTGTT + HHHHGGEFHHHHHHGEFGGFHHGGHHHFHHHHFFHFFFHHHHHHHHHGF?CFEFCEGFFFF<<6%::>9;'-;?>@@@:-CA@EHHFGHE@?89F @read_150_200/1 TGCATGTAGCTGTTCACTGATGTCACCCCTCTGCTGAGCCTTGTCCCAGTGTTGCGGTCACCAAAATGCATGGCAGTGAGACCTCACTCTTGAAGAGTTT + HHHGHHHGGEDC@8>GHHHHGHHHHHHFFFEGAEAFFFE@>D<8(-'.4>?DGGGHFFGGEHHHFFED96ADGBFFFFFFHEHFEGGHHHHGFFFCFBEE @read_150_201/1 GAGACAGGGTTTCACCATGTTGGCCAGGCTGGTCTTGAACTTCTGATCTCAGGTGATCTGCCCGCCTCTGCCTCCCAAAGTGCTGGGATTACAGGCTTGA + HHHHHHHHHHHEBEEDD?>GFHHHHHHHHHHHHHFC?GCEGHHHFGCBFHHFFFHGGGGEHFHHFHHHHHHHHHHHHHH@=7DA?72235= @read_150_202/1 GCTCAGTTCTGTCAGACTTTAGTGAAGTACCTAGACCTGGTCTTGTCAGAGAGAACCAGGGCATTGGGCAAAGCAGGATTAAACCCATCTTCTCCCCTGA + HHHHGHHHFFFHHHHHHFFGHHHFF4>@AA=@/>>/ @read_150_203/1 AGAGTTTCAACACGTTGGCCAGGCTAGTCTTGAACTCCTGACCTCAAGTGATATGCCCACCTCAGTCTCTCAAATTGCTGGGATTATAGGCCACCACACC + HHHHHGGFFHHHHHHHHHHHHGGGGHHHFDFFHHHGG=EBFFBFHHHHGHHHHHHHHHHHEEHDFHEE8@CEEEHHHHHHHHHHHHHHHHHHHHHHHGCF @read_150_204/1 AATGTAATCACGAGATTTCTTAGAAAAGAGAGGCAGGATATTCAGAAGTTAAGGAGGAGAAGACAATGAGAAGATAAAAGCAGAGAATGATGTAATGCAG + GGEHEA@GGHHHHHHHHHFHHHEHHHHHHHHHHFEEHHHHHHHHHHDHHHHHFGGFFGHHFHHHHFDD@B?FEFHB@@DGEC((3,?A7@@HHHFFG @read_150_206/1 CTGTTCTTGGTCGTGGGCATCTCTGGGGAGCTCTGAGTGGATGAGTTCTCCGACTTGGGCTCCTGTGAGACGTGCCCGCTGTCTGGGGTCTTCTGACCAG + HHHHHHHHHHGHHHFFHHHHHHHHHHHHHHHHHGEHHEFHHHB@@ECFFEHHHGDHHHGHHFHHHHFFFHHHDE('%444D.DGE:;*GHFGEB5BF(,% @read_150_207/1 TTGAGACCAGTCTGAGCAACAGAGCAAGACCTTGTCTCTGCAAAAAATTTTTTAAAAATTAGCTGAGTATAGTGGCACACACCTGTAGTCCCAGCTACTT + HHHHHHHHHGGHHHFHHHHHGCGHHHHHHHB*>;?AAHBDHHHHHHHHHFEHHHHHHHHFHFHFEHHFFFFHD7EGGHGGGHFFHHHFFHGFEEAE;EFECDHEHHFHFHHA>3(+644A78BEEDBB;7>=)1?BFD:68=D93AD @read_150_210/1 AGAGTCCCCCGCAGCAGCGTCACGGCCCAGCTCTGGTTCTCAAGTTGGGCTGCTGTTTTTCCCCTTTTTCTCATCCGCCAGGATGCCAGGCGCTGCTGAA + HHHHHHHHHGHHHGAFGGGGGHHHGGDFEE2ABFFHFEEC-4,+FGHHHHHHHHGFCCHHBGF=E9CDC@CFEGGDDEE0=ADFHHHFHBDD?EH:A)12 @read_150_211/1 AACCTTTGACATAAAAGATTAGACACACATTTAATAAACATATATATACACACACTTTTTATTTATATTTAATGAAAATTTGGTAGTTGGCTTTCACATC + HHHHHHHEEFHHHHHHHGGDFGHHHHHHHHHHHHC.A?ADFHFHHHHHD?FHHH@FE978?EDF?BHH@HHHHHHHHHHHFEGHHHHHEFFGFHH@EFCC @read_150_212/1 TTTGTAGGAAAGCTAATGCTATTATACTGGTTTTTGTTTTCATGAGGAGCTAGAACCAGAGCAGCCCTTCCATTACATTGACATATATTTACTAAGGTTT + =;CC=DFFEEDDB=BBCEGGHHHFF=:6<>DCHGHHHFHHHHHFFHHHFHHHHE:DGGHHHFHHGDDCFFHHHFBHHGFFCEFFFFB/1;8EGFFGG??E @read_150_213/1 AAAGGTGAAATGACATTTGCTGTGTAAATTTCATAGTTTGTTTCAAAAAAGAACCTTGAAAATAAGTAAAATTAAAAAGTAGAAGAAAAAAGAGAAAATG + HHHHHHHHHHHHHHHHHHHHGGGFHHHHFHHHGFFHHHF?C3)0<2@@DFEHHHHHFBAAD1CCHHHEEFHHHFEH?;.9@HFEEF@DHEHFHHHHHHHFBHHHHHHE>EFFHHH@C=B @read_150_217/1 CAGACACACACAGCCTCAAAACATTTACTTCCCATGTACCCTTCTCAGGAAAATACTTCACAAACAACAGAGGGAACCCCAACCAAGAAGCCATGAAAAA + HHHHFEC/D?EEB/B;IEHHHHHGHHHHFHFHHHHHHHEEHHHHEFFFGFFHHD29.15BHHHHCHHHFB539EFG=558?ECFGHHHHHHHHGFC;ECF @read_150_218/1 ACTACTTTTCAACAAACAATTCCAGTACCAAAATCGTATTGCTGCTGAATTTAACACCTAATTTGCCGTAGCGACGTACTTCAGCCTCCAGGAATTGGAC + HHHHHHHHHFGDDBBEEEGGHHHGGE@;CCFHHHHHHHC?==CFHFHHBGFFHHFCFFHHFHHHHHHFB<'3966CDEGHHHHHFHHHHHBBFHFHHEHG @read_150_219/1 AATTCAAAAATTGTTTTGTCTATCCTTCCAGTTTTGAAAATATAAGCAAGTATTTTATATCTGTGCATATATATATACACCTTTTAGATAAACAGAAGCA + HHHF?AGGGGFHHGGHHFHHGEEEFHF><EEHHHHHHHHEFEFDDCHHFEEDD?@@EGGHAEEEHHHHHHHGFHBF @read_150_220/1 AAGTCTCTTGGTAGGTCTCTAAGGACTTGCTTTATGAATCTGGGTGCTCCTATATTGGGTGCATATATATTTAGGATAGTTAGCTCTTCTTGTTGGAATA + HHHHHHHHHHHHGGHHHHHHGGGHHHGFHGC@FEBGEEFHHHHA>603ACEEGFHHHEDEDFHHHHFHHFEACHFGEBAEFHHHHFGBEBEFHHHHGGFF @read_150_221/1 ATCAATGTAGACTTGCTATTTTCACTGGTATTTTTTTTTTTTTTTGACTAGCCACTTAAATTCTGATGTGTCTCATGTTTGGTTATTAGTGTCACCTAAA + HHHHEE<::<@FFGGFGGGGHHHHHHHHFFGGGEHHHHHHFHHFFGC;8DHHHHHHHDHHHEEEEHHDDDEEFCDHHFDDF?5@DC?EBDGDA7?HDGCD @read_150_222/1 TTGGGTGATGGGGGCGGATCCCTCTGGAGTGGCTTGCTGCCGTTCTCACAGTAGTGAGTAAGTCCTCGCTCTCAGTGAAAGAGCCTGGCACCTCCTCTTT + HHGEBFD=6:DGGG?@CGEEHHHHFGHHHHHHHHHHHHHHHHEFHHEEAGEA52:0<9EF<4/6AFBDEBE::''@>7;?,.86509770EE?DCHHHHF @read_150_223/1 CTTGCTTAGAGGTTTCCGGTTGGGAGGATTGATGAGTAGGACATTTGGGAAGACTAGAGAGAAAACACAAGAGGGTTCTAGACAAATTCAGCTCTTTCTT + HGFEFFHHHHHHHHHHHGGHHHHGHHHHHHHHHHEHHHHHHHHHHHHEFHHHHDFHD?=EFHBDDD87ABBEDBEECC=FEGGFFG9-%5;D9DAE2>>A @read_150_224/1 GGAAATCACAACACATCTAATTGGAGTGAGGTACCAAACCCATTTATACAGTTTATTGCCTATTGATAGTTCAGTGACTACTGAGATTAGCTTGTTAGCA + EEFD@=:GFFGEHHHHFFGCBCGGEC@F?:A@@4 @read_150_225/1 GTATCATTTTGTTACTTAAAAGGTCTAGAATTTACACTTGAAATAACCTTTTCAGGTGGAACCAGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACC + HHHHHHHHDFFHHHGD5<ABFEFEGF: @read_150_226/1 ATGACGGGTTGATGGATGCACCAACCACCATGGCACATGTATACATATATAACAAACCTGCACATTCTGCACATGAATCCCAGAACTTAGAGTATAATAA + HHHHHHHHHHHHHHHHHHHFFHHHHHHHFDEHHFFHHHFFGGGB@GFHFFHHHHHFEEEEGDD@ECHGGEHHHDDGDCE=91ADGBEHHEFHHFFHHHGB @read_150_227/1 CCAGGGTATACTGTTAAGTAAAAGAAGAAAGCAAAGTACAAAAGAGAATATAGAGCATGCTAACTTTTGTGTAAGAAGGGTAGGAAAACACACATAAATT + HHHHHHHGHHHHHHFFGGGEBGBHFHHHHHHAFFHGEHFBDDHHHHHHHHHHHHE?))4@/,/C@FBBFHHFFHHHHHHHHHHHCCFHHFCFB@DAAB7E @read_150_228/1 AGAAAGGAGAGGTGATGTGTTTGGTTTGTGCATCTTGAGTTTGAGTGCCCAGTGGGATACCTAGTGAAAATGTCCAGCCAGTTGTCAGAATGTCAGAGGT + HHHHHHGHHHHHHHHHHHHHHHHHEDE?GFGBEFFFHHHHHFHHHGHHHFBFFC>;EHHHFHHHHHHHHCEFFDEFEHHHHHHFFFFFC77?EFHHFFFD @read_150_229/1 GTTAAAATATTTACTGAGCACCTACTGTGTGCCTGGCATTGTTCTTGGTGCAGGGAAGACAGCAGAGAAGAAGATAAACAGATAAACGCAGTCCCTGTGC + HHHHHHHFFHHHHHHHHHHHHHHHHHFHE??>>HHHHHHEHHHHEEHHFFCFGED1%>?FHHHHHHHCBFFF>?EBC7>C4DEEDE8<>?AEFHHHFCDF @read_150_230/1 CTGCCTCAGCCTCCCAAGTAGCTAGGTTCATACGACGACGACCAATGGCACACTTATCCGGTACTTGCGTTTCAATGCGCATGCCCCATAAAAAAAAAAA + HHHHHHHHHHHHEDHHHGHHHHHHHHFFHEBAFF?FFHBFHHHHFEHHHHHHHHHFFFFEEHHHHHHHHHFDEFCHHHGHD?DDHHHHHHHHHFHHHHHG @read_150_231/1 AGGCTGAGGCAGGAGGATAGCTTGAGGCCTGGGGTTCAAGACCAGCCTAGGCAACATAGCAAGACACCATTGCTACAAACAATTTAAAAATTAGTTGGGC + HHHHHGFDGFHHHHHHHHHHHHHHHHHHHHHHFHHHHHHFHHHHHHHFHEBGHHFBEHHHBFHHHDF@<<>0BEFHFGFHHGHHHHHGFHHHHEEDFFHH @read_150_232/1 ACCAGGTCAGCGATGAAGGTATCTTCAGTCTCCCCCGAACGATGAGACACCATGACGCCCCAACCATTGGCCTGGGCCAGCTTGCACCTGGAAGCCAAGG + HHHHHHHHCFGDE/EHHHHHHHHHHGGHHGGHHHHHHEEEFHHFGBEHHBCAHFDHFHFFEGGGBHHHHHDA?AEFGHHHHGGECEFGHHEGHECEBDDF @read_150_233/1 AACTAGAACCAATCCAGGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCACCTAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAA + GHHHHHHHHDEFFFFHEHHHHHHHHHHGHHFHHHEEEDBD?6>5@EFHGGBGGHHHHHBFHGHHHHFHHHFDA:(C=@@5BDFHHHHHGFGEEFBFDFFD @read_150_234/1 CAGGGATGCTTTATTACTATTATTATTTATCTTGATGTTTCTACTAATTTGCCGTAGCGACGTACTTCAGCCTCCAGGAATTGGACCCTTACGCACACGC + HHHHHHHHHHHHEEGC@GGG>>11:;171:@A;/3;DGGGGEHHGFACFFCH @read_150_235/1 AATTTGTCCCCCAGCAGGACTCAACTGTTTGCGGTTCCTGCCTAATTTGCCGTAGCGACGTACTTCAGCCTCCAGGAATTGGACCCTTACGCACACGCAT + HHHHHGGEEEGEDHHGHHFFFHHHDF?GEHHHHHHHHGGEFFHHHHHHHHHHGGFFHHHHHFFHHHEHECBEFFDGHHHHEDFFHHHFA>BDEHHGHHHH @read_150_236/1 CTATCCTTTTTATAAATTCAAAGTGGGTTAAATCTTACTAAAGTTCAGAAAAATTAAGTAACTTGGAATCAAAGTTCACACAGCTCATAAGAGGCAAAAC + HHHHHHHHHHHHHHAEEB<4=FEHHHHHHFGHFFHHHHHHHEBHHHHHHEF9< @read_150_237/1 TTCCCACCCCCTGTCGGGAGTGCTGAGCAAGGGGCCCCTCAGGTTTTTCCGCTTTAAGAATCGGGTCCCAATGTCCTGCTGGCCATAGCTGCGGTTTTCC + HHHHHHHHHHGHHHHHHHHHHHGGC?DGGF=BGGGHHHGGEEHHHFFHHHFDDEEH@ADCHHEFDD9851)03%95BBFAEEB@@66<:>FHHHGFEEDH @read_150_238/1 TAAAGACACATGCACACGTATGTTTATTGCGGCACTATTCACAATAGCAAAGACTTGGAACCAACCCAAATGTCCAACAATGATAGACTGGATTAAGAAA + HHHHHHHHHHHHHHFDDD4>FFBHHHHHHFHHFGFHHFEEFACCFE@@;BCGGBBEDFEHHFHCEGECDDFGHHHEHHEHHHDEDEEGFE @read_150_241/1 TTTGGTTGGTAAGCTATTAATTATTGCCTCAATTTCAGAGCCTGTTATTGGTCTATTCAGAGATTCAACTTGGTCCTGGTTTAGTCTTGGGAGGGTGTAT + DHHHHHHHHHHHHFEAFHHHHFGDEBE@EFFFHGHHFHHHHHHHHFFFGFHFDE7CFEGFFG97B4382*+%%'<>67'6/2CFHGG38:BGG;EEEEFF @read_150_242/1 CTTGTAGGGTACTCTCGTTAGCTTTAAATCAAAGCCTAGTTATTCTTATTTTAAACACAATTTTAATCAATTAGGCTTTCTGGTTTCCTAGCCTGTGGTT + HHHHHFFFFDEA>7CEHHHHHHGHGHHHHHHHGGFEHHFGFH?CEFGFDFHHHHHGGGFDCDCFHHHHHFHHHFFHHHHGFHHHHHHHHHHFHHHHHHHF @read_150_243/1 CTCATCTGGCAAGAAAGAGCCCATGTAGGATCTTGAGTGTTGAGAAGGTGGGAGTTGCAAAATGGAAAGCAGGGTTTTAGAAAGATGAGAGGAGATCGGA + C>6DHHHHHHHHHDDEGFD?FFBFHHHHHHDEEFHHHCHFEHHHHHFGEHHHHHFD45>@DFHEHHGGBBFFHFHHFFD<:?EHHHHHHHHHHHGGHGBHHFHHFBBFG.3+7F @read_150_248/1 ACTTTCTGTCTTGTTGATCTGTCTAATGTTGACAGTGGGGTGTTAAAGTCTCCCATTATTATAGTGTGGAAGTCTACGTCTCTTTGTAAGTCTCTAAGGA + HHHHHHHHHHHHHHHHHGHGGBEGFGHEEFHHHHHHHCHHD<95=BFFBDED??HHG@C?GFHHFHHHHFHHCEFHHHHFFHDDEHHHHDEHHFEFD<8> @read_150_249/1 AAAATAAAGTAAAATTTCAGGATTTTTTTCACACTTGAGGTTATTTTTGAAATTTCATACAAAGCCCCTGGAAATTTGCAATAATTTATTTTGTGCCTTA + GGGGHHHHHFEHHHHHC6DEGB=@@8EEGGHHHGGE?:AFHHD6@FHHGHGHFFFHGHHEFFF::?FHFAEHHFGDDEEFHHHHHHHHFFEBBEFGFHHH @read_150_250/1 GAGGCAGGCACTTTCTTATCACCTCCATCTCTAAGATGAGGAAACTGAGGCTTGGAGAGGCTAGTGACTTGCTGAAGGCCACAGAGCGTGCTGGTATTTG + <<=?HHHHHHHD89<DEEEFF;@?HHEEHHHHDAEF?GFGEEHFFFHBGGE;0<*4(2DDFF @read_150_251/1 GAGCAAAACACTAGGTAAAAGAAGGCTGACTGATTACTTTGTATAGCACAGCTACCATATTACCTTGGGCCTTTAACTCGTGAGAATAAATGTCTGCCTT + HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHFBHHHHHHGDDGHDDFBD:AADFHE@C9.64A @read_150_253/1 GTCCATACATTTCAGACAAAACAACATATCATATCACAATAGATTGAAATTTCAGGCAAAACAACATATTATATCATAATAGATTGCAGAAGCAGATATA + 6:GFGHDFFGGGGHHHHHFHHHHHHHHHHHHHHHHHF?GHHHHFEHHBDEHHFHHHHHHFHH?AAA;?-5)26;FB:8@@EFFCCGHHHGHC@E/)&-=G @read_150_254/1 AGTTACACTTTCAGTCCTCCAGGGCCCCATCATCTCTGGGCCCATTCTATATTCCCTCCTTCCCACACCCACCTCAGTGTGCCTCTCACCGCAGTAATCT + EEBFDGGHHHHHHGHHHHGGGBHHHHFEEEGHHHHHHHHHFHFHHHA,(EFBDD>@@BBHHHHHFAAE@7DDEFDGDC;>+'9951A?CEGGGG@2>?.: @read_150_255/1 GTACTCTGAAATATTATATACCACTTTCTTTTTTCTAGAAAAGAAAATAATTTCTGTTTATATCAAAAGCACCAGTTGATTCTGTTTATTGGATAGTCCA + =><<:@EEEG@DEHHHHGB?DBGGGGFFFGGGGGD8EEDBEE?BEGFFF @read_150_257/1 TGGCCAGGTAGGTTGGCAAGACACAAGCCAATCATGAAGGGCCTTGTCCACAAGGACTTTGACCCCGGACTTTAGCCTTGTGGGGGTGGTACACCCCCGA + HHHHGHHHHHHHHFHHHHHHFGGGHHHHFFGGHHHHHHHHHGHFDGHFHHEB?8;;>6@:EECEED;:FHEEFHHFHHHEGFHHHEAECAEHFHHFCGBF @read_150_258/1 GTCCACTGATGTTTAAGCTGCTTCCATGAATAACAGTAATAGCTAAAATTGGGCTTTACCTTTCATTGTAAAACCACCACAGTCCTATGAATTATTCCTA + HHHHHHHHHHHHHHHHGHHFGGFHDGGGFFHFGGEDE@CEFCCEEFHHHHHHHHHHHHHHGFHHHCFFBFHHHHHG=?FFHHHC>EBFDFEEEDEDHFFH @read_150_259/1 AATTGAAGTTGCTTTTGAAAGTCAACAAATGCCTCAGCAAATACATCAAAGCTTCCCTAAAACAGGGTCAATATCAAATCTTCCTAAGGGAGCTTACTGC + GFDDD?AE-9CHHE;EFHHHHHFFGFHFFFFHFHHEHHGBEBFDDEFHHF8?FHHHHHFDCC4AHD;FF=?FFF?0@BHFHFFFHEHGHHHHFGHHFEFBED?HFHHHFDCCHFG=AF6?DDFEHHHHEH @read_150_261/1 TAGTTTGAGATGTACATTTATATACGTACCTCTTATTTGAGATAGGCAGGTGTGCAAAGTTAGATTCACCATGACACTAACGAGACTTAAACTGTAGGGC + HFHHHHHHHHHHHHHHGGGGBBFBC<@80@HHFD@HF?DCHA9:EFFHHFGHHHHBBA:<4DHGGFGBEEFF @read_150_263/1 GATGGGTGAGTGGTAGTAATAGTAATAGCTGAGTTCATACGACGACGACCAATGGCACACTTATCCGGTACTTGCGTTTCAATGCGCATGCCCCATAAAA + HHHHHHHHHHGGGGHHHHHHHHHGFHEHGHHHHHHHGGGEFFHFG@BEFEGF?EFGDD?.;9BHHHEEHHHHFBEED<5007EF37B?GGFFFFGGGEAA @read_150_264/1 TTGTCTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTATTTAGTTCAACCAAATTTTGTCACATGTAGATTAAACTTGCTCTGTGCCCGCTCCGTATGTCA + HGGHHHGGHHHHHHHHGHHFD@@?BHHC=EBCBBHHHHHHHEGFE>@EFFEFHFFHHHEEEHHHHHFHHFGFDAEHD/(-<:@HG8;@:.5.1-;FGEEE @read_150_265/1 TGCATTCTCTTAGAATATTTTTATAGATTTATTTTTTATATTCAGATATCTATCTGAAATGTATTTTTATATAGTATAATGTAAATGTATTACTTTTTCT + HHHHHHHHHHHHHHFHHHHHHHHHHHHHFBFHHHHHGGGGHHHHHFGHFHHHD@;@(77AEFHHHHHHHBEFCCDFHHHHHHHCDBEGGEBBHH85;EGG @read_150_266/1 TCAGGGGCAGTTGGGATCGATGGATCTCTGAGCTGCCTGTGGGCACCAAGATGCTAAGAGCCTGGTTTTGAAAGTGTGTTGTATGAAGGGAGAGAAGGTC + HHHHHHHHHHHHHGFBGHHHHGHHHHGGGGHHFHFHHHHHHHHHHHHHGGFEFFFGEGHFEED@AHHFHHHEED:DDD57>8<947BFFHHHHHHABDEC @read_150_267/1 TATCAATTTGGCACCAGGTTTGATATATAGTAGAGGGAGCTGTTTAACAAGCCATGTTCTTCATCCTGTTGATAAGGGAGAAACAGGAGAATATGAAGTC + HHHHHHHHHHHHHHHHHGGGHHHGFHHHHEGGG;EDHHFFBCFGGHHHF@6>2:3:3;EEHHHE?EEBFGFHHHHGGGGGHHHHHGGDGBHFFE7EEG;F @read_150_268/1 CATTATTTCTGAGGGCTCTGTTCTGTTCCATTGATCTATATCTCTGTTTTGGTACCAGTACCATGCTGTTTTGGTTACTGTAGCCTTGTAGTATAGTTTG + HHHHHHEHHHHGFHHHHHHFHHHGHHHGHHHHHHHHB?7?@DD@FHHFHHHHHHHHEFDFHHHHFHHHHEEEDHHHHFEEF@>>CGHHHCEF@DFFAHHHHHEA16-88@D @read_150_273/1 GCGCCACCACACTTGGCTTTTTTTTTTTTTTTTTTTTGTATTTTTAGTAGAGACAGGGGTCTCACCATGTTGTCCAGGCTGGTCTGGAACTCCTGACCAT + HHHGFHGGGHGFFFBFFHGDBBDFGHGGFFHHHFGHHFHHHFF@E9=BEEHHFGGFCCBCGFEADHHHHHEFFHHHHHGGDDDBC=DFHHHHHFHHHHHH @read_150_274/1 CTGATAAAACTGATGAGGAAAAAAAAAAAGAAATAGACCCACTCAGAGACAAAGAGATAACCATGCCCCGAAGATTCCTATACCCTTAAGGTCGCAATTG + HHHHHHHHGGGEEGHHHHHHHHHHHFFHHHGFGDHFDFHHHHHGBEFHHFHEEHGFHHHAEFEEE:EEHFFEFFDGA>CCEFGGGHHEFE@DAADDDDBE @read_150_275/1 TTGAGGAAAAGCAAATGGATTTAGTTTTGGTCATACAGGGTGATCAGTAGATGGCTCTGGAAGGTCTTGGAGGGCTTTGTATGCCATTCTAAGGAATTCT + GGGGFCEGEFGDEGGBBB=CAGFGGHHHHHHHHFGEBFHHHHHHHGHHBB@@BFFF8DFEEGGC?C @read_150_277/1 CTCAATCACAAAGAGAAACTAAGAAACTGACCTTTAAGTTCTTTAAACAAGTCCTAGAATTTTGTGATAACAGAACATAGCCTAGCCTTACCAATAGCAA + GFGGHHHGGHHHHHHHHHHGFHFHHDB<:>FFEE6876*<2409DEHHHHHD;FFHHHHHG<727CHHB<,BCFA@37>7@FGGHFHFHHHHHHHF>DDC @read_150_278/1 AATCTGGAAAGAGAAGATCCTTAAGTATTGCTTTAAAGTGAGCACTGAAGGACAGCCGTTAAAACAATCCCAATTTTTAGAAAAGGTATTATTCCCTGAC + AAAECFGFECHFHHHHHHHHHHHHHHHFHDDFGFGF=;EEFDEGGGFBE@7')7(74 @read_150_279/1 GTTGGAGCAGAGCTCCTAGGCCCACCTTCTGAGCCTTTCCTTCTCCCCTCCTCCTGCCCAATCCATGCCCCGAAGATTCCTATACCCTTAAGGTCGCAAT + HHHHHHHFGHHHGHHHHHHHGGFFHHHGHGHDEAEFFHHHHFGFEHF>DFHHHHHHHHHFFBGFE?AADFF?DFFGEFGGEB>;D;99AA@<>>ECFFHH @read_150_280/1 CCCAAGCATTGATTTTCTAGACATAATTCACTCCCATTGCAGATGTCCTAGGAAATGGAGAGCTCTATGACAGAAGTACACATCATGTGTCCAAAGTAAC + HHHHHHHHHHHHHHHHHHHHHFHHHHHHFHHGHHFHHFCDFFDBHHHHHFGGGGEF@EGHHH80;;@D=6EEF?DHHHFHHEFBHHHHHH>6D@6><>@DFEHHFFFHF@42><4?D @read_150_282/1 CACTGTCCCTCGTGGTGTCAGTGTCGCGATCTGGGCTCACTGCAACCCGTGGTGGAGCCTTTACATAGGAGTAGGTTGTGTTGGAGCAAGCAGAGGCCCT + C=FFHHHHGGDDDGGHHHFHHHEDHHHHHHHHHHHHHHFCFBHHHF>BHHHHHHDHHFHHHHHHFHFFHHHHHHHGGGGFFHHHHFCDBCG,3,&(1&/6 @read_150_283/1 GTTAGAAGTATGTATGTTTTGTATATATCTCACTCCTATAATATTAGGTATATTGTCTGCATTAGACCTTTGCAAAAGACATGGATTCTTATCAGCTCAG + HGGGHHHHHHHHHHHHHHGHGDFGB4;@GGHHHHHHHHHHFEEFHHHHHHBCEEHHHHHHFFFFHFHFHHHHEEEHGGGGHHHDA???;HEBHHHDDB49 @read_150_284/1 AAAAAATTCTTTTATCAATTGAGGAAATTTGAAAATGAACTAGCAATTAGAAGATATTATGAGGCAGGGCATGGTGGCTCACCCCTCTAATCCCAGTATT + HHGFEFFGEEGGHHHHHHHGHHGHHHHHHHHHHHHHHHGHHHHHAAA?CBEFHHHHHFCEEHHCF@:,)*6CBAFHHGGDFFHHHHEEHHHFHHHHHHHG @read_150_285/1 TTGAAGTGGCAGAAGATAAAATCTCCCTCTCTCCTGTGTACCTTGGGCTAAGGATTCTTCTCTGGATAGCCAGGACCCTGTTGATCCTGAGCCCCCATTG + @67@@;DEEEFGHHHHHGHHHHHGGGHFGBDDGGG7><=EHHHFFGEHHHHHHHHFHFHHHHHHHGGFFFHHFHFGG*&7CDDGBGFFFHHHHHHHHDCF @read_150_286/1 ATCCTGTCCCTCTTCCCAGTCTCCACCCTGCAATAGGCCCCTTTGTGTGTCCATGTGTTCTTATCATTTAGCTCCCACTTATAAGAGAAAACATGTGGCA + HHHHG:@ADHHHHHHHHHGHHHHGGGGCCBEGFG@E=EH8-EHHFB5FFHHFB@FFFFFHHDFEFHHHHHHHFHFEFFEGHHHHHHHHHHHDHE/&7+)3 @read_150_287/1 TGTCAAAGAAAGAGCTTAAACTTCAGGCTTAAATACCATCATTTTTCTGAAATGAAGGAAAAAAAGACTGTTGGGAAAAGGCCCTGTTGAGATGACCAAG + =BGGGGEGGHHHFGGGGHHHHHHGEED..7(49DEFHFBHHFFHHHHHFHFFFHHHHHHBBFDHA5454EFCB?1(208-DGHHF<16FGHGFCFHHHHE @read_150_288/1 AAAAAAAAGGACAATATGTAATATTGATGAGTATTCCTAGCATTGTTATATGGGGAGTCTTGTCTAATGCACGTCTATAAATATTTATACTCCTTGGGAA + HHHFCD@EHFE@CCGGBGEEGHEEBHHGGFHGGEHHHHHHC49@FFFHHHHHHECEHHHFBCCDFHHHHCBA77296@BGHHEE@FCEHCDD:;A%)4=; @read_150_289/1 TGACTCCAGAAGGAGGAAGTGATCAGCTATGTCAAATTGTGCTGCTAGGTCTAGTAAGATGAAGAATAAGAACTAACCATTGGGTTCATACGACGACGAC + HHHHHHHFFGGHHHGGFDEF;CD;FHHGBD3(EHHHHHHHGGG@AFEG?FFCC;HHHHFHE@DEFECFHFHEEHHHHHHF@HHHHHGEFHEFBBBFHHHF @read_150_290/1 TATTCTCTTGGAACTTACTTTTTCACCGTGATATTTTTGGTCACAGTTAAACTAGTTGGTAGATACTCATTTTCTAGTGTCCCTGAGGTTCCTTTAGGTT + HHGGHHHHHHHHHHHHHHHHE6<9<;EHGGBEE@BFHHHHHHHE @read_150_291/1 TATGTCAGGTCTACACACTTATGTCAGGTCTAGGTATATTATAGGAATTTTTCCATGCTTTATTTTTGTCTCTTTCAATAGGATTATAACTTTCTTGAGG + HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGHHFC;9EEBDHDHHHHHHHHHHHHFFHHFFFGGFFFDDEEHDDEEFHHHEHED>?FHHGDDFBFHH @read_150_292/1 TAACTGCTAATCGCTGATTTAAATACTTAAACTCTGCAGAAGTATTTATTGCATTGACTTCAATCACTCCTTCCACGGTATTTTCTAAATATTTCTGTGT + BBGGEFGGGHHHHHHHHHEEDHHHFFEFFHHHHHHEGGGHHHHHHHHEHHF?A9?EBFHEFDDDEGCGFFHHHHFHGBB75CDHHHHHHGHHHHGHHHGH @read_150_293/1 ACTAGACCCCCACTTGGTCTCCCTCTCCCCAGGCTACGCCTGTCCCCCAGCCCTACCTCGCAGCGCAGCCGTGGCCGTGCTTCCTCTCACTCATCCCAGA + HHHHHHHG9<976=GHHHGGGFHGGHHHHHFEHHHHHHHHHHFEGHHHFHHFFGFFC>DB@EFGHHHHFHHF @read_150_295/1 CACATCACGCAGCAGTTTCTGAGAATGATTCTGTCTAGTTTTTATACGAAGATATTTCCTTTTCTGCCTTTGACCCCAAAGAGCTTGAAATTTCCACTTG + GGHHHHHHHHCCFHHHEGGCFF7 @read_150_297/1 TGGGATTACAGGCACCCGCCACCATGCCTGCCTAATTTTTATATTTTTAGTAGAGACGGGGTTTTACCATGTTGGCCAGGCTGGTCTCGAACTCCTCACG + HGGGDCEEGHHHHHGFHHHGHHFCGFFHFGHD<@CEBEECFFHFFCCB?>BHHHDEFHHHHHHHHHFH?BHHHDBGFGFBF87.>>?;?FHHA>>0&&<@ @read_150_298/1 TTATTGTTTCATTGATCAAAAAGATTAGGTATATAATCTATTCTTCCACAGCCCCCTTCCCATTCGTGATTTCCTCTAATGATACATAATATTTCCAGTT + HHHHHGHHHHHHHGGFHHGGHHHHHHHEEGDHHHHHHHHHHHHHHHHHGGD@?ACFFGGGEHHHHGEDEBGHCHBGHGDGHHHHHHHHHHGDFHEFB:54 @read_150_299/1 ATCTGCTGATTTCCATTCACCGTTGTTATATGTATCACAGAAATAGATGTTCATACGACGACGACCAATGGCACACTTATCCGGTACTTGCGTTTCAATG + >?=GFHHHHHHHHHGGGHGFFEEHHHGGHHGHHHHHHHHHGGGGFCEEHFBBHHHHHHHFEEE?3?D@94>;91AEFHHHH?:>A@DCDEHHFGGHHH@E @read_150_300/1 TTTAGCTTCCTTTTGTACCAGAATTTGTCAACTATAACATCTCTTTCACTAAAGATTGAATATATTAATCTGTATACAAATCTTAGAGCATATAATAAGC + GGGGGGGHHHHHHHHHGDDFFGCEEHHFFHHHHH=5:FEE=@BHHFHGHEFBHGGGHGGEHHHHHFHHHHHHHD@3:*6'1->799?;)2:94<-B5DB; @read_150_301/1 TTCTGCTACTCAATATATTGATGTTTAATCTTCTACTAACATGACAAATTGTTGAAAACAGACTGGAATTCAACTTCAAACTTGCTCTGTGCGCGTTCCG + HHHHHHHFFHHHHHHFHHHHHHHHGHFGHHHHHHHHHHHHHHFDBFCBGFHHHEEFHFFHHHHFFFGGGEHHHHF>EEDDD??>CHGFGGCC(AD+4E@FCEDDEBCFBBEDE @read_150_303/1 TGTGTTTGTATATCTATTAATGTATGTTATGTATATGTGATATTTTCTGAACTCCAGAGAGCATTGCAAAATTCATTTATGAAATCCAAACTTGCTCTGT + GEE=CCCBHBEEHHHGHHHHHEEHGEEE@1:<>:A?> @read_150_304/1 CCCGGGTTCAAGAGATTCTCCTGCCTCAGCCTCCTGAGTAGCTGGGATTACGGGCATGTACCACCATGCCCAGCTAATTTTGTATTTTTAGTAGAGACAG + HGGEEHHHHHHHHHHHHHHEGHH?/CCGHHEBHHHHHHHHFFEEFBFBADDECDDD62-3(+=?HHHHHHEECC=HHHHHHHFFHHHHHHHHHH?BBEDH @read_150_305/1 CACTGTTGCCCAGGCTGGAGTACAGTGGCACATGATCTCGGCTCACTACAATCTTCACCTCTTGGGTTCAAGTGATTCTCCTGCCTCAGCCTCCCGAGTA + HHHHHHHHGGHHHGEHHHHHHHHHHHHHHHHFHHHHHHFF7=@FFBFFHC?FHGHHHHHHHHHHA<:81*1*47=ECBGFHFFBHHGHHF:>C5GGHHE: @read_150_306/1 TAGAATCTTCTCTGTAAAATGAGGATAATATGAGTACCTACCTCACTGGATTAGTACCTTAATTGTGAGGATTAAACCAATTAATATATCAAAAGCCTTT + HHHHHHHHFHHHHEHGHGGF@@DGHHHHFFF33EHHHHHHHHD??@FHHHHGFFFHHFFDGFHHFFHHFFFHHHHFE?GEECCFHGHHGHFEGFCGEGHE @read_150_307/1 CAAATTCTTCCATAACGTTTTATGTCTAGATGGAGCCGTGACAAAGGCAATAGGTTAAGGCTTGAACATCTACAAGTTCAACTTCAAAAGGCTTATTTTA + HHHHHHHHHFDEEFHHHHHHHHGGCHHHGEAGEEDGHHG>DEEGGHHFEB@@/%/:'',,=?DD7;@>HHFFEFEFHHGGEEFFHHHHEEAABDHHHHEG @read_150_308/1 TGAATGACTGTGGGATTGGCTTATGTACTTCCTACACTATACTTTTAATTATTATTTTGGAGGATACTCCTTCTTATACAAAGAAGTTAACTATAAACAC + GEHHHHHHHHHHHF?FCCDH@F6DDGGHHHHEBDFDFCCEED>81?EHHHHHHHHHCHH@DHHFHHHHFFF?DE0<BEECEGHFFFEEEFGHFFFF@;CC==FFFFAEHHHG @read_150_311/1 GCCCGGTAGACCTCCATGGACCCAGACATGCGAAAAGGCTGCAGGAGCTGAAGGCAAAGGGAGAGCTGGTGGATTGCAGGGTGTCAGCCCAGAAACGGCT + HHHHHHHHHHHHHHHHFFGFEBEFHHHHHHHHHHHHEDHHHGDFHHHHB*5EF*'0=@DBDHHHHHHHHE>A3<3/*671C6',A=EGHHGFHEDCHCFF @read_150_312/1 AAAGCCCCTTTTCTGAACAATACCAGTTGGCATCCTGCAGAATAATCTTTGGGAAATGCTGTTCCAGGCAAATGCTACTGTGAATCCCTCTACCTTAATT + 6><>@@DGDCGEEED38CC@BDGGGH>D@@<>FEEFHHHHHHHHHCCEFFEHHHHFD@BE@@4BFHFDFHHHHHEHHHDDHHHFC@FHGDHHHHHHHHHD @read_150_313/1 TATTCTAGGTTTTCTAGGTTCCACAGCATTTACTTATATCACAGCTATCTTCTCCCCAAGAATTACAACAGTGTTCATACGACGACGACCAATGGCACAC + E@GHHHHGGGHHHFFEHHHHHHHGBBFHGHHFFFFFFB?EGDDEHFE:3)33@CFFHDEFEHGGHFHHHFCBFFHHHGFDGFFFFFFFHGFHFHFHGHE,>0D@ @read_150_315/1 CTGGGTGGCCATGCGGTCACCCATGGTGTGGAGCTGCTCAGGATGCCCCTTCTCCTCATGACAAAGCCAGAAAGATGCATGACCAGATTCCCCATGATTG + GGGHHHHHHHHGDDHA@A;AEHHHHGGB68==DAHBE?HHHFCFHFEFHHHHHHHHHB>AEG=EBFHHHHFEE?:@@DDDHHGFHHHHFDFBHHHFHFHH @read_150_316/1 ATCCTAAATCTGTCGTCATAATTAAGCCAGAAATTATCCAGTATATACCAGGTTTATTAGAGATTTGAGTAAAACCTACTGATGCTTCTAACACTCCATT + HHHHHHHHHHHHHEGHGGHHHHHG<=/?EDDFHC=:>;97AFHHHHHHHHF@GFFFFHEEBDEHC @read_150_317/1 TTAAGAAGGAACGGAAGTGGCCTGAGTCATGAAGTTTAGATTATTCTGATTATTTTAATTCCTCAAAGAAACTTTTTCTGATTGAAATTTAGCCTTTAAT + HHHHHHHH@FFHHHHHBE=FHHHHFFHHHHHGGGGACDBGHHHHHHHFHHHHHHHHHFDGHF?>FHHHHHFHFFGA@GGGHHFHHHHHGEHHHHHHHGGB @read_150_318/1 TCACCACTTCAGAAAATATATCACCTATTGCAATACTGCTCATGGTATTTGACTCACTATAATGCCACCATGCCCCGAAGATTCCTATACCCTTAAGGTC + HHHHHHHHFFA9)@BHHHHHHHHGHHHHHHHHHHHHHHHHGHHHHHFHHHHFGHFEHHHHHHHD=FHGGFFFHHHHHHHECHECCFFFHHHHHGC<;771 @read_150_319/1 GGGAACGTTCAACTCTGTGAGTTGAATGTACACAACACAAGGAAGTTACTGGGAATTCTTCTGTCTAGCCTTACATGAAAAAAACCCGTTTCCAACGAAG + HHHHHHHHHHDBDFEGGGGHEEEEHHHHHD@?FGGFFHHFHHHHHHHHHHHHHHFHHHAGFFFEFEFHHFHHHED:?D?AGHHHHHFDD<@BEEEDEGHH @read_150_320/1 ATGCCTTTGACCAAAATGCTGACAGTGATTTGGACAATAAAGTCCAGGCCGAGGTTGTCTCAGATGGAGATGAGGACTTGTTGGGAACTGGAATAAAGGT + HHFGGGGHFEGFEB/=BGA=FG=@FFGFDDGGFGHFFBBDHHHHFHHHHBFFHHHFHHHHHHHHHDFHHHHHHHHHHHHE;EFGEFFDB<=DBHHHDDEC @read_150_321/1 GTCGTGGTATGCTGCATCAAACTTAGTTCTGAGTAACGCCTAGAACAATGCATAGTATTTTATATTGGCCAATAACCAATGTTTTATAACTCCTGAACAA + HHHHHHHHHF?@@BEFFGHHGE0>EGGHHGGHDEHFFFCFHHHHHFDDDBEEFEGGGHFHHHE@:;9<@A@CBDD@A.;;<<+?FF @read_150_323/1 AAAGCGATATAAAGTAAATGAGACTCTGATTATCTGTTTAAAAAAAGATAATTACTTGAGGCATATGATTTTTAGACACTTGTCCTCTACAGTATGATAC + HFFHHHHHHHHHHHHHHGHGHHHHHHHHHFGGHHHDFHEEHHHHHHHFHHE:=2?FFHHHHHHEHFCFD?<@CCDHHFG@BFFDDFEADCFFADGFHHHF @read_150_324/1 CCATGTTAGTCAGGATGGTCTCAATCTTCTGACTTCGTGATCCGCCTGCCTTGGCCTCCCAAAGTGCTGGGGTTACAGGCTTGAGCCACCGCACCCGGCC + HHHHHHHHHHHFDEHHHHHHDDAGGGGEEEGHHFFHHHHHHHHHHHHHHBGFFHHHDFHHEHHHHHHHHHHHHDCGHHHFGFFEFGHHEGBGEFFHGEE9 @read_150_325/1 ATTTTCTTTTTTTGAGACAGAGTCTCTGTCGCGCAGGCTAGAGTGCAGTGGCACGATCTCATCTCACTGCAGCCTCCAGCTCCCTGGTTCAAGGAATTCT + HHHHHHHHHHHGHHHHHHHHHHGBEGHHHHEED=BB@FGBGHHFHHHHHHBE(46DBFEEHHFFHFB3/;GFCFBFFHHHHHHHHHEAADCBEFGHHFHH @read_150_326/1 GTATGGCACAATCATATTATTTCACAAACAGAAAAAGTAAAGAAAGAAAGAAAGCTAATCGAAATGCCTGTGGATTATAAAATACGTATTTGAAATCTGG + CCEGHHGHHHHHHHHHHHHHHHHHGHHHHGHFGFFFFEEAFHHHHHFHHHHHFH@ADAD>@;9CGEFCEGGEGBFDHHHDEHE @read_150_336/1 AGGCACCAGCTTTGAGGGCAGCTGTTTTCTTACTCTTGTTCTTCATGGAGTAAGCTAGAGAGAGTCTTTTGAACTAAATGCACAAGTTATTTGTTCAAAG + HHHHHHHHHHHHHHHHHHHGFFGHHHHHHHFHHHHHHHHHHHHHHHHEHFHHHHFFFFFFFFBBEFEBCBDGGEEAAGFFHHFB@G?ECGGGGFGGGEGE @read_150_337/1 CCCATCGTAGGTGGGACAAGGGTCAAAGAACGGAGTGGGTAGGGTGCAGGCAAGGGAGTGGGATGTGGTATTGGGTGAGGTTGAGGGCCGGACCATCCCC + FHHHHHHHHEAADFGHHHGHFGGGGGHHHHHHHHFHHHHHHDFHHEDEEHHHHHFEGBHEFDDDAA:A<>9)<@3>CCD@EEDDHHFCEHHHHHHHHHHEBHHFFGEEHHHHHHBEGFFEHGHHHHGHHHHGFGGHHHHHBD.&& @read_150_339/1 TCCCTGGCTTCCACCTCTTCTCAAAGAAGAGAAAGGCATCTCATTATGTAGCACCAAAGCGACATTTTAAAGAGTGCTTCAGCATTGACTTTATTCCCAA + DDDDEFHHGGGG=@A4+;EEEEEFEGD@DFFFEGHHHGHHHHHHHFC<@@FFFHFEGGHHHE??HHHHHEFFEFFHHGHHEFFFFHHHHHHE=:>C+*++ @read_150_341/1 TGATGAATGTCAAAAGTAATATATTCTTAGACAGTAAAAGGTTGAATTTATTATCAGTAAACATACATTATTAATGAGATCGGAAGAGCACACGTCTGAA + FFE2-8;@.3;CB7FGHHHGHHHHHHHHF?GEFHHHHHHHHHHHFHHHHEDFFCHHFHHHGGFHHHHHFFFH>BBHHHHHHHGGHHHHFHHDAA?CGFEF @read_150_342/1 TGAGAGGGTAGTGGGACACTGAGGCCCATGAGGGAGAAGCGGGGAATCATTAGAGCTGCCTCACTTCCCAACAACTTCTCAGTTTCCATTCAAGTGTTTC + DCEFHHHHHHHHHHHHHHHHHHHHHHHFD:@DBHGHFE=DGGFHEEEHFHHHHHDD=?BHE884;FHB7EAEEFHHHHHHF?FGBB:=9E @read_150_349/1 GACATTGACTTCTACCTTGTAGAAATCTTGTCTGAGAAAATTCTGAGACATCTTTAAAGAAATACCTTTTTTTTTTTTTTTTTTTTTTTTGAGACAGAGT + GDCDCGHHHHHHHHGHHHHHFFFHHHHGFFHHGGHHDGGGCGHHHHHDEFHE>5@CEFFHHFBD4EBC1=.2;;ADEAGGHHHHHEHEEEFGGBBEHHEG @read_150_350/1 GAGGTTGCACCCCTGTGGCTTTTCCGATAGGGAGATGGATGATAGAGCTGGAAGCTCATGAGCTAATTGAAGTAGCTTTCAAATGATGTATTTATAAGCT + HHHHHHHHGHHHHHHHHHHHHDCDDHFHHHHHHHEFEEHHHHHEBFHHHHGEFHGGFHFFFCDHHFGEHHHHFBDHHHHHHHEGHGGFFFHC>>EGGFHH @read_150_351/1 GCTCCATTGTGGCTTCCCTTTGCAGTCACTCAAAGGCCCCTCCAGCTTTGCTTTGTCCTGCAGAGAACTCATTGGTCCCCACCGTCTCCCTCCAGCAGGT + HHHHHHHHHHHHHHHHHHHBGFHHH?ABHHHHHHHHHHHGE+@@:ECFFCHHDHHHHHHHHHHHHHHHHHHHHFCDGFC@@ACDE8A>EGGDFEFHDFE9 @read_150_352/1 ACTCTGTCTCTACTTAAAAAAAAAAATAGGCATGTTGGCCCATGCCTGTAATCCTAGCTACTCAATAGGCTGAGGCACGAGAATCAAGAATTGCCTGAGC + FFDDDHGGFGGHHHHHHHHHDHHHHFGGGHHHHG,CFC?FFD98FHHHHHEEB.:BGGFFHHHHHHHHHEDAA9ACFEEADEE@BGHCGFHBFED@@.FB @read_150_353/1 GTCACACAGTATCTAAATTTGGACTCTCAGAGATGTATCCTAAAGCAACAGGCTCATTCAGTCCCCAGAATAAGGCAGTAGGATGTACAAAACTCAGTTC + HHHHHFGGGBEHHBEE5GHGHHHHHHHHHHHHHHHHEDDDGGEHHHHHHHHHFFEHFBFFHEFHF@AHFBAABFFHHHHGFEHGGGFEFBDEFB3DE48> @read_150_354/1 AAGGCCATGTGCAGTGGCTCACGTCTGTAATCCCAACACTTTGGGAGGCCGAGGCATGCAGATCACTTGAGGTCGGGAGTTTGAGACCAGCCTGGCCGAC + HHHHHHHFHHHHHHHGFFEEHHHHHHHHGGFDCCGGGGHHHFFEHE?DFHHFFHHHHHGHFDCEFFHHFFFF0910?DEB9<= @read_150_356/1 TAGCATTAGGAGAAATACCTAATGTAGATGACAGGTTGATGGGTGCAGCAAACCACCATGGCACGCATATGCCCATATAACAAAACTGCATGTTCTGCAC + HHHHHHDA;=EEGGGGGGHFHHHHHHHGGHHHHGGHHHHHHFFDHHHFFFHHHHHHFC138C>(4DD>>>A>CBEHHBEDD?D?83;;DBCEFEFFGHHH @read_150_357/1 ATATCCAGTTTTCCCAGCACTGTTTGTTGAAGAGACTTTCCTGACCCATTGTGTATTCTGGGCACCTTTACTAAAGAGCAGTTTTATGTATGTGGATGTA + FA@BGGGH@BEFFHFGEFGHHHHHHE@A?GHH@@<;DA@DFFFECHHHHFHHHHHHBB3'633EEGECHFHHFFHGGE-BFHFEH@@B>EHFHCECC1AEHHHHHHHHHHHFHHHHHFFFEGHHH @read_150_359/1 ATTATTTAAAACTCTGGGCTGGGCGCAGTGGCTCATGCCTATAATCCCAGCACTTTGAGAGGCCGAGGCGGGTAGATCACTCTAATTTGCCGTAGCGACG + HHHHHHHHHHHHHHHDDBA?96FGFHHHHHHHHHCFFD?FHFGGDGHHFCAABFD225FHHHD?FFHHF=ED?FFFFDDEFFHHGG=:;9DACEFFFG?B @read_150_360/1 ATTTCATAGTGTATGCGTACCACATTTTGAAAATGTATTCATCCATTGATGAGCACTGTAGTTGTTTCTGTGTCTTGGCTAGAGCGGAAGAGCACACGTC + HHHHHHHHHHHHHHHHHHHFHHHFB>C@DCG?FFHD?ECHHCAA=:7>;,4A;B@DHF:(-/3:.BG@FEEHHHHB @read_150_361/1 CAGCCTGGTCGACAGTGAGACTCCGTCTCAATTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGGGCTGGGCACGGTGGCTAACGCAAACGGGCTCTGTGC + HHHHHHHHHGGHHHFFEDEHHHHHEFHHHHHHHHGHHGGEBGHHFGGHHHHHHHHHFEHHFHHEEFFFHHFFFHHGGGBEGGEG8(/+6'%'-77DBBEE @read_150_362/1 CTACGAATCCAAAGTTGTTTACCCTACGAAAGTTGAGATTCCAGTTCATTTGCTAACCTGCAGTTTCTTATTTCTTGTCTTGGTACTTCAGTTGGCTCAT + HHFFFFFHHHHHHHHHGGGHHHHHHHGHHGHHHGGHHGGGA=@8?FFGHHHHHFFA;AA?GFCEHHGE5.3<>EHHHHGGHDHFHHHHHHHFFEEHHHFF @read_150_363/1 CTTGTTAATGTTGATATTTTGATCTCCTTCTATGAAGTATGAGTGTTCCTAATGGTGTCTGGAATAGTGAATCCTTTCCAGAAGGTTTTCAATTTACTGT + HFF@CFGGGHGDDHHHHHHHHHGHHEFGHHHHHHHHHHGEHHHHHHHHHHHHFGGD:43>*6FHEHFGHHCHHHHFFFC;GHHHHHHEHFHHEEBDDDHH @read_150_364/1 GTGGAAGGTTTGGGGGAGAATCAGAGCTTAATGTGTATGTGATCATATTTACACATATAGGCTGGTAGCCCCATAAGTGGGGGGCCATAAAAAAGAAGTT + HHHHHGGGHHGHHHEEFGHHHHHFHHHHHHHHHFFHHHHHHHHHHHHHHHFFFHHHHEEDCEDHBEDBGGBFCEEHHHHHHB>FE?5;&765,DFGGHHH @read_150_365/1 ATTTAATCATTACACATCATATACATGTATGAAAATATCACATGTACTCCCAAAAGAAGTAGATCTGATATATCAGTTAAAAAGTACAAAAACAAGAAAT + HHHHHHGGHHHHHFDHHHHGFGHHHHHHHHGGGG@D?EAHHHHHHHFHHHFFGFAF?EEEEFHFHHHFCHDGF?EHHHFD:9?EEHH @read_150_368/1 CTCCTCAATGGGCCAGGATGGAAAATCCAGGACGGATGATCCTGCCTCCTGGGCAGGGAGGGGCAGAAGCTGAAATGGAAACTCTTTCTTGGGAGAGAGT + HHHHFBFGHF2GGG9CC@4<8@FGGHHHHHHHHHHHHHEDHHHHABFHHHFFHHHFHHHHFBH?F97EFHFE?DFHHHHHHHHHE>7B?EFHGHHHHHHH @read_150_369/1 TTTGGTTGGATGAAGTTTATTCTCTCAAAGTTTGCCCAAAGGAAAATCAAGAATACAATATGCCTCAAGTTATTACATGTTTAAAACTATTTTTATATAC + @>77<39CC6EBGBEGFHHGHHGGHHHGD=FEHHC@EEFFFHHEC>(-7306DHHHFGGHHHHHHHFHHHDFHHEFHHHHHFGHHFFDDHHHHC=C@?F; @read_150_370/1 TGACCAACTATGATGCCCAACCCTAGAATGAGCAATCTAATTTGCCGTAGCGACGTACTTCAGCCTCCAGGAATTGGACCCTTACGCACACGCATTCATG + HHHHHHGGGHHHHHHHHHHHHHHEGHHHHHHHHGGHFGGEFHHHHHHFFCCEEHHHFHHFHGFEFHFFFHFDFFFHHHHHHFFF?.5036390>>BFGFE @read_150_371/1 TGGTTCTAATTCATCCTGTCCTTCAAAAACATTAAGAACGTTATTGAGCATCTATACCACCACATCAGCCCTGGTCTAAACTTGCTCTGTGCCCGCTCCG + HHHHHHHHHGFF=DEDDFFGGHGCBCDBGGHHGDDFFCFHHHEEFEHF?D@?C>@>C>@E?DGG;@2DEE7 @read_150_372/1 GACTTGCTACCCCATGCCCCGAAGATTCCTATACCCTTAAGGTCGCAATTGTTCGAGTAAGCTGTACGCGCCCATAAAAAAAAAAAAAAAAAAAAAAAAA + GHHHHHGGFFEEHHHHHHHHHHHHHGFHHHHHEBD?@379882?BBBFHFEBFFCHHHHHHHHGGGHFHHFFHEFDCDEFFHEHHFF@GHGEGHHHHHHB @read_150_373/1 TATTTTTTGTTTGTTTGTTTGAGACAGGGTTTTACTCTGTCACCCAGGCTGGAGTGCAATGGTATGATCTTGGCTCACTGCAGCCTTACCTCCTGGGTTC + HHHHHHHHHGGGEEEFGHHHHHEHHHHGH=6<<<< @read_150_374/1 CTCTCAAGTCCAACCCCCTTCCAATTAAGCAAACCAGCTGCAGGGTAAACGCTCCCAGTGGCAATAACTTAAGTATAGCCTTAGAATGGATTGGCCCTGT + HHHHHHHHHHGBDBEFGHHBFFGFHHHHHHDDDCAEGGGHHF@EDHGHHFFHHHEFBFHHFFA>>;>DEEGFHHEB*5< @read_150_377/1 AGATCAGGAACAAAACAAGGGTGTCTACTCTCACTACTTCTAATATTATACTGGAAATCTTAACCAGTGCAATGAAAAAAAAAGAAAGAAAAAAAAACTT + HHHHGGFFGFEHHHHHHHHHHHHHGEGEE@0C@AFEEHDCEFGGGHHHHHHHHHHHHF?ABBHHHHFC:.77EEDGEEEGHGHHHHHFFFHHHHFFHEAE @read_150_378/1 AGCAGGCCTTGCTCTAAAGTCTTCCTTGGCTCAAAAAGTAAGATACAAGACTGGCTCCATACCTCTCAGCAAGTCTAAAAAAGCAGAGCCAGACCAGAGC + HHHHHHHHHHHHHHHHHHHHHHHHHHHHEFHHG@BHHFFFHHHHHHHDEBD?C***7+67DEFFHFHFFDEEFBBEB?BGGFFF=CD @read_150_380/1 GACATCCACCACAACCCCAAGCAGACTGGATCACACCCATCTTCACACCATTACTGCACGTTCATACGACGACGACCAATGGCACACTTATCCGGTACTT + HHHHHHHHHHHHHHHHHHHHHHGDHHHHHHHHEHHHHHHHHFGGGGBEEHFHHHHHFHHHHHHFEDEDCBBHFFDEFHEFEFE>>>@2<9EEHHHH @read_150_381/1 ACCATAAGACAAAAAGGAGCACAGAGGATCACTTGTAGAAGGGTTTTATGAGCCAGACCTGGAAGGAGCACAGATCACTTTCATATTCCACTGGCTAGAA + HHHHHHHHHHHHFFEF@=88?=4DGFHFFGCDBHHHHHHHHHHHFECCBFF:/;9:>DDGEHHHHHHHHFF?@*EGHHHHFGH@<=EFD4<<1/8@FGHF @read_150_382/1 GAGTTTCCTGATAAACCCATTCTTTCCATTTTATTTATTTATTTATTTATTTATTTATTTATTTATTTAATGAGACAAGGGTCTTAGTCTGTCGCCCAGG + HHHHHHHHHGFHHHHDHHHHHHHHHEEBHDEDBEFHHHHHHA?FHHHHHHGFEHHHHFHHHHF8:<85@7359?CGGFGHFHHHGHHFHFEGFFFEFHGH @read_150_383/1 TACAGCAGCCCCAGCAGGAACGGAGCCCTGGGAATAAAAACTCCAGCTGCTCTCTGTCTCCTGCCATGCCTCCCTTTGGCATAACCAACCAGAGGGCAGA + HHHHHHHHHHHHHHGGDDFFHHHHHHHHGHGFFHHHHGHHEGB=@DDGGGGFCEHHFFHHHHEFDFEFHHHHHGGDG?EBBGHGFHE?FDDG @read_150_384/1 AGATGCCCCACCCTGGACTGAGGATCTCATCTCCCAGTCACTGGGAATGTTGCCTCCTGCTGGCTCGCAGCTGAGTCCTTTCTGGGAATTGCCCTCAGCC + FDFHHHHHHHHGHHHHHHHHHHEHGCCHHHHHC@GFHHHHHHHHHHHHHHEBFHHEBBDEGHHFEHHFFGGFFHA@B@BDA:>.>@B@FHHHGECEB?>F @read_150_385/1 GCAAACTGAAGTCCCTCAGTTCTACGCCTGAGCAAGGTAAGAAACTGGGTATAACTGATGCAGTAGACTTGTGTGTGAACTACTGTGTTATAGAGGGGAG + 95@DC@EEHHHHGGHHHHHHHHHHHEGGHHHHHHFFFGGGHHHFEFHHHHHHHHHHHHFHHHHHHHHHHBFGDD?FHGGGFEHFG@;?FHHHHFFF@DD('&%01.+GGGFHFHHFFFFFFFFFH>9 @read_150_388/1 GAGGAAGGGCCCAAATAATCTCCTGGGTGGTTAAGAAGGGCTCAAAGTTAACCAAGTGATGGGCTGTATACTTTGAAACCTGGAGTTCATACGACGACGA + HHHHHHHHHHHHFGGDEEGGEEEEED5ADD2:@@=BEHHFHHHHHHHHHHDGHHF>GGFBFEECC=>0>@>D8<)39:ADGGHHHHHHHE@D@EHFEHHH @read_150_389/1 ATCTGTAATAGACAAATCTATAGACCCGCAGAAATTATTTTCTCTTTTTGTCCTCTCAGGGTGTGGGGATTAACGAATAAATTCTAAAGGAGCTTTCAAG + DEEBDHHGDEDCEDBB8.D5>@ABDECFCC=1;7:?G @read_150_393/1 GCAGGAGAACTCACATCGGGCAGGCAACAGGGTAAAGTCCCAGCTAGTCCCTTTCCCTCCCTGGCTTGAGGTACGCACCTTCACGAACCAGACAGGCACA + A-'566CDE;+@EBEGEGD@=@B?/3)3@CG=EC@ADDDHHHFFDD?2*@CEGDDFEFHHE@HEEC2DFHEBEGIHHHHHHFHFDHHHHHHEEFHHHHCC @read_150_394/1 ATGTGGCTTGCAGAAGTCATTTATTCATTGAAAATGTATTGAGCCTCTTCTTTGCACCAGGTCTCATGAATAATTGACAAACCAAATAAACATGGTCCCT + HHHHHHHHBEFGEEHHGGDGGGEBD;ACADFFHDFFBFFFHHFHFFHHFGFHHHHFFDCFFCBHBACFFHFCAADE=8EEBGDHEE>CDC?HHEAFFHFHHHHHGHHHHFFFGFCCD>+>,9=C9 @read_150_396/1 TTTCAAAATAGTTTGGTAAAGGATTTTGGAGCCAATGTTTGTGGGTGTGGTAAAGTGTTTAGGTGAAGTTTTGTTTTTGGAGAGCCAGAAGCCGAGGCTC + GGHHHHHHHHHHHHHHHHHHHHFCDE@BEEFHEGGHHHHHHHHHH:,=HEHEEDHGHHHHHHEHHHHC;D>:@FFHHFHHHGBHHFHHHHHG@@>CFHFH @read_150_397/1 GTAAGTTTCCTGAGGCCTCCCCAGCCATGCAGAACCGTGAGTCAGTTAAACCTCCTTTCTTTATAAATTACCCAGTCTCTGGCAGTTCTCAGATCGGAAG + HHHHHGHHHFHHHHHHHEDFEEEDFGGEHHHHHHHHHHHHHHHHHHHHHEDHCEHHE84;@HFE9?DDBDFHHHHH?FHHHHHHHFFGHHBDA?A,8FHDDBFFEBFE:DEEE @read_150_399/1 CTCCTTGGAAAAAGTAAAAGGAAAATGTAAAATGGAGTCTACCTTCTGGATGCAAAGAAATTCTCATCATCACGTGATAGCAAGGAGATCGGAAGAGCAC + GEEEHHHGGGF?DDEHHHHGBEGFEHFFFFCGFEEEHHHHHHHHHHHHHHHHHFEFDFE?>6FEDEGEHGD=CFBGGHHF?8:>FGHHHHHHBE954DFA @read_150_400/1 GACTTAGAAAGCCTTGTCTAAAACCATTGTGGAAATAAGTGGTGGAACTGAAACTTGAAGTCCACACCAACATCCCATGCCCCGAAGATTCCTATACCCT + HHHHGFDDFBFEFFF=FHHHHHHHHHHEHHHHHHHHHHHGEFHHFHHHHFEEFGHHHHHHHFEHHFHA @read_150_401/1 AATTTTTCAAACTTTTATGCTCTGCTTCCTCTTGAATGTTTTGCCACTTAGAAATTTCTTCTACCAGATACCCTAAATCATATCTCTCAAATTCAAAATC + HHHHHHHHHHHHGHHHHHHHHHHHHHGFHHHHHHHHH:@?FHGE=AGHHHHHHHHHHHHEFHHGFHHBFFDCHFCHHHHHHHFHHHHG=;E8C?:93''' @read_150_402/1 GGACATACACTGGTAGCCCACGCAAAGATGAAACAAGCAAGGTCTCATCTCCCAAGATGGCACAATTTAGTGAAGGAAGAAGGAAATGTTCTCAGCTGTC + HFBGHHHHHGGGGGGGHEEBGHHFHHHHHHHHHGFFFFHHHC4DGDHHHFFBFBHHHHFHHHFE?GHFFFBHFHHHHHFFEGFHGFBGE<1+?ECDFD??.,0;EFGGHHH @read_150_404/1 ACATATGCCTTAGTTCTGTCTGTTTTTTGACTTCATATGAATGAAACCACATGTAGGCATGTATCGCTGCTTACTCTACTGCCTCATCCTTATGAGATTC + D@?A?68EGHHHHHHGHHHHHHHHEFCHHGFHHEHHHEEHHHEECCGGGHHHFCHFFFHHGGEFFFFC@A@DEE>GGGGGHGHHHGHHHHHHHHHHHEAC @read_150_405/1 GCAAATTGTTGAGCCTCATCTCCACAAGTTTCATTTTGGTAGGTTTTGGGTGAGGTCCCAAACTCTGTATTTTTTTTTTTTCTTCTTAAACTTTATGGTC + GHHHHHHHHHHHHHHHHHHFFHHGGGHHC@EGGDHHHHHHFFHHHFHHDDFBFFHHHHHFDD@>;5FFFEEBFEDFHHHHHHHFEGHHHHHHHHHHHHFG @read_150_406/1 CTAAAAACACAAAATTAGCTGGGCGTGGTGGCGCATACCTATAATCCCAGCTACTCAGGAGGTTGAGGCAGGAGAATCACTTGAACACGGGAGGTGGAGG + HHHHGFF=?:DCBFHHHHHHHHHGEGG@2*-9AHGHGCC/;>DDAEEHFFDBFHHHHHHFHHEEEFHHFHHHGFHGGHHHFHHHHG99>5@5=HGGFFDC @read_150_407/1 ATCTGAGGGGCCCCATGATGAAATGGCAGGCAGCATCGCCCCTCTACTTTGTAAAGAAGGCAGACCTGTCTGGAGTTTTCGTTCATACGACGACGACCAA + GGHHHHHHHHHHHHHHHE@@@C5FBBHHF>@BEGGGGFFBFHHHHHHHHHDA99EHHHHFFHHHFFG663=DFF;DDCEEHHHGGFFGFHFGE><+:@GG @read_150_408/1 TGGGCTCAGGGTTGACTTCCTTAAGCCGTGTATTACTATGCTAGAGCGTGAGGAAGAACTTATAAACTTGCTCTGTGCCCGCTCCGTATGTCACAACAGT + HHHHHHHHHHHHHHHHHHGGGGHHHHHHHHHHH5FGHHHHHB@7;7EHHHGGFHHHECC//:DDDFFGHHFFFFDHHHF=:417.ADHHHFHHHHHHGGH @read_150_409/1 TCTGGCCTCTAGTTCTGGTTTTAGATGGAAAGAGTGTTGAGTACCAAAGATCTAGCTTTTTGAAAATTTTATTTCAGGCCCTGCCTTTATGTAAACTGTA + GHHHHHHHGFGEEGHHHHHHHHHHGGGGGHHFHGGDDEE=A@4;6@CDBFFD==CHHHEDDFFFHHHHHF0*2=/>AABGHHGF;FGHHHHHHHHHHHHH @read_150_410/1 TTCTTTGAAAAGCTTGCAGTTAATATAACGGCTTCACAAAAAGCTACTTTTATGTGCATAATAACAGGTAGAAAGCGAATATGCTCCAGGCACTATATTA + HHHHHHHHEEGHHFEGGGFFFDEGGHHHHHHHGHHHFHHHHHBFHHHHHHHECBDEHHHHHHHHHFGFC5<>EDEGHHHHHHFEFHHHHHHHHHHHEFHH @read_150_411/1 TGCAAAGCAAATGCTGTGTGAAAGACAGGTTTCCAGTGTAGCATATGTGGGCCACTAATGGGTGTAGATTGAACTGTTCTCTTGCCAAGAGTCATCAATA + @BEDDBDAEHHGGGGGGHHHFHHHHHHHHHHHFFGHHHHHHEEDFDD?FFHEBHE>FHHFEFFDBFHHCBFGHHHHHHHHHFFFHF=EEFHH @read_150_413/1 CTATGAGCATGTAACTTTTTAATTACAAAAACTATTACCTAATATTAGATAGTTTTTACAATTCTGAAATAATTTTTATCATAGGAAAAAGCCAAAAGGG + HHHHHGGGHHFFGFHHHHHGGHHHGEHHHHHEGEEDDHHHHHG@AEGGFG=CFFCEDADDFEFHHHFBHFEFB>9EEDGEFB?EG@EGGGFHHFHHEA74 @read_150_414/1 GAGTCCGTGAGAAAGGTGTCCACAGCAAATGCTTATGTGTTTCTCTTGTATGTAAAGTGCACAAGTACTACTAAGTTGCACAAGACTTTCATTTCACATT + HHHHHHHHGHFBFDFHHFA8EHHHHHHHHHHHHHHHGGGFBCBBBHHHHFHHHHHFFHHHDFHFFHHFFHHHHHHHACDECDHHHHHHHHHFFHHF?EEE @read_150_415/1 GATCACTTGAGGCCAGTAGTTTAAGACTAGCCTGGTCAATATAGTGAGACCCTGTTTCTACAAAAAAATAAAAAATGAAAAAAGTTCTAGTTTTCCTAAA + HHHGGHHHHHGGHHHHGEHHHHHHHHHHGHHHHHGDD?BEFHHHHC?E2@EAA><*DDACHHHHHHHB?EHFGFHHHHGHHHHHHFGHEDEHHHHHFEHH @read_150_416/1 AACATATTTCTAAAGGAGTAAGTTGTAAGTGTAATGTTTAAGGCAAATAAAGTTTAATGCAATTCTAGTAGCAATTTCTGAAGCTCTTTAATTAGTGGAA + HHHHHHGHHHGFHHGGEDGHHEHHHHHHHHEADC<;G=B>@>+EEBBCE @read_150_418/1 CCCTAAAAGGAAAAAAAAAATTATTCACTGCTATCTATTTATTGATAATCTTTAACTTAGATTCTAAAACCTGGGATTTAATAATCAAATCCCAGTACTT + HHHHHHHHHHHGGHHHHHHHHFGHHGGBEEGHHHGHHHHDEEEHHHFEEHHHHHHHHED<)5FFHBFHHH?@+DCGEEBDA;GGFGEBDD?=EEGHHB5C @read_150_419/1 GTTCCAGGATTGGATATCCAAGCTGTTGGCTTTTAGGATACATCCCCAAATGGTCATCTATCACTCTTTTTTTTTTTTTTTTGAGACGGAGTTTTGCTCC + HHGGGGHHEFFG???EGHGGGGBC@EGFGGFGHHHHFFHHHHGFFHHHHHHHHFHHHHHHHHHHFHDACEHHFF9EEEECEGGGGGHHDHFHHGGEFFCB @read_150_420/1 GGGATTGATCGAGGAGTCCCGTGTCCTAGTCAACTTACCACTTTGTTCACTTATCCATCCACTTGCTCATTTTTTGGCCCAATCAATCTACAAATGTGTA + HGGBD@EHHHHFFFHHHHHHHHHHGFFHHHGGGCDHHHHHHHBECB>ECEEHHHHFFEHHHHHHFHHHHHFD@>91G?FGHHHHFGFBBEDDB=330?GH @read_150_421/1 GACTCTGCTTCCCCAAATGTGGGGAATCTGAGGGAAGGATATGAGACATGTTGAGGCAGGAAGAAACTTGGCCTTGGAAGAGAAAACACTCATGATCCAG + HHFGFGHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCFEEDA=@>79FHHHHHBEEEFEC,)/(/)630>DDEEBEBDDDEGF;59D6*499:+4>0><- @read_150_422/1 AAGAAAGAAAGAAAAAGAAAAGTAAAAGGAAACAATTCAAGTGTGAATGGAGTCATAGTGGAAAAAAAGAGTTCCAGCCAAATTCTTTTCTATGCAGCAT + HHHHHHHHHHHHHHHHHHHHDDGGGHFHHHHHHHGAGGEHHHHFFFFGFHBFFHFFDEEHHFBFHEEFDD=?3>-,EDHHHFHHHHHHHHHHHCFHHHFFG2GHFHHHHHHHHHHHHHHHHHHHHHEHHHHHHF?79@@HHHFH7C99+*4CFHHHF65+:,48DEF5EGHHFCFHB;7B @read_150_425/1 TGCAGCCCTGGTTGGTATGGTAAATAGCAGGACCAGTGAATAACATGGTCATGTGCTCACTTTCTCCATGGCCATGTTATGGGGGGTTCATACGACGACG + HHHGGGHHFHHEEEAFAGFB25FGGGGGEC2@EHHHHHHHHHHFGBBFFHHHHHEDDEFHFHHFBCFHEHBFHHFHHHFFEHHHHFFHHHHHGFGGFHEB @read_150_426/1 TACATTGTCCACGAATTTATCAACTTCTGCTAGGTTTTTTTTTTGTTTTTTTTTTTTTTTTTGAGATGGAGTCTGAAAACTTGCTCTGTGCCCGCTCCGT + HHHHHHHHHHHHHHE0EEEFHHHHHGGEEB?GGHHHHHHHHGHHHHHF<5=FHFFHHHHHGFFHHHHEBFBDFC>EFFHHHHHHFEBHBD?DD:6GEHHH @read_150_427/1 AAAGCCTGCAGAACATTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCACCTAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAA + HHHHHFHHHHHHHHHFE=@@@B@@GHHHGGHCBGGCD@B?CA=:)-<<@>/)4EFHHHHHGGHF89CCFHGHGHEHEHH43'@A@<1A;=> @read_150_432/1 GACAAAAGAACACTTTCACTTGTGTCTTCAGCCAGTTCCCATCTGTAAAATGGAGTGATAATAGTATCATAGGTTGTTGTGACATTTTCCTTTGAGATGG + GGGGGGE@DC8,=:BGCEHHHFGGGFDDFFHHHHHHGGGHHHHHHHHHFDDEHHFHHHHFGHHHHHFFFFAADDEGGGGGHHHCFFHHEHHFFFGGFEGH @read_150_433/1 TTTTAATAAGCTGTTGATCTCTTGATGATACAGGAAAAGATGAGCAAGTCCTTAGAATCTGTATATCTTACTTCTTTGGTTTTCGATGACAGAAAAATTT + HHHHHHHFFHHHHHGHGGHHHHHHB=@=GGGHHH>B34EEHHHHHHHEHHHHHHFEFEBHHHBBAFB=@DFFADDDA;1,149C@CCB=EGHHEC00B-; @read_150_434/1 GTGGAGTGGAGGCCTTCGTTTTAAGACCAGGGTTCTGATTACACCTGACAGGGCCGAAACTTGATGCCCGCAGAGCTTACTGATATCTTATCTTCTTCCA + GGCHHHF@EFHHHHHHHHEBEEEDHHHHHHHFHGGGHHHHHHBFCHHEHHHFFFFFFFHHHHHEHHHHHHFHHEEGHGHHHGHHHFFGGED@GGGGDF;7 @read_150_435/1 CTATGTTTTCTTTTTCTTTTTTTTTTTTTTTTTTTTGAGATGGAGTCTTAGTCTGTCTCCCAGGCTGAATGAAGTACAGTGGGGTGATCTTGGCTCACTG + HHHHHHHHHHHHHHHHHHHHHHHHHHHHFFFBBGGGHHFDFEABCEFFFHHHHHHHHHHHFHHHFE>BF?D=>><><;8;FFHHGEAFEFFC8-;EEFF? @read_150_436/1 ATTAATTGTGTCCTGGGCACCTACTGTTTTGTCACTTGTTGGTGAGCCTTCTGAGGGCAAATACTCTGTTTCATTAATATTTTTTATCTCCAATGTCTAG + HHHEEEE@@?556&0=>9@ADEFFEHH=CHFFEHHHHCCDD>?FB@?FEE?BGGDDDEGE=7+ @read_150_439/1 TACTTTGGGTCAGACACTGTTCTAAGTGCTGAGTGATGAATAAGGTAAGAGCCAGATGATTATACTGTCATGGAACTTAAATTCAAGGGGATGAGGCAGT + DCEGGFGGHHHHHFFHHHHHHHFHEF=FHGHHHEEEGGGGD85AF6FFFHGGFHHGG;:EFHHHHHC,>;A@FE?A7.34AGHGHD;DFDBDEGGHHCFH @read_150_440/1 GGAAGCGAGGCAAAAAGCTGTGGCAGGCCGGGCACAGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCCAGGCAGGCAGATCACCTGAGGTCAGG + HGGGGHHHHHHHHHHFD@HHHHHFBEGHHHFHHHHHHFHHFFEEEGHHHHHHHEHHHA+5'*>:@DFEE?<>@-6 @read_150_441/1 AAACCACCATCTCTCACCTAATTTTTGCACTCCTAACTAGTCTTCCAGATTTTATGCTTGCTTCTCTGTGGTCTATTTCCACACTGAAGCCAAAGTGATC + HHEEEFFFHHHGGGGGGHFHHHHHFD?95/@DGHB@GFBEDBHHHHHHHBCGGDHHHHHHEFEGD=FHFCEBHFHHHHHFEECEBEGHHEHFHHFGHHFF @read_150_442/1 TCTGTAAAGTATTTAATATAAGGTCTTAATCCCAGTTGCAGAGTTGTGTGTAATTTAAAGCACAGCATTTTGTGGCATCTGGGCCATTTACTGCCTTTGT + EGHHHHHHGF@?@EBEDFGHHHFFHHHFFBEHHHHHHHHHHHEFHFEHHHHHHHGGFHHDBCADHDD?C??A?EEHHHHHFHHHHHHHEHHHHG79EGEBFGG @read_150_446/1 ATGATAAAGCTGCCATTAATATTCCTGTACAGACTTTTGGTAGATGTCTACACTCTTTTCTCATAGTTATGTTCCTAGACATGGAGTTGCTGGTCGTAAG + A3AFGGFGGHHHHHHHHCCEGDFFHHHHHHHHHHHHHHEFGHHHHHHHHHG<099EC?>9DDHHEEHHHEAACFEGHHHHGHGEDCAEEFGG==5BCDHF @read_150_447/1 CAGAACCAAAGACAAAAACCACATAATTATCTCAATAGATGCAGAAAAGGCCTTCGACAAAATTCAACAGCCCTTCATACTAAAAACTCTCAATAAACTA + HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHFGHHHHHHHHHFG=7'.;D9EEHHHHFDFHHEFEEEEEFHGEEDDHFAD=DCDFBFCECD;DD// @read_150_448/1 ACAAAAAAACAAGAATGGCTTATAGGCTCTGGCCATCATCTCTCTAGCTTCATCTCACATCATTCTTTCCCTGAACCTCTAAGCCCCAGCATTATGGCCT + GGGFEEEEBHHHHHHHHHHHHHHGGHGGGGHEHHHHGFGGGGDADF>D=1A?ACDFGEHH=A?@ACCFHGFG @read_150_449/1 CAAAGATGTACAAGGATGCCCGGTTCATACGACGACGACCAATGGCACACTTATCCGGTACTTGCGTTTCAATGCGCATGCCCCATAAAAAAAAAAAAAA + C,9447CC8?DFEFE@BBHHHEBFHHHHHHHGGGGHHHGFEFHHGEBCBHHFA>> @read_150_450/1 GGTTGTGGACTCACAAGTATTTGTGATTCCACAATATTATAATCCATAACTTGCATGTGTATTATTTTGTAGGTATCAAATACTATAATGTTAAAAAATA + HHHHHHHHHHHHHHHHGEBHHHHHHHHHHHHHGFEHHHFFFHHHFHHEEEGF?EDFFGHHHHFF@??5:=98>CBGGGHHGHHHHHHHHHHEEHHHHHHE @read_150_451/1 CTTACAACTTTAAAGAACTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCACCTAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAA + HFFED@=?EEFHHHHH@DBEFGFHHFHHHHFFFFHDEHHHHHHHHHHHHHBFFFBFFGFHHH=>91AFD?FEHHFFHHHHGFFFGHHHFGE=EHDG?BB0 @read_150_452/1 CTAACCACAGAAATGTCAAAAGAAAATAAATGGAATTCTTTTCGGCTACAGGCAATACAAAGAGAAGTATAATCAAACATATAAAAGCTGCTTTAGGCAC + DCDHHHHHHGEFGGHHHHHHHFFDD@@BBEFHHHHHHHHFFE?DFEEAAAGGEHHFFGEGDC4==CEEFFED@<1;EGFFFHEGG@FGEEGGHHHHHBEG @read_150_453/1 ATGTAGAATTATGAAGGATCTTATTTTTAATTTATACACCCAGATATTACTTGTTACTTTTAAAATAATGGCTTTGTAGTTTTTATTATTATAACAGCTA + HHHHHHHHHHFE@EFHHHHHHDBCFEHHHGHHHHHHFDHHHHGFGFGGFEHFEEGHHHHHHHHFFHHGEADBD>CDB@BDGFFFFHHGDAFC@EFHHEFB @read_150_454/1 ATAAGATTCCTGGAAGCCAAGTGAAGAATAGGTTTCAAAGAAGACAGCATAATCAACTCTATCAAATGCAGCTGCTAAGTAAAATGAGGCCTGAAAACTG + HGGFHHHHHHHHHHGHFFDGEEHFHHHGGFHHHGHHFHHEB>CCGHHH?EFHDFFHFDHEBDGEDF9@=GHHFHFEBDCFHHFGFDAAAFFDDEEE?DGG @read_150_455/1 AAGAAGGCAATGATGTCTACTTTTGCCACTGTTATTAAATATAACAAATACCTGAAGGCCTAGCTAGAGCAATTAGGCAAGAGAAAGAAATGAGGGCAAC + HGB<=CDEEHHFCHHGGGGHHHHHHHHHHHHHHHDEHHHHHHHHHHHFHHHHHGHHFGHFFFHHHHHHHEBCCCBGBBEEFF(?8EHHFGGEEECCHHBD @read_150_456/1 CCTTGCCTGGAAGTAAGTTTACATTCTTTAACTTTGTATTGCCTCCTATATTTTCCAGTCTAAGAAATGGTCTTTCTTTGTAGACTCAATTTTGGAACAT + FFFGBDBHHHHHHEHFBHGF@?DGHHHGFG895@HHHHHHHHHFFFFFHHHHFFEHFHHFHHFHEBDCBFHHHDDHHHHHHHHHHHHHHHD?*++)--54 @read_150_457/1 TTGGCACGTTTTTCTGCGCCAGGACCCTCTGGCTGTAACGGTGGCTGTCTCCATTTCTTCCAGTGGTGGCTCTGATAAAGGGAACCTAAAGTCTCAAATT + HHHGHHHHHHFFF8>EGGGGGFBEBGHHHHF@BFHFFHGFHHHHFGGE.FAGFE?FHHHEE992*''9CHHHCE4;=>@HHHD5CECF>@:<+BB?DD @read_150_461/1 AAAAGGCCTTTGACAAAATTCAACAACCCTTCGTGCTAAAAACTCTCAATTAGGTATTGATGGGACGTATTTCAAAATAATAAAAGCTATCTATGACAAA + GGGGGFB=D>FHHHHHHFEHHHHHHHHHGHHHEGC:CFFA?DD.01=@A5>*7A4BHC1:4)+;5:ADE@>.5A<@A>54<(( @read_150_465/1 CCCCAGGCTGTTCCCAGCCAACAACTGAGCGTGGCAGGGACACTAAGACAGGCCCATTCCCAGGAGGCCTAGGATTCCCATGACAGGTAACTTTGGCTCA + HHHHGHHHHHHFFGEEFFHHHHHE7EEEBF=:E?DEHFGEFFBEBDAFCFHHHHHHHFE@HHECCFE>FB@GDHHBD/.BBG@@AEEFHFGGHHHHHHHH @read_150_466/1 TGTCTCAAACAATAAATAAATAAAATAAAAATAAAGAAAGACTGGTTAAACCATGAGCACAGAGAGACTGCCCAGCACACCAGGAAGAGACAGAAAAACA + EB=EGGEEFGHHHHHHHHGGBHFFBFHHHHC?>FHGFHHEFGHGHHHHHGGEFFFHFEGGHHHHHHEE?FEFHHHFHHHHHHHHB?<)>@5A@CFHHHHH @read_150_467/1 GGTATCTGCAGGGTTGGTTCCTTGCTAAGGCTATGAGGAAAGCATCTGTTCTAGGCCTCGTTCCTTGGCTTAACATGGCCCGAAGATTCCTATACCCTTA + HHHHGHHHHHHHHHHHHHGGGGGGGGHHHHEFEHHHHHHHGGGG;.)0:ADGGGHHFEDHHGGHHHHFFDAD44@ED,62=DDHHHHHHF78<8898;EF @read_150_468/1 AAAGACAGGGTTTCACCATGTTGGCCATGCTGGTCTCAAACTACTGACCTCAAGTGATCCACCTGACTCGGCCTCCCCAAGTGCTGGGGTTTCAGGCATG + GEBFGDFG=CABBCB:@;DDF535A>?BDG @read_150_469/1 TCTAATGAAGTTAAAGATGAAATGAAGATGTGCTGAAAGATTCGGTAATAAGACCCTGTGCACTTACTGAGCATGCAGACTGTTCTTTAATAGATGTGTG + HHHHHHHHHEHHHHHHHHFHHHHHHHHHHHHGGDEEFEEEFFHHEHFDGGFGGGGGHEB?2<.%&)5:@@GEHGHGGEFFHFFFFFHHGHFD/36;?C?< @read_150_470/1 AGAATGGCATTAGGATTCATTATGTCAATAATGATGAGAAATAAGTAAGCAATTCAACTGGTTTTCTCAAACATGGAAACTATTCTCCTGAAAGCCTTGG + HHHEEBHHHHHHHHHHFFGGGHHHHHGHHHEEGHHHHHHHHHHHHHHHHHFHFHHHDEHHHHDBD6>BEECCBHHHHG?<91)88;5DFGDBHFHHH78; @read_150_471/1 ACCTGAGAGACAGGAGGCCGCAGAGAGGCTTTTCTGAACATCTTGGGCATTCAGTTGAGACCCCAGAAAGGCCACACCCTAAAATTAAGATTGTCCTGTA + HHFEGGHHFHFHHHEFHHHHHHFFDEHHFHHHHHFHHHHHFADA9EEHFHHFEEFHHHHHHEEGE9;E.:;>4E?:;<7;EGHHHHHHFDFEEA').'1* @read_150_472/1 TTGTGCCTCAACCTAGTGTTCAGTAACTGAAAACAGCAGTGGGACCAGGCAGTCTCCAGAGGAAATGTGCAATCCCAAACCATGATTCTTTTACAGCTTT + DC-9?GCDDFHG;:A?FEGFGG==BHHHHHHE>HHHHHHHFHHFHHFEHHHFHHFHDHFBE?=,5F?AEHHHHHHHHHHGHHFHHHBCHHFFFAD?CE @read_150_477/1 ACTTCTGCCTCCTGGGTTCAAGCGATTGTTGTGCCTCAGCCTTCCGAGTAGCAGCTGGGATGACATGTGCACACCACCATGCTCGGCTTTTTTTATTTTT + HHHGEHHGGHHHHFGF?FHGHHHHHHGHGGGEGFHHHHHFHHHCEFFFHHDD?EE?DABHHHEEHGFFHHEEHHHHHHHGGEEFHHHHHHHGFDDAF?:; @read_150_478/1 GGCATTACTCTATTATTTGTGTTTCCATATTCAAACTCTTCAAGAGAGTATCTGATTGGCTTGTCAGTTACTCTCCAGTATAAATGCCAGATTGGCCATA + GGGGGGGGC7BHHHEEHHHHHFGFHDEFGGFHHHHHHF<@EFHHEHHHHHHHHHFFGHFFHHFFDHA?CFFFDDDGGGFGHHHHHHHGH:DEGGHHDEHG @read_150_479/1 GTCTTAGGGCAAGTTAACAGCTCTGATATTCAGTTCTCTCCTTTGCAAAATTGGAGATTATCAGATGTGACATGAACATTTCTCTGTGGACTAGGGGTGA + HHHHHHHHHHFFDFFFGG@>CDEBFFGGG@@:;HDGGGFHEGHHHHHHFFAEFHEHFHHHFFE?2>5/EHHHFGHHHHHHCCEDD @read_150_480/1 CCGCCTCTGGCATCAAGTCCCACCTCCTACCTCAGGAAGGCAAATAAAATAGAAATAGAGGGGAAAATGAAACTAATACAAAAATTTGGTAAGTTTATAA + GEEFHHHHHHHHHGGHHHHHHGGHHHHHHHHHHFF0/92DFHHHHHHGGCFHGGGHGGGGHHHHHBEHFECFHDD>8FHHHHHHHHHH94>FBEDB:@FF @read_150_481/1 AGTTTTTATCCTATGGGAAGGGAAGGAATATCCCCACTAAGCAGGTTTAACAATATTGTGGGAAAGAGAAGAAAACCGACCTAATTTGCCGTAGCGACGT + HHHHHGEDFGGHH@F=DDFD6;EEHHHFHEHFFFGHHHD9BD=DDHHHHEFHHHHGFFBEHHFHHHHHFF@CCGEDFHHHHHGEGGGFEFHHHHFB<@BF @read_150_482/1 TTCAAATCTACCAATTCAAAGCCCTTACACCCAACCACCTACTTTATCTGGCTCTTGCACTCTGGGTCACTATCCACTTGCCCTAATCACCTCAGGACCA + GFGFHHHHFFHHHHHHHGHHDEEHHHGFFHHHHHEB<<2EHHHFEDHFHHHHHHHHFFFFFHHHEHHAFHHHEEEFFFEEGG@@GFHHGHEHHHHHGEGE @read_150_483/1 TTAATTTTTTGAGAAACCTTCATACTGTTTTTTAAAGTGGCTGTCCATGCCCCGAAGATTCCTATACCCTTAAGGTCGCAATTGTTCGAGTAAGCTGTAT + GGGGF@FHHHHHHFFHHHHHHE@@HHHHHHHHHHHGCD38CCADD@??EHHDBAA?FFHECF@=DFDFFHHHHFFHHHHHHF><=E9DECD;7( @read_150_484/1 AGTGACAATATGATGTAGTTAATATGAAGAAAATGAAGGGCGACTACAGACTGAGGTATACTGGGTGTTGTGTGGGATAACCATTTGCTTTCTTCTTTCA + GEEHHHHHHHHBEGDAGHHGHHHHHHHHEGFFDDDFGHHHHHHFFHHFHHGBEGE9:DFDEHGGFBHHHHHHHHHHHHE>EGF?; @read_150_486/1 CTGACTCTCCTGCTTCCATCTTCTCTTCTGTAATGTGGGGCTAATCATAGAACCCACCTCATAGGGTACAGTGATAATTAAATACTTTAAGCTAAATAAA + HHHHGHHHFEBC@FFGEGED3=5C9>?DB@>C:>A:BEFFFEDFHGBD:>:@ @read_150_489/1 TTTTTCCTGGCTCCTAAAGTGATCATTTAAATATCTTTCCAATGTGTTGAGCCTCTCAAGAAGCAGTTTCTACACATGTTGACACCTATTGGGTGTAACT + HHHHHHHHHFGFHHEFB=>EBD?B@EEHHHBAB3DEC;9DHHHHHBDDDDCCFHHFBB9)/:7=C4DCGFHHCADFFGFDDGGHHHGHFFFHDAGEEEDF @read_150_490/1 CTAGATCAACAGTTCTCAGAGTGTGGTTCCTGGATCAACAGCATCAGCATCATCTGTGACATTGTTAGGAATACAGATTCTTGGGCCGCATTCCGGCCCT + HGGGEGBFFD@GHHHHHHEEFFGHGBE?C:EBF>;/);2 @read_150_491/1 CGTGGTGGTTTAAACACTGGTTGTAAAGGAATGTGCCTCAAAAAAACAGGAAGGAAATCAATACCAGATCTATTGATTTAAAAAGCTAATGGATGGAACC + HFGGGHHHHHHHGGD9<@+')??DBFFHHHHHF @read_150_493/1 AAAAAAAATCTCCACATACACAAAACCAAACATTTAGGTTTTGTGATTGATACCTTTCAAGGTTTTATTTGGATGAGCTGTTATAAGAGCAGGCCTCTCA + HHHHHHGGHHHGHHHFEEEEGGGHHHFHHHHHHFFEEHHHHFEEEHHHHHFHHHHHECD4@>>?FGG<:DDFGHHEEF?DFFGEHFB5DCGD(>@HBHHHFEG @read_150_495/1 TGCAGGGAGTGGGATGCGCAGGACACAGCATGAGGGGGCTGCTGGCCGCCAGGGCTGGGTGTGTGGCCCCTGAGGAGGCAGGTGAGAGGTCATCTGGCTG + BA=8=BDEGHHHHHHHHHEHHHHHHHHFFA@@GFHHHHHHHHHHHHHHHFFHHHHEE=CBHHHHHHFH?DEFFDEEF?EDDFDC@DFHHHHHHHC>:DEF @read_150_496/1 AGTTTAATGTGTGTTGGATTGTGTTCATACGACGACGACCAATGGCACACTTATCCGGTACTTGCGTTTCAATGCGCATGCCCCATTAAAAAAAAAAAAA + HHE@FGFDGEHHHHHHHHFHHHHHHH=EEHHHGGGEHHHHHHFFH?DBEBAHH@9.5?E=@:?GD?ACCF4CFHHFBHHHHG8=?2-<>@EHCCFFB>?C @read_150_497/1 TCAATAAAAGATGAAGAACCACTGGAGGGTTTTTGTTTGCTTGCTTGCTTGGTAAATTGGTTGGTTAGTTGGTTGTCTGATTTGTTAAAAAATTAAATTA + HHHHHHFHHHHHHHHHHHHHHHHHGHEDD=<4FFGEFHHHDEFFFFHHHFB?FHEF;8GGHFFFEGHDEEHHEEEGB@EBBEFHHEDD<>40?C=EEFHH @read_150_498/1 AAACAGAGGAGGAAAAATACTCAAAGAAGGGGAAGATAACAGGAAAAGCTAGAAAAAAAATGGCTAAGGAATAGGACAAGTTCCCATACAAATATCCAAT + HHHHHGGEED*@@CFHHHHHHGFFDHEHHFHGHHHHHHHHHCEEEHHHFHHHHHD?E@56.:7,DE5>>EHHFC@EE993EGGGDFFHHHHGHHHHHHHG @read_150_499/1 TTTTATAATTCAATAAAAAGATAAATTATCCAATAAAAAATGGGCAAATGTTTTGAATAGACAGTTCTCCAAAGAAGATATACAAATGGCCAGTAACACA + DHHHHHHHHHHHHHHHHHHHHHHHFGGGADG56A?FFFGHDGHHHHHHHGHHHFHHHFHCEDFFEFHHB@EEEEHHHDFHHHFFGHHHGFFGGGFGEHHH @read_150_500/1 TCTTAAACTCTGTGATTTTGAGTATCATTTCTTCCTTTACAATTATTTTAGAGGTTTCCAGTTGTTGAGTCTTTGTAAATTAATCCAAACTTGCTCTGTG + HHHHHHHHHHHHHHHHHHHHHHHFGBEFHHHEGEEEHHHHHHHHHHHGGGB@H?C,BGHHFHHEHHHHHHHHHHHHHGGFEEHHEHHHHHHHHHBD?:EHDCBD?DFHE??@?DDBDDBGE @read_150_3/2 AATACTAGCAATAATAGGAACAGACACTGAACTTTTATGACTTATTACAATTATTAACGGAATGATTTACCCAACACAGTCTTAGAATACTGAAAGTTGG + DG@HHHHHGGFFFHHHHHHHHHGGHGGHHHHH>HGBHHHHHHF5EFDAF?GE@GGIG@B47CEGEGHDDFE@+--&;5(+:;?CC1=004;57)+:+5=A @read_150_4/2 TGACTGTCTCTCATCCCCCACTCCTGCAGAATGTAAGCTATATGAAGGCAGAAGATCGGAAGAGCGTCGTGTAGGGAAAGAGGGTAGATCTCGGTGGTCG + HHHHHHHGFG7/@FEEEIFDHFHHHHHGFEFFHFBBBDEEEEBFHFFCGGFGGGBCBD8'9:C5<=>HFDFFCGBEE @read_150_5/2 CGTTCTAACTATCTATACTGTGTAACAAATCACCCCCAAAACTTAGTAGCTTAAACCACCATGGTTTATTATTTCTTACAAGTCTATAGGATAGGAATTC + @.2>AGHHHHHHHHHHHHHHHHEBE:CFG@:4<:-88ACHHHDEEFFEFHHHGE932;8/CC @read_150_6/2 TTACATATTTAGCTCCCCTGTTCTTCTCAATACCTCTGTGAGTATTTGATTATTGCCAGTTTATGGACAAGATATCTGAGGCCCAGTTTGCTTGAGATCA + GGGHHHHHFGGFHHHFHHHHHHHHEHHCDCGHFHBHHHHHDHH?AEGHHHHHHHHHHHGGHHHHHHHHGGEFHHFHGEEEFFHHHHFGEE*1@97-4AED @read_150_7/2 TCAACACTAAGAAGCCTAAATTGAATAAACACACACAAAACATTGTTAAAATTTTGCAAAAGTTTATAAAAAATTATTTTTGTCACTATTTATTGAGAGA + BCD95?DHHHHHHHHHHHHHHHFHHHHHHHHDGGHHDDBHHFFHHHHHHHGHHHHHFDFGGGDDFGFEHH@7-64).@?B?HHHHHH@>?ED?FFFEBFH @read_150_8/2 TCCAACAATGCTTCGAGCTGATACCAGGGGAGGAGAGGGTCAGCCTTGGGGCCGGTGGGGGGGTGCGGGGGCAGAGAGCAGGTGCCTTCGTTGGATTCTC + HHHHHHHEFEEAB,5?=@@?CEEHGHGHFG7'045-.5:;GBGHHHHHHHE8@DCFEEFHHHHHHEB@@HGHHHHG=HHHHHEGHEDEEHHHHHFHHHFE @read_150_9/2 TACAGGCGTGAGCCACAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAACAAAAAAAAAAAAAAAAAAAAAA + HHHHHHHHHHHHHHFGGHHHHHHGEHFDEGGDBBGHHFHHHFGAEHDCHHGGGGIHGHGHHHHEBEFCGGGGEEEE>+,;>BD@@7368EAD=F @read_150_10/2 AATTAGCCAGGCGTGGTGGCGGGCACCTGTAGTCCCAGCTACTCGTGAGGCCGAGGCAGGAGAATGGCGTGAACCCAGGAGGTGGAGCTGGCAGTGAGCC + HHHHHHHHHGF=BGHHHGA55><00>>CEEHHHHHGGIGDACEHHHHHFGEHHHHHHHHHHHHFHHHHHGFFHFGGEFEHHHGE7 @read_150_12/2 GAAGGGACACGGCGGAAGGCAAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAA + GFFHHHHFGHHHHHHHHEEHGHHHHGHHHHHHHBE@DC@GFCGHFHHHH?E @read_150_13/2 AAGACTGCCAAGCATAAAACATTGATTATTAGCATAATATACAGTTGCATTGACCCGAAGGGCTCGCTGTTTAGGGAGGTCAGAAGTTGAGCGGGTTCAA + HHHHHHHHHHHHHHHHHHHHGFHHFGHHHFDBHHHHGDDHHHHEF@=B@.@DHHHDD8@CAG?E6-*8EEEG8GHHHHEEBGFFDFFFF=.;9@EEHF/@ @read_150_14/2 GTATTTTAATTTTTGATGGATTGGTGCTTATTTTCCTATCTTTATTGATATTAGATACTGACAGTGAAGAATAATATTCAATAATAAAAATTTGTGCTTC + FHHHHHHFHHHHHHHHH;;-((/ABGGBFHHHHHHHHHHHHHHHHHHHHHHHHHHHHGEF=<53=E7AC>EFEHHHHHHHHEHF:3-DFGHHHHHHHHHHGGG@?>D?DHHHCDDHHHHHHHHHHHHHFHFC53F@BDEEHF @read_150_20/2 GTAGTTTGTATTTCTGTGGAATCCATTGAGGCTAGGAAGAAACTGCATAAACTAACGAGCAAAATAACCAGCCAGCATCATAAAGACAGGATCAAATTCA + HHHHHHGGDEBFHHHHHGGGGEFFC?476*,:6B?A@?>ADFHHHHDFB:EGHFHHHHHHHGFCDGGGHHHHHHE6+=9FB>856>9A>@75DE7.,,3DBEF @read_150_22/2 GCAATTGTGGATGCTTAATTCTGTGTTAACACCTGGAGGCAACAGATTCAGGGAAACCAGAGTGTGTTTAATGTCATGTTTTCAACGAAGGCTGAATTAC + GFDHHHHHHHEEHHHHFEEGEGHHHEGHHHDC/8@@GEECGDG?@EGFFEHHHHHGHHHHHGGGGEE:<*&,7:3?EHHHHHHHHHFHBFFEEFGEH@>; @read_150_23/2 TTTCTATTTCAGTTAAGAATGTCATTGGTATTTTGAAACAGATTGTATTGGGTTTGTAGATTGCTTTGGGTATTATGTTCATTTTACAATATTAATTCTT + D98DEE?D;=,+6:HHHHHHF@?FHHHFDDEEFCFGEHHHADHFFDEGGFHHHHDFHHHHHHHHHHFG@=D=-E?8<8F>0*1:FFHHHHHHD7FGGHHHGHGHDHCFFFFFDE64.36DBHHHHHHHHHHHHGHEEEGE@EEGFGGFFGGGG<8CGFFEBED@@+5@@@3)0%3A>?A?C @read_150_26/2 GACAGGACTATGGACAGTTTGTACACCAACAAATTGGATAACCTAGATAAAATGAAGAAATTCATAGAAACACAAAACCTATCAAGACTGAATCAGGAAG + BA@=DHFEEEHHHHGHHHHHHHHHHHHHHHHHHHHHHHHHHFGDGHHHHHHGDFHHHFHFHHHFE844@HHHGGFHHFGHGHHHFFECDFHFGGGCCEB? @read_150_27/2 AGTGAGCCGAGATCGTGCCACTGCACTACAGCCTGGGCGACAGTGAGACTCCATCTCAAAAAAAAAAAAAAAAAAATTAGCCAAGTGTGGTGGCACGTGC + HHHHHEHGBIGHFHHHHHHHHHHB=DA;ABG:@BFHHHH?DE=-927>23EGGGHHHHHHHHEEFHGGDBBEFF>BHCFCCHHHHDB.9.74,4CACFGF @read_150_28/2 TATTGCAATTAAATAATTTAATATTTAAAGTAATGTGTTGGAAATCTTCTATGTTTTGCTACTAATAAGTGAAAACTTGAGCAAACCAATAAGTAAAAAT + =CBHHHHHHEEHHHHHHGGHHHHFF@GHHHGG?8FHHFE066GHHHFFHHHGEEEIFFFHHEDFD6(48@>);.97EBHHGGGGE:@>@C @read_150_29/2 TAAAGAAGATAGTAAAAAGAAATATTATTTTTATGATGAACAAGAGAAAAACAATTATGTTCTTCAACCAGACAAAGATAATCAGGCGTCAGGAAACTTC + GHHHHHGFHHEEGDFF=47;D>>>HHHHHHHFHHHGGEHFHBEEHHHGHDGGF@D@=3.,0&=G=@<8GGGE8;CCCFBCDC< @read_150_30/2 CCCTCAGTACTGGTGTTTGTGCCTGCCATTGTAGGACCTGTAGGTGGGCTTGCATGGTCCTTCCTCATCCATCTTCTCCCCACTCAGTGTCTGAGCACAC + HHHHGHHHHHHHHHHHHDA?EE@BF=EEFFFGGHFA@6A526@HHHGFBFHGFFHHHHHHHBEEHHHHGCHFGG8/,?DDB<;5.>EEHH<70EDDFHBF @read_150_31/2 CTAAGAAGGGTATTTAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAAA + EGFFHHHHHGGEDFFEGG@EDHHEEGGHEHHHEFGHHHHGBGHHFEDBFFE@@DGCHHHHGGDGGEGHGCE'',8?GGGFFGGGHHHBGFFDHHHHHHHHDDECBBDHEHGGGGBHHHHHHBBCFHHHHHEFFHFGEGG @read_150_33/2 CCACTGCACTCCAGCTTGGGCGACAAAGTGAGACTCTATTTAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTA + HHHHHHHHHFHHEHGHHHHEEGGHHHHHHHHGFHHHHHFHHHHHHFHHHHHHHHBEHHHBDBFEBCBB??(CD@:&.?AFBFFEEGFE<;BFGDEHFDEB @read_150_34/2 CAGAGAAAGAAATAAACACTGTGAGCTCCTGGTCCTATCTATAGTCTTAGTACCAGGTATCTCTTAGAAACTTAGTAAGTGTTTGGAAAGAAAGAAAAGA + DC8-946,(/6?>ADG?DCBGGFEEA:CF@@@GGGEEEEBBFDGBCEGGG<=EBEDEEEGHHHGHHHHD=EFE?3+<>ADGGEEE?CBD @read_150_36/2 AGCTCAATAGTTTTCCATAAAATATGCTCAAAATTCGATGCAGTGGCCATGAAAGTACAGCTTTTGAAGTATGGTCAACCTATGGTACGTTAGGAAATGA + HHHHGEHHHHHHH@>CGHFGHHHDC;>'<5:ECD@CFFG?FFGFHHHHFDDA997AHHHHHHFEEB=<@E61>><5735+=GGDGGGHHHGHHGFHHF<;9<@;@@9>;C>18?CC7 @read_150_39/2 TTGAATCAGTAATAAATAGCCTACCAACCAAAAAAAAAGCCCAGGACCTGATGGATTCACAGTCAAATTCTATGAGATGTACAAAGAAAAACTGGTACCA + A>;66/=EGGG?@GGDEEG=@EEHFHFB8GHHHECCAAEFHHHHHDCC<5>CDDEEEB@=EHHHHEFA?EFFGGHHGHHHHHHHC078D;12CA*:DDFH @read_150_40/2 TTTGCCTCAAATTCTTTCTTGTGTAAGATCCAAGAATCCTCTCTTGGGGTCCGGATCAGTAACAGCTTTACCGTCACGTAGTTCTGTGACAGATCGGAAG + HHGHHHHHHHHHHHHHFHHHGB;7B;7@7)7;><( @read_150_41/2 GCCTGTATCACCACTTAGCTCTCACTCTAGCCTCAGTTAGGTATCAGCAAGACCTCACCAAAGATTATTGTTTCGTTGTATGTGCGTGTGTCTTTTTGTT + <8CCBBDDDHHHG@4BIEHHHHHHHHHHHHHHHFHHHHHHHDGFGFBEEFGGGGGHHHHHHHHHHH=27@;+3,8:6GEEEFHHFFFFHHHHHHHH?HH @read_150_43/2 AAGGGTCTGCCTGAGTTGTGTCCTGTTGGACCAGAAGGAATTAGTCAAGCACAGTGGGGAGGAAAGCATTCCAGGTACAGGGAACAGCATGTGATAAAAG + <53.@EEHHHHHHHHHHHGHHHHHGG5<.76EFGGHHHHHF@;47336DFGGGGGHHDBFGE=FHHCDGGFEHFFHHHHHGGH==/@@BFFIDBFBAAEG @read_150_44/2 CCCGCATACGGTCACCAAAACTCAAACATTAGAATGTTCATTCTAGCTGATCGGGAGTAATTTGGAGGCAGTAGTTCGTCGAAACTCGGAGCGTCTTTAG + HHHHHHEEFE<<5:EHHHHHHE?@@CFGGEHHHHGBDEFBEEFEHHHHHHHHHHHHHHHEHE=EEHHHHHHHHGBFHFGFDDFG@DGEE=EEEFGEDHHF @read_150_45/2 GTAGGATTGGTTTTTGCCTCTGAATGCTTGGGATAAAACATGTTTTATCCCAAACGCACTATTTGGTAAATATTATAACAATCATTCATTAACCACCTAT + DA<;<:<<GGBAC<.)/)0,+A @read_150_48/2 ACCAATAATTATTAAATCATGTTTTTAAAATTATGGACCAGTAAGTTCTCAGGAAAAAAATAAACAACAAAACTAACATTGGTTGGGTAGAAAAGTTGAA + HHHHHHHHHHHHHHEHHHHHFFGDDFDEHE@GEEDHHFFHGEEEFEEGG@<3/AB=:5/EAA@;=EBC8EHHHHGEEHHHGBBGGHHGHHDDCBEFGEDC @read_150_49/2 TTCCATCAGAAAGTCTCCTATTACAAATGTCAGTTTATTTCTTATGCTTAACATTTTAAACATGATGTCCAGAAGCCCTTATTTGCCATAGGTACAAATT + HFGGF@?861/CDD5=FCFEHHHHHHHHHHHHHHGGFC2D0>>A01157.DHEE @read_150_51/2 GTTATGATGCAGCACAAAAGCCTTCACCAGAAGCCAATGCCATGCTGTTGAACTTCCCAGCCTGCAGAACCATGAAGTAAATAAAACTCTTTTCTTTATA + HEDGDB=EEEHHHHHHHHHHHHHHHHHHGAEFFFEHHG>CHHHHHHHFF@EEHHHHHHHGHHHHGGEFFD913<<@.9;:5:FHHFFD? @read_150_52/2 CCCTTTCCCTAGGTAGCCAAATTAATTGGGAAAAGAAAAAATGTGTTCATTGGAGTGGAGTCTCACACACTATCACAGTGCCCTTGACAGCACCCTGTTG + HHHHHHHHHHHHHHHHHGFEGHHHHHHHHFGGFFGGFFGHHEHHHFI9<.DDG@@67=HHHHHEHEGDE;-.5>=EFHHH@CDBHGFFFHDHADEFGE9< @read_150_53/2 AAAGGTAACCAGAAAATAAAGGGAGCTGTTAGAATATTCTCCTTGTTTCAGTTTCATTCTCTAAAAGATGGAGAATATAATAGTACATGCCTACAGGAAT + FHHHHHHGBFEFFHHHGGGFG=DADEBFBCG@;=EFHHHFHFFHHHHFDABB@CA=??7839;GFHHHGHHHHHF@EHH?HHHHHGBGD?5@'*31>:.5 @read_150_54/2 TAAGTACCTTCCCTCTTTCTTCCCCTACCTCCCCAACCTCTCTTTTTAACCCACAATCAGGGCCTGCTGGTAAGAAACTCGGAGTTTGGCCTGCGGGGTA + GHHHHHHHHHHHHHHHHHHFHHHHHHHHHHHHHHHHHHHHHE:@C?HHFHGIGGFFGGF>ED8<7F=@AE<<=>4@CEHHHHHEGB,5<:28)/6&,4:< @read_150_55/2 TTTGCTTGCATAAAGACAATATCCCTCATTTCCTGCTAGAGAGAAAAAAAAAAGACAATATCCCTTGTGCATCTGGAGTTTTAGCAAAAATGGAAGTTTA + HHGHHHHHHHHGGHHGHHHHHGEEDAACHE=EB=BGDFHHHHDEEFHHEE.83731;;>FHHHHHHHHGGHACBC5AEFHHEDHHHHHGDBGHHEH;4DF @read_150_56/2 CTAAAGCACTGCCAGTATCTTCTGCTTTCAAATTTATATATAATTTAACATCATAACATACCTTTTCATTTTGTTCTAAGTGTTTCGTAAACTTGAATTT + HHHFDGHHHHGGHHHGEGGHFHHHHHHHHGEHHHHHEEDDGHD@@@D55>.@5C?ABFHHHH @read_150_58/2 AAACAAAAGCAAATTTATTTTCTCCATGCTAAAAGGATATGTTGGTCACACAAGTTTTACCTATTAGTACTGACAAAACAATAAGAAACTCGGAGTTTGG + HHHHHHHHHHHHHHHHHHHHGEFFHHFFEEDDCD42,'>49138@419<7?BECBHHEGGGF=DFHFHHHEHHHHECFBFEB;.>:<61<=GGDA@BFFGGHHHGHHHHHHEEFGH=;E>A)79<.-0(0/ @read_150_61/2 GCTTGTTCTTCCACCATGTGAGGACACAGCTAGAAGGCACCATCTGTGAACCAGAAAGCACACCTTCACCAGATACTGGATGTTGCTGGTGGCTTGATAT + HHHHHHHHHHHHEEHHBGHHDFHHHHHHHHHHHHHHHGHFFHHDE?=)31?/D=?-BEEHHHFHHHHHEHBEA>DDD9DF>*34 @read_150_62/2 AACTTTCTAACCAAAAATTAAAAAAAAAAAAAAAAAAAGAAACAAAAAAATCAAAAACAAACAAAAATAAGTGAAAGGACTACTTATCATTTCCAGCAGT + HGGGGFDHHHHHHHHHHEEEEHHFHHDFHHHFHHHHHHFH@>BHHHHHHHHHEFHFHHHFFGED?EE.;=93>CGHHHHHHHHFEHFGBABBFH?@@@EG @read_150_63/2 TTTTCCCAATGTTTAACATAAGCATTCTATTATAGATATACAGATATTTTTCTGAACCTTTTGAGAGTAAGTTACAGATGTAATGCCTATTAACTACTAA + HHFHHHHHHHHHHHHHHD=FF@GHHHFDBCHFH=299.7CHHHHGA=9:G8BGGGHHHDC@ADDGGHGEA@CADEFFEGBBBGBC*,1>C86:>>DB?DA @read_150_64/2 ACATAGTCATCAGGTTATTGAAAGTCAGGATGAATGAAGGAATCTTATGAGCTATGAGGCAAAAGCATCAAGAAACCTATAAAGGAAAACATGTTAGATT + HFHHHHHHHHHGFHHGFDF?GFBGGFHHFGHHHFGHHHFFHHHHHH@4>ABECDDHHHGGGGHHHHHGEHHHHDBEFBHFHEFGCDD6,-:'>DEGBD>A @read_150_65/2 TGGTGAAATCTCAGCTCACGGCAACCTCCGCCACCCAGGTTCAAGCGATTCTCCTGCCTCAGACTCCCTAGTAGCTGGGATTACAGGCATGTGCCACCAC + EFHHHHHHHHHGHFE5A3:./EFEEE:ABCE6-@DGHHHHHEGHHHHHHHHHHHFEHHGHHHHHHEDDFFBFHH<(1;6DHHHHFFCFB:,C4/ @read_150_66/2 CCCAGCCCTGATGTGTTCCTTTGGAGTCTGATTCAGGGAAAGTTATACTAATGTAGTAAATAAATTCACTGACTGAGTATTAGGTTTTGCTTGCTCTTTC + HHHHHHHHHHHHHHHHEGHHHHHHHHHH==BEHHHHHEFHHHHFFHFFFHHGBCCFEGHHHHHHHHHHHHHHHHHEEFEFFHGE4,,=@BHHFHHHFEBD @read_150_67/2 GCCATGGGGGACAAGGGGAGGGAGAGCATTAGGACAAATGCCTAATGCATATGGGGCTTAAAACCTAGATGATGGGTTGATAGGTGCAGCAAACCACCAT + @DFHHHHHHHHHHHHHHHFEEFFHHHGFFHGHBEFHHHHHG8@@FHHFHHHHHHHHHHGHGBDB4FD>:@A:;>>C:;HHHHHHHH@EFBEHHFAC@AFF @read_150_68/2 ACTTTAAGCAGGTGAAATGTGTGGTATGTGAATCATATCTCAAGTAAAACATAAGAATGTTATATAAATGGAATCATAAAGTGTATAACCTTTTGAGATT + FHHHHHHHHHHHHHCG:1+BDHHHHHHGGBHHHHHGHHHHHHFGGDEFHHHHEEDHFHHHFGEHHHHHHFEFGGHEGGHGHDFHHHFHHHD@DHFFEFBF @read_150_69/2 AAACTGTGGTGAGGTTTTTCTGGGTACTAGGGTGCCAAGTGAGCCAGTCCTTTGTTCCCTAGATGCTATCCCCTTGTTGGTTTTAGAATTCTCTCTTCAT + HHHHHHHHHHHHHHEHHHHHHHHHFHG=GFHHHHHHFADFG>>:FF@.>>6*(9B?@EEFHHEFGHHHHHHHHFHGDEGEFHHDFBG @read_150_71/2 CAAAAAGAGGGATAGCAGAACACAGACAAAATCCTTTGCAGAATAAGTACCTCTATTTTGCAAGATAGTCATCAGCATTAACATCACTTAACATTTTATT + HHHHHHEEEHHHHHHHHGHHHHEED>>96@+>9?6@CGHFHHDAE?84:6EG>>7);8994,@@B?:B7@7@8?FAHHGGGCGADHHHHHHHHFGGF@C;HEGFDFE @read_150_73/2 AGGCTCCTCACTTCCCAGACGGGGTGGCAGCCAGGCAGAGGCTGCAATCTCGGCACTTTGCGGGGCCAAGGCAGGCAGCTGGGAGGTGGAGGTTGTAGCG + HHHHHHHHHHHHHHHHHFHE?DGEBAE<>?CDG<<34BFHHHHFHHHHHHHHHHHHDEGEFHHHEEEHHH@:>DDHHE@4@GGHHEGHBFHHHGEG.48? @read_150_74/2 TGGAGGCATCACATTACCTGACTTCAATTTATACAGTAAGGCAATAGTACGCAAAACTGCGTGGTACCAGTATGAAGGTCGAGACATAGACCAATGGAAT + EDDGHGD8==DFHEB::25EEIG8>CCD67<>CDDEFEE?D=/897.<,CFBEEHHG+9BE=CCB?GHHH77*-+-*5<<CGBHHHHBEHHHHHGDD@@DEBB@A=DHEE=9;.663DEEB>BBFHECA?:=4DEHHHE@AB @read_150_77/2 CAGAGTGCTGAGATATGCCACACCTTGATTGTTGCATTGACCCGAAGGGCTCGATGTTTAGGGAGGTCAGAAGTTGAGCGGGTTCAAAAAAAAAAAAAAA + EHHHEEHFFHHHHHHHFGHHHHHH@8<>@F?ABEE>>6CGHHHHHHHHD?GGGFFFBBBFHHHECFFFABGGHHHEHHHHHHHGHHHHHHFCCA>DGEHH @read_150_78/2 TGTCAGCCTTTATCTTCCTTGACCCATTAACATTTGATACAGTTGATCATGACCTATCAACATTTGATGCAGTTGATCATGCCCTTCTTCCTGAAACATT + GE9@BFFHHHHHHHE@BCHHFHGGGGG6GHHHHHEGGGEECEHHHHHFHHHHHHHHHHHGF89;+2,<<9/=EHHHGF?GGGHHEGEHHCHHHHHHHHH@ @read_150_79/2 TATAAATATAGTGTCTGGCAGAAATTGCTTTATATTAAATATCAAAAACAGCAATCAATAGTGACAGCGATCCATGTATATTAGTATTTTCCAAAGTATG + GGIEEEGDEDFHHHHHHHHHHHDHHFHHHHEC>BHHDEFGHBE>><7;=AHHHFFBCEFFDE@DDHHHH@:>59.>:>>HHG@EBDHHHHDFHHHEFEBG @read_150_80/2 CAGGAGTTTGAGACCAGCCTGGCCAACATGGTGAAACCCCGTCTCTACTAAAAATACAAAATTAGGCTGGGTGCAGTGGCTCATGCCTGTAATCCCAGCA + HBHHHHHHHHHHHHHHFFBDBFGD@:C=FEGE;EHHFDHHHHHHHHEHHFEFE/--8D+8;BBEFGGHHHHHGGGHHHGHHHHFFFEF>CFFBDEBGGDF @read_150_81/2 TTTTCTCAGCACCCTTTATTGGATAGATTGGCCTTTGCCCAATGTGTGTTCTTGATGCCTTTGTTGGAAATCAGTTGGCTGTAAGAGCATAGATTTATTC + HHHHHHHHGFEEDGFHHHHHHHHHHHHHHHEHHHHHHHHHHGGGGFFF@FCA@GGHHHHGHHFEHFEFEEHHH=/AFHFC;8B(4>:?GHHH=EEDA5<, @read_150_82/2 TGGGCTCGGTCTCCTGAGGGAGACAAACAGGGCTTCAAGCAGGGCTTAGGCTGGGGACGCTGTGTGGAGCAGAGTCACTGGCTATTTATAGCCCAAACAG + AB=EDDDDCDEEFHGF@@DFHHFEGGFHHED>>>>66.AE=EDBBGGHHHHFFFFHHHGHHDFGF@BHHHHHHHHHHHHFHHHFGGHFCEGGFE4AEBC8 @read_150_83/2 TAATAGAAGTAAATAAATAATAAAAATTGGAACAATAACGAAACAGAGACTAAACAATACAAAAGATCAATGATACGAAGAGTTGGTTTTTTGAAAAGAC + HHHHHHHHGGEHHHHHHHHHHDD/@DDHHHHHGCCEEFHHFHHHHHBGGGGHHHHHHFGIDCFFDGFGEFHDAE<(125CHGDCC44545)/=EGHFB5E @read_150_84/2 AAGTGACTACAGACATCTGTCCCAGGACAGTAAACAAGAAAACAAGGTGTCACAAAAACAAAAACAGCTGACCCCAGCATACAATCACTGAGACTGAGCC + HHHHHHHHHHHHHHHHGHEEHHHHHHHHHHHHHHHHHHHHHHHHEBBDEGHHHHGGGDHH@DHHH=83*2-'9'':??D?EBDFHHHHHHE>BD5)786>5<96C@HHDDGFHHHGFHHFGCFHFGDGFHGGCCEE=1 @read_150_86/2 TTATTTTTTGCAACTTTGTCCAGTTTTATAATTGTTTTTTGGGGAAGAGAATTTATCAATTGCTTCAGTTCGACATCACCAGAATGACTTCCTCATTGAA + HHHHHHHHHHGGHHHHHHHHHFCBHHHHHHHHEFCEHHHHFFHHHEECDCHGGGGGFHHEBGGEHHHHHHFE(41:@5<9EEHE>D:A.:GGGHBFD@5< @read_150_87/2 CACTCATTCAATGTTTATTGTGCCTCCTCTATGATCCAGGCCTTAGGTGGGTTTCAGGTGTTAGGAGATTTTAACAACTCCGATCGGGAGTAATTTGGAG + HHGHHHHFHHHHHHHHHHFFHHHHHHHHHFGGHHEHHHHHHHHHHHHHHHHHHHHHHFGGDGHHHHH87.-;CC/2,0*6):@EAGFDEEFHHHHHG9>4 @read_150_88/2 TCCGATGTGGTCCTGTGCTCATCACCTTCCCACACCTGCTGCCCTGCACCATTCCCAGGGGCTCCTCTGTGACATAAATTATAGTTGACCATAACTGATC + HHHHHHHHHHHHGGGHHHHHHGHGGC@HHHHH?EHHHHHHHHHHHHF:>7FHHHHHHHHHHHHDACEFHHHFBDC55?4<%-1-5,>BGEEGDH @read_150_91/2 GGTGATAGGAATTTGTCAGCTCCATTATAATCTTACTGATCTGTCATTGACTGAAATGTCATTATATCGTGCATGAGTGTGTGTGTGCGTGTGTGTGTGT + HHHHHHHHHHHHGFFHHHHHCHHHHD=;575EHHFFH @read_150_92/2 AGTGCCAACATGGGACTTGATAGTCCTGGGGAATATGAATGCAGCAAAGATGAAGTCCATAATGAAGAGTAAAGAAGACTGGTAAGAAACTCGGAGTTTG + HHHHHHHHHHHHGEHHHHHHHHHCAHHGGGEHHHHHHFHHHHHFHHHHHHHHHHHHFHHHHHHHGEGGHHHEFE?EB@A.-5?A65433*83.:03CBCB@EFFHHHE;>;3;@@ED6DCEDFGFHHHHHGE@@CFFGEHHHHHGHHHHHHHEEDHFHHHHHHHHHHHHHHHGGHGFFCFHHHHHHGFEH @read_150_94/2 CAAAGTAGGATATGCATAAACTTGGTGGCCATAGTATCCCTAGGACTAAAAAGAATTCATTTTATATCAATGAAAATCCCTTCTTTGTGGCTTCTTGAGA + HHHHHHHGHHHHHHFG=,@D=:BDEEHHHHHHHHHHHHHHHHHHHHHHFHHFHFGHHHHHHFHHHCDDGEEFGHHHHHHDGIEGHHEHGGHH?@2*6:;))1 @read_150_96/2 ATAAATATATATATATAAATAAATATATATAAAATTCAGGGCTTTTCAATTTTTCTTCCCTCTTGGGAATATTAGTAATTTGTAAGTCTCATGGATATAT + HHHHEGGGDDFHHHHHHHHHHHHHHHHHHHHGF=B.@-2>@EFHH>:FDCFEGGHHHHHHHHHHHHHH;><(1>9.@24=CE5>)<=77@A( @read_150_97/2 GCGGCGTGTGCCTGTAGTCCAAGCTACTCGGGAGGCTGAGGCAGGAGAACTGCTTGAAGCCGGGAGGCAGAGGTTGCAGTGAGCCGAGATCATGCCACGG + HHFIEGDFFHHFFGEBD:::*<19=DEBBEFGDEGEHHHHFFHHHHHHHHHGIGGE252726.D=<6-1ADEGECDHHHHHFFDHHFDDGFBBCFFFFBF @read_150_98/2 GCAGTGGCTCACGTCTGTAATCCCAGCACTTTGCGAGGCCGAGGCAGGTGGATCACCTGAGTTCAGGAGTTCAAGACCAGCCGGGCCAACATGGTGAAAC + HHHHHHHHHHHHHGGHHHGFFHHHHFD;F@C:>ECFFD?E@;@EEGHHHFCDD@=GHHHHFHHHHGGBDD:EEBHHHCHE@/*7512/ADDEEHFHHD?5 @read_150_99/2 AAAGTATCATATCTGTACTGGTTACATTGGCCTATGTCTGCCCTCCTTTCCTATCATCACAGACAACTTTAGCTAGCCTTCTGTCTTCAGAATTTTCCAG + HGB:EHHHHBFCGG>?>56GHHEGG?EDDEFDECC;GG@AHHHGGFHCFEFGEEEHHDD=98-4<5-2*5?GHECDEEDEFHHHEDFHFHEGEE@C.9DD @read_150_100/2 GTACTTTGTCTTCTGTTGTACCTTCCAGAGAAATATCTATAAAAGCCCATAATCACCACCACCATGACCACCCACCACTGCCACTGCTCCCACTACTGCC + >+>9>88<98GBBEHHHHHHFEHHBCFHHHHEFFFHHHHHHHHHHHHDHHGEE9HHHHHHFEG6>7')-0CFHHHFDDFFBC@BF @read_150_101/2 ATGTTCATCGGGTCCATGGATCAGGAAGACTCCGGGGTTTTTAGCCCCTTTACCGGCATCTACATGTGGAATTAACACATCTTCTAAACCCAAATCAAAG + GEGDGGGHHHFEHHHHFHHHBCFHHHHHHHHBEGGHHCBEEBHFFGHEDFHHHHGHHHB@FFFEEFHGFGFHHHHHG=DCBGHHEFFFD95*:4568BBD @read_150_102/2 GTGGAGTTGGGAGCTGTGTGTGGCTCTGCATGTGTGTTACATGTGTGTATGTGTATGTATGGGTATGTGCAGGAGCTCTCTCTAGGTTGTAGTCAAGGAG + HHGHHFGFEGGGGHHFFHHHHHHFFFGGGDFFEE@FEHHHHHHHHHHHFHHHHHHHHHHHE/.?;>=DHHEFFHHHHHHGHHD=GGGFDDHHHHFEHHHB @read_150_103/2 CCAAGGGGACTTCCAAGAGATCATCTCAGGAGGCACAAGTCTGGACTATAATGTTGCATTGACCCGAAGGGCTCGATGTTTAGGGAGGTCAGAAGTTGAG + HH=BEHHHHHHHGDBHHEIGHHHHHD=DF?GHHHHHFFEHHGGHHEHHHHFEEHHHHHHHHHGHHHFHHHHHHHHHHHHHGEHHHGG--4*-@>.,7DD@ @read_150_104/2 AAAATGCACAAGATTCTCCAATTAACTGAGGGTGCACAGTCAATTGGGTGCTCATAAATAGGACAAAAAAAATGAAAATTCTTCACTTAAAAAAATTTGG + HHHHGDE@@@@@>?@EE@GHHHEB@CGEGFB529;.802AF?=EB8+<74BEHHFHHHFHHHEFG6/;?@>?2'07D@?>BB3@C@A.FHHFEHEFFFG@ @read_150_105/2 TTAGGCCCTTATTTATCTTTTGATGTTTTATTTTCAATTTTTAAAAGTCAATAATAATTTATAATAATAATTATAGTAAGAAATTATGTGCCTGTAATTC + HHHHHHHHHHHHHHHHDB@@CFHHGHFHHHHBDEEF>FFFFFHFHFHHHEEEGF@EGHHHHHHGGHHGHHD@DDHF?D=D9>@A?=EAAA;59EFEHHHB @read_150_106/2 TTCTGGTTCTCAAAACCTGACTACACTCTCTCTGGCTACCTGGCAAATCGGTTTTTGGTGCCCAGTCATTTTGTCTGTAAAGCGAGAGGCTTAACTGAGA + HHEEHHHHHHGFHF:=FFFDGDGFHHHHHHHHFHHHHHHHHHHEG@?>,AFGFBEFFHFHHHHHHHHHHHHHHHHGHGEGHF<9'77,2,@D5>FHGFFEGEHHHHHHHHHHHHE@?>>>BEGHHHHHHHD?FFEBCGHHHGGDCC?EHHHHGCD?9(.9C57*+5-2/5<*<93@BHHFFE>CC @read_150_108/2 TGAGCTTTTTTCTGAGACAGAGTTTCACTCTGTCACCCAGGCTGGAGTGCAGTGGCACTCCACTGCAACCTTGGCCTCCCGGGTTCAAGTGATTCTCCTG + 26;94BFHHHHHEEHHEHHHHFEEHHHF=FHHBDFGBDDGFBCDGEEEE<;@DDB@FFCBFHHDDEGHGHHFHHH @read_150_109/2 GACAGTTAAGACCATATATTCTCTGAACATTTAAAGAATTCTGGAGTCAGTCATAATCAGCCTGAAAGCTGAAAGATTATGTTTTCTCCGAACTCACACT + HHHHHHHHHHHHHHHDDDFHHHFGIEHHBEEEGHHHHHHAGHHHHGFDEFHHHHHHHFEEFGGFHFHHH@GGGEDHHHFHEBCCB@E.:'CED;FEF.<4 @read_150_110/2 TAAAATTATGACTGTTGACATAACCTTTAAGGATTATCCCTCAGATTCATGATGAGGCTTCAGTCATCTCTGAGCCCTTTTCCTTACACCCACATGCTAA + HHHHHHEB=>)24@HHHHHHHHHDDHHHHHFFHHHHHHHHEEEBE=BB=AFFHHHHHHHHGBHGGGHG+.)89CEFHHHHHHED7'*;,=FGHFFDBEGG @read_150_111/2 ACTGCTGTTGCCCTGGGTCCATCTGCCATCATCTCTCACCTGGATTATCTCAGTAGTTTCCCAACTGGTTTCCTTGTTTCCATTCTTGCCTCCTTCTGTC + EGEE@@@CDEHHHFHGHHHHHHHA8=DDB/9.DEDGEBD7CDEHHHEAAEHHHHHHHHHHHHHHHHHHHFEBCEEFCDGHHHHHF?B@5><=>:67.DEEFHHHHHHHD:4CDC8=DGGBCCBBE@CHHFHHEHEGGGCB@@@GGHHFHFHF<:@FCFHHHHC @read_150_113/2 CGTCTTCTGAGCCCTCCAAACTATTCCAACCTTTGCCTGTTACCCAGTTCTAAAGTTGCTTCCACATTTTTGTAAGAAACTCGGAGTTTGGCCTGCGAGG + HHHHHHHHHHGGGGGGFFEFGBEHFC@E;@<>50BHHDGCGDGHGFFHHHHHHHGHHHHHFGHHHHGGIGFCDDHHHHHC?57:@B5GHHEFHDCBF?=? @read_150_114/2 TCAGGTGGGTATATATGCCACTAATTTGTTTGATTGTGTTTTTTCCTTGTTTCATTTTGTTTTGGCCAAGTAATATCCTATTGATGGTATGACGATCATA + FGGHHHHHHHHHBGGHHHHHHHHHHHHHHHGGEEBDEHHHHHHHG.8:?@;:,7BFDFBDHHGHFG=418EHHHEHHF8<9;.74672@@FHB.,-4=<( @read_150_115/2 CAGGCATGGTGGCACGTGCCTGTAATCCCAGCTACTTGGGAGGCTGAGGCAGGAGAATCACTTGAACTCAGGAGGCAGAGGTTGCAGTGAGCCGAGATGA + HHHHHHHHGGHHHF.A?C@;DGHHHHHF=BHHHHHHEEHFHHDDE>0<,598BCHHGFGFGHGEEFHGGB@AGGFHHHCEEEBGEEFHHFFBDDD78-(4 @read_150_116/2 TTCTGAATGCAAGAAGCAGCACCCTTACATACTGCCTCTTTTCTCTTAAAGGCTAACTCCACCAAAGACAGGGAAGAGAAAACGAATAAATCTCTCCTAA + GGF;?EBGHHHHHFFGHHHFG@CHHHHHHHHHHHHHHHHHHHG>(')).?>>B@?EDEGCEBA<:69=EE5;:1===FF @read_150_117/2 AAAAACTTCCTAAAAGCATCAAATGGCCAAGGCAGTATGGAGTTACTGGGCTGAGATCTGGAAAGACTGGAGCCGAGAAAAGTAAGTCTGTACTTGGCTG + HHHHHHED@4/DC;8>?BBBGEA?C?HHHCBEEHHHHHHHHHHFFFGGHHHHHHFEGHHFBHHHHDA@EHHHFBEHHHHHHFHHFFHH9EHHHHEBFCHE @read_150_118/2 AGAGATTGAATCAAACGTGGTGGAATTGAGAAGCAGCATTGACACTCCTGGGAGCACACTCCTTCCAGGAAACAACAAAGGAGTCCTCTTGTGGTTGGTA + FEEEDDHHHHHHHHHGGHHHHFFGGFFHHHHHHHHHHHHHEFDDD@6A;<87,6HG @read_150_119/2 GGACCCACTCAGTCAAGATCACAGGGTGAGGGGCGTGTGGGCAGAGGGGGTTTGGGACAGCAGGGTTTGTGCTAGGGGCTCTGGAGCCTGCCTTGGGTTC + HHHF=GGGFFHHEEFEE.>9>117:.>@CBGGFG=GBG=DGHHHHHHHBB26;<==GCA9>2B6CC58>.9:4,)%. @read_150_124/2 GAGGAAAGACCTGAGGCAGTTCCAGGAAGTGCCAGGAGGCCGATGGTGCTAGAAGGAAGAGGAGCATGGTGAGAGTGAGGTCAGAGATGAGCCAGTAGGG + )93:FHHHHEEBEFHHHHHHHHHGHHHHHHHHHHHHHHHFBBBDDDDHHHHHHFFBGHHEDHHHHHEHHHFCE??EFEEGHHEEEC?DDDHHHHFFE9F? @read_150_125/2 CATGACAGTGCTGTCCACATTGATCTTGTTTTAGAAATGGGATTTTGAGGTACCGTGAAAGGTGCGCTTAGTGGCATATGCGTTAAGAGCTAGGTAACGG + HHHFHHHHHHHHHHHHHHHHHHHEFHHH?DBD?<75>DFEHHHB?=C:<=HHHHHHHHHHHGGHHHEBEFHHHEEEFHHFDHFH?DDFB=CC><6;>ABC @read_150_126/2 GCTGGTACTACAGGCACACGCCACCATGCCTGGTTAATTTTTAAATTTTTTGTAGAGACAGGGTCTTGCTATATTGCCTAGGCTGGTCTTGAACTCCTGG + HHHGEHHHHHHHHHHHHHHGHHHFHGF=FHGHHFDDC@AE;ADEE:.<;B8:?A8AACFFHFFGGFFHHHHHFFFEEHEFHDFDDHHHHHHHF?>EGHHHHBHHHHDHHGHGFBHHHHHFHHHHHHHHHHHFGGHHDHHHHHHHDFEFFGHHFFHBHGGGHHHHDEEEFF @read_150_129/2 GTGTGTGTGTATGTATGTGTGTCCATCTGTGTCTGTGTGTGTGCCACTGAGAAGAAGAGGACAATACAATTTTTCATTTTTATTTTCCATGTTTCTACAT + HHHEGE=DCF@C=GGBFFHHHHHHHHHFEBEEEE?GGHHFGEFFFHHGGFHGHHFDGHHHBD.-24FEEEF7)776.5:AGHHHHHHHHHHFHHHEFG@@ @read_150_130/2 AGTCATCTCCTATCGAGTAGTAGCAGGATACTTAGCAGTGTTGGGGTTAAACCTTCCTTGCCTTCAAGTTTGTTCTCTCCAATGTTAGCAGGCTCAACTT + HHHHHHFFDG8@BFFHHGHHGEC?@DHFFHHHHHHHHHDD9DHHHHHHHHHHHHHHHHHEFHHHHDHHHHGEHHHEHGDD>+.5/.35=?D@EDEEHHHHHHHHHHEFHHHEA:?GDGGFI@EHHHFFFHG5;@CC5(,+GHHHHHHHHHHHHHGG@?@A@FFHFFD8DAB @read_150_134/2 TTGAGGGCTTTATTCTAAGGGGTCAGTAGTCCTCAAAAGGTGACCACTGCCCAATTATTGCAGGAACATGGGGATGCTGGTGAAAAATGAAATTCCAGGG + @CECDGGGHGHGGHHHHHHHHHHHHHHHHHHHHHHHHFHHHHHHDED;;*057@@@@=FFFEEDB<125>EGDB?FG@@GGBGDEBGG?4>A,4,%,38; @read_150_135/2 CACAGGCTATATCCTAGTTGTTTAGCCCCTTTTGTTTTTCACTGCATAAGAAACTCGGAGTTTGGCCTGCGAGGTAGCTTGGGTGTTATGAAGAACGGCA + HHHHHHHHHFHHHHHHHHCBAHFEGA=FHHHHHHHGGFHHHHGGEGEGFHHHHHHHEDGGB>DDD685*8994<=HH7-3?EHHHFGFEHFFHHHHHHFF @read_150_136/2 ATTGGATTTCTCACAACTTGCATTTTGAATATTGTTTTCCAATTGTTTTGTGGTCTATACAATAATATTTGAAAAACACAACAGCATAAAACATTTAGAA + EHHHHHHHHHE2<@.>CGGHHHHEEEDEEGBEHHHHFEHGHHHFFFEEDEGGGGFHHGEEBBFHHHHDEDDIHHHHD?.C>;5:)5<4@DBHHF8DEFFF @read_150_137/2 GTGGATAGATTTAAGATATATTTTAGTAAAGTTCTTGTCACACAATTTGATTTTAGATTGAATACAGGATGAGATCGGGAGTAATTTGGAGGCAGTAGTT + HHHHHHHHHHHHHHHHHHHHHHHHHHGFHGBHFFDE@DDDGHHHHHHHHHHHHFFEE@@DDB= @read_150_140/2 CCTTCCCTGAATCCCCCAGCCCACAGCGGCAAAGTCTTGGTACTCAAAGTTGCTTGTGCATCTTTGGTATCATCCCACTGCCAAGCACACAGGTACGCAA + HHBGHHHHHHHHHHHHHHHHHGFGGHEFHB=HHHHHHHFGFFFB/;AD9CGHFB7>&9C @read_150_141/2 TCATGTACCCAGTAGTCATTCAGGAGCAGGATGTTCAGTTTCCATGTAGTTGAGCGGTTTTAGTGAGTTTCTTAATCGTGAGCTCTAGTTTGATTGCACT + HHHHHHHHFDHHHHHHHHHHGGIEGHGEFGFFHHHHEIEBFGGHHHHEHHHHHHHHHFFGEEGHHGIGBEHDA.,<1&161?AEFE=5:CFHHHHEA=A; @read_150_142/2 GACACAGCGCCAGGTCCACAGCCAACACGGGCAGATGTATACTTGTCTTGTGCAGTGGAGAGAGCGCTCGTCATTGGGAATGCACGTTATCAGGATGAAC + FGGGGHEHHHGG@FFHHHHHHHHHHHHHEBHGGFHHHHHHHC;DDF<9:89;/EGHGGHHHGGFGD?GHHEFFC;;GFADCCBEAADDD8@CHHFFFHC@.B. @read_150_146/2 TGAGCTCTCCCTCTCCTCCTCCCAACCCCCAACTCTTGCCTCCCACAGACTCATGTGGACACTTCTCCAGTCATAAGAAACTCGGAGTTTGGCCTGCGAG + HHGHHHHHHFHHHHHHHHHEFGHHGHHHGGHHHHHGGFHHHFCFEEHFFHHHHHHHGGDFHHHGGDA9;E5-8;FE?=AEFBFHHHHC:DEFHHFFDDFC @read_150_147/2 GTTCAAAGTATTTCCCTCTAATGTTTGATCTACCTGTCTTTCCCTTCTTCTCTCCAGTTCTGTTTTTCTTACCGTGAAAGGTGCGCTTAGTGGCATATGC + HHHHHHHHHHHFFHHHHFEEBHHHH36FBIDEIEEBHGHHEGHHHHHHHHHHGFHFACD<8=DFHHHHHHFHHGEBGGHHHHE@?CEFGGDDDDBHHHDF @read_150_148/2 AGGGAGAGCTGTGAGAGGACACAACCTGAGTGTTTGTTGGAGCACAGAGGAAAGGCAACTGGCCTTGTCTTGGAGGATCCAGATGGGTTCCTAGCAGAGA + HHHHHHHHHHHHHGHHHHHHHHG?AFFHHHHG@@;59E@BCEHHFHHFE@@BB@@GCBGGHHHHHHFGFHHHHHHGGHGDEHHEEFHHDCFCFHHCDFFH @read_150_149/2 GGCAACCCTCACAGGTTACTAAGGGGGGGTGGCTAAGTGTCAGGTGCAGCTCATCAGTGAGCAAGGCCACACTGAGACAGGAGCCTGAGTTGGCAAATTA + HFGFDHHHHHHHD?=HHHHHHHH?8.BFFGHHHHHHHFHHHH?EC/BBBEBGHHGHHHHFHHHHHB6.,6>8/,478>5@;(90&&4ECC@DGGHB;;6= @read_150_150/2 AAAATGTGGCACATATACACCATGGAATACTATGCAGCCATAAAAAATGATGAGTTCATGTCCTTTGTAGGGACATGGAGATCGGAAGAGCGTCGTGTAG + EGEHHHHHHHHHHHHHHHHHHHHHHHHHBBEEGEHE8EEHHHEHFHFHGHHHGF;CCBFGEEEDDGEEE:+0,CFHHHHHHHFGA=?C@A3*5'+3,34* @read_150_151/2 ACATCTATTTCTAAGGCAGTCACTCCCTCTGCACATCCCTCCTATCAGAGTAATTTCCATATTAAGAAGGCAGAGAATGAGAGGGAATGCAAAATCCATT + =54--=:6@@@BGHHHHHHHHHG=D<<>AFCDHGEGHHHHHHHFHHHFHHHHHEGFHFHHGHHHHGE;+'B=A36(7.'7(-*-3%.11-<=8GFFFHFH @read_150_152/2 GGATCCCAGCAAACCAAGGTTGAATTTTGTATTTTATTTCCTATGTTATATGATCAGTGGAAATACAGTATTCCATTGAAACAAAAATGATATTATAAAA + HHHE@EHHGHHHHHHHHHHGEEGDCE@EHHHHGFHHHHHHHHHHHGHHHFFGGHHHHHHHHHHHHHHG>B62?@EHHHHEFFHFHFCD?EGBF7>@DCGF @read_150_153/2 TATCACAGATAGTTTTTGTTTCTTTTTTCTTTTTTTCTTGGTATTTCCCAAATTTTCAACAATGAATATGTACCACTTTTCTAATCTGAAAAGCGACCAA + HHHHHHHHHHHHHHHAB7)?8.FHHHHHHHGE8GHHG9--,&&<>=EEHHHHHHHHHHHHHHHHHFEHHHHHHHFHHHHHHGG7350%2-;93 @read_150_154/2 CTAGGTCCGGATCTTTGCACTTGTGTTCTCTCCCAAAATAATGGATTTTCTGTGGATTTTATTTTGGAATAGGTATTTCTCCTATGAAGTCTGATAAATG + HHHHGEEB?FGGGHEFE82;BGHHDFHHHFEEEDHHEFHHHHHH>=?DBDHHHHHHC99*7@;DCEFEFBFHDCEHHF:76;77C=FEGFHHBDHFGBFH @read_150_155/2 ATTTAAGGTTGCAGTGAGCCATAACTGCACCCCTGCACTCCAGCCTGGGTGACAGAGGGAGACCCTGTCTCCAGAAAAAGAAAAGAAAATTTGGATTATA + HHHHHHHHHHHHHHHHHHHFEEEFHFHHFFFGHHHFGGGCGFHHHHHFHHHHHHHHHHHHFEHHHHHHGG?7932'9;BEHEHHDHHHCFHHEEGHB;:3 @read_150_156/2 CAGCACCATTTATTAAATAGGGAATCCTTTCCCCATTGCTTGTTTTTCTCAGGTTTGTCAAAGATCAGTGGGTTGTAGATATGCGGCGTTATTTCTGAGG + HHHHHHHHHHFHHHHHHHHEBEHGF@B?GEBHGD*3CEFEHHGGFEBEE6GGGHGHHHHHHHGED:?:,'&+,AFDDEFE@4)=<:DEE?2EEBCGGEBH @read_150_157/2 TTGGTGAATCAGCTTTGAAAATGTCATATAGGCCTCATATTCAAATTGATCTTCAATATTAACTGACTCTTAAACTAGTGCAATTTCTTCATCAGTCGAT + HHHHHHHHHHHHHHHGGHHHHGGGHHHFFCAAE/*9.>DCHHHHHHFFFFHHHHHHHHH@@?&,-'2DFHGFHHHHHHHAAFFDBC.:DEHHF;?FA,7% @read_150_158/2 GCAGCCTCTAGATGCCAGAAAATGCAAACAGACAAATTCCCCACAGCACATCCAGAAGAAACACAGCTCTGCCAACACCTTGATTTTAGCCTACAGAGGC + DHHHHGHHFFHGGEDBGHHHHHHHGEFGHFGGGHHDIDDE;>9=FBDEFHDIIDECABEFFHHHG? @read_150_160/2 GGTCATTTTTGCTGCGGCAAAAACTTGCTTGAAAGTGAAAACATTTGTCCATGATTCATATAATTGTGCTAGAGGTTACAGTTTGCTACCATGAAGGCTA + GGGHHHHHHHHHHFHHHHHHHHHHHHHHHGBCDHHGHHFCCEGHFHHHEHHFHB @read_150_161/2 TTTTAGTAAGAAGTTATTAAATGTATGAAAGGCTATTGGGACTTTAACTCTTCTTCTGTATAGAATATTCACTAAACTTAGTGGTAGAAACCTTTTTTTT + HHHFHHHHHHHHGGFF<<-;ADDDHHHEHHHGEEB=B?FFGGGEBFFFFHHHHHHHHHHHHHHHHHHHHFHHHEHHHFFC,<5DF=EB89478EA9*8=: @read_150_162/2 GTACTTCGAGGCAGGGATGGATAAAACAGGAATGTATAATGAATGGCTTGGCTAAGTATACATATTTAGTACACAATAGGAGGAGTCATGAATATTTATG + HHHHEGHHHHHHHHHHHGHHHHHHE@CHHHHHHHHBEFFHHCHHDCCDD=DDD;=CFGGEEHHHHHHHFFGHHFGFHHHEEFHHHH>9EGE?:GGEC>CFFHFB;DEEF?BFFE@BBACDCFEGGHHHHHHFGHHHHHHHFDDEHHGACFDDEHB@@>=9,,. @read_150_164/2 CTGGGTTCAAGCAATTCTTGTGCATCAGACTCCCGAGTAGCTGGGACTACAGGTGGGCACCATCACACCCAGCTAATTTTTTATATTTTTAGTAGAGACG + EHHHGFHHHHHHHHHEBEFGFDBEHGHHC@6,.+FGFFEBE?BHHHHGGFHHHHHHHHHHHHHHHHHHEHHHHFHEHHHHHHHHEE@:9=FD31/<.<<, @read_150_165/2 TCTGTGTGTTCCATAATGCTCCAAAAGGCGGTTTTTCATCACAGTAATAACAGCTACCATGCATGTAAGGCCTATAAATTAAGTGTTCTGAAGTATTTCA + HHEBCGHHHHHHD@BGHHHHHGH@FHGGGEDCA-AEHHFFEBEFFHEFEBBCDHHHHHHHBDDDGHHGFHHHHHHHHHHHHFGBFBDFFHHGDFHHHHHF @read_150_166/2 ACAAGTAAGCAAATAAATAATTACATGTTGTGATTAAGTGCTATAACAGAATTAACAGAGTGACTGTGGAAGGGCAGTCAGTATGGCCTCTATGAGGAGG + HHHHHHHHHHHEGFHHHHHHHHHHHHHHHFHDBFFHHHHHHFFHDGHFEGHHHHHHHFG838B9<@CHHHHHHBE?FGGFGGGB?BEEE7=BGHCDAGGG @read_150_167/2 TGAACAGTTTGGTGTTCATCCTGTCTACCATCCCCCTCAAAAACAAAGAGACAGACAGAAAGAAAAAAAAAGCAGAAGTTTTGCTTTTCTAAGCTACGAG + EEGEEFBHHHHHHHHHHHHHHGHHEHHHHHGGGGHHHFHHFFFEEEEFB==AHHHHHHHHHHHFEHHGA@HHHHFHA>:@EAGGEFGBFGGFEBFFHHHHHHHHHHHHHHHBEEB==HFGDDDA7EGEGF0BBGBD @read_150_169/2 AAATATGAATGCCCTTTATTCAAAATTTGATGGGCATTTCTAGCTAATGTAATAAATATAATAGAAATCAGAGGCTTAGGAAGTAGGAAGAGGGAACACC + HHHHHBGGGDEDDB?BGE=CHHE=DGAGGGHHHHHHHHHE>GHHD=*8>5@GC @read_150_170/2 TGATTGTAAAGTCTGCAAGTGGATATTCAGAACTCCTTGAGGCCTTCGTTGGAAACGGGATTTCTTCATTACCGTGAAAGGTGCGCTTAGTGGCATATGC + GGFGGHHHFGGFHHHHHHEHHHHHHHHHHHHHHHHHHBHHHFGHHHEBC?3913,?BFGHHHGHHHHHFHGHHB%*-65DFHFHHHGGHED<,ECCEADB @read_150_171/2 CAAAAATTAGCTGGGCGTGGTGGTGCACACCTGTAGTCCCAGCTACTCAGGAGGCTGATGCACCAGAATTGCTAGAAGATCGGGAGGAATTTGGAGGCGC + GGGEFHHHG=GGFHHGAAGGHHDDGHHHHHGBFHGHHHEBCDHHHHHFFGHHHHHHHDFFGEHFHDB791933))/6>5AC?@G6%%;<<:792>@E9)' @read_150_172/2 CGGTCAGGCTGGTCTCAAACTCCTGACCTCAGGTGATCCGCCCCACCTTGGCCTCCCAAAGTGCTGGGATTACAGGCATGGGCAACAGCACCTGTCCCTG + HHHHHHHHHHHHHHHHHHHHHGFHHHHHHHEGG75<<*BHFA;36-12;;5:968BDD@@@85@FHHHHHFHC@/A.-1)&+),==<=EED?;?9DD>HH @read_150_173/2 AGTTCCCTAGTGGCCAAAGTAAAAAGGGATGAGTGGGCCTTTTATCCCACTTCCATGGGAGGATTGCAACAAAGGCCAAGTAAGATCCTAGATATGAAAG + HHHHHHE@FHHHHHHHHHHGEHHF=)93336FHHHB/.>>>CDBA@EGFHFFGD=?=?EHHHFAHGHHHHHFFEFFFEF @read_150_174/2 CATGTGAGATATGCCTTTCACCTTCCACCATGATTGTGAGGCCTCCCCAGCCATGTGGAACTGTTGCATTGACCCGAAGGGCTCGATGTTTAGGGAGGTC + HHHEE:IGHHHHHH?BAAEA:FGG@CDGGHHHHHHHHHHHHHBEE?EFGFGDF@FGGHHDGFHEEF>6+5?6?EEB @read_150_175/2 GTGTCTTCTTAAAACAAATCTTCTCTGAGAATTGTCTTTCCACTGTTGCCTAGACCAGTTAAGTATACAGGTCATTTTCTTGTTCTTGACAGAGTTTTGG + E8;:@ABDDAFHHHHHHHHHHHDHHF<>>9<:66=@DCFEEEEGFBFFHHHHHF=EGGHHHGG@DE5=EF;.:A=FGHHGHHHFB80CHFFHEBCD?EFC @read_150_176/2 ATGAAACTTTCTGCTTGCAACTCTTTGCCTGGAGAAATAGTTTCTTGAGAAAGTATTTCAGCAATCCTTAGAATTTTTTTTAATGTTGTCACAAAATATA + GBGHHHHH@@BGFHEHHHHHGHHHHHHHHHHHHHHHHHHHEE@DECCIFF=@<>BD.=.@+--2'38B=@@GHHHHHHHFF=DFHHCEDDC?EBBFBFFG @read_150_177/2 ATGCTTGTAATCCCAACACTTTGGGAGGCCGAGGTGGGTGGATCATTTGAGGTCAGGAGTTCGAGAACAGCCTGGCCAACATGGTTAAACCCTGTCTCTA + HHHHHHHHHB-:ACEGG?>>-@;+:CHHHHHHHHEBFHHHHHHHHHHEFEDFGHHDGEEIEHHGFHBE8CGHHHB6?5EBGHGFHHHGHEHEAHHG?1%1 @read_150_178/2 TGGGGCCCTGACCAAGCACGCCTGACTCCAGCCCCATGAGGAGCATCCTGTCTTGGTTCCGTAGGGATCATGGGTCCTCTTACCACTGTGCGCCAAGCCC + HHHHHHE@ACGGGGGHBB=GHHHHHHFFFHHG@@HGGGHHHHHHHHBE@<9??:>=?:9>D@DGGHHHFCFE=>FFDDDFE74?DBBB-BEFGGG/BEFFHAFFGHHHHHHHHHFHHHHHDHHFEE;?.<>4<,9<5+686GHHHHDGGFFBFHHEHHHFBF?ED>6<;.851?EEC @read_150_182/2 GTTCCAACTGTATGGAGGGACAGTCAATTTGAGCCCTCATCTTGAACAGCCTCTAGGTTATGTCTTCTGGCCCCCTTTACCGTGAAAGGTGCGCTTAGTG + HHHHHHHHHHHHHFGEFEHHHHHE;.;EH@DDDHHFFFHHHCDEHHHHHHHHHBCEHHHHGGGEFHHHFFEEEFHFHEHHFHHHHHF<EHHHHFHHFFEEHHHEEHGF?FGEF;/3BDGGGEHHHHGDEGGGGEFH @read_150_184/2 CACCAGAAACCTTGGCAAGTAGCCACCTCTGGAAGTGACATGTAAGCTGAGAACTGGATTGAGCAGGAGCCAGCCCCTAGAGTGGCAGGGTTGGAGTGAC + HHHHEFFHHFGFC@;2/B;?BGFHHHHHE<8BEEHHHHHHFHFHHHHHH=EFDHFEEDBGHHHEB>BEGHHGDDDBEGGHHHHHHHHGC?8=DFD:=G:. @read_150_185/2 TACTCTAAATGGATAAAGGGTAACTGTCCCTGAAATGAGTTATAAAACCCTCATTTTACAAAATAGGAAAAGACCGGGAAAGGTGCGCTTAGTGGCATAT + GGFHHHHGGFGFFGGHHHHGFHHHHHDHHHHHHHHHHHHHHHHHDD4::>:9*??FCA?5>&39.))+=HEGHHFFHGEHHD<55*ACGB @read_150_186/2 GAAGCAAAATGAGGTAATGAAACAAGAGGTAAATACAAATGGTTGAAAGAATAAGACAGGTAAGGAAAGACAGAAAAAAATTGTACTTAAGGAAGCAAAG + @EFFE=@AGHHHEBFFD@GEHGGGGGGEHHHHFHBA?>EEDGHHHGCC@?41=;98?A<96??ECGGGFFFFHHDEEGFFGHGHGFCFHFC>179489AA @read_150_187/2 GATTAATGCTATCACCTTTTCAGGAATACAGGCTTGAAAACTGACAATCCTAGTCTCTCTCTCTCACCCTCGAAGCCAGTTGTTATCAAATTCTCATAAT + HHHHHHFGG@CHHHHHHHHHHBCHHHHGGFEHHHHHHHE==FHHHHHHFHFB89>FF>=FBEBGEFED01+7D.<+8995361,, @read_150_188/2 CTTCAGAGTTTTATAGTTTTCCTCCTGTAGAGCTTGTACATATTTTTTTAGATTATACCTAAATGTGTTTTTTGGTGGTAATATAAATGTTAAATTATTA + FHHHHHHHHHHGEGE=93;47>G@.11.<9**177CFFFFHHHHHEEFFHHHHHHHHHHHGGHHHFHGG@DIB8AGDDED<:.;79=DGFEDGGGFEGE? @read_150_189/2 GTATATAATGCCCATGTAAGAAGCTTCTACTTTAAGCAATCTGAGCCTTCTCACCCAACTACCTTCTTCTACAACACAGCTCATGACATCCTAACTTCGC + FEDDABGGEEEEHHHHHHHHHHHHHGF@BBDFGHGFFGEEEHFHHEHHEE@CEEE7)**6;D:,;48@C7'7=EG @read_150_191/2 AATTGTGTCCTGTTATAAATGTAAACAGGTTCTTATGGCACTTATGCAAGTAACTATATTGCCATAAGTTAAGCATATTCATAATAGTTTACAAATTCTG + HHHHHHHHGG>BEG9>.67A@AA8DHHHHGHGGEEGHHFHHHHHHHH=><::5861=9EE9>CAHHHHHGBE??DEFFHHHFHEE;ADBGHHHHHHHHHH @read_150_192/2 TGCGGCACGCAGGGCATCTCCCAGCTTCAAACACACTGTCTTCCCATGAGCCTCTTCTCCCCATGCCCGGCTCCCTCTCGCCTCACAGACTGCTTGGAGA + HHHHHHHHHHHHHHHHHEG@@GHHHHHHFFHDFGHFC.A+?GGGBFHHHFDGFEFFHHHHHHHGB@BC5;@ @read_150_193/2 TAGATTCCAAGTAGAAAGTGACTTGTAGGAAGTTGGACTCTTACATTACCACATACTTGAAACTTGTTAAGAAACTCGGAGTTTGGCCTGCGCGGTAGCA + HHHFHHHEFHHHHHHHHHHEHHHFGGHFFHHHHHFCGHHFHHHFC7=EBFHHHHG5-?GE.=//EFHHHHHFHGDHHHEHHHHD(3FGGGFC4EHCCC/- @read_150_194/2 CCGCCTCCCGGGTTCAAGCGATTCTCCTGTCTCGGCCTCCCGAGTAGCTGGGACTACAGGCGCCTGCCACCACGCTTGGCTAATTTTTTGCATTTTTAGT + HHHHHDDE@B8ECDDDEHFBBB>HHIFGGHHHFHHHDD@@HHHFDFA??@6<>;?E=881-2>=GHGCFHE@DDDDDHHHFF?@,295?>:;FHHHHHHEGEEHHHHHFHFHHHE6BFFFHHEGEABC@68349 @read_150_196/2 AGAAAAGTTAAACTCTGAGAGTTGAACGCACACATCGCAGAGCAGTTTCTGAGAATGATTCTGTCTAGTTTTTATACGAAGATATTTCCATTTCTGCCTT + DB>9-1.AHHG?GHHHGGHHHHHHHHEHFHHHHHHHHHHHHDDEHGGGGHHHHHGEFFDFFDGAAEFHHH>?DEBGEGHHHHHHEAADGHHHHE?FA=4/ @read_150_197/2 TCCAAGGGACACCATTCGCATAGAACACAATGTACAGGGAATACATTTTGCAGTACAGGCCCTGAGGCCACTGTTCCTCTGCCACTGCCACAACTGTGGA + HHHHHG?EGGGHHHHHHHHHHGHHHFHHHHHHHHHHHHHHBBGGH@BBE>@C@EGIDGGHHHHFGCFGFH?5.66F+)7.82(-2B745)7079'55DBFGGHH?.=A<464 @read_150_199/2 TGCAGTCTAGTCCAACTGTTTCTCCTTTCCCCTCTGTCCCTAGGAATCTTCCTTCAGCTTCTTTTCTGCTGGGGCTTTAGTATCCTTCAGGTGACCCCAC + HHHHHHHHHHHH@GB-9713.9:;AECF@DEGGHHHHHHHHFGACFFFFHHGFGGHHHHHHHHHHHHHFHHHHHHE.DDAAFEEFBCFFHHCEFE8>>;= @read_150_200/2 TCCTTCAGGTCTCTGTTCCTGTATTACTTCCTTCAGGGAGCCTCCCCTGGCTGCCCAGTTAGGAGGTCCCTCCCTGGGTTTATATATCACCCTGCATAAT + HHHHHHHHHHHHFGFHHHHHHHHHHEGGHHGHHFE:;:=4;?3?=+1>D6@GGGHHHHHHHGHHBGBFHHGB=;85?EFAAA>D9>ABGGGE @read_150_202/2 GCCTTAAGCAAGCTTATTTTAGTTGGGCAAAGGCCTTTCTAGCCTACAGTTCACAAATAAGACAGTGAGTTTTAGCTGCCTGAGTCCCCTTTATTAGGTG + HHHHHHHH;FFDCDDGHHHHHHHHB5*3609B@?EGD@GGGBEEEHHHHHFGDDABEGFGHHHDGE730/A89:06<:.+'>)+=DBEFFCGB<>7 @read_150_203/2 AGATTACAGATGTGAGCCACAGCATCTATCCTATAAAACTCTTTAAAGAAAATAGGCCAGGTGTGGTGGCCTATAATCCCAGCAATTTGAGAGACTGAGG + /?FFGHHHHHHFCHHHHHHHFGCFG>8EFGGHHHHHHHHHHHHDEBE8EFHHHHHHHHHHGGHEED;.GGHFFFFFFFFHFB>EFFAFEEBBH<39/8DC @read_150_204/2 GAGTTCTACTGGGCTGGAATCAGGTTGTCAGCGGGGCTGTTTTTTCTGAAGGCTCCAGGGGAGCCTGTTTCTTACCTCTCCCAGTTTTTAGAGGGTGCTA + HHHHHHHHHGGFHGEGHEHHHHHHHHEFHHFADDHHGG8?GEGGGHHH=EIGHHFHEHDDHHFHE:>:89DDCD:*18<-673;GGEEHBHHEHHHHF97GHHHHHHFEB?>:@:7(0:AC>< @read_150_207/2 TGCCTTAGCCTCCCAAGTAGCTGGGACTACAGGTGTGTGCCACTATACTCAGCTAATTTTTAAAAAATTTTTTGCAGAGACAAGGTCTTGCTCTGTTGCT + HHHHHHHHHHFHHFEGBBHHHHHHHHHHHHHHED8HHHHHGGHHHHFHFEDEHHHHHHHHHHHFHHHHHHHHHFFHHGBGH=4A@EEHHGGEEE+7DHFG @read_150_208/2 TTTTTAGCGTTGTGAATACTTACATAAGCTGTGTAGAAACACATCTTCAAGTGAAGATATTTTCTCCATTTGGCAGAATATGCAGGCTCCAAACTGGATA + HHHHEBDEFHHHHHHHGFGGHHHHGHHFEHHHHHHHBEED>@EBGGCGFE?9<<9BHF=ECDA>5:@??BE;@<;>9FFBFHF/D?FHGA.8;CDEEHGC @read_150_209/2 TGGTCTGTTTTCCATGTCTAGATATTAGAAGAGAAGGCTCAAACATGAGGTTACTCTCTGTAGTGCAGTGGGAAAGAGTATATTCCCAGGGAGCCTGGCA + HHHHHHHHHH@@.795>BHGHHBECBBB==DGGHHHHF5;DDDCB(B@@1/(01=EGHHHHEE@@<<:;@D>>;GFFBFHHHFHHEHHFGHHHF>?FEBG @read_150_210/2 CGTTGTAAGGAATTCTAAATCCTTTCGGCTGCAGCTTTCAGCAGCGCCTGGCATCCTGGCGGATGAGAAAAAGGGGAAAAACAGCAGCCCAACTTGAGAA + HFG/===DH?<<<<6=GAGB;/&53@DDEBFGFEGGGDBDEHHHHHFEDEHHHHHHHHHFEHHHHHHHHFHCDEECFHHDBFF@9FGGFC<;@<26.39H @read_150_211/2 TTTCTAAACATGCATCAGTGCCAATGATAAACAGTGCTTTCCTCGAACCACATGATGTGAAGGCCAACTACCAAATTTTCATTAAATATAAATAAAAAGT + HHHEEFHHHFHHHHDFHHHHFEEEE?DFFGGGGEEF=CFFGFFD6'>1<>8AFGGHHFFG<-268>8DEHHHB>:EED;.FBFFFEHFEE>FEE>E44%& @read_150_212/2 AGCAACTAGCACAGTAACTGGCCTATCACAAAACCTTAGTAAATATATGTCAATGTAATGGAAGGGCTGCTCTGGTTCTAGCTCCTCATGAAAACAAACA + HB@EEHHHEBEHGGGEDGEHHFGED5.FHHHHHFGHHHHHFFHHHFHHHEAGGEEEBHHHHHHHHHHHHHFGGFHGDH@:DHHHHDDCAEHHFHB@,C.D @read_150_213/2 TATCCATAGCCCTACAATTTTTTTTCAGTGTGACTATAAAGTAATACATTTTCTCTTTTTTCTTCTACTTTTTAATTTTACTTATTTTCAAGGTTCTTTT + GGHHHHHHHHHHHHFBGGGEHHGGEFFFFHHHHHHHFE@.AHHFGDFHHHFE8=:=2.>:7<=CFHHFFHGGHHGHHHHFFFB8:68*?DHFHHHHHFDHHHHFEDHHHGEG<>339AD8>397@@@7CD><=CG=G=D-CDEFDD7CGHDAFFG7(<.*:?=>FHHHFFB @read_150_215/2 TGGTAAGAAAGGCAAATTCAAATTTGGAAGAACAATGTGGAATATGTTGTTTTAAAATTAAACTTTTATTTTTGAGATAATTGTAAATGCACATGCAGTT + HHHBGEGHDEG@EGHHHHHHHFF@;G86<6-*>@DEF?EEGGFFHHEHHFGED=>EHHFEHHHHEHHHHHFGHHHHHGD,+=GG;D,0:DDDCDFHHHDE @read_150_216/2 AGTTAGCCCTTTCAGCAAGAATGTATGTATCCTTCTTCTAATCTCCACCACATGACTCTCTATGCGTCTTTATCCACAGAGGTAGATATTATTCTCCATC + @@8?GHHHHHHHHDAHHHHHHDDGHHHHHHHHAC7*:(7:??@=79>ADADHHHHHHGHHHHHHHHEEHHFHHFGEEIFDEDGHHFHECD0>EEEDFFFF @read_150_217/2 GCCTTGGTGCTATCCTCCTGGAACCCATTGCCTCATTTTGGTGTCTAGATCTGCCACTGAGTTGTTGGAAGAAGACTTCCCTTTCATATGACTCTCAGAT + HHHCBBC@FHHHFHHHHHHHHHHHHHHHHEGA@2CFHD7@@=9CDFEBBCEEDDCGGGGHHGFDEHHHHFBFHHHGHHHHHHHEFHEEHFB;,EHFCFEF @read_150_218/2 GTGTTAAATTCAGCAGCAATACGATTTTGGTACTGGAATTGTTTGTTGAAAAGTAGTTACCGTGAAAGGTGCGCTTAGTGGCATATGCGTTAAGAGCTAG + DBDDDGGDHHHG//DHHHHFFFHHHEEGFEEBD>CGFHHEFHHHFHHEFEGEC@BDFHHHHAGFGHHGFFHEEFEDC=>EHE:6AAD643@@FFB @read_150_219/2 GTTGTCAGCTGAAAAGAAGGTGGAAAAAGTGTCTACAGTATGCTTCTGTTTATCTAAAAGGTGTATATATATAAGCACAGATATAAAATACTTGCTTATA + .@HHHHHHHHFB@AEDFEGGFGGHHHHHHDHCDCE=CBHDGE<76DEGCCHHFFFHHHHH>)+;DBE=BFHDD(/C/DEGHEB7>A=C?D@FEEEECDFC @read_150_220/2 TTCAAAATAATATTTCAGATAGTACTACACAATCTATATTGATCTAACCAGAAGGAGAATATTTTATTCCAACAAGAAGAGCTAACTATCCTAACTATAT + <;/GHHHHHHHHGHHHGHFHDHHHHHGH?GEEDFE=..BGDEEGFGFDD69&'+37;,956@GGHDEFCDHGBB0@@6?D+@FFADDDA:.8;@CA @read_150_221/2 TTTTCAGAGGTATTAATCTAAAAGCCATTTCATGGAAAAAAGCAACAAGGAACTGGTTTTATTTCTTTTAGGTGACACTAATAACCAAACATGCGACACA + HHHHHHHHHEFFBFHFFFBHHHHHHHHFEHFGDEA755=D<.85(;GGCCGGHHHFHHHHHHHHHBEBE;EEEEFEHGHFHHFGFFFFFHHHHHDIFHHHHHHEE:0,>DBEGHHHHFFFDA=>.D:A.8BCEEHFGFGEEA @read_150_223/2 ATCTGTTGGTTCCAACTTATATTTCTGTGTGTACAAATAATACACCCTGTGCACGAAAAATCAGTTTCAAAAGAAAGAGCTGAATTTGTCTAGAACCCTC + HHHHHHHHHGHGFFHHHHGGHHHHHHHEHHHHHHHHHHHHHHHEGBCEDD:@?,/1?;EEEEFHGEFHGED @read_150_224/2 TTTCCTAGAGTAGTGACCAAGTTTCTGACTATCCATTAAATCAACCGTAGAGAATACCCGCAGTTCTTTTTCAAAATGTGATGCTAACAAGCTAATCTCC + HHHHHHHHHHHGHHHFFHHHHHHHHFE=FFHDHHHFGHHH?HHHHGFHHEBGDDB.5 @read_150_225/2 CTGGTTCCACCTGAAAAGGTTATTTCAAGTGTAAATTCTAGACCTTTTAAGTAACAAAATGATACAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAG + GEEB@FDCDGGHHHHHHHH>;DHHHHHHHHB:GHHBFFHBF=@DGHHHHHHHHHEEEHHHHHHHHHDGGEBCHHHFHHHHHHHGB4+DEFHFFEEAADEG @read_150_226/2 TAACCTATAAACATTTATGTTTAGTATATACAATCTTTTTTTTATTATTATACTCTAAGTTCTGGGATTCATGTGCAGAATGTGCAGGTTTGTTATATAT + HE:.FGHHHHHHHHHHHHHGGGHHHGHHEHHEHFGHHHHFGFBEI:=CBD=DGIEFGHHHFHHFFBHH87@CEGD>@??:9FDEBB @read_150_227/2 TTTGTCCTTATCTTTATGGATTTAATTTTATTTTTAGAATATATAGAAAATTATCTTGCTTCCAAGAGTCAAAAGTCATACAAAACATTTACTAAGAGAA + G@GFHHGHHHHHHHHHEBFHC@AA?=>@AC35-(')<7:99EFFHGE32(><<'*:D=:=BHHHBB@@?DG>FEFBGHEFHHHHHHHEFGED.>+.1:;C @read_150_228/2 TCTTCAAAGGCTAATGCTCTGCAGCCTGTAATCCTGCAGGTTGCCTTAACAGGCTCCCCAGCTCTGTTCCATTAACTATTTTTGGCTCAGTGATTAGAAG + HHHHFDGHHHHHHHHFHHGBDE@HGHHHHHHHHHHHHFHHHHEGDDEGGGHHHHHHHHHEFGGF@739@;44017BDEDFGE@BB@D??GGGEADHEEE;B>ECFCFFHHHHHHHHHHHHHHHHGHHHHHHHGEBEGHHHHHHFFGG?CC@>*,<>9.938<854>;EEFFHHHHGBECBDDEHFBHHHHHHFHHHGHHHB=FDDHHGGD0:5-4(/8@FGEGF;?A>BD?FCD @read_150_233/2 CCTGGATTGGTTCTAGTTAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAGGAAAA + HHHHHHHHHHHHHFFHGHHHHHHHGGHFE>CFDCBFHHHHHHHHDEFF4==ABCHHHGHHHHHHHHHGHHHHFHHE89DDHHFBFBD=@C1.:7&&>>DC @read_150_234/2 TAGAAACATCAAGATAAATAATAATAGTAATAAAGCATCCCTGTACCGTGAAAGGTGCGCTTAGTGGCATATGCGTTAAGAGCTAGGTAACGGTCTGGAG + EE=CCEBFEFBEG@BGHHHHHFGDHGHHHHHFGGEFFFFHHHHHHFB:@@EGGHHHHHGDGHHHHHHFEBFFEGF5/DGD>>?6?2>@+8/68,8DGB@@9>EF?@ED.EFBBEEHDEEED.HHHHHHHFFEEHDBFHC@=)3:?;;DDCB::+@B> @read_150_241/2 CCACAGAAATACAAACTATCATCAGAGAATACTATAAACACCTCTATGCAAATAAACTAGAAAATCTAGAAGAAATGGATAAATTCCTTGACGCATACAC + HHHHHHHHHHHHDBGGGGHHHHHHHHHGFFBHHHHHHHHHFEHHHGGFFEHHHEEHHHHHHDDGGFHHHHHHFEDGFA@EHFEHBHHFHEGBFHB4%/3/ @read_150_242/2 AGAAGTCTCACTTTAGTTTGCTGCTTCTAATCAACCACAGGCTAGGAAACCAGAAAGCCTAATTGATTAAAATTGTGTTTAAAATAAGAATAACTAGGCT + HHHHHGGGGGDDDGGHHHHHHHHHFHHHGGB;=?60,;99HHFE=:DGIGHHHBBGGFFBBEFFHHHHHHHHB;;GGHEGGFHHHHEGHHB<189-9A@4 @read_150_243/2 CCTCTCATCTTTCTAAAACCCTGCTTTGCATTTTGCAACTCCCACCTTCTCAACACTCAAGATCCTACATGGGCTCTTTCTTGCCAGATGAGAGATCGGA + HHHHHHHHHFEGGB?CDHFGGIDGGGFGGHHHHHHHHFGGHHD>6<5?HFHHHHHGGGGDEEHHHGHHHHHHHHHHHHHFHHHHHHHHEHFHFDBBGFHF @read_150_244/2 GAAAAAAAAAAAAAATCAGACATGAGCCCCTCACCCAGGGTTTCCTTCCTTGGGGGAACTCAGGCTTGTACCCCTCTTGGTTTGTGGCAGACTGCACTGA + <@AEGEDCDFFDE=6DBHHHHHH@HF=ADGGHHHHFFFGHFHHHHHHHHHHHHHHHHHHHHGGGFEEHHEGGHHHHHFHHFDGGFHFA;AGDHB=))A?B @read_150_245/2 GTCTTCGGAGACCTTACTTCTCTGACTTTCACATTCTAACGTTCTGAGGCTAATACTGCGATGTTGCATTGACCCGAAGGGCTCGATGTTTCGGGAGGTC + HHHHHGFEEEEGFHHEFFHHHHFHGEGGDEGGHFGGGHHGB+0>CB&*4@HHHEEHHHEGGFFHHDB,5<@'5:1: @read_150_246/2 GAGCCAATTTGATGCACATGTAGGATCTCAGGGGTCCCCTAAAACATCCAGTAGGGAGAGCTTGATAAACCTAAATCCTAGAAGATACCGTGAAAGGTGC + HHHHHHHHHHHHHHHHHHHF=GEEGGEEBGHHHHHGDA@;F@;87GGDDA5D?EE8).@5@DHDFHEEDA>GGEHHGBFA@AAEFHHHHG4@?B;GED4??HF @read_150_249/2 TCTATGAGCAGCACATTTCCTATACAAATGTAACCTAGGATAGACTGGGCATCTTTTCTGATTTGACTATTCTTCCTAAACAGCTTTTATAATAATGTTA + HHHHHHHH?GE8@CCBE@C>FGAEGHFGGGGB@@GHHHGGHHFHH@A?>>8*74>FEHHGE=?@.?=FFHHHHHHH@C.CHFFDAHHHHEHHGB;@BGEEDDFHHHGHHFHHHHFEHBAFFGFBCE;@A-@EHHHHEEG9@=EGFGHGGHFHHHHHHGHHHGGHEHHHHHHEC=6ADGFEFHHGDDEH@CEFF @read_150_251/2 ACAGGATATATACCTTGCATTTTTATTACATACATTTTATATACAGTATTAGCAATGGCTTAAACAAGGCAGACATTTATTCTCACGAGTTAAAGGCCCA + FGGFHHHHHHHGEHFFEDGGHEFEHHHHHHHEEEHHHEEFHHHFHEEHHHHHHHHHHHHHHHHFGHHGFBFEDDGGGHHHFGHFF=CCBCGHHCHDF?DE @read_150_252/2 AGCAAATTAGCAAAGTCGAATTTTAGTTCTGCTTTTCAGGGAAAAGAACTGGAACTCTGCTATTCAGAAATAAACTGTGAAGAAGAGTGGCCAAAACCTA + HHBHF?HHHHA@>>>B7@GGEEHHHHDE=FGHEGAHDD=@=18>DCE=CFCGHHHHHHHDFGGCBGGG=CGHHHEBB=@HEBDA?GHHHHHHHHHHHHHH @read_150_253/2 AAAAGTAAACTCATCCATCAAGATACATCATTATGAAAAATAACCATATTTTCCAAAACAAAATTAGTAGAACAATGAAATTGTTCTAAATTTGTGCAAA + FHGEBHHHHHHHHHEHHHHHCGGHHGHHHHHHFHHF?EFFGCGEB>7@AA75<>>DGGFEGGGDHHHEFDHHHHHHFEEG@>BAFHEB?&%7CFDDH @read_150_254/2 GCCAGGCAACCTGGGTCTGACTGTCTACCACCGGGCATTTCTCCTCTATTCCTTCCTGCGCAGTGGGGAAGCACTGAACCCTGAATATTACTGCGGTGAG + GFFACGD>:>EEHHHHHHGBE?>>DGHHFHHHHFHHFHHHHHHHFBBFFG@BFGHGDIHEGGGHFHHHHBC=CDEFHFFHHHHHFCGBDHECFFF@A@>A @read_150_255/2 TTTTTGTTCATTCCTGGACTATCCAATAAACAGAATCAACTGGTGCTTTTGATATAAACAGAAATTATTTTCTTGTCTAGAAAAAAGAAAGTGGTATATA + HHHHHHHDBBDFEHE=BCHHHHHGHHGFGGFEHHHHHHFFEEHH=H<8DFHHHHHHHHHHHE@??@CGGG21*+.7EHHBCBEHHHHBEECBDCDDF5GF @read_150_256/2 TTATCTGAGTTCCTTCCTCAGGAAAGGACCTTTAAAAAAAGTATCAGAGAACTGAAACTCACCAGATCACTGCACCAGATGCCTCCTTGCCCCTCTGTAG + HHHHHHHHHHHHHFFDFE.8FIGGGHHHHHHHGGHHHHHHHGDCD57@FGGGGGGD@GDGGGDBEHFHH?EFFDGBF?DHFEDBDHHB@<45DGGHHFDF @read_150_257/2 GAAGATGAGCGGACGCAAAAGAAAGAAGGATGAGAAGCGCCTGAACGAGCTACTTAAAAGCCAACGCCGGTGACATCACAGCCTTGCTTTAAACCCCTCG + HHHHHHHHD=BGHHHC@;33A.>CDDAEHEHHHHHFHHEEGHHHHHEFEFEGHHHHHH=EHHHGGHHHFHHHHHFHHHHHHBGFFFF58'BD@@>::E@< @read_150_258/2 TGGTAAAATAGGAATAATTCATAGGACTGTGGTGGTTTTACAATGAAAGGTAAAGCCCAATTTTAGCTATTACTGTTATTCATGGAAGCAGCTTAAACAT + HHHHHHHHHHHHHHHHHHHHGD>BGGEHE@EEEGHD6>GAE<8EB5CGGFHHHHHHHGGHHHHFHHGCADF@CDBEE/:DGHHHHHHHDBEEHHHHFEFH @read_150_259/2 AAACCTCTTTTCTTTGTAAATTTCCAGTCTCAGGTAGTTCTTTATTGCAATGCAGGAACAGCCCAATACAAACAGGTATAGCAGGTGTGTCATAATTTAA + HHHFFGHFHHGFBFFHHGFBBFHHHHHHHHHHHHHHHHHHHHHHHFFFEEHEGFHHHHHHHHF<>EGHHHHHHEHHHHHEDDGGFBEHECFCHF5311,< @read_150_260/2 CAAAAGCTCCCCAGCCAGGCAACAGGCCCTAGGAATTGGCCTTCTGATGCCTCTTCCCTTCCAAGCTGAGATCAGACCCACTTCTCTGCTGCAGACGGAA + GHHHHHHHHHHHHEGHBFFHHHHHHFGHHFHGEEBEEFHHHHHHHHFDFHHHGEEDFHGHHHHEEIEGGFHHHHHC)BEE+:BHGDFFFHHHHEE=FHFA @read_150_261/2 TAAGAATGCCAAGTTGACAAATGCAGAAATGGGAACAGAGTTTTCAAAGGGGCTCCTGCAAGTGGAAGGCCCTACAGTTTAAGTCTCGTTAGTGCCATGG + HHHHHHHHHHHHGGGHHHD:4<9<5>D?HHHHHHEBGHHHHHHHEHHHHFHHGHFGEEE2BGA7:16EFFGFHHHHGHEHEHHHHEGHHHHHHD;3&;EE @read_150_262/2 ACTCAGTAAACTAGGTAGGGAAGGAGCATATCTCAAAATAGTAAGAGTTATTTATGACAAACCCATAGCCAGTAAGATCGGAAGAGCGTCGTGTAGGGAA + HHGD>7A=FB<>:2;-**'00*-3>BFHHHHHHHHHHFHFHHHHHFGGCBF.8=CIEB@?=B7BC<*2/CEEEA?:CCE@A.8EEED245==:9%BFHHH @read_150_263/2 TCAGCTATTACTATTACTACCACTCACCCATCTAAGAAACTCGGAGTTTGGCCTGCGAGGTAGCTTGGGTGTTATGAAGAACGGCATGCGAAAAAAAAAA + HHHHHHHHHHHCFHHGEHHHGDHHHHFEHHHHHHHFHHFBHHE83('.36BDHGIEHE8E7BEEEGGGHHHHHHH/3&AFFEGGGFD?6BAFFGFHC<06 @read_150_264/2 AATCTACATGTGACAAAATTTGGTTGAACTAAATAAACACACACACACACACACACACACACACAGACAAGATCGGGAGTAATTTGGAGGCAGTAGTTCG + HHHHHHHHHHHHHHHHHHHHHHHHHHFDBE<=@-1-25:BFHHHHFBGECDDCDGHHHHHHHHHHHHFDHEFHHHHHHFEBE:776>:-)48ECCAAEEF @read_150_265/2 TTAAAAGTACTAGTAAAATAGCCTATCTGGACAAAGAAAAAGTAATACATTTACATTATACTATATAAAAATACATTTCAGATAGATATCTGAATATAAA + 8DHHHHHHHHHHHHHHHHHHHHHHHEHHHHHHHFHHHHHHHHHHB;@BFHGGHHHB06>A7.;@@FHD@@6=@BIHFHHDGGFFA=>;7B@?C?C?;,55 @read_150_266/2 AGACTTGTTCTTATTCGGTCTATTTTTTGTACCCATCAAAAACAAATGATGGTTAGGTGTCACTAAGTAGGTGACAATGGCTTAATCTGTCTGTGCTCCT + HHHHHFHHG8>=?HHHHHHHHEE?CEAHHHFHH@D2-(20.(?EHHHFHHHHHHGDEGBBD==<:A?FHHD@;GEC8=CCDHHHFEGHGE43A@BCGHEA @read_150_267/2 AAGACATGCTAATCCTCAGATCACTTCAGCAAATGAAATTGTTTCAGCTTTGGACAACTCACACTCCGTTACATGACTTCATATTCTCCTGTTGCTCCCT + HHHHHHGGGHHHHHHHFHHHHGHBCBDFHHHEF?@DGBBDHHHHE.1?HHHFGGFHHHBF=CF4720).BFHHHG@=A6EHHH=CCBFFE=,%-FFEHFF @read_150_268/2 TGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAGAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGCTA + EEHBEBDDB9'1'04?GGBC=DFHFBBBHHHEE897E@HHHGE=:?.<8DFHGGHHHHHHHGHHHHHHHHFEE(/7&,1:99<>4;51D?C:6438.8(ECCA5 @read_150_272/2 ACAAAGCATTTGCCACTAATAAGACTTTAACACCAGCAATCTGTTAATATTACAGATGTAAATTAAATATTTCCACCACAGAGATGCTTCATCAACTTCA + HHHHHHHHHHHHHBDFFHHHHHHHHHHEFHHHHGEHHHEHHGEHHHHHHHH9<<;A;BEFFFFDF>?AAAEHH;%1'.3 @read_150_275/2 CTGTTTCCTTATTTAATACCATTAGGTGCTTCTCCACTAGGATAAAGTAGTCAGAATTCCTTAGAATGGCATACAAAGCCCTCCAAGACCTTCCAGAGTC + HHHHHFHHHHHHHHHHGD?=C9GHHBBBHHE@FHEC@,@.:DEEEHHHGEFHHHHHHGGDGGBDFHGHHHHHFHHHDD?BFHHHG<<.CHHHHHHHHHHHHHFFEFHFHHHHHHFEEDF=EHHHHHHHHHGHHHHHB@B@*3BBHHEGGGGHHF;<;D@A=:>;5>55>:& @read_150_277/2 CCAAATTGTGCTAATTCTGCTCAGGATGAAACAAATCCCCACGCTGAAGTGGAGAAATATTTTCATAATTGAAGGAACATATCCCATTGATTGTCTACAC + E@E=ADBGHHIGEGEHHHHFFHHHHGCDG>@@7?436GGHHHFHHHHGBCGGGEGGHHHBHGGGFHHEHHGH@>>A?>43DDBEHHHG@>FBEHFC@EDF @read_150_278/2 AGCATCTGTCCAAAATGTGTCTTCAGATTGAGAAGGGAATAAAACAAGTAAATGTCAGGGAATAATACCTTTTCTAAAAATTGGGATTGTTTTAACGGCT + /?7495AE @read_150_279/2 ATTGGGCAGGAGGAGGGGAGAAGGAAAGGCTCAGAAGGTGGGCCTAGGAGCTCTGCTCCAACGTTGCATTGACCCGAAGGGTTCGATGTTTAGGGAGGTC + IE@=F@BEB@@;EDFHDHHHHHGDBCFHHHEGEDF?-6;>),271899BDGHHHGECHHFG7BEHEFFF;ADFFA..;<=>+6<>?E6BFHHHHFG?D9< @read_150_280/2 CTGCAATGTTTATTCATATGGTGACATTTACTGTAGCTTTCCTCTAAAAGGCAATGGTTTCTTCCTGTTTTAACAACCCAGAAACCATTATGAAGTTACT + HFHHHHHHHGGFHHHHEGFHHGFHHHFHHHHHHHHHHHHHFHGEEDDFHGHHFF=ABDFFHHHHHHGGGHHHHHHFDHHBG7'-100.7;@6041:>DGEEFHHCB9:,6;<<.8CA'386.(5:@E9869@@FFGFBBE8BCD6.19AACCFHBCHHFGF @read_150_284/2 TAGAGACAGGGTTTCGCTATGTTGCCCAGGCTGGTCTCGAACTCCTAGGCTCAAGCAATCCTCCAGCCTTGGCCTCCAAAAATACTGGGATTAGAGGGGT + HEB@@GGBDHHHHHHFGHHHCGHGFGHHHBGGEHHHHHHHFDFFFHHHHHDCCCB:=B:;>>@HHHHHEAGHHHHHHHHHHF>9.9=@EEFHEEGFFGGG @read_150_285/2 TTCTGTGGGGCCATTGCCCACTTACTAGGGGGAAAGTTTGGTGCATGTTTTCCCCAGAAAATGTCCTGTGACATCAAAGAGTGACCTAATGGAACCAAGA + HHHHFFGEBC@CFHHHHHHEDFHHHHHHGGEHFBFHHHEBEFFEHHHHFHFHH:)50365:??ABD,2@DEEECEEEEFFFHDCDGEFCDE+%5=FHHBH @read_150_286/2 TAGCAAACAAACAGAGGAATAGAAAACAAAATACCACATGTTTTCTCTTATAAGTGGGAGCTAAATCATAAGAACACATGGACACACAAAAGGGCCTATT + HHHHHHHE>B@ECF8DEACHHHHHHHDGDE;FHHHHHHBHFFGFHHGGHH=EEGFHEFGFHHC:7..;;A9,AEEHHHFDHHHHHHHE=4'>9AE63;57 @read_150_287/2 CTTTGTTTAATGTGTTCTTCTTGGTCATCTCAACAGGGCCTTTTCCCAACAGTCTTTTTTTCCTTCATCGCAGAAAAATGATGGTATTTAAGCCTGAAGT + EHHHHHDECCHHHHGHHHEEGFF:<=DFG?E869DEE>B@DFHHHDCDFHHHGHGDFHGGEHHEE6--+))=G??FF@;AHHHFHDDFHHHHE@HHH9=3 @read_150_288/2 TCAAGAAAAATAATAATAAATAAATAAAATAAAATAAAATATACATACATTTTGCCAAAAGACGCTGGAATAAAGTTCCAAAGGAGTATAAATATTTATA + HHHGHHHGCBHEGGHHHHHHHHHHGEEEHHHHHHFHHHA@GFHHHHHFFHHHCB75412,)&1010GEEFHHHHHHHHDBECBHHHHHHHEE><;6;>CEHFHFHHHHGHHHGHHHHDHHFF@@HHFFEEGHHGHHHHHGFFFHFCBHHFAEF?FFFHHHHHHH @read_150_291/2 ACAGACACTTTAGAAGTACAAATATAGTATTTTTCCTCAAGAAAGTTATAATCCTATTGAAAGAGACAAAAATAAAGCATGGAAAAATTCCTATAATATA + HHHHHHHGHHGFFHEHHFHHEFGHHHCBHHHHHHFD@BB>BCC.BC;>;CHHHHHGGHHHHHHHHHHHHEGEGFHFGHHEFFFFHHHHEEHHFGBEBGEE @read_150_292/2 GGCCACAGAGAGGGAAGAAGGGAAAGAAGGACGTACAGATGTTCACTCATTCCAGTGGAGCAGGGGAAGGAAAAGAGAAATAAGCTGACCTGAGGCATCA + FHHHHHHHHHHHHHHHHHHHHH?CDA>AHF;CBEDHHHHF?AHHHEGB,@GHHHHHHHHHHHHHHBF=>>E:>>@F?=DDEFFHCCBEBDC+&+BGHHHF @read_150_295/2 TTCCTTGTGTTGTGTGTATTCAACTGACAGAGTTGAACTTTCATTTGGAGAGAGCAGATTTGAAACACTGTTTTTGTGGAATTTGCAAGTGGAAATTTCA + HHHHHHHGEBC@=FHHHHGHHGFFGB@@;@DDFCHHHHHEE?BHHHHHHHHHHHHHHHFHHHGEHHHFAAIGGHHHHHHG;AGFFHHHH=GGHHHHHHEF?FHHHGHHDE;FGHHEGECE=DDDGIBGBBAC@FHHCFG?4-AEGHH@<8.2DFCFHHHHHH@CEEF@:.?ACFHHEFFEBDBFHHHCHFGGGFFDDD @read_150_301/2 GAAGTTGAATTCCAGTCTGTTTTCAACAATTTGTCATGTTAGTAGAAGATTAAACATCAATATATTGAGTAGCAGAAGATCGGGAGTAATTTGGAGGCAG + HHHHHHHHHHHHHHHHGBGHHEEEFE@CDCF@DDDHDDGGFDA:HHFF77)3.;BBGGEHGHHFEHHHHHHHHHGADFEGFGFBGHFGDEEHHGFFHE?C @read_150_302/2 CTGATATTTCCATTTCAGTTACCGTGAAAGGTGCGCTTAGTGGCATATGCGTTAAGAGCTAGGTAACGGTCTGGAGGAAAAAAAAAAAAAAAAAAAAAAA + DBEDEDD@<@B=CGGFHHHHHHHHHHE5ABDGEEEEHHHHFCFHBF=C>914-54CEGDHHHHEEHHHHHGFHHHC76GGHHEEEGCEAEEBEHHHFC?9 @read_150_303/2 GGATTTCATAAATGAATTTTGCAATGCTCTCTCGAGTTCAGAAAATATCACATATACATAACATACATTAATAGATATACAAACACAGATCGGGAGTAAT + FBB>HHHHHHHHHHBEBHHHHHHFE@5.@G@6+:/DEB@HEHHHHEDBADD@=EEHHHHHHHGB8CC@6->4A;?DHHHHHF@HHH?,;>33:300BCHE @read_150_304/2 GGTCAGGAGTTTGAGACCAGCCTGACCAACATGGAGAAGCCCTGTCTCTACGAAAAATACAAAATTAGCTGGGCATGGTGGTACATGCCCGTAATCCCAG + GFFEFGD?4?CBDBGHHHFHGHHFHHFEHHHHHFGGD@><5<.D?EE7<&('5DD?>EEE:48EEDBFFHHHHHGF+@EEFG@E36@=?AHAAACBFHFE @read_150_305/2 CTCTACTGACAATACAAGAATTAGTTGGGTGTGGTAGCACGCAGCTGTAATCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATCACTTGAACCCAAGAGG + BAEAB@.?EEBDGFCHHHHHHHHHFEDBHHHGDAAEHFGE.D??E@+BGB7:D@7/6@BBGFHBFEGHHHHHB? @read_150_306/2 TCTGCAATCCCTGTTACATATGACAAGTTGAACATAAGTCTTTATATCACCTCTCCCAAAATTCTACTAAAATGAGCACATCAGAAATTAACCATGGATT + HHHHHHHHHHHEHHHHH@.6>C/55DHHHHHHEFHHHHHGHB:@A*59AEEFGFGHEE0;BDHGGG:6<<,2C>>BEEHGHHHFFHEE?+7BFFGBCGFFGBADBHHHHHEGEEF @read_150_308/2 AGGATCAACAATATCACTGTCCTCTACCTCCACATCTTGTGACACGGGAAGGTCTTCAGGGGCAATAACAGGCATGGAGCTGTCATTCCCTATGATAACA + DAA@FHHHHHHHHHHHFFFDGHHHHHEEHHHHGGDGGGFHFHHHD;;DC2,'/)..?A8HHHHH @read_150_309/2 ACACATATATATATGTTTCTTAAGGAATCATATTGTACATACTGTTTCTTTCCACTAACACGGAATCTCACTCTGTCTGCCAGGCTGGAGTGCAGTGGCG + HHHHHHG=C@=GFEHHHHHHDGHHHHHHHHHFFGFHHHHHHHBFHAB@DHHHHHHHHHHHHHGFFHBIFEHHHHHHHE:@DB>.2>937.635CF?@2<- @read_150_310/2 CAAAGCAAGACATATTTCAGGATAAAGAGAGCAATTCATCAAGAGGATATAATAATCTCAAGTGTATATGCACCTAATAAAAGAGCTTCACAATACATGA + GGHHHHHHHFFGHHHHHHHHFEC=BF<5:DED=DAAC5:.>.:E=D?G=FE @read_150_311/2 TGAACACCCCCTTTTGCAGCGAGATCAGCCGTTTCTGGGCTGACACCCTGCAATCCACCAGCTCTCCCTTTGCCTTCAGCTCCTGCAGCCTTTTCGCCTG + HHHHHHHHHHHHHHCEFFHHGD=+CDGFHHHHHFHHD>>8:>@EFHHHHHHGGIGGHHHHHHFHFHHHFHHFIBEDD;C==EFFFEEBCA::557ECBCF @read_150_312/2 ATCCTAGACCTTGAGGAAGAAAGGCAGCGGCATGCACAGGATACGGCTGAAGGAGATGATGTCACCTACATGCTAGAGAAGGAAAGAGAGAGGCTGACTC + HHHHHHHFEGHHGGHHHHHHHHGFFGGHHHHHFFFFHHHHHB><(ACFFHHHHHHHDC88<'/CHHHHHBA:>=5BFFG@DC;CFC>DDBF=@@EE?97-836)&&:59(*0%.AF>94 @read_150_316/2 GAACCTGGGAGGCGGAGGTTGCAGTGAGCTGATATCGTGCCACTGCACTCCAACCTGGGCGACAGAGAGAGACTCCGTCTCAAAAAAAAAAAAAAATTCA + HHHHHFGHHHHHHHHDFGHHHHHHHFFHGEEEGGF@CFHHD@@FHHHFEEFFFFFHHEHF7;DBCFBGFFEEHEE?FHFHHHHFE4A:D/=FHFGBCEEBA;9@C@FFC8GFHBGFHHHGBFGGFEHHHHHHHHBHHEEEE@B<8=FGHHGB @read_150_318/2 TGGCATTATAGTGAGTCAAATACCATGAGCAGTATTGCAATAGGTGATATATTTTCTGAAGTGGTGAGTTGCATTGACCCGAAGGGCTCGATGTTTAGGG + CD@EGHHHGFHHHHHHHHHFFFGCBGHHGGGHEEDCC:<>C>CHHHHFB7.A8937558,5:EHGGDFFHHHHGHHHHBG.9<<9=AAACHHBEHFFBHD @read_150_319/2 TGCGATGTGTGCGTTCAACTCTCAGAGTTTAACTTTGCTTTTCATTCAGCAGTTTGGAAACACTCTGTTTGTAAAGTCTGCACGTGGATAATTTGACCAC + HHHHHHHHHHHHHHGHHHHHHE+:CFHHDDFHHHHGHHHHHHHHHFEGGHFGGGHHHHHHHHHHHHHHHHHHFFEHHDDGGIDGG=CD>?*>8 @read_150_322/2 TCCCCCAAAAGGATCATCATTTTCTGTGTCCAGCTCCAAGCCCAGGAGCTCTGGGTGATAGCCATTCCTCCAATTCTGTCACCATCTCATCTCAGTTGCA + FEEDGHHHHHHHHHHHHHHGHHHHHFFHHEHHHHHFHHHEHHEBDHEHHHHHHHHF?<8BF>EGGEHHFFBGEDEBC<7-5EEGHHHEFFDEHHHA@@AB @read_150_323/2 TGCATTCAGTTTGTCCTTTCTCTCTCTCAAAGAAGGTACAGTATCATACTGTAGAGGACAAGTGTCTAAAAATCATATGCCTCAAGTAATTATCTTTTTT + HHHHHGFED@DDF?ABCEGGFHHHEGGDDGGHFGHHHHBDGHBGBADEFGEFFHHHHHGHHHC@D;=EDBHHHHFFDCFHHHHHHGGGGGFHHHHHHDA< @read_150_324/2 CATAAGCAGACAAAAAACTGGACTGCTGGCCGGGTGCGGTGGCTCAAGCCTGTAACCCCAGCACTTTGGGAGGCCAAGGCAGGCGGATCACGAAGTCAGA + HHHGEGGFGHHHEHHHHGB@:?C@75?8EE?<@DE@EEHHHHF?.=9EBEGGGHHHB7GBD?BCEEGGHHHHHHHHH?HHHHGFHBEDFC92BHHHFEHH @read_150_325/2 CCAATTCAAAGTGCTGGGATTAACGCCTATAATCCCAGCATTTTGGGAGGCCGAGGCAGGTAGATCACTTGAGGTCAGGAGTCTGAGACCAGCCTGGCCA + HHH@F8D=DGDFDHEGGGD?;5:96+03.5'AFGFHHHHCEFCGHFGGEEHHHHHHHCC2(?A79;A?AD @read_150_328/2 TAACCACTGCTTTCCCCACCAGGCTAAGAAACTCGGAGTTTGGCCTGCGAGGTAGCTTGGGTGTTATGAAGAACGGCATGCGAAAAAAAAAAAAAAAAAA + HHHHGHHHHHHHHHHHHHHHHHHHHGHHFGHHHBBHHHHHHHHHHHHHFEHFFDDHHHHFGECB>EGHHHHHFHGDFGGEFHHGFDEFB@B>D>D?ADDF @read_150_329/2 GACTCGACCCACTGCTCCTGTTCCAGGCATTTTCTAGACATTCAAATATGCTTTCACCCCCATTCATTTTTAGAACTTCATTGATGAAATTCCACTGAGG + HHHHHGHHG@A@@/BBIFHGEDHHHHDBHHF?DC?8CBHH?3:;A?;EGBFFGCEHHHGHHHHHH@CDHHHHHFFG;;@A4D@?<761))9 @read_150_330/2 GGGGTTTTCTAGATATAGAATTATGTCATCTGCAAACAAAGATAGTTTTACTTTCTCTCTTCCTATTTGGATGCTCTTTATTTCTTTCTCTGGAATGATT + HHHHHHHHHGHHHGGHHHHGGHHGHHHF>@8DEBFHHHHHHHEDGGDEIGCEGFGEHDB@<.505DDEHHHHHHFHHHHHHHEDCDFB;A<>11/;59?? @read_150_331/2 GGATGACTGGTACATTGCTAAAATGCAAGCCCCATTCTTTTTGTCATTAACGAAAAAGAGTTGGAATATAGATTGAGGCAATCACTGTATCCTATTTTCT + HHHHHHHEEGHHHHGE?BBEB@DBAHHAFEEHHHHHHHHHHHHHHFEGFHEFHHHHHHHEBHHHHHGDGHFGDDGGGFEFHEFHHHFEGD@A?FFDFBEH @read_150_332/2 ATGCTAGAAGTGTGATAAACTAAAAGAAAATTTGTATTTTTGGAAAAGATTTCTTGGGAAAGATTTCTGAATTTCATAAGTAACCTGGAAACTCTTTAGT + HFHHHHFHHHHHHHHHHHGFEHHGHHHABEBGFEHHHHHHHHHHHFFGGDFGDGFHHHHHE@EBFHF=@<9<:))*@B70+@CCFHHGGAD4;:99?EBC @read_150_333/2 TCTCCACTTGCAGATTCTGCAGAAGGAGTGTTTCAAACCTGAACTATCAGAGAAAGGTTCAACACTGTGAGTTGAATGCAAGCATCACGAAGAAGGTTAG + HHHGHHHHHHAFA?=FHHHHHHHHHDHDB)*-*->2?A?>FGDGHHHHDDHHBA..?DCCC?@FFFHFEHHFHHHFFHHHD@26>CDADD>,,:BFADAB @read_150_334/2 GGGACGACAGAATTTCACACTCATTTTATAGATGTGTTTCTCCAATAGCCAATTCCTAGGTCATAATACCGTGAAAGGTGCGCTTAGTGGCATATGCGTT + GEBEE:AGGHHHHHHHHHHHHHHFGFHHEEHHFFF;@EDCHFFEDCEHFDDDGEE@8/D=GFHHHGHHGHHHF@=9<@EADA>0&&;FHE@;E9G@BIFE @read_150_335/2 CAAGAATAGGTTATCAAAGCCAGAATTCACAAATGGGATCACATCAAGTTAAAAAGCTTTTGCACTGCGAAGGAAACGATCAACTAAGTGAAGAAATAAC + HHHHHHHHHBGGHGGHFEHHGGGDGDFFHHHGHHHHHEBEEEEFFHFEFHHHGGGFHEEEFBFHFEGC@9DHHHHGHHHHFFHHHHFHHHHHF<4@GD.A @read_150_336/2 TCTAATAGAATGGATTTCTGTATACCAGGATCAGAATGATTTAGATTTAGTAATGCTGCTTCTTGATTCTTTGAACAAATAACTTGTGCATTTAGTTCAA + HHFGGHH@GHHHHHHHHHHHGGABHHHGHHGHHEGDDD<<:5<>>B?A?DD6836=DFCB<;:44>A?<@16&:DHHFE:>><75, @read_150_338/2 ACATGGTGAAACCCCATCTCTACAAAAAAAAAAAAAAAAAAAAAAAATTAGCCAGGCATGGTGGTGAGCACCTGTGGTCCCAGCTACTCAGGAGGCTGAG + 44+(/A5<.76:>7<-=EHHHHHFHFHHFEECD@EHHHHGEHHHHHEE7EFHHHHHHHHHFBEHGGFHBGCGGEHHHFAFHHHHHEDEFFHHHHHHHGFF @read_150_339/2 TGCATCAGAAAACAGGAGGGACACTGAGGCTAGTGTGGAGGAAGGTAGCACAGGTTCAGTGTTCCCATCACCCATGGTGATGCTGTGGTGTATGACACAG + DHHHGGEDHHGGGEEHHHHHHHHFD?A@=3';DHHHFFHFHHHHHHHHHHB@@E=BB@DCGGEEHHHFEGID@BHHHDDG=@66:CBGFEBACFFFHHHH @read_150_340/2 TTTCACATTTTGTTTTCTTGGCTAAATGATTGTCTGACTATCTCAGATGAGTGGCTTATCTCAATAACCCAAGTGCGTGTGAAGAATGGAATACATCAGA + HHHHFEFD<48CDFB;924FGAFHHHHHGHHGIEEHHEB?DF7108DBHGHHHHHHHHGGHHHHHFDD=FGB76EGIG?A?C@HHHHFGCDD(,5:64%7 @read_150_341/2 CATTAATAATGTATGTTTACTGATAATAAATTCAACCTTTTACTGTCTAAGAATATATTACTTTTGACATTCATCAAGATCGGAAGAGCGTCGTGTAGGG + HHHEEEGEHHHHHHHGGBB@/B=DD?HHEEBBFHHHHHHHHHHHHEB@EHGHHHBGGHHHHDHHH@<B;@DB9-3C4><=?BDEFHFFHHHHHHGEA7@HHHHGFHHHFHFHHHHHHHEHFFDFHHHFBDEHFEHHHDCBCC @read_150_345/2 TTGGTACAGATTGACCTAAATGGAACTCTGAAAAATACTCACTATATAATCTAATTGCCAAGTCCAACCCCCATTATCAAATTAATGAGCAAAACGCACC + 95331).-8EHHGDGFHHHHHGGDEHHHHHHE@BEEDGCF;7,*:@H @read_150_346/2 TGATTTTCCTCAGGGAACACAGAGGAGAGATTGTGATCCCCAGGGGTTACCTGGTAGAGGGAGAATATGGAGGCCCAGAAATCAAGGCTGTGCCTCTAGT + HHHHHHHHHHHHHHHHHHGHHBGGHHHHFHHHHG@@@HHHFHHEBHHHFEHHHHHHHHHH9<*<.EGDE8=DDGFBC>=CFEG?GHHFE?CHHH@BDDBEEFGHHHEEFCFFG @read_150_349/2 GTGGAGGTTTCAGTGAGCTGAAATTGTGCCACTGCACTCCAGCCTGGTGACAGAGCGAGACTCTGGCTCAAAAAAAAAAAAAAAAAAAAAAAAGGTATTT + CDCDDHEEEDHHHHHHHHHHGHHHHGHHHHHHHHHFFFHHHHF,<>>ABF89==HGFFDBC570)*6;;/=DCCDBCF@AECBFGB?;FHGFFFCGGEHH @read_150_350/2 AAAAAAAGTCCGAATAAATCAGTGTTAAATAACAGCAAAAACATCCACAAACTCATATCAAAGAGACCATGTGTTTCCAAAGCTTATAAATACATCATTT + HHHHHHHHF<=EHHHHHHHHGBFHHHHHHHHHEEFHFHHHHHHHHHEHHFFHHFDGGEEGFDHHHHHBGGGFFFEEHBF?BFFFHGGGFBED,,DFFFFF @read_150_351/2 AAGCGAGGAGGACCCGAAGGTGAGCAGAACCTGCTGGAGGGAGACGGTGGGGACCAATGAGTTCTCTGCAGGACAAAGCAAAGCTGGAGGGGCCTTTGAG + HHHHHHHHHHHHHHHHHHAEEBCDHHGCHGHEEBFEE??CFHHHHEEHFE:@EEEF=+-CHHHFFDGHHHFGHHDDGEBDG?DDB:CEEEBDFBAC@DDD @read_150_352/2 CAAGGTGACTTTTTTTTTTTTTTGAGACAGTCTTGCTCTGTTTCACAGGTTGGAGTGCAATGGCACTATCTTGGCTCACTGCAACCTCTGAGTCCAGGGC + HHGHHHHHHHHHHHFFHHGHHHEDHHEEGHEDHHHHHEEEE2FFHHHHHHHHGGFD@8BGHF@DEEGFEE,-88EGFHHHHHHHHHHCBEEGHHEFFGHH @read_150_353/2 GGAACCTGAACTGAGTTTTGTACATCCTACTGCCTTATTCTGGGGACTGAATGAGCCTGTTGCTTTAGGATACATCTCTGAGAGTCCAAATTTAGATACT + HEEGGEGHHHHHHH>:>>@HGDB@;HDFFHHEDAHEE986D;FF@EBGFFFGGFHHHHHC@5=F>BEHHGHHHG@HEG5DGEHHHHH?6;@@BCFGHDAA @read_150_354/2 TAGTAGAGACAGGGTTTCACAATGTCGGCCAGGCTGGTCTCAAACTCCAGACCTCAAGTGATCTGCATGCCTCGGCCTCCCAAAGTGTTGGGATTACAGA + CBHEHHFDBBDHHHG?BGGHHHHHHHHHHHHHHH@BGFAAHHHH?))07;>828@HHHHEGDDDEFHHHFAB;>GFGFD=CGFFDFFG77BEEEFFEFGF @read_150_355/2 AGTTTCTTTCCAGCAACAATGACATGAGTTCAAGCGATTCATCAACATTACTGCATGTAACTGTAGTTCATACATTCTCGTTGCTGTGTAATATTGAAGA + HGGEHHHHHHEEHHHHHHEHFDDCDEGHHHGEEFGEFHHEHHHHHDCF?>GFHHHFB@DEHEHFEFHHHEFFGEHHHGGFHDFGGEHBEIBDB)):5BDD @read_150_356/2 TAAAATTATACTTTAAGTTCTGGGATACATGTGCAGAACATGCAGTTTTGTTATATGGGCATATGCGTGCCATGGTGGTTTGGTGCACCCATCAACCTGT + HHFHHHHHHHHHHHHHHHHHHHHHHHHHBEEEG?:2')BBFHHHHHHE=:FGIFGGCDCEDFGHHHHHHGGFHECGEFFFEA/D8AEDC47BEDFH6 @read_150_357/2 TTGATTTTCTGATTTCAAAATATATAACAAAGCTGTAGTAACTAAAACAGTGTGGTACTGGCCTAAAGACAGACATAGAGATCAATGGAACAGAATAGAG + HHHHHHHHHHE8=BGDDEEFEE=EHHFHEHHHHEGHHHHFHHHHFFFD49FGDBHHGIED:BFFEFHHFGE=D=DA96.>CDDEBFGHHDA<<:6))1%) @read_150_358/2 AAATTGCACAAATAGAGTGTTTCAAATCTGCTCTGTCTAAGGGAACGTTCAACTCTGTGATCGGGAGTAATTTGGAGGCAGTAGTTCGTCGAAACTCGGA + EGFFBG@<71DFFFHHEDHHHHHHHHHEGGFFHHHHHHFHHHHHHHHHHH@5.>FHGEEHFEFFHHHHE=.93<>4-37I@?HHFBDCA=FFGG:BC?F7@9:@205C=GDB<.1/EEDGFEEGEDDBHHHFBFHHHF?AADACCBFD@<<6CF @read_150_360/2 AGCCAAGACACAGAAACAACTACAGTGCTCATCAATGGATGAATACATTTTCAAAATGTGGTACGCATACACTATGAAATAGATCGGAAGAGCGTCGTGT + HHHHHHHHHHHHGGHHHHHHHHGHHFEGHHHHGHHHHCFFB?@D;1,59788.76FFHHHFHHHHGGGHHHHHEHHHFHHHHGGEFHGGHHHHHHHHFCC @read_150_361/2 GCGTTAGCCACCGTGCCCAGCCCTTTTTTTTTTTTTTTTTTTTTTTTTTTTTAATTGAGACGGAGTCTCACTGTCGACCAGGCTGGATCGGGAGTAATTT + HHFHHHHHHFGEEEFGEEFHHEGE@C@@>>@66EHHHHHHHFHFEGGEEFHHHHHHHHHHFGHHGGGGDHHG?F?DCGEEFFHHHHHHGE.;5>=E @read_150_362/2 GAATTTCTCTCTCCTTCTATCACTGTATCTGAGGAATGGGCAACAGATGGATCTAGTAAGATGTACATAATAATTAGTTTCCTCTAAATCAGGACACATT + HHD@;C;ABBFEBGFGFGGHHHHFHCEHHFEEE<>99:;.D987DD8DF?FEGB@DADFHHHHHHHFEG=?:3'=>BGGDEA9:>FABHCA<.<59:-=CCDHHH?HHHHH @read_150_364/2 CACCTTGGTCTCCAGCTTCTAGTTAACCTTTACTTTCTAATTTGCAACTTCTTTTTTATGGCTCCCCACTTATGGGGCTACCAGCCTATATGTGTAAATA + HHHHHHHHHHHHHEHHHHHHHHHHHHHHGGHHHHEDHHHHFC>B?DCFE>..:46@C@GDA:*36>DDGHFHGGB@AEEGHHE8>539,8&.3DDD=.@: @read_150_365/2 CTTCCCTCCAGGGGAATCAATTATCCGGCTTCTAAATATTATATATAAGACACAAGTGTTTTTATGCTATTTTTAAAAATTTAATATTTCATATGATTTC + BE/BBHHHHHHHHHHHHHFFHHHHHHHHFHH>=GHHHHEHHHHHHHFHHHHDAB>EGGFGDCCEGGGFEHHFHHDDFFHHHHHGGB4EIBGDBGHHEDFF @read_150_366/2 TTATTTCGACATTTAATATCAAAAGTATTTTGGTTTTTATTTAGAAGTTTGGTGACATTTTTGTGGCCAGTAGAAACCTAACTCTTGTTTACATCAATTA + HHHHHHG@FHHHHFHE26:8DFHHHHGHHHHHHFCC@DEEBIGCDEFDD@EEEGFDDGHHHHHGFEGHHHEEFF=FCAC=EHBHHHHFEGGDBA*@EEEE @read_150_367/2 ACTCCTTCGCCAGAATGCTTCCTTCCATGCGCAGAGGGGTCTTCCGTCTGTAACCCCTGACCTCTCTCTGCGCCTATGCCCTCTTCTCTTCCCCAGGAAG + BCC?:?..9;CDBFFHHHHHCFHHGBDDDGHHHHHHHHHEGFHHHFDCCHHHHHHHHHHHHHHHEHDHHHHHHHHG?BHHFBFFHEEEFEEEEAFFFEFF @read_150_368/2 GCCTGATAGGGCCCACCCTCTACTCACTCTCTCCCAAGAAAGAGTTTCCATTTCAGCTCCTGCCCCTCCCTGCCCAGGAGGCAGGATCATCCGTCCTGGA + GGFHHHBECC>GHHHHHHHHEDDDDECA4>=FHHEGECF?CFHHHHHEBFDC@EC@@@-.7-6.GHFFHHEFFHEEHHHFHHHFE@+>C/86CFB1'7?C @read_150_369/2 TATATAAAAATAGTTTTAAACATGTAATAACTCGAGGCATATTGTATTCTTGATTTTCCTTTGGGCAAACTTTGAGAGCATAAACTTCATCCAACCAAAG + GGDBGEFEEGHHFHHHHHFHGGHEHHEEFC-/..++>EB1>>EHDFHDIE:6@B4<8=CDDGEFFHHECEFEFHHHGG9ADHHHHHHHHHHFGEHEHHEE@>:47;,CC?AHHBDGEE?=?DD>ED @read_150_372/2 GGTAGCAAGTCGTGGCATTGACCCGAAGGGCTCGATGTTTAGGGAGGTCAGAAGTTGAGCGGGTTCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA + 949BEEFGGHFFC/)GFGGHHF:3-<<6@CBGHHHHHHHHCGC57A?:EFGIGEHHHHHHGGHHHHHGGF5<@CDDGBFHDA<8EDFGHHHFEE<<@5/> @read_150_373/2 ATTCGGAGGCTGAGGTGGAAGGAACACTTGAACCCAGGAGGTAAGGCTGCAGTGAGCCAAGATCATACCATTACACTCCAGCCTGGGTGACAGAGTAAAA + HEFHHHHHHHHHHHEBDA@.EFHGGGG?@='(3538DBFGEGHHFHHHFHHHHHFEEHHHHED<>C((6.+(-=EIGGGGGDAEAEDFHHE=DBEF=DA; @read_150_374/2 CTCTGGGTTGGCCACTCCTGAATTCCCTAGTTTGGAAAACATTTTCAGGTGGGAGTCTGCCAGACAGGGCCAATCCATTCTAAGGCTATACTTAAGTTAT + HHHHHHHHHHHHHFHHHHHG=B;HHHHHHHDDA?73-5>CDEBDD;-,54CDHFGHHGBC--',;GHHHHHHEGEHHHGD:;AEEHFHHHHHFDCCCCFF @read_150_375/2 AAGAACTCAAATGAGGTACTAAGGAAATCTATAAAAGGAATAAGGAATTTCTACTCTCTAAAAACCTTAGAGATGATGAGTGTGAATTTCTTCATTTAAT + HDDDHHHHHHHHHHHHGHHGHHHHGHGD=GFFHEEHDHHHFDC=FHHHHFHHHHHHHHGFHGGGGFHHHHFFEGEFFFGF@DCFEHFDEHE<6AE2)6.7 @read_150_376/2 AGGTTGTCTGTTTACTCTGTACCGTGAAAGGTGCGCTTAGTGGCATATGCGTTAAGAGCTAGGTAACGGTCTGGAGGAAAAAAAAAAAAAAAAAAAAAAA + FHGFHHHHDHHHHHHHHHHHHHEGHEFEHHHHHHHDEGGHEGEFHHFHHHHHGFG5AACA@CEBHHHHHHHHEGE@GHD>)=DB=HEE/DCFHBHHHHEE @read_150_377/2 TATACTTTTTAATATATGTGTACAAGTCTTTTGTCAGATATATATACTGTGTGTCTTTTAATTAGCAGAATTTTAAAATTTTGCTAAAATTTCTGAAAAC + HHHHHHHFHHHGGD@BB8G@FHF@E88BCDGFBEBEHHG<@=;AD<4;EDGB@C:;BBDE@B?A;1692-?E@B;CFFEHHHFAHHHHHHEHHHFDHGFF @read_150_378/2 TGTAATTCATATATCACATATATGAAAGTCTGATGACAATTATACTCATGTACTTGTATACTATGTTTCAGCTCTGGTCTGGCTCTGCTTTTTTAGACTT + B885D@D7>GGEHHHHHHHHEHHHGHHHHHHHHHHHD?ABFFCCCDEGHHHHGEFEHHHFGGHHHHAA=EC;?108AGDBHHHEHHHFHGFHHHGC>;:? @read_150_379/2 ACCACCACGCGCGCTACTTTTTGTGTTTTTAGTGTTGCATTGACCCGAAGGGCTCGATGTTTAGGGAGGTCAGAAGTTGAGCGGGTTCAAAAAAAAAAAA + HHHHHHHGGGHHHHFHHHHHFCEEFB?BHHHHHHHHHHHHHHHHB>:>;2FE??B?63.<@:@BA>@4.(816.5(29DDGF@:D.737?7?GIFHAEFE @read_150_380/2 GTGCAGTAATGGTGTGAAGATGGGTGTGATCCAGTCTGCTTGGGGTTGTGGTGGATGTCTAAGAAACTCGGAGTTTGGCCTGCGAGGTAGCTTGGGTGTT + HEGHHFG=BA=EI?DFGHHHHFGGGGGGHGE5>8FFGAHFHHHHFHFFFGHFHFFB/GBEFDHHHHHHHHDFHHHHHHHHBHHFGFCDEHHHHHC@>A?BEDFGHHHGFD@@BCHHHHHHHF67BFHHFCDFFFHH>;661A9:)-.>5,).@5 @read_150_382/2 GGTCAGGAGTTCAAGACCAGCCTGGCAAACATGGCCAAACCCCATCTCTACGAAAAATAAAAATAAAAATAACAAAATACAACAATTAGCCGTGGCTAGT + HHHHHCA/EG@EB==0:3;7ECFC;A@@>.EF@BDEG=FHHHHHHHGG7&@...3C/6BA@?6BHHFFHGFGHHGHHFBF @read_150_384/2 AGGGAGGTTATTGGGCAGTGTTGTTGGACCATCTTCGTTGGGTGAGTGAGTCTGGCTATTCCAGGAAGGGAACATGGTCTGGCTGGGACTCTCTTTGGCT + HHHHHHHHHHHHHHHHHHHHHHHFGFGFDFHHHHHHHHHHFGEGBBEBEFHHHHHHFHHHHHEHFHHHHHHHDDEHHHHGCFGFFFDEHEEGGGEG@@DF @read_150_385/2 TTGCTCGTCTATCCCCACTTCCATATGTGAAACTTGGACTTTCTTTGAAGATCTGGGTAAAATGCCACTTCTGAAAAACCTCTTGACTCCCCCAGGTACG + HHHFEHHGEAGHHHHHHHHHHHHHHGHHHHHHHHHFHHFEBFEEFHHFFHHHHHFHHHHHHHFFHHHHEFFFGHHHHEHFGFHHE?DEBDAG==@C>)%% @read_150_386/2 CCTAAGGAAACAACATGAGGTTTCCTCAGTTAAGAATGGCCGTCCAATATTCACATGCCAACAACTGAGTGTCACAACATCCAATAAGGAAATATACAAA + HEGHFEEHHHHFD@EEBHFEB??>9>3-@CGHHHHHHHHHHHEFHHFFEGFFDDDGHHHEHHGFHGGHHHHHE/GHHHFFBHFEDEGECDB*-(97IFBH @read_150_387/2 AAAAATATTAGACATGTAACATAATTTTTTGCCTTCTTTTACTTCTTTTGTAGCTGGGTGTGGTGGTGTGCACCTGTAATCCCAGGTACTCGGGAGGCTG + HHHHFGDEGGGHHHHHHHHHHHHHBEHHHHFHHEHHG.23@DBEHHC>>>BA?CHHHHHHHHHHHFHFHHHHHFHHDFGDGHHHHD+:9BDDCHEEEFCD @read_150_388/2 TCCAGGTTTCAAAGTATACAGCCCATCACTTGGTTAACTTTGAGCCCTTCTTAACCACCCAGGAGATTATTTGGGCCCTTCCTCTAAGAAACTCGGAGTT + EHHHHHEBBBDIGHGGGC55EGGEGD.@/EHHHG=G4DCDEBHFG>@@9-D@C@<>,/;@B@GGHHEEGDGEHHEGEHHE@?:ABGGDDD26@; @read_150_389/2 GCACCCCACTCCCCAACAGGCCCTGGTGTGTGATGTTCCACTCCCTTTGTCCATGTGTTCTCATTGTTCAACTCCCACTTATGAGTGAGAACATCTGGTG + HHHHGGGGGDHHHHHHHHDGGEEFC=CGHGHHHHFHHHHHHHHHHHFHHHHHHHHHHHHHHHHHEFGBEHHGG=ECGHHHFHHHHFFHEBGG8++D@4@EHHHB;09FHHHHHHDFF=CBE;@GB=GGDD=8>;6D5DHC@HGGHHBDHHHHHFHHHFHHHHFBBACB8=F @read_150_394/2 GGAAATTACTCATACTATACAAATTCTTTTGTCTCAGAAGTTAATTTTGAAAATATGGCTTTATTTAGAGTTGTCAATTCAGATAAGCATCTCTGTGTGG + HEDFFFHHHHDDGGHFGEEHHHHHHHHGHHHHFHHFDFFHHHFHHHHHHGEF;(;BGHHHFBHHHDDE=GHHHHHHFHHHGGGBHHHHFCFHHBHHHBFH @read_150_395/2 GTCTTAAAGTTTAGAAATTCTTTCTTCTGTTTAAACCTGTCTGTTTTTGGTGTTCTTGCTTTTATTTTTTATTTCAATCATTGAATTATTCAACTCCACA + HHHHHHHHHHHHHHHHHHFEEEEHHDDEDEFGHHHHHHHGHEBHEFHHHHDEGFFEHHHHHHGHHHHHHFBDEIEEEC=:DGFFHHHHDFEFDDHHHEGF @read_150_396/2 GCAACGCCCCACTCAACCGCTCCTAACTCACAGATGACCTCAGAGCCTCGGCTTCTGGCTCTCCAAAAACAAAACTTCACCTAAACACTTTACCACACCC + HHHHFHHHHHHGG;FHFHHHHHHHHHHGDDADBGFHHHHHHHHHHHGEFFGGGFGHHHHHHHHHGFGHHGHFHHHFB>BHDECEFHHCDBFHFFF5?;2< @read_150_397/2 GAGAACTGCCAGAGACTGGGTAATTTATAAAGAAAGGAGGTTTAACTGACTCACGGTTCTGCATGGCTGGGGAGGCCTCAGGAAACTTACAGATCGGAAG + HHHHHHHHHHHHHHHHHHHHFHHHHDHHHHHHGHHE=FFEGFHHEFHHHHHHHHHCCCDDEF<<4>.E@?-0BFHHFHD=DFHHFGFB<;?%3BDFFHHHGFHHFHFEFEC:6GHB.;BF6; @read_150_400/2 GATGTTGGTGTGGACTTCAAGTTTCAGTTCCACCACTTATTTCCACAATGGTTTTAGACAAGGCTTTCTAAGTCGTTGCATTGACCCGAAGGGCTCGATG + HHFBFGEEFHHHGHHHEEGE???:?G@@@DFEHHFHHHHHHHHHHCEBGHEDGGFFEFEE25<+;>>>:.>;+98:5*56E68EFDCCDEHGH?AD=EBB @read_150_401/2 TAATATAGTAAGTTGGTATAGGTAAAGTGGGATGCTGCTGTAAAGATACCCAAAAATGTGGAAGCAGCTTTAGAGCTGGGTAACAAGCAGATGTTGGAAC + HHHGHHHHFGGHGHHHHEHHHHHHHHHHHEFHHFHHHHHHHFG=>CD822>>>:=;DD@CEEGGGHHHHHHHEHFGHHHHE;CDHHHEE>CCE@AGHHFH @read_150_402/2 TTTTTTTAAATTTGTTTTTTAGGACAGGGTCTCATTGTGTTTCCCAGGCTGGTTTAAAACTCCTGGCCTCAGGCGATCCTCCCACCTTATCCGCCTGGAC + HHHHHHHHHHHHHHFHHHHHHHHFHHFCHHHB9@@CAADEFHHHHHFFHHHHHEEHEFGGHFD:@9:;?C>GHFHE@@EDE=30(8261::>.@AAA5+, @read_150_403/2 CCTACAGACATAGACTTCTTGCATTTAGCAGTATCACTCACCTCTTACTCCATCATTTCTTCAATAACTCCATCAACACTGAACCTTCTAACTCTAACAT + HHHHHGGGGEE801*+8GHHHDEGGEGHGGGGFFB5::<.EBEFFHE@=BFFG@CBBCDEB/,9:@EBEFEHHHGHHHE<@DEGDD@8AAEEE?B?FEHH @read_150_404/2 GAATACTATACATCAGTGAAAATTAGTGCCTATAGGTACACATATCATGATGGAGGAATCTCATAAGGATGAGGCAGTAGAGTAAGCAGCGATACATGCC + HHFCFHHHHGDDE8CDFFHFBGGGHCCD@DBGFGHHHHHHHFFHHFFFFHHHHHHHHHGEHHHGHFFFFDGEHHHHHHHHHHHHHFCFF?C?BHHHHFBB @read_150_405/2 ATTCCACAGAAGCCTTTTGTTAGAATCTTCAAAGGATGAGAACCAGGATGAAGAAGAGTTTTCAGTAGGGAAGTATTTCTCAACTGTAATTGTACATAAA + HHHEEBCGHHHHHHHFB;@@DBA;BCFFHHHFHHHH@?FFHHHHEHFHC:;<:= @read_150_406/2 GAGTTTTGCTCGTTACCCAGGCTGGAGTACAATGGTGCGATCTCGGCTCACTGTAACCTCCACCTCCCGTGTTCAAGTGATTCTCCTGCCTCAACCTCCT + HDFFFHHHHHHHBEE@DABFHHHHHHHHHHFGDB@DCFHHFEHHB98'..,3.,12==@BGGEFHFFF=BAFFHHF8CCGB@C<('12(8@>@GFEF?9* @read_150_407/2 GAAAACTCCAGACAGGTCTGCCTTCTTTACAAAGTAGAGGGGCGATGCTGCCTGCCATTTCATCATGGGGCCCCTCAGATTAAGAAACTCGGAGTTTGGC + HHHHHHFHHHHHHHHHHGHH=EEEEEHFHHGHGGGHFHECFEHHGGHHHFHHHHGB;;<9.A7@BHHFA=EGFFFGHHHGGGFHHHHFFHHHHHCEHEFGGCBHHHFBGHFHFF @read_150_410/2 GTCTCTTAGCCTCTCTAAGCCTGCTTCTTCACCTCCAAAGTGGGAGAATAATAGTCCCATGTGGTTGTGGAGACAATTAAATATTTGATGTACTTAATAT + FGGHHHHHHHHHHFB((08=GHHHFHGGEDCEHHHEHHHHHHHHHHDDEEGGGDDHHHHHFFFBFC=EBHHHHGHHHEGDGG=CAFFGHHDD.0>8@@@. @read_150_411/2 TATTGTTTACTGAGTTAAACACAGAGATCTTCATGCCAAAATACATCTATGAACTAAGCCATCATTAAAGAGTTCTTATTGATGACTCTTGGCCAGAGAA + HF?6898=CEGGGHHHFBAHHHHHFGEF@HHHD.AHHHDDGHCFHHGFGGFHHHHHGGEE?@EFEHHHHHFEBEBBEFGHHHHHHEEED?(;7):BEFBE @read_150_412/2 TCTGGGGCTGTTATGGGTTCAGAATAGGTGAGTATGTGCTGATTGGTTTGTGAATATGCAAAAAAGGCTAAAACAAAGACATCACTCAATAGTGAACACA + HHHHHHHHHHHHHHHFHHABHHHHHHHDEFEGFEEHHEBFHHHHDEDCGHGGFFD66@=GEFHFGHHHHHFHGHGHGHHHEGDBD@B>==EAAHEGBDG? @read_150_413/2 AAATTATAAAATTCAGTGGTTTTCATTGTATTCACAGAGTTGTGCAGCCATCACCACAGTCAATTTTAAACCATTTTTATCACTCCAAAAAGAAAGCTTA + HB=EGHHGGHHHHHHHHHHHHEFHHHHHHGHE@HFEFFFFDGI?HHHECBFEGGE=BFEGA/B;55&<4))2B=6;.29@EEEEHHHHHHHFHHHED>8: @read_150_414/2 CTTTCTCACAAAGGGAACAATTTCAAAAATAAGAAGTTTTTTTTGGGCTTCAGGTAGCACATTAGGGAGAAACATCTGCATGGTTCAACAACATCTCCCA + HHHHHGGD@?BCBDDHHE8<@@FEFHEFDBHHHHHHHGG?GCEDFFGEHHHHGHGHHHHHHDEE/DGC>@EDEDDFHHBFGFHHHHHG896>4-?6DGHHHHHHHHHHHHHHFBEHHHHHHHHHHHFEEDHHHFHHD>>DDBDGHHHHHHHHHEDFB?@B8GGGEDEE<,1'9'), @read_150_416/2 TGAAAAGTGTTAGCTTATTTCCACTAATTAAAGAGCTTCAGAAATTGCTACTAGAATTGCATTAAACTTTATTTGCCTTAAACATTACACTTACAACTTA + EGGDDHHHHHHHEEABBCCHHHEEEHHHHHFFFFFHFHHHFEEFFGHHHEFE@DHGGHHHGHEDGHGH>7@HHGGHHHFHFEFHHHFFFFFF753.;HHH @read_150_417/2 GAAACCCTGTCTCTACTAAAATAAGAAACTCGGAGTTTGGACTGCGAGGTAGCTTGGGTGTTATGAAGAACGGCATGCGAAAAAAAAAAAAAAAAAAAAA + FHHHGF@FFHHHHEHHHHHHHHHHHHFGABB4:5E<::5.5@CH<2.DFHH @read_150_419/2 CAGGAGCAAAACTCCGTCTCAAAAAAAAAAAAAAAAGAGTGATAGATGAACATTTGGGGATGTATCCTAAAAGCCAACAGCTTGGATATCCAATCCTGGA + GHGDEDGFGHHFF@EC@6;>:CHHHHHHFFFHHHFFBDDDHHHFEC:5'&46:<<=EGCCB,=<:FGFEDHGFHHHHHEF@=HHHBGFCFFBEDD@BB@E @read_150_420/2 TCCCCATGTCTGTATGGATGCCTCTGCCTGGCACCTTGTAAGTAAGCACTCATTACACATTTGTAGATTGATTGGGCCAAAAAATGAGCAAGTGGATGGA + HHHHHGCDBDFIA89,75'6936BDHG=FFC>CFFHGEFFFEDHHFFEGBDGGFEEHGHHGG?HHHHHBGHHHHHHHHEHHBFFHHHFGGFHHHHHFEEF @read_150_421/2 ATCCACCCACTCAAAGCATCCCTTTAAATCCAGCAAGGCAGGGCAAGAGGCTGAAATTCAGCCTCTTGGAGGGATGATGCAAACTCTACGTTCCTTCCAA + HHHB@DDBGHHFHHHHHHHHHHGGHGGGEEEDDDFHFGBAAEHHGHHHFF@DFFGHFHHHHHGBEDGHHHHB2:FHHHHGFFHFG@:3@DEHHHHHHFHHHHFHH:C:>6BEBF=5<:5<41079BEHHHHGGHHHGHHEHHHHHHHHGDFHHHHFHHFC7E;;735 @read_150_426/2 TCAGACTCCATCTCAAAAAAAAAAAAAAAAACAAAAAAAAAACCTAGCAGAAGTTGATAAATTCGTGGACAATGTAGATCGGGAGTAATTTGGAGGCAGT + //C@=EHHHHFFFDFHHHHHHHHFEGGGB<<@@HHGHHHFFHG:?FGGDGGEFFHHFDHHHHECEB>A7F @read_150_428/2 TTCTGTGCTATTTAAAATTCTTTGGTTTCTTTTTGATTAAAATATTCTCATTTTCTTGTATTTTAAGGCATTATATCTGTCGCATTATTTCCTCTCCTGT + EEDGGHHHGHHGDBB?:9>C*+94=GFHHGBFHHGIE@CECDEHHHHHHGHHHGFFE8671*665@FFGFEEEEEC/3.>8?'17:<<8@FDBD?HHHHD @read_150_429/2 GCTCCTCCTCTTCTCTGGAACGAGATTTTTACCTTTCTCAGCTTCCTCGTCTCTCCCATGTCTACCATGGCAGTCTGGTTACTTCTGTGTTACGGAGTCT + GGHHHHHHGEGGFHFGFHHHHHHHHHGFGGHDCBEHHHHHHHHHHB=EHFEEHGB?BBFHHHE@@B=DAEEGHHH@@4:<=A8>DEE?BEHHHHHFFH=F @read_150_430/2 AACAGGGACCTCCCCCCATCCCTAGACCCCAGTACCCAGCAGACAACTGTGGGATTCTTCACATGATGATGAGGACATGCTCGGGCTTCTTGAGAGTTAG + FFFHHHHHFAACFHFHHHHFHEEBIHHHHHHDDDFHHHHHHFHHHHFEHHHGGGFD.@CD>DDGHHHHHH@84&)9>?EEHFGFFECDDB@GGB5,.A<5 @read_150_431/2 TCCCAATTTGAGAGGCGCCATTTTTTTGGAGGGTAGTGAATTTTGATTTCTGTCTCCTTTGCATCCTTCCCAATGAAAACTGCTTTCAGCCACTCTCTGC + HHHFG:?DDFHHHHHHHHHHHHHHF@>>:>EEGDHHHHHHHFFFB@@?EFHHHHHHHH@DF=C;DHFDDFHHHHHHABGHGFDBEEHHHHFCCFEHGDFC @read_150_432/2 ACCTGTAATCCCAGCACTTTGGGAAGCCAAGGCGGGCGGATCACCTGAGGTTGGGAGTTCAAGGCCAGCCCGACCAACACGGAGAAACCCCACCTTCAGC + HHHHHFHHHHHHEGGGHHHGDGGEFHHHHHHHHHHB5<6?CEHHHHHBHHHGHHHHEBDFHHHHD=;GHHHHHHHHHHG>FHHEFFGGGCDFFGHEGHHH @read_150_433/2 GAGGTGGGTGTGCTATAAAGTATCCCATGCTAGTTTTGGGGCTTTGACTCCGCAGAATAGTTTAGTCTTAAACTCTAGCTACCAAAATATGGATTAGCAT + D@A:94>->8>@DEEHHGGGBHHHFHHHB;+?HHGEHGCB5@A;CGDCFFDCGGIGBF?4-6=AGFHB3:B7,2;FE@@?CB@FB@BE@EEFCED2:1<3 @read_150_434/2 AGCCTTGAGAACAAAACTCTTTATGTTGACCAATATTTTTAAAAAGATGGAAAGAACTCTCTCTGGAGCTAATTTCAAGGAGGACAAAAAAGAATTTTGT + HHHHHHHHHHHHFGGHGGHHHHHHHHHHEFGHHHHHHHHEFHHFHGBAABGGFD/>GEEFEHDBFHHHEHGGHBBEEHHEHHG@EEDBHFHHFBHB;DDF @read_150_435/2 TCTACTAAAAATACAAAAGCTAGCCAGGTGTGGTGGTGTGTGCCTATTATCCCACCTACTCGGGAGTCTGAGGCAGAAAAATAGCTTGAACCTGGGAGGT + HHHHHHHHHHGGGHHHHHAFHHEGDBBGD.B59.BBB?=CHHHFEF?>CFFEFHGFEEEGHHHFFF=:ACE8BFHHHFDD>0/DB72::FHHHHDDDCF= @read_150_436/2 TGTATTAAGTTCTGTCTATGTACTAGACATTGGAGATAAAAAATATTAATGAAACAGAGTATTTGCCCTCAGAAGGCTCACCAACAAGTGACAAAACAGT + D@@B=DFHHHHHHHHHHGFHHHHEGGEGD@6657*FHFFFGFFBGHHHHFGFHHHHHHDGBFGBHHHHDGFG;==FHHGFEEFDC@;*/2AHHEGDDFHH @read_150_437/2 TTGTGTTTGTTGAAATGAGTAGCTAAATTCAACTATATAAGGAAACATATATCAGTCTCATGAATTTCAGTTTTGATTCATAAACTGTCTGCTAATGTTG + HHHHHHHHHHHHGFFHHE>@BFFHHHHE;=FHHHHHHHHHHHCDFFEGD.>>>=EGHHHHHHHHHHHHHHHHHHGGGHHHHHB?::;<@:*EE6C:AHHC:;?@6..>DGE @read_150_440/2 GCGTGTGCCACCATGCCCAGCTAATTTTGTATTTTTAGTAGAGATGGGATTTCTCCATGTTAGTCAGGCTGGTCTTGAACTCATGACCTCAGGTGATCTG + HHHHEHDBDDFEHHHHHHHHHHHCCHEDHHHHFHHHHHEGHHHHHFEHHHHHHHHHHHHHF?FHHHHHHHHHHFHHHGFB03+,.<?:@C/-23:EFFC>5DAEGF @read_150_442/2 CTCACAGTTGAGTAAACTAAAGTATGGAGAATGTTAAGGAACTTGGCCCAGAACTACAAAGGCAGTAAATGGCCCAGATGCCACAAAATGCTGTGCTTTA + 66A5@;@CBAFCEBFHHFFHHHHHHFHGGHFHHHG39B5>DB/0?EEEFGHHHHFDDCGHHHGGGHHHHHHHD::ABDDE=='@HHC6A3'%%).:86,1 @read_150_443/2 CATCAAATCAGGAGCGTTTTCTACTTGTCAGACACACGTACCAAAAAAGGTAAGTCATCTTGCCCTTTCCTTGGGGCCACCAGCATCTAATTGTGTTCAT + HHHHFFGGHHHHHHHHHHHHHHHHEEFFGHHHHHFFFHBEHHHHHDEEEHHHHEEEFHGGEBDBAEEFHHGHFDFHGHHHFFFDFHE--6EHH@DFFFEE @read_150_444/2 CATTCATTTGATCTTCCAGCACTGATACCCTTTCTTCCAGTTGATTGCATTGGCTCCTGAGGCTTTTGCATTCTTCACGTAGTTCTCGAGCCTTGGCTTT + HHHFCFEBHHHFFEABD8.:3BGEHHHHFHHHEEHHFFFGGHHHHHHHHHHHHHHHHHHHHHHHHHHHGHEGGG@HHHEHHD@HE@+@A922@0-5>?;9 @read_150_445/2 GATATTACAGACAGCCCCAGAATCACTGTGTGAGTCAGAAGATTTGGGCCTCTGAGTTTCACTTTCCTCATCCTAGAAACTGTGGTAAGAATTTATCCCC + HHHHHHHHHHHHHHHHHHGHHHEEDEHHHFHHD5139B?HG=DGHHHHHHHGDDBFHHHHHHHHHG0@?>GHHHHHHFFFGD?DDHHHHDDDEEE@DFFF @read_150_446/2 GTAGCTGGGACTACAGGTGCATGCTACTGTGCCCAGTTCAATTTCTTTTTCTTTCGTTTGCTATAGAAACGAGGTCTCACTATGTTGCCAAGGCTGATCT + BEED=B//34)2=5-+EFEBFHHHHFFHBHHGHHHHHHHHHHHFGHHHHHHHFFFHHGG=D:++471:@EGEEDGC?AC>+178:>?;6(;DDCCGGFHHHHF@EFHHHHFFFFFEE><,@1*,2(%))/=>CF @read_150_448/2 TACTAGGTCTGGAGAGTATATATTTTAAAAATCCTACCCAGGTTATTTTGTCAATCATTTCTGAGAGTTAGAGAGAGGCCATAATGCTGGGGCTTAGAGG + HHHHHHHHHHHHHHHHHHHGGHHHHHHHHHFHHHHFC3.59>B@?D<0@DHHHHHGGHHE83)7?DDGGGFHHHEEBAFBECA@BHH?EHHH??<>6=ED @read_150_449/2 CGGGCATCCTTGTACATCTTTGTAAGAAACTCGAAGTTTGGCCTGCGAGGTAGCTTGGGTGTTATGAAGAACGGCAGGCTAAAAAAAAAAAAAAAAAAAA + HHHHEFHHHHHHHHGGG=@@CEGEFEEGG8EFG@<>:BEHDFBEEFAEGGEEDDDIFHHHHFEGHHHHHHHHFGC:(%(+%&2(;DG>;;@ADFCG@BE= @read_150_450/2 TTTTGATAACTAAGGCTAAAGAAGTTCCTTCAATTCATTTTTTTTTTTTTGCTAAGTGCTTATTTTTTAACATTATAGTATTTGATACCTACAAAATAAT + HHHGHGBHHF@6?>.607>@DD;8.DGBFFHHHHHHE651;>.-@@.>CDF=;?=EHHHHHHHHHE;=7>GEFHDHGGEEHHHE@HFHHEHHFHHDEBEG @read_150_451/2 AGTTCTTTAAAGTTGTAAGAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGACGTATCATTAAAAAAAAAAAAAAAAAAAAAAA + HHHHHHHFHHHHHHHHHHHHHFD@;EHHHFHHHHHEE=>>EHHFHHEGHHHHGEDHHHHHGHC=20&))2(/45.;@B>@FGBHFGHFDBCEEF@>.8DEHHHHHHHHEEEFH@CCGED@GDB;@B;CG@.5GGGHHHHHHHHHHHHHEBDB@DBDA=ADHGGHHGHHDEEEBFDDBHFEDDIDDB0:74:=A:2'2--,>7CFHGFFH @read_150_455/2 TTTAGCATTTCTTAAATACAAGATCATGTCATCTGTGAACAATAATAATTTTTCTTCTTTCTTTTCAGTTTTGGTTGCCCTCATTTCTTTCTCTTGCCTA + HHHHHGHHHHHHHH@EE@?DEB=B<11468:DBFHHFHHGHHGHHHHDF@95-5-))(*@?@C@>64>;E<95<:@>;?>EDGFEFDEC2==DGD@C>?E @read_150_456/2 ACAAATTTCCAATACAAAATTAGAAATGTTCCAAAATTGAGTCTACAAAGAAAGACCATTTCTTAGACTGGAAAATATAGGAGGCAATACCACGTTAAAG + HHFHHHHHHHHEEGHHHGHHHHHHHHHHHHBEEHHHHHHHHHHHABG6?DFFHHHHEEDBEDFHHHHFGGHHHHHHHHHHFFFHHHHA@%,<'@A3772F @read_150_457/2 TTTCCTTTTGTTGAAGACATGGGGGATTAATTTGAGACTTTAGGTTCCCTTTATCAGAGCCCACACTGGAAGAAATGGAGACAGCCACCGTTACAGCCAG + HHHFHHHHHHHHHHHHHGHHHHHHHHHHHGHFFHHHHFFEEBAHFFD;CDGGGHB@;::;?@@;<;B?<4(-')69DDDC5:.F;FFBGF @read_150_459/2 AAGCAGTGGCTTTTACAGCTCTCATGCAAGTTAGCACTCCTCTTGTTACAAAGTCTGTTGGCTATAGCACCCTACAGGATTATTTAGATCGGAAGAGCGT + HHHFHHHHHHHHHHHED=D?FEHHB:@DDBBGHHFHHHHHHHHHFHHBFBFGHGBGHHGHHHHHGHHHHHHHHHHGDC<<;5?:B>=@D2GBDEGHHHHH @read_150_460/2 ACTGAGCAAGGAATCAAGGATGCAAATATGAATAAAAGTACAGTCTAGTAAGAGAATCAGATATGTAAACAACTGTTGTATGAGAAAGAATTATATGGCT + HHHHHHHHHBB?DFGEGGHHHHFFHHHH?ADGHHHGFGHHHHE9/>5@EED@C;BDBA33>BCG@HGHHHHHGFFFGDEBEHGGGHHHHGGGHF<5=<(% @read_150_461/2 AGTTTTCAAAGGGAATGCTTCCAGTTTTTGCCCATTCAGTATGATATTGGCTGTGGGTTTGTCATAGATAGCTTTTATTATTTTGAAATACGTCCCATCA + HHHDG7*7//386A@EEE=EFGHHHHH@GEEEHHFHHFHHHHHHHHHHFFHHHFHHHHHGEHHHFHHHHHEBD>>FH:2>(= @read_150_462/2 ATTAGAAAGACTGCAAAACAATGATGTCTACATTATTCATGAAACAAAATTTGGAAAAATTTTGCCCACTTGGATGTTTTCTTAGCTTCAACTTAACGTT + DA;DHHHHHHHHHHBEGHHHHFGFFHHHHHHFCHHHFHHHGE=EG>:5,/99414@-;@::<;HHHHHHHHDEHHHFFHHHEDEHF;;5B>=DGEEFFF= @read_150_463/2 ATTAATTATCCTTAAATATAAAAGAGCATCATCTCTGCCATCCTGTTAACAAATCCTGTTTGTTTAGTCAGCCTGATTTCCATGGGGAAGCAGAAAGATT + FHHHHHHHHHHHHHHHHHHGHHFHHD=6GFFHHFE;CDGGGGB:;DBF @read_150_465/2 GCTGAGGCTGTCAAATAGTTGTTGAGCCAAAGTTACCTGTCATGGGAATCCTAGGCCTCCTGGGAATGGGCCTGTCTTAGTGTCCCTGCCACGCTCAGTT + HHHHHHHHHHHHHHHHHHHHHFHHHHHHHHHHHHHEHHDBFFFHHHHHHHHHHHHHHHH@@8?DC6>C>2'+AHHHHHHHHHHHHECFADFCDBFHF<<> @read_150_466/2 GGGTGGCTGGGATGCATGGGGTAGGTAGGGGTGGCAGTTTTTCCAAATTATACATTCAGGCCATATGTGGAACCCTTGCAGAGACCTGGCTTGCTGTTTT + @/HHHHHHHHCBHHHEEHFFCF@GEG@=GGHHHHBEGHHHHHGFEFFFFGCDDEEGHGGEF??EFEFGFFHHEEEGFHFGHHHHFHHF@EBB<<E>><6;HHHE?EDGHGF8DHHHHHFFHHHHGFHHHHHHHHHHGCCC96154.7@@>DD@FHGEHHGGHHHF5CGHHCFFGDECE:?:4,,= @read_150_468/2 CTGTCCTGTCATTCAGATAAATAAACCAAAAGAATAAAATATAGAATAAATCAGGCTGGGTGCAGTGGCTCATGCCTGAAACCCCAGCACTTGGGGAGGC + DFGGDDDGHHHHHHAGD55GHHHHEFHHHHHHHHH5EFGGHEHHHFEEGBGGIGGFEEGHHHE93EDEDGEGGG=BEHHH@@EEBFFHHE@FHFFHFHF8 @read_150_469/2 ATTTAAAAGGAAGTGAAACTTCAGACAATGTGAAACATGTCAGAGTCGTGTTTGCATTCTAAATTGCAGTAATGATATAAACATCATTATTCCTAATCTG + HHHHHFGFGEGFFFHHHHHHHHHHHHHHHFHHHHHHHDGGFEGFB0@BFF?;29>C@EHHHHHHHHEHHEHHHEECGGBEFGGHA=B0;/1<6, @read_150_470/2 TGTCTAAAATGAATGAGCAACACTATCATTCCCTCACTCTTTAGTGCATATGTGTTATAACTTTTAATAACTCTTCTCTACAATTAACTGAGTTATTGCA + HHHHGHHDDEGGHHG?D8EHHHHHHFGGHHHCHHHHHHFEHHHHHHHEHHDFCBEH?78D@CBFFHHHHHHDDA2<<4)&&85DGFEEFGGHHHHDEE?G @read_150_471/2 GTTTTTGAACTTAGTCCTAAAGTACAATCTTAATTTTAGGGTGTGGCCTTTCTGGGGTCTCAACTGAATGCCCAAGATGTTCAGAAAAGCCTCTCTGCGG + A?CBC@EEE@?<9E@6@FHHHHHHHEDDEEEHHHHFHEEIHHHHHHG@23.),,39@FHHH @read_150_472/2 TCTTTCATAAAAACTACTGCGCCTCAGCTCTGCCGTGGGGTCACCCAGTCATATGAAAACATGAACTATGTAAGAGGAAAGACATAGGCATACACTGAAA + FFHHHHHHHHHHHDGHHHFHHHHHHHHEBIH?GGBA;/DDHGBBC@-.EG=5<>DDHFHHHHHHHHHHEGEHHHHHGHHHHADDEGFCDD<3-273(@EE @read_150_473/2 TGGTGACTCTGAAAAGTGAGTTATCAGGAAGAGGAAAGGGACTTACAGAATAGGTCAAGAAAATCACCGCATTATGGCCGGATGCAGTGGCTCATGCCTA + HFHHHHHD-5:5?=A;@<@/CDHHHHHEFD,<=FHHHFGHHHHHHD:;CFEEEGEGCEFHBCEGC?FFA:EHGGGHH@.G @read_150_474/2 AAATATCTGGGTAGCTCCAACGATCGGGAGTAATTAGGAGGCAGTAGTTCGTCGAAACTCGGAGCGTCTTTAGCAGGAGAAAAAAAAAAAAAAAAAAGAA + HHHGHHHHHHFHHHHHHHHHHHFH;BGHHHHHHHE.6BGFHHHFHHEHHHHHHHGHHHHH?EGGFDCCDHHHHHHHHHFFFHHHFHHHFGF>B9>@>,6- @read_150_475/2 ACTTGTAGTTAGTGACCAGCCAATACGAACTTCATGTATGTCAATATCTTTTGTATATAAATGCCTTACTGGGATCTTCTCTGTAACCTGAAAGTCAAAT + HHHHHHHHHHHHHEEHHHHHHHHHHGHFHHHHHGEHHCGHEHFFEFBEEFGGGGE:@>2,2'&1/9:=GHHHHHFEF:A=DFHHHHCBEGHFE?FDHHFE @read_150_476/2 GCACTCCAGCCTGGGCAGCAGAGTGAGACTCTGTCTCAAAAAGAAAAAAAAAAAGAAGAAAACCAAAACCCAGTTAATCCTAAAGTGACTTTTTGCTCCA + 8D;2,<@FHHHHGEHHHHHHHHHFHHHBBD3-DEFHFHH8EEGCFDD/.>BEDCDEGHHHHHEFGHHHHFCCDDDCEC@GCFFEEGBDDGHEE95=D8F> @read_150_477/2 GCGCGGGCAGATCACTTGAGACCAGGAGTTCTGACACCAGCCTGGCCAACGTGGTGAAACCCCGTCACTACTAAAAATAAAAAAAGCCGAGCATGGTGGT + D@GFHDDCCGHHHGHHHHHHHFCGHHHHFBB=FDBEHHHHFGEEHHHEE535-CCGHHHHHHHHEGHHFHHHDGFBA?EE?.0FGHHFGEEBA?86155AFE @read_150_480/2 CTGATTTCCTACCTAAAATGGGTCCCTTCAATTCTCTCACTCAGACTCTTGATTTCCCATGATGGCACTCATTATAAACTTACCAAATTTTTGTATTAGT + HHHHHFHHHGDD;FFHHHHHEBE@@FGGFHCFFHFBHFHFGFCFHEHHHHHHGHHHHHHHFHHHGHFHHFG=@@C78>:<9CEE<>>?BHHFEFHHHHHHHHHFHFFH>:5BHHHHHHFHFEEEDAEEEHHHHHHHHHHHHHHHGGGF?5BAADBDFHCCGEE @read_150_482/2 AAAACCCTTTATTGTGGTTTCTGCTGGAAGCAATGGCTGAGGCAGGGTGAGCAGGCTGGTTTGTTTCAATAATGTCAGTGGGCTCTAGGGTAAAAAGGCT + 97B>>HEED<6=BGGBGGHHHHHFHHHHFHHHHFHFHFEEEB??8FFBBEDDCCEGHHHHHHHHHHGHHHFHHFHHHE?GEEHHHFEGGFEFGBEEFFBA @read_150_483/2 ACAGCCACTTTAAAAAACAGTATGAAGGTTTCTCAAAAAATTAAGTTGCATTGACCCGAAGGGCTCGATGTTTAGGGAGGTCAGAAGTTGAGCGGGTTCA + HHHHHHHHHHHHHHHHHHHFFFHHHBBHHHFFCBC@@56?EHHHHHHHHGFHGHHHHHEFHHHHHGEE6AFFEGHHHHHHHHEEEEBA=ECC@BHFFF?D @read_150_484/2 ATCTACTTCACGAAACCTCTTCAGTGAAAGAAGAAAGCAAATGCTTATCCCACACAACACCCAGTATACCTCAGTCTGTAGTCGCGCTTCATTTTCTTCA + HHHHHHHHHHHHHHHHHHHHHHHEGBHHHHHHHHF?=ADFGHGHHHHHFHHHGGFB732EEBEE?EC<:@C=@<->A,6@E>4<=4>DE @read_150_485/2 AGGACTGTTAAGAAATCACTGCTTCATTTCTTCAACTGGGCAGCAACTTGTGCTAATGAAACTCAGGTGGACATTAGACTGCCAGCCCCAGGGTTTCCCT + HHHHHFEEDG24531)-)6=2,30?:.9 @read_150_487/2 GCACTGGCATGAAGGATTTTGAGGCTGTGTCTTAATAATGCAGAAAAGGTTGTGACTGATTTATGATCTCAGGCATTGGAACAGCACAAAACACACATGC + HHHHHHHHHHHHHEEEEHHHHDF=EFD<43+'6(*?EGG?EEFGGEE<3.4@DDDGHHHHGHHH?>DCF?83CEEHHHHHF=HHD.;:6.(19+))*07, @read_150_488/2 TATTGACATTTTGCATCAAACTTTTGCTTCGGGCGATTTATTGTGTATTGTGTCTTGCTTATAGCATCCTAAACCACAACCTACTAGATGCCAGTAGTCC + HHHHHHHHHG8DGHGEHHF@CCAHHHHHHHGHHHG;:>==DFHHFDDDC;>;>78-,569-FHHHHHHHHHEFFHGHH>0>BCE/?=DEGIGEFGHHHHHBGA<@E9;7:>:@EGGG@555:@C:DBF<7EEE @read_150_490/2 AAGACAGTGGTTCTCAAACTTAAGCGTGAATCAGAATCACCTGGAGAGCTTGTTAAACGAGACTACTGGACAGGAGGTCCGGAATGCGGCCCAAGAATCT + HHDA=;FHHHHHHGEDFHHHHHCFHHHHH?@E@DD?BFHHHHHHGC?CCBGHHHEHH=;49<./%& @read_150_491/2 CAATAGTAATGGGTTCCATCCATTAGCTTTTTAAATGAATAGATCTGGTATTGATTTCCTTCCTGTTTTTTTGAGGCACATTCCTTTACAACCAGTGTTT + HEHHHHHHHHHFGFHHHHGHHEGGGF@DDHHFHHFHHHHFHHHHHFEGFHHHHHHHHHEHGHHHHHFFHHHHHDDC@0':FEGGFHHDGHEHHFFFEEEF @read_150_492/2 TCCAGCTTGTGCAGAGCAGCATGACATTCTTAACCAGGAGATATGGACAGCCCACTTACTTCCCATTTATAGTTGGATTTAAATGTTTTATTTTCATATA + HHHGGHHHHHHHHHHHHFFHHF9=DHHHG@FE;FFEFHHFAADBHHHHF=DFGHD@<<@D,3330/?<>CBFFFHHHHHGEHHFEGHFFGFE4;AEDHHD @read_150_493/2 CATTATGTTGCATTTCCTGTGCTTATTTCACAGTAGCTGAGAGGCCTGCTCTTATAACAGCTCATCCAAATAAAACCTTGAAAGGTATCAATCACAAAAC + EEEGCFGGGHHHHHHHHHHHHHF:.A:=GBDHGGHHHHHHBCC=?=;@EGGGDD>C@>C<@GGEG?@EEHBEEHFFFGHHHBHHHHB@HHFHHHFDCA5= @read_150_494/2 AACATATGTATGCATGTGTCTTTATAGTAGAATGATTTATAATCCTTTGGGTACATATCCAGTAATGGGGTGGCTGGGTCAAATGGTATTTCTAGTTATA + EEIHHEHGEEHHHHHHHHHFGHHHB:8AHGFHHHHGGHHHHHHFFFF3@2?>7:>DACDE@CDFHHCFHEBFBB;C,@HHHHHHHHHFFCDGD22)))AF @read_150_495/2 TGCTGTCCCTGGGGTAGGCTTGCCCCTCCTCTGTTCACACCCCTCTTTGGGTGGTCACCTCGCTTCCCATGGACACAAGCACCACGTTCAGCCAGATGAC + FHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGEEHHEFHHHIE?FGGHHHHHHHEIFGGF=<669GCA,-8AHGGCA;>04=DD@DDFDDCA>A>EE>,> @read_150_497/2 ACCTCAAAGAAAGAGTCCTTTCTTTCCATGGCCACTGATACGGTGTCATTTAAGACCCTGATTTTTTCTTGTCTGGGCTATTACCACAGCCTCCTCTCTA + HHHHHHHHHHGHBHHHHHHHHHHHHHHHHGFHHH;EEHFC=8;AD=@DGIGEEEEGG/BBDBBBE4->/)EBDDGFC@BEHFHHHHE8CECHHHHFBDEF @read_150_498/2 ATATCCAAATGAAAATAGCTAGAAGCTTTTATTGGATATTTGTATGGGAACTTGTCCTATTCCTTAGCCATTTTTTTTTTAGCTTTTCCTGTTATCTTCC + HHHHHHFIGEFGEEHHHHGHHHGFG889<:?HHGDEHHHHHFGFDFGIGGEEEDDHG=BGDC@?GD==73:31:CDECB @read_150_499/2 TCCTCATTCACCCCTTTCCCCACTCCAGTAATGCTGAGCATCTTTTTATGTGTTAGTGGCCATTTGTATATCTTCTTTGGAGAACTGTCTATTCAAAACA + /+>>@BEHHHHHHHHHHHHFEEGFHHHHHHHHHHHHFDCDFFFGGFHDEB6>>21*(,7;-4EHD;BBF@HHHHFEHHHHHHGHFA7.7%.=:.;.C?A? @read_150_500/2 GGATTAATTTACAAAGACTCAACAACTGGAAACCTCTAAAATCATTGTAAAGGAAGAAATGATACTCAAAATCACAGAGTTTAAGAGATCGGGAGTAATT + FHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHFBGEFFFFDBDFHHHHFHD@86<3=GGFHHHHHEHHHHHHHHHFD166>5<;;ECHGGFIGHHHHHHH adapterremoval-2.3.1/examples/reads_1.fq000066400000000000000000003265041350370616400202260ustar00rootroot00000000000000@read_150_1/1 CTTGGGTACTCAGCCTTAGGGTACCACATAGAGTTATCTTATATATTATAATTGCTCTTTTAACATAATTTTAAAAAATTTATATTAAACTTTCTCTGTT + HHHFFFFBBDGGGGGHHHHHGGFCDHGEE<@;+@C792A.CEEGGFFFFDEFGFHHHH@C2;@F;EDDHFDCCC@.DEEEG=BGEDC5>:=2@GFHHHFF @read_150_2/1 GAGTGGGCTTCATCCCTGGGATGCAAGGCTGGTTCAATATATGCAAATCAATAAATGTAATCCAGCATATAAACAGAACCAAAGAAGATCGGAAGAGCAC + HHHHHHHHHHHHHHHHHHHHHHHGC.@CFGHHHHHHHHFBFFHEHHHHFBGHFFFFFFHEDE@EBHHFHB<<>099BEB@=?*59/''.CCFHFHHHHHH @read_150_3/1 TATGTAATGACATAACTCTTATGGGCAACTTCACAAAAACACAGAAGAAAGCCCTCCTAAAGAATGAAATTCCAAAAAAAATCAGGTTACTGCTCACTGA + HHE=EE@DBBBGHGBFGGDDDDFFFHHHHHGHHHHHHGHHHE7BFHHHHHHG@4FEHHFHHHHFHHHHHHFFFE?EGCDE>CD:9=>+*;=37::ADDHF @read_150_4/1 CTCCTATATAAAGATAGCTCTGTAAAACAGGCCAAAAAGCAGAGTGGGGTGTGGGAAGGCAGGGAAAACTGTCCAGGAATAAAGGCATGAAATGAAACAA + HHHHHHHHHHHHHHHHEG@:EEB4DFHHEHFHHHHEGFFEEFCDHEFF:+1;?GFFCFHHHHHHHHHFHBB>>BEDGCDHHHHF @read_150_5/1 TACTCACGGACAAAGAATAAATATAGCTCCTCCAGGAGCTTAATAACTCAGTGCTGTCTAAACTCCTTACACCTGATGTTGATGCCATGGTTAGATAGTT + HHFFGGFDBHHEHHHHHHHHHHHHFHHHHFHHFEEDFD8=GHFFHHDHHHCHHFDHBHD:> @read_150_7/1 TAAGTAAGGTAGACAGCTAAGTCTAGTTTGTTCCCAGTGTTGTACCAGTCTCATCAGTGCCGTGTCTGGGTCTCACAGCCTCTGGTGTTCTATGCTGGAT + GFFEEDHHGHHHHHHHHB?GG77-/:>>@?6AC5GIB?BEBHHHHHHHHHHHHFGFHHHHHHEFEGF9?EHHHE@8BB12BEHHH @read_150_8/1 TAAAAACAAAAACCCTGATGAGAGTATTGATGTGTGCATAAACAAAGAAAAACATAATAGGAATAGAATGGTGAATTAAATTTTGTGAATTTTGGAAACC + HGGGGGHHHHHFHHGHHHHHHHEHHHHHHFHHEEHHHHHFE:/CGBHHHHHGFFGHHHHCEHEFECEFHHFEEE>CFFFCE?DEBD @read_150_10/1 TATAGATGAACTCTGATTTAGAATTTGTATAAGCTAAAGCATTATAGTAATAACTTTTAAAGTAGTATTTAAAATATCCTTATCTTACGTATATATGACT + <506@6?GHHHHGFHGFCFHHHHHHHHHHFGFF<3@C43F>AAEEFBFDFFHHHHHHHHED(0DAEBEFC?BFBEHHHHHC@85@GBGGFDCHEHHFCFB @read_150_11/1 GCCCAAGCCATACTTCAATAAACGTACCATAGATGTGAAATACAGGATAGAGAGCAAGAGCTTTTGGCACGGTAATCTTAGATGTGGAAATTTACTCTAA + HHHGEGGHHGGFGGGFHHHECDDCCDDHHHHHHHHHHHHHFGGGHFHHFFHHHHHHHHHHHEHFFHFG?HHHFEE=EE8@8EEBEDHHHHHHHHBCDDHH @read_150_12/1 AAGGCCTTTGAAAAATAGTTTTTTTTTCTCTGACTACGTATTTGTTGTCATTGTCATCATATTTCCTCTTAATTCTCCAAGATAGTTTTACTTTGATTTT + HHHHHHHHGGGEGGGGGHHHHHHHHFCEBFGHHHEEHHHHHHHHHHBDGBHHHHHHHHHHHFFFFEHFFCDDDHHFGGHHHHHCCEHFBGHHFGHHEEHH @read_150_13/1 CCTGAAGCAGCTGGCTAGTGGCTTATTACTTGTGACTGGACCTCTGGCCCTCAATCGAGTTCCTCTATGAAGAAAATACCAGAAATTTGTCATTGCGACT + HHHHGCC8EF@E8DB'/DDEFGCEHHHGGBHHHGGDD>>?DHHHHHHFGCGC@DHFDHHDDFFHFHFDEFHFFFGFHHBBGFFHHHHHHH=>:8BE @read_150_15/1 TTTGATGGGAGACATTTTATTACAGATTTAATCTCTTTACTCATAATTTGTCTGTTCAGATTTTCTATTTCTTCTTGGTTCTATCTTGGTAGGTTGCAAG + BB;:DGEGGEEFHHHHHGHHHHHHHHHFHHGDHHHHGGHHHHHHHHHHHHEF77BFGGHFFGEDDF@GF;DCFFHHHHHHHHHHHHHFEBC@FFFFHHH; @read_150_16/1 TATTGCTAATTTCCCAGATTTTTAAATACTGCCTGATGCTTATATCCTGCAAGTCCTGTCTAAAAATCAGTCAAGATCGGAAGAGCACACGTCTGAACTC + B@EHHHHHHHHFGHHGGBB@?CFFHHHHHHFEEHE@@CADAFFC>AHHFHFHHHHHHHGGFHFGE6A=@8.>HHHHD4*BFHHHB=BEHHHHFFFFEEDE77<+(>4@EFDF @read_150_23/1 CAAGGGATCTAGACTGCTCTGTCTATGAGAATCTAATGCCCTCCCCCTCCACCATGGAAAAATTGTCTTCCATGAAAATGATCCCTGGTGGGAGACCACT + HHHFHHHHHHHHHHHHHHHHHHFFH@EHHHF8@;@DD=EEHCFFAEFGFHHFHFGD<+(4EDFHHEFHHFFFFFHHHHHDFGGHFHHGB=CF?@>CD?CG @read_150_24/1 GGTTTTGTTTTAGGGAAGAGGATGAGAGTCTTGGGCATCCGAGAGGACATGAAGAACAGGTTTCATTAAAGTAGGAACTCAAGTAAAAATAGTCATGCTG + HHHHHHHHHHGGGGFFFHHHHHHHHHHHFGGGGGHDBEHFEHEEGGHHFEDD?@>&7;>HHHHFHHHHCHFHHHDFFFHHFHGHHHHHHEHHHFHEHHHG @read_150_25/1 GCTGTTGGTGAAAATTCTTGTGATGTGTTTATTTATCTCACAGAATGAAACCTGTGTTTTTATTCACTGGGTTGGAAACACTGTTTTTGTAAGATCTAAG + HHHGGGD8/=B>:CCEGFHHFHCFDAFAEFHHHHHHHFDHHHHHHGGGDDECD@FFFGD8,;1 @read_150_26/1 TTGCAAGTAATTGCAGATGACTGTATTACCACAGGATAACATGAGCTGACATATTTTTTTGCTACATCTCCAATTGACTACTAGGCCAAAATCTTCATGG + HHHHHHHHHHHHHHHFGGHHHBGEEEGG=GDEFBEHHHHDHE?EHHHHHHHHFFBFHHHEHFFFHHHEED?BFB=DA?E?HHHEEHHHHH=>DHHFGHHH @read_150_27/1 ACAACAATTTCTTCAGATAAGTCCTTTAATTTAACCACATGGACCCAGCCTGGGATCTCCGGGACATACAATCCTGTCTTAGGGCTCAGAAGTGCCCAGG + HHHHFGHHHHHHHHHHHHHHBGDFHHHHHFHHGFEE?/8<2>CEA?7CG?FDE3FCFFCFHD?@FHHHHF79573>EDD;FHEFFFGHHFHEHHHHHHFFHHHHHHDD3,>DDDDDEEEEGCEHFBFFHHHHGGH @read_150_29/1 AAGAGGTGTTTAGGTGAATGGGATTAGTGACGTTATAAAAGAGGCTGAAGAAATCTCCCTAGTCCCTTTCATCCTTTCGGCCATGTAAGGACATAGTGTT + HHEHGHHHBDDFHHHHGHHGGGHHHHHHHHHHHFFHHHHFHHHHHHFHHHFFHHHHHHFD@FF<.+->@.;?,4FFHHHHHHHHHFB @read_150_30/1 CTCTCCCTACAAGCACCCAGAGCAAGCTGTGCTGCAATCCCAGGGACTTGTACATGGCCCCTTTCCCTCCCTTACCGCCCAGTCAGCCCCTGCATACATC + EEDFGDBB@CGFHHHHHHHGHHHHHHHEEEGGDHHHHHHHHHHGB=@FCHHHFEHHEEDD=+E?FHHDA>>12+(D8?FDHHHFHHCFF9:>FF@CDBEE @read_150_31/1 TCATTCAACCCTGTGGAACTCATCTCATCATTCTCTGTCTCCTGCTTCTGAATGCTTTAAGTCACTTATTTGTCTATCTTCCCCAGAGAGAAAGCCTGCT + HHHHHHHHHHHHHHHHHHHHHHHHHHHEEGHHHGGGGFFFEEDFCDHHFFHHEAD?FHFGEEE5<@;=>49GGHFHGHBEFB>ABBEFFFECEHFH @read_150_32/1 CATGAACACCTTTATGAGTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCACCTAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAA + GGFGEEE9DC346GGHHHHEFEGGHHHHFHHHHEGGGHHHHHHHHHHHHFAC=E7ADFFFBEFEEFH@DHFCHHHFFGHHHHHHHHEHHHHHD@?>CBFB @read_150_33/1 GCAACCTCTGCCTCCCAGGTTCAAATGATTCTCCTGTCTCAGCCTCCTGAGTAGCTGGGACTACAGGTATGCACCACCACGTCTGGCTAATTTTGTATTT + HHHHHHHHHH@@D?GD8GEHEB=EGH??:@GGGHFEFFFHHHHGFHHECFHHGHHHHHFEHHHHHFBFFHHHHHHHE<>@EFFC=9=GFDEEED65@BB@ @read_150_34/1 AAGAAAAGAAAAATGTAAACAAAGAACTGAATGCTGCTGAATAACAAAAGAGTCACTTACTTAAAAAAATAATAATTTCAGCTCATCTAAGAAATAGATA + HHHHHGGGGFFGGGGHHHHHDEGDGGGGGEFFGGFHHHHDB@FGGGHHHHHGHHHEFHHHFF@EFHHFAF>FDHEGHHHHHHHHEGGHHHHHHHHHHFED @read_150_35/1 TCAATACAGAATGATGCCAGCACAATGATACACAGGACAGCTGGGACCAAGAAATTTGAGAAGGTACAAATAAAAACTAAAAAAAAAAAAAAGTTTAATT + HHHGBBGGGGHHHHHHHHHHHHHHHHHHFHFFHFFHHHHHHHHHHHHHHFFHHHHHFHHEEHGHHFDFFHC?BFFFHHEHHHHHHGGBBEHHHFG86EFH @read_150_36/1 GGGTTTGTAAAATAAATAAATAATGTGAACAATACCATCAGTGTTTGCATAGAAACAATATGATATCATTCTTAAAGAGATCGGAAGAGCACACGTCTGA + HHHHHHHGFHHHFHHHHHHHGGEHHHHHHHHEEHHHGGFHHHHHHHHHHHHHFEHHHGGE=EDEFHHGEEFD@?E::;24>6383;(.501>HHHHHHHH @read_150_37/1 GGTCTATATGTGCCACATTTTCTTTATACAGTCTATCATTGATGGGCATTTGGGTTGGTTCCAAGTCTTTGCTATTGTGAATAGTGCTGCAATAAATATA + HHHHHHHGGFFEGFHHHHGBGD@??37=FFDAEFHHHHHHHHHHFEHHGGGHFEFFHHHHFFFHHHHEB-DHHEHHEEGFHHHGGHHFHECFGHHC@AFH @read_150_38/1 CAATGTCTGTTTCACCTTCACTGCAGTCTGTTTATCCAGCCTGGGAAAAAAACTGGCTCCACTTAAACAATGAGACAAAAAAGGTGCAAACCTGACAGCT + GFHHHHHHHHHHE=GGFFGEG2@BHHHHHHGGGHHGGGHHHHHHHEFFFFAHHHHFHHHHGHHFFFDA2<<@FC:;44:>2?@@69BDAHHHHHHEBHCH @read_150_39/1 TCTCCCAACCTTGTATGGTCCTAGGGGCTGTGATATGGTTTGGCTGTGTCCCCTCCCAAATCTCATCTTGAATTGTAGTTCTCATAAACCCCATGTGTCA + C?8>?EFF?E@@C@6C.5EFEHHHHF>;::)04>?EFG @read_150_41/1 TTTTCCCATTGAGTGTTCTTAGCACCTTTGTTGAAAAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCACCTAATCTCGTATGCCGTCTTCTCCTT + HHHHHHHHGGGDA@BCDGGHHHHHHHHHGGEFFGBFHHHHHHHHHHFHHHCC??.AABC5DDHHHHEEEFFHHHHHD=FBHHHGGGGHHDD-%-&2 @read_150_42/1 ACGGAAACTAGCCAGAGTGGACTCTGTTGTCTACATGCAAGAAGATCGGAAGAGCACACGTCTGAACTCAAGTCACCACCTAATCTCGTATGCCGTCTTC + HHHHHHHHHHHHHHHHHHHHHHHHGGGGGGFCCHGHHHFBDDEFHHHDHBFHHHHGFBFHEDFFEHHC63@@<.119;C@B@BHDFGHHHHEE?CBCEFF @read_150_43/1 GCAGTGGTGACATGCATGACAGGCATTTGGGATCAGATGTTGCTGATCCAGAAGCCTAGGTGTGGCCATTTTGTCATGGCAACTGATAAGCAAGTAAATA + HHHHHHHHHHHHGGEB@C?HHHFCCGEFEEIEHHHHHEFF>4:>B:4C@9CAFHHHHHG.DEE@D77=BEHGGBA+,-(+7,7GC'5BDD;B?FDHGGGH @read_150_44/1 CCTCCTGTGCCCTGACCCTAATGACTTTTCTTCTCCGGGAATGAAGAAGCCAGAACCAACCAAGGTCTCACACCTTCACCTCTTCCCGAAAACTAACTCC + HHHHHHHHHHHHHHHHHHHEEGHECGGHHEDHF<7;BAHHCBFFFHHHHHHHHFFHHDCE928D@6<@@>>FHHHFBC+8 @read_150_46/1 ATTGGTTTTTTTTTTTTTTTTTTTTGAGATGGAGTCTCGCTCTATCGCCCAGGCTGGAGTGCAGTGGTGCGATCTCAGTACACTGCAAGCTCCACCTCCC + HHHHHHHHHHHHHHHHHHCDD@EFCGHHHHHHHHHFHCDDFHHHHFDDDB>BHHHHHHHHHFEEFFGFDHHF/AF?CF8FBEFFFFFHFEBEEE @read_150_47/1 CCTGTATATCTTAAGACTTCTTTCCCTTAAATTATTACCTTCTCCAAGAAGATTTCTATAACCCTCTAGGAGAAAAAAATGGGTGTTCCTCTCCCCCAGG + HHHHHHHHHHHGFHHHHHHHHHHFHEEEEEGGHFB6D?CD@@DDBGFHFHHFF973:9@DDFFFGGHHFGCFFDGFGEEFFBFFFH @read_150_50/1 ACTGATCCCAGGGAAGCTTTATCTATAGTGAATATTGTCTTAAATTATAGACTTTTTGCCAGTCTGTACTAGATCGGAAGAGCACACGTCTGAACTCCAG + FF;:?GGHHHHHHHHHHHHEHFFGHHHHHHGGHHHEEHEFFHHHHFHHHHHGGDDECBDDEBBCD74AABEFF;B@<@@@FEGHHEEE>,E=ACHHHHBE @read_150_51/1 CAGAGGTGGCAAACCCTCCTTGCATAAAATATCACACTTGGGTAAGTGCAGTATGTTATGTGTCTTTAATAATGCCACATCAGCCCCAAGTATTAGATCG + HHHHHHHHHGD@3--5EFGHHHGHHHHHHEGHGEEDGGHHHHHHHHHHFHFFHHHHHHHHHHFD.CFCD4=E=DFHHHHEHHHFGHHHHHHHHBFF;;?> @read_150_52/1 GGCCAAAACAAGAGGCGGTAAAGAGAAAGGCAAGAATTGGTGGTCAAGTCCTGGCAGGGAAGGAGGACATCAGACATCCATAAATATCAAGAAGTGAGGG + HEEGGHHHHHHHHHGF?A;B57.+&1:/' @read_150_53/1 GATTCAGGAAGCTCAGAGAATACCAGGAAGGAAAAATGCCAAAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCACCTAATCTCGTATGCCGTCTT + FFFGHHHHHFFFHHHHGHHHHHHHHHHHHHHDDEEG7DFEGGHHHFFGDHGGHHFBF?HFHHHFHHHFFDFF=EDFGFA@DFHHHGFHHH>CC;<61)&5 @read_150_54/1 AGTTAATAACACCTTCCTCTTCTCTGCTGTTGGATTCTAGCTTAGGTCTAATCTGTTCTAGGAAGACTTCCTAGGCCACCCCGTCAGATCGGAAGAGCAC + HHHHHHHHHHHGHGGEFDEHGHHHHHHFED>EHGHE?=?ECHHHHHHFHHHHHFHHFFH?=?BFHHEFEEFBGGHHHHHHHHHHHHGFFHHHHHGF;D<8 @read_150_55/1 TCCCTTCTTTTTCTTTTAATTTTATTTTTTACAGAGACAAGGTCACACTGGTCTCAAACTCCTGGCCTCAAGTTATCCTAAGGATTTTTATTATTTTTTA + HHHHHHHHHHHHEGGGGHHGEFGGGHGFEDDEGGEDGHHHHHHHHHHHHHFDHHGE?HHHHHEEEFFFHFFFHFDCEGHHHHHHEEEEFGGGGDGHFHHH @read_150_56/1 CCCAATCTGGCTTCACCTGGTGGTTCTCAAACCCAGCTAAGGAGTCATTATTAAGCAAATCCAACTGCCTGGGCCCCATCCCAAATCAACTAAGCAGAAT + HHHHHHGGGBCEEEHHHHHHHHHHHHHHHHFEECHHHHHHFCFDFHHHGHHHHHHFEHCBEFEFHH>EEEFDFB>EEACABGGHHHHG@@EGGHHHEE>@ @read_150_57/1 GTCATTTAAATATAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCACCTAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAA + HHHHHHHHHHFE?GGHHHHHHEEB>?D7>*CB?FHHHHHFHEHHDFHGHHHHHHHEHHGFHFHHHFHHHHG>BCEFGE=;CFFHHHHHHGFHFGGHGG?F @read_150_58/1 TCTGATATAAAATAGGAGCTCAGTCAGTGAGCATTCAATCAATAGTATCATGTTTCTGTCTCTGTCCCCAGCTCCCTCACTAACTCCCTTGGCCCTTATA + HHHHHHHFHHHHHHFGHHHHHHEAGHGGHFHHFHHEFFHHHHHHE+8>://6-3>FA7;@DDAED?FDF< @read_150_60/1 CTCTGTCATCTGTTTCTTGGAGGCTTGCCCCACATCAGGTGGGTGGGACACACCCAGGAGGCTGTGCTCAGGATTTCTGGCCCGTGTCCCAGGTCACCAG + HHHGGCEHHHEEGGCDGGBDGGHGGHHHGHHEFGFHHHHHHHHHHHEHEBCDEHEEEBHHHHFEFHHHHHF;@8,BDDEB>:.EE@>??BB>AA=CC??DEGGECD?;E8GGFHHHHHBE @read_150_63/1 TGTGGTGGCTGGTGCCTGTAATCCCAGCAGTTGAGGAGGCCAAGGTGGGTGGATCACCTGAGGTCAGGAGTTCGAGACCAGCCTGGACAACATGGTGAAA + HHHHHHGBEFDBGGGHHHHHHHHHHHFFHHHHHHDD@CGGBEHFGGGHHHFHHHHHHEBHGGEED<).3FGEFGHFHHGFHFH< @read_150_64/1 TAAATTATAGTTGTCTTTTGTAAACAGGATGTCAAATACATCAAAACCTCTCAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCACCTAATCTCGT + HHHHHHHHHGGGHHHHHHHHHGHGHHEH?;C@EFEEFE?AFHGGC:EEHHHHHGFFHHDBHHHHFHHHFFFGFDFHHHHHHHHHHHHHCD=CEACCCHBD @read_150_65/1 AGACCATCCTGGCTAACACAGTGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGCGGTGGTGGGTGCCTGTAGTCCCAGCTACTCGGGAG + HHHHHHHHHHHHEEEFFFHHHGFHHHHFFHHHHFFHHHHFFHHHHHHFHFFHHHHHD?C4DDHFHHHDBFHFBB,8DBDE*2,)37?DDFFHGGGFGHHEFGHFEEGFE @read_150_67/1 ATTGATTATTGCCACAATTTCAGAGCCTGTTATTGGTCTATTCAGAGATTCAGCTTCTTCCTGGTTTAAGATCGGAAGAGCACACGTCTGAACTCCAGTC + HHHHHHHHHHHHHGGGHHHHHHHHHHHHEFGHHHFHHHHHFDCBFHHHHHFHHHFHHFHHFFEFHHBF0?CHHHGD,92>>9;DE?FEEEEEDEHCHHHHHHHHHEFFFECC @read_150_70/1 TAGAAGAGGTGGCCGTAATTGCTGCTTGTCATTAATATTTTTACCAAATGGATTTCTCCATATGGCAGTTCCTTTCTGTCATGGGTTATTTATAATCCTT + EFGGGHHHHHHHHHHHHGGHHHHGGHHF?DEHHHHHHHHHHHFHHHHHHHHGGAA4EBEEHHHHHHFCCBDHEEDHH??EHFFEFDEDCCFHHHHHHHGGHHBC,DHHH@E;CEGHHGHDFGGEEC@@A?HHHHHHEBEBADFHHFFDCEFEHFHHHFBEEHHHGDDEG;48ECEHHHHHFBD=CFHHHHHHGFFEC @read_150_74/1 AGTGTTTTAGTGATTGTTCAATGCCATTTAGCTAGACTGTGCACAATCCATTCCAGGCATCCCAGAGTCCCTGTAATACCACAAATGTACCATTTTATCT + HHHHHHHHHHHHHHHGHGGHHHHHHHHHHGGGHHHHHHHHHHHEEFGFHHHHHHBE?@FHHHFHHHFE5BEG?ABDDDDGGFGHHHHBFHHHHDGFFHHH @read_150_75/1 GTCCAGGATCCTGCTGTTGGCTGGGCTCTTCAATTATCCTCCAGGTATCCTCTCCCTTATCCCACATCCCCAGCTCCACCTTGTCTTTTCATGTGGTGTC + HHEA9<=DDEGFBGHHGEG@EGHHHHHHFE?:<<>FHGHHHHHHFGHHHHFFHHGHHHHHHHHHD==??=FFD=4?DIGED8EGGHHHGADD-?=EGDDFAHHHHHHHBEGHHF6@HGFHHHHHHHHHHHHHHGFFHHHFEE?HCEFFFHHHHEHEFHHHHHHHHHHHHHFGFF @read_150_79/1 GTGGCCGGGAGCAGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGCGTGTGGATCATGAGGTCAGGAGTTCAAGACCAGCCTGGCAGATCG + HHHHHHHHFEGGGGHHHEEE:>?HGEEE>><?BEHHHHHHHHHHHHHHHHHEGDGEB@8?B?=>CHHHDHHHFHHHHHHHHH<-=FEGHHH=?@>EEDDDDHEB:?BEA561 @read_150_86/1 TCCAGCCATGAGCCACCCCACCTGGCCTGATTTTTTTATTTTTAGTAGAAATGAGGTTTCGCCCTGTTGCCCAGGCTGGTCTTGGATTCCTGAACTCAAG + HHHHHE>DGFHHHGHHHHHHHHHGGHHHHHEGECHHHHHFHHHHHGFFDDD??@FHHHBFGBHGHEEBFFHFFFFEBHHEHHH=DHHEECG?DHGHGGHE @read_150_87/1 TTCTGACACACAGGAGTTTACTTGAAGACCACTATTTAACCTTTTGATAGCCTTTTATGGCTACCCTGGTCCCTGAGAAAAATGAAAATGCATTTGCCTT + GHHHHHGGHHHHHHHHHFEHHFHDHGHHHGHHHHHHHHFGEHEHFHHHHHHEEBFHHBD>(6E96DFHFHHB90%%&913>FEG@EBDFGHHHHHHHHHG @read_150_88/1 CCTGGTTCATTTACTAGCCACCTTATTGAGCACCTACTATACTGCTGCAAGCACCCCTTTTCTCGTGTCTCCCCTCTTTCTGCTGGAAGTTGCTTCCTAG + HHHHHHHHHHHHHHHHFEHHHHHHHGGGEE:?5CGHHHHEFHHHFD??B<=@=EDG@EDFHHHCGFHDFCFHHHEFFGHHHHHHHHHHHHHHHHHF?;-% @read_150_89/1 GCATTACGTTATGTGGCAATATTTACATCCTCTTTTAAATAAACTACATTCTGGATGCCACTGAAATTTATTTCTATTTAGTATTAAGTTTAGTAACACC + HHHHHHHHHHGGGGBBBAFHHGGGEDGDCEEBHHB297BCCBEEHEHHHHHHHHFFGFHHHFCDHHHFEEGHHHFGEHHHHEBG?HFDA9EFB@/;@?HF @read_150_90/1 AATTATGAGCTAAATAAATACTTCCTTGAAATCACTAAGTTTTGGGGGAGGATAGAAGATAGGAGGATATACTGAAGAGGAAAATACTGAGGACTTATTT + HHHHHGGFGGGGFHHGGFHFG>>=6FFHHHHHHHHEFFFEHHHHHHFFFGFFHHHHHDC?BDDDEHHHGFA795,@?HDDEFGGGF<(52:1-6:FE.-& @read_150_91/1 TTGACCTTCTCTCCTGTTAAGTGCAGTAGGGCTTCCCCTCTTGACTTTCCTGGTTATAGCTTTCCATCACAGCTCCCCACATTCTCTCTTGATGTTGAAA + HHHHHG@4-256EEEEHHHHHHHHHGGGHGHHHHFGG20=CA>9C6427HHHFEFHHHHHGGHHHHHHED @read_150_92/1 TAGTTTTAGATCTTAAACATTTTCAACCCTTTTGTGTGAATTACAAATTGTTTGACTAGTAGAAAATAAACAGGACAAAAACTGAGCAGTAGTCTTGTTT + HHHHHHHHEEBGHHF>>G>EGDHHHHHHHHHDDAFGEAD@<GCFCGDEEEEFGEEEHHHH@?EA7<6&0(2BGGHD @read_150_95/1 AAAACCACAATGAGATATCATCTCACATCAGTTAGAATGGCGATCATTAAAAAGTCAGGAAACAACAGGTGCGGGAGAGGATGTGGAGAAACAGGAACAA + GGHEGGHHHHGHHHHHHHHHHHHHGGGHHHHHHHHHEHHHHHFHHHHHFCHFFFGGBB@EFHDHHHHHD;4A(2*3C?A@=6)>DGGEGHHHFHHEEH=B @read_150_96/1 TGAGGAGGTTTAGGCTCAAGAGAAGGAGCAAAGTGTAACAAAAAGAGCACCAGGCAGTCAAGACCACTGACTTGCTAAGACCAAACCACTTTTTTATCTC + HHHHHHHHHHHHHHHHEEFGGGGHHGHHHHHHHGFHHHHFHHFF8@79@BDGFFFFHHHHFHFEFHB:BCFEFEFHHGGGFCACD>CEAC=9.3*/7/,99@< @read_150_99/1 TGACATTTACAAGGATGTTGATCTTGTTTTCCTTCATAATTTGGAGATGTAAATATTTCAAACTTTCCTATTGGTTCTGCTATTTGTAAATATACAGCTG + HHEGGGG?A>;EFHHHHGF?64>?FHGBHHHFCC>HHHHHHHFHHFFFFHFHHHHFEEDDEEHHHEHHHEBEFHFDHHHHHHHFGHHHHGGGHHHFFHHH @read_150_100/1 AATAAAAGTGAAAAAAGCAATCAACAGTTGAAATTGTTCATCACTAGCCCAACATCTTTCCTATCACATGCCCCTTCTTCTCTGCTAATAGAACCCCTAT + HHHHHHHHGGHHFCD=DCHHHHHHHE;@BGGCEGHHHHHFFGGGGHHHHCFGGEEEFCHCFF<;EFDBDCGGGGFDEGGEFHFFHHHFBFGGG;BD4>?E @read_150_101/1 GATTACAGGTGTGAGCCACCTTGCCCAGCCTATTGTCTTATCAACAGGATTAACGGCATTTTCACAAGGAGTAGATTCCATCTCAAGAAACCATTTGTTT + HHHHHHHHHHHHHHHHHHHHHHHHBCEBFFGGGCGGEEFHHHFEEHE?B;6DA;DEDHHFHHHHBBBEDBFAEE@CEGBCDBGBEB@?=@@>GFHEFGEF @read_150_102/1 TCTAATTTTGAAACGAAGATATTTCCTTTTCTGCCATTGACCTTAATGCGCTTGAAATCTACACTTGCAAATTGCACAAATAGAGTGTTTCAAATCTGCT + HHHHHHHHHHHHHHHHHHHHHHHHGFGGGFHFEEEFHHHHHHHHH?EEFGFGH=GGEBHABD@9@DFHFEDC8;9DDFHHHGE=GGFHHGHHECBDFFHH @read_150_103/1 CACACACACACACAATAGAATACTACTCAGCCATAAAAAAGGAAAGAATTAATGGCATTCACAGCAACCTGGATAGGATTGGAGACCATTATTCTAAGTG + HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGGEBGGGGHHHHHHHHEFHHHHHHEFHHHHHHHGEEDEGFHHHHHHHHHEEEEFE@);@;AADDEFADHH @read_150_104/1 ATACTTCAGGGGATGAGCCTGGGTCCTCCCCTCCTGGCTGACAGGAGCCTGGTGGGCAGTGGGTATGTGGGGCCCGTGTAGGGGGGTTGGGCAGCACTGG + HHGEEGGHHHHHHHHHHHHHHHHHFEG@>BFHHHHHHHHHHHHHHHHHHHHHHF=DEDGE,-AHHHHHHFEHFD9DEEGEHHHHHHHHFHGFFFACEFHH @read_150_105/1 CATAGCCCTTCAGTGGATACGTTGGGGAATGGAAAATGAGTTATTCAATTGACTCATTCAAATGAGTCCTGGTTTTTCTTCCATAATATACAGATAAGCA + HFGGGFFFFFHHGGFGGHFFGGGDHHHFFBDEDGHHHG>;;?GHHHHHHHHHHHHHEHHHHHCFHHHH @read_150_108/1 TGATCTTTTCCTTTCTAGCTTAATGGCTTTCCTAGAAACAGAGCCTGAGGTAAGTATTGAATGCTAATGCTTTATTTAGGAGGTATGTTTTTATGGCTGC + HHHHGFBHHHHHHHHHG=2BGGHHHHFHGHHHHHE;>BBFDEF9BCC:,0FHHHHHHHHHEFHHHHBFFHHHHHFHHHHGGE=>>7DFHHHHCD.3>CDD @read_150_109/1 CTGGGCAGTGAGCCAAGCTGGCAGAGAGCCAGCACTACAGGAAGACACACAGGGAGAGTTACCTTGAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC + DDBBDD=DGFGGHHHHHHEGHHHHHFGHHGHHGFFHGC@CBHFE=CDA9FFHGGGEHHHHFHHGFDFF6<>9DABHHHHHHHHHHHFEEHFHHAGEFGGG @read_150_110/1 CGGTGGCTAACGCCTATAATCCCAGAACTTTGGAAAGGCAAGGTGAGTGGATCACCTGAGGTCAGGAGTTCGAGACCAGCCTGGCCAACATGGTTAAACC + GGFHHHFHHHHHHHHHHHHHGDGFA/10*=(,CGHHHHHHCD42:A>:CGGGGFFGHHHDEFFHHHHFFFGD;AC.3CCFGGEHGFEFFD+/>3+2;29; @read_150_111/1 GGAGCTCAGAAGGGTCTATTGGCAAAGCCCCAGAGACGATGTCTCAGGATACAGAGTGTGGGGCCCATTGGTACACAGGTGTCTCCACGCAGGGGCTGAG + HHHHHHHHE@EEEBFHHFFFGHGHHHHHHEHHHHHHHHFDEGDEEFFFDDACBHHHHFC;@FHEFFFHE4EEE>ABE?CDGEDFHDEEEHHHHHHFGFGF @read_150_112/1 TCACCATGTTGCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCACCTAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAA + HHHHHHHHHHHHHHHHHHHHHGGGGFGDFGFFHDDC?EACFFHHHHHHHHHHHHHFCGFFFHHHFEFDEFB@D@A4?7773,5*, @read_150_113/1 TCACGCTTATTCATTGATGGGCTGCCTTCTTACCACATGTCCTTGACATGTTTTAATTCCTTAAGTCCTCATAGTAACCCTAGTACATGTACTCCTGTGA + HHHHGFFEB2GGHHHHHHHHHHHHGFGE8EAEFC97B<7DDEC@FHHFDFDGD=HHHHHDGHEE??CCEHH @read_150_114/1 CATTGACTAACAGATAGTAAACTCTCAATATATTTTTACTGAATGAATGTGAGAATTATCTTCCCAAAGGTGTTTTATTATTCTTTATCAAGATCGGAAG + HHHFFFEEHHHHHHGGHHHFBGGGFGGGGGHHHH?@799;6DHHEHHHGDEEEDDBEEFHHHHHHFHHFEFFFFCHEEEFGGG=?BFEGGGHBBBEHHHH @read_150_115/1 ATTTCAAACGGAGCCTCTTCCTTCACAGTTTTCCTTCAGAGCTCCTTTTTTTGTTTCCATTTTAAAGTTATTGTTTATTCTAGACAGGGAATCCTGCCAG + HHHGDCHHHHHHHHHHEAGHHHHHHHHHHHHAFGFHHHHHHHHHEB=EDEHEEBGHHHDFHE4DCFFFGFG@FHHFFGEFDFFHHHHHHHHHECCFFEFH @read_150_116/1 GATGGCAATGAGGCGCCACCAAGGTTTTTATTTTTCAACTTTTTACTTTGGAAAAAAACATTTTTTTTTTTTTTTGAGACAGAGTCTCACTCGGTCACCC + HHHEFFFFB=DA?CFEHHHHHHHHHHFHHHHHHHHHEHHHHHHHHHFHEDHHGGHHFBBHH?CBDDDB;:*3>HHGEE:61<<;+7?>?D@(%C5<FGHHEFHHEHHEEHHHHHFHHHHGDCC823*/%2/1DHHHG @read_150_120/1 AGCAATTCTCCTGCTTCAGTCTCCTGAGTAGCTGGGATTACAGGCATGGGCCACCACGCCTGGCTAAATTTTGTATTTTTAATAGAGACGGGGTTTCTTC + GGGGHHHHHHHHHHHHHAHHGGHHHHHHHHHHF@?GFHHHHHHCFFFFHHHHHC?FFED=/BGHHHHHHHGEGHB=59ACA @read_150_121/1 CTCTATCTTTACCTCCAAAGTGCTTCCGCATCTCTTGTCCCATTTTCTTTTTTTTGCCCTATATTTTAAACCAGGATTCTGTTGCTGGCCATAACACATA + HHHHHHHHHHHHHHHHHHHHHGGHHFGE>>DDDDDEEEEHHHHHHHHFHFFHHHHHHHDDCEHCCFHHFHHFHHHHHHHHACC>?A?EFCHHHHHHHGFH @read_150_122/1 TGTGTCCTCTCTGATTTCACTGAGCAGTGGTTTGTAGCTCTCCTTGAAGAGGTCCTTCACTTCCCTTGTTAGCTATATTCCTAGGTATTTTATTCTTTTT + FHHHHHHHHHHHHHHHHHHHHFHHHHHHHFGFGGHHDFEEGDBBBDDCFFHHF;>;B)')6GDAACE @read_150_124/1 CTTGTTCACCTAGCAACATTTAACAATGATACCTCTTTTAACAATTCAGGATGTGAACGACATAAATGAAGATGGTGAACATAGATCGGAAGAGCACACG + HHHHHHHHHHHHHHHHHGFBGGGGGFFFEGHHH;FFF@ABCCE;@EEEHHHHFHFHFEHHEFEEEHHHHGBFDHHHHCHHHHGHHHHHHHHH9CHGGHHE @read_150_125/1 GACACCAGGTGGGCCTGAGCAGGGGGACCAAGCGCCTGATGGGCTGTGGGGCTAAGGGGGGAATCGGGTGGCTCCCGGGGGTACAGGCTGGGTGTTGGGT + FEEEDDDHHHFHHHHHHFHHHHHFEGGDFEGGHHHHHHFHHHHHHHHHHHEFHHHHHHHFHHHEHHHHHHFGB2?GDAAGHHHHBEHHHHHGCFHHGFFD @read_150_126/1 AAAGTAAGTGAACATAACATTAAAAAAATTCAAGGTGAAAATATCAAAGGAAACAATAGTGACTATTTCACTGTGATAAAAAGAAAATAATTGAAGGACA + HHHHHHHHHHHHHBGFDFHEBEBEEFHHHHHHHHGHG@CE829A-,>FHDEEFBHGHHHHHHFHHHHHHHHFEFFFBDHFBE756DFFDBE;BGHEHHEE @read_150_127/1 GCCTCATTTCTCACACATGTATAATGAAAAAATGGAAGTCCAAGGTCCTTCCAGATCTAAAATTCTACAATGTTATGAAACTAAATCATAATAGCAGCAA + HHGGB@@EEGHHGGGHHHHHGHG@;9>CAFDFFGGFFE:DDA>FHEBFHFFDFFFHHHHHHHHHHHFFFFCGGFFGEFFGHHHHHHHFGEBFCBEH @read_150_129/1 GGTGACAGAGCAAGACTCCAGTCAAAAAAAAAAAAAAAATGAGACCAAGGAAAGTGAAATAATTTGATTAAGAGCTACAGGATTTCAATACATTTGCTCT + HHHHEFEGG?>?D@CFGGG?AHHGFHHHHHHHGEE?EEHHHHDA=>EEEGHHHEEFHHHHHH?HHFFHHHHHHHHHHHHHHHHGGFHB8;E+'+8;CHHH @read_150_130/1 TGCAGATGAAGCTTGTCCGTGCCCAGTGCCTGAGTGTCTGGAGCTGTCTGCTGACTGGAGCTGGTGGCGGGATCCATGTCTTTCTCCTGCACTTGATCTT + HHHHGGGGHHHHHHHHGF?C=FGGDE=::2/&-6FFHHHHFFGHHFHFFFFFEEHHHFHH?D>FEHFFCDHFFDD4,04>DCFFHEE@CCDD4B-+)35D @read_150_131/1 GGTTACATCTTCACTTTGTAGAAGGCTAGAAGGCACAGTTTTCTGGCAGTTCAATGTAACTCAAATTGGTAACCTCCTTTTATCAGCTCCAATATTAAAC + GGGHGHHHHHHHHHGBEEHD;DHHGGDBGHGFFHCAFDEHHHHFFEHHGGFFHFGDEDGFFHFFHHHHHEHD@ADDDDDC>@8DHHGECCE@EHHHFGGB @read_150_132/1 AGTCGTAGGACACCATTGGGAGACCGGGCTGTCTCCAAGAGAAAGATGCCCAGTGGCCCCCAAAGCCTTCTTGAATCGCACACTTACCCCAGCTCTCCAG + HGGGGHGGGGHHEHHHHHHHHHHHBHHHHHHHHFGHHFHHHHHHHHHGHHHHHHFEFHHHFC?;DCFBFEHFFFHHHFFHHGEEE=9A<)84>CDEE;BFFDHHHHFFFDFD?EEA4D @read_150_134/1 CACAAACTTGTAAGAAACGTTTTAATTTGTCCTGTCAACTTCAACAAATTTACAAGAAAAAAACAAACAACCCTATTAGAAAGTGGGCAAAGGACATGAA + HHHHHHHGHFHGGGGGF8%9DBBHHHHHHFFFGGHFFHHHHHHH?E@:?BFHHBEHGGHHHGCEB,:0:))4;%');6=AHHHHFFHHD@FHH?=EEEEHHHHHHGHHFCHHFEHGGGGG @read_150_140/1 TCTAGAAGTTGTATTTCTTAAAAATAAATGTAATGTGGCTACTTGGAAGAAAGAAGAATGGGAAACGTTGATTTTTCTTGTAATCATTTATAGGCTATTG + BCDAADHHHHGFEHG=@;;>D@HHHHHHHHHHFHHED>AFHHHH @read_150_141/1 TCTAAAAGTTTTAAGACCATTAGGTTTGATCGTCTTTCTTCTTTAATCTGGAAAGTTTGTCTTCAATTCCTGTATGAGACTTTAGGAGTTTCGAGAGCGG + HHHF=FHHHHHHFFGHHHHFFHHHHGGHHHHHHEE=6FGEFFHHHFGFHHHHHHFHHHHHHHHHHHEFHCEEHFHHGFBD:;2E8BGFE6EEE@C2%9;F @read_150_142/1 CTTTCAGGCAAAAATTTTGAAGTAAGATGTGATGCAAAATTTTTTATTGAATTCAGTATATTTGGCCCTATATTCTTGACTGTAGTAGTCAGAGGAGGCT + GGFFDBEACBDBBEEEHHHHHHHHHHHFEEHHHHGHHHHHHHGBDA:EGGHDB??GGGFFDHFHHHA9>EFEDCFGFEDDHEEBDEGGHHHHHHFGF:DF @read_150_143/1 AGTCTCAGAAGATTTCTCTCCACACATATGAGTAATACCTGGCAAAAATGCTGTCCTCGGAGCAGAGGGAGAAGATGGAATGATTCGGTGTTTGATTAGA + HHHHGHHHHHHHGFEBDCHHHHHHGBEHHHHEHFFHHHHHHHGGG??/7DHHFHFFHHHHHHHEEHHHFFFBEDAFF6:.)35@:&+AGF7.33/BD>CD @read_150_144/1 GCACTCCAGCTTGGCAACAGAGCGAGACTCTGTCTCAAAAAAAAAAAAAAAAAAAAAAAGGATTTGAGCTAGAAAATGGGACCATTCGTACAATTCAAAC + FFE?@EFBGEFGGG:>CDEHHHHHH@0'-.6;@EFFFFGGHHHFED=CE/->99=FBB+3> @read_150_145/1 ATATCAGTTAATAAATGTTAGATTCATTGGACAGTACCAGGCACATAGTTAAAGTGCAGTAAATAGTAGTTATTGTTGGTATTGGTGTTATTTTATGTTG + HHHHHHHHHHHHHFGHHHHHHHGHHFFEHHEHHFFHHHHEHHDDBCDFHHHHGGGEHHHHFDB9BFHHHHDEEHFFHHHHHHHDE;:BGDEHHHHFHD3( @read_150_146/1 GGGGATGATTTTCTTGTGGTATGCCAGTGACATTGCCTCCTCAAGAGACCTTTTTAATTTAGCTTTATGGAAAGTAATATAAGATCGGAAGAGCACACGT + HHEEEBCCGGGGHHHHHFFHHHHHHHHEGGEHHHHHHHHHHHFHEEFAAFHHHHGGGFEHHHHHFHHHC@CBEC:;::=D?HHHHFHFEDEDDFFHHHFF @read_150_147/1 CAGGTTCTCCAAAGCAGATCGGTGCTCAAGTACCAGGAGTTTAGGAGTCATGAGGCTGAGAACCTCTTCACAGGGCCTGCTGCCCCACCCAGGGGGAAAC + GEEEGFFFHHHHHHHHHEHHHHHHHHHFFA9=CBHHHHHHHHHHFHECHFFFHHHHHHHHFHHHFFFHHFD349EDDDFHHHFEHHHFHHHHHFFEEHHH @read_150_148/1 TAACCTTGTCTCTCCTAAGGAATTAGTCATTTTTATCCTCTTAGTAAGGAGTTGTGAAATACATGACGTTTCCCTATGCACCTCCGTGCCAGGAATGTTA + HGCCEFGGHHHHHHHGE@AACCCGBEFHHDHFFFGHHFD8FHHHFADAAEAHHHC?AADDDGGADFGHHEF=B:>F>BDHGFFGHF @read_150_149/1 CAGGAGTTTGAGACCAGCCTGGCCAGCATGGTGAAACCCCGTCTCTACTAAAAATAGAAAAATTAGCCAGGCATCGTAGCGTGTGCCTGTAATCCCAGCT + HHHHHHDEEHHHHHHHHHHEGHHHGHGHHHGFA@HHHHC?GGHHHHHHHDBDB%395>@DEEFFAHFHEFHF@9EHHHHHHH@GGHHHHFFEFHHHFFGF @read_150_150/1 ACTGTGCATAGGGCCAGTGCCCCAACTCCTGCATTGTTCAGAGGTCAACTCTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT + GGHHDHGGHHHHHHHHHHHHHHHHFGHHGGGEHHHHGGGGEADFHHHHH@FFGHFHHHHHHHHHFCHACFE=ADFFHHFHHHHHHHHHHHHHHGGHHHHH @read_150_151/1 GAAAATGAGAAAGAGTATTTAGAGATTTTACTGTCTGTGGTGGGTGATTTTAACGTAGGTCTTGCAAAGTAGGTAATTAGATCGGAAGAGCACACGGCTT + HHHHHHHHHHHHHGGGHHGHGFGFGGGHHHHH@HEEFHEGHHGDFECDAA=A?FEHHHFFFGGHHFHHHHHHHHHE26@CEHHHHHGHHFHG?B8.*>>> @read_150_152/1 AGTTTTATTATTGGTCTTCAATCAAAAGGCAACATGCCATTGATAGAAAAGGGTAACTTTACAAAATAAAATACACTGTTTCCCTAAAGGAATTAAAGAA + HHHHGGGFGFGHHD4FHEFHGGHHEFEEDFFHHHEFGHHHHHHHHHEHHFHFHCBDHHCHHHHHBAEDC8@EEEB=C=/1&;EDDHHHHHHHGFGFDDDC @read_150_153/1 TCTGTCTCAAAAATTATAATAATAATAATAACTGTATATAATTTGTGAAAGGAAGAGAGGAAAGAAGGAAGGGAAGGGGAGGGGAGGGGAGGGGGAAGGG + HHHHHHEEEHHHHHHHHFE:CHHFHHHHHFFGBGEFHHHHHHHHHEEBEFHHHHHHFFF@CDHHHDB>@CEA3;CFHGGEGHHHGFGHGB??DFBFBFEC @read_150_154/1 TTTTTTAAAACCTTTGTCTAGTAACTCCAATTTCTGTCCTTCCTCCAGGATGGTTTCTGTCAATTAACCTTGGTCCTTTGAATTAGTCATATTTTTGTAA + FEGGHHHHHHHHHFBDHFHHHHFGHFFFHHHGHGHHGFHHFHHHHFHHHHHHHHEFDEHHHHGGGD?DCDFFFFEHHHHHHHC@7CGHHE:?EEHHE><> @read_150_155/1 AAGGCTCTTGAGCACATTTTGGGAATATTGCTCTGGCAACAGCACATGGTAGAACGGAGTTTCACCAGTTTCCCTGGTGGAAAAACATGTTCCATGGCAA + HHHHHHHHHHHHEEBFCFHHHHHHHGGGGHHHHHHHGGHHHHHHHHHHHHFHFHHHHFECFGDFE?DHHHFEF4??ABHHHHFF?@DF< @read_150_156/1 GGATAAGGCACACACAGAAGAGTGTCATGAAAGCCTCCCACCCACCAGTATTTTCTGAGCATGCACCACATGCAGGCCCCGCAGAGGGCCTTCCACACCT + GGGHHHHHHHHHHGGHHHHHHHHHHHHGHGHGBFFHHHHHFGFF?EHHFGEEHHHHHHFHHFFFBFHHFGGGB:BFB?CAEHHHHHHFHEHHHHHHHGGHHHHHHGHHHHHHHHHHHEE @read_150_158/1 ATGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCACCTAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAATAAAAAA + HHHHHHHHFGHHGGFHHDFF;CEEEEGC=@?19@A@C@BCCEHHHHDHHHHHHFFFFHHHHBBFDDBDGGGHBGFGCAFG?EEEHH;@1<7>C=BHHHHHHHFFGHFHHHE;-*.<09CC@8A?GEB@FBGB@9>2?91:./- @read_150_161/1 ACTAAAAATACAAAAAATTAGCCGGGTGTGGTAGCGGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCGTGAAACCGGGGGGCGG + HFFGHHHHHHHHHHHHHHHHGHHHHHHHHB-0:;6:EEHHEBFHFHHHHHHHHDFHFFHFFBBDFEDDEGHDBHEHHHHHHEHF5CD-5@;8;-&3DHFE @read_150_162/1 TCAAAATTTTATAACTCCTGAAGACCTGACACAAATACCACTTAGTCCACAAACCATGTCGATTTCCCTGAAATTCATCCTTTCCTTTAAATACTCATGG + HHHHHHHFHHHHHHHHHEEFBHHHHHHHEEBDDDE@?DHHHHHFHEEEHHHGHHF>,2>9%1>FHHFC??FHHHHGGEGHHGHHHGHHHHHHHHHH @read_150_164/1 TTAGGAAATAATACAGAGAGATCCTGCATGCCTGTTACCTGGTTTCTCCCAGTGATAACATCTTGTAAACTACAATACAATATCAAGATCGGAAGAGCAC + HHHHGEBGGFHGEGFHHGAAEEGHHHHHHHHGGHGHHHFFCBC.E>F9BHHHHHGEFHHHHHGD=FFDEEEC>EHHHHHHHGGEB<6=A>@>ADGFB>5* @read_150_165/1 CCCCATGAGCTAAGAATGGTTTTTACTTTTTTGAATAGTTGATGAAAGTCAAAAGAGAGGGATAATATTTTGTGACATGAGAAAATGATATGAAATTCAG + HHHHHHHHHHHHHHHHHFEEHHHE=BEHHHHHHHHE@916FHHHHHHEEHFEFFFH?HHHHHHFEF=CCC?@6,:GCCDHHGGGHHHGG703:(5(33&( @read_150_166/1 CTTAACAAAAGAGAAAGCACAGCACTTTCTGATCCAAACTGTCTTTTTTTTGTATCTGTTATTTAAAGCCCAGTGGATATTTCAATTAAAAAAAAAATCT + HHHHHHHHHHHHHHHHHHHHFFGF>EHHGGGBFFHFGGGFHHHFHFEBB;GCFHHHHHFBDDDEHHHHHHGD=@?CFFF@BHHH@F @read_150_167/1 TTGATTACTGTAGCATTATAGTAAGACTGGAAGTTGACAAGTGTCAGTACTTCACTTTGTTCTCCACCAATATTGTGTTGGCTATTCTGGGTCTTTTGCC + DBFGGGGFDFFHHHFEGCC>DFHHHHHEEBGGHDCCEBHHHHHEDBEFBEHHHCBCHHHH@FEHEHEDDD7:@C52>?ACGGGHF=GEGH@E@3DA?A>5) @read_150_171/1 CCTTCTAAACAGAATATAAATAAGACCTTAACCAAAAGAGAAAAAGTCTCTCTACTTTCAGAAAAGCTAAAAACTATTCATGTCCCCAAACTTACTATTT + HHHHHHHHHHHHHHHHHHHHGGHH7;EFHFF;EGGGEFH @read_150_174/1 CTCAAATGATATGAAGCAAAATCTGGCATTATAAGAAAGAGATAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCACCTAATCTCGTATGCCGTCTT + HHHHHHHHEFHHGBBGFHHHHFHHHHHHHHHHHF?FAGDFFHHHHHHHHHHHHHHE7>AC7:BFFFEEHHEEEFFFFFFHHHHHHFGHHGHHFHFHHHHH @read_150_175/1 CTAATTTTTCTAGAAAAAAATAGAAAATTTGTCACTGTTATTTACTTGCACTTAAAAATAAAACAAAATATCACTCAAAAGCAATGACTTATGTTTCTTT + GHHHGGHFHHHHGB=DDGFGHHHHHHHHHHHB=4>@HHHHHHC?DGD11<9@HD;GA?;@CABHHHDFHHHHDFEHHHHEEE.8(5>H @read_150_176/1 AGGGAACACAGGGTATTTCAAAAAGCTCCATAAGCAACTAAATTGAGGAGTGAAGAAAAACGGACAAAAATAATGAGATTTTAAAAGGGTCTTTTGCAAA + HHHHHHHHHHHGFBCEHHHHHHHHHHHHHHHEEHHHEEFHHHHHHEHHHHFAHFFHE@A7-/11-+5=GHGEAA @read_150_178/1 CCTTCTGGGACGTCTTTTGAAATCTGGATGGAGGCTGCTAAGAATTCGTAAGGCCCTTGGAACAAGCAAGAAACCCTATGTTGGAATTTGGGGAAAAGAG + HHHHHHHHHHHHHHHHHHHHHHGGGGGGEFHEFGGFGGHHHC=;@F9CEE19DDCDDF?FHHHFCBEGA::/DCDFG===6<>EFHHHHHFHHFBCFGEHHBDBA??@D=BHHHF/)?9>>AD=C4@ @read_150_180/1 AGGCACCTGCCACCACACCTGGCTAATTTTTGTATTTTTAGCAGAGACGGGGTTTCACCATGTTGGCCAGGCTGGTCTCGAACTCCTGACCTCAGGTAAT + HHHHHHHGGGHHHHHHHHHHHHHHHHHHHHEFEAA4FHHHEHHHHHHHHHHHHHFEHEFHHHEFFDDB?;>ACGGEFGDFHHFEHHHHEED67@;*28,B @read_150_181/1 TTGTTTAACAAGCTTATTATGATACTGAAAAAGAATGGTTACCATTAGCAGAAGCAAGAAGAGATGAAGTTTTTATGTAAGTAAAACTTCACCTAACAGA + DGGEEDBGFGGHHHHHHHHHHHHGBEFHGHHFCDEHHFFGDHHFHHHFFFHHHHHFHHHHHHHHFHHEFEFFFC?7)/(187179><@@BFF@C893>3/ @read_150_182/1 GTCTTGAACTCCTGGCCTTAAGTGATCCTCTCCCACCTCGGGCCTCCCATGTTACTGGGATTACAGGTGTGAGCTCGGAAGAGCACACGTCTGAACTCCA + HHHHHHHHHHHHHHHHGGHHHHHEGHHHHHF;=>FHFE @read_150_183/1 AGGTGACTGGTTGCTGAAGAAAGAGTACCAGGTGGAATAGGACAGCAAAGCTATGGTGACAGAATGAAGAGATTGACTTCTTTGCTGCCTTCAGAGAACA + HHHHGHHHHHHHHEBFEHHGGGHHHHHHGGHHEEHHHHDEEAFHHGDEFGEHHHHHHHHHFHEFFEFCFF?2D;DGDD@GGCBF?FEGGGEEGG@ADEGC @read_150_184/1 GTTCTGACTGATCAGAAGCAGCTTCCACTTACCATCAGTGTCACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCACCTAATCTCGTATGCCGTCT + HHHGHHHHGGGHHHGGEEEEGGGDCCFEFFHHHHHHHGG:EFFFHHHHDFHHHHHEDCEHHHDDABDFFGG?CEHHHHHHEFHHGHFHDGFEDBD9EHFC @read_150_185/1 GCTATTGCACATGTGCCGAAGAAGATATTATAAGATTTGCAGAAAAAGCAGTTATGCTTTGGAGATAAGAAAGATCGGAAGAGCACACGTCTGAACTCCA + DDGGHHHHHHFFHHHHGHHHHHHHHEHEEEHGGHHHHHHHHHCDDGDB>CDDFHHEFF=9EGHHBFFDHFHHHFHHHHGFHHFFHHFFHFBEHHHHEFCA @read_150_186/1 GCTTGAGAGGCAGCAATATGATGTATTCTTTTCATAATAACAAATAGGGCATAAATAATAAATTTATTTATTATTTTGTTATGTTTAATAAATACACATT + HHHHHHHHHHHHHHGGBAADGHHHHHHHGHHDGHHHHHHHHHHHHHHHEEDEA305;ADB?FHHGFFFB?A=DDFFHHHHHHF>BEFHHHED097BDBEH @read_150_187/1 GACAAAATGATTCTCATAAACTCCTTTGTGATGTGTGCGTTCAACTCACAGAGTTTAACCTTTCTTTTCATAGAGCAGTTAGGAAACACTCTGTTTGTAA + HHHHHHHHHHHHHHHHGHF@EEEEEEEGGHE.6HGFEEGED4:>DFE<@HEGGHHHHHFEFHHHHD.=@? @read_150_188/1 GGTCCCCAAAAGATCCCCAGACCTGGGTCAGGCACAGAGCTGGTACTCAGGAAATGATTCGTGGATGCTGGATGGGGAGGAGCCGAGCTAGTGTGACCCT + GHHHGGGEFE:5?BEEHHHHGHHFGHHHEDHHHHFFHHHHHH?FFHHG@DFFFHHHFHHHHHFFFFHHGHFFEGB54,2@C47@GG=FEBHFHHHHBFFD @read_150_189/1 AATGGCCATTAGTCATTCTAAGCAGAATCTGCTTCTTCTCTGTAAAATCAGTTGTATCTTGAATGGCCCTTTTCTTAAATCTTCTGGGGCTTTTTACCCT + HGGFGFHHFFHHHHHHHHHFHHHG@HHHG=G?HHHHHHHEGEHHHHHHFFHFEHFHHHHHHHHFFHHHDDF@CCCEEEBBE=HHHGHEACHHEHHHFDHF @read_150_190/1 AAAAAAAAAAAAGACTGGGAATGGTGGCTCACACCCGTAATCCCAGCACTTTGGGAGGCCAAGGGATCACTTGAGGTCAGGAGTTCAAGACCAGCCTGGC + HHHHHHHHHHHHHHHHHGGGGHFH<9@@GFAAHHHHHFHHHHHFFFHHFF7=?>@A-B=<>36EFHFDG=FEEEC?@CEEHEDHHHHHFE?GGFEHHHFF @read_150_191/1 TTTTGCGTTATCTGTTTTATATTTTAGAAGAGTATATTTCACTACATTATCCAGAGGGATTTTGCTCAGAATCTCATTAGTGTGTTTTGAGTCAGATCGG + GGGGGGGFFD=C?<6BBFHHHHHHHHHHHHHHHEGGFCCCHHHHHHHHDDGFHHHHHHHHHEEEHHHHFFHFFHFHHGGGFBHGGCDDB4>C@1817EDCFH@ @read_150_193/1 TTACATTTCCACCAGCAACACATGAGAGTTCCAGTTTCTCTGCATCATCAACACTTGTTATTATCTGCCTTTTTTATTAGAGCCACCCTAGTGGGTGTGA + HHHHHHGG@>CGHHHHEFF8@HHHEBFHGGB?<55BBFHGGFHHHHHFFHHHHHEDD3>CEF @read_150_194/1 AGGGCCGTTCCATCTGAGGTGAAGACAGGCAGGCATTTGTTAGGTTTGCGGGACTGCTGGGTGACATGGTTCAGCTGTGTCCCCACCCAAATCTCATCTT + GGGHHHHHHHHFFGGHEEEEGFHHHH@GG>-79.EFBBGGGGHECFEFHFFFFHHHHHFH @read_150_195/1 TTTGTTTCCTTTGTTTCTTTTTCTGCTTTTCTTCCCCACTGCCTTCCTTTGGATTGTGTTTTTTTTTTTTCTGGTTCAATTAAAACATTTTTTAACCGAT + HHHHHHHHHHHGGGGHHHHHHHHHFDCHHHHHFHHHHHFFHFHHHHHHBDFEHHHDFFEEHHHFFFFFFBEGEHHHHHFFDEGHHHDDFHHHHEFFFFBC @read_150_196/1 ATTTCTTCAGAAGGAGGTTGTCAGCAGTGGGGTGGGGCTGGGAAGAAAGCCACAGTGAGGCAACAGGTGCAGGCATGGAGACCAGAGCAAGCACAGTGTC + HHHHHHGGGGGFFGGGHHHHHHHGHEEE@@GHHHHFHHHHHHHHEHHHHHB=CFEEFFHHFHHHHHFGEHB@:BEBDGGGF>HHEHHHHHHHHHFHHDE, @read_150_197/1 TTCATCTTTTTATTTTATTTATTTATTTATTTTTTAATTTAAGAGTTAGGGTCTCACTGTGTCACCCAGGCTGGAGTGCAGTGGCACAGTCATGGCTCAA + FFFFGGGHHHHHHHHHHHHHHGHHGBFFHFHHHHHFEB@9)4CFGGGGHHHF@DHHHHHHGHHCEGFHFHECB49DEFAFFHHHHDDBBHHHF>EHHFBH @read_150_198/1 CTGCCCAGCAGCAGCTAGGATACAATATTGGTCTCATAGGGTTGAGGGGTGAGCGTGTTATCCACGTGGAGGGTTATCCAACAGAGTGTTTGGCTGGCTG + HHHHHHHHHHHHHGGGHHHHA4E@CD;DDFHHB@BGGFFGHHBEFDDCFHFHHHHHHCB@EEEEEBGHHGD?GHHHHHGEAHFECDDAFFFEFBB2<.CDFFGHHHHHHBHHHCDED=.6:2687?CEBDBGHHBHHHHHGEFHH @read_150_201/1 AATGAAAAATCAAGTAATGAAATTGTCAGCTGCATAGCCAGTAGAAAAGACAAAACCAAAAAGAAGAGAAGGAGGGAAAGAGGGTGGCAAAATGTAATGC + HGFACDEE@?BCGHHHHHHHHHFHHHHHHHGEFEGHFD48./6@FFFDEHHHHHHHFHHHHHHHEFFHHHHHHHHHHHHGHHHFHHHHGFFD/%7?5CBB @read_150_202/1 TCATCATGTTGGCCAAGCTGGTCTCAAACTCCTGACCTAAGGTGATCCACTCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCATGAGCCACTGCACC + HHHHHHHHGGGGFHHHHHHHGEHFHHHHHGHGHHHHHGHHE?DHHFCHHHHHHGHEDC<.9(7:9FHHCCFHH?DFEEEDEFFFHHHHHEGGBFCA:DDC @read_150_203/1 CTATAATTACTCAATATATTGTTACTATTGTTACTTTAAACATATAATTATAGATCAATTAAGAGTAAAAAGATGAAATATTATCATTTACCTTCATTTA + HHHHHHGGGHHHGHHFHHHGGHGHDDDGGBDB@HHFEHHHHHCFFCFFDEFFF;?F;DGFFFHHHDFHEEEHFGFHFDB?B9C @read_150_204/1 CTTTAGAGAAAAAATTGACTAACTTCAGAAAAGATTTTGTAGTTGAATTAAATCTCGTAAACATGAGTAACAGTTATGGCCAGAGAATAGAGTTTATGAG + GEHHHHHHHHHHHGGCGGHHFHHHHHD@FFHEFFGGGC??59>,>DFHHHHHGBHHHEBAB?DC>FHHEE?1772=>@BHHHHHFGGGGHHHEHFFHHHH @read_150_205/1 CTTCCTGGCTAGACCACGTCAGAGGCCACTGGCAAGCCTGTAGCTTCCTGCCGGTTGGCTTAGGTGTTCTGCTGTGGTCCCTCAGCTGGGGTCGCTATGG + EGGGBEHHHHHGHGHHHHGGDFFHHHHHHHGGFAHHHFD8:9EFFHFFFHHHHDDHAFHHEFHHHHDFHHHFFHHHHECEFADBE9+,1;3:8.924:'8 @read_150_206/1 ATCTGTGTAGTTTTAGAACACTGGGAGTAGCCTTTAGAATCGAGAGGAAGAGGCTCCAGTGAGTTATGAAGACAGCATTTTCTTGAAGATCGGAAGAGCA + <=DBGGGGGFDHHHHHHHHFCGHHHHHEEFHHHHFDDEE@HHHHHHHHHHHHHHHE/36GHFBHEHEEFHFFFDADAEDED.EBGHEFEHEFHHFFHHHH @read_150_207/1 AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCACCTAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA + GGFHHHHEHGHHHHHHFEEHHHHHECHHHHHGGFFHHHHHHHHHHDCDFHD?AAD673ADDFHHDFFFFFHHHHHHHHHHFDDBGD>CDCDCHEGHHHHF @read_150_208/1 TAAGCATCTTAAAAGAGAGCAATATTTTAAGAATAAAATATGTTATTTTTAATCATTAGCCATTGTTAACTGCGATGTAATGCAGTTTTGTCAGCCAGGC + HHHHHHHHHGFHHHHHHHHFFGFFHHHHHHHDCBGFHHHFHHHHHHFHHHHHE<+A@FEFBDDFFHHHFHEBDFHHFEDHHHHFFDFHHHFEEHHFGFD? @read_150_209/1 GCTTGGGCTCAGAGGCCTGACACCAGGGAAGGCTTCTGATTGATCCAGCTTGAGTCTAGACTCAAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACC + HHHHHHHHHHHHHHEGGGEHHFFFFHHHHHHGEEFHHHHHHHGHHHHHHFF=5D@>?DFHHHHFFHHHHHGGHHHHHHDGFFHECFDEFGHHHFFHHGHG @read_150_210/1 ACAGTCAAGTCCATGGGACTTTTTTTAATAGCAACTCAGTAAATTTATTGACTTATTTTAAGACTGTAACAATAGAATTGTTTTCATTTTAGCACTTAGT + HHHHHHHHGGDFBFEHHGHHFGGGFGGGGHGGEEDD/EBFEHHHHHHHHHFB?DDFGFHEEHHFGHHE@E3)'9?GGEEDFHHHHHHGG@G=DDE5BBGG @read_150_211/1 TTTATAATTTCTAATATATTTGCCACTACTAAGACCTTCTTCATGTTGCTGTCTAGTGTCCTTCCATTTCAACTTTTTAGCATGCCTTGTAAGAAAAGTC + FDEDDEEFGECD=CFD?FGGHGG??GHFFBG;@CG<9>EIHHHHFHHHHHHHHHACDCEFFHHHEE@BFHHHHEFHHHGGH?@@BHHHHFECCABHHHHH @read_150_212/1 GTCTAAGACACAGACACTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCACCTAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAA + HHHHHHHHHHHHGGHHHHDFHHHHHGFFHGGA<6?GDDAFBGFHEHHFHEADCBHHFFFHFEEHHGHEGGFHFEEFFG@GHHGHGHHHDFHHHFHHHF@F @read_150_213/1 TATGGAAAGCTTCAGGCTCTCAGAATTTGCAGCAGCAGTTCCAACTTGCAGATGGCAATAATTTTAGTAACTGCTGCCACCACTTGGCCCCAGACAATCA + HHDGHHHHHHHHHHHHHHHHHE@<=BE@@>FGC54@DHHHHHHDAA:??9EHFD;7AF-C??+9>BE=DDDEHHHHHHHGGGFCEHFHHF<86CHFHHHFDBCBEHEHHHHHDDADGGBGGBEABDBDFHHHHHGE@C>DF @read_150_215/1 TGATACAGTCTCATATAATTTCCACAATAGTTCCATGGGACAGATTAAATTATTAGCCCAGCCAATGGATGGGAAGGGCAAGTAGGATTTTATTTGCCAA + HHHHDFBEGGHHHHHHHGHGHHHHHHHGHGFHGA5ACE @read_150_216/1 CATAGGTACATACCATCATGCCTGGCTATATTTATTTTATTTTATTAAATTTATTTTTTTTATTTTTGTAGAGAGGAGGTCTTGCTGTGTTGCCCAGGCT + HHHHHHHHE@:CHHHHHHHGHHHHHHHFGHHHHFFFBDFEHHHHHHDHEEEHHHHGGDGHFGD>@HHHHDFC9*>,(, @read_150_218/1 CAAGATTTTTGTCTACTTTGTTAACTGATGTAGCCCCAGAGTCACAGTAGACACTAGAAAAATAATCATTAAATGAAGGGAAAAAAACTCAGTGGTTTAC + CDEECBFFFGHHHHHHHGGDEGHHHGGGHGE?86ADEEEHHHHHCGEB@HHEGHGFHHGDD;;@GE?;<)/-8*11 @read_150_219/1 ATCTCATTTAAAACACAAGGGACAAAAGATACTGTATTACAACTGGGAAGCAGAAAGTTAAAGCTCCTTCAGTATCATCTGAATTAAAACAGAAAGATAG + @FFFGHHHHHFDEGHHGGGFHHHHEHHHG@EGGGFHHHHHBEFGFHEGGGHHFGGHHHHF>>@=>FFHHH;?HBGDGHFHE;'/07. @read_150_225/1 CTAAAGGTAATAAGAGCCATCTATGACAAATCCACAGCCAACATTATACTGAACACAGAAATGTTGAAAGCATTACCCTTGAGAGATCGGAAGAGCACAC + HHHHHHHHHHHHHHHHHDFHHHHHHHGGEFFE5?BEHHHHHHHHHHHFHFHHFDDFFHF>GFHHF@DHFH?EFFFE9ECFHHHHHHHBHHF9*,>CHFGC @read_150_226/1 CCTGAGAGTGGGAGGGAAACTACCGTCATTCTGCTCATGTTTCTTCTTGACCTCTTGCATAATCTTTTTGTTTTCTAGACAGTTCACTAATTGTTGAATT + HHHHHHHHH<=DDFHHHDE?DFDGEDHHHHEDDBBHH:DCFFFHHEFFGDGGHHHHHHHHHFHHDC9@BED??:CFEEEFEEHFDDFFFCC@CFIGFFGH @read_150_227/1 AGAAATTTATGTCCCTGGAAGCAAAATAGGCCTTTGAGTCTTCAGAACCATTTATGTTTCCATCTGAGAGGAAAAATATATGTTCATCTGTCACTTTATA + HHHHHHGHHHHHHFGHHHHHHHHFEGBFEEFFHBHHFHHHHHHHHFHHHHFFEFFHHHHE9CFFFHHHHHHHDFHC@CCCFFFFGHGGFHFBFFHHE<>; @read_150_228/1 AAACGGGAGTTCCTCTGCACATGCGCTCTTGCCTGCTGCCATGTAAGATGTGTCTTGCTTCTCCTTCACCTTCTGCTATGATTGTGAGGCCTCCTCAGCC + GGGFFFGGHHEEHFGGGFFBHHHHHHHFHFGFGHHHHHHHHGHHHHHHFFGHEHHFCCF=>7,5>;4DDEHHFCDDDFFHEHGFGGHHHGHA5.*.(-(A @read_150_229/1 AACTTATGGTAGTTATTTTATTTTTTTGAGACAGGGTCTTCCTCTGTTGCCCAGGCCGGAGTATACTGGTAGGGTCATAGTTCGCTGCAGCTTTATCTCC + GHHHHHHHHHHHHHHHHEFHGGHHF=GGEEHHFGHHHHGHHCEHHEBEFHHHHHG5*;AB479>FFHHHDA;3DDGHHHHHHHHEHDEGHHHHFHHHH?F @read_150_230/1 CAAGAATGGAAACAAGGCCAGAGGATTGAAGTAGCCTGGTGTGTAACAAAGTGATCCTTGAGTTAAGGTCAGTTTCTTGGGAAGACTTGGAGGCTTAAGA + HHHHGEEEFHHHGGHHHHHHGHFGGHHHEBGGGGHHHHHHGHHGCEHHHFFCF<>ADFHFHGGF;FFG?BEEEFGHHHHHHFFFE @read_150_231/1 ATTACCCTATGAGAGAACGAGTAAAAAATATGCATGATGGATAGGGTTCAATTAACTATAGCAACAGACAGAGTTCCTAGTATGAATCAAGATGTTCTAA + GGHHHHHHFHHHHHHHHHHHHHHHFHHHHHHFHGGGGHHEHGHHFGGFFHHHFHFDFHHFHHHHHHHEFEFHHHHHHHHHFHHHHHGGGHEC=DDDHF?B @read_150_232/1 AGTAGCTGAGACTATAGGTGCTTGCCACTATGCCCAGCTAATTTTTGTATTTTTAGTAGAGGCCAGGTTTCACCATGTTGGCCAGAGATCGGAAGAGCAC + HHHHHHHHHHHHHGGGGDGD@AD>;2.5@>EBGGHHEFBGCBBGH@CEEHEHDFEEEECEDFHFHFHHHHEB7:FGGDDDD8E6<><<:>GGB@BBFFHHHFFGHHHEHHDHHHEGGA;?ACCHFFGDFEHEHHHGHFFGG@C:FFEEFFH @read_150_236/1 TCAGTCGAGTTAACTTCAATGAGTGTTTCTCAGTGTTGCACTAGGTGCTATAAGAAACATAGAGAAGTACAATAACATCTCAGCTCTCCAAAGATCGGAA + GHHHGGGGGGCGGDEGGGHHHHHHHHG@DHHDBGFHHHFFHHFF?314?ACFGEB44228B?FF @read_150_238/1 CGTTGCTCCAGCTGAACTGCTCTATGCTGAAGCCCTGCAGGTCTCAAGTGTTTGGTTCAGAGTAATTTCAGGCCATATGAATGCTTTCTTAAGTATCATT + >>CC@BEEFCCEDGGGFFHEDHGEGBBFHHHHGFGFGGGFHHHHHFFFHHC:;?A:=@@ED:ACCEFBBHHHHHFHHHGGGBFEHHHHHHHH?@HHHHEE @read_150_239/1 TGCACTCCCACCTGGAGGACAGAATAAGACCGTGTCTCAAAAAAAAATTAGGCAAACAAATTCACTAATAATTGCCATGTGATCAGTTGAAAAATCCAAA + HHHHHHFHHHHHEDGFCFHGGGDECHHHHGHHGBGFHHHHHF=DEFFE:AD4D>7D6< @read_150_240/1 CTCTTTCACTGCAGTTAATCATTGTGGATGGATGGATCAGTGGATGAATGGATGGATAGATGAATGGATGGATGATTTAAATAAATAGATACTTCTACCA + >AGHHHHHHHHHHGGGHHHHHHHHGDDFHHGHHHHHHFF<>+17<BEECGGGHHFGGFGEEEFEHHFHHHHHHH @read_150_242/1 TAGTCTTAAAACCTTGCAGTTTTGTGGGGTTTTTTTTTTGTTTGTTTTGCTTTACTCTGTCATTTACTTGCAACATGCTGCCTATTATCAAGTTGTGATG + HHHHHHHHHHHHHHHHHGEEHHHHHHHHHHHHHHHGBDCC/BHHHHHHHHFHEBHHHHHFDEGGHHHFEHBBFHFHHEBBA9&+DFFFHHHHHFD+1)3< @read_150_243/1 CTAGCATAGGGGTCAGGACTTTGGGTTCAGTAGTCCAGATGTGTGTTTGAGCTCTTGTCTCCTCCACATGACTGTAGCAAATCACTTAACCTCTTCAAAT + HHHFHHHHHHHHHHHHHHHEHHEGGHHHHHFHHHHHHHHHHFHHHHHHHHHHFEGHEAGEEB7>DH?DHB@ADBEEEE?DHHGE.E=B/99.>EFCH?9;EFFFACCADD@>BGHHEHHHHHHHHHC<@BEFFFHHHHHHHHEFEDEHHHFFGEECEG>>;2>,15ABB>?06):BB@89+3)/*:BHHHEFFDFGHH @read_150_251/1 TGGTCTCGAACTCCTGACCTCAGGTGATCCACTCACCTCAGCCTCCCAAAGTGATGAGATTACAGCCGTGAGCCACTGAGCCCAGCCAAGTTGTAAATAT + FFFHHHHHHHHHEEFGGGGGGHHHHHHHFEHHC?@EDGHHFEHEFHFHBFFBHHFBDFHHF:5:,>>>?AEEGB9F>894??HHFGHHFH @read_150_256/1 TTTTTCTTCATCATGAGGCTAGCTTAAAAACTTTGCATCTGTTTTCATGGACATTAGTTTATTTGAAGGATTAAAACCCTAAAATTGGTCAGGTCTGTTT + GHHFED@EGHE@<>=FHFHHHHHHFGGHHFHHHHFEGGHHH @read_150_257/1 GCTCCTGAAGGAAGCACTAAACATGGAAAGGAACAACAGTACCAGCCACTACAAAAACATGCCAAATTGTAAAGATCATTGATGCTATGAAGAAACTGCA + HHHHHHHHHHHHHHEGGFFEHHHGFHHHHHGFCA,1-(:<6:CFCFE6ADEHHGHGGGG?3;8ADDAC>GFHGDHE@<:/DGGGAEGFHHHHHCFFFHHHHCEF@DHHHHHHHGGHFFDDB1.:5>A=B? @read_150_260/1 GTCAATAAGGGTGCCACTGGCAAATTCGTCATTTAGGATGCTGTATTTTTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCACCTAATCTCGTAT + HHHHHEEHHHHHHHHHHHHHHHHHHHHHHHEEEGGHHHHHHHHHHHHHHBH@EBB1AFHHEFF>CFHHHFGBHBEHHHHHHGGGHGHGFGHHFEFHHDHH @read_150_261/1 TTTCTGAGACTGTGCGTGGATTTAATACGTCACATTTCGATGATTTGAGGGAGATGGTGATGGGTTGGGGAACTGAGGAAAGATCGGAAGAGCACACGTC + D?DDFEEEDCE?DFEHHHHHHGFEDGGEHHHHHHBGFHHHH@<@==9+)8>>?5?CGGHGFHHHGGGDDFHHHH @read_150_264/1 TTCTTTTCTTTTTTTTTTTTGAGACGGAGTTTTGCTCTGTTGCCCAGGCTGGAGTGCAGTGGCGCAATCTCGGCTCACTGCAAGCTCCGCCTCCCGCGTT + F6939DFFGEGHHHEF?=CB@@F@AHHHHGGHHCDHHHDHHHHHHFFHHHEEG><9E9=07FFGFFHFGEAE@CCEHHFEGCEHHGGGBB;>5;BGFHFE @read_150_265/1 AGGCTTGGGCCTTCTCACTCCTTCACCATCTCTTGTGCTGGAATACAGAATTTTGTTCATTATTACTATTATTTTATAGACATGGGGTCTTGTTCTGCTG + HHGHHHGHCDHHHGAAA?GHHHHHHHHHHHHHHHBEFFC?CEFDEEHHHGHHEHHD5:BEEHHBBHHHHFHH?AF@EFGG@=>4=FHEBDEEEDGBGHG6 @read_150_266/1 CCTCCATTTTCTCATCTGTAAATCAAGATAATAGTATTATACTTTCAAGAGCTATTGTGAGCACAAAATGAGTTAATATGAGGATTACATGTATACATAA + D8EEHHHHHHHHHHHHHHHHHHHHEHHFFGHHHGHHHHHHHHHHHHHHHHHHFDDC>HHHHHHDDEFFBEEBHFFGFHHFFFHHHHHHHFGFHHGHHH@B @read_150_267/1 ACTATTGATGGTGGACAAGAATGTTTTCTTGTCAAGAACATACGATTTAGAATGAAAAGATGAGGGTTTGACTTTTATAGCATTGAACAGGTTAACCTCT + GDC>>FGGGEEFFEGBEHHGGGGGHGDDHHHHHCHHFHGGGEFB?@A=??AEHHHFFFEHHHEDFDCBDEHHHHHHA<5>47;@EHHCE @read_150_268/1 GTGCAGAGTCTAAGACAAATAGGGAGGATCAATGACCCTTGGAAGTTCCTTCTAACAAGACAGTAAATATGGTCAAACAGTAGAGCGAAAGAGCAAACCT + HFFEGFHGHHHHHHHGHHHEHDEF<(9>@CFEHHCEDEDBBCFB5BED;*DBBED>6774),%'7 @read_150_269/1 CTCACTGCAACCTCCAGACATGTGTCTGTTCGTGTCGTTTGCCCACTTTCTAATGGAGTCATGTTTTACTTGTTGATTTGAGTTCCTTATAGATGCTGGA + HHHHHHHHHHHHHHHHHHHHHHHHHGHFBFBED9AEEHHHE;@ABFBADACHGF502DBDD@@EFFHHFDHFFHHHHHHHFGGHHBBEEEHHHHHHHHHG @read_150_270/1 CACACTCCTTACCCTCTTTAATAAACTGATGGTTATCTCAACTGGTACAATCTTTCCTTCTTTAATGTACTTTTCAATAAGTTCACCATACTGTGAATCT + HHHHHHHHHHHHEEDGHHHGHHHHHHGHGFHHHGGFFFFHHFFHFBEFCC9?DBBBDFFF9=3=DFFBB>AADFHHHHFEBD?HHHHHHGGGAB?FGBHF @read_150_271/1 GCCACATAACACTTGGCATTTCCAGACTGCTTGACATGTGCTAAGCACGGTGCTGGGGGTAAGGGGATGAGCAACACTGGCAAGGCTCCTGCCTAACCTT + HHHHHHHHHHHHHHHHHGHHHFFFGHFFGFFB<*2CHFHHHHHFHBEDBFHHGDBCC?AFHHHHFHBF<>:F;5=6>DD?D=BDGFEF @read_150_273/1 TTTTCTCTTTTTAAACCCAGGATATCATTTGAATAAAAGAAAGGGTGAAAAAAATGGACAGAAGCTTTCTTTTTTGTATTTATTACTTTTAAAGATCGGA + HHHHHHHHHHHHEEB@@>GFIGHHHHGGEA:1)<3CFBEDDHHHHDHEEBFEHHHFFHHFF??GGHHH @read_150_274/1 GTCTTCCTCCAGGGAACACAAGATGGTGGGGAAACTGTCCACCCTGATCTCACTTTTTCTAGTGTAAAAACTGTGAGATGAGTACGAGAACATTGTCCAC + FGGHHHHHHGHHHGGHHHHHHHHHHBCFFBHHHFFHHFDEFFFHHHHHHHEFGHHHFGGFFFHHHDFFF?H??E=EFFCDEHHHHFCHHHEC@;0.7BD= @read_150_275/1 TTTTGACTAGTATGGGAGAGGATCAGACCACAGGACTCAAGCAACATTTTATTTCTTCATCAAGGAAAGGGCACCGTCTAGTGGCACACACTTCATAACC + HHHEBE@FGFHHHHHHHHHHHHHHHC=EHHHHFGFFGFFFFHHFFHHHFFFHHFHHFHFHHHDDHHHHHHFHFBEHHHHHHGDBABBABE?>BHHFHHHHHHEEBC>DBHFFHHHFHFHGHECDDEEFFFEFHHHFHH@DEHHFBFFGGFHFHHB>F @read_150_277/1 TAGTCATGTAGATTTTAAGTGGTCTGCTTATAACCCTATATTCTCATAACCCTTTTTTTAGTGCATGTTTTTATAGAATATGAGGTTTTTCAGGAACAAA + <=DB>9-7GHHHHHHGFFGGGGD??B/:8D=BGGFGE=FFD<:8CB=FEEEHFGHHHHHBFHBFEG?9>3?DHHHHB@DBFFFHFF9FCDDEDDDHHGHGE<>4>EBEBDG@CFEFFFGH @read_150_279/1 TAGAGTTCTCCAGGGAAACAGAACCAATAAGAGAGATTGGTAAATATTATAAGTAAAAGATATATAGAAATAAACATATAGGGAGATATAGATATATAAA + HHHHHHHHHHHHHHHHHGGHHHHHHHHFFGHFA@<:BEFBHF@75791<9DDDDE2=09EEGGGD@;=CE @read_150_280/1 AGACTCCTATACACTTCAATTTTCCAGCAATCCATAAAATTGAAACATAAAAATAGGATTCTATTTCCCTTGTTCATTCTATATCTTACCAAGATCGGAA + HHDDDA-?HF979>(DB=0>FACDFFHHHHHHHHGB?6>BGHHGFHHFFHF @read_150_281/1 GGTAACAGGGAAGGTGGTGGGAAGTGGTTGGATCCTGAATGTATCTTGAAGGTAGAGCCGATGAGGTTTGCTGATGAGTTGGATGTGGGTGTGAGAGAGA + FBGGHHHHHHHHH9GE@BBD<9::8BHHHGGHHHHDDD?EGG@@EFHHHFAAAABGFHHFGD>=DHHHHHHGGGHHGHHHHHGHHHGHHHHGFECDHHHFEFHHFHF?FFHEAEEHFB@@CFHE?FFFGFEGHHADHFCDGBBGB=DHHHHHHFHHHHHH @read_150_283/1 GAAGGACAGCCAGCCAAGAGAGGAACAGGCCAACTATGTTCAGTCTCTACAGCAAGAAGCACAGGATCTTCCACAGCCAGACTCAACGATTTCATGATGC + GDFBBGEEHEGHHHHHHHHHHHFHHHGGCF@FFGD=FEHHHHHHHHEFHHF9EHFFHHHC@6DFHHHFHHCFFCBHHHHGHHHHFEE7??@A=CFFGDDD @read_150_284/1 TTCCTGGTGCTTCAATTTCCTGTTTGTAAAATGAAGAAGTTGGACAAGATGATATCCAAACATTCTTCTAACTTTCACCTTCTGTGATTGTCTGTGTGGG + GHHHHHHHEGHHHHHHEEFHHHHEBBDDFCFBEF=HHFFHHHHHHHHHHHHHEFGEHHCCHHDDFDEDHFFDC9<@A?DBFGHEHHHHHHEE=<>;DDFG @read_150_285/1 ATGCTAATTAACCAAATTCTGCAAAACAGAGGGTTCAGGAACTAAGCTGATAAAGACTGAATTCTCCTGGAAAGGATATGTGACAGAGGGAGAGAGTATG + HHHHHHGHHHHHHHHHHHHHHHHHFDFFGHHHHHHHHHFFHHDDDADHHGHHHHHHHHFFHHHHGGGHHHD@CEEGHHGEEGHFFEHHHHGB?GHHHBAB @read_150_286/1 TAGTTGAGCGGTTTGGAGTGAGTTTCTTAGTCCTGAGTTCTAGTTTGATTGCACTGTAGTCTGAGAGACAGTTTGTTATAATTTCTGTTCTTTTACATTT + HGGHHHHHHGHHHHHHHHHHHHHHHHHHHHHHHHHHHHFFHHCHHHCCEEHHBHE9DFEE>17(.:=DHH@D?E?FFED?FFFGHHHHHHHHHFFGHGFH @read_150_287/1 CAGACATTGTATTTTTCATCTCTAGAAGTTCAGGCTGGGTCTTCCATGTCTCTGCTTCCATGTTCAAGCTTCCCTTTACCTTCTTGTTGTGGAATGTTAT + HHHHHHHGEHHHHHHGGHHHHHDHHHHHGGHHHHHHFGDBEHFFFHHHHHFDEEEHFFHHEHHHHHHFFHFFFHFHHGGGHFCFBEE6:48*2AEHHFFH @read_150_288/1 CAGCTACTCCGGAGGCTGAGGCAGGAGAACCGCTGGAACCCAAGAGGCGAAAGTTGCAGTGAGCCGAGCTCGCACCACTGCACTCCAGCCTGGGTTACAG + HHHHHHHHHGBBEHFHHHHHHHHHHHHHHHHHHHEHHHHHHHHADCHFHHFHHFBCF;>,;0A3,/6A+E8EED2DEC:,'/.?;;'%*0>E=GEDBH?A:@@@ECC<19ADDFCFGFHFHHHFCDHFHHE5;C=BA88>.*'01;C>DDGHHHGHHHEDEGFGGE452( @read_150_290/1 GATGATCTGTGCAGCAAACCACCATGGCACACGTTTACTTGTGTAACAAACCTGCTCATCCTCCACATGTACCCATGAACTTAAAATAAAAGTTGAAGAA + HHFFGHHHHFGACAFHFHHHHHHHFGGFEFHHH?<5<>@>,32=:>>FHHHHHFHHFFGGEGEEFFDDDFDDDF@GGHHHHHHHHHFE?FGFFEHHFGHF @read_150_291/1 CTAATCCTGCTTTCTTCCTCTTCTCCGTTATAGGGGTCAAATCTACAGGCTCTGTCCACCTTCTCTGGTTTGCTCCGCTTTATCCTCTACTGGTATTTCC + FGGGFGGGFGDGFGGHHHHHHGFHHFGGEHHHHHHHHHHHE6@@)7,:7967>-====FHHHFFF?EFFEDFHHHHHHHFHFFHHEHHHHHEHHHD?4FH @read_150_292/1 TGAGTCTGATTTTGCTGTGGACAATGTTGGGAATAGAACTCTGCGCAGGAGGAGAAAGGTAAAACGCATGGCAGTAGATCTCCCACAGGACATCGCTAAC + FEHHHHHHHHHFFHHGG@DFHHHHHHHG=CCFHHHHHG @read_150_295/1 TGACTTTCTTTTTTCCTCCTAAATAAGGACAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCACCTAATCTCGTATGCCGTCTTCTGCTTGAAGAA + HHHHBD=EEHFHHHHHGF@DHHHFGHHHHHHHBGEADA<339CBEEFFEFHHHHHHHDFFCB9;9BFFHHHHFFBEGHHGGHHHHGHHHGEDC:>A0'7: @read_150_296/1 TAGAGGATTATACTACCCAAGTCTGACTGGGAAGGAGGAGGACCATTCTATTTTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCACCTAATCTCG + HHHHHFHHHHHHHHHHEFFEHHHEEEDDDDBGHHHHHEHHHGHHHBFFFHHFHFEGGHHHHHHHHHHHHHHFFHHHFHHHHHFHHHHHHB5'*=ADFGHH @read_150_297/1 GGCTAGGCCAGTCTGTTTCCACCACATGAACAGGCAGATAGGTTCAAGGGTGCTTGGCAGTATTGTGGGGAATGTAGATTAGAGTCCAGGGGACCTGAGT + DGHHHGHHHHHHHHGHHHEGEGGEGHHHHHHHHHHHF>,4BFFHHHHBCGHHHHFFHFHHHHHHHHFFHHHHHC7:<<-),6EFHHHHHGDBBGB@':>A @read_150_298/1 ACTTCTTGTGCATCCCTTGTTTCCCTGGCTAAGGCTTTCCAAGACTGAAGGCAACACTGTCTTGAGGCACAAGAATCCAATGTTTCTTGGTAGGAGCGGG + HHHHHFGGGHHHHHHHHHEDHHHHHEED@>76D4=FFBGFHHHHFGGFFFHHFDDEBFFDDGFFGH?@CB>>+BEHHHHEEHHHHHHFE<7@DBBA:*0; @read_150_299/1 GGATCACCTGAGGTCAGGAGTTCGAGACCAGCCTGACCAACATGGAGAAACCCGTCTCTACTAAAAATACAAAATTAGCTGGGCGTGGTGGCGCATGCCT + EEE?@BGGGGGGGEBDGHH@AEGHHCC>?4@FEFGHECFBDB>5??DB?@EHHHGHHHHB@;B?;?39:ADFGGGGHHHHHC>E?DEHHHFH5(*:BHHGGHHHHHH @read_150_302/1 GAGAGGTAGAGTCTCAGTCCTGTACTACAGAGATGAAAACACTGCAGTCAGATAGGCTAGTAACGTTCTGTGTCCTCATCACTTTTGTCAAGAGATAACT + HHHFFFHHHHGGFHHHHHHHHHHHHHHHHHHHBFHHHHHHHHHHHHHHHCEHG@BGDBA>EGEEFHHEHFHHFHFGEGGGHHHHHGHHGGGGE?G/><*4 @read_150_303/1 GGGCCCATCATTCTCCAGGGGAGATGGCTCTTCCTATACAGAGTCAAGGACCTCTGGAAACACAATATTCAGAGTTAATATATTCCACAAATACTTATCA + HHHHHHEEEFEF982<@G?CBGFGH?DCFEGFDBFEFEEFC??=GHBHFFHHHFHHHHHHCCBBC@:>DHGFHGFGFGEHHHEEHHHFHFFHHFFDBF=< @read_150_304/1 TCCATGGGGGATTGGTTCTAGGGTCTTCTATGAATACCAAAATTCATGGATGCTCATGCTACTTATATAAAATGGCAGAGTATTTTATATGGCTTCTGTA + HHHHHGGGEGHHHHHHHHFFGGFHHHBHEHEDEBEDHHHHFHHHHHHHHHEBDBGFFCA@BEEFGB6CCDFDBD?C88GGFFHHHHHG=6>BD70)&8C> @read_150_305/1 CAAGAATAATGTGCCCAGCAAAGCTATTAAAACAAGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCACCTAATCTCGTATGCCGTCTTCTGCTTG + FHHHGGBEGBDEHHHHHHEHGGGFFHFGEGHHHHD,::=AFHHHHHBHFHHHGGEFFHHFFHED?DHFHHHDFEFHHHHHHEEHFED65@CC;:ADHFC?D;:;>?FEHFF @read_150_307/1 GGCCCTGACGTCACGCACGGTCACGTGGCCCCGCCTCCCGCTGGATCTTTAAGTAGAAAGTAATCTATCAGGCCAGTCCTTAAAACGGGACTTTCGACTA + HHHHHGHHHHFGGHHHFHHHHFHHHHEDGD0==GD7;?FFHHHHFHHFDFHFHHHEDDHHHFFFF7DDGG<:> @read_150_311/1 GAAGGGTGATTATTAAAAAGTCAAATAAGGCCAAGTGCAGTGGCTCATATCTCTAATCCCAGCACTTTGGGAGGCCGGGGCAGGCGGATCACCTGAGGTC + HHHHHHFF=CEGHHHHGGFDHHHHHGGFHGAEBFGHHHHHHHBHHDE?GBFDBGHHHFFFEEEECHFEHHHHAAHHHEFE,>7BAE5@38,/@CFFHDDA @read_150_312/1 CGTGTGTCACCAGGCCCAGCTAATTTTTGTATTTTTAATAAAGACGGGGTTTCATCATGTTGGCCAGGGTGGTCTCGATCTCTTAGATCGGAAGAGCACA + HHHHHHHHHHHHHHGEGFGGHCGGECBEEEE@/D?HHHHHHHHHHHGFHHHEHFFHHGEDDEDHFCFFDCDBA>;EEEEF@>5:?GHFHHHHHHHHHFH< @read_150_313/1 TCAGGCTATGCTAATTACTGTCATAGATTCTGCAGCAGCCCATTAAATATACAAATTACAGAATTAAAGAGCCAGAGCTCTTCATGATTAATCTCTAAAT + HHHHHHHHHHHHFBCCB@7=DDDHHFGHHHHHHHHHHHHHHHHHHHHFGGG@EHHFHHHFHHFHHFGFHHHHHEDHGH=8@9ADHHHGGGHHHHHHHHGB @read_150_314/1 TAATGTTCTGTATCTTGACTGTATTAACATTGATATTCTGTTTGTGATGTTGAATTATAGTTCTGCAAGATGTTACCTTTGGGGAAAATCAGGTAAAGAG + HHHHFFEEEFFCFFFFHHHHHHHFBGBAEHHHHDDGEEFHGCFCGGF>>@D@EFHFFFFFGHHHDGEDDDDEFHHHHFGADDGHHHHHHHFFFHF@DDBG @read_150_315/1 CCATGACTCCAGACTTGCTTTGACACCTTGCACACCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCACCTAATCTCGTATGCCGTCTTCTGCTTG + HHHHHHHHHHHHHHHHHHHHGGGGGFCGHHHHDE6B@9<8C?AA8<1B>B247E>@A>CFFFFDDH?:FHHHHHHHHHHHHHHHHEDHHHHHHFCHHHHFEDBA.;@ACFGHGHHHHFF00>BE16.%)3((5 @read_150_319/1 GTGTGTGTGTCTGTGAATCTTTAATTAATCTCTTGAGTCCTTTTTGAGAAAGAAACCCTGTCTCATTCAAGTTTGTTCCCCAGGGCCTGACATAAAACTG + HHHHHHHEEGGFHHHHHHHHHGHHHGGHHCHHHHHHHHHHHHHFGBDDFHHHHHHHFFFEHHCHGFFHHHF:CHEDDADDGEEBADD?489.159HHHFF @read_150_320/1 GCTGAACTCGTACTCTCTAGCTGAGCACATAACTTGGGTGAGCCTCAGTTTAGATCGGGAGAGCACACGTCTGAACTCCAGTCACCACCCAATCTCGTAT + GGGGHHHHHHGGGGGHHHHBEEHHHHHHHHHHHHFEGGGFHHHHHHHHBDFHHADE72)0??DDEHHHEF?@6:FFFBBHHFD>>D;GFHFBFGHHHDE@DDGHHFHEEFEFEHHHHFHHHHF?DFHHE=DC@?EC9>CHGEA@FDBB?ADGGB@EFFB @read_150_322/1 AGAAGAACCTATGTGAGCAGCCCTCTCGCCTGTTCTTGAACGCCTGTGCTTGGTTACATAACATTGGCAAGGATTGCTCAAACTGGCAAGAGGCAGGATG + GFDDFGGHEHHHHHGHHHHBFFHHHHHGF9GHHHHHFHHHHHFHFHHHHGHEEHF?7;@E9DD>HGHHFHFFFFDHGHHHHGFHH><8;-0?E@DEEEFF @read_150_323/1 TACCTATTTACATTTTGATATCTGCATTTTACCAATAATTTTTAAGGCTGTTTTTATTTCTCAAAGATTAAAGTCATGTGAACTAAAAGGGACCGCAGCT + HHHHHHHHHHHHHHHHHHHHGGGHHGFFHHHHHFBHHFGE?EFEFHHFFFBFHFHHHFFHFHDFEHFHHFFDHHHFBFHHHHGHHDGGGA'2,-%,27:: @read_150_324/1 CATTTTTCTCCTATGTTTTCTTAGGAAAATTGCCAAATTATCTAATCTGCCTTTTGTTTGTAGGTAGGGAAAATTACATGACTTTTTTTCACTTTCAAAA + HHGHHGFCBCBEH?FGDCBFGHHHHHHHHHHHHHEHHHHFHHHHHHHFEGHHHC.1;BBCFDBGFHFHFFHHHHHHG@>DEDCDFHHHHEFFHFEHHHFF @read_150_325/1 GAGGCTACTCTCATATGGCAGCAAAAACCCTGGGGTTCTCATCCAGGCCTCTCAACACACTGGTGGTTGGGAAACTGCTATATAGTATGATTCTTTGTCT + HHHHHHHHHHHHHHHHHHHHHDF;@FFHHE?ABHFHHHEBGE??CA9A=DHHHA?HB?=FHHBEGGD4 @read_150_330/1 CCAGGCCAACTGGCTTCCTTTAAAGTCATGATCTCCAGCCATTAAATGTCTTCATTCCTCACAGAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACC + HHHHHHHHDDFDEGGGGGG=DAGHHHHHHHHHHHHHHHHHHFHHHHEGGHHHHHCGDEE=HHHHHFFHFGDFFFFGHHFGGHHHECGGGDGG@ACHFHHH @read_150_331/1 GTGGTACCAAACACAGCAACAGCCTCCACATCTTTTAAGGCATTACACACTTGAACTCCACAAGTCTAGGAGACAATCAATAATAGATAATTATTATCCT + HGGFEHHHHHHHHHGGHHHHHGGHHGHHHHGCGGFHHF>FHDFEEFEHFHHHHHHHHHHHH@???FHFF?=?<649781)<9?FEDDCHHHHFHHHHHHH @read_150_332/1 AGGCCTCAAAGAGGTCTGAATATCCACTTGCAGACTTTACAAACAGAGTGTTTCCTAACTGCTCTATGAAAAGAAAGGTTAAACTCTGTGAGTTGAACGC + GGGEDCFFFFB;GGHGGHHHHHHHHHHHHHHHGHHEHHGCCFFF<.BDEBHHHEEGHHHHEAB>CCCCFHHE9FHGGHHHHGEGEC>>DDDHH;<9DBHHFHHFCHHHHHHHHHFEFHHFHHBFCHHHHFHEFHHHB8?FC@@DFHHGHHHHHHF46( @read_150_335/1 ATTAGAATATAAGCTCCATGAAGGCAAGAACTTTTTGTTATCTGCTATATTCCAGTGCCTAGCACAGTGCCTGGAACATGGGAGGCACACTGTAAATATC + GGGGGGHHHHHHHHHGG5@EGGGFECAGGGHHHHHHEFHHHHHFDFBEBDHHGFCDCGGGGHHEDC>-%3B933DEEBFDGEEEGG@DDGDHHHGFFHHH @read_150_336/1 GAAAGACTTTACCATCTAGGTTCGATAGCTGGGTCTAGGAAATACACTGACAATACACAGATTTAACAGGAAAAAGGGTAAACAAATTTATTAATTTTTA + F@@GGEGGHHHHHHGHHHHHHHHHHHGHHHHHHGDHHHEHHHFFD;=-*B?DEEFEGECHEEEFHHHHHHHHHFFFD40?ADFGGFHHHHHHHHHHHHH? @read_150_337/1 CCTCTGATCAGACAGGTGTGGCATCAAATCCTGGCCCAGACACAAAAGCTGTTTGACTTTGGACAACATACTTAATCTCCCTGAGCCTGGGACTCTTCTA + GGGHHHHHHHHHHHFFFHHHHHGHHHHHHHGG9;47DDGHHHHHFBFBBBEFEHHHHHHFBGFFHHHHFF@>CDAABB@CGHEFHHCDHEGGG=ACEHFHHGBCHEGHFHHHHHFHHHHEEFFEEEFD8EEG@CEHHHCCFGFDEEHHHHH @read_150_342/1 CGCCCGGAGGCTGGCCTGGGGTCTGACATCAACGACACAGGCGGGGAGTGGAAGTCCTTCCGCACAACATGGTGTGGGGCTGCGGGGGTGTGGACGCGCC + HHHHHHHHHHHHHGGGFFHHHHHHHHDFFGHHHHHHHHHHGBHHHFGGHFHHHHHHHHHEEEBC;E?HHBAEBFFGEFHHHHHHECHHHHHHHGGHBGEH @read_150_343/1 AAAGAGCAAGAGAACTAGAATGAGAAGCAGAGCCTAGGCCAGGCATGATGGCTCATGCCTGTAATCCCAGTACTTTTGGAGGCCAAGGTGGGGGGATCAC + HHHHHHHHHHHHHHFFF<DADFFHFDBGHHHHCBA9BCBEB39FCAEACDHHHHFBEFHHHHH @read_150_347/1 TAATTAGTGGAGACAGCTACCAGGGATCAGATGCTAACTACTGATTCAGTAGACTATTGAAAGTAAATTAATACAAGTATCTACCATTCACAGAAGAAAG + HHHHHHHHHD=@FHHHHGFHGGHHHDBFF?HHFFEEFHHHHHFHHHHHHHFFHFGGHCHHHHHHHHHHHH??DFEFEECDHFFHHHHHHD9FFFHHFBGF @read_150_348/1 ACCAAGAAAATATCTTCATTTTTTTTCCTTTCTCCTTTATCATGTGACATAAGATTTATTGACTTCACATTAGCATTTAAGTATCGTTAACTTTATGTAT + @C@DDEE>>?ECD:;GHHHHHHHHFHFFFFFEGGGHHHHHHHECHHHHHFFFHH@FFHHDFB?FHHFFCAACA?DGHHHHHHFHHHFGGGEFHEHCED;4 @read_150_349/1 AATTACTACCCAACTATTTCAGCCTTGATTTCACCTTTGTGGTTTGCATTCAGGTTGCACCCACTGGCCACTTTGTCTCCATAGAATCCTTGACCATCCA + HHHHHHHHE=@HHHHHHHHHE=BHHGFGBGHHH@AFFGGEGGGHHHCFEHF3?E>EDDFDHHHHFFDBBBEEDCEBEFFG=4:6:6@:'DHGHHFH @read_150_350/1 AAGTTTGAGGTGGCAATGAATACTGAGGTAGGAATTTCCAGTAAGTAGAATAGAAATGTCTGGAGTTTTTTTTAGCTAAGAGTGGAATTGAGATAACTAT + HHHHHHHHHHHHHHHHHHHHHHCHHHHGFFHHEHHHBFGE@=HDHHG?A9DDEGHHHHGHHFEECCBF9FFHHHHEDDDBBFFFHHDEFFFHHFDHE?.E @read_150_351/1 AATGATGGGATAGTAGAATTTTCTAAGAGATTAATAAAACACAAAAACAGCCTTTGAAACTTAGCTGTGACCCCAATTGCATCCCTTTATGAATCACAAA + HGFEGHHHHHGHHHHGHHFGFGGGDGE>@@GGGHHHHHHHHHHHHHHHHHHHHHHHHHHHFHFHHHHCD=AGGAFFGHHHGGHHGHHFFFCEH>9FGGD: @read_150_352/1 GTTCTCAACTCTGGCCGCACATTCGCCTCACGTAGGAAGATTTTTACTTACTTATTTATTAATTAATTTTTTTTTTTGAGACAGAGTCTCGCTCTGTCAC + HHHHHHHHHHFBGHHHHHHHHGHHHHGGG=9@CA@DHHHHH@CHHHHHHHGFHHHHHHHBFGG>EEFHHHHCDGHGFHEEDHHHHHHHHHGBHBF68*?EBDDECFCBF @read_150_355/1 CTACAATTGTGGTTTTGTAAGAAAAACAGTCTTAAAGATTTCCAATAATTCCCACAATGGCCATAAATTATCCTGGGTGTCATTTTCCCATCAATTTAAA + HHHHHHEDFHGGHHHHHHHHGEFGHHHHHGFGEDDBEFGFGF@DGGGGHHHHHFF=D?GDFHHHGHHEGE.4=A@AA79>FHHGE?FHD/,23;7@GGFF @read_150_356/1 ACCCCTAAGGTAGAAATAAGCTTAGTGTGTTTGAGGAAGAAAATGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCACCTAATCTCGTATGCCGTC + HHHHHHHHHHHC><);,:4??FHHHEHFDBD<8DEHCFHEEHFFEFD8GGDDHHHHFB@DHCEEHFEAHEBCGGGGGGGGCCFHHGGE,705BDFGH @read_150_357/1 TTCTAGGGCTTAATTTACTGTTTTAAATAAAATAAACATAAATAGAAGCTTCACTATTTTCCTTTCACATGCCAACAGATCACCTTGTGCAGTCACTGGG + HHGGGGGE@:BHHHHHHHHHHHHHHGGGHHHHHHHHHHHFHHHHHHHHHHHHHFHFHHBE>AGEFHHHDGADHHFHHEFGHHHHHHHHGGB78>=@DFDA @read_150_358/1 AGCCCTAGCCTCATAACCACCTGGGGTGAGGACCCTGACATGGTGACCAGAGCCAAAGAGAATCCAGGAAAGATTTCTCTGATATGAGAATGAAGGTGAT + GBCCGEHHHHHHHHH89EHEEGGG;@>??AGEEGGFHCDFFB/BCCDBEBEHHHHHHHDHHHHHHGDE@AHHHFEHHHGGHGEEDHHHHHHG52?9AA=; @read_150_359/1 ACCAGTTAAACGTAAGTGTTTCTCTGAGTTCCTTGCGCCACTCTAGCAAATCAATGGACTTCAAAGAGAGGATCGTAGGAATCCCAACTTGAAGTCAGTT + HHHHHHHHHHHGDHHHHGGGHHHHHHHHHHHHB4)'&*7110) @read_150_360/1 CAGGCTGCCAGGCCAACCGGGGAGAGGGAGGCTAAACCTGGAGCATCTCATGAATAGGCCTAGGATATCCCTGCTGCCTGGGCCCCTCCCGGGATGACCA + HHHHHHHFHHHGFGHHHHEEHHHHHEFGE>>BGF;FFHHHHFDFHHHHGDFEDEEGGGGHGGFCEHFFDEFFCFFFCFFBBEB3E8*8>FDB=EAFHHFF @read_150_361/1 AGAAGACTATGAGACACTAAGAGAAAAATTAAGGTAAAAAAGACACACACTTAGAAAAACACACATAAGGAGGAGGGAGGAGGTTAAGACATTTTACTAT + HHHGBBHHHHHHEEHHAFHHHHHHHHFGHHHHHHHHGHHHHHHHEHHEHFC?HHFHBEBHHFC<6))60AEA5AEFFC59>>AC/--7DDHGGHHHHHGE @read_150_362/1 TTGCAGCAAATATGGAAAACTGTTGTCCTCTTATAACATAAAATTTATCTTATAACAAGAAAAAAAACACCAATGCACCAAAAAATAAGCAGAGGACAAG + FFD@GGEF@GGGGHHHHHHHHHHHHGHGDBE=@DHHHHHGGHEGHHHHFHHHHFFHHHHD+)4,;DHHFFEEA5FGHHHEBFHHHHHF@@@*39BCC4>= @read_150_363/1 GAGAGGTGTTTGGGACATGGGGTAGACCCCTCATGAGTGGCTTGGTGCCCTCTCGTGATAATGAGAGAGTTCCTGTTATGGTAGTTCATATGAGAGCTAG + GGHHHHHGHHHHHHHHA5.E? @read_150_364/1 ATTCTGAGCTCCTGGGGTTAGGGCTTCGCCTGTGAATTTGAGGGGACCCAGTGCCCTTCCTCGAAATGTCGTGTTGACTGGCAGTGGCTCTTTGTTCCGG + HHHHHHHECCGEGHGHHHHHHHHHHHHHGFHFFFFHHHHHHHHGFHHHHHHHHDFHHHFHHHHHHHFFDHEFEBFFFHHA=@8DC3::B@BFHHHHDDCFHHHFHHHHHFHCHDFHHHHHEHHDCC@HHHHEHDHHHFEBA6)8=53-21(A @read_150_367/1 TTATCTATTGCACCTTTGCATTCACTCTTTTCACTTAGTTATAAGTCTTTTTAATTTGCCTAAAGTGTGAGGATCTCTCCTTACCTGTAGGCTACTAATC + HHGGGFHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHFGGEEFFFCFEEF9DGHFFHCHFDCFEEGEFFFCFCDDDHHHHHHFBF/DGHF?FFGBF?E?DE @read_150_368/1 AAATGCCCCCAGGGATGGAAGTTTACTGCCTCACAAGGCAGCCAATTATCTTTCTGACAGGTGCCATTCTTCCTAATACTGAGGTAAAGTACATTGTTCT + HHHHHHHHGHHHHHEGHHCB@@CHHHHEHHHHHHHHHHHHGCFHFFDEGGHF::)6'%1;ABD=6;F @read_150_371/1 CCACATTCCCTTGGTGGCAAGTCAATTGCGGGGACGCCTGCTTTGGCTGCTCACTCACATTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCACCT + DCDDDBDECHHHHHHHHHEHHHHHFHHHGGDGGHHHHHHGGEDDDGBCFF:9?ADHHEEBEEFFHAEFEEFHHCDGFHHFFFFFEFFDDHHHHHHHHHFH @read_150_372/1 AAAAAAAAAATAGGTATGGGCAAGATGACTCTAGGAGATTAGAAAAAATATTTTTGGCTGGGTTCAGTGGCTCACACCTGTAGATCGGAAGAGCACACGT + GGGGGEECCHHHHHHHFHHHHHF=DFFHHHHHHHHHHHHHHHHHHBFCBFHHHHHHHFFFGDAA9CEHDDEEBEFHHHED8EEE9FHHDFFC4@C@-1D9 @read_150_373/1 TTTAAGACCAGCCCTACTTAACTTTTAGGTACCTACTCTGATTTTCTGACTTATGTTTTAACAGATTGTTCCAGAGCTTATTTAAATGTAAAGAAGAGAA + HHHHHHHFFFHHHHHHHHHHFFECCGGGHHHHHHHEHHHHHHG>HHHEEEHEGHEFHHHEECEEBFHHHFCCEBBGGGFFHHHHGFEEBF4*..>FFHHH @read_150_374/1 CTCTTAACATAGACTAATTTATCAATGATCCTATTAAATATTAATAGGTACTAATTTTAGATCCATGTTTACAGACGAGAAAATGGTACTAATTTAGATC + 98DDBGHHHHHHHHHGHHHHHHHHHHH30CBGGHHFHHHFEHHHHFFEFHF;5<:(?49AA@BEBCE @read_150_375/1 TCATTGTACACCTTAACTGTATACATTTTTTATTAAAAAATAACAGAACAGTAACATGTGAGGTTGTGGCTGTTATTATCATTAGTTGTAGTAATAGCAG + GEGGGHGGB>HGHHHHHHHFGHHG9DBEHHFHHHFHHHHHHHHFGBHHHHHHHHHFDEB::*HGEDHHHHAFHHHEHHHHHHHFGFCHHHHHHHHHHHD6CEFFFEHHHF @read_150_379/1 AGACCTAAAGTGTATGGGGTTCTATGTGAGCTGATAAAAATGCTCTAAATTTGACTTTGTTGATGGTGGCATAGATCGGAAGAGCACACGTCTGAACTCC + HHHHHHHHHHHHHEBEGHHHHHHHHBGHHHHHHFDFHHHHHHFFEEGG?=@CCF??GEDFHEHHHFHC?4/>71?HGGGD5C5BFFCHHHE>DDEGGFFH @read_150_380/1 CGAGAGCAGCCCTTTTAAGTGTAAGGCAGTGCACATCCACAATCTAAGGTTCGTTCTTTCTGTAAGCATTAAACAAGACCATCTGTGTACCAGGCCAGTG + 8FFGGGGGGGHHHHHHHHHHHHHHHHHHHHHHGFHHHHHHHHHHHHHHGGHHHEFFGHHEE=E?FEFCHFDDE;.0.+%'::GGHHHHGHBGDB?HHGHH @read_150_381/1 CAAATAGCCAGAAAATGGCACTTTGAATTTTTCCATCCTGCAAGATCTAAATAATTCTCGTAAAATAGGCAAACGGTCTGAGGTGCCTGACATCCAGGCA + GFCFEGHHHHGHHHHHHHHHHHHFHHHHHHGGGDDEGHHFHHHHHFHHHH=CHHHHHHHHHHHHHEED?HEG><>><=A@DD;;>EBDADFGCHB=BDGFDEEGGFFEBGFHHHHGGBHHF??HHHHHHFHHHHH?DEDBEEBA?DHHHHHHHFFHHEEHHHA>: @read_150_383/1 GTGCCTCAGCCTCCCAAGTAGCTGGAATTACAGGCAGACGCCAACACGCCCGTCTAATTTTTGTATTTTTAGTAGAGATGGGGTTTCACCATGTTGGCCA + FFFFFFHHHHHHHHHHHHGHHHHFFEFEFC767;EHHHHHHBGGGEDFEHHHF?=4646>BEBCBE9DC?AA@FFHGGGGFFFF=:D>9DEFF?BEB;52 @read_150_384/1 AGGTTAACTGTTATCTGAACTCCGAGTTACAAAATGATGAAGATTAGTTTTGTTAAAGATTCTGACTGTGAAATCATCAGGAAATATATTTGTAATAGGC + GEFHHHHGHHHHHECFHHHHHHHHHHHECGDFFGGHHHHHHFFECGGFHHHDFHHHHHHHHH>@F9?<->GGGHHHGEGFEEHHBDEG @read_150_386/1 CTTTCTTTAAAATGTATATAGATATTACTTTTAAATAGCATGCCGTTTTGTTTAGTGGATGCTTTCTCTGGCCAGAAGCAAAAGAAAAGAAAAGAAAAGC + HGHHHHHHHHHHHHHHFHGFHHHHHHHGGHHHHHHHHHHHHEEA646BCDFGGG=CDA??HHHHHHHHHEHHFEAG @read_150_387/1 CCCAAAACTAAGTTCGCTTCATGTCTCTCATGACAGGGAGGAAACTTAGTGTTCCTTGGAGACCTGAAGGGATGCAGTGAGCTTAAGAATTTTCAAGAGC + HHHHHHHHHHHHHH@:@EGGGHHBGF@*>CBCGBEHHHFFD@DGHEE<>EFHHHEEDDFEHHHHHE16,::1)2%&85 @read_150_389/1 ACCAGTCCCAAAAATGTTTTTTAGGAATAAAGTACCCAGTTTCCAGTGATGTTGTAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCACCTAATCT + HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHFFEEBDDD>GHHHHHDFHHHHHHHHHFHEACEEHHHHHDEEBFFHHHHHHHFFHHEFHFFBFFDHGEEE9 @read_150_390/1 AGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAAAAGAAAATGGCTGTAGCAGTTCTAGGTCTCACATCTATGTACCACACCATTCA + HFHHHHHHHHHGGGHHHHHHHHHHGHHFG@@5;4;BGGEAB?FEHBHHHED?BFHHHHF<(0?FF===<@DEEBHHHHHFFCFFDBEECCEEHHHHHHHHHHHFE?FF95:;0+5 @read_150_396/1 TCCTTCAGACTTCTGAACTTTTGCATTTGCCGTGTCCTGTGCTGGAAATGCCCTTTTTACCTCTTGACTGGGGGTGGGGGAGGTCTTGTTCATTTAAGTT + HHHHHHBDFF@DGGGHHHHHHHHHHHHHHHGFHDGGGFFD>7@EDHHHHHHHHFFHHBFDDDAD=B=3GDEHHFGFFGGGHHGHHHHEFHHHHHHHHHHG @read_150_397/1 TACCTGGGTTACACAGTTTCCTGCTCTTGGATTCACCAAAATTCATTTAATGCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGACCTAATCTCGT + GGHHHHHHHHHHHE=DFEEE@DFHHHGDDGHHHEEGFFDFHHFGB8EFHHEHHHHHHBAC=;=BCC>EEBDBFEHGGEDHHDEEC>1(8GEFHHHHHHHH @read_150_398/1 GGACACTTCTATCAATCAGGTTTCCATCAGGTTTCTTGCAAATGGCCGCTGCTCTCTGTCCACCTTTAACTGTGAACTTTTCCAGGACAGGGACTGTATC + HHHHHHHHHHHHHGHHHHHHGGGGHHHHHHHHGHEHHHFFHHHHHHFGHGGDDFFFFHHHHFBGCGEHDAEHHE6*3?:>EBHHHFEEFEEEFB:FHHHHBGC?GGHHH::F@F @read_150_400/1 TAAAGCAACCACGCCGTGCAACCTATGTAAACTTGTTCCTCCTGTGGGCCTCAGTTTCTCCCTGTAAAGTGAGCAGCTATGCCAGCCATGCTTCACCTTG + EEBFGHHHDFC8ECEBFHFHHHHHHHHHHHHFCBFHHHHHHHHHHHHHHHHHHHHHGCCHFHHHEHF>086848:>E7%(5.BF @read_150_404/1 ACAATAAACTCAAACAAATTTACAAGAAAAAAACAACCCCATCAAAAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCACCTAATCTCGTATGCCG + GHHHHHHEHHEEDD8FFHHHGHGGHHHHFHHHHHGDHHHFGGFFCEHFEFEHHGHFHHFHHHCCBFFHHHFCHHFGGHCGEHF?DDFF4CFHHHHGFHHHHHFHHHHE;+/-9EHHHFHFBDGGBEFHHFBDF?==BHHHHHDFDEE @read_150_407/1 AGTTGAGATAAAAGCCTTTCTGGTGACCTCTAACCCCCTGGTCTGGCAGCTGGTTTCAGCTTATAATTGCTGAGAAGGTAAAGGTGTTCTAGGATAGTAT + DCDDDHHHHHHHHFGGBEHHHHGBGEEEEEHHHHGHHHHHHHHHGGCAAFFECDF:EGGHEHHH@@EBGHHFHHHHHHG4DHHBDFFFHHHHFCDAAFC4CBEEEFFC@HHHHHHHHHHHGFHFHHHHHECCBEB @read_150_409/1 GCATGAGATGTCCTGGTGTTCAGGGAACACAGTTAAACAAAAGTGTGATGCTGCTGTGGGAAAGCCTGCCCCAGGACACCACCATACCATGCTGTCTTCA + FGFBEGHHHHHGHHHGGHHHGFFGHHFBFHHH?;;DDB.EFHHHHHHHHHHFGHEFFDEFECEBEHHCDB?HHFHHHHHHHHHHHHHDFHHFB596 @read_150_410/1 TGCCCAGCCCTTGGTACACCACTGAGCCCTGGCACCTAAAATAGTGGCTACTCATAGCAAGCACTCAGTATCTGCAGAATGAACCAATAGATCAGATGGG + HHGFBDEDHHGHHHHHHHHGE=AADBEDDGIGHHHHHHHHHHFF?;=>EFHFCDFHHHHFHHFFHHHFFFAAEEFHGHCDD5A9DEADHF24/;@GE8.2 @read_150_411/1 GCATCTAAAATTTCTGAAGAACAGCAGTGTGTTATGTCTCTGAGTTCTAACAACAGACCATTAACCTACTCCGTACCGAGGGAGATCGGAAGAGCACACG + HHHHGGEFFFFGGHHHHHHHHHHHHHHEBFGGHG?HHHHHHDHHEGGGGGFDDGHFDA???FECBFFD4@A9%3/:A@F?DGGEBDFCFHHHHHHDD@,; @read_150_412/1 GATGTAAAGTGAAAAATTAGAAGTACATTTAAGAGTGACATATGAGAAAATCATTAAATAATGCAGAAAGGGGTAATTAAGATTCATACCAAGATGAACG + D7036@DBEGGGGFHHHHHHGFFDD-*:5B@FHGHHHHHFHFHHHHFFEFEHHHHHHHFE=AD@?.4CDD<-/539BCDDEEEHH=5A5''0,8=DFHHH @read_150_413/1 ACTGGAAGCATTCCCTTTGAAAACTGGCACAAGACAGGGATGCCCTCTCTCACCACTCTTATTCAACATAGTGTTGGAAGTTCTGGCCAGGGCAATCAGA + HHHFFGA>>8BFHHGHHHHHHGFHHHHHHHHHHHHHHHHHHHHHHFFHHGHHG@EEDDHHHFFFHHGGHHFHFHFHGGA9=<=@E@?EE.CCCEFDEGFF @read_150_414/1 ACGTGTATGTGTAAGGGCTATCACGTAGATTGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCACCTAATCTCGTATGCCGTCTTCTGCTTGAAAA + CDEEFB27DD@CDFGHHHHHHHHHHHHHHHHHGHHHHHGDDHHHEBFEFGGHHHHHFFHHHHHHHFHHHHHHEE@FGGFHHHHHHHHHHHHHHDC/,7/< @read_150_415/1 CAAATGAGACCAGACTGCAAAATGAGTTTATGTTCCAAGACTCATTCATTTATTTTTGGGTTTCAATCAAGATCGGAAGAGCACACGTCTGAACTCCAGT + HHHHHHHHHHHHHHHFHHHEEFC;D65666FDHHHE?<'@>?CFHHGGGGFHHHFBEHEFGG?GFHHFHEBBFFFHHFFFHHHHHHGGHHHHFFBHFHBG @read_150_416/1 TTTTTTTTCCATTTAGCATAATTACTTTGAAATCTGCCCATACTGTTGTCTGTATCAATAGTGTATTCCTTTCATCTCTGAGTGTCATTCCATTTTGTGG + HGGGFGBBDGBEGGGFGHGGGHHGGHHHHHGGHHEDGDHHHHHHHHHHHFFGEHHHHFHGFHFHHFFBEHHHHFFGGHE?GGE8A?AD.DEFFHGEBEFD @read_150_417/1 AGAGTGGTATTAGAAGCCAACACGTGGATGCCATGTATGCTCATTGTTACTGAGGCATCATTGTTTCTATGGGCTCCTAGCTGACAGAACCTGGAAATAT + GHHHHHHHHGHHFHHHHHHHHHHHHFHHBHGGHHHHHHFEGHFFFHHCHHHHHHGB=A996)AAHHEEH9CA.DDGDEFAHHFGFFGGFHHHDHHGGFG( @read_150_418/1 TATTGGAGGAACAGACACAGATCAATGGAACTGAATATAGAACCTGGAAATAGCCCCACACATGTATGCCCAACATGTACAATTTTTGACAAAGATGCAA + GGFBGHHHHHHHHHHHHHHHHHHHGHGGEHHFEHD=GF:FHHEEEDDFHHGHHHEFDFHHFFBB>FDEB?E?>7A*16DDEEDDBFFHHHHG=DEHHHGD @read_150_419/1 TAGATTGGGAAAGTAAAATGAACTTTGTCTGTAACTGAAAGTCATCAGTGACCACATTGTAGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCACC + FHHHHHFFGGHHHHHHHHGGHHDDHHHHGFE=FHHHHEHHHHHHBHHHHGHHFEEHHHFE?C=EFFHHF?ED6?>D>CA;>FEFEBCFFBHHHE @read_150_421/1 CTCTCTAGTAGCTGGGACTACAGGCGCCCGCCACCACGCCCGGCTAGTTTTTTTTTGTATTTTTAGTAGAGATGGGGTTTCTCCGTGTTAGTCAGGATGG + HEFHHHHHHHHHHHHHHHHAGHHHHFFFEEGGHHGGGGFHHHHHHHEGFFHHHB?FGGGFHHHHHHHHFEB5@9&);?EFFFEFDEEEFB>@59DDEBCFBGFGGH;A:DBEEEEE @read_150_423/1 GTAAAATTATCCCTGTGTGCAGATGACATGATCCTGTATGTAGAAACCCCTAAAAATTCCACAGTTACTAGAATAAATGAATTCAGTCAAGTAGCAGAGA + HHHHEHHHEHHHHHHCE@DGHHHHHHHHGHHHECGGHHFEHHHHH80?EHBBBGEEHHHHFFEEBEFHHFHHFEEHHFEE8>ADD@C:<66@514ADAGG @read_150_424/1 CGTCTTCGTCCTCTCTCCAGTCCTCCTCTTCTGAGGTTCAGGGAGTGGCCGCAGCGGAGGGGAAAAGCGAGACAGGTTAGTCTGGGAGCAGAGAGCACCC + HHHHHHHHHHHHHHHHHGHHHHE=BBCCF=BFGHHHHHFHHHHD@HHHHHHHGFEHFGHHHHFEHHHGHFHHFEC@A8BHFHEFDCFBED@1/+. @read_150_425/1 AGACAAAAATAAACAATGGGAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCACCTAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAA + HHHHHHHHGAAGDFH?FHEEDFGGHHDHGHHHFHHHHHHHHFFGHHHHHHHHHEBHHFD?@DFDEF?A-45BCAEGCFFGHGGGCEDHHFGGHHHEFC48 @read_150_426/1 GAGAGAGAACATGTGAAGGAGGAACTGTCAAACACTTATAAAACCTTCAGATCTCATGAGAATTCTCACTTTCATGAGAACAGCATAGGAGAAACCACCC + HHHHHHHHHHHHHHHHFFEHHGEEHHHHHHHDFHHHEGEGG?FG-5>-@=CFEGHHHFFFEH?7BAGHHHEEEFFGGGFFDBFFHHD.?AFEHG51739: @read_150_427/1 TGGCATTTTACTGGTTAGAATCTCATTTACTGCATACAATAAAAAACTCAAAGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCACCTAATCTCGT + GHHHHHHHHHHHHEGHFHHHHHHHHHFHHHHH=>+BDHHFGFFHHHHHHHHHHHDFFD8,47EBCAHHEEEFB@9GGFB<@FHHHFHGGGEBBEGGHHFADGEBF@;:?>E @read_150_430/1 CAAAGAGAGCCAACTGTTCAAACAGTGTTCAAATAAGGCAAATGCTTAGTTGGAACCAATACAGCTGTTTCAGTTTCCTTTTCTGTACATCACTTTCCTT + HHHHHGGHFFDC@BBFFHHHHHHHHHHHHHHHHHEE<<@@98:246EEHGFFC=>BBDB@:CFFDFHFEBFDB @read_150_433/1 TGCCCTGGATGGTCAGGGACTTGGAAGAAACATGATTGGAAAACTGGTGATGAAAAAATTTGGGCAAGAGGAATGTGGATGGACCTGTCTGAGTGATCAA + HHHHHHHGEHHHHHHGHHHHHGHHHHHHHHHHGFFDBFFHFEFFHHFHHFFGGGHFHHFFHH@<ECDHHDDDDEGAAFFCBGFEGBB@>FGGGHHGHHHHHHHHHFDDDDBCFE @read_150_435/1 CCATGATGGATGAGGAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCACCTAATCTCGTATGCCGTCTTCTGCTTGAAAAAGAAAAAAAAAAAAAA + HHHHHHHHHHHHHHHHHHHFHHHH?HD@HGFHHHHHHFGHHE==FHHFGF5;(7>;;6;=EEE>:A@CCHHGFBHGGBB/:AC@A(.>EFEFFHHHGBEH @read_150_436/1 GGGATGATTTATGGGCTTTGTGCTTAAGAGTATGAAGGTGTATAAAAGCTGGTGTGGAGTATGGTAAGGTTGCTGAGTAGAGATGAGGAAAGGACTGCAG + HHHHHGHHHHHHHHHHHHHHHHHHHHHHHFHHHHHHHHHHHHHHHHHFCHHHEHFHFHFCFDFFHHHHHHDDDBCAHHHHFGED.:-2;>6.GHHA@:31 @read_150_437/1 ATCTATGTTCATCAGGGATATTGGCCTGTAGTTTTCTTTTCTTGTAGTGTCTTTGTCTGGCTTTAGTATCAGGGTAATGCTGGCCTTGCAAAAGGAATTG + HHHHHHHHHHHHHHHHHFGHHHHHHHHFFHHHHHHHHHHHHHDBHHGGHHFFFFHFDACFFHHFHHFF?EACFFDHHHGGHFHHHHGDBE<1(503BEBG @read_150_438/1 TGGGTGAGGGGAGGGGGCAGGACTGCAAGCATCTAGAGGGTAGAAGTCAGTGGGCTGTTAAACATGTTCTAATGCACAGGACAGCCCCCAACACAAAGAA + HHHHHHHEE2DGHHHHHHHHHHHGGHHGFFHHHHHGF7:=D@8CHFFFFFGHHFHEFGGDGEGGHHHGHHHHHEGGFHHHHEBAEEEBHHHGGFEFEE@@BECC:CDFHBHHGG @read_150_440/1 CTACTAGATGGTGCTATGATTGAGGGACCCAAGACCAGCTGAATCCCATTATGATGAAGCCTCCTTTTCTTCCCTTTCTCCTGTCAATGTTTCTAAGGAT + HHHHHHHHGEHHHHHHFFEFHFHHHHHHGG@BAHHGECDFEHFHHFFGFHD+80@>@FHDHHHHDFHFHHFFGFDHHHHEHHHHGHHHFGFFEHHHHHFE @read_150_441/1 AGCTCAAGTGCCAATAGACATGAGAGAGCTTATAGCTGATAGGGATGTAAGGAAGGGCAGGGGTATCTCCACAGCCCTGACATAAGGCAGGCTGAGGTAA + GGGHHHHFGGGHHHHHHHHHHHEBEGGGHFGHHHHHHHHHHHHHHHHHFHHHFHHHHHFHHHHHHHHHHHHEEDHHHHHHHHGEHHHHHHFE90:ADFGC @read_150_442/1 GAAAATTAACAAAGATATTTAGGACCTGAATTCAGCTCTGAATCAAATGGACCTAATAGAGATCTACAAAAGATCGGAAGAGCACACGTCTGAACTCCAG + HHEEDFEGHHHHHHHGHFHHHHHHHHHGHHGHHFFFHHHHHHHHHHHHHHHEDDDEECBFHHFHHHHHBFAAB?CG=423595EBGHHHFHEE4%6,1+: @read_150_443/1 CTTATTCCAAATTTGAAGGATTAGGCCATGTTTTTCTTTTTTGCTGAGTGCATGATTTTTCCCATGTTGTACCACTTGAAAGAAAGGTTTTCCCTTTTGC + HHHHHHHHEHHHHFE=@FFGHGEHF?EGHHGHEHHHHHDCF>8HHFFDEHHHHHHHFHHHHHHFHHHHFFED5DEGHHHHFBFHHHHFEHHHHHHGHHGG @read_150_444/1 AGTTAGTGATGTTGACACCTCTGCATTTTAACACTGGGATTTCTTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCACCTAATCTCGTATGCCGTC + HHHHHHHHHHHHHHHHHHHHHHHHHHHHFHHHHFGGHHHHHHHF?C=9CEEDBFFHHHHHHHHFFD?F>478-1>DDBD;6>;?A?DFHFDFHGGBDGB9C>G@39<'178<:BFHEH @read_150_446/1 AGTAGATAGATCCATGATATATTCATAAAGTAGCTCTCCTAAGTATTTCTTTCTAAGTATTAGATTAAAAACATTTGGTAGCCAGGTGCAGTAGCTCGCA + GGHHHHHHHHFHCB@FGEDD:EHHGGHHDHHHHHGDEFGFHHHHHEB3:6EHH?AHHGGHHFHGGHHHHF=DGBGFEDBFGG @read_150_447/1 GAGTGTGGCCCATCTAGGGAATGTGGTTCATCTAGGGAGCGTGGCCCATCTAGGGAGCGTGGTTCATCTAGGGAGATCGGAAGAGCACACGTCTGAACTC + HHHHGGED?EHHHHHHHHHHHHBFEHGFBDFDGHFHHHFHHHHHHHHEHHEHGGFHHGGFEHHHHGBFCFHHHFCHHFFE77EEEGGHHFGDGB@FHGF6 @read_150_448/1 GAGGCTCGAGGATCACTTGAGCCAAGGAATTCAAGGCCAGACCAGCAACACAGTGAGACCTTGTCTCTAAAAACAACCAAAATCCCTCTGCTGGGGGCAG + HHHHHHHHHHHHHHHBEFFGHHHGHHGEHEEEGHHHHHHHHHHHFHHHFFHHHFCHHF>;DA>AED4??E @read_150_449/1 ATTTTCCAGTCAGATAATCTAATTATAACCATGAATAGAACTGAAAGAGTATTAATACTGTAATACCATATCAAATATACAATATGGAAACACATTAAAA + HHHHHGGGGHHHHHGEGFHHHHHHHHHGHHHHHHHHHHHHHHHFDC=DDHHHF9FFECHGEBE=HGFHHHHGG?;7CDFHFHHH @read_150_452/1 TTAATGTACATGATATGAATGTGAAGCATAAAATTAAATAAAATTTTTCCCCATTGGCTTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCACCTA + GEEG@FDE=CCB@CCC6CDDFHHGEHHHHHGFHHHHHHHHHHHHHHHGHHHHHDD<&*&)3@HHD,:AHHHGA?EEDE@CHHHHGCFHDHHHHHHHHHFGHGDDC @read_150_455/1 AATGATTAAAACTATAAACATACATCTGTAACATTTCTTTCTAAACTATTCTAGCACTTCAAAGCCTGAAGCCTATTACTGTTATATGGAGAAATGTATA + EEEEGHHHHHHHHHHHHHHGGHHHGGEE8HHHHHECFHHHEFFHGHHHHCFGFGFFEF>:<;BDFGG;AEHHFHHHGGGGHHGFFHGFGGFFHHHHHHHE @read_150_456/1 GGAGGGAGAGAGAAATAGAATATGAATAGAGAAAAGAGAACCCACAAACCTAACTATAACAGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCACC + HHHHHHEFEEBEGGGGHHHHFHHHHHHHGGGHHEFGGGGEFFHHHHHGHBFBGFD:061:=DFEB,>(C@FGGGDGGGEHFD,:>*&+BEEFFEHHDHG6 @read_150_457/1 TAATAACAGCATTTACAGTATTGTGACTATGTAAACGTTAATTCATGGAGGAGCCAAGTAGTATTCTATGAGTATAATTTCTTTCCTACACGTTTTTATT + HFEHHHHHHHHG@FEGGGFEEHHHHHHFFGEEHHHHHHHHFFHHHHHHBGGAFHHHHFFBEF6EGFBAEEEBEBEHGGFD9:+'21)0?CHHHFEBHHFH @read_150_458/1 TGCAGCGCTCTTTACTTCTGGGTTTGGCCCAGATCTTAAGTCATCCACATATCTTCTGGTTTTCAAAATTTATTCATTCAATCAATATTTATTAATATTT + HHGHHHHHEFGEFHHHHHHHHHHGGHHFGGHHHHD@GFFFECBECFFHGHHHHHHHHHHHGGE@HHFDEEDFFHHHGHHHDBAFFHHHFFFBB=GGGDDF @read_150_459/1 GAGTTGGAGACCAGCCTGGGCTACACAACAAGACCCTGACTCTACCAAAAAAAAAAGTTCTTTAATTAGCCAGGCATAATGGTGCACGCCTGTGGTCCCA + F@BEB<:8:9CC@BGDHGDGGHHHHGDBAGGEBGHHHHHHHHFGGFFGHHHHHHHHHHHHHHHHGFFFFHHHHHHHEEHHHHHEHHHGHHDDFHHHHHGF @read_150_460/1 TGAATAAGTGAAGGATGATGAAAAGAAAGGGACATGATTATATTTATGAATTCATCCCCAATCTTCCCTTGGGAATTATTTTCTGGACAAATCCTAAGTA + HHHHGFFFHHHHGGGHFDEEBC896EEEEG;B>HHHFCD?GEBHHHHHHEHHHFFHFGG63:@FFHFFHHHHHHHHHHGEC9FHHFDHHHHFFFGEFFHH @read_150_461/1 AGAAATAGACCCAGGCATATCTGGTCAGTTGCTTTTCAACAAACTACCAAGATAATTCAATGGGGGAAAATAATCTTTTCAACAAATAGTAGATCGGAAG + GGGGHHHHHHHHHHHHHHHHGEEGC+B>@>CFDAHHHHHHHHHGHHHHHHHHHHHHHHHECGFHHHHHHHHHHHHGE78.3>DDH>FEDFB=HHDDFFFGHHHHHFHHHGGHHEGB,5;EHHFH @read_150_463/1 AGGCTGCCGGGCTGAGAGCGCGGAGACTCCTGCTAGGCTGTAGTCTGGCAGGCCGGGGGACTGGGTTTACTGGAAGAGTGTGAGGTGGGGATGCAGAGGG + HHHEGFFDDDHHHHFGGBAHHGHHHHHHHHE@DFEHHFEGGGHFBHHHFHGFFHCEFFFHCF72)77::>><9FFGGEHHHHFFB:D @read_150_464/1 GGCCACCAGTTCAATTCAACAAAAAACTCTCTGGGAGTTCCAAATGTGCCAGGCACATTGCAGGGCACTGAGATCGGAAGAGCACACGTCTGAACTCCAG + GGGGEEGGFGFHGGHHHHHHHHGHHHHHFGHFFHHHHHHHHHHHHHHHHHHFFFHHFEFHHFGDFHHBCBHHC?FDEEEHFHHEBEDC5FFDCDHHF.79 @read_150_465/1 TCTTTCAACAACTCTAGTAAGGAGGCGTGTTCCAAGATGGCTGAATAGGAACAGCTCTGGTCTGCTGCTCCCAGCGTGATCGACGCAGAAGACGGGTGAT + GGGCEE56CDEEGGHHHHHHHGDHHHHHH@/8BBGECHHFFHHHHFFCE=FHHHHHFBHGHHBB?5<0;9+02>D>>EEBEF@HFHFFGGC@B:9AADHF @read_150_466/1 AAAATGTAGGTAGGTCCTAGGTATATCAGGATGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCACCTAATCTCGTATGCCGTCTTCTGCTTGAAA + HHHHHFDGGFDDDA?GBDDEHHHHHHGD-D,1-98;??==;FFHHHHHHFHHGHHHHHHHE?863:FADE>CDCCGHGFGHHHFFHHHHHBHF=B(9:CF @read_150_467/1 TCATCAATTAAGGAAGGAAAAAACTCTGAAGTTAGTTGTTTTGCATCAAGGAGACAGAACAACTGGTTGATTGTTAGATGTTTCTGCTTCTCCATTAGTC + HHHHHHHHHHFFFHEFEFHHHHHHGGHGGGEHHGEAEA(;-208@>4.AFHHHDEHHHHHE=:BDGGBDAFFFHHHHHHHGGDBFGGGHFBGACBGHGHH @read_150_468/1 TGTTTTAGAAACTTTGTTCTCTGCTGGGCGGGCCTGGTGGCTCATGCCTGTAATCCCAGCTCTTTGGGAGGCCGAGGCAGGTGGATCACAAGGTCAGGAG + GFF>>=CGGBDGHHHHHHHHHC?E=@F@CBE7>C/=DEEE@FBFFHHHHHHHHFFDDD;7(6CHFFFCHHHHHHHHFEFFHHHHGFABDGGFFFHF@@+C @read_150_469/1 GTCAGGAGATCGAGACCATCCTGGCTAACACAGTGAAACCCCGCCTCTACTAAAAATACAAAAAATTAGCCGGGCGTCGTGGCGGGCGCCTGTAGTCCCA + F6DB8;EDBBFHHHHHFFDHHHGGGFHHHHHHGFHHHHHHHHHFF@BBFHHHHHHHFBC?HHDDC2BHHHHFHHHHHHHHHHFGGGHCCFFF @read_150_470/1 CAACAAAAACAAAACCAAAAAAAGTGGGCTGTGGAACACTGAGAGGGGCTGGCCTACCCTTGGGGCATGGATCCCCTCCCCGCTACATCTCCCACCATTG + GEGGGGHHHHHHHHHHHHHHHHHHHGFHHHHHGGGGGHCDEFFHFBHHHHHHF6=EBFGB;EHFFFCH?BDDDCFHHEBGFFDFEGFEFHDDDAE<>=DG @read_150_471/1 CTGAGAGGGGTGCTGGAATGTAGAACAGAATGAGATTGGACTGGAGGTTCCAAAGGTTGGTTTGGCTTAATTATGTCAGTGCCAAGTAGATCGGAAGAGC + HHEDFFFHHHCHHE+5@EHHHHHHHGGGHHHHFDDEHHGGHHHHHHHHEHHFHHHGEFHFFHHBFECC?FFDHDDCCGGDHHH>?FHDGHHEHB9EEHFE @read_150_472/1 TTTGAATTCCTTGTCTTATAGATCACACATCTTCTCTTTAGGATCTGTCACTGATGCCTTATTCTGTACATTTGGTGAGGTTATAAATCCCTGATTGTTC + HHHHHHHFFHHHHHHFFGGGGGHHHHHHHHFHHHHECHHHHEHEEFDFFHHHHHFHHHHHFEE@DDHHEGFHEEBGGGBFHGGEEHHHHHHHHFFHGBFF @read_150_473/1 TGCACACCCACCCTCCCTCCACCCCACCCCCCTTTCCCTTTTGCACCCCCACCACGGCCGCAGGCATCTCAGCACCATGCACCTCCCCCCCATGCCCTTG + HHHHHHHHHHHHHGGHFHHHHHHHHHFEFHHHHH?DFEDHHGHHHHFHHHHHHF9FFBEFFGEFHBBFF?8:1@@HHHG.,3;;+::AD?:DFF@FFFFF @read_150_474/1 TCACCTTGTTAGCCAGGATTGTCTCGATCTCCTGACTTCGTGATCTACCCGCCTCGGCCTCCCAAAGTGCTGGGATTACGGGCGTGAGCCACTGTGCCCG + EFFFEFFHHHHHHHHHHHHHHHHHHGEEDHHHHHFHHHHHDHHHHHHHHFHFEEDCDDBEEEGGGBEFEBHHHFHHGHHHH; @read_150_475/1 TTGTGTGCTCTTGGTTCCCTAGTTCTTTTAGTTGTGATGTTAGGGTGTTGATTTAATATCTTTCTAGCTTTTCGATGTGGGCATTTAGTGCTATAAATTT + EDEEHHHHEEAGFHHHHHHHHHHHHA7,;:CBC@BGFEBGHCFC7HHHHHHDHHE??EB@9EEEGGA@HDBHFFFHHGFE@AD@DFFFECGEE<5C=?67 @read_150_476/1 GTGCACAATTATATAAATTGCAAATAAAGATCATTTTACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCACCTAATCTCGTATGCCGTCTTCTGC + GFGFGEGFGHHHHHFHHHHHGGHHHHHHHHHHHHHFHHHFGFHEFHHHHHHHHFEHEHHHHHHHHFFDCCFFEHFHHHHGFGGEDFHHHB=E;A>><=,? @read_150_477/1 TCAAACGAGGCAAGTAAGAACATAACTGGAAATGTTTTGAAGACCCCCTACACAAACACACCTGCAGAGGCTCAGGCCATTTTAGTGTTGCACTCAAAGG + HHHHHHHHHHHHHHHHHHHHHHHHHHHHGGGGFHHHHHHHHHHHHFFFB@GHGFHHHHHFHHHHEFGGFHHHHHHHHHHHHHHHHFBHHFF@FDFFFEHHHFHHHHHHE?EE>>55<8;5-? @read_150_479/1 AACACTGGAGCTCCCAAATTTATAAACTAATTACTACTAGACCTAAGAAATGAGATAAATGGCCACAAATCCATTTGCTAATGGACTTAACATTTGTTAA + HHHHHHHFFHHHHHHHHHHDCDGGEB>7EEEGHHHFFGFFGGHHFC0@-5GE??DAEGGHHHHFHHHHHEEHFDBHC?<>@ @read_150_480/1 GGTACAGGTTTATGTACATATTGAACTACACTTTTTGTCATTATCTTAGAGTGTACTCCTTCTACTTACAAAAAAAAAAATACAACTGTAAAACAGACTC + HHHED=BDGBDECDEDGHFHHHHHHDDDEHHGHHHHHHFHHEEED@BDDDBBFFFHFA5AFBBGHHC<9?FHHHHGFGGEHHHHHHGFFABCECD98399 @read_150_481/1 TCATGATTTGCTTTTGGTTATAACTGAAGTTTGTAATAACATTGCTAATATTATTTCATTTTGTCTAAGAGTGTGTCAAGCTTTTAACACTTGGGGAGAT + HHHHHHHHHHEEEHHHEEEAGDGFHHHFDD@@?GGEFFHHHHFFFEBFFHHGFHHHHHHHHHFFBEE9>ED8?BEGGGGGGG=EEEB8*/:6,2)749EG @read_150_482/1 AAAGTCTGAGGCCCTGAACAACAATTCCCAGGATGTCTTAAGTCCTGGTTTCCCATACTGATTCACGTTGTGCCCCAGTATTGGGAGTCATTGGATCCAC + HFFEFGGFGGGGGHHGFGGHHGEHGGGGGHHGCDFHHHFFDHHHHHHHDDAC?GE;A? @read_150_483/1 AAAGTTTTACTACAATGTCATTTTAAAGTCATAGATAAAAGTCAAGACAGTGGTTATTAATTTGAGAAAAAAATATTTTACAAAGAGGAAGTGTAGTCAC + GGGHHHHHHHHHHHHHHHHGHHFHHHHHGF.6AFHHHHHHHHHFDHEHHHHHHFFFE>9BBHHBCFF@@70:CC @read_150_485/1 TCCTGCCAAATGGTCCCCATTGCCAGTCTTAGAATGAAATCCACCTCGTAACAGCTACCAACTGATCTGCCCCCAGGGAGAGCTGTTATTCCATATTTTC + EEEGGEGGHHHHHGEFFFFHHHHHHHHHHHHHHHHGGGEEGFEHHHHHHEFHFHHHHHEEECGHHHFDDFEEHHHHHBDHHHHHHHHDBBFCED694?EC @read_150_486/1 ACTGTTGCTTTTCTCTCCTCCTTACCCATTTTCCAAGCCTGATGCACTTCTCAAGATCCAATCTGAATAGGTGAATTTACCCTTGACATACACTGCCTTG + HHHHHHHGGHHHHHGEB@B<@C@EDGEEHHHEE?FF?@BEGHHHHHGG9AFHH?B?9EEHHHHHFDCHHHHHHHFHFFFHHHHFGHHHHHD=FGGHHHFH @read_150_487/1 GGAAAAGGGTAAATTGCACAAGCAATTTCTGGGGAAAAAATGGCCCCCACCAACAAATTTTTTTTTTTTTTTTAAAGCAAACTTGCCTGTGGAGGAATTT + HHHHHHHHHHHHHGGHGDDGHHHHHHHHHBFBDEEB@HFFDFFFFBEGFHHHHHHHHHHDEAAEADBEEBDFGGFHHFFBCC>:5@BEDFA@CFHFHHHFHHFEE9CDHHHHHHHGGFFHHHFHHHHH@7CHF @read_150_494/1 TGGGGATAAAATATGGTAGGGAATATTTCAAACAGAGCATTCCAAGTAAATGCAAAGGCCCAGAGGAGAGAGAAAAACGGGGCATCTTCCAGGCAGTGAG + EGGGGHHHHHHHHHHHHHHHHHGHHHHHDEEFEFFC:2B<;@FA:<;CFGEGGDHHEE?CFHHHHHHHHD @read_150_499/1 AAAATTTAATAGGAAGTACTCATGTCCATTTATATCAAATCATAGAAGAATTTCAAAATAAGTAGCGCCATATAGAAAATGAATGTGAACACATTCTCCA + HHHHHHHHHHGGGHHHHHHHHHFEHHGDGFFHHHEGGFFHHHHFBFFHHHHHHHHECFBFFHHFFHHD9:@FFHHHHGHEFFHHHHFHHGEDEGHHHH=@ @read_150_500/1 ATGTCTGTTCATGTTCTTTGCCCACTTTTTAATGGGGTTGTTTGGTTTTTCCTTGTAAATTTGTTCAAGTTCCTTATAGATTCTGGACATTAAGTCTTTG + HGFFFHHHHHHHHHDFDBDFGGGFFDA9DDBFHHHHHHHHHHGHHHHHHHHHHHHFHDHE5EEFFHFBHGFHHHHHHFGHHHHFHC<>EBEEGHGGGFHH adapterremoval-2.3.1/examples/reads_2.fq000066400000000000000000003265041350370616400202270ustar00rootroot00000000000000@read_150_1/2 AGAAACCACAGTGACTTAAACAGAGAAAGTTTAATATAAATTTTTTAAAATTATGTTAAAAGAGCAATTATAATATATAAGTTAACTCTATGTGGTACCC + HHHFFHHHHHHGFBGHHEFBDG?B=GHHFGFHFHHHHHHHFBFHHHHHGGEEG=DGGGGCHHHHHHHGEA%5ADHHHH=G&&*>>E6,735@GG @read_150_3/2 GTCATTAACATTCACGAAGATAAATTTCTCCATTTTAAACAGAGACACTCAGTGAGCAGTAACCTGATTTTTTTTGGAATTTCATTCTTCAGGAGGGCTT + HHHHHHHHHHHHHHHHHH?GF5:@AFHHHGHFDDGGFFFHHFGHHHGGHHHHHHHHFGHFGEGC.18984>1BC=GFFAC<>E?..59&&-81:<<5.@ABCDBCE>:>@CDGHHHGEBFE/38@EEFBFGHHHHHHEGH?DHHHH>'9DEC**'*6 @read_150_5/2 TGGGGCCATCAGGAATTTTGCAGTGGTAATGGGGGACATTTTAGCTGAGACTTGGAAAAATGGTAGAATTTGCTCCAACATGAGGAAATATGAGCATTGA + HHHHGEGHHHHGEG;/FHHHHHHHHE;@==G=DC>DGFHHHHHHHHHHHHHHFD;>A5<(@<4 @read_150_7/2 ACTTGCACCTCTTCATCAGAGGAGCAGATCCAGGAACAGAAGTCCTGCATTTACAGGCTCTTCATATCTTGTGCCGGGTTTGGCTGCCAGGTGGCCAGCT + HHHHG=BDEDFFGGHHHHHHHHHHHHFHHFHHHCGHHHHHEBHHHHHHHHHHHHHHGEEE??6BCFHE624@7=1AFGBDHHHFFE<<.>,1349EEHHHHHHHGFHFHHHHHEHHD=:>-7@BC2BHHHHHHHGBHEFFHHGGHFGFHHEEFHFBEBEFHHFFBCA?B @read_150_9/2 GCCTTCCCTCTTCACTCCCTCCCTTATCCCAAACCTGCCTAGGTGGGGCTGATACAGACAGCAGGCCTGGCTCTACTTGTTTTGACAAAATATATGCCCT + GGGEBGHHHHHHHHHHHHHHHHHHHHFADHHHFHHHF?DEF@B>C;CDGEHGGHHHE@@DBFGHHHHGB>BBFEGEGHFHF8ADCFDEE4D?>H@:>DD= @read_150_10/2 TAGTCTTCTCTTTCCTGAGAATATTTTTATTGCAAATATGTAGTCATATATACGTAAGATAAGGATATTTTAAATACTACTTTAAAAGTTATTACTATAA + HHHHHHHHHHHHHHHHHHHHHHHHHHHHHFFFGHHHHHHHHHHHHEBDG>CCBB?FHFHHDEFHGDDGHHHHHH@BECHHEHGDHHHHHFHHHGEHHHHH @read_150_11/2 TCCTTCTTAATAATCGTATTAGAGTAAATTTCCACATCTAAGATTACCGTGCCAAAAGCTCTTGCTCTCTATCCTGTATTTTACATCTATGGTACGTTTA + HHHHHGEHHHHHHGHHHGGGHFGHHHHGGDHHGGHHHHHGHHFHHHFBD@FDFFHHHHHHHEHHHHHDDB=DA@@5DBC<.&9=AEHGFHGGD=1A;3CC @read_150_12/2 TTGCCTCAGATGTGGACCCAGTGTTAGATTTAGCATATAAGGATTTTAAACCAGATATTACAAATACGTTCAAAAATCAAAGTAAAACTATCTTGGAGAA + HFB<95>:5226A>>DDCB@--3;BFFH @read_150_13/2 ATGTTCTGGGATTTTTACATTGCTGATATCAATTTTGGTTGAAGTCGCAATGACAAATTTCTGGTATTTTCTTCATAGAGGAACTCGATTGAGGGCCAGA + HHHHHHHHEGHHHHHHHHHHHGEGGFHHHHHEHHHHHH@E>FHHHHHEE;EFHHGHHB@FD:<.?DDGHHGBDDEE=ACEGHHHHF=CC?DGBBHD@DF8 @read_150_14/2 ATTATTGATTACTCTGGAAAATAATCAGCATTGATATAGCAATAGTAGCATGGCAGTCAATAAATAATGTTTGTAACGTACCTGACATAATCAAAATAAC + HHHHHEE=/?<*>FE;-53>>8=FEEFHHHHHHHFHHHHHHHHHEHHHHHHHHHEFEEHHHHFEBFEBC>FHEGE9?D @read_150_16/2 TGACTGATTTTTAGACAGGACTTGCAGGATATAAGCATCAGGCAGTATTTAAAAATCTGGGAAATTAGCAATAAGATCGGAAGAGCGTCGTGTAGGGAAA + HHHGHHHHHHHHHHHFFHHHHHHFFDEGDHGHHHHHHHHHBBAB>.6HHHEEFFGGHHHHE@?=EGGFBFHHHHHEHHHHHHHHBEEFFGHG5CBCACDG @read_150_17/2 GCTTCGGTCCGGGTGAGACAGGCCAGTGGCTGCAGCTGCTTTGCCAGAGGAGAAAAGGGCATCCTTCCTTGACTAGGAATAAAGAATGAATGAATGATGT + HFHHHHHGFHHHHHHEBHFFHHHHHFEHHHHHHHHHHHHGHCCGGHHFEGHD=FGGGHHHHEEHBGHHHHGG),BAA?>5%4:FGGDHFE@614A= @read_150_20/2 TGTTGGGGTCTGTGGCATAACACAAAATATACTTGGTCTTTGTCCCCAGCTCCTGTGCAGGGCAAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTACA + HHHGGFHFHGHHHHHHHHHHHHHHFHFGHHHHHHHFHHHHHHHHHHHHGGFHHHHHHGGHE><.??D98EHEC:.B @read_150_21/2 CAGAAGGAGAAGCTGGTAACTGTCAGCCACTTTATGGTAGATAAATCGAGGCCGGGAGAAGAAAAAAAATCACAGTAAGAGGCAGTGAGCAGAACCAGAT + HHHFABEHHHHHHHHHGHHHHHH@:ABHGGHHHEEHFHHHHHH>>=FFHHHHHHHCEHHEGEGFD-%%5CGCEHEHHFHHGFEH>>BDEEBDBFE.1%88 @read_150_22/2 AAATGAGGCCTGAGTGAAGAATCTTGATACTCATAGGTCATTAGCTTCATGTAAAAAAAAAAAAAAAAAAAAATAAAAACCAAAAAAAAAAACCTTTGAT + HHHHEEFEGDHHFHHHHHHHHF8BCDEHHHHHHHHHHFFDEHHHHHBAADGFGGBFFFGCGGHHHHHHB.057(+2-9GGHFHHFHFA@@;>DEDEBEFG @read_150_23/2 TCATAGTCTTCAGTGCACCTTAGATTGGGGTATTGTTTTGTTTTATTCCAAGTGAGCAGGGAACATGTTAATGTTGGACATGTTCTGAAACAGTTGATAA + GGFFGGGHHHHHHFHHHHHHGHHHHHHHGHHGFF=BDHB84DB@AC5(('97B?@E=6>@AHHHHFFEGEGHHHHFHFDGHHHHHGGHGHHGEDD?7>29 @read_150_24/2 CAACTTAATGTGACTGAACTTAGAATTGGGAAGATTCACGTGCAGTTGACTCTCATGAGCCAATACAAATTGGCTCCAACACACCATCAGCATGACTATT + HHHHHHHHHHHHHHHHHHHHHEFHHHHHHHEHHGFDEFHHHHHHGHHHFDHHHHHHHFFDG@BCFFHGFHHHHGHEE@AD?2&5.544DE82EDHH=<45 @read_150_25/2 AAATATCACTTGTTTCTAGTTTTATGCAGGATATTCAGTTGTTCACTATAGGTGAGAAAAGCTCAGAAATGTCTGTTCTTAGATCTTACAAAAACAGTGT + HHHHGDGGGGFGGHHBAB=??CCDDBGCDEGHHBHHHHHFCECBFGGDFFGHHHHHBB@.<3,+6<<9=DCBGGFHGED@GHC@GGEEFEGB?>DB>58E @read_150_26/2 AAAAATTATCCAGGCATGGTAATGGGCGCCTGTAGTCCCAGCTACTCAGGAGACTGAGGCAGGAGAATGGCGTAAATCTGGGAGGCAGAGTTTGCAGTGA + HHHG>:>98633131><>>??BFGHHEHHEHGC8=8@DDCHHHHHFD;7EHHHHHHHHHHGGHHHHHHHHHHHHHHHHHHHHHHHEEBEBGECDEEEE<8 @read_150_27/2 ACACACCACCACACCCAGCTAATTTTTTTTTGTATTTTTTTAGTAGAGACTGGGTTTTACCGTGTTGCCCAGGCTAGTCTCAAACTCCTGTCCTAAAGTG + GHHHHHGHHHHHHHHHGHEGHHHHHHFIGGGGBDEEEEE6BHDHHHHHFHHGE@HHHHHHC8//4*)5>CGFHHHDFHD=EE;)--7:ADHBFFF @read_150_28/2 TGTGAGGATATAGTTAATTAAGCTGCATTAGGGCAAATATACACACTTGTTAAAACACTTAATTTGCCTCAATAAGATCGGAAGAGCGTCGTGTAGGGAA + GDD??<9;:=EEG:?CCCC@FFGHHBGFFHFD=D@@>18>=<3=FHGGFHFFHGGHHCBHHHHFFFAFFFHHHHHHHDGHEFC9=DDBDDHHHHHHBGHH @read_150_29/2 CTTGCCTTCTGCTTCCAAGATGGCATCTTGTTGTTGTGTCCTCTGGAGGGGTCCAACACTATGTCCTTACATGGCAGAAAGGATGAAAGGGACTAGTGAG + HHHHHHHGGDEDG;DHHHHHHHFBDAGD@EDEE@C:DBDEFHHFBDDHFFGGGFHHHHHHHH=:A+/BHHBBF==EFFFHGGEED;3/@7E=A>87)*.: @read_150_30/2 CTCTCATCAGTCCCACTCTGGCTCTGGGTGTCTGTTAGGGCTGGATTCACAGAGTGAGGGGCCTCTGCTGACGAGGATGTATGCAGGGGCTGACTGGGCG + IGDDDHHHHHGHHHHHHHG=CBCB>&-+BEHHHHEGHHHHHHFBHHHFHD/5=60CFGHEEFGEHHBFC.2':.9?FBHHHHGFCFEEEHHHHB=A?@A4 @read_150_31/2 CTAAGCAGCAGGCTTTCTCTCTGGGGAAGATAGACAAATAAGTGACTTAAAGCATTCAGAAGCAGGAGACAGAGAATGATGAGATGAGTTCCACAGGGTT + HHHHFF?FGFHHHHHHHHHHHHHHHFFFHHG7D=CB<9>4;4>AFHA@>>EDCDBHHHHHHHHHHHHHGHHFHHHHHHFHHHD=5@DHG6CA58=DD>AE @read_150_32/2 ACTCATAAAGGTGTTCATGAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAA + HGGGGHHHHHGHHE8DHBGGGGGGEHHHHGGBHHHEFDCFEHBDEGGGHFFHBD555ADHHHHHHEGHHHHHFD43 @read_150_33/2 GTTCGAGACCACCTTGATTAACATGGTGAAACCCCATCTCTACTAAAAATACAAAATTAGCCAGACGTGGTGGTGCATACCTGTAGTCCCAGCTACTCAG + HHHHHHHHHHHHHEEHHHHHHHHHGHHHHGEEEHEHHHHHHHB6DHHFCDEDEGFHGGGHHHB8><)0-<9@;@HHGBFFHEEEGCFFEFFBFBCEDHFE @read_150_34/2 GTTTCGGATCTTGATATTGCCCACTGTTGCTTGCTATCTATTTCTTAGATGAGCTGAAATTATTCTTTTTTTAAGTAAGTGACTCTTTTGTTATTCAGCA + FGGFDGGIBBEDB/9)/:HHHHDD=GGCEEFGBADA7EFEBC@DEGG?:C-/EDEDEG?BEGG4(4CCGFEE6EBFCCEE @read_150_35/2 AGAAAGCACTGTGAACTTAGTCATTAAAAATGAATATTTAACAGTTCACTTTTGACATGCATTTTTAAAATTTAAATTAAACTTTTTTTTTTTTTTAGTT + HHHHHHHEEEEE/?636BGHDAEBDEBD@GEHHHHHHHHCD*1::CEDCCDB@GGEEFGFHHHHHGHHGHGHHHHHF8=FHHHHHHHBFHHHHHHFFHHH @read_150_36/2 CTTTAAGAATGATATCATATTGTTTCTATGCAAACACTGATGGTATTGTTCACATTATTTATTTATTTTACAAACCCAGATCGGAAGAGCGTCGTGTGGG + EF@@DEGHHHHHHHHHHHHEEEHHGHHHEFHGGCBHHHHHGHHHHHCCC>DDD;DHHHFIHHHHHHHHHGEFGFGHEHFGHHHH@*66G?1(03 @read_150_37/2 CCATTTGACCCAGCAATCCCATTACTGGGTATATACCCAAATGATTATAAATCATTCTACGATAAAGACGCATGCACACGTATATTTATTGCACCACTAT + BEED@FBFHHHHHHHHHHG;8CD=HHHHCB6>563<5?D432>..<6<>@923@CFGHHGEHCEEDEHHFHHHHHHHGHHHHFHHHHEHFCB:.<<><@CGGEDEECBEEHFFBE @read_150_40/2 AAAACCAAATCACCTCATTAAAAAATGAGCAAAGGATGTGAACAGACACTTCTCCAAAGATGACATACAAATGGCCAACAAACATATGAAAAAAATCCCA + EGGHHHHFEHHEGHHHHHHHFFHHHHHGF=@E8CCHHHHFEHGGIGEEBD<47.5?GGGHHHC8CFHHHHHEG=CHHHHHHHFHHDEEGGFFFEEGEEF= @read_150_41/2 TTTTCAACAAAGGTGCTAAGATCACTCAATGGGAAAAAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAA + HHEHHHHHHGEEEBEEHHHHBFEEEGGGC?EG6:;BGGEGEHHHHGFGDDHFEGGHHHHHGA>.?,47>6ADHHHHHHFGHHHEDDCDDFEFHHHHHHHH @read_150_42/2 TCTTGCATGTAGACAACAGAGTCCACTCTGGCTATTTTCCGTAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + HHFFGE@.'8>>@DHFFDBHHFGED>13=699D=,>66EDEG669?CCCDE@44@6GHFHHGFGDA@>@?=HGECGG>@CFFCCBD?FFHEEFFC>.*/( @read_150_43/2 TTCAAAACAAACTGAACATCGCTGGAGATAAGTCAGATGACTACTCTACCCTATTTACTTGCTTAACAGTTGCCATGACAAAATGGCCACACCCAGGCTT + EHHHHHHFHHEIIEBE=@<-;AAFGHHC@>>BBGHHFHHHFHFE?EEHHDEGF7BHHHHHHFHHHHHHHHHHHHHHHHHHHG?@?DFFHE:.54HFH57@ @read_150_44/2 AAACAAGCACAAACACTTGTGTACCAACACACCTGTCCTTTAAAGCAGGGGCTGGACTTAGAGGTGGAGCTTTGCCCACAACTTCAGAGCAGTGCTGAGT + HHHHHHGFGFADDFGHHHHHGGHHEEEDEFHHGCAEFHHHHFE/9GHHFHHHHHHHC862<@8DGH@<6.CGGE87<7@HHGD=CDHHHF?5:74AFEEE @read_150_45/2 TTTGCTCTCGTTGCCCAGGCTGGAGTGCAGTGGCACAATCTCGGCTCACCGCAACCTCCACCTCCCGGGTTCAAGAGATTCTCCTGCCTTAGCCTCCTGA + FHHHHHHHHHEHHHHHGGHHHHHEECDFFCHHHHHDHHFHHF@HHFGFHHHDDGGFGFB><>+923:7/DHHHHHHHHHHHGCDF@>76&>D;<;GGFHF @read_150_46/2 CCGGAGGCTGAGGCAGAATAGCGTGAACCCGGGAGGTGGAGCTTGCAGTGTACTGAGATCGCACCACTGCACTCCAGCCTGGGCGATAGAGCGAGACTCC + HHEGDEEFHHEGHHH9000;.252-DGFE9&7FFCBFFF*).>:,4 @read_150_47/2 TAGAAGCCTGGGGGAGAGGAACACCCATTTTTTTCTCCTAGAGGGTTATAGAAATCTTCTTGGAGAAGGTAATAATTTAAGGGAAAGAAGTCTTAAGATA + HHHHHHHHHFHHHHHHGHHDEBGGEDF2/EDEBHHFE=9.;@B@EDGFE4<@ACDHFF;;BGGGHHHBBHHDC?HFFAAGDE;331=>AC>8CDHHE>)1 @read_150_48/2 TTGTAGCTTAAAATCTAAAAAATAGATCACTGAAACTAGAAAACTAAAATGGCTCTCATAAAGATAGAAGCCAAAAATAATGATGACAAATTCAATGAGT + HHHHHHHH4>??A>+-:<7BF=DBE82@7>EHHGGHFHDDHHHHHHFHFHFBBGGHHHHHHHGGFEHHEFHHHHHHHFGEBDGEFHHHFDHEED=;46D7 @read_150_49/2 TTTAGGCTCCACTTCTAATTCTAGTTCTGTTGCTAATTCTATCACATCTGTAATTACTTCTTCCACTGAAGTCTTGAGCCCCCTCAGTCATTCATGAGGG + C@DHHHHHHHHHGEEFHHHEF;:47::2'-4.>CEIGGFFHHHHD=ADEEFFFG;@CCGHHHGGHFDEGE;8EHHHHHHHHGFF6BDFHEDFBHFFFHH? @read_150_50/2 AGTACAGACTGGCAAAAAGTCTATAATTTAAGACAATATTCACTATAGATAAAGCTTCCCTGGGATCAGTAGATCGGAAGAGCGTCGTGTAGGGAAAGAG + FFGHHHFGGGFDD@FFFHHHHHHHHH?BEGEEHHEHHHHFF?;A=::-*DGHHHHHHHHHGHHHHHHHHHHHHHHHFFGD699D69<<;ADF:99DD?.E @read_150_51/2 AATACTTGGGGCTGATGTGGCATTATTAAAGACACATAACATACTGCACTTACCCAAGTGTGATATTTTATGCAAGGAGGGTTTGCCACCTCTGAGATCG + HHFHHHHHHHHHHHHHHHHFHHHB@',364.,& @read_150_52/2 TGGGTCAAGACCTGCCCTTATTTCTCATCTGTTTACTCCCTCTATGTAGGAACACTGCCAATATTATTATTATTAGTCTGTATTCTGAGTCTACCTACTG + HHGEHHHHHHGHHHHHHHHHFHGHFEG@C@CD=9EGHHFHHHHHHHHE@CD<@>9.AFCCECFHHHHBEFEEEI/1-BHGHEEEHHGEHHHHHHHEHHHHHHGGBHHFGGHGG@9.CCEBFDGHFFIA?7?<+ @read_150_54/2 GACGGGGTGGCCTAGGAAGTCTTCCTAGAACAGATTAGACCTAAGCTAGAATCCAACAGCAGAGAAGAGGAAGGTGTTATTAACTAGATCGGAAGAGCGT + GG8EAGHHHHHHHHHHHHHHGGCDEEHHHHHHHHHHHHFHHHHBB=EDHHHGIFFHHHHHHHHHHGHHH=DGFFGHHHHFFCGEHFBGFEADB?C9DCE? @read_150_55/2 AAAAAGGAAAAAAGAAAAATAATAAAAAATAATAAAAATCCTTAGGATAACTTGAGGCCAGGAGTTTGAGACCAGTGTGACATTGGCTCTGTAAACAATA + GGEBGHHHHHHHHHHGGGHHHHHHGG<=8=:>>:+-,BEEHHHFHHFGGCGFFGGHHHFEE=@?DEGEHGB@9;=;DD1--*3.2%,:EG731)0%49'/4?@5@=FDBCF8:EH @read_150_57/2 ATATTTAAATGACAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAAAAA + HHHHHHHHHHHHGHHHHHHHH>ADEE/GGFD=:0(+@AD@DFHHHHHHHHHHH@?EEEEHHEHHHEHHFFHHHHGGHFEA5847@HFHFHF@BEHHHHGGEFHFFEBEEFHFFHHHHF:> @read_150_60/2 GACCTGGTGACCTGGGACACTGGCCAGAAATCCTGAGCACAGCCTCCTGGGTGTGTCCCACCCACCTGATGTGGGGCCAGCCTCCAAGAAACAGATGACA + HHHHHGGGHHHHDEEEHHHHHHHGHCFFHHHHHHHHH?IHHHHHHHEFHHHGBBBHHHHHGHHHHHHFDDHHHHHE6138:CCHHFGHHHHEGGEEFEEH @read_150_61/2 AATAGATTTTTCATCAGTGGAATTAGCCACTTCTTTGAGAAGAAGAATTCCTTGATCAGGACAGAGCAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT + HHHHHHHHHHHHHHHHHHHHHHHHGE8>EEGBBEEEEEEHHHHHHFHHHEEFBEGEGBGHHGGGG?GGHHHHHBEFDEDCEFACBBGGCFHHDEFCBG== @read_150_62/2 CTTGTTAAGGTCTTTTATTAATTCTACTATGCTATCTGTGGATTTTTAACTTCAATTTTATCATCTGCCATCACGACAGGTTGTTTTTTGCATTTCGATA + EFEEHHHEHHCGDBHHHGGH@/A=BFEEFFHHBEBHDG>1>GEDHHFHHHHGGG@><>>>DB814DEE6&3;<>=BHHHE@BECAAI=DEFCHHFHGHHHHHHHHH @read_150_67/2 TAAACCAGGAAGAAGCTGAATCTCTGAATAGACCAATAACAGGCTCTGAAATTGTGGCAATAATCAATAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTG + 7=BDDGHFCEF8929EE;;GHFHBHGFHHEHHHHHHHHBFFFDCCHHHHHHHHHHHFED.)5BCFHHHHHDGEEGAA=+EHH67@39%%->>;><33273 @read_150_68/2 TGGGTTTCCCCGGTTTGCAAAGTATTCATTGGAGTAAAATCTCTTTTTTCCAAATTATCATTCAGAGAACTTAGATCGGAAGAGCGTCGTGTAGGGAAAG + HHHGHHHHHHHHHHHHH@DGGGHHHHHFB=8C=@FEEFEBDDDDFAAFFEFGFCDB@211,<6(D;D@>@C=CCFHFFFBFHDEBBBCEGGEE?==?C;E @read_150_69/2 AAATGAAACAACTTCTAAAACCTGTGTGATAATGATAATACAGATTGAGATGAAGAACTTTGAAAAGAGTTGGACAATCAGAATCAGATATTTGAATTCA + HHHDHHHHHGHDFEFDHHHHHHFHHHHHHBGGHHHHHHHHHHHHEHHHHHHHEEFFHHEHGB5*0GGFGAE=B2(;>=D>,@BB/5?>.A:991/+1%*) @read_150_70/2 GAATCCTATTTGATATTAGCCAACAAAGCCACATGCAGGTCTGTGCTTATTCAGCCTTCACTTTAATAGCCCTGCCTCCTGGAAATGACATAAGGGAACT + EHHHHFHHHHHHHHHHHGGEEHHGFHGDBGHE=C*:284<;=?BDCBDDF;DBHHHGGFHHHHHHHHEHHHHHFA.:.30DA6= @read_150_72/2 GCTGATCTAGAACTCCTGGGCTAAAGCAATCTTCCTGCCTAAGCCTCCCAAAGTGCTAGGATTACAGGCGGGAGCCATCACACCCAGCCTCCTCCCGTCC + HHHHHHHHHHHGHHHFFFHHGHHEFHHHHHHHHHHHDAE8.:1:7FFHHHHHHDEHEDCACBFHHHHHHHHHHF89?AFHHHHHHHHHGECFDDDE*>4. @read_150_73/2 TGGTTACCCAAACTAATTAGCTGAGCTTGGACTGTACAAATACCTTTTTACCTGGAATCCAGGTTAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAG + GE8BEBGHHFECDIFFHHHHHHHGHDFHHHFHFDBDIGBE-.@4*BHHHHHHHHHHHHHFB=ECHHHHHHHHHHCEGEBEBEFE?EADDF=C>97<.@G@EHD>7@4DDGEFHHEGGHHHE?6/52'64AD<, @read_150_75/2 AAAAGACTGAAGCAGAAGTGATGTTGTGTCATTTCACACTTAGACTTTAAGAAAACTGGCAGCTTCTGCTCCCTCTTTCTTGAAACCCACCTACCATTCA + GEFGEC@<.DHHHHHHGFDFGEEHHHHHHFHHHHHFDGHGGEGIGGHHHHHHHGHHHHHHHHHHHHHF@BFFFE@FGHC@:EEHGGHHHH?C=EDEFFFH @read_150_76/2 CCAGAATTCTCAGGAATCTGCACTTTACCCAGGCGAAAAGCCCAAGGGCTCTCCCCACAGCTTCCCAACATCCTTCTACAGAGTTTTTAAATAGTAGACT + HHHHHGHEGGGHHHHHHHHHHHHHHHHHHHHGH>FHEDBGHHHHHHFFHHHHHHEEB=EBEHHHHHHFHHHHHB@.@A6HFFF>@@5BHHHGGFFFDDFEFGGFFGHHEHHEDHHHFBHFFEGEHHGDHHHBFDD<6*/EEFGE86C2638 @read_150_78/2 CTGAAAGTAGAAAAAGGAAAAATAAAAATAAGAACAATGAACTTGGGCAACACATAGAAAACAACAGCTAATGCTACTCAAAAGAAACCAGGTGTAGTCA + HHHHHHHHHHGHHHHHHHHEHHHHHHHF8;+ @read_150_79/2 GCCAGGCTGGTCTTGAACTCCTGACCTCATGATCCACACGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACTGCTCCCGGCCACAGATCG + HHGHHHHHHHHFHHHHHFHHGEFGEGBEGFGGGFFHHHHHHFD?D5@A.6'CCDBEHHH>6:5;7-2>< @read_150_81/2 AAGGCCCTTCTCTTTTGTTTCAGAAGTCTGCAGCTAGGTCAGCAGTGTAGTATTCTGTGTTTACTTAGAGAAGCCAGGGGAAGTATTCCAAAGATCTATT + HHHHHHHHHECGGGFFHHDDC5;G?:>@DB9EEDGFDCFHGHGHHHHHEGGDDDEHHHHHHFGHHHHHEEADBEA,(6HGDCD=>>C@BFBFHHBFDACE558:BEEF:>ADFDEHBEFHHHHG @read_150_83/2 GTGAGAGTTCTGCTGCTTTCTGGACAGTCTGTCTTTAAGCACCCGTTTGTGATTGTTTCCACATCTAAGACCTCTCCGGGCTAAAAGCACCTTGAAAGCA + HHHHGGGGHHHHHHHHHHHHHFDDGHHHHHHHHHHHHHADHHHHHHHFFHHHHHHGHFGHHHHHHHGFHCDFDBHHH=,BCFGD@DDGDCAEDC9=*/DF?EF=BB::78C*57=D><<@EEHFF @read_150_86/2 ACCACACTATGCCACAAGCTTGCCAGCTACCACTTCCATGTCAACGTATCAAGAAATACATCTGGGCCGGGCACAGTGGCTGACACCTGTAATCACAGCA + DBBFHHHHHHHHHHHHHHHHHHHHHEGHFFHEEGBDFEGEEDE@HFHEHFHHHHHHHGHFHHHHHHHHHHHHHHHFEFHHHB@*6CCCE;;.37+B79<: @read_150_87/2 CGTTGGTGGAGGCTGGCTTCTTGGTGCGAAATACAGACTCGGGCATTCTTGCTGAAGGCAAATGCATTTTCATTTTTCTAAGGGACCAGGGTAGCCATAA + DFHHHHFEHHHHHHHCHHHHHHGHHHHHADG@@BFHHHHFHHHHCCFFHHFGHHHFHH@DFHHHHEHHFGGGGGHHHHHHHGFDCEEDFGFBG?CB??B: @read_150_88/2 AAGAATTATAATTACCTTTGCAGAAAGATTTATCCTAACAATTAGGAAGCAACTTCCAGCAGAAAGAGGGGAGACACGAGAAAAGGGGTGCTTGCAGCAG + HHHHHHHHHGGFFDCDFFHHHG@;@6>>CEHE@GHHHHHHHHFD?HHHHBBFHHHDCCBBDEEEFEEEHGHHFFF@11;646=D=C?6@&/)6C@.:/-< @read_150_89/2 TGATCTCAAGTTCGGAATGACTCAGAATTTCAAGACATTTATTTTGGCACCTAAAACTATTACAGACTTGAGTCAAGTGAATTATGGATTTACATGTGGG + HHHHHHHHHHHHHHEDGEBB236+:9<.<5EBEG9?.(;D8EHHHC=FGFHHHEGHHHHHHHHHHHHBB:EHHHHHFHHHFHGGHHHHHFBBD5=?DGBD @read_150_90/2 TGAAATGTTTTTTCATTTGTTTGTGTCCTCTCTTATTTCCTTGATCAGTGTGTTGGTAGTTCTCCATATAATTTCTATCATTTTTTAGTTGAAGAAAAAT + HHH8A:6BCEFHHHHFEEGGHFHHHGGGHHGCGGHHHHHHHEHFC:EGGEDCC@@@FFBFDE8FGGHHHHHGDDCD296CFFDHHHFEHHBFC;ECA:+2 @read_150_91/2 TACTATCTGTGGTTTGCGAATCTACTAGGGGTCTTAGAACATATACTGCTCAGATAAGGGGAACTACTGTATTTTCTTGGGCAGGAGTATGATTTGCATA + HHHHHHGHHHHHHHHHGGHHHHHHGDCDD>.@>ABFHHHHHHHHHFFGEFFHHHHHHHHHHHFGGEEHHHHHHHHHHHEHHHH>C?D;EEFEHHHHHHHH @read_150_92/2 TGAACTAAACAAGACTACTGCTCAGTTTTTGTCCTGTTTATTTTCTACTAGTCAAACAATTTGTAATTCACACAAAAGGGTTGAAAATGTTTAAGATCTA + HHHHGHHGFFFFHHHDGHFFHDHHHF=/>?GGFHHHHGHHHFCCCBEHDBGGGGGHHHHHHHHHHFCCEHHEHHHHHHHHHFHHHHGD88=@FEFE8=64 @read_150_93/2 AAAGCACTTTCTTATTTTTGCCTTTTATAGAGATTTTCATTTTCAATATTAAAGGATAAGTAGGCCAGGTGCAGAGACTAACGTGTGTAATCCCCTCAAT + C5@HHGHHHHHHHHHHHEGGBDGGHGGHHHEFFFGCFFHHH@CHHHG>@DDGGGFDCB76?ADEHHFFHCCGFHHEGB@EHHHHHFHHHHHFEG9AF6BH @read_150_94/2 TAATCCCAACACTTTGGGAGGCAGAGGCGGGTGGATCACAAGGTCAGGCATTCGAGAACAGCCTGGCCATCATAGTGAAACCCTGTCTCAACTAAAAATA + EDDC6-<56;CAHHHHHHHHHHHHFHHHHHHHHHHHHHHHHHHHHFHHHHHHHHHG8EGGHHHDCFHHHHHHFHHHHHHF=E=FFHHHHHE<76EDCHHH @read_150_95/2 TGTTCCTGTTTCTCCACATCCTCTCCAGCACCTGTTGTTTCCTGACTTTTTAATGATCGCCATTCTAACTGATGTGAGATGATATCTCATTGTGGTTTTA + HHG@EGIGHEHHHHHHHHHHHHHHHHFHHHHHHHHHHHHHHG?BHHHHFHFIGGHHHHGHHHEEF:;8GGHHGGHHFHEEDBEHHEF6655BDEGCEHDE @read_150_96/2 ACCTTACAGATGAAGATACAAAGGTACAGGGAGATAAAAAAGTGGTTTGGTCTTAGCAAGTCAGTGGTCTTGACTGCCTGGTGCTCTTTTTGTTACACTT + HHHHHEGFHHGC86BEA=GEEHHHHHHHG>EBGFHHHHHHHGGGGGFFHHHFHHFFEEDDHEFFEEHHHFGHGGFF0:+,-(+A @read_150_98/2 GGGGAGGGCAGGAGCAGGGTGTGGCTGGAAGAGGAAAGGCTGGTGGAGAGTGGAGACTGGTCAGCAAACACTCTTCATCCTGTCATTGGCTGGGACTTGT + GHHHHHHHHFGBGFGHHHHHHEFHHHGHHHHHHHDHACHHHHHHHFF9E?EGDCFDGHHHHDB=GBBBBBEEEHHHHHHE<6-7,:;))%4><;9CDFFC @read_150_99/2 CTTATGTGTCCAAGGACAGCTGTATATTTACAAATAGCAGAACCAATAGGAAAGTTTGAAACATTTACATCTCCAAATTATGAAGGAAAACAAGATCAAC + HFFFGHEFHHHHHGDDFGHHHHBF>HHFHHGGFHFGGFHHFHGEDCFHHHHHHGEFB4,*2E @read_150_100/2 TTTCTACCGATACCTAGCAAATAGGGGTTCTATTAGCAGAGAAGAAGGGGCATGTGATAGGAAAGATGTTGGGCTAGTGATGAACAATTTCAACTGTTGA + HHHHHGFHHHFEFEBEDEFFHGFHHHHDGGE=B@FHHHHHHHHHHGDE.ABGFDFFEF@FH @read_150_101/2 ATAACTAGACAACTGAAAATATGATTGAATTGCTGCAATCTCACGATCAAACTTGAATGGATGAGCAGCTATTCTTACGGGTGGGCAAACAAATGGTTTC + E@8<5<=D=DHHFDD>@.C>@BD== @read_150_103/2 GCCTTTGCATCCTCGTAGCCTAATTCCCACTTATGAGTGAGAACATACGATGTTCGGTTTTCCATTCCTGAGTTACTTCACTCAGAATAATGGTCTACAA + HHHGHHHHHHHFGBBDFGGHGD@HFDGEEHFHHFB.%3)331)%%-*'4()&*/ @read_150_104/2 ACCAGTCCCTGGCTCCCTGGCCAGGCCCAGTGCTGCCCAACCCCCCTACACGGGCCCCACATACCCACTGCCCACCAGGCTCCTGTCAGCCAGGAGGGGA + HHHHHHHHA?HGHHHFDBHHHHHGFHF9>ADD7828.?EEDD35:A<.A@><9ADE@@@C@7&%< @read_150_105/2 CGAAAGGCACATAGAAATTACCAATGGGAGAAAGATGGCTAAAATTTGATACCATACATCTTTACTAAGCTGGCTGTTTTAAACCTTTGTCATAGCTTTA + HHFHHHHEEHHHFEHFHHHHCHHHGGDGD=EEGD@EHHHFHHF??99;HHGFGFDHHHHHHG>10+8<@B5<+)6(8;EHEFF:AHDGGHFHF)85CD6: @read_150_106/2 ACATCAGGATGTGAGGCAGCCTTGAGTCATATGAAGAGGGAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAA + HHFFHE>?<<@GGDDGD@EHHHHHFGHHHFHHHHHHHHHHHFFHHHHHHHGGGHHHHHFHFGGHHHHHHDHHFFHGHHHHFGFHH@@EBGE=GGGHHHHH @read_150_107/2 TTTCCCTATATGCAAATCTGATTGATTTCTTGCTCCGAAAGGGAATGCAAACAAGACTTAGTAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATC + HHHHFFGGGGHHHHH@50)6C599;D?>HHHGGHHHHHGAEBFFFFBDHCHHHHHGGHHHHEHDHEGF@@EFHHHHHHHHHF><>BDDGBCE0<+>FCC; @read_150_108/2 TGCTTCAAACTGCCTCGCTTCCCTTTTCGCTCAATTTTGCAGCCATAAAAACATACCTCCTAAATAAAGCATTAGCATTCAATACTTACCTCAGGCTCTG + HHHHHHHHHHHFFFHHHHHHHFGEEHHHHHHHHHHHHHHHHGGGFE;?CBFGIGGEHHHHHHHHHHHHEEEGHHHGFBGEHDHHHH?;DFBHHHHHH>@?>6.?;DGFHHHHHHFEHHHHE??EE<*.::.@GGHHFH?HHE:.<4.:@GFHFHHHHEGFHHEHHHHHGGHHHHHCDGFFGHGFHHGFCHHHHHHH @read_150_112/2 GCAACATGGTGAAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGCTCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA + GGFGBAEHHHGHHFHHHHEEA8CADD:.8DEDFHHHFGHEDCEBE>:*EFFDDBDGHGGFEBGF@>>B=336BDHHHHHHEBEE.659=AFHHFFBCA?E @read_150_113/2 CACAGGAGTACATGTACTAGGGTTACTATGAGGACTTAAGGAATTAAAACATGTCAAGGACATGTGGTAAGAAGGCAGCCCATCAATGAATACGCGTGAA + @><855@5D8BEE>DDDCBA1=58:<6;=B@GEEBFDC= @read_150_115/2 CAAAAAACAAAAAAAACTAGGTAGAATGTGATACATGTGAAAAGAGATCCAGCTCAAGTGCCTTGGGAGCTCAGGGGCGGGTGAGATTAATCTCTTTTTC + HHEHHHHHHHGF;9EE21,*60(2FFF@<<<:,A6,=D@@A@ @read_150_116/2 GGAGAATCGCTTGAACCCAGGAGGCAGAGGTTGCAGTGAGCTGAGAGCATGCCATTGCACCCCAGCCTGGGTGACAGAGTGAGACTCTGTCTCAAAAAAA + HHHGD8>@@BHHHEGGECGG=@B8CDFFG;8EEIFFHHHHHHHHHHHFHHHHHGHHHHHHHHHHFHHHHFBE2?EFE.5,41-<5>AEFDCFBCFHFADG @read_150_117/2 TTTCTATAAAGGGCCAGAAAGTAACTATTTTAGGTTTTTAAACCTACTGTCTCTGTCATAACTTGTCAACACTGCTGTATGAAGCACAAAAGCAGCCATA + HHHHGFHC>HHHHHHHHGHHHGGHHFGFGGHFHGGHHHH>@<59>AFH8@EGGGGHHHHHFBEHHGIGHHHEGHFHGEGGGBHE=)4E7403A@D?DFBC @read_150_118/2 TTTTATATTTGAGCCATAGTTCACCCTCTATTAGCTACAACTAATCTTGAAGAGACAGAGGATTGGCACGGTTGATTTTTAGATCGGAAGAGCGTCGTGT + HHHHHHHHHHHHFHHHEHHHHHHHHHGFHFGBEEHCDGBHHGHFHGHHHHFFGGHHHHHHEEGEEDGEBBDDGADD?CHHH?HE@49:=CDHHHHEDGEE @read_150_119/2 TTGTAGTAACTCGAAGAATCAAGAGAAAAGCTAAATATTAACATCTAGATAGCAAGATTTAATGTGCAAAACTTTAGACTTCTTCAAGCTGAATCAGCCC + HHHHHHH@*?-5>9-><;=HHHHHHFHHHEDEEG/+86;2DDHEFHBEDCGBEFFB5CBE@FGGGDBFF?=;@<1')-/BGE@+6<5,@FBAE@AHHHFF @read_150_120/2 ACTTTGGGGGGCCAAGGAGAGTGGATCACCTGAGGTCAGGAGTTCGAGAACAGTCTGGCCAACATGAAGAAACCCCGTCTCTATTAAAAATACAAAATTT + HHEEE?BGHHHHFHHHHHHGHHBH<@FFHHDDCDFHHHEGH?DDC>F?<3)+3*90>@;C@>DB3?ADGH@ACBC05ACDCEEGCFD=ADDDHH @read_150_121/2 CAGAGATCTGGGTTCTAATCCCTGAGATGTTACTGATTTGGGGTATGTGTTATGGCCAGCAACAGAATCCTGGTTTAAAATATAGGGCAAAAAAAAGAAA + HHE=EHHHHEHHHHHHHHDDHHFEHHDDEEHHHHHHHHHGF>@@:FHHHHHEEGHHHHHHHDHHHBEEHGEHEDD72EEGHHHHEEEEHHHHHH;45,4C @read_150_122/2 CATTCACAATCACTGCAAAAAGAATAAAATACCTAGGAATATAGCTAACAAGGGAAGTGAAGGACCTCTTCAAGGAGAGCTACAAACCACTGCTCAGTGA + HHHHFFFHHFBBFBFHHHHHBEIGGGHHEFGFGGGFFBC@:BFFFFE@/7)/=DA5<8CHHHHHHHGE/08ABBGBHHFIIGCDHHE@ADEEEHHGGBHHGFEHHHGBE@GFE7()9>,:FF@FG?>5 @read_150_124/2 ATGTTCACCATCTTCATTTATGTCGTTCACATCCTGAATTGTTAAAAGAGGTATCATTGTTAAATGTTGCTAGGTGAACAAGAGATCGGAAGAGCGTCGT + GBHHHHHHHHEBCC;<87CEHGHH@FEG>HHHHGFEHHEBEBGFHADCDFHHHHHE=B9CD(6EF @read_150_125/2 GGAAGGGAGCAGGGCCAGCAGGGGATAGGGGGCACTGCCAAGCTGTCAGGGAGGCCAAGGCACGGCTCATCCCTTCGGGGCCCCATTTGGTGCCTACTCT + HC?FFHHHHHEGHHHCBGHHEE.DHHHHHF<<7BGHHHHHGGFHHDCFHHHHHHDBEEGGGGEE;A<974<>:783:BAG=<>,86??GADB;57>@CB? @read_150_126/2 ATTTATTCTGACGGTGCATAAGTTTTAAATGTCCTTCAATTATTTTCTTTTTATCACAGTGAAATAGTCACTATTGTTTCCTTTGATATTTTCACATTGA + HHHHHHHHHHHHHHHHHHHCGGGGFFFHHFFGBBGGGHHHHHFFAEA>6=EEBDGHHHDD<><;8<.77DEHHHGHHHGC+797E.;>EDHHHHHHHHHHHHHCHHHHHHHHHHHHGHHHGE/@=@BCDBB69B:ABEDEEHHHGGFHFHHHHHHFFHFDEHGHHHFFDDD>@,9)+(4B8EHHHHGGGFHHEDCDD45EGHHHHHHHHHHHGGHHHHFFHHHHHHHHHHHBGDCDB@87CC? @read_150_130/2 GGCACTCTGCAGACAGCTCCAGAAAATCAGGCACTCGTCACACACAGAATTCCTCTAGTGGACAGGCTGCGTCATCCCATGAACAGGCAAGATCAAGTGC + DBBEG;<@@FDHHHHHGGHHHHHHFGGGHGHHHHHHFHHF=DHHEFGB/8:=785B9>@HHHHHHHHHHEC@@?@GHHHFHH@7EHEE@B55477&0:11 @read_150_131/2 TCACAGGAAGGTTTAATATTTGAGCTGATAAAAGGAGGCTACCAATTTGAGTTACATTGAACTGCCAGAAAACTGTGCCTTCTAGCCTTCTACAAAGTGA + HHHGFC@6?@@EFIIHD?FHHA@..45@??=EE@GGFGGGHHHHGGEHHHHFDDDAFEEFF=>8DHHHHHHHHHGGFBDC>CBBGEEDB95.55;HHHHFEA=EE@ @read_150_134/2 CATGGCACAGGTATACATATGTAACTAACCTGCACATTGTACACATGTACCCTAAAACTTAAAGTATAATAATAATAAATTCAAAAAAAAAAAAGAAAAA + HHHGEBB/0,)=CDHHHGHHHHEHFEEDEHHDDHHHHHGHGGFFGGG4@@DGGDDB@=CDGGHHHHHHHHHEEBGHDHHHGDFFHHHHGGHHBFC;5>CD @read_150_135/2 CATGAAGAATGCACCTACCAAAAATCTGAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAA + HHHHHHGEGG=EHHHHHHHHFECBHEDF??FGFH;@GFD9@FIGGF@@>GGFEHHHHHHHHHHHHHHFHE8(<@)..:>CD,9 @read_150_137/2 CTCCTGAGTAGCTGAAACTACAGGTGCCTGCCACCATGCCCAGCTAATTTTTTTTTTTTTTGTATATTTAGTAGAGATCGGAAGAGCGTCGTGTAGGGAA + HHHEEBEHHHHHHHHFHHHHHHHHFGHHHHHHFGGGFHFGF?EGE566/)20?GCDEGDEHHHHHHFHHGFC=88BBCEEEDEFHHHE4G8:?;DFFHFE @read_150_138/2 TTTCTTCAAGTAGTAAAACAGCCTATTCCTGGAATGTCCCCTGGAATGCAGAAGTGACAAGGATGCTAGGGGAATTTCTTTGAAAACCTGGAACAAGAAC + HHFCDDEHHHHHHGGHHHHHHHHHHHFHHHHGHHGHHEDDHHHHHFFFDFHHGHHHHBFFBGBGBEAE?E1DDHHHHEE5<= @read_150_140/2 ACAGAGCGAGACTCCATCTCAAAAAAATAAAATAAAATAAAATAAAATAAAATAAAATAAAATAAAAATAGAGCCTCTGACATGAGTTCCACCAGAAAAC + :>>>:14D @read_150_141/2 CGAAACTCCTAAAGTCTCATACAGGAATTGAAGACAAACTTTCCAGATTAAAGAAGAAAGACGATCAAACCTAATGGTCTTAAAACTTTTAGAAGATCGG + HHHHHHHHHHHHHHFFHHG@EGG8CHHBDCEEDCDHHHHHHFHFFHFFGGEECCA>DHHEGDB?C.:FHHHF??=DBFFEG=EHHHFFIGE?>2:(8>.1 @read_150_142/2 TCACTCCCCACCTTTCACTGAACTAAATTATTATGGGCTTTTAGGTGAGTGGGAACCAAACTTTTTTTGTTGCCTCATTGTATGTTTGAGTCCATTTGTT + GGED=FGHHHHHHHHHHHHHHGGGDGGEDDDDEEEFHHHHHFHHFFHHHGHHHGFHHHABGHHHHHHHHFEEEGFHGHEHHHHHHEGCDFBB..DHHFGHFHGDAFHHH@=AC<;CB/3(8D:EHHHHEEHHHHDEGGGHHHFHHHHHHHHHHDEFGFHFF;= @read_150_147/2 TGAGATTCCCTGTCATACCAGTTATGGATAAATTTGCATTTTGGATGGGACATTACTGGACCAGCCCATTTTAGGCAGTTCCGTTTCCCCCTGGGTGGGG + HHHHHHHHHHHHHHHCE@GHHFGGFGGFCFHHHHHFGHHHHGGFHHHHA.GBCDDEGEC@GGHHEFGGGF@572(5-<>?2?CBC::>CHHHEG @read_150_149/2 GTCTCGCTCTGTCGCTCAGGCTGGAGTGCAGTGGCACAATCTCGGCTCACTGCAACCTCTGCCTCCTGGGTTCAAGCGATTCTCCTGCCTCGGCCTCCCG + HHHHHGGE=DEFFBCEGHHHHGHHHHHHFHDGHCEB?17/.;EBEFGFDD6BGFFFBGHEB=:80.6607FHHDFBFGHGHEFC/3:+=6115DHGGG80 @read_150_150/2 GTATACAGGATTTAGTACTAATCTAGTTTTAGACATCCACTGGGGGTCGTGAAATGTAATCCTCATGAATAACGGCAGGGGGATTACTGCAGCTTTGTGT + GGGGFHHHHHHHBGGHHEHHHFHHHHHHBDFFHHCGHEFEFHHHHBFFGEHHHHHHHHHHHHFABEEDDHHHHHHFEHFDC?DBBDFFF49=7,6)%4>B @read_150_151/2 AATTACCTACTTTGCAAGACCTACGTTAAAATCACCCACCACAGACAGTAAAATCTCTAAATACTCTTTCTCATTTTCAGATCGGAAGAGCGTCGTGTAG + FEHHHHHFFBF=@DCGGHHHHGGHHHFFFEDA;>B@GHHHHHHBDEEFHHFHHHHHGGHHHHHHHHHHHHHHHHHHBDBFFHHHGHHHHE;@AHFH?DD, @read_150_152/2 GATTATATAAACAGATATTTTCTTTATCTATAAAAATCAGGTAATGAGTGCTCTGGGAATTTGAGTAGGATAGGATAGTTTCTTTAATTCCTTTAGGGAA + B@GDCEEEHGHHHHHHHHHHHGDGGHHHHHEHHF@A?@:=%1/D=8,?ABDHHEECFHEHHHGHGB@8<8CC>>.6>CHHHHHHHCC=.:1*++<@:DEB>4@58@:FHHHHHHHEGGHHGGGGG46-,31,:FFHFFHHDABC< @read_150_154/2 TACAAAAATATGACTAATTCAAAGGACCAAGGTTAATTGACAGAAACCATCCTGGAGGAAGGACAGAAATTGGAGTTACTAGACAAAGGTTTTAAAAAAA + 95<<@@DDDEBEHHDGDHHHD?C@BBBHHHFHGB>FHHHHHHHFI8><<?GEFFEEFHHHHHHHHFFEDFDF?D?6/CCD;A:;A7C>>;:.@CEHHFFFHHBE<.60(''64B@D/;<<5ADGGFHHHHHHHHHGHHHGCBEAA?BCFHH @read_150_156/2 GGTCCTGGGGTGCCTGGAGAACTGGGGAGGGAGGTGTGGAAGGCCCTCTGCGGGGCCTGCATGTGGTGCATGCTCAGAAAATACTGGTGGGTGGGAGGCT + HHHFE:BGGHHHHHHHHHHBEHHHHEGBHEHHFEHHHA<4@BFHHHGHHHHHHHHHHHHDGGGGGFHHFFGEHHHHGGGH.5?00,/EABFEG @read_150_157/2 GTCCAATTTTTGTATTTTTAGTAGAGATGGGGTTTCACCATGTTGTCTGGGCTGGTGAAGGTGGTAGGTTTCAATGACAGCAGCATAATGCCGTGGGAGT + @ECDCD>6.>7CEGHHHHFHHHHHHFHHHHHBEGBHHHHHHHHHGCBEEEHHHHHGHFHHGGHHHHFHHHHHFHH9EFHHHHHHF@CCDFHHHFH:?AA? @read_150_158/2 CATAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA + GIIGHHFHHGCFHHHHHHHHDDB@;B@D?>5BBGBGEBDHHHHHHHHHHGGDDCDEHFHHFHHFFFGHHHHHHBG51?HDEEHHHBFHHHHFDEBEBGFH @read_150_159/2 GTGTGGGTCTCAAAGGAACATGAGGCTACTTATTCATTCAATATTTGATATTAAGTGCCTACAGTAATGACCTGGATGACTGAGAAATCACCACTGACTT + HHHHHHHFHHFFHHG><><>BFHHHHHHHHGFFFHHHHHFHFHHFGGD.FGGEEBEFHHHDBGHHHHGGBCEDEEGHHHHEEEEEFCFHGDF5<:A;6FF @read_150_160/2 GTAGCAGCTTCCTGAAGGGTCAGAGTGTGAATATGAGTCTTTGTGAACCAACAGGGACATAGCCCACCCACCCTGTCCTGAGATCGGAAGAGCGTCGTGT + HHHHHHHHHHHHEE@EGEB/5<73BFHHGC1<:<>?HHF<8=A=<;-1<.2-,:22HHHHHHFHHHHHHHGHEGGDEFEHFD446GFHHE=+@AFHH @read_150_161/2 TATTGCCCAGGCTGGAGTGCAGTGGTGCCATCTCGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCCTGCCTCAGCCTCACGAGTAGCTGG + FBHHGEGHHHHHHHHHEEEFBHGEGHHGGHHHHHHHFHHHHHHHHFEHHHFHDDGHHHHEAB74/>=B=GBFFHFF?EDH@EHHE?=5C6?DE8CCC@@HHHHHHHHHHHHHGHH>EHHGGHHFEHHHHFHFCB5;<;ABE @read_150_164/2 TGATATTGTATTGTAGTTTACAAGATGTTATCACTGGGAGAAACCAGGTAACAGGCATGCAGGATCTCTCTGTATTATTTCCTAAAGATCGGAAGAGCGT + HHHHGGG@EEGFFHHHHEDDDHHGHB=@FHHHHEDHHHHH@;EFGFCGGADDHHHHCDDFHFED5DDDCAGFHHFHHHFHFG;EEB><>,;@6-&/3:6C @read_150_165/2 GAGCAAGACTCCAACTCAAAAAAAAGGAAAAAAAAAAAAAGAAAAAAATATCCAGATGAAGAAACATGCCCGGGTTATAACAAAACTTTATTTATGGATG + >--;BGHGDGED7-9HHHHGHBBBB@FFCHHHHHHHHHHHEEHHEHHHHHE=EEFGBFGDBBEFFE?HHGGFHHHHFHHFFHHHHHHGHHHHHHHHFIHHHG@=?DECAB@ABFHHHHGGEDHEFEHFCFF @read_150_168/2 GGAGTCAAGGGCTAGGAAATGTAGAGCCTTTAGCCATCGTAATCTGTTAGAATTCCATTGTAACTGAAATGGGAACTCACTGGAGAATCTTAAGCACAAG + GFGDGGHHHGDF?6:.2+===;;BHDHHE?=AD8CHFHHCDFHHHHHEEGFDG/A9.;CGGBBDCHBB5:8DCBBDEHHHHHHHGFG?BFHHEF? @read_150_169/2 GACTTTTTTTTTAGAGACAGGGTCTTACTCCATCACCCAGGCTGGAGTGCAGTGATGCCATCATAGCTCACTGCAGCCTTGAACGCCTGGCCTCAGGCAA + HHHHHGHFFF.GBGFI8;HHHGHGFHHF?>77DDD48EEGHFB>6=CDDDEAB=6C@859@DGHHHHHDBCGHHFFFCBC=<<%)62-32=A(/@&(6D> @read_150_170/2 GGAATTAAAGTAAACGGTTTTTGAGGTCACAAAACTGATGCAACCGTGCTCAGAGAAGTCTAATGTCTTTTCTAGGTCACAGCTATAGCAGAGCTTGGAC + HHHHFBFFHHHGFGHHHHHHGHHEBHFGGHHHBDGGHHHHHHHHH?DHHHHHHHHHHGHFGGGHHHHHFHHHHHHHEC2C=?=>DCA?H @read_150_172/2 GACATATATTAAGAAGGCAAAAGCTGGAAATTTAAATTCAAGGGGGATTATAATAGTAAGGTGGGGGAAATCATAGATTTAGCAGGGAAGTATGGGAGCT + HHHEFG8?FGHFABGG<GIDDFFHHFDC7@>CBDGFB<488:.>.5?7:6:AB6<40..8=CD?AA*6EB?@EFGDGEEEH @read_150_174/2 ATCTCTTTCTTATAATGCCAGATTTTGCTTCATATCATTTGAGAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCAT + 8DDHHFHHHHHHFFGGHHHHHHHHHHHHFGHHG:HGGHHHHHGF?8'53CHHHHE@C2:67@FG;6>@CHHGGEFDHHHHHHHHD?CADE??FHHHHGHF @read_150_175/2 GTCCAAGGGAGGAGGATTGCCTGAACACAGGAATTTGAAACCAGCCTAGGCATCATAGTGAAACCCTGTCTCTGTAAAATTAAATATATATAGTTTTAAA + EHHHFHHHHHHHHHHHB?CBGE7555<4@=GHHHHFFEHHHGHGHHHHHHHHHHHGHEGFHHHHHHHB<@6416@ADGEFHHDCHHHHHFHHE-5BB @read_150_176/2 CCATATATGAGTGGGAATATGTGAGATTTGCAAAAGACCCTTTTAAAATCTCATTATTTTTGTCCGTTTTTCTTCACTCCTCAATTTAGTTGCTTATGGA + HHHHHHHHHGGHHHGHHFGGHHHHB@BEGFDFGGEDDGGG=2)0>A49.?<;.<<.7.>323=GHGGGHGHHHHHHE=GHHHH@DGFFF?=DEDHGFHHH @read_150_177/2 TCCTGTTCTACACCATATGATCAGATAAAGGAAAAAAAATTATAAAGCCATAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGC + HFBHHHHHHHHHGGHHHHHHHHHHHGD.38:;;EGGGDHHGEFHHHHEECDDDFFHHFFD846==HHHGHHHHHG>.*63;;BEHHHFFC>,5?EHFGCHDHHHHHFHHGGFFDBGEEACB@FFBFFEE=BHHHFED;<@:-13<:;13(32 @read_150_180/2 AAGAAAAACAAACCCCAAATTCGAGAGGAGTTCTAGAAATATATAAGAAGAGGGCCAGGCGCAGTGGCTCATGCCTGTAATCCCCGAACTTTGGGAGGCC + EDHHGHHHHHHBEHHHHHHHB?;EGHFGEEDB8(<<@B.>FC;CA-1/)(9 @read_150_181/2 TTCATTAAGGGTTGCAAAATGGAGATATCCTAATGCTATCATTTTTTCATCTGTTAGGTGAAGTTTTACTTACATAAAAACTTCATCTCTTCTTGCTTCT + GGHHHHHHHFEHHHHHHHHHHHHHHHHHHHGGHHEHHHHHHHHGFDFHHGFFDGEGGHHFHHFH?FFFFHHFH=6=@7<<3%0FFFFHHHBDE9>EGDA> @read_150_182/2 CACACCTGTAATCCCAGTAACATGGGAGGCCCGAGGTGGGAGAGGATCACTTAAGGCCAGGAGTTCAAGACAGATCGGAAGAGCGTCGTGTAGGGAAATA + HHHHHHHHHHHHEGBEGGGFAFF>@-8>>-,/EHEAHHHHHHGGDBBBEGFGHHHHHE=@CDB:.4@ED>FAAFHHHGFHFHFHFFFEFFE<@=DD@5,? @read_150_183/2 AGGAACTTGTTTAAATTGAATCAAAGGCTGACTTCCTGGCAGATTTTCTCTGTGTATTGGTTTTGTTCTCTGAAGGCAGCAAAGCAGTCAATCTCTTCAT + HHHGGGHHHHHHHFGDB4@@FEHHGHHHFGHHHF>GGGGBFEGGFGHHHHFEEHHHHHHHHHHHH@GEHGEHHHBGGFEEEEGG<;EBFECDDEFGGFA> @read_150_184/2 GTGACACTGATGGTAAGTGGAAGCTGCTTCTGATCAGTCAGAACAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCA + DDEB@DBBFCDFHHHHHHHH@CAEEB3376EEE::?FHHC@@.3-5=99EGDCE @read_150_185/2 TTCTTATCTCCAAAGCATAACTGCTTTTTCTGCAAATCTTATAATATCTTCTTCGGCACATGTGCAATAGCAGATCGGAAGAGCGTCGTGTAGGGAAAGA + HHHHHE=C2.67BEDIGCHHHHHHHHHHHHHHEFHHGEGCFE?BEHEIB?CDDFHHHHHHHHHHHHHHHHHHDDFDHHHGFDDC+?B@HHHGGB=BDA16 @read_150_186/2 CTTTAGCTTTACAGAAAAACTGAGAACAAAATGCAGTGTTCTCATGAATTCCTTCTACCCTTTGCACAATTTCTCTATTATTACAACCTTGTATTAGTAT + HHHHHHHHHFHHHHHE@<>:5C;EGEGG?EHHGEE<))18EFHHEE>BBDDCCFHHFHHHGEGHHHHHHHHEEECDC69BGHH<66;+196FBE;EFFD81'CGFHCFHFFEFGHHHEEC8EHGHHHG@CFD8<-'7388GGBA?6?=A618)59DE@/DBDB @read_150_190/2 ATTATAGACGTGTACCACCATTCCCGGCTAATTTTTTGTACTCTTAGCAGAAGCAGGGTTTCACTATGTTGGCCAGGCTGGTCTTGAACTCCTGACCTCA + GGHHHHHHECDEHHHB8=FHHHHHHFHHHHHFEEEFHHHHHHHFFFFFBHGGGGGGGHBHHHHHHHHE8:BEFBEBDHHHGFHD=<5,59496/:5=C88 @read_150_191/2 GACTCAAAACACACTAATGAGATTCTGAGCAAAATCCCTCTGGATAATGTAGTGAAATATACTCTTCTAAAATATAAAACAGATAACGCCAAAAGATCGG + DCDGHHHHHHHHHHHHFFHHC?G@FHHHHHFGHHHHHHHHHHHHHHHFD;CD8EGHGEDFHFEGGHHHHHHGDCEFB(AEFFD@9<<91'67...5>:@77AHHFG/DEFHHFHFG8CCA>FHHHD@EFHF8B<396=>?@?>DDD;C;DCE=GFEAA @read_150_193/2 TAAGCACAAAAAAATATGCTCAAAATAGTCATTTGGGAAATGCAAATCAAAAGTGTGACATACTTCACACCCACTAGGGTGGCTCTAATAAAAAAGGCAG + EEBDBFHHHHHGFFFHHHHHFHHHEGDDFFHHHHHHHHHFBEEFHEBEEEGHGGCEEED6-DHHHHHHHHHA6GFFDF78C95BEHFEDDB@@ABAFFHF @read_150_194/2 CATGAGACTTTTTCACTACCATGAGAACAGTATGGGGGAAGCTGCCCCCATGATTAAGGTATCTCCCACTGGGTCCCTCCCACAACACTGGGGAATGATG + HHHHHHG=ECEHHHHHHHHDGEGGE;FEHGGHHHHHHHFFD>?CFHFHHHHHHHH@>4724:BBFFHHHHHHHHHHHHHHHHEGBEEB/DBACFEE;A@5 @read_150_195/2 ACGCATCGGTTAAAAAATGTTTTAATTGAACCAGAAAAAAAAAAAACACAATCCAAAGGAAGGCAGTGGGGAAGAAAAGCAGAAAAAGAAACAATGGAAA + )0+/AEHHHHHGFFHHHHHHHHC.BGHHHGDC@HHHHHHHHHHHHHHHHHHHHHHHHHHHDC='=BFHEEEGEHHHHHHHGECEE?GHHHHHHHHHHH@GE@EEHHHHHHHHGGGGFHHHHG=C@AFHHHHHHHHG@HHHA @read_150_199/2 TTCCCGGAGTCTTCTTTGTAACACCCTTGACAACATTTAGTGCAATACCAATAATGTGTAAAAACAAAACACAAATCCATAATAATCTCCCTCAACATCA + HHHHHDCC>CEECFHHHC;7B>>BDDHGDD@EHHHHFHHHFHHFHHHFABHHHHFHHHHHHHHHHHHHHHFHHHHHFF@EEDBHCFHB0&%-(78DD@.C @read_150_200/2 GCCAATGTCATATGTCTTGTCATCCTGCCAGTCTGCATGCCTGCTGGCCTATTCATAGCATAGATATTTTATGGTAAGGGGTGATATTTGAATTGATACT + HHHHHHHHHHGGGFHHHHHHHHHHFGGG8?-2>>=FDEEEDFHHHHHHHECFFFHGBGEHHHHDB8*::+31).>E6.0.3?>@.DGHFDEEHHHHEEA; @read_150_201/2 CCAACCCACCCCAGCCTCGCTCCTCTTCTGAGACTCCCACCTTCCCAGGGGAGAGTGTGCAGTAATTCACTGTCACTGTGCATTATATTTTGCCACCCTC + HHHHHG@A3EGEAC;?GHHHFHHHFGHHHEHF;?FDHGBHH @read_150_204/2 TTGCCTAGTCTTAGTGTCTCATAAACTCTATTCTCTGGCCATAACTGTTACTCATGTTTACGAGATTTAATTCAACTACAAAATCTTTTCTGAAGTTAGT + HEHHHHGGEHHHHHF?:;EFHF=>DGGBAC@>@@HF=FHHHHFEBFFHHHFGIFGGGDHDBDGGFEHHHHGDCBFFBEBCDHHHGHGEEHHED0&%%?BD @read_150_205/2 ATCGGGTGCAAGATACTTCCCTGATCAGCCACCTCTACCTCAGTTCCTGGTAAGAAACGTGGTCACTGGGGACCACGTGAAGTCATTTAGCTGAGGACAG + HHFD=@9BFHHHHHHHEHHHHFHHBHHGB?GBGB096?EHHB65/%53355 @read_150_206/2 TCAAGAAAATGCTGTCTTCATAACTCACTGGAGCCTCTTCCTCTCGATTCTAAAGGCTACTCCCAGTGTTCTAAAACTACACAGATAGATCGGAAGAGCG + E8B<<74DD=EC663?GGGFHHHHFGFFHHHHHBEEHEFBFHFFHHF5EEEGHHHHFGB=GGHFGFFB8DB@HHHEFHFEEFHA@EGHHHFACBFFE-80 @read_150_207/2 AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA + HHFFHHFDDHHHHBDDEFHHHHHHHHHHHEFFAD8=FHHHHEHHHHHGHHHHHHGGGGHHGGGHHGGGGHGEEDEHHHHHGDFBDHCDHHHFB>BHHF?B @read_150_208/2 CTCATTTTTACTCATTTTGATTCTTGTTTTCTGTAGATGAGACTTTCACTGTTCAGCCTTGCTTTACTGTGCCTGGCTGACAAAACTGCATTACATCGCA + HFHHHHHGEGHHHHHHHHHHHHHHHHFHHFFFGHFHHHHH1'''+6EEHHGGGIFHHHHEGGF@8666,DHHHFFDGGGFFA@EGHHFFGGHHHEHHHFF @read_150_209/2 TTGAGTCTAGACTCAAGCTGGATCAATCAGAAGCCTTCCCTGGTGTCAGGCCTCTGAGCCCAAGCAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAG + HHHHHHHFHHHGHHHHHEGBBGHHFEHHHGHHED83@>DFHHHFHD>)1CEGBBBGBEEGDFGGHHHHHHGHHHHHGHGHHHHHHCDBEGGGDEGHHHHH @read_150_210/2 TAAATGGATAAATAACAGTAGAGTGTTTACAACAGTAACTGGTACAGGGCTTGTTCAATAATCATTAACTGACATCATGTATGCTAATTAAGTTACATAG + GEFEGDB,2,*0EBEEE;6EFFEHHHHHHHHDGHHHHHHHGFGDBDA9<'<>DFGHDABFFHHHHABBHHHHEB?@43+AEFGG>9729+.7;.A><<.A?7>*)12-EEEHFHHF;@6,EGGGDDD=?EGEECCEGHHHEGE@FHHDEFGFGGFEE@53,2<9AB=@;@ @read_150_214/2 CTTGAGAAATGTGTTTCCTTTGTTCATCTGAGGAAATCTAAACTCTATTCCAAATAAGCTTTCTAGGCTGCTTCTGGGGCCGGGAACAGGAGGGCATGTG + HHHHHEGEEGGHHHHHHHHHGDB?GEHHFBFFFGEFGFHHHEFHHHHHHHFBCCEDEEG=EBGGGHHHGGHFCDDHHHHH?..AA@=E53)3*;<)/*6' @read_150_215/2 TGCAATATTATTCATAATAGCCAATATATGGAATCAACCCACCATCTCCTAGCTATGTGTTCTTGGCAAATAAAATCCTACTTGCCCTTCCCATCCATTG + HHHHHHHHHHHFDEEHHFEEGBBFGEEB@<2/C>?AFEGHGBC:2'..;2CCGHHHHHHHHHHHFGHHHHE@AHDDB.,;C;77/0-,@BFHFE?A=?>= @read_150_216/2 TTCCCAATCCTACCAAGTAAAGGATGCTAGATAAAAGAAAACCCAAGTCAGGCCAGGTACAGTGGCTCACACCTATAGTTCCAACAGTTTGAGAGGCAGA + HHHHHGGGGGBGHHHHHHHHHHHHHHHHGG0-28/BEE@C&(09)26@B581@;:4AEEHHHHHHFHHHHHHHHHFHFHHCADDHHGD<:DGDEBDD9DE @read_150_217/2 CTTTTGAATGAATATTACAATTGATCCTTATTTAGGTCATTTCTCTTAAGCATACTACATCAGCAATGTTAAAAAGTGCCCAGAAATCAAAATTACCAAA + GG?.;GEHHHHGGEHHHGHHHHHHHF.>=FFGHHHDDEGHHHFF>FHHC?<<>>>;7;CHEEDDD=DBEFBFGHC@BHHEGHHHHHHHHGHHFDE@AGBF @read_150_218/2 TGAGAAGGCCATGGAGCAGGGATGCCTCCAATCCTTGAAAGGCATGTGACATGAGTAGGGAAAATATTTGCTATTGTAAACCACGGAGTTTTTTTCCCTT + HHHHHHHHFFEGFHFHHHHHFDEBHE:2<38:GGHHHHHHEGGFHFFHHHHHHHHHHHHHHHHGHFFFBEFHHHFHGG6?G?>D%7;@DFFGEED<,5F;=D6--B?EADADBC<<FGGFEFGGHHHHHBEEGGHHFBHHHHHFFDFFHHEF9*.@@GDFEFFFCFEE;82 @read_150_221/2 TGCATAATTTGACCACTTAGAGGCCTTCGTTGGAAACGGTTTTAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCAT + GGGGGHHHHHHHGGGGFHHHHHHHGHHHHHHHHHFHHHHHHHGFFFHHHHGGFHHGFE@:;3<:=E=EEEHHHHHDDHHHHFHBE=<<<>FHHGHGGDGE=EGECEHHHHHHHHEEHHBBEEEHF9';EEA41566.;82>>=DEFD @read_150_223/2 TGCATATTTTGACATGTGCCCCTCAATACACACACACAAGACACTCTGATTCTCACTAATCATATTTCTGGGGTTTTTTTCTGACATGAACACACAGATT + HHHHHFFIBHGGFFHHHHHHHHHHCGEHHHHHGGGGGHFGEEF?EHFFBAFFDCBD=-+9:34EF?GGHHHHHHHHHHFGHEB363+>A<@@.>CFB>FEIEHHHHFFFEFEEEEEE=;:<<@HHH>=.ADEHHHEGGFHHHE<;<127(=DEBFEE/; @read_150_225/2 CTCAAGGGTAATGCTTTCAACATTTCTGTGTTCAGTATAATGTTGGCTGTGGATTTGTCATAGATGGCTCTTATTACCTTTAGAGATCGGAAGAGCGTCG + HHG=CCFHHGFHHHHHHHHHHHHHHFFFFBGBGHHHHHFHHHHHHHHHFHHHHHHHHHFHHHFHHHHHHGGHHHEFHHHEGHHHHGE,>;DHHHHFB1=> @read_150_226/2 TATACAGTAAAATTCAACAATTAGTGAACTGTCTAGAAAACAAAAAGATTATGCAAGAGGTCAAGAAGAAACATGAGCAGAATGACGGTAGTTTCCCTCC + HHHHHHHHHHB74BBHDGGFFGEEHHHHHHHHHHFHHDEEGE=FHE?FFFHGGGGHHHHHHHHHEGG@GFHHBE;68;>BHGGGG666::166568EEB@DE8@DGFHFFEFFHHFCABEGHHHFE8BHHHHHHHGHGEDB;>A? @read_150_228/2 CAGGGTAATTTATAAAGAAAAAGAGGTTTAATGGACTCACAGTTCCATGTGGCTGGGGAGGCCTCACAATCATAGCAGAAGGTGAAGGAGAAGCAAGACA + HHHFFG;CBDHHGEGHHHHHHHHHHHGEBEGFGG?HFFBGHHHFFGD?EEGGHHHHHHBHHHHHHHHHHHEGD:>@BBA@AEHHHEAEEEHHHHEDCDBE @read_150_229/2 AAGAATTGCCTGAGACAGGGAGATAAAGCTGCAGCGAACTATGACCCTACCAGTATACTCCAGCCTGGGCAACAGAGGAAGACCCTGTCTCAAAAAAATA + HHHHHHHHHHFFFHHHHHHHCF8?EEGFDDGHHFFHHHHHHGGEFHHHHHFHHHFGHDB=1,8FHHHEEEB?DDDFGDBFHGDDC&&45BEFFDD @read_150_230/2 TGTTTGCATCTTCCCAAGACAGAGTTTTCCCTGTGACCACTTGTGCCTACGGATGAGTCTTAAGCCTCCAAGTCTTCCCAAGAAACTGACCTTAACTCAA + BHHFGHHHHHHHHHHHHCA:DCEHHHHHHHHGGHHHFDGEHHGIEFFHHHDDEHHHHHHHHHHED?DD=FGE>CE;<2:0--;5.<>CGGHH@B/<((7A @read_150_231/2 ACCTATGTGTGTTCATAGGCCTAAGGGTAGGAAGTGTGTTTGTTTCCTACTCTTAGAACATCTTGATTCATACTAGGAACTCTGTCTGTTGCTATAGTTA + G@@EHFFHHHHHHHHHGGFFHHHHHHHEFFHCHHHHHHHHHHHHHHHHFFFFHHHGFFFHFFEGGFFG5.*<-84F=EEGHFHHHHHFHFFEEGGEFFDD @read_150_232/2 CTGGCCAACATGGTGAAACCTGGCCTCTACTAAAAATACAAAAATTAGCTGGGCATAGTGGCAAGCACCTATAGTCTCAGCTACTAGATCGGAAGAGCGT + HHHHHHHGGGHHHHHHHHHHHHHHHHHEHHHHHHHHHHHHHHHHEGHHHHHHHHHHHHEDEB?;,33-,>:;@BFHHHHHFFCFFHHGBGGIFBBFFCG; @read_150_233/2 TTAGCTGGGTGTGGTGGCATGCTCATGTAGCCCAGGAATTTGAGGGTGCGGTGGGTTGTGATTCACCACTGCACTCCAGCCTGGGCAACAGAGTTAGATC + HHHHHHHHHHHHHHHHHHHDDC57.C@E:+16FFHHFEFHHFFF7%&8FHHHHHHGHGEG;@@:=HHHH@DFG=30)),6EHHHH?4GHFCEFFFGBCCGEFGHHHH@5--,G?GHHGHF.8-2>D:7:<:<>CFBFBH8-7=<< @read_150_235/2 TGAGTCGGTAATTGTTGAAGCTAGGTATTAGATAATGGGGATATTAATACTATACTGTGTAAATATGTATACGTTTTAAAATTTCCACAAAACTTTTAAA + HHHHHHHHGEGEHGG=FHHHHHHHHHHGFHHHHHHHGHGFHHFF@57>=CCB@=FHHHHHEGHFFHHFF3EHHHGHHHDBE><>?FFHFGHHFEEHHE@F @read_150_236/2 TTGGAGAGCTGAGATGTTATTGTACTTCTCTATGTTTCTTATAGCACCTAGTGCAACACTGAGAAACACTCATTGAAGTTAACTCGACTGAAGATCGGAA + DACD=:?HHHHD8EBDCFFFEG<>>.8F@@BEEGGFGHHFDGEHHHFHHHHHGGDE7@7>5BGE>?;DEEFHDBABEGBBGEHHHHHGFB=3DAB>==<.:4C8F5BGGGGFDC59, @read_150_238/2 CTAAATATGGTAATAGCTGGCAGACAGCCAGCCCAGTAAATTCCAATGATACTTAAGAAAGCATTCATATGGCCTGAAATTACTCTGAACCAAACACTTG + GFFHFFHE=87;GGA8E8:=83EHHCHHHB@GGGGEHHHHHHHHFGGFF?GHHHHHHHHGCEEG@8.?FA@HHG=CAEEFFFHGHHHFC>FE=GGBCDHA @read_150_239/2 GTTCAACATGCCAAAATTCTCATGCTTTCTTTTTTTGGATTTTTCAACTGATCACATGGCAATTATTAGTGAATTTGTTTGCCTAATTTTTTTTTGAGAC + HFD?GHHHHHHHHHHHHHHHHGHHHHFHHGE/2HFDAEED869EEHHFFGFGDD=DC@G=:GHHHHGFHHHEBFFFHHHHHFH@BC@<=AEBCHHHHHH @read_150_241/2 CATCTACCACAATCAAGACATAGAATAGTTCCGTTACTCTAAAAAATTCCCTTATACGTTTTTGTAATCAGTCCTGAGCCTCAGCCCCTGGCAACTGCTG + ..*65;EEFFHHHFHHFFDGBEFDHHHHHEHEGHHHHHHHFFHHEEDFHHHH@EDFGDBCHHHGHHFGDHHHHHG@EEEEGEHA=><;CDHF7).8?-7; @read_150_242/2 AGTGATATTTAGGAAAAATAAACATCACAACTTGATAATAGGCAGCATGTTGCAAGTAAATGACAGAGTAAAGCAAAACAAACAAAAAAAAAACCCCACA + HHHHHHHHGGHHHHHHHFFHHFHHHFGGHHG?GGHGGFDHHHBD=GFC>?@A7*43-->GHHHHGHHHHCB-*6BHHHHHHG:;EDFGFHHHBEBEFHHD @read_150_243/2 TTGAATGCTACAATGGCAAGAAGTCAAGGGAGTCTGATGCATCAAGGTCCAAAAAAAGGATACAAGCCACAAATAAGAATCAAGTCCAGGATACCCAAAA + GHHHHHHHHHHHHHHHHHHHHFFHHHHHHHHHHHHHHHHHHFFHHHHHHDF=DFHHHHHHHHDFGF@BGFEFF>55;=F@GFGHHHHHBC>>DD:A>?@GE?A@D4A?CDEFFHEFFGEEDBCBBD;=EEGFE<;6C8;01,60A9EFHHFEFEEEHG6;D?B>=5CCEF?GEEFDD?7>7FBE?G..* @read_150_249/2 CCTCCCTGGTGAGTCCCAAGAGGGTCAGAGGACACAAGGTGGGGTGATATGCCCTCCCCAGCATGGGCATAGCAGTCCCAGCTGAGGCCTAGATGAGTTT + HHHFFHHHHHHHFEE/78DHHHHHDGGIC@@EHFGHHHHHHHHHHB?F9CHHHHGHHFGHHHHE?A?E::)(*:.(5CCBGGHGD5@@>AFE>,,,+)*? @read_150_250/2 TTTTGCCATTTTTGTCATGAAGTCTTTGCCCATGCCTATGTTCTGAATGGTAATGCCTAGGTTTTCTTCTAGAGTTTTTATGGTTTGGGGTTTTCCATTT + HHHHHHHHHHHHGHHHHHHHHD.DA8CCEHHHHGGE@@BHHFB=FBFFFHDDC@=C=65()9<5AGHHHHHHFHHHHHHHHHHHHHEEEFHHHF(@;4:3 @read_150_251/2 AACATAATGCTTGATGAAGGAATGTTTTTTAGGGCAATTGCCATTTACAATTAAGAAGAATATTTACAACTTGGCTGGGCTCAGTGGCTCACGGCTGTAA + HHHHHHHHHHGGHHFGGGA@@>.7>,48CGHHHHHBFFHHHB9;:=A=:AE<5'-)-,>+ @read_150_252/2 CAAAGAAAGGGTGGGTGAACCACAATCTTAGAAAAATGTCAATGCTGTAAAAGACAAAGACGAGTTGTAGACACGTTCCAGATAACCGGACACTAAAACA + HHHHHHHHHHHHGGGGBGHHFFHHHHHHHHHHHHH@EDCEGEBBEBE4>AHGCCBEBB@ED;GHHHHHHHHHGFHGBGFGFFG=@&'+CGHHHHFHEE@* @read_150_253/2 CTTGAGCCCTGGAGGTCAAGGCTGTAGTGAGCCATGATTGTGCCTGCCTCTGCACTCCAGCCTGGGCAACAGAGTGAAACTTTATCTCAAAAAAAAAAAA + HHHHHHHHHHHHGGGHHHHHHHHHHHHHFGFEBGDFHHHHHHHHHFGGGGGGGAEHHHHCBGGBBEGGHHCD@E/<@<@AHHE>>CDHHHHHHHFD9DGA>CGGFFHFBCFFG=< @read_150_255/2 GACATTGGAAGGTTAGATGAGACTGAACAGGTGAGAAAACTCTTAGGGTCCCCAGACAGCATTGAGATCTCACAGAGGGGCCCCAAGGGCGTGCGACCCC + EHHHHHHHHHHHHHHHFFHHHHHHHGHGAFGDCEHEBEHHHHHHHHGIGFHHHHFHHGGFGHHHHHHHHHHHHHHHHGGCE8:>D?EGHHHHHHHEEEFFHE?HHGFFHHHHHEDDHHHHEFFHFGGHHHHGHHGGEGFCC@;C<7<&(3;??EE@B@CFECDADH07A4008 @read_150_257/2 TGTGAATTTGATCCTGTCATTATGATGGTAGCTGGTTATCTTGCTCATTAATTGATGCAGTTTCTTCATAGCATCAATGATCTTTACAATTTGGCATGTT + HHGGHHEDDBEHEEEFHHGFFFHHFHHHHHHHHHBGEGGFGFHBEHHHHHBA=@@DHHFFHEGEEFHHHHHHFGHHHHBGEFEHFFHHFEEGE9'8118; @read_150_258/2 TGGGAGGCGGAGGCTAGAGTGAGCCGAGATCACCCCACTCTACTCCAGACTGGGCGACAGAGTGAGACTCTGTCTCCAAAAAAAAAAAAAAAAAGGTCCA + 7?DEEDBABBHHHHHHHHHHHFGHHHGGHGGC8=B;>;>)5A3:@EFEHFGFFHHFD8:,639@:++6CBB66?EGGFFHFC=FBFHHHHGHHEEDF<6& @read_150_259/2 GAGTTAAACATACCTCTGATTAGACAATTCCTCTCCTAAATATATTTATCGTGGAGAAATGAAAAACATATATGTCCACAAAAAGATCGGAAGAGCGTCG + G7;<;G:FGHHHHHHHHHHEHF8,:<972/22589EEHE;DCDHHGHHGGHHHHHHF:8=I@@><6<:9BFHHHHGGGFHHBGGFHHHHHGHFDAC-5&( @read_150_260/2 GAAAAATACAGCATCCTAAATGACGAATTTGCCAGTGGCACCCTTATTGACAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGC + DEE89;<=>ACCBB/7BBHHDDE5@GEDHHHECCEDFCDAGFFHFCGHHFGIBDBGHHBDFHHHHHHHHH?.FIDA41<6??A=?2<57?DA8<9DEGD@ @read_150_261/2 TTCCTCAGTTCCCCAACCCATCACCATCTCCCTCAAATCATCGAAATGTGACGTATTAAATCCACGCACAGTCTCAGAAAAGATCGGAAGAGCGTCGGGT + EHEFFHHHHHHGHHHDGFBB=GGGDE@DDCEHHHHHHHHHHHHHHHHHBBB>GHHHHGHHGEGGFHHHHFHHFHFAC=HHHHHHHHHHHHFDGB<38+4A @read_150_262/2 TGAAACAGTGCCACAATTCTAAATATTTCTTCTGTGGTAAGCAGATCACATTTCAATAATCATACTCACTGTAACAACTAGACAATTCTTAAAAACCTAA + GGEGHHHHGHHHHHHFDCDFBB;C==D48FEHHHBHHHHHFHHHHDEFCFHHHHHHHHHFHHGHHHHHHHHHHEHHHFHHHHEHF?G;>CB8GFC5CDDF @read_150_263/2 AAATCATTAAAGAAATTGAGAAGATAGAAGAGCAAATTTGAATGAAGTTGATAATTCATGATAGTATTCTTACAAATATAAAGCTGAGTAGGTTTTTGCT + HHHHHHHHHHHHHHHFHHHHHHHHHHHHEEHHHHBFHFHHHHHFFE/BGBDE:@@EGFFHH??=C;3-5BFBGGHBFHHHGEDEEG?@=8@FDDDDBC>= @read_150_264/2 AATACAAAAAATTAGCCGGGCGTGGTGGCGGGCACCTGTAGTCCCAGCTACTCCGGAGGCTGAGGCAGGAGAATGGCCTGAACGCGGGAGGCGGAGCTTG + DCEFFGHHHGHHHHFHG:5@C=<.BB?FHGGC=DFHHHHHHHFHEHDCABEEEBB3CFFEGBBHHHHFGGHHCFEHHHHF@EEC@%25:12>11/9645' @read_150_265/2 AGGAGTTCATAGTTACAGCGAGCTATGATTGCACTTCTGCATTCCAGCCTGGGCAGCAGAACAAGACCCCATGTCTATAAAATAATGGTAATAATGAACA + HHHDHB5EFGGFBDDDD>9FHHHFHHHHFHHHE4;?GHHGHFFGH6AAEBEEGGEEFHFFHHHHHHHGGHHHHFHHFHEEDCF@@='.8/1/%,4>;?DD @read_150_266/2 GTATATTGTATGTATATATGTATGTAGGTATGTATTTTTCATAAACATTTATTATATATTTATTATGTATACATGTAATCCTCATATTAACTCATTTTGT + @EBFGGG8=2@BHHHHHHHHHHHEEHHHHHHHHHHHFFFHHHED/GGG.:BCDEDGFB;HHEEGHDHHHHHHHFHHEEEFEGEG@<:6EFFHHHFDBGDB @read_150_267/2 CAACTGAAACCATTTAAAAATGTATAAAACTGAAGCTCAGAGGTTAACCTGTTCAATGCTATAAAAGTCAAACCCTCATCTTTTCATTCTAAAACGTATG + HHEEGHHDCCFHHHHHHHHHGHHFGHHHHHFHHHHGHC?>E4?:38GBC@HHHHHHHHHHHHHHHHHHHHHHHHFHHHHHGD@F/<99.BF@<+/7AFFF @read_150_268/2 ACTGTTTGACCATATTTACTGTCTTGTTAGAAGGAACTTCCAAGGGGCATTGATCCTCCCTATTTGTCTTAGACTCTGCACAGATCGGAAGAGCGTCGTG + FHHHHHHHHGF8FD>=DGFEBGFBI<@ADA?FFHHHHHHDCB@C,6::==408E@CEBEFGHHHHFAFFEGHHCHHHHBCFHHHHH @read_150_269/2 AATATCTGCAAACTAAGCATCTGACAAAGGTCTAATATCCAGCATCTATAAGGAACTCAAATCAACAAGTAAAACATGACTCCATTAGAAAGTGGGCAAA + HHHHHHHHHHHFHHB@GBCHHHHHHHHFFBHHHHHHHBGHG>;DE<5;B>DGHFFFFBDDGGFFEBEE??BIHH?DEGF?EEEHHHHD(.AD?AC>BEGG @read_150_270/2 TCTTAAATTTTTCTTTATTATTTAATATACAAGCAAAACTTCTTTATTGTAGAAAAATTAGAATATAGAAATTAACACAAAGGAAAAAAAGTATAGTCCT + C@EGHFHHHFEDDGGEE=@BEGEEHHHHHHHHHFEEBABDHHHHG?GB@DHHFFHHHDHHHHHHHE@CEH@A?HHHHHEH9511GGHFFF>.?GGGGHHH @read_150_271/2 CTAAGACCCTCCTTGCAAACAGGAGTATTATTTCTTTGTTTTTGATCTGCATCTCCTCTTCCCTTTGAATGTAAGGTTAGGCAGGAGCCTTGCCAGTGTT + FDGGBFD=DEHHHHHHHHFFGFFGHHHHHHHHHHHHHGFFHFHHFDDFFEHHHEFHFHHHHFGD2,19?D@FEAA4*8*42(1?DF=77EC? @read_150_272/2 CTCTACCGCCAAAATATATTTAGAACCAGTCTATTTTTCAGCTTCTCTACTGCTTTTATGTTTGTATGAGTCTTCTTCACTTCTAGATCGGAAGAGCGTC + HHHHEBBFEHHHHFGHHHHHHHE.C+)7CHHHHHHHHHHGDFHHHEE@EHHHHHHHHFFHGGE/8CEE>CFFFHHHE@ @read_150_274/2 CAGCGCCAAGGTTAGCACCAGCAATATCCCAGTACTCGAATATAAGGATAAGACAACTCTTGGGGCCACAGAGAAGTGAAGAAACTGTGAGTACATGGTA + 2-24@<:?>DG@??>2;>:=;55.CHFHHGHHHHCHFHHHHHHHHBGGFBGGIGFHGBCHEDEEEGF@GEGF=HHHHHHHHEEEEGGAA6(,,55@CGHHHGFFHGHHHGHGFHHGGHHHHGCDDG;=GGHHFFEHHHHHB5::@DE@99D71CBGHHHGDGDGGGFHHHHHHGD>=8EGDHHHHHHHHHHHHHHHHFFHHHHHH>96BGCEEHHGFDGHHHFE?4FHHHHHH @read_150_278/2 ACAATATGTCTCAGGGATTAGCTGTCCCAAACCTATACTATTAAGCTACAAACATGCAGGCAGGGGAGAACAATGAGAATTTTCTTTCCAAAACGAATGG + HHD?:DGGEHHHHHHHHHHH<466HDG=D@DFFCDEHHHHHHHHHHHHFEGFFHHHHHHHHGGGHHHHHHHEFFHHHHHFGDEHHADIDFHDCHF=FHFH @read_150_279/2 AATAAATACACATATATTTATATATCTATATCTCCCTATATGTTTATTTCTATATATCTTTTACTTATAATATTTACCAATCTCTCGTATTAGTTCTGTT + HHFE8CA@@;.:-@GHHHHGFA=@BHHHHHHHGE>A:EHHHC>>@EEGGGFIGHHDCDHHHHHHHHHHHBEFBB=CHHHFHHG=49.;52)->;EED>:; @read_150_280/2 TGGTAAGATATAGAATGAACAAGGGAAATAGAATCCTATTTTTATGTTTCAATTTTATGGATTGCTGGAAAATTGAAGTGTATAGGAGTCTAGATCGGAA + 9--8;7-0,BGF8GHHHHHHHHHHHHHHHGHHHHHBFHHHHFF?<..:5FGCEEFGFGC5C@EGHHHHHHHFDFFGHFGGHHHDD@8-)4:>.EHHHDB? @read_150_281/2 CCAATGCCCGATATGAAGGGAACACGTCACCTGCAATTCACCACCTCTACCCCAAGCTCTAACAGACATCTCATGTCGAACAAGTCCAACAGAGAATGGC + EHHHGEGHHHHHHHHHHHHHFFHHGGHEHH;@@BHCBHHHHHHHHHD89>FF8::,>1FHFHHHHHHHHHFFFHFDGFGGEAGHFEFF?=EEDEHB?=CC @read_150_282/2 CTCCCAACTCTTCCTTCCTCCCCACCCCCCTCCACCACCCAAATTATTGTGTATAATTCCCTTTGGGCTATATCTTGTTGACTATCTTGGTAATTACTTG + I?EEEHHHHHHFFGGHHHHHHHHHHHHHHHHHE@,9EEEGEFFHHHFEHHHHHHHHHHHHEEGG6;CGHHHHHHHGHHHHHHHFFGD=C5.=65FHHFFA @read_150_283/2 TTTGCATCATGAAATCGTTGAGTCTGGCTGTGGAAGATCCTGTGCTTCTTGCTGTAGAGACTGAACATAGTTGGCCTGTTCCTCTCTTGGCTGGCTGTCC + HHHFIFGGFHHHHHHHDDDDGHEC;@<=G?EFFFFCGHHHHHHHHFHCGGFGGEEGFEB8),+;EFFFHHFFADFC,4DAE6E=8DADFFBA==FHFFFH @read_150_284/2 TCTTCAGAGTGCTTATAAAATACAAACCCACACAGACAATCACAGAAGGTGAAAGTTAGAAGAATGTTTGGATATCATCTTGTCCAACTTCTTCATTTTA + C5FGGHHHHHD=DGFCFGHHHC26DBEHHHEG<@BE>FFHHH03<*1:BGHHEEHHHGFFHHHHHFFEHHHHHHEEHGCB8D,>@B@BDDHHCC@EC @read_150_285/2 TCTAAAACTGACAGGGAAAAAGTTAATGTAAATATTCACAGTCCCTTTGCTTCAGTCATACTCTCTCCCTCTGTCACATATCCTTTCCAGGAGAATTCAG + GBBFGHHDDD;B><<:=><;<-.CCHHHHHHEFCBGGGEBHHHB@4BABDFFD:7DC>8'01->EEF6GBBEHHHHBF @read_150_288/2 CCAGGGTAGATCTGTTTACCCTGTGACTCTTACATACCCACTGAATCCCAGCTCAGCAGCTATAGTTTTCTTTTTTCTTTGGAGACAGAATCTCACTCTG + GFFHHHHHHHHHHHGHHHHHHHHHHHHHHFG;4EEHHFC@DFGHHHEHHHHHHGGHHHHHHFHHB;99CGHHHHHHFFHHHDDD.>.>*:,*<;?=>:BB @read_150_289/2 TGAATAACATGATGCCCTTTGAAAAATATGATAACATAAGGGTATAATGATCAACAAAGTATCTTTGTGGTTAAGAGTCTCAGAATAAAAATTAGACAGA + HHHHHHHHHHHHHHHHHHHHHH<41AFEGFDHB?AGHEEEFFHHHHHHHHHHG@94:GD?.AB2?*; @read_150_290/2 TCCAGATTTGTTCTTTTTGCTCAGGATTACTTTGGCTGTCTGTGCTCTTTTTTTGGTTCTATATGAATTTTAGGATTGTTCGTTCTTTCTTTTTCTTTTC + BB?HHHHHHHHHHHHC@@8B@>CG<5.<; @read_150_292/2 TGACTTTGTTCTTGGTAAATTCTTGATACTGGTAGGCTCTATCACTGTCCATGTCCTGATCTCTACAACCCTCAGGTGGCTGGGTCATTGTCCGTTTGTT + HHHGGEGHHHHHHHHHHHFDHEDDDBGDHFE?8'3DECHHHHHHHHHHHHHHHHHFHHHHHHHHHHHFH@CCDDFHHHHHHHHGFFFFGFHHGF?@::2D @read_150_293/2 TACAAAAATTAGCCAGGCATGGTGGTGTGCGCCTATGATCCCAGCTACTTGGGAGGCTGAGGCAGGAGAATCACTTGAACCCGGAAGGCGGAGGTTGCAG + HHHHHHHHHHHHHHHHHHHHG=D52?A//;EFEEFGHBAAFDDCD>>@73ACA>>FHHHHHFHHHHHGHHB/A9CFDGG=)5,*087.4*19ADCDDB?A @read_150_294/2 TACATCCTCTAGAGGGAACATAAAAAGATACCAATAAAATTTTGTAGCTGAACAGTTATGAAAAAGAAATGCTGTGGGATAGATCGGAAGAGCGTCGTGT + FHHHHHHHHGHHHHHHHHHHHHHFHFEBCFHHGGFG4<>>E><,)45:>526?6>E;@2,5.<8@<):D@BBFHHHHHHHHHHHHEEEDHFBGB???>?> @read_150_295/2 TGTCCTTATTTAGGAGGAAAAAAGAAAGTCAAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAA + HHHEDHDFFEHHFHHEEEFEGFFBFHHHHHEHHHHHHG@>BCGGGA@::B@BEHFGFDGHGHHHGGHHHHHHHHHHEDHHHHD6(BA=>.<79=?E=?HHHHHG@A=CDGGBGHHHHHCDGHHHHHHHHHHHHFHDEEHFFFHCBEEEDC@B8CHHHHHFDCG>>6@@BFBH>DAE @read_150_297/2 GGCCCAGAGAGCCTGCAGGGTGCCCAGCACCAGGCTTGAAACAGCCCTGAAGCAGCTACGTCCCATTTCCCGGTGAGTGGCACAGCCCACCTTTGAACTC + HHHHHHHHHHF@G@@56<55F@E/?83:.=BE401<:?HHHHHHHGAC=;29:;.FHHHHHHHHHHHHHB:6GFHHHHHHGGHHFHHFHGGFDGBD8<<9 @read_150_298/2 TTGTCTGATAGTAGTGCAGTTTGCATTCCAGCTCCTACCAAGAAACATTGGATTCTTGTGCCTCAAGACAGTGTTGCCTTCAGTCTTGGAAAGCCTGAGC + HEGHHHHHHHHHHHDCEHHHHHHH@FFGGFFBGFHHHHHHFDEGHHHHHHHHDFFHHHHHD>@:4B@DC?GFCBEHDBD491);:2,'),22,,)*%',5 @read_150_299/2 TCTTGTTGCCCAGGCTGGAGTGCAGTGGCACAATCTCGGCTTACCGCAACCTCCGCCTCCTGGGTTCAAGCAATTAGGCAATTCTCCTGCCGCAGCCTCC + HHHHHHHHHHGHHGDEFFHHHHHHG.9;@CEGFGHF8E<.5=GHHFFFB<=C7?EEHHHHEHHHHHHHHHBG@DDFHB@HHHHFGGDD=<='699D5?.@BCBC2<>4875CF@ @read_150_303/2 TAGCTTATGCAATTGGCCACTACTGTACCACTGAAACCTGGTACATTGTAGGGACATGATAAGTATTTGTGGAATATATTAACTCTGAATATTGTGTTTC + HHHHHHHHHHHG@>:GEEFFEHHFFFEHHHHHHHFGEBCDDGFHHHHHGBBEHHGDB;?C;CDFEBCHHH@@CHHHHFFDFBA?FHHEGFFHFGHFDEFF @read_150_304/2 TGGTCATTATTCAATAAAGAATAGAGTATAATAACTATTTACATGGCATTTACATTGTATTAGGTATTACAAGCAATCTAGAGATGATTTGATGTATATA + 8@@GFGGGGGD@<173=((2GGFGGFHHHHHHHHHEHHHEHEHHFFFFBDHHC:>EFFHHEEGEHHGG.?EEEGGFHDGF.:22:EFGBD738?D@6AFF @read_150_305/2 CTTGTTTTAATAGCTTTGCTGGGCACATTATTCTTGAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAA + HHHFFDFFGFDFEHHEGHHHHHG<>@:FGGGGHEHG8DE<<8DDBC?CCCFBECEBHF @read_150_306/2 TGGCCTTTTTTCACATCAAGTTGTGCTACAGTCAGTTTAGAAAATGACACTTGCATTGTGGAGTGGAAGTTGAGGAGCCAGTGAGTTACATTAATTTATA + HFDHHHHHHHGEHDFD@BCD@GHHHHHHGBEEEHH@CBC8E@6?HE2-33;>;=FFGGGHBGGG?,+<<2FBGEHHH?B;918FEEEHFGFDGGGH;>/B @read_150_307/2 GGGCGCCGAGCAGCTCGGGAGGGCGCGGGCAGGGACAGTAGCGGGGGGGCAGGGGGCTGGGTGTCAGGGACGCCGAAGCCCCGGTAGTCGAAAGTCCCGT + HHFEHHHHHHHHHHHHHHHHHHHHHHHHHBEDDHHHHHG=7.EEF?>::<>AFHHHHHHHHFEGHGFBCFA@@>:EEEEHHHBFC5?FDGEFHHFHHFHEFD @read_150_310/2 GTCCCCAACATAAAGAAATTATAAATGTGTCAGATGATTGATATGCTGATTGCCTGGATCCGTTCTGATCACTATATATCACATGTAGCAAAACCTCATT + GGEDC:><=GGEFFFGGGHHHEFHHHHBD=FGGEFHHFCDEHHHGGHHEAFEEHFFHHGHHHHHHGHDEGFEDAFHHHGFDDHEEDHEEFEEFFD359.) @read_150_311/2 GCCGGGCTGGTCTCAAACTCCTGACCTCAGGTGATCCGCCTGCCCCGGCCTCCCAAAGTGCTGGGATTAGAGATATGAGCCACTGCACTTGGCCTTATTT + HHHHHHHHHHHHHHHHHHDGHHHHHHHFHHGGHHBDGGEEF?AHFHHHH+8>-*9GHEBEDGDHHHHHHHFFGAB<6:>9;9%',;96=D4DFGHHHEFC @read_150_312/2 AAGAGATCGAGACCACCCTGGCCAACATGATGAAACCCCGTCTTTATTAAAAATACAAAAATTAGCTGGGCCTGGTGACACACGAGATCGGAAGAGCGTC + HHHHHHFGEHC8@=HHGHHHHHHHHHEEGHHFFFHHHHHHHHHFF+C=IGDDDDGGFBECD>;BFCFFF?/A?=9DE?:7:@/5FHHHHB<7@D?FFHHC @read_150_313/2 GTTCATTGGGCTCACTCAGCCAAAAGTAGAGGGAAACTTTGTACAGACATCATTAGTTTTTCTCCATTTAGAGATTAATCATGAAGAGCTCTGGCCCTTT + HHHHHHHHHHHHHEBHGFDDA@DFHFHHHHHHHHHHBHHHDGEHA78A@BHFHHHHHHHGECGG<:-CCD=DGHHHHHHH=DA,2>78HG=C;97GHHHHG?@BEEGEGEABBC@?AEGECDDEFFEEFD@?GGGHHHHGBEEHHHHHF?EEFA71=BFCCD==9,1,2 @read_150_315/2 GGTGTGCAAGGTGTCAAAGCAAGTCTGGAGTCATGGAGATCGGAAGAGCGTCGTGTAGGGAGAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAA + FHHFHHHHHHGFHHHHHHHHHHHGH?EDGGE=CBEFFHHHHHHFHF?HFHGHHHHG@GC=G6?B@CE;G87@CHHHHHHBFEHHHGGFHHHGD=?EFEEF @read_150_316/2 ATCTGGGAGGCAGAGGTTGTAGTGAGCTGAGATAGTGCCATTGCACACTCCAGCTGGGTAGTAAGAGTGAAAACACTCAAAAAAAAAAAAAAGAAAGGAA + HHHHHHHHHHHHHGGEGHFHE@<-?BGGEHFHFCHHHHHHEEF?EE?EHHHHHHHGHHHGHGHGHHHG=?BG?EGHHHHFFHHHHHHHFE@D<46<:*8; @read_150_317/2 AGCATATAGTAGCATAAGTATACACATTTGTTTCTTTTAACTCACTTGTCTTACTAACATTTATTAAAAACTTTTATTTTTGCAATGTTATATTATTACA + HHHHHHHHHHHGHHHHHHHGHHHHHHHHC-DGGHHHHF?E;.@HHHGGCABHHHHAGEGGDGEEHHFC6GHHBEGHDBBEACDFFDFE@A,<74>DD>5= @read_150_318/2 GAAGCTGAGACAAGTGAAGCAACTTATCTATGTCCATACAGTTCTTATAACTAGAGGAGGCAAATTCTGATCAATGGATCTAGTAAGTCATCTTGCTTTT + HHHHHHEGFDB@GFHHHHHHB@FHHHHHHHHEFEAB@;<5@**)8?GFGCEG=DGHHHGGHHHHHHHHHHGDC@HHHHHGEEHFFFFFCBCFHD@*5BCB @read_150_319/2 CTGCATCATTCATTTGTTCATTTTGTCATTCATTTGCTTGTTTATTTAGGCATTCATTTACCAAACACTGTGCTTACAGTTTTATGTCAGGCCCTGGGGA + HFHHHHHHHHGHHHEFHHHHHHHDEEEGGEGFECB=DDBDBD:B;>BDHC>=4<=9+3:@<>.DGFCEHHHGEGHHHBEHHFBBBBDEBFA;,A;EB@FD @read_150_320/2 AAACTGAGGCTCACCCAAGTTATGTGCTCAGCTAGAGAGTACGAGTTCAGCAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGC + HHEBHHHHHGHHHHHHHHHHGGHHHHHFFFFF<368>>CA@FHHHD;.DCGIGGGHHHHHHHHHGHHF@GGHFF7EHHHHHEG@HHHHFF@BDA@DHHBE @read_150_321/2 TGTTCGCTGGAGTCCGGACAGTTTGGGCTCGGAAATGGCTCTGCTGCCATTCGGAGCTAAGAGCACAGCCCGTTCGCCCTTTCACTGTCGCCTTCCGGGT + DCDHFGHFDB65CGHHBBCDDHHHHHHHEHHHG@AHHBGHHEGHHHFHHHHHHHE@,07EEFHFEGHHFHHHHHHEEDCD@.5.> @read_150_322/2 TCTCTCACTCTGAGTCATGGCTGGCTTCAAGTTCCCCAGCCTGGCAGGCAGGGCCAGGAGCCATTTCCCAGCCTGTGAGAGTATCTTCCCACACCCCACA + HHF<93*+=GHHHHHHHHHGBHHHHHHHHHGGGGGH?EHHHHHFFHHHEDGFD@A@<:DDD=F.>AC:?EHEGDH3;AEEHHHFDGHFEBHHFEHHHHHE @read_150_323/2 TGGCCTAAAGGAATACAAGTGCTTGGATCAAATATTTTTTAAAGGGAAGATAAAAGCTGTGGTACCTTTTAGTTCACATGACTTTAATCTTTGAGAAATA + HHHHHHHHFHHHHHHHHHHHHHEGIDE9/@>DEGHHHHHHHHHHEGDHHFHHHHHGHFFGDGHEE?GFFEHHFE>G?CCBHHHFEAFHHHHHFH?BEFEE @read_150_324/2 GTTTTTATTTAATACGGCACTGCAGAACAAAGAGGAAATAATAGTTTTTAGAGACAGCTACTGTGGCAACTTCTGGAAGTGAAAAAAAGTCATGTAATTT + 7<:?@EGHHHBGHHHEHHHHHHHF@FFHCCHHGBEFHHFFHGHHHGECHHHHGGGGFBEDCDG>43<<>8<)*(6(:;<91BFHHFHHHHFHHHHHHE*8 @read_150_325/2 TCTTGTTATCTAGTAACTATCAGTTGAGGCAGGGAGGGGATAAATAGACAAAGAATCATACTATATAGCAGTTTCCCAACCACCAGTGTGTTGAGAGGCC + HHHHHHHHHHHHGGGHHHEEEGFHEFGDA@@EFHHHHHHHGHHHHHHEFE673/1+87CBB@AF@AI==>>FFFHHHHEEECDEEDC89FEEEEBFFCA, @read_150_326/2 TCCCAGTGACTGGTCCCCTTGGTTTTAAACTCAGAATCAACCTCGCCGAGCCTCCAGCACATCATAAATGACAGGTTATGTTTTGCTAACCCAATACTGG + FHHHHHHHHHHHHHHHHHFGBCDDDGHHGGFHHHGHHHHFDA(,82)=DGHHHHHHHHE@DCB5@4:DDHHGHHHHHHHHHFHHHB:9'6AADA@EGFGGDDDEEEEEGEGFDFG=EFHHHHHHHHGDHFA>B)>*4.CGEE? @read_150_328/2 GATACTATGAATCATACCCGCCTGAACCCCTCCAAATCCCTTCGGAGCTAAATATCGCTCACATTCAAGAGCAATATCAACCCATCGCCATTCAAACAGA + HHFGHHHHHHHHHHHEB?*(9E86@?FHHHCHECCCGEHE>;CEDEFFHFDBHEGHFHFCCHH @read_150_329/2 AGTTTTTATACGAAGATATTTCCTTTTCTACTATTTACCTCAACACGGATGCAATCTCCACTTGCAAATTCCACAAAACGAGTGTTTCAAAGATCGGAAG + HHDHHHHHHHHHHHHHEG@@93@@6BHHDBFGEGHHHHHHBFEE/1-1*8.'*2*<0'>?6;?DHHHHHHHHFB>.:<=EFFH@B.:,3AC=..3?DFHHFA?%+ @read_150_331/2 GTGAGGTGAACCAGCAAGTGCACTGGCTGAGGGGACTGGAGTTCTAGCCTCTGAACCAGTTTCCTCCTGTGCCAAAGGAGGATAATAATTATCTATTATT + HHHHHHHHHHHHHFHHHHHHHHHHHHEGHHHHHHHHHHHHHFHHHHHHEHEECEE/32'38EA3AEFFEHHHEHHHHHHHHGGEHHFEEDFGGABBE??< @read_150_332/2 AGAGCAGATTTGAAACACTCTTTTTGTGCAATTGGCAAGTGGAGATTTCAAGCGCTTTAAGGTCAATGGCAGAAAAGGAAATATCTTCGTTTCAAAACTA + HHHHHHHHHHHGGHHHHHHHFEBDGGHDGDFB;BBGC;C8EF/HHHHHHHHHHFEGGHHHHHHHHHHHHHHHHHHHHGHHHFA=GG?C>EFHHHHA5.>F @read_150_333/2 TAATGAGCCCATTGAACAATGACAAAGGGGGCTAGGAAAAGAACCTGGAATCCACAGGGTTGGTTATCCTATCCACTTGGTTATTAAAGTTTTCTGCAGA + HHEFHHHHHHHHHHHGHHHHFHH=<5C??AD @read_150_334/2 TTCTTAGATTCTTGCTTGTCTTCCTTTTCATAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAA + HHHHHGB=/@<9@GGBE/@FBBGHHHHHHHHHHBECFHHHHHGFDD8AE6.:8D;GEHE@BHHHHHHHHHHHHHHHHDCC@>5CHHFGGGHHGGEGBDGDFHHGG4FEEFHFFD/)1: @read_150_337/2 TTCACAGCAGCACTGGGAGGTGGGTGTTAGTGCCCCTGTTTTCAAGACCTAGAAGAGTCCCAGGCTCAGGGAGATTAAGTATGTTGTCCAAAGTCAAACA + @:<7@A7/;EHHHHHHEHHHHHHHHHHHHGGGHGGGGHFFHHHHFGGBFHHHHHHHHFHBHHHFHHHHHHHHHHHHHHHHHHEHFDGFB=5,AD?DHHFF @read_150_338/2 GCCCACTAACTAGAAACTGAGAACCTAATACAAAAGTGTAACTCAATAAAAGTGATTCTGAGTGATCCATGAAAGTAGCTTGCTGCCAATCCATCAGAGA + HHG@CHHHHHHHEEDGHHHHBGBHHHGHHHHHGGGFFCEEHHHFFFFGHEHGGGFEHHHHHHEEFFHHHHHEGHHHHFFHDEGFBFHHHHHEDFHHHH:9 @read_150_339/2 GTCATTGCACTTAGTCAAGACCTAGTGGCTTCTGTTTGCTCCACTAACTTTAGAGTAATTATAAAATAATAAGCTTGTATTGGTAATCTATATCTATCAA + HHHHHHHHHHHHGEEEEHHHHC?BFHEEBABGHHHGGF=?GHHHHFEHHFHHFEEHH@7=E@GFFB=?328HHFF+78*;>. @read_150_340/2 AATATCTTTGCCTTTTAAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAA + DBGEDHHHH89=BGFFGGGBBHHHGHHHFGHHHHGHHD@E>BGFFF??FFHHHHGHHHD?GFHHHHHDHFDBBGEGFBE7;A:>FACEHFFFHE0>(0)) @read_150_341/2 GGTAGCAGAGATTGCAGTGAACCAAGATTGCACCACTGCACTCCAGCCTGGGTAACAGAACAAGACCTTGTCTCACCAAAAAAAAAAAAAAAAAAAAGAG + HHHHHHHHHHFFEBGHHHHHGHHHHHHHHHHH=AFHHGFHHFDDF=GFHHEGDEHE @read_150_342/2 TTTGATTTGCAGCATCTTTGAGCCTCTACGACAAAAAAACCGCGAAGCACGCCCAGCCCTCCCCCGGCACCCCGAAAAGCACCCACTCCCTCCCGGGGAC + HHHHHHHGHFEHHHHHHFHHEHHHHFGCFGHFEHHHHHHHA=CEGHHHGHHHHHHHHHGGGFFFGHEHHHHHHHHHHGHHHHHHHGGGDC08==?EEBBH @read_150_343/2 ACAGATGCTCTAGTACAGTGGTATAATCATAGCTCATTGTAGCCTTGACCTTCTGAGCTCAAGTGATCCTCCTGCCTCAGCTGTCCGAGTGGCTGAGACT + DHHHHFDGD?<2-3>?<<>@9->>:A:((6.DCBCGHHHHHHHFHHHHHDGEF<58EHHHHEHHHHHHDFGDHHEC?BEC--->.8>4>AFHF>>@?;CH @read_150_344/2 GCATCGCTATACTCCTTCAAGTCAAATGAATTATTTCTTTATCTTTCATCCTATAGCTCTATGGCAGCGCTCAATGTACTATATGGTGCCTCTATTCTGG + HHGGHHHHHHHHHHHHHHHHGDGHHHH?BFHHHFHHHFEHHHHHHHHHHHHHHHHHG@CBCABEEG=:-0;+(:;DHEHHDBFGFFCGGHHHHEF/+ADE @read_150_345/2 TATCCCTCTAGGCAACCACTAGTAGATCTTTCTGTTTCTAGAGATTTCCCTGTTCTGGACTTTCATATAAGTGAAATAATATAACATATGGTCTCTAGTG + GHDDHHHHHHHFHHHHHHHHEEF@BEABHHHHHHHHHHHHHHHHHHHHHBEHGHHHHHHHHHHHHHHHHHHHHHHB?=EE3C*8.5CC3.:7EBFHG=@5 @read_150_346/2 CAGAACACGACAGCAGTGCAAAGGCCCTGCAGCAGGATGGTGCTTGCTGAGTTTGAGGAAGAGCAGGAGGCCCTTGTAGCTGGAGGAGAGAGTGGTGGAG + B@GFHHHHHHGEHHHHHHHHHHHHHGFHEGHHHEEFEEHHHHHHHGFFFHHHHHHHHHHC:<<>:EGFHHHHB@HHHHHFHHHGD?ICFHHHECE6;B,/ @read_150_347/2 ATTCAATACTTATGAGATATTTAATCAGGTCATTAACTCTAACTTGTGATAAAATTAGTAGCCCTGATGAATTTCTACTTGCAGTTTAAATCAGTGTCAC + HHHHHHHHHHHHHHHFGHHGGHHHFEAG<.BDGGHHHF?CEIGEFHHHHD=BCACFHHHHHHHDGGHHHHHHE63>DCDEEB=CEDGHEFFHHHHHHGGF @read_150_348/2 CAACTATCCTTCATACAACCAAAATGCACCAGTCCCCAACCCAAATACATAAAGTTAACGATACTTAAATGCTAATGTGAAGTCAATAAATCTTATGTCA + FFHHHHHHHEDGHHHHHHHHGHHFFEDEC@B<>>GHHHHHEFEEGHHHFF;7.:EHHHHHHHHFHHHHHHGHFHFFEHEACEEEHFG@?EHGEHFDFE=C @read_150_349/2 ACCAGATGTGGAAACAAGGAAGTGAAGGTACATCTTAGCATTAGAAATTTCCGTGGCCAGAATGGTGGATGGTCAAGGATTCTATGGAGACAAAGTGGCC + HHHHHGGHHHHGHGFG?FHHHGHHHE;DCCEBHHE93EFFHHHHHHHHFC..14;.7 @read_150_350/2 AGTTGTCTTTTCTTTGAAATGTTGGTATTCTTTGATACTCTGTTCTCTTGTCACTCTCTAAATTCCCCATGGGTTATTTTATCCATTTAGTTATTGTGTT + HHHHHHHHHHHHHHGHHEEEFBD6-/@A@@HHHHFHHHHEHHD/CGGEHHHHHHHHHHHHHHHHHHHHHHHGHEHHHEFFGG=ACGA7<5><52DGFHF? @read_150_351/2 TCGCTGAGCAATTTGTTCTTTATTTTTTACACTAAGTTTGTGATTCATAAAGGGATGCAATTGGGGTCACAGCTAAGTTTCAAAGGCTGTTTTTGGGTTT + HHHHHHGHHHHHHHHHHHHHHEF=A@@@EHFEGGGHHHHHHBC>>57>=@BB?46A42*5:6-9-36:??HHHHHHHEFCHGFA?;??-/>:=.0&79EBHH?><:DEFHHHHGGEHHE=B@6>>.>:C@.CHHHHEEEGFFGHFHHD@?BEDGHHFFFDHHHHHHHH @read_150_353/2 CTGCCAGCACTAGAGATGATGTGAAGTGGTTGCATCTGGGATGCATTTTGAAGCTATAATCAACAAAACTTGCTGATGGAGATCGGAAGAGCGTCGTGTA + HHGFGGHHHHHHHHHHHHHHIDBGGAE?>CHEB31>EGEDA>CEEEAGHHF @read_150_354/2 CACTCTCTCTCCTGCCGCCTTGTGAAGAAAGTACCTGCTTCCCTTTCCGCCATGATTGTAAATTTCCTGAGGCCTCCCCAGCCATGCAAAACTGTGAGTC + CCC;<89>?DEEEDGCCHFF3:6.?6@BB4BH?:FHHHHHFHE@+56FEEGEEEGHHHHHHHHHH@FBEDE?<58:EEHHHHFHGGFEA52 @read_150_355/2 TGTGCCTTTTTAAATTGATGGGAAAATGACACCCAGGATAATTTATGGCCATTGTGGGAATTATTGGAAATCTTTAAGACTGTTTTTCTTAGCGAAGCAC + HHHHHHHGGGFHHGHHHHHGFEHFCCDF@<@.6EBBHEGFHHFFHBDCFEEEIEEGGGHHHHHHHHHHHFFDEEEHFHHHHHFDHHEAA.@+-%-5&3EG @read_150_356/2 CATTTTCTTCCTCAAACACACTAAGCTTATTTCTACCTTAGGGGTAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATC + HHHHHHHHHHHHHB?@=@>CDDEGGFGGHHHHHHHHFFHHHF?GF?FHHHHHHGHHHHHHD@06FHHBFEHBGGHHGHHHHFHHGBFDEHHHC>>@E=E@ @read_150_357/2 CTTTACCTTTTATTACCTAGCTTCCCTTTTAGGTCTTTAAGACAAAGGTCAAGATCTCATTCCATTACCTAATCTATACCTACAGGACAACTATTTGATA + HHHHGHHHHGHHHHHHGBA.38@EEHHHHC@>A@=>.5,(@C=@=?@EHHHHGDHHHFFHHBGFHHHHHHEEG=HHFBDGHHH?DFEGFDFEEHHFFBEG @read_150_359/2 CACAGCAAGCAAGCGAGCAGTTCTGCAGTGGATACCAGCTGGGCTCCCTCCAATTCTGTTCCAACACTATCTACCTGGCGATAGCAGTAGAAACCACAGG + GHHHHHHHHHHDCGEDHHHHHHHCDHGHHHHHHHGECCFF=:5?FFHEDHHHHHHHHHHF@FEHHF@AGGD@AEEFFEEEHHGFEHHHHGH@=,6;EEDD @read_150_360/2 AATGTTGTGTTTTCTCCTAAACTGGTTTTCATCCAAATCTTGTGTTGCTCAGAAAAACATGGAGCCAGAAAGCCAAATTCCAGAGTCCTCTCTGTGGTCA + HHHHHHFFFHFHHHHHHHHHFHHHHHHHHHHHHHHHHHHHEBDEEFHBGECD@757631:6B9DD:GGB*09A?EGGDDDBDCCEHHHHHHEHEDBA.@. @read_150_361/2 GTTTCCATTCACAGCACATAGGAAAATGTCTTAACCTCCTCCCTCCTCCTTATGTGTGTTTTTCTAAGTGTGTGTCTTTTTTACCTTAATTTTTATCTTA + HHHHGFHHGEEHHHHG@=9965;=DDFHHH<>:B@D5:;5=.>59@DDGFGGHHHHHHHHHFFEGFHHHHHHHHHHHHGGGBHHHGHHHH28EC,+)6); @read_150_362/2 TGTCCTCTGCTTATTTTTTGGTGCATTGGTGTTTTTTTTCTTGTTATAAGATAAATTTTATGTTATAAGAGGACAACAGTTTTCCATATTTGCTGCAAAG + HHHHHHHHHHHHEE9*CFHHHHHHBEEHHFE?BDCGB@BEFE@;=FFHHFGHHHFHHHHHHHFB=64E=EEFDGGFEECBGHHHHHD=?@,,.<7CC@AC @read_150_363/2 AAACAACTAGCTCACATATGAACTACCATAAAAGGAACTCTCTCATTATCACGAGAGGGCACCAAGCCACTCATGAGGGGTCTACCCCATGTCCCAAACA + HFE;;??CBDFB8.@DHHHHG8DDEHCGE?011/%+:DGGBEFDBGHHHFFGGFGHHHHHHHHHHHHHHHHHHEEHHFCEFADFFHHFFFCDFDDCBF?@ @read_150_364/2 CTGCACACCTGCTTAAGGCGATGCCCAATGGCCTGGGCACCCTCCACAGGTGTTTCTGCACCACCCCTCAGGGGCTGGTGTTTTTGGCGGTATGCGAGGT + DHHHHHHHHHHHHHHHHHHHHHHHHCD@5>CEDFGHHHGEDHFHHHHHHHHHFCGHHGHGFHHE3);<,4(D>ECCEG? @read_150_365/2 TTACTTAACATTTAACATTGAAATCAGGGCATACCTTACAATCGATGATGTCAAATTACCAATGCTATAGCATCACTGCCTGCCTACAAGTACTTGGTTA + HEEGGF=EHHHHHHHHHHHHHHHHHF<>8FGGHEDF??(9605DHECF=BGFHHHHHHHHHHHHHEEDEHHHBFBHHHHFHHHHHFFEGB+.=AA@D @read_150_369/2 TTCCCAGAGGAATTGATATTTTAGTGGGATCTTGACAATGGGTCGGAAGGAAAGTAAGAGGCTTCACAAAGAAGGTGATATTTTTTGGTGGGATCTTACA + HHGGBDGFFDGHHHFGCDF85-5-9;A9?BFHHHHFFGGGHHHHHHFEBCB@DEEHHHEHHHHHHHHHHBGI?;GI::FFFHHH?CC<39<@,+.>9C?@ @read_150_370/2 CATGTTGGAATGATACAAAGTTTGTTAACTGAGGGAATGAGTTAAAATATGTAAATTGAAATGTTGCAAATATGCTCATAATTGTAAAATTTCTTTTTGT + HFHHFGG;?9BD@59:6DDGGGGGFDBHG@HHHHHHHHFCFFHGEGGFHHHHHHHHHHHHHGHHHHHHHFFDBGBGBEFHHHFHEEAEFEBA58(>FBBA @read_150_371/2 AATGTGAGTGAGCAGCCAAAGCAGGCGTCCCCGCAATTGACTTGCCACCAAGGGAATGTGGAGATCGGAATAGCGTCGTGTAGGGAAAGAGTGTAGATCT + HHFHDGGEEEEFFGHG9129DHHHHHHHHHG?@?<6:72GE?7)+>=DHHHGHHHHHGGFHEG4>ED><.+6(5D:CHHHHGDH:GHHFFHHHFHDG@DF @read_150_372/2 ACAGGTGTGAGCCACTGAACCCAGCCAAAAATATTTTTTCTAATCTCCTAGAGTCATCTTGCCCATACCTATTTTTTTTACAGATCGGAAGAGCGGCGTG + HHHHHHH?;1@BDDGGGDDDFB@CGE(5?.:EFHE?::7@EHHFGHHEHHHHHHD<=?@CE?=EC;?:C-,;9 @read_150_375/2 GGATTCTTAAATCAACCTTAGCTGTAAAACCTTTACAGAGTAAAGTTGCCAAAATCCCACTCACAATTCTGCTATTACTACAACTAATGATAATAACAGC + HHHHHHHHE?BEHHHHHBAE6634>CEHGFEGFHHH @read_150_376/2 AGCCAATGGCTCATAATAAATGTCTTTCTACATATCTATACCTATCCTGTGGGTTCTGTTTCCCTAGAGAACCTTGAGTAATAGAAATATAGTCCCTATT + HHHHHHHHHHHHHHHFHHHHHEHHHGG8/>,709@EE645EE>*;?GFFDDABGCHHHHHHHHHDHHHHD459;,';??42:.5?CFFHHHHFHFHHHDEFGGDHB<:9-3E9>?CAAA @read_150_379/2 ATGCCACCATCAACAAAGTCAAATTTAGAGCATTTTTATCAGCTCACATAGAACCCCATACACTTTAGGTCTAGATCGGAAGAGCGTCGTGTAGGGAAAG + =8EFEGCDCDEFHEDEEEGGEBHHHF@BFDFDCACG:2<64A*+CE6;;8@B/>8:.=BGCFDDABFFHHHHHHHHE@HHGHFHG@5EEEFFGHEGHHB= @read_150_380/2 CTTACCCATCCTGTACTGTAATTGTTTGTATCTTGTGAGGGCGGGGGTTGTGTCTCACATCCTGGCATTCCCTGGGCACAGCACTGGCCTGGTACACAGA + HHHHHHHHHHHHHHGHH=GGHHHHHHHHDDHHHHHHHHEEBHD?DABC@5AC?GHHHHGGFE?DHHHGCGF=EEFHHHHGD6=<B>47BFHHHHHGHHHHHHEHHGG:<=65937BDH @read_150_382/2 AGGATTATACTTTCACTCAAGCCTTTTCAAAAGATTAATGCTCTATTTATGAAATAGCATTGTTAACATTTTTGGTTCTTAATTTATTCTTTTGATAAAA + HHG=EHHHHFEBGFHEEEEHEFHHHEEDDC@@886BHHHC/DBEFHEDBDEGGCBDFHHFFHFBBHHHHHHHH?;42E=DEDBF@>FHHHHFHHGEHH=:@DB<75:9E @read_150_384/2 TGCCTATTACAAATATATTTCCTGATGATTTCACAGTCAGAATCTTTAACAAAACTAATCTTCATCATTTTGTAACTCGGAGTTCAGATAACAGTTAACC + GGGGABB;577BE:CC@==EEEEEEHHHH@6ED;EHEGGHDECDDHHHHHHHHHHFHHHEDDGEDEAFHHFGGHHHHA;6*4':;BCD7=;>/=EFF@BD @read_150_385/2 AATACAGTCAGTTTTAAATTGAGGACTACAAATATCTAGCAATTTAACTGACTGAGTTACAAACTGTAGAAGCCTCTGACTTCTGAAACTGTTGTGCTGG + :88DBHGHHHHHHHHGHHHHHFBEE?HFF=DBGGGHHHHHHGEHHHEHHHHHHDDFFHGFFFFE=.*&/;CHHHHCD@FFD(>>,,@GHHEHFHHEF@:' @read_150_386/2 GGAACCATGATCCCTCTACTTGTTCCTCATCTTTCCCCTCTTCCTTGAGAAACCCTCTCCTCTGCTTTTCTTTTCTTTTCTTTTGCTTCTGGCCAGAGAA + BBGCCCBDDGGHHGGHHHHHHHHE=DB<<79E@@@?>:??946+8ECFFHHFF@CFEB=@BD.EEDF;@GFAA?@;DDHGDDGHHHHHEEEEEAAEHHHF @read_150_387/2 ATGAACAAGGGCTGATTGATACATAAGCTCTTGAAAATTCTTAAGCTCACTGCATCCCTTCAGGTCTCCAAGGAACACTAAGTTTCCTCCCTGTCATGAG + HHHHHHHHHHHHHFHGHHEHHHHGDEEEHHD?@59EHHGHHHEEBFFHFAGGGGEEEEEEFHHHHHHHHFB:.+*(58ADD@A7@>AAEDHHFDFEE77@ @read_150_388/2 GAGGTCAGGAGTTTGAAACCAGCCTGGCCAACATGGTGAAACCCCTGACTCTACCAAAAAATACAAAATTAGCTGGGCCCACACTGGTGGGTGCCTGTAG + HHHHHHHHHHHHHHHHGF75>2-<@C7@GE9EECDEECCB??GHFE@A@D93;GGGBFHHHGFFEGFHFF@.<354,2*'>AABB8EEHHHHHEG?F??F @read_150_389/2 TACAACATCACTGGAAACTGGGTACTTTATTCCTAAAAAACATTTTTGGGACTGGTAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTG + DDDDHHHHHHHGG==:641265>DDBE?6GDFHFGDEDFHHHHHHHHHHFCFHHHHHHHHHHHHHHGFFFHHHHH8>@=FHHGBHGGF5&0EDDGEE5;< @read_150_390/2 ATCCTTCCGTTTGAAGAGCAAGAAAAAAGCAAGAGAAGAGTGTAGAACTTTCAGTGATTAGAGAAGAGCTCTGAATGGTGTGGTACATAGATGTGAGACC + HHHHHHHEFD=CEEEDBBC8DFHHHHHCGHHF<@?D:7FEGHHHHHHFECGGIGHHE@FEHHHHHHHHHGHEHHFHHHHHGEGHHHFD(DD=CDC>=?<= @read_150_391/2 ATCTCCATCCTGGTTTTGGTGTTTGGGGCAAAAATAGTGCCTAATGTTGCACAACACTGTGTGCTCTTGAGTGTAGTTTGCGGATGAGTTATATTAATGA + EHHHGG@;;<08:<=FGHHGHHHHHGEEHHEAGHHHHHHBEFEEDEGHHHHHHBCDCFEGHHHHHGHHFHHHGDF>.6>=EBGEHHFHHHHHHB>D?DD; @read_150_392/2 AGAGACAGATCATGAAAAGATTCTGGTAAATGGTTGGAGTTTCAGTGATTCAAAGCTGAGCACCACACTCAGTACTTTTTATTCTCTTAACCCTAAAGAC + HHHHHHHHHHHHGGGHHHGG7C?GGHHHHHHHHHEHEHHEB?B6.:DFFHEFBBAECC=B9+CEE5BD@HGHGB-8:.9EDAC=B?C@B@GGFHHHHEF4 @read_150_393/2 TGCAGTGGTCGGCTCACTGCAACCTCTGTCCCCCAGGTTCAAGCGATTCTTGTGCCTCACGTAGCTGGGACTACAGGCATGCGCCACCATACCTGGATAA + HHHHHHHHHHHHGHHHHHHHBDGGHHHHHGC>.A@.GHBCEC= @read_150_394/2 AGGTGTTCACAGCCCCCGAGGCTTTGAAAATGGGAGGGCTTTTGAGGTCAAGTAGGATGAGCTGCAGGTCTAATTTGAAAGCAGTGAGCATGCAATATCT + HHHHHHHHHHHHHHHHHHHHHHHHHCDCFCEHGGFHHFEHHGFGGHFD>CD@>CGHHHHHFEHHGGEFHCA@CAC6DHHHCCFHHHHH8.BBDEHEFDFD @read_150_395/2 GAGCCCTCAGAAATAATGCCACACATCTACAACTAACTGATCTTTGACAAAGCTGACAAAAACAAGAAATGGGGAAAGCATTCCCTATTTAAAAAATGGT + DBBEGDFGHHHHHHHHHEECEHHHHGGFHDBD6629C8BB5CCEBEB9;@GGGHHHHHHFHHHFHHHGGFDABGG@BCE@>+>=>CFEEE=B)6;29,4A @read_150_396/2 TAAATGAACTAGAACTTAAATGAACAAGACCTCCCCCACCCCCAGTCAAGAGGTAAAAAGGGCATTTCCAGCACACGACACGGCAAATGCAAAAGTTCAG + HFHGGB?C/;97<68FHHGBF@EHHHHHHGFB>@@HHHHHHHHHFFEFEFHHHHFGGHHH=@ACB@GDC853F98DCDHHEFFFFHFF @read_150_397/2 GCATTAAATGAATTTTGGTAAATCCAAGAGCAGGAAACTGTGTAACCCAGGTAAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCACGGTGGTC + HHFHGGHH@EHHHHHHFHHHGGGHHHFFHEGF*BF@<-=<@@EHHHHHHHGEC<.>>5>EHHEC?EEG@D@CB:AFHHHHGFAB?<>39-,.GHD366BF @read_150_398/2 AGCATGGAGGAGCTTCTGCAGGTCCCGCAGCTGGTGGATGGCAGAGCTTGATTCCCCATTCAAGCCCACACACAAGCCACTCCCCTGGCCTGTAACATCT + HHGGD?@@EEGGHHHHHFGHHGBBA:C8=BHHHHHFHHHHHHHHHEHFHHHHHHHHH@BFFFHHHEBGFFDDDCHHHHHHHHFHHHGGGH=EBDDBB.*, @read_150_399/2 TTTGGGGCTATTTTTCTAGATCTCATAGGTGTGCTTCATTCTTTTTTATTCTTTTTCTTTTTGTTTCCTCTGACTAGATCGGAAGAGCGTCGTGTAGGGA + E?DEDGBEGGGGGB@CDEEDGHHHHHGEHHGGGEDFFHHHHFHHHHHHHHHHHHHEDBD8<5535AB=A@DDEDE@),836BE.3.777(70-2BFFEFCD/HHHE9DFADHHGGHHGFHHHHHHHHHHHFHHHGFFE@AFH=FGEFC?E4DDDEBFGGBHEE6E @read_150_402/2 AAGCATTTTTTAAAAGTAAGAAAGAAAGAAACTCATTGAATTTTAGACCTGGGTGGGCCATAGATATCTCCCATGCTGTCCATTCATTCTGTAGATTGAT + HHHHHHHHHHFHHHFBDHHHHGHHHHHHHHHHHHHHBFGHHEEGHFHHDE0EFGFEHHHHHHHHHHHHHHHCDC>>DDEEEFDFGFHHHHHHHGG>;@E-0:>190<68.EHHHHH@5BHHEA9FF @read_150_404/2 TTTTGATGGGGTTGTTTTTTTCTTGTAAATTTGTTTGAGTTTATTGTAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTA + G87BEEBCHHHGDFBEEEHHBG@GGGGGDDHHHFFHHHEEHHHHHHHHHFHHEEDFHHHHHFHHHGFGDD:9:GGHGEHHFHFHHHHHHBBG=D@>/&9? @read_150_405/2 TCCCTGAGGCCCACCTGCTGTCCTAGAGAGCTGTCCCCAAGCCTAAGCCCCTGTCACTGCTGGGAGCCGGATGCCCGGGCCCTCTGCTGGGTAACTGGGG + HHHGGGGFCHHHDGGHHEGCFGFHHHHHDFEGGCHHHHHHGBFHHFDBFCFEFHH@>F,,'0-32257(6;GGHHHHGHEDCHHHFHEBBE@D @read_150_406/2 ACTTTTTTGTGTTTTCAGTAGAGATGGGGTTTAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGTCGTATCATTAAAAAAAAAA + GHHHHHHHHHBGGGGFFBD?;>5@D<8629 @read_150_407/2 TTCTTGGATACTATCCTAGAACACCTTTACCTTCTCAGCAAGTATAAGCTGAAACCAGCTGCCAGACCAGGGGGTTAGAGGTCACCAGAAAGGCTTTTAT + HHHHHHHEHGGF7@BGHDDGGFGHHHHFCHFGFF@B53.51-2))*843=FGIGBFHHFHHHHHHGHEHEEBDFHHHB@@EGGGFGFECDFBHHEFHHGB @read_150_408/2 GGAAGGATTGCTTGAGCTTGGAAAATTGAGGCTGCAGTGAGCCATGATTGCACCACTGCATTCTAGCCTGCATGATGGGAATGAGTCCCTGCCTAATTTA + HFCDHHHHHHHHEBCEGEEDBGGFGAGF>>FGGGGFFHFFG@A?HHHHHHHHHHHHHHHHHHHHHHHHHC@@HHHHHDG6EACFEHHFHFD4*7BD29>2 @read_150_409/2 AGGAGAAAGCATTGCCTGGGAATAAAACTTCAGCTGGCAGGAACTGAAGACAGCATGGTATGGTGGTGTCCTGGGGCAGGCTTTCCGACAGCAGCATCAC + HHHHHHHHHHHHHHHHHHHHHGGGB@CFB=FHHHHGEB:BE//8=HHHHFHHHHHHHHHHHHHFHHHHHHHHHCDDHHF@HHHGBD,.4743=FF.91/A @read_150_410/2 GATCTATTGGTTCATTCTGCAGATACTGAGTGCTTGCTATGAGTAGCCACTATTTTAGGTGCCAGGGCTCAGTGGTGTACCAAGGGCTGGGCAAGATCGG + HHHHHHHHHHHHHEHHHHEHFGGHGHHFF?DB@EHDDDAEFFEHHDDGFHHHHHGED84+;*3?BBFHHFEEHHHHEEHHDDEBHGGGFGG9;37@>>>: @read_150_411/2 CCCTCGGTAAGGAGTAGGTTAATGGTCTGTTGTTAGAACTCAGAGACATAACACACTGCTGTTCGTCAGAAATTTTAGATGCAGATCGGAAGAGCGTCGT + GGGHHHHHHHHHHHFG:;/422>EEDD;EEEBFFEE @read_150_412/2 TTTGTAACCAACTTTTGTCATTAACAATTTACTGGACTTGTCAACAAACCTAAATCTGTATCGTCTATAATGGCTACGTTCATTTTGGTATGAATCTTAA + CEEGBGB@@5EHHEGGHB@GFF@DDCC=:?EFGHHEE93ABHHFEEHHHHFGC@?FFGHHHFHCGH@CGEHHHHB41<@DCDDDGGHHHHFDGG?2<>3 @read_150_414/2 CAATCTACGTGATAGCCCTTACACATACACGTAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAA + GDC@A@EHF@*3@?,6CEG@FFEFDBGA?CDEFFHCA @read_150_415/2 TGATTGAAACCCAAAAATAAATGAATGAGTCTTGGAACATAAACTCATTTTGCAGTCTGGTCTCATTTGAGATCGGAAGAGCGTCGTGTAGGGAAAAAGT + HED@:BGHHHHHHHHHHHHHHHHHHHC=EDBGGEHHHEFGHHHHHHHHHHHGHHHHHHHHHHHHHHHFHHEHHEEGFEBE>CEFHHHHGHEFC@D>)5D@ @read_150_416/2 GCAAATGAATAAGCAAATTATGGCATTTCCACAAAATGGAATGACACTCAGAGATGAAAGGAATACACTATTGATACAGACAACAGTATGGGCAGATTTC + HHHGEBCEEGGHHHHDHHF8>3(8?HHHGHHHHHGDHHFFHHECBC5DEEFFHHFHHHHHBDDGDGHHEHHHHHHEEE?GFHHF:-388861,=FFEFBA @read_150_417/2 ATTATAGATAGGTGTATACACACAGGTCAGCATATTTCCAGGTTCTGTCAGCTAGGAGCCCATAGAAACAATGATGCCTCAGTAACAATGAGCATACATG + HHDA@=B/66*A.>>C;A?@FGGHHHHHHHHHHC+:<-8)11?EHEA @read_150_419/2 CTACAATGTGGTCACTGATGACTTTCAGTTACAGACAAAGTTCATTTTACTTTCCCAATCTAAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATC + HHHHHEEB8=BHHGC4>;.39>CD=*BHG=:BEEG@D5>=CA@<7EDCFFFGFFFHHHBAGGH=D@FHHB=DD?EGGHF=:>.39=ECCFHHHHGHHH;@ @read_150_420/2 TTGCAAGTGGAGATTTCAGCCGCTTTGGGGGCAATGGTAGAAAAGGAAATATCTTCGTATAAAGACTAGACAGAATGATTCTCAGAAACTCCTTTGAGAT + FFBGGGGF==.75,98@BHEHHHHHHHHHC',DB@@FFEEFHGGFFHHHHHHHHFHGHHHHHHHHFFGEHEHEGEEC9>=:@BFF@>EFFHFHE<.0%)1 @read_150_421/2 AGAGGTCAGGAGATCGAAACCATCCTGACTAACACGGAGAAACCCCATCTCTACTAAAAATACAAAAAAAAACTAGCCGGGCGTGGTGGCGGGCGCCTGT + HHEEGGGFGHHHHEGHHFFFD8,=55<-;CGHHHHHCCEFHE=0.35?==DDGG@>:352FGGGHHHDHHFHHHFFFFEHHHHHFFGHCGGEE@FHHEFF @read_150_422/2 TTTGGTAAGTAGTGTTCTTATTTTCATTAACTTCAAATTTTTTTTATGTATGTCCTAATTTTGATGTTCATCCAGGAGTTATTCAGGAGTAAATTGTTTA + HHHGG?>@FGHHHFFHHGHHHFB=>07;/A,9<67HHHHHHHHFFDDBGGFFFGDEGHHGEFBBB7:;0,:.6@+,-:>6GFGFHHHFHFGD@9,7<>)>?CF @read_150_424/2 GTGGCTTGGGAATTGGAATGCCGGCCTAACTCCAAAGCCCACACTCTTAAAACCACTGCGCTGGGTGGCTGCTCCTGCCGAGCGCTCTCTGCTCCCAGAC + HDE@BHHHHHGGEEHHGHHHG@BEHHHHHHHHHFDDDA.:-49<-ABB=FBFHEGECFHFHHHHGGFHHBBD85>EEHBABDFHEECHFDEEDGDEGFEBBFFHHHEEEG @read_150_427/2 CTTTGAGTTTTTTATTGTATGCAGTAAATGAGATTCTAACCAGTAAAATGCCAAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTC + HHBHHHHHEEGE?@)'9)BHHHHHHHHHHHHHGGFGHHFGHHHFFHDGHHHEHHHABG83.??@HHHHFHHHFCBFEGDHEGGGEGF?ADDDHHHFFFG? @read_150_428/2 AGGAGACATTACCACTGATACCACAGAAATTCAAAGGATCATTAGTGGCTACTATTAGCAACTATATGCCAATAAACTAGAGAATCTAGAGGTATGGATA + HHHHHHEHHHHHHHHFGHHHHHE27EEBHHHHHHHHHHHFHFHHFHFGE?FFFHHHFGFHFHHGHHFHHHHEGHHHHEHHHDEDDFF@A?EHHHFHHHHF @read_150_429/2 GCATGGCATGCCATGTTGGAGGTGGAAGGGGGCACTCTCTTCTCATCCTGTCTTCTAAAAAACAAAACCAAAACTCATCTATTGACCCACTGGCTAAGAA + HHHHHHHHHF@2<=@@DD?:6GGG;<.83CDEEHHHHHHFHD0CACA7B@:EECBGHHH..6>:>@AEHHHFGHF@EECFEHHHHHHHHHHHHHFGG<><@CBE;B=.DEHHHHB:--+2EHHHHHHFGFDDBFEFEECFFEFD/C@A @read_150_431/2 CCTCTGAGACATGTCTCCTGGATGTCCCACTGTACCTCCAACTCAACACGTCCAAGACAGAATCTGCTATCTTCCCCCAAGTGTGTTCCTCCTCCTTGAT + HHHHEFHHH=B@FHHGFHHHHHHECHEFDEEHHHEHHHHHHHHHHHHHFEHHHHHHHHHHDGG=>GFHHHHHEEHFHHGHFGFGACAC>@EBFHHHHHHH @read_150_432/2 TGATTTACCGAAGCCTAAGCGTCTAGATTGAATGGGGAGAAGCAGATCAGAGGATATCATTCCACTACAGTAGACACCCTTATCTATGGGGATATGCTCC + DDDGGHHHHHDDCGFEEEEHHFFEEEHHHHHHHHHHFDGFFFFEEFHHHHGGGHHHHHHHHHHBHHHHDEHHHHHFHHHFFHHH@;:;C/*8>:?7,4:A @read_150_433/2 ACATTTGTGAGCACTCACATGGGATACAAATATCTTTACAGTTTTTGATCACTCAGAAAGGTCCATCCACATACCTCTTGCCCACATTTTTTCATCACCA + FBHHHHHHHHHHHHHHHHHHGGEHBHHHHHIGHHHHHHFFHHHED;D;6:BD@EFF?GEGFE @read_150_437/2 TCTCACAGGACTTAATGGCTTCACTGGTGAAGTCTACCGAACAATTAAAGAAGAATTAATGCTAACCCTTTTCAAACTCTTCCAAAAAGCTGAAGAGGAG + HHHHHHHHHGDD8GE=CBDDEEEHEGGEBG;EFFEHEHHHHHD?:>DFFFHHHHHHHHFHHHHFF?FFHHHHHHEHEFF??7>A;DEFFHFFHEHECCFF @read_150_438/2 TTTTCAACTTCTGCCCTATTGACATTTTGGAATGGAGAATTCTTTGTGTTGGGGGCTGTCCTGTGCATTAGAACAGGTTTGACAGCCCACTGACTTCTAC + HHHHHHFDDEHHFGGGHHHHHHHHHHFEBB8DEEEHHHHHHHEHHHHHHHEHHHHHHHHGBADECE=FHG?@'(,.6.=B;-:.(0H@8AB4<4C<>@=<5>5<:BFFFDEB@:6@DBE?FHHHHHHHHEG=@@HBBDFBEDADHHHFGDHHHFEGHBEHHEEE @read_150_440/2 TTGGAATGAAAACCTCAGTTTAGAGTAAAGCATGTCTGCGCGCTCCAGTTGATTTGCTAGTCCCCACCCTGTGCAGTAATATCCTTAGAAACATTGACAG + HFHHHHHHHHHHHHHHHHHHHHHFHHHHHGGHHHBFF@?@DDDFHHHHEHHHHHFEHDGGHHGF<C@<79>578-9DBCCFFFE/&(/6<, @read_150_445/2 CCTGGAAGTCACGCTGATTTAAAGAAAAAATAAATACAACTTTAGTCTAGCTCTGCAGGCTCTACTGCTCCTTTGTGCCTGTCCTCTGTAGGTACCTCAT + HHHHEEEEGHHHHHDEHHDBDEFHGE?HHHHHHHHHHHHHFEDE@EFEHHFFCHHGEEGGEFGBHHHHHHGHH:GFG>CD>CEGFBEB/,;5;><.9:;@ @read_150_446/2 TGCTGGGATTACAGGTGCGAGCTACTGCACCTGGCTACCAAATGTTTTTAATCTAATCCTTAGAAAGAAATACTTAGGAGAGCTACTTTATGAATATATC + HHHHHHHEEHHHHHHEEEEHHHHHHHHHHFHHHFHHHCHHHHHDGHHHHHHHHHG8A4;HHHHDGD??EGGGEBFE5@@/3;A@;;BHHHFEBF6ECFHHFHHGHHHHHFHHHHHFDBEHHHHBFIGHHHEEC;HHHHGDFEHDFHHHHHE@/...<;?FDHB7BFHHHFEDFF?C9 @read_150_448/2 CTCAATATTAATTCTCACTCTGCCCCCAGCAGAGGGATTTTGTTTGTTTTTAGAGACAAGGTCTCACTGTGTTGCTGGTCTGGCCTTGAATTCCTTGGCT + >><<<;<3@@@=D<:;FDDEHHHFHHGHHHHHHHHHGFIGDHHEG?DA+>7EFAEE>6&0A?GHHHF@CDGEBCG= @read_150_450/2 AGCAGCTGGATGACCTTCATGGGTGTCCATTGCCCTAGCTTAGTGACCCTACCAGTGCCTGGACTGGTTGTGTATAGGCTGGAGGGGACTCTGTGTCTGG + HHHFFFHHHHHHHHHHFHHHHDCGGFFGG;DFFFEGFGFHHHHHHFGEEEHGGHE;DDB8.86A<33,B9BHHHD6.A5EHFECB?@DDDCEHHFDGFHH @read_150_451/2 AAGGAGTATGTTTGTACTTTTCTCAGCTCCTACTACAGGATTTGCCACATGGTGTTTAATAGAGTATTTGTTAAATTGCTAATTGACTTGTATATGGAAC + BCB=?;=EHHHHHHHHFFHHHHHHHHHHHHHHHHHHHHHHFHHFFBFCDIEGDEHHHHBGHHHHFBBCDD@C7<>=@DDAD2.59::@BEGFEBFEFDFH @read_150_452/2 AAGCCAATGGGGAAAAATTTTATTTAATTTTATGCTTCACATTCATATCATGTACATTAAAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTC + BHHHHHHHHHHHHHHHHGGHHGGEHE@HGHHFGFE>1:EBHHHHFEAEGHHHHHHHHHHHDBCGD=EHFD9?EEGHDICEGHHHHDFDHHHHHFFBEEFH @read_150_453/2 GGGCTTCCTGGCCTCCCCTCCTTTTGTTCTAATATGAGATTTTCAATCAGGTGAATCCTGTCTGGAGTAGAGGATGGGATATGTAAAACACCTGCAATGC + HHHEFEGGFHHFFDDFHHG/(01)2=<>DHHHHHGEGHHHHHHHHHHHHCEE@@76>BGBGDDBDFGB>>D9;;7DHHHHGHHHHHHHHHHEFHD>;:,6 @read_150_454/2 ACTTTTGAGAGTTCTTCCTGTATTTGGATACAAGTTGTTTATCAGTTATATGTTTTGCAAGTATTTTCACTTTTCTGTGCCTTCTTTTTATTCTAGATCG + .,.@B/<@B8<=@CBDFFHEBB:6+))6<=@HHHEDGHHGGAGFEEGGGCD=.5--%,,5:--1 @read_150_455/2 GTTTCACCAAATAACTCATTATAGCCAGAAGAGGGTATTGCTTCTTTCATTTGTGGCACTAGATAGGGCCCTATGTTTTTCACTATTTAGTATGTATACA + HHHHGFFDCEFHHHGHHHGGHHHHHHHHFHHFEFHHHHHHHB>E<@DEGEB/1419:<7DCD:CBC.:2E@@878BEGGGHHFAHHHHB:52(4:>E>GF @read_150_456/2 CTGTTATAGTTAGGTTTGTGGGTTCTCTTTTCTCTATTCATCTTCTATTTCTCTCTCCCTCCAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATC + HHHHHHH=E@BEBEABEHHHHFHHHHHHEHHHFHHHC+>,:*346@D9AAEEGGGHHFC@EDAA6+?@FD<@D@<86:DCFGHHHFFEF?GHHHFHHHHE @read_150_457/2 CTATGACACGTACAGAACAAAACATCCAGGTCAAAGCGGAGGGATGTAGAGCCTGGGGAAAGAGGTCTCCTGGGCAAAAGGGGGACTTCCTAGAAAACTT + HHHHHHHHHHHHHHHHHHHHHEEEHFGGFGHHF8FHHHHHBFFFHHHHFGEFGEEHHHHHHHHHHHHEFGGFABGFDFC?A5675DDACB@EF6CA98;: @read_150_458/2 TATTTTTGTACTTACCACATTGTATAAGTTTTGCTTCTACCTCTGAACTCTAAGCATGTATTTTGTCTTATTTTGTACTTCCTATACCTTGTACAGTATT + HHHDEGGHHHHHHHHHHHHHHFFBFHHGFHBGFFHHHHHHHEE5%,4(DEGEEGFHFIHHHHHEEGBEFGFHHEHHHHHEGBEB=.D/?CFA56'>87@/ @read_150_459/2 TGGCCTCAGCCTTTAGAGTAGCTGGGACCACAGGCGGGCACCATTATGCCTGGCTAATTAAAGAACTTTTTTTTTTGGTAGAGTCAGGGTCTTGTTGTGT + HHHHHHHHHHHHEGGHDEEHHHFHHHGFHHGA?=)5'2AAG>FEE?EGFHHF?AED5)26+4 @read_150_460/2 GCTGAAGTACTTAGGATTTGTCCAGAAAATAATTCCCAAGGGAAGATGGAGGATGAATTCATAAATATAATCATGTCCCTTTCTTTTCATCATCCTTCAC + HHHHHHHHHHHHHGGDDAAGHGEEHHGIGHHHHIHHHHHFFHFD9=;.*1FGGHHHHHHHHHHFFHHHHFHFDDD;GEHFHHEDCHFHH>EEEEADDB58 @read_150_461/2 ACTATTTGTTGAAAAGATTATTTTCCCCCATTGAATTATCTTGGTAGTTTGTTGAAAAGCAACTGACCAGATATGCCTGGGTCTATTTCTAGATCGGAAG + HHHHHHHHHC6>BF@GGHHHHHHHEADGHHHHHHHGBEHHHEGHHHH@DDGHHHHHHHHF8EGGHHHHGIHBBBHHDCFB46A7BGGGFHGEEAC.5851 @read_150_462/2 TTTTAAAAAATCAAACCTAATTGCCAAAATCTGATGTTTACACATAGTTAAGAAAAGAAAGAGCTAAATTGATTTTAAACGAGAAAATAATGCTTTGATT + HGGGGC<4>DEEGGHHHHHHHHHHHHHHHHGE6+;GCEFFHHHEBDC;=HGFGGFEHHHDD<4GEGHHHHHHGHGFFDE@:8DFF=C??D1+7DD=EGFF @read_150_463/2 GGGGATTTCAAGGACCTCCCTCTGCATCCCCACCTCACACTCTTCCAGTAAACCCAGTCCCCCGGACTGCCAGACTACAGCCTACCAGGAGTCTCCGCGC + HHHHHHHHHHHHHHFHHHHHHE8FHHF6:?D@FGGHHHHHHHHFHHHD8=FGHGFC=DGGHHHC?18=7FFEE@EFFEGGH<6,*;.DHHHEEBFDBADG @read_150_464/2 CAGTGCCCTGCAATGTGCCTGGCACATTTGGAACTCCCAGAGAGTTTTTTGTTGAATTGAACTGGTGGCCAGATCGGAAGAGCGTCGTGTAGGGAAAGAG + HHHFHHGFHHHHHHE;?>GBDFHHHHHHHHHEFGGDHHHHHFGGBECAHHHHHGIFGBED@6:60,/+2,A;CE7(9<<:EGFGB9- @read_150_465/2 CTCAGTGAGATGAACCAGGTACCTCAGTTGGAAATGCAGAAATCACCCGTCTTCTGCGTCGATCACGCTGGGAGCTGCAGACCAGAGCTGTTCCTATTCA + .66:@B>>BEHHHHHHFHHHHHHHHHHHGFGEHEBGFFD@FD9EEHFFAA:DDC?=6GEEBEEEHHHHEGD@@@45.;1*7CDF5EEECCEEGE4C@/'3 @read_150_466/2 CATCCTGATATACCTAGGACCTACCTACATTTTAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAA + HHH=GHHHHHHHE+EACGGGGE;>79?@CEB/BGHHHHHHFHEGGECDAHHGEGGEHHHHHHHHHHHHHHHHHHFDC?DB?GFDGHHHHHHHDFD?E<@) @read_150_467/2 CTCCAGAGAGCCCCTCAGATTCTTTATTGATTCATCATCTTCAAACACCAGAAGGACTAATGGAGAAGCAGAAACATCTAACAATCAACCAGTTGTTCTG + @@EGFHHHHHGEEB@HGHHHHEHHDHHHHGEIGEEEHHHHHHHFFDD<.@*3689E65DAEBD>>4GFHHGFF4&:DBEGGGHHHHHHED5@FDFFHFHHHHFE @read_150_469/2 CTCCTGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACGACGCCCGGCTAATTTTTTGTATTTTTAGTAGAGGCGGGGTTTCACTGTGTTA + HHFC@=EBDEGHH@A@CCDDHHHEEEE*:<@@BGFAFCGFHFHHFHFHHHHHHG8<4(34362-EFBE;A.@ @read_150_470/2 TGGCAACTTCCTCACTCGCCGCTGGGCCAGGATGGATGACTCGATGGGCTTCAGCTGGGGGGTGGGCTTGGAGCTGTTGAGTGCGGAGTACGTGGCAGCC + HHHHHHGGHGHHHFEEFF:BCB=36>B587<=>-63-4-0><36?=EGCC,@@>?FB>BFFHHFDFEEHFE<9AECCA @read_150_472/2 AAAGAGGAATGGGCAGAGATCAACCCAGACTATGAATATTAGATTAAATACATAATTATTTAACGTGCAGACATCAACATGCATCCACATCCATCAAGAA + G=CBDEGGBGHHHHHHGFGGFBEHHGCHB59@74>A*,,1:9><-@GHHHHHHHHHHHHHHG=EC24.-BEHHH86A@BEEHDHHHEDCAD8&-11399A @read_150_473/2 CAGCTCTGGGGTGGGGGGCCTGGCCCACCTAACTGCTTCCATGGTTGAGGCAGGAATGGGAGCATTGCTTAGAGTGCAGCAAGAGGCTGTGTCCATGGTT + GGFDHHHHHGDEE@72:/.09496<+36@@845FFGGDFGHHGHHHHB@@5>>=>BFEHHHEFD<@BFEEDFF@/2<<;75=6EE4+ADE7----(,3': @read_150_474/2 TCATATACTATGAAAAGTAGTTTTGTTTTTTTTTTTTTTAGCAGGGCATGGGGAACCAATGAAGAATTTAAAATAATAGGCCGGGCACAGTGGCTCACGC + HHGEHHGHHHHHHHHHFDEBCFFGGHFHGHHHB@;4*&67=FHD7@DHFFHHHDDEEEHHHHHHFHHHHHHHGGGC22)>CGF=@FFEGHHHFDCD.=A@ @read_150_475/2 GCTAAGTGGAAATTTATAGCACTAAATGCCCACATCGAAAAGCTAGAAAGATATTAAATCAACACCCTAACATCACAACTAAAAGAACTAGGGAACCAAG + HHHFGHHGGGGCDD?BGFHHHHHHHHFHHHHHCCD6B<<15@EBHHFFHHGGGGGHGFHHHHHHGEDEHFDHHHHHFHHHGD9;4*.>;5'73/9>57;1 @read_150_476/2 GTAAAATGATCTTTATTTGCAATTTATATAATTGTGCACAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTACA + GFGFDGFHHHHHHHGHFGFHHHHE@CFFHGHHHHEEECDEHGFHHGHFHHHHHHHHGG<-5,)8CGEEHHEFFIGDCDDCFEECEHE@FA9GF8E*4<.- @read_150_477/2 TTAACTCTCCAGCTGTCTGCAGTTTCTATGGATCCATCAACCATCCTTCTGACATTCCTTTTAGTGCAACACTAAAATGGCCTGAGCCTCTGCAGGTGTG + HHHHHHHBHHFGG=CGGDCBHHHHEG8DHHHHHHFFGGC8+1=DGEEHHHHHHHHHG@1;EE?7DEHHBFGHHHHFHH8>DBEHHHHBDDCFE9:6>EEF @read_150_478/2 TACTTACAATAATGACTAATAAAGATAATAGGACATACCTCACCAACTAGGGGGTTAATTCAGAGATTCAGTAACACATTGTATAGACAGGGGACTACTA + HHGHHGHHHHHHHHGGHHHHEFHFHHHHHFHHDFFFHHHHHHHHHHGHE@4*2(((08EE@@DFHHHHHHFGEHHHHF7EGGGGGGHHHGGHHF@<;BHH @read_150_479/2 ACCTGTCTAGTGCTGTCAGTGGAGTATTAAAGTCCCCCCACAAATGGACTTAACATTTGTTAAGTGATTTATTGTTAACAAATGTTAAGTCCCTTAGCAA + HHHHHHHGGHHHHHHHHHHHHHHHHHGHHHHHHFB=?;ADFFGGHGGFHHHHFFFDCEHHHE@D@GDGGIHHHDFFFB485EHHHFHHGB8>,DEBFE2- @read_150_480/2 TATTTTTTAAACTTTTTGTTAAAAGTGAAGACACAAACACTCACATTAGGCTAGGCTTACAGAGGGTCAAGATAATCAGTATTACCACTGGAAGGTCTCG + IFHHHHHHHHHHHHHHHHHHHHBEEEEEEGGEHFDHEFDHHFFEF @read_150_483/2 AAAAAGTACAGTAAAAATACAGTATTATAATCTTATGGGACCACCATCATAAATGCAGTCAGTCATCGACTGAAATCTCATTATGCTGCCCATGACTATA + HHHBE@EHHHHHHHHHHHHHHHFFHHHF==HE8FGHHFHEFEBFBDCBBHHHHFHFGHHHHHHHHHHHHGCGGF738FFGHFHHAGFHGGFG9=A:??AG @read_150_484/2 CTGGTGTTACTGAGAACTTTAAGGCACTGGCCTGTTCCTCCACTCCTATACATCCCCCAGTTGGGCCTCTTGGCATCGCCTTAATATCAAGATAAGATCG + <;DHHHHHHHHHHHHHGGGGGBGCHHHF@=EGHHHHHHHHHHHHHFFDDDEFFFFFH=7>:GHHHHHHFHHHHHE>7,/;@95CDGHFHHFEFFFFB77@ @read_150_485/2 CTTATGGGGACGCTTTCAAGATGAATAGGATAATGCATGTATCTCCCATAGCCCTGCAGCCTTATGCTTCATCCTGTCAGTGCAATCTTTTTAGGCAGGG + HHHFGHHHHDECBFDFGFEEHHHHHGFHHHHHHHHHGEEEDCEHHHFFF @read_150_486/2 GCGGGGCTGGGGGGAGACTCAGGCAGAATTGTGAAGATATTCAATTGCTCCTGACTTTATCAATAATCTAACATTTCAACCTAACATTGATATCTATTTT + HHHHHHHHHHHHHHHHHHHHHHHHHHHH?AGEGHHFHGHHGHHHGD??B=EEHHGEGGEFCCB>,15793<*15FFFEFH9@@DBD9->@BCEGFHHHHHHHHFDBHHHHD@:9?/;A2:@.=@;D=D>8@555=BHE @read_150_489/2 AGCATATTTCCCTTCCACACTGTGTAGATATATAATACGGGGAACTGAGAAATAAACATGAAAAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGAAGAT + DEHHHHFHHHHHBHEHHFCC<.@C8CDGGGHHHHHHHHHHHA9<>?CFEFEEFGGHHHHHHGGFHHGFHHHHHHH8GHEBADDB?@C9EGHH:6A%'1>B @read_150_490/2 TTTCAAGTGTCTTTAATACTCAACATAGAAGGTTTTTTTTTTTCCTATGTAAAGCCAGGCACATCAATAAAACTCTCCTCAGTGAGATCGGAAGAGCGTC + HHHHHHHGGHHGHDDHHHEHFHHHHHHE8EFFFEGHFBEFHHHHFHGGGDCBEHHFGHFEHHHHHHED@GHHD=CDDEADEGHHF85.=ACFFFHGFD@? @read_150_491/2 TCCAGAGTGAGGGAATGCCTCGCCCTGCTTCGACTCGCGCACGGTGCGTGCACCCACGGCCCTGCGCCCACTGTCTGGCACTCCCTAGTGAGATGAACCC + HHHHF=FEEGDEGHHHHHHHHHGBDBGGHHHEEEFC=EAFHFHFHGHFEFHFGCEFB717;9:>EFHHHHHHHHEGDGFFHHHHHG@AGE?B7GHHFE3< @read_150_492/2 TCATCAAGGTGTCCAAGTTCACCAGGCGTGGTAGCTCGTGCCTGTAATCCCAGATACTCGAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGAAGTTATC + HHGGHGHGHHCD@FHHHGGHHHHHHHHDE9:>6=AEEHHFHFFHFDFFFFGGGBHHGHHHHHHFHHHHEE@D=EDEG9:.@=@.*8.8F8:&-2-&158: @read_150_493/2 TCCTCCTTACTCTACCATTGCACTGCTAAGTAGGCTTTTATTTTGCTGTATTTGCCACCTTTAAAATTTATCCTTCGCATCGTAGTCATAACAAGTGAGG + FHHHGEBEHHHHHHHGHHHHHHHHHHGGGHHHFFDHHHBFFHHHHHHHEFHHGHHHHGCECAGGHHHHHHFHHCEEEFFFBFGE2:?C@@?FFBEC==?? @read_150_494/2 TTCTCAGAACCTGGCATCCGCCAACCTCTCCAGCTTTTGCTTTCTTGTCTGTGTCCTTTAAGCTCCTCACTGCCTGGAAGATGCCCCGTTTTTCTCTCTC + 9-8CDFBBBE?IGEEHHHHHHHHHEFHHHHHGG>9,;84+790AHEHDBHHGHHHHGHHHFC8>9DD?@A<@CDCAHHHHHHFBDHHCABHCA*4ACDBD @read_150_495/2 CCTTGACCTCTTGAGCTCCAGTGATCCTCCCACCTTGGCCTCCTGAAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTAT + HHFIGHHHHHHHHHHHHHHHHHHHHHEBBCHHHGFFHHHHEED=6C@FGGGBEGBCCDEEFHHFFHHHGGGGEBECHDGHHHHHHHHEHFHHHBHHHHBHHHFFDC0CEFHHHHHHAA @read_150_497/2 ATTGCTTGATATGTACCACAGATTGAGGTACCGACCTCAATGTACCAAACACACCTGCAAATGTGGTTGGTAACCACCTCAAGATAAATGAATCCAGTGT + HHHHHHHHHHHHHGBBDGFHHHHHHGHHCB@68ABDFCGHHE:7<55;.5:;@BCHHHHHHHHHHHHCEHD8DHFHFHF=;@D;7?FHHFBEFEHHHAE? @read_150_498/2 ATTCTGAGATTTTAGTGCTCCTGTCACCCAAGTAGTGTACATTGTACCTAATATGTAGTTTTTTTATCCGACACCCCTTCCACCTTCCCACTTCTGGCTC + HFGHHHHHHHHHHEFGGF@FHHHDCA>GGGCDEHFHHGFHHHHHHHHFHF?.EEE=CCDGHHHHHGGGFHHHHHEHHH@HFHHFBE<=@>08><.::*4; @read_150_499/2 TTCTTTTAGGGTGTGTCTCTCCTTGGAGAATGTGTTCACATTCATTTTCTATATGGCGCTACTTATTTTGAAATTCTTCTATGATTTGATATAAATGGAC + HHHHHHHHEHGFEFHHHHH>GFHA6CDBHDHHE88CAHHHHDGD=@..7ECGGGHGB8>?BEEFHHGGFCCGGFDE62@>=DBBAFHFHFFGHHHHEFF6 @read_150_500/2 ACAGAATGGGAGAAAATATTTGCAAACTAGGAGGGGAACAACAGACAAAGACTTAATGTCCAGAATCTATAAGGAACTTGAACAAATTTACAAGGAAAAA + EHHHHGDGEEGHHHHHHHHHH@@BEAHHHHEBFHHHHHHHHHHHEHHHHFHHHHHHHFHHHGFDHHGGE>B@?GHFE?ACEHHHHFDHHH<59FFEF. * \*************************************************************************/ #include #include #include #include "adapterset.hpp" #include "debug.hpp" #include "linereader.hpp" #include "strutils.hpp" namespace ar { typedef std::pair named_fastq_row; typedef std::vector fastq_table; typedef fastq_table::const_iterator fastq_table_citer; bool print_parse_error(const std::stringstream& message) { std::cerr << "ERROR READING TABLE:\n" << cli_formatter::fmt(message.str()) << std::endl; return false; } std::string trim_comments(std::string line) { const size_t index = line.find('#'); if (index != std::string::npos) { line.resize(index); } return line; } bool read_table(const std::string& filename, fastq_table& dst, size_t min_col, size_t max_col, bool row_names = false) { AR_DEBUG_ASSERT(min_col <= max_col); AR_DEBUG_ASSERT(min_col >= 1); size_t last_row_size = 0; size_t line_num = 1; try { line_reader adapter_file(filename); for (std::string line; adapter_file.getline(line); ++line_num) { fastq_vec row; std::string name; std::string field; std::stringstream instream(trim_comments(line)); for (size_t index = 1; instream >> field; ++index) { try { if (index == 1 && row_names) { name = field; } else { row.push_back(fastq("sequence", field)); } } catch (const fastq_error& error) { std::stringstream message; message << "Failed to parse sequence in '" << filename << "' at line " << line_num << ", column " << index << ": " << error.what(); return print_parse_error(message); } } if (name.empty() && row.empty()) { // Ignore empty lines, e.g. those containing only comments continue; } else if (row.size() < min_col) { std::stringstream message; message << "Expected at least " << min_col << " columns in " << "table '" << filename << "' at line " << line_num << ", but only found " << row.size() << " column(s)!"; return print_parse_error(message); } else if (row.size() > max_col) { std::stringstream message; message << "Expected at most " << min_col << " columns in " << "table '" << filename << "' at line " << line_num << ", but found " << row.size() << " column(s)!"; return print_parse_error(message); } else if (last_row_size && last_row_size != row.size()) { std::stringstream message; message << "Error reading '" << filename << "' at line " << line_num << "; rows contain unequal number of " << "columns; last row contained " << last_row_size << " column(s) but current row contains " << row.size() << " column(s)!"; return print_parse_error(message); } else { last_row_size = row.size(); } dst.push_back(named_fastq_row(name, row)); } } catch (const std::ios_base::failure& error) { std::stringstream message; message << "IO error reading '" << filename << "' at line " << line_num << ": " << error.what(); return print_parse_error(message); } return true; } bool check_barcodes_sequences(const fastq_pair_vec& barcodes, const std::string& filename, bool paired_end = false) { if (barcodes.empty()) { return true; } const size_t mate_1_len = barcodes.front().first.length(); const size_t mate_2_len = barcodes.front().second.length(); string_pair_vec sequences; for (fastq_pair_vec::const_iterator it = barcodes.begin(); it != barcodes.end(); ++it) { const std::string& mate_1 = it->first.sequence(); const std::string& mate_2 = it->second.sequence(); if (mate_1.find('N') != std::string::npos) { std::stringstream error; error << "Degenerate base (N) found in mate 1 barcode sequence '" << mate_1 << "'. Degenerate bases are not supported for " << "demultiplexing; please remove before continuing!"; return print_parse_error(error); } else if (mate_2.find('N') != std::string::npos) { std::stringstream error; error << "Degenerate base (N) found in mate 2 barcode sequence '" << mate_2 << "'. Degenerate bases are not supported for " << "demultiplexing; please remove before continuing!"; return print_parse_error(error); } else if (mate_1.length() != mate_1_len) { std::stringstream error; error << "Inconsistent mate 1 barcode lengths found; last barcode " "was " << mate_1_len << " basepairs long, but barcode " << (it - barcodes.begin()) + 1 << " mate 1 sequence is " << mate_1.length() << " basepairs long! Variable length " "barcodes are not supported!"; return print_parse_error(error); } else if (mate_2.length() != mate_2_len) { std::stringstream error; error << "Inconsistent mate 2 barcode lengths found; last barcode " "was " << mate_2_len << " basepairs long, but barcode " << (it - barcodes.begin()) + 1 << " mate 2 sequence is " << mate_2.length() << " basepairs long! Variable length " "barcodes are not supported!"; return print_parse_error(error); } sequences.push_back(string_pair(it->first.sequence(), it->second.sequence())); } std::sort(sequences.begin(), sequences.end()); string_pair_vec::const_iterator prev = sequences.begin(); string_pair_vec::const_iterator curr = prev + 1; for (; curr != sequences.end(); ++prev, ++curr) { if (prev->first == curr->first) { if (paired_end) { if (prev->second == curr->second) { std::stringstream error; error << "Duplicate barcode pairs found in '" << filename << "' with barcodes "<< prev->first << " and " << prev->second << ". please verify " "correctness of the barcode table and remove any " "duplicate entries!"; return print_parse_error(error); } } else { std::stringstream error; error << "Duplicate mate 1 barcodes found in '" << filename << "': "<< prev->first << ". Even if these " "are associated with different mate 2 barcodes, it " "is not possible to distinguish between these in " "single-end mode!"; return print_parse_error(error); } } } return true; } bool valid_sample_name(const std::string& name) { for (const char c : name) { if ((c >= 'a' && c <= 'z') || (c >= 'A' && c <= 'Z') || (c >= '0' && c <= '9') || (c == '_')) { continue; } std::stringstream error; error << "The sample name '" << name << "' is not a valid sample " "name; only letters ('a' to 'z' and 'A' to 'Z'), numbers (0 " "to 9) and underscores (_) are allowed."; return print_parse_error(error); } if (name == "unidentified") { std::stringstream error; error << "The sample name '" << name << "' is a reserved name, and " "cannot be used!"; return print_parse_error(error); } return true; } bool check_sample_names(const string_vec& names) { if (names.empty()) { return true; } for (const auto& name : names) { if (!valid_sample_name(name)) { return false; } } string_vec sorted_names = names; std::sort(sorted_names.begin(), sorted_names.end()); string_vec::const_iterator prev = sorted_names.begin(); string_vec::const_iterator curr = prev + 1; for (; curr != sorted_names.end(); ++prev, ++curr) { if (*prev == *curr) { std::stringstream error; error << "Duplicate sample name '" << *prev << "'; combining " "different barcodes for one sample is not supported. " "Please ensure that all sample names are unique!"; return print_parse_error(error); } } return true; } /////////////////////////////////////////////////////////////////////////////// // Implementations for 'adapters' class adapter_set::adapter_set() : m_samples() , m_barcodes() , m_adapters() { // Default name if no barcodes are used m_samples.push_back("main"); } void adapter_set::add_adapters(const std::string& adapter1, const std::string& adapter2, bool adapter2_read_orientation) { fastq adapter1_fq("adapter1", adapter1); fastq adapter2_fq("adapter2", adapter2); if (adapter2_read_orientation) { adapter2_fq.reverse_complement(); } m_adapters.push_back(fastq_pair(adapter1_fq, adapter2_fq)); } bool adapter_set::load_adapters(const std::string& filename, bool paired_end) { fastq_table raw_adapters; if (!read_table(filename, raw_adapters, paired_end ? 2 : 1, 2)) { return false; } for (const auto& row : raw_adapters) { fastq adapter_5p = row.second.at(0); fastq adapter_3p; if (row.second.size() > 1) { adapter_3p = row.second.at(1); adapter_3p.reverse_complement(); } m_adapters.push_back(fastq_pair(adapter_5p, adapter_3p)); } return true; } bool adapter_set::load_barcodes(const std::string& filename, bool paired_end) { fastq_table raw_barcodes; if (!read_table(filename, raw_barcodes, 1, 2, true)) { return false; } m_samples.clear(); m_barcodes.clear(); for (const auto& row : raw_barcodes) { fastq barcode_5p = row.second.at(0); fastq barcode_3p; if (row.second.size() > 1) { barcode_3p = row.second.at(1); } m_samples.push_back(row.first); m_barcodes.push_back(fastq_pair(barcode_5p, barcode_3p)); } return check_barcodes_sequences(m_barcodes, filename, paired_end) && check_sample_names(m_samples); } size_t adapter_set::adapter_count() const { return m_adapters.size(); } size_t adapter_set::adapter_set_count() const { if (m_barcodes.empty()) { return 1; } else { return barcode_count(); } } size_t adapter_set::barcode_count() const { return m_barcodes.size(); } fastq_pair_vec adapter_set::get_adapter_set(size_t nth) const { if (m_barcodes.empty()) { AR_DEBUG_ASSERT(nth == 0); return m_adapters; } fastq_pair barcodes = m_barcodes.at(nth); barcodes.second.reverse_complement(); fastq_pair_vec adapters; for (const auto& adapter_pair : m_adapters) { fastq adapter_1("adapter_1", barcodes.second.sequence() + adapter_pair.first.sequence()); fastq adapter_2("adapter_2", adapter_pair.second.sequence() + barcodes.first.sequence()); adapters.push_back(fastq_pair(adapter_1, adapter_2)); } return adapters; } string_pair_vec adapter_set::get_pretty_adapter_set(size_t nth) const { fastq_pair barcodes; if (m_barcodes.empty()) { AR_DEBUG_ASSERT(nth == 0); } else { barcodes = m_barcodes.at(nth); } string_pair_vec adapters; const fastq_pair_vec adapter_pairs = get_adapter_set(nth); for (const auto& adapter_pair : adapter_pairs) { fastq adapter_1 = adapter_pair.first; fastq adapter_2 = adapter_pair.second; adapter_2.reverse_complement(); std::string seq_1 = adapter_1.sequence(); std::string seq_2 = adapter_2.sequence(); if (barcodes.first.length()) { seq_2.insert(barcodes.first.length(), 1, '_'); } if (barcodes.second.length()) { seq_1.insert(barcodes.second.length(), 1, '_'); } adapters.push_back(string_pair(seq_1, seq_2)); } return adapters; } const fastq_pair_vec& adapter_set::get_raw_adapters() const { return m_adapters; } const fastq_pair_vec& adapter_set::get_barcodes() const { return m_barcodes; } const std::string& adapter_set::get_sample_name(size_t nth) const { return m_samples.at(nth); } } // namespace ar adapterremoval-2.3.1/src/adapterset.hpp000066400000000000000000000104351350370616400201670ustar00rootroot00000000000000/*************************************************************************\ * AdapterRemoval - cleaning next-generation sequencing reads * * * * Copyright (C) 2011 by Stinus Lindgreen - stinus@binf.ku.dk * * Copyright (C) 2014 by Mikkel Schubert - mikkelsch@gmail.com * * * * If you use the program, please cite the paper: * * S. Lindgreen (2012): AdapterRemoval: Easy Cleaning of Next Generation * * Sequencing Reads, BMC Research Notes, 5:337 * * http://www.biomedcentral.com/1756-0500/5/337/ * * * * This program is free software: you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation, either version 3 of the License, or * * (at your option) any later version. * * * * This program is distributed in the hope that it will be useful, * * but WITHOUT ANY WARRANTY; without even the implied warranty of * * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * * GNU General Public License for more details. * * * * You should have received a copy of the GNU General Public License * * along with this program. If not, see . * \*************************************************************************/ #ifndef AR_ADAPTERS_H #define AR_ADAPTERS_H #include "commontypes.hpp" #include "fastq.hpp" namespace ar { /** * Class for reading sets of adapters and barcodes, and for generating * per-barcode sets of adapter sequences as needed. The class further checks * for the correctness of these sequences, and detects duplicate barcode * sequences / pairs of sequences. */ class adapter_set { public: /** Initialize empty adapter list. */ adapter_set(); /** * Adds a pair of adapters to the set; by default it is assumed that * the adapter 2 sequence is in read orientation (e.g. can be found as is * in the raw mate 2 reads). */ void add_adapters(const std::string& adapter1, const std::string& adapter2, bool adapter2_read_orientation = true); /** * Loads barcodes from a table, returning true on success. The value of * 'paired_end_mode' is used to set the expected number of values. */ bool load_adapters(const std::string& filename, bool paired_end_mode); /** * Loads barcodes from a table, returning true on success. The value of * 'paired_end_mode' to correctly identify duplicate sequences. */ bool load_barcodes(const std::string& filename, bool paired_end_mode); /** Returns the number of adapters per set. */ size_t adapter_count() const; /** Returns the number of adapter sets; namely 1 or barcode_count() */ size_t adapter_set_count() const; /** Returns the number of barcodes. */ size_t barcode_count() const; /** * Returns the nth set of adapters; when barcodes are specified, the * raw adapters are merged with the 'nth' barcodes. If no barcodes are * set, the get_adapters(0) == get_raw_adapters(). */ fastq_pair_vec get_adapter_set(size_t nth) const; /** Returns get_adapter_set(nth) formatted for printing. */ string_pair_vec get_pretty_adapter_set(size_t nth) const; /** Returns adapter sequences absent of any barcodes. */ const fastq_pair_vec& get_raw_adapters() const; /** Returns the (pairs of) barcodes. */ const fastq_pair_vec& get_barcodes() const; /** Returns the name associated with the nth set of barcodes. */ const std::string& get_sample_name(size_t nth) const; private: //! Names associated with barcodes string_vec m_samples; //! User-supplied barcodes fastq_pair_vec m_barcodes; //! User-supplied adapter sequences, without barcodes added fastq_pair_vec m_adapters; }; } // namespace ar #endif adapterremoval-2.3.1/src/alignment.cpp000066400000000000000000000435171350370616400200130ustar00rootroot00000000000000/*************************************************************************\ * AdapterRemoval - cleaning next-generation sequencing reads * * * * Copyright (C) 2011 by Stinus Lindgreen - stinus@binf.ku.dk * * Copyright (C) 2014 by Mikkel Schubert - mikkelsch@gmail.com * * * * If you use the program, please cite the paper: * * S. Lindgreen (2012): AdapterRemoval: Easy Cleaning of Next Generation * * Sequencing Reads, BMC Research Notes, 5:337 * * http://www.biomedcentral.com/1756-0500/5/337/ * * * * This program is free software: you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation, either version 3 of the License, or * * (at your option) any later version. * * * * This program is distributed in the hope that it will be useful, * * but WITHOUT ANY WARRANTY; without even the implied warranty of * * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * * GNU General Public License for more details. * * * * You should have received a copy of the GNU General Public License * * along with this program. If not, see . * \*************************************************************************/ #include #include #include #include #include #include #include "alignment.hpp" #include "alignment_tables.hpp" #include "debug.hpp" #include "fastq.hpp" namespace ar { #if defined(__SSE__) && defined(__SSE2__) #include //! Mask representing those (sparse) bits used when comparing multiple //! nucleotides. These are simply the least significant bit in each byte. const __m128i BIT_MASK_128 = _mm_set1_epi8(1); //! Zero'd 128b integer. const __m128i ZERO_128 = _mm_set1_epi8(0); //! A 0xffff... 128b integer. const __m128i ONES_128 = _mm_set1_epi8(-1); //! Mask of all Ns const __m128i N_MASK_128 = _mm_set1_epi8('N'); /** Counts the number of bits set in a __m128i. **/ inline size_t COUNT_BITS_128(__m128i value) { // Calculates the abs. difference between each pair of bytes in the upper // and lower 64bit integers, and places the sum of these differences in // the 0th and 4th shorts (16b). value = _mm_sad_epu8(ZERO_128, value); // Return the 0th and 4th shorts containing the sums calculated above return _mm_extract_epi16(value, 0) + _mm_extract_epi16(value, 4); } #else #warning SEE optimizations disabled! #endif /** * Compares two subsequences in an alignment to a previous (best) alignment. * * @param best The currently best alignment, used for evaluating this alignment * @param current The current alignment to be evaluated (counts are assumed to be zero'd!) * @param seq_1_ptr Pointer to the first base in the first sequence in the alignment. * @param seq_2_ptr Pointer to the first base in the second sequence in the alignment. * @return True if the current alignment is at least as good as the best alignment, false otherwise. * * If the function returns false, the current alignment cannot be assumed to * have been completely evaluated (due to early termination), and hence counts * and scores are not reliable. The function assumes uppercase nucleotides. */ bool compare_subsequences(const alignment_info& best, alignment_info& current, const char* seq_1_ptr, const char* seq_2_ptr) { int remaining_bases = current.score = current.length; #if defined(__SSE__) && defined(__SSE2__) while (remaining_bases >= 16 && current.score >= best.score) { const __m128i s1 = _mm_loadu_si128(reinterpret_cast(seq_1_ptr)); const __m128i s2 = _mm_loadu_si128(reinterpret_cast(seq_2_ptr)); // Sets 0xFF for every byte where one or both nts is N const __m128i ns_mask = _mm_or_si128(_mm_cmpeq_epi8(s1, N_MASK_128), _mm_cmpeq_epi8(s2, N_MASK_128)); // Sets 0xFF for every byte where bytes differ, but neither is N const __m128i mm_mask = _mm_xor_si128(ONES_128, // This is a bitwise NOT _mm_or_si128(_mm_cmpeq_epi8(s1, s2), ns_mask)); // The oddity above is because SSE doesn't have a bitwise not operator, and // `~(some __m128i)` doesn't work on Intel compilers. XOR(thing, 0xff) // is the same, so we use that current.n_ambiguous += COUNT_BITS_128(_mm_and_si128(ns_mask, BIT_MASK_128)); current.n_mismatches += COUNT_BITS_128(_mm_and_si128(mm_mask, BIT_MASK_128)); // Matches count for 1, Ns for 0, and mismatches for -1 current.score = current.length - current.n_ambiguous - (current.n_mismatches * 2); seq_1_ptr += 16; seq_2_ptr += 16; remaining_bases -= 16; } #endif for (; remaining_bases && current.score >= best.score; --remaining_bases) { const char nt_1 = *seq_1_ptr++; const char nt_2 = *seq_2_ptr++; if (nt_1 == 'N' || nt_2 == 'N') { current.n_ambiguous++; current.score--; } else if (nt_1 != nt_2) { current.n_mismatches++; current.score -= 2; } } return current.is_better_than(best); } alignment_info pairwise_align_sequences(const alignment_info& best_alignment, const std::string& seq1, const std::string& seq2, int min_offset = std::numeric_limits::min(), int max_offset = std::numeric_limits::max()) { const int start_offset = std::max(min_offset, -static_cast(seq2.length()) + 1); const int end_offset = std::min(max_offset, static_cast(seq1.length()) - 1); alignment_info best = best_alignment; for (int offset = start_offset; offset <= end_offset; ++offset) { const size_t initial_seq1_offset = std::max(0, offset); const size_t initial_seq2_offset = std::max(0, -offset); const size_t length = std::min(seq1.length() - initial_seq1_offset, seq2.length() - initial_seq2_offset); if (static_cast(length) >= best.score) { alignment_info current; current.offset = offset; current.length = length; const char* seq_1_ptr = seq1.data() + initial_seq1_offset; const char* seq_2_ptr = seq2.data() + initial_seq2_offset; if (compare_subsequences(best, current, seq_1_ptr, seq_2_ptr)) { best = current; } } } return best; } struct phred_scores { explicit phred_scores(size_t index) : identical_nts(IDENTICAL_NTS[index]) , different_nts(DIFFERENT_NTS[index]) { } //! Phred score to assign if the two nucleotides are identical char identical_nts; //! Phred score to assign if the two nucleotides differ char different_nts; }; phred_scores get_updated_phred_scores(char qual_1, char qual_2) { AR_DEBUG_ASSERT(qual_1 >= qual_2); const size_t phred_1 = static_cast(qual_1 - PHRED_OFFSET_33); const size_t phred_2 = static_cast(qual_2 - PHRED_OFFSET_33); const size_t index = (phred_1 * (MAX_PHRED_SCORE + 1)) + phred_2; AR_DEBUG_ASSERT(index < PHRED_TABLE_SIZE); return phred_scores(index); } string_pair collapse_sequence(const std::string& sequence1, const std::string& sequence2, const std::string& qualities1, const std::string& qualities2, std::mt19937* rng) { AR_DEBUG_ASSERT(sequence1.length() == sequence2.length() && sequence1.length() == qualities1.length() && sequence1.length() == qualities2.length()); std::string collapsed_seq(sequence1.length(), 'X'); std::string collapsed_qual(sequence1.length(), '\0'); for (size_t i = 0; i < collapsed_seq.size(); ++i) { char nt_1 = sequence1.at(i); char nt_2 = sequence2.at(i); char qual_1 = qualities1.at(i); char qual_2 = qualities2.at(i); if (nt_1 == 'N' || nt_2 == 'N') { // If one of the bases are N, then we suppose that we just have (at // most) a single read at that site and choose that. if (nt_1 != 'N') { collapsed_seq.at(i) = nt_1; collapsed_qual.at(i) = qual_1; } else if (nt_2 != 'N') { collapsed_seq.at(i) = nt_2; collapsed_qual.at(i) = qual_2; } else { collapsed_seq.at(i) = 'N'; collapsed_qual.at(i) = PHRED_OFFSET_33; } } else if (nt_1 != nt_2 && qual_1 == qual_2) { if (rng) { collapsed_seq.at(i) = ((*rng)() & 1) ? nt_1 : nt_2; const phred_scores& new_scores = get_updated_phred_scores(qual_1, qual_2); collapsed_qual.at(i) = new_scores.different_nts; } else { collapsed_seq.at(i) = 'N'; collapsed_qual.at(i) = PHRED_OFFSET_33; } } else { // Ensure that nt_1 / qual_1 always contains the preferred nt / score // This is an assumption of the g_updated_phred_scores cache. if (qual_1 < qual_2) { std::swap(nt_1, nt_2); std::swap(qual_1, qual_2); } const phred_scores& new_scores = get_updated_phred_scores(qual_1, qual_2); collapsed_seq.at(i) = nt_1; collapsed_qual.at(i) = (nt_1 == nt_2) ? new_scores.identical_nts : new_scores.different_nts; } } return string_pair(collapsed_seq, collapsed_qual); } /////////////////////////////////////////////////////////////////////////////// // Public functions alignment_info::alignment_info() : score(0) , offset(0) , length(0) , n_mismatches(0) , n_ambiguous(0) , adapter_id(-1) { } bool alignment_info::is_better_than(const alignment_info& other) const { if (score > other.score) { return true; } else if (score == other.score) { if (length > other.length) { return true; } else if (length == other.length) { return n_ambiguous < other.n_ambiguous; } } return false; } alignment_info align_single_ended_sequence(const fastq& read, const fastq_pair_vec& adapters, int max_shift) { size_t adapter_id = 0; alignment_info best_alignment; for (const auto& adapter_pair : adapters) { const fastq& adapter = adapter_pair.first; const alignment_info alignment = pairwise_align_sequences(best_alignment, read.sequence(), adapter.sequence(), -max_shift, std::numeric_limits::max()); if (alignment.is_better_than(best_alignment)) { best_alignment = alignment; best_alignment.adapter_id = adapter_id; } ++adapter_id; } return best_alignment; } alignment_info align_paired_ended_sequences(const fastq& read1, const fastq& read2, const fastq_pair_vec& adapters, int max_shift) { size_t adapter_id = 0; alignment_info best_alignment; for (const auto& adapter_pair : adapters) { const fastq& adapter1 = adapter_pair.first; const fastq& adapter2 = adapter_pair.second; const std::string sequence1 = adapter2.sequence() + read1.sequence(); const std::string sequence2 = read2.sequence() + adapter1.sequence(); // Only consider alignments where at least one nucleotide from each read // is aligned against the other, included shifted alignments to account // for missing bases at the 5' ends of the reads. const int min_offset = adapter2.length() - read2.length() - max_shift; alignment_info alignment = pairwise_align_sequences(best_alignment, sequence1, sequence2, min_offset, std::numeric_limits::max()); if (alignment.is_better_than(best_alignment)) { best_alignment = alignment; best_alignment.adapter_id = adapter_id; // Convert the alignment into an alignment between read 1 & 2 only best_alignment.offset -= adapter2.length(); } ++adapter_id; } return best_alignment; } void truncate_single_ended_sequence(const alignment_info& alignment, fastq& read) { // Given a shift, the alignment of the adapter may start one or more // bases before the start of the sequence, leading to a negative offset const size_t len = std::max(0, alignment.offset); return read.truncate(0, len); } size_t truncate_paired_ended_sequences(const alignment_info& alignment, fastq& read1, fastq& read2) { size_t had_adapter = 0; const int template_length = std::max(0, static_cast(read2.length()) + alignment.offset); if (alignment.offset > static_cast(read1.length())) { throw std::invalid_argument("invalid offset"); } else if (alignment.offset >= 0) { // Read1 can potentially extend past read2, but by definition read2 // cannot extend past read1 when the offset is not negative, so there // is no need to edit read2. had_adapter += static_cast(template_length) < read1.length(); read1.truncate(0, static_cast(template_length)); } else { had_adapter += static_cast(template_length) < read1.length(); had_adapter += static_cast(template_length) < read2.length(); read1.truncate(0, static_cast(template_length)); read2.truncate(static_cast(static_cast(read2.length()) - template_length)); } return had_adapter; } std::string strip_mate_info(const std::string& header, const char mate_sep) { size_t pos = header.find_first_of(' '); if (pos == std::string::npos) { pos = header.length(); } if (pos >= 2 && header.at(pos - 2) == mate_sep) { const char digit = header.at(pos - 1); if (digit == '1' || digit == '2') { std::string new_header = header; return new_header.erase(pos - 2, 2); } } return header; } fastq collapse_paired_ended_sequences(const alignment_info& alignment, const fastq& read1, const fastq& read2, std::mt19937* rng, const char mate_sep) { if (alignment.offset > static_cast(read1.length())) { // Gap between the two reads is not allowed throw std::invalid_argument("invalid offset"); } // Offset to the first base overlapping read 2 const size_t read_1_offset = static_cast(std::max(0, alignment.offset)); const std::string read_1_seq = read1.sequence().substr(0, read_1_offset); const std::string read_1_qual = read1.qualities().substr(0, read_1_offset); // Offset to the last base overlapping read 1 const size_t read_2_offset = static_cast(read1.length()) - std::max(0, alignment.offset); const std::string read_2_seq = read2.sequence().substr(read_2_offset); const std::string read_2_qual = read2.qualities().substr(read_2_offset); // Collapse only the overlapping parts string_pair collapsed = collapse_sequence(read1.sequence().substr(read_1_offset), read2.sequence().substr(0, read_2_offset), read1.qualities().substr(read_1_offset), read2.qualities().substr(0, read_2_offset), rng); // Remove mate number from read, if present, when building new record return fastq(mate_sep ? strip_mate_info(read1.header(), mate_sep) : read1.header(), read_1_seq + collapsed.first + read_2_seq, read_1_qual + collapsed.second + read_2_qual, FASTQ_ENCODING_SAM); } bool extract_adapter_sequences(const alignment_info& alignment, fastq& read1, fastq& read2) { const int template_length = std::max(0, static_cast(read2.length()) + alignment.offset); if (alignment.offset > static_cast(read1.length())) { throw std::invalid_argument("invalid offset"); } read1.truncate(std::min(read1.length(), template_length)); read2.truncate(0, std::max(0, static_cast(read2.length()) - template_length)); return read1.sequence().length() || read2.sequence().length(); } } // namespace ar adapterremoval-2.3.1/src/alignment.hpp000066400000000000000000000215741350370616400200170ustar00rootroot00000000000000/*************************************************************************\ * AdapterRemoval - cleaning next-generation sequencing reads * * Copyright (C) 2011 by Stinus Lindgreen - stinus@binf.ku.dk * * Copyright (C) 2014 by Mikkel Schubert - mikkelsch@gmail.com * * * * If you use the program, please cite the paper: * * S. Lindgreen (2012): AdapterRemoval: Easy Cleaning of Next Generation * * Sequencing Reads, BMC Research Notes, 5:337 * * http://www.biomedcentral.com/1756-0500/5/337/ * * * * This program is free software: you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation, either version 3 of the License, or * * (at your option) any later version. * * * * This program is distributed in the hope that it will be useful, * * but WITHOUT ANY WARRANTY; without even the implied warranty of * * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * * GNU General Public License for more details. * * * * You should have received a copy of the GNU General Public License * * along with this program. If not, see . * \*************************************************************************/ #ifndef ALIGNMENT_H #define ALIGNMENT_H #include #include #include "fastq.hpp" namespace ar { /** * Summarizes an alignment. * * A single offset value is used to represent the alignment between two * sequences, with values ranging from -inf to seq1.len() - 1. The alignment * of the first base in each sequence against each other is defined as having * the offset 0, with each other offset defined as the relative position of * seq 2 base 0 to seq 1 base 0: * * Seq 1: aaaaaaaaa * seq 2: bbbbbbbbbbb * Offset: 0 * * Seq 1: aaaaaaaaa * Seq 2: bbbbbbbbbbb * Offset: -11 * * Seq 1: aaaaaaaaa * Seq 2: bbbbbbbbbbb * Offset: 8 * * The meaning of the offset is slightly different in SE and PE mode; in SE * mode seq2 is the adapter sequence, and the offset therefore unambiguously * shows the starting position of the adapter, regardless of the size of the * adapter sequence. * * In PE mode, while the alignment is between seq1+PCR2 and PCR1+seq2, the * offset returned is relative to to seq1 and seq2 only. Thus, if '1' * represents PCR1 and '2' represents PCR2, the following alignment results * from PE mode (ie. offset = -9 rather than 3): * * Seq 1: 22222222222aaaaaaaaa * Seq 2: bbbbbbbbbbb1111111111 * Offset: -9 * * Note that the offset can never be greater than len(read 1) - 1, but can be * less than -len(seq 2) + 1, if a positive shift is set in PE mode. In PE * mode, an offset <= -len(seq 2) indicates that no non-adapter sequence was * found, while an offset <= 0 indicates the same for SE mode. Offsets less * than -len(seq 2) for PE or less than 0 for SE indicates that bases have been * skipped during sequencing, and are discoverable if a shift is set: * * Read 1: ...22222222222aaaaaaaaa * Read 2: bbbbbbbbbbb1111111111... * Offset: -12 * */ struct alignment_info { /** Defaults to unaligned (len = 0), for adapter_id -1. **/ alignment_info(); /** * Returns true if this is a better alignment than other. * * When selecting among multiple alignments, the follow criteria are used: * 1. The alignment with the highest score is preferred. * 2. If score is equal, the longest alignment is preferred. * 3. If score and length is equal, the alignment with fewest Ns is preferred. */ bool is_better_than(const alignment_info& other) const; //! Alignment score; equal to length - n_ambiguous - 2 * n_mismatches; int score; //! Zero based id of the adapter which offered the best alignment. Is less //! than zero if no alignment was found. int offset; //! The number of base-pairs included in the alignment. This number //! includes both bases aligned between the two mates (in PE mode) and the //! number of bases aligned between mates and adapter sequences. size_t length; //! Number of positions in the alignment in which the two sequences were //! both called (not N) but differed size_t n_mismatches; //! Number of positions in the alignment where one or both bases were N. size_t n_ambiguous; //! Offset describing the alignment between the two sequences (see above). int adapter_id; }; /** * Attempts to align adapters sequences against a SE read. * * @param read A read potentially containing adapter sequences * @param adapters A set of adapter pairs; only the first adapters are used. * @param max_shift Allow up to this number of missing bases at the 5' end of * the read, when aligning the adapter. * @return The best alignment, or a length 0 alignment if not aligned. * * The best alignment is selected using alignment_info::is_better_than. */ alignment_info align_single_ended_sequence(const fastq& read, const fastq_pair_vec& adapters, int max_shift); /** * Attempts to align PE mates, along with any adapter pairs. * * @param read1 A mate 1 read potentially containing adapter sequences * @param read2 A mate 2 read potentially containing adapter sequences * @param adapters A set of adapter pairs; both in each pair adapters are used. * @param max_shift Allow up to this number of missing bases at the 5' end of * both mate reads. * @return The best alignment, or a length 0 alignment if not aligned. * * The alignment is carried out following the concatenation of pcr2 and read1, * and the concatenation of read2 and pcr1, resulting in this alignment: * * pcr2-read1 * read2-pcr1 * * Note the returned offset is relative read1, not to adapter2 + read1, * and can be used to directly infer the alignment between read1 and read2. */ alignment_info align_paired_ended_sequences(const fastq& read1, const fastq& read2, const fastq_pair_vec& adapters, int max_shift); /** * Truncates a SE read according to the alignment, such that the second read * used in the alignment (assumed to represent adapter sequence) is excluded * from the read passed to this function. */ void truncate_single_ended_sequence(const alignment_info& alignment, fastq& read); /** * Truncate a pair of PE reads, such that any adapter sequence inferred from * the alignment is excluded from both mates. * * @return The number of sequences (0 .. 2) which contained adapter sequence. */ size_t truncate_paired_ended_sequences(const alignment_info& alignment, fastq& read1, fastq& read2); /** * Collapses two overlapping PE mates into a single sequence, recalculating the * quality scores to reflect the added support offered by two reads at the same * nucleotides. In the case of different bases at the same position, the * highest quality base is selected; if each base have the same quality score, * a random base is selected. In both cases, the quality score is updated to * reflect the lower quality implied by these observations. * * If rng is null, different bases with the same quality are set to N and !. * * @return A single FASTQ record representing the collapsed sequence. * * Note that the sequences are assumed to have been trimmed using the * truncate_paired_ended_sequences function, and will produce undefined * results if this is not the case! */ fastq collapse_paired_ended_sequences(const alignment_info& alignment, const fastq& read1, const fastq& read2, std::mt19937* rng, const char mate_sep=MATE_SEPARATOR); /** * Truncates reads such that only adapter sequence remains. * * @return True if either or both reads contained adapter sequence. * * Reads that do not contain any adapter sequence are completely truncated, * such no bases remain of the original sequence. */ bool extract_adapter_sequences(const alignment_info& alignment, fastq& pcr1, fastq& pcr2); } // namespace ar #endif adapterremoval-2.3.1/src/alignment_tables.cpp000066400000000000000000003277451350370616400213550ustar00rootroot00000000000000/*************************************************************************\ * AdapterRemoval - cleaning next-generation sequencing reads * * * * Copyright (C) 2011 by Stinus Lindgreen - stinus@binf.ku.dk * * Copyright (C) 2014 by Mikkel Schubert - mikkelsch@gmail.com * * * * If you use the program, please cite the paper: * * S. Lindgreen (2012): AdapterRemoval: Easy Cleaning of Next Generation * * Sequencing Reads, BMC Research Notes, 5:337 * * http://www.biomedcentral.com/1756-0500/5/337/ * * * * This program is free software: you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation, either version 3 of the License, or * * (at your option) any later version. * * * * This program is distributed in the hope that it will be useful, * * but WITHOUT ANY WARRANTY; without even the implied warranty of * * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * * GNU General Public License for more details. * * * * You should have received a copy of the GNU General Public License * * along with this program. If not, see . * \*************************************************************************/ #include "alignment_tables.hpp" namespace ar { // Original algorithm: // Hardcoded results are used to ensure identical results across architectures. #if 0 /** * Calculates the phred scores to be assigned to a consensus base based on two * bases, depending on the Phred scores assigned two these two bases. A phred * score is calculated for both the case where the two bases are identical, and * the case where they differ. * * The returned vector is inded by (phred1 * MAX_PHRED_SCORE) + phred2, where * phred1 is assumed to be >= phred2. This is because we always select the base * with the higher Phred score. */ std::vector calculate_phred_score() { std::vector Perror(MAX_PHRED_SCORE + 1, 0.0); std::vector Ptrue(MAX_PHRED_SCORE + 1, 0.0); for (int i = 0; i <= MAX_PHRED_SCORE; ++i) { const double p_err = std::min(0.75, std::pow(10, static_cast(i) / -10.0)); Perror.at(i) = std::log(p_err / 3.0); Ptrue.at(i) = std::log(1.0 - p_err); } std::vector new_scores((MAX_PHRED_SCORE + 1) * (MAX_PHRED_SCORE + 1)); for (int i = 0; i <= MAX_PHRED_SCORE; ++i) { for (int j = 0; j <= i; ++j) { const int index = (i * (MAX_PHRED_SCORE + 1)) + j; phred_scores& scores = new_scores.at(index); { // When two nucleotides are identical const double ptrue = Ptrue.at(i) + Ptrue.at(j); const double perror = Perror.at(i) + Perror.at(j); const double normconstant = 1.0 + 3.0 * std::exp(perror - ptrue); scores.identical_nts = fastq::p_to_phred_33(1.0 - 1.0 / normconstant); } { // When two nucleotides differ const double ptrue = Ptrue.at(i) + Perror.at(j); const double perror_one = Perror.at(i) + Ptrue.at(j); const double perror_both = Perror.at(i) + Perror.at(j); const double normconstant = 1.0 + 2.0 * std::exp(perror_both - ptrue) + std::exp(perror_one - ptrue); scores.different_nts = fastq::p_to_phred_33(1.0 - 1.0 / normconstant); } } } return new_scores; } #endif const char IDENTICAL_NTS[PHRED_TABLE_SIZE] = { 0x22, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 0x22, 0x22, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 0x22, 0x22, 0x24, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 0x24, 0x24, 0x25, 0x26, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 0x25, 0x25, 0x26, 0x28, 0x29, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 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0x7d, 0x7c, 0x7a, 0x79, 0x78, 0x77, 0x76, 0x75, 0x74, 0x73, 0x72, 0x71, 0x70, 0x6f, 0x6e, 0x6d, 0x6c, 0x6b, 0x6a, 0x69, 0x68, 0x67, 0x66, 0x65, 0x64, 0x63, 0x62, 0x61, 0x60, 0x5f, 0x5e, 0x5d, 0x5c, 0x5b, 0x5a, 0x59, 0x58, 0x57, 0x56, 0x55, 0x54, 0x53, 0x52, 0x51, 0x50, 0x4f, 0x4e, 0x4d, 0x4c, 0x4b, 0x4a, 0x49, 0x48, 0x47, 0x46, 0x45, 0x44, 0x43, 0x42, 0x41, 0x40, 0x3f, 0x3e, 0x3d, 0x3c, 0x3b, 0x3a, 0x39, 0x38, 0x37, 0x36, 0x35, 0x34, 0x33, 0x32, 0x31, 0x30, 0x2f, 0x2e, 0x2d, 0x2c, 0x2b, 0x2a, 0x29, 0x28, 0x27, 0x27, 0x26, 0x25, 0x25, 0x24, 0x24, -1, 0x7e, 0x7e, 0x7d, 0x7b, 0x7a, 0x79, 0x78, 0x77, 0x76, 0x75, 0x74, 0x73, 0x72, 0x71, 0x70, 0x6f, 0x6e, 0x6d, 0x6c, 0x6b, 0x6a, 0x69, 0x68, 0x67, 0x66, 0x65, 0x64, 0x63, 0x62, 0x61, 0x60, 0x5f, 0x5e, 0x5d, 0x5c, 0x5b, 0x5a, 0x59, 0x58, 0x57, 0x56, 0x55, 0x54, 0x53, 0x52, 0x51, 0x50, 0x4f, 0x4e, 0x4d, 0x4c, 0x4b, 0x4a, 0x49, 0x48, 0x47, 0x46, 0x45, 0x44, 0x43, 0x42, 0x41, 0x40, 0x3f, 0x3e, 0x3d, 0x3c, 0x3b, 0x3a, 0x39, 0x38, 0x37, 0x36, 0x35, 0x34, 0x33, 0x32, 0x31, 0x30, 0x2f, 0x2e, 0x2d, 0x2c, 0x2b, 0x2a, 0x29, 0x28, 0x27, 0x27, 0x26, 0x25, 0x25, 0x24, 0x24, }; } // namespace ar adapterremoval-2.3.1/src/alignment_tables.hpp000066400000000000000000000045321350370616400213440ustar00rootroot00000000000000/*************************************************************************\ * AdapterRemoval - cleaning next-generation sequencing reads * * Copyright (C) 2011 by Stinus Lindgreen - stinus@binf.ku.dk * * Copyright (C) 2014 by Mikkel Schubert - mikkelsch@gmail.com * * * * If you use the program, please cite the paper: * * S. Lindgreen (2012): AdapterRemoval: Easy Cleaning of Next Generation * * Sequencing Reads, BMC Research Notes, 5:337 * * http://www.biomedcentral.com/1756-0500/5/337/ * * * * This program is free software: you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation, either version 3 of the License, or * * (at your option) any later version. * * * * This program is distributed in the hope that it will be useful, * * but WITHOUT ANY WARRANTY; without even the implied warranty of * * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * * GNU General Public License for more details. * * * * You should have received a copy of the GNU General Public License * * along with this program. If not, see . * \*************************************************************************/ #ifndef ALIGNMENT_TABLES_H #define ALIGNMENT_TABLES_H #include namespace ar { const size_t PHRED_TABLE_SIZE = 8836; /** * Table of Phred scores to assigned for identical positions during collapsing. * * Position is calculated as phred_1 * (MAX_PHRED_SCORE + 1) + phred_2, * assuming that phred_1 >= phred_2. */ extern const char IDENTICAL_NTS[PHRED_TABLE_SIZE]; /** * Table of Phred scores to assigned for mismatching positions during collapsing. * * Position is calculated as phred_1 * (MAX_PHRED_SCORE + 1) + phred_2, * assuming that phred_1 >= phred_2. */ extern const char DIFFERENT_NTS[PHRED_TABLE_SIZE]; } // namespace ar #endif adapterremoval-2.3.1/src/argparse.cpp000066400000000000000000000316501350370616400176340ustar00rootroot00000000000000/*************************************************************************\ * AdapterRemoval - cleaning next-generation sequencing reads * * * * Copyright (C) 2011 by Stinus Lindgreen - stinus@binf.ku.dk * * Copyright (C) 2014 by Mikkel Schubert - mikkelsch@gmail.com * * * * If you use the program, please cite the paper: * * S. Lindgreen (2012): AdapterRemoval: Easy Cleaning of Next Generation * * Sequencing Reads, BMC Research Notes, 5:337 * * http://www.biomedcentral.com/1756-0500/5/337/ * * * * This program is free software: you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation, either version 3 of the License, or * * (at your option) any later version. * * * * This program is distributed in the hope that it will be useful, * * but WITHOUT ANY WARRANTY; without even the implied warranty of * * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * * GNU General Public License for more details. * * * * You should have received a copy of the GNU General Public License * * along with this program. If not, see . * \*************************************************************************/ #include #include #include #include #include #include #include #include #include #include "argparse.hpp" #include "debug.hpp" #include "strutils.hpp" namespace ar { namespace argparse { typedef std::set consumer_set; /** Returns the number of columns available in the terminal. */ size_t get_terminal_columns() { struct winsize params; if (ioctl(STDERR_FILENO, TIOCGWINSZ, ¶ms)) { // Default to 80 columns if the parameters could not be retrieved. return 80; } return std::min(120, std::max(80, params.ws_col)); } parser::parser(const std::string& name, const std::string& version, const std::string& help) : m_keys() , m_parsers() , m_name(name) , m_version(version) , m_help(help) { // Built-in arguments (aliases are not shown!) (*this)["--help"] = new flag(nullptr, "Display this message."); create_alias("--help", "-help"); create_alias("--help", "-h"); (*this)["--version"] = new flag(nullptr, "Print the version string."); create_alias("--version", "-version"); create_alias("--version", "-v"); add_seperator(); } parser::~parser() { // Track set of unique pointers, to handle parsers assigned to multiple keys. consumer_set pointers; for (const auto& parser : m_parsers) { if (pointers.insert(parser.second).second) { delete parser.second; } } } consumer_ptr& parser::operator[](const std::string& key) { AR_DEBUG_ASSERT(!key.empty()); if (m_parsers.find(key) == m_parsers.end()) { m_keys.push_back(key_pair(true, key)); } return m_parsers[key]; } const consumer_ptr& parser::at(const std::string& key) const { return m_parsers.at(key); } parse_result parser::parse_args(int argc, char* argv[]) { const string_vec argvec(argv + 1, argv + argc); for (const auto& arg : argvec) { if (arg == "--help" || arg == "-h") { print_help(); return parse_result::exit; } else if (arg == "--version") { print_version(); return parse_result::exit; } } string_vec_citer it = argvec.begin(); while (it != argvec.end()) { consumer_map::iterator parser = m_parsers.end(); if (find_argument(parser, *it)) { if (parser->second->is_set()) { std::cerr << "WARNING: Command-line option " << parser->first << " has been specified more than once." << std::endl; } const size_t consumed = parser->second->consume(++it, argvec.end()); if (consumed == static_cast(-1)) { if (it != argvec.end()) { std::cerr << "ERROR: Invalid value for " << *(it - 1) << ": '" << *it << "'; aborting ..." << std::endl; } else { std::cerr << "ERROR: No value supplied for " << *(it - 1) << "; aborting ..." << std::endl; } return parse_result::error; } it += static_cast(consumed); } else { return parse_result::error; } } return parse_result::ok; } bool parser::is_set(const std::string& key) const { const consumer_map::const_iterator it = m_parsers.find(key); AR_DEBUG_ASSERT(it != m_parsers.end()); return it->second->is_set(); } void parser::add_seperator() { m_keys.push_back(key_pair(false, std::string())); } void parser::add_header(const std::string& header) { add_seperator(); m_keys.push_back(key_pair(false, header)); } void parser::create_alias(const std::string& key, const std::string& alias) { AR_DEBUG_ASSERT(m_parsers.find(alias) == m_parsers.end()); m_parsers[alias] = m_parsers.at(key); } void parser::print_version() const { std::cerr << m_name << " " << m_version << std::endl; } void parser::print_help() const { print_version(); std::cerr <<"\n" << m_help << "\n\n"; print_arguments(m_keys); } void parser::print_arguments(const key_pair_vec& keys) const { const size_t indentation = 8; cli_formatter fmt; fmt.set_indent(indentation); fmt.set_column_width(std::min(80, get_terminal_columns()) - indentation - 3); for (const auto& key_pair : keys) { if (!key_pair.first) { std::cerr << key_pair.second << "\n"; continue; } const consumer_ptr ptr = m_parsers.at(key_pair.second); if (ptr->help() == "HIDDEN") { continue; } const std::string metavar = get_metavar_str(ptr, key_pair.second); std::cerr << std::left << std::setw(indentation) << (" " + key_pair.second + " " + metavar) << "\n"; std::string value = ptr->help(); if (!value.empty()) { // Replace "%default" with string representation of current value. size_t index = value.find("%default"); if (index != std::string::npos) { const std::string default_value = ptr->to_str(); value.replace(index, 8, default_value); } // Format into columns and indent lines (except the first line) std::cerr << fmt.format(value) << "\n"; } std::cerr << "\n"; } std::cerr << std::endl; } bool parser::find_argument(consumer_map::iterator& it, const std::string& str) { it = m_parsers.find(str); if (it != m_parsers.end()) { return true; } // Locate partial arguments by finding arguments with 'str' as prefix if (str != "-" && str != "--") { key_pair_vec matches; consumer_map::iterator cit = m_parsers.begin(); for (; cit != m_parsers.end(); ++cit) { if (cit->first.substr(0, str.size()) == str) { matches.push_back(key_pair(true, cit->first)); } } if (matches.size() == 1) { it = m_parsers.find(matches.front().second); return true; } else if (matches.size() > 1) { std::cerr << "ERROR: Ambiguous argument '" << str << "'; " << "Candidate arguments are\n\n"; print_arguments(matches); return false; } } std::cerr << "ERROR: Unknown argument: '" << str << "'" << std::endl; return false; } std::string parser::get_metavar_str(const consumer_ptr ptr, const std::string& key) const { if (!ptr->metavar().empty()) { return ptr->metavar(); } std::string metavar = key; metavar.erase(0, metavar.find_first_not_of("-")); std::replace(metavar.begin(), metavar.end(), '-', '_'); return toupper(metavar); } /////////////////////////////////////////////////////////////////////////////// consumer_base::consumer_base(const std::string& metavar, const std::string& help) : m_value_set(false) , m_metavar(metavar) , m_help(help) { } consumer_base::~consumer_base() { } bool consumer_base::is_set() const { return m_value_set; } const std::string& consumer_base::metavar() const { return m_metavar; } const std::string& consumer_base::help() const { return m_help; } /////////////////////////////////////////////////////////////////////////////// flag::flag(bool* value, const std::string& help) // Non-empty metavar to avoid auto-generated metavar : consumer_base(" ", help) , m_ptr(value) { m_value_set = m_ptr ? *value : false; } size_t flag::consume(string_vec_citer, const string_vec_citer&) { if (m_ptr) { *m_ptr = true; } m_value_set = true; return 0; } std::string flag::to_str() const { return std::string(m_value_set ? "on" : "off"); } /////////////////////////////////////////////////////////////////////////////// any::any(std::string* value, const std::string& metavar, const std::string& help) : consumer_base(metavar, help) , m_ptr(value) , m_sink() { } size_t any::consume(string_vec_citer start, const string_vec_citer& end) { if (start != end) { m_value_set = true; (m_ptr ? *m_ptr : m_sink) = *start; return 1; } return static_cast(-1); } std::string any::to_str() const { const std::string& result = m_ptr ? *m_ptr : m_sink; if (result.empty()) { return ""; } else { return result; } } /////////////////////////////////////////////////////////////////////////////// many::many(string_vec* value, const std::string& metavar, const std::string& help) : consumer_base(metavar, help) , m_ptr(value) { AR_DEBUG_ASSERT(m_ptr); } size_t many::consume(string_vec_citer start, const string_vec_citer& end) { m_value_set = true; string_vec_citer it = start; for (; it != end; ++it) { if (!it->empty() && it->front() == '-') { break; } } m_ptr->assign(start, it); return static_cast(it - start); } std::string many::to_str() const { if (m_ptr->empty()) { return ""; } else { std::string output; for (const auto& s: *m_ptr) { if (!output.empty()) { output.push_back(';'); } output.append(s); } return output; } } /////////////////////////////////////////////////////////////////////////////// knob::knob(unsigned* value, const std::string& metavar, const std::string& help) : consumer_base(metavar, help) , m_ptr(value) { AR_DEBUG_ASSERT(m_ptr); } size_t knob::consume(string_vec_citer start, const string_vec_citer& end) { if (start != end) { try { *m_ptr = str_to_unsigned(*start); m_value_set = true; return 1; } catch (const std::invalid_argument&) { return static_cast(-1); } } return static_cast(-1); } std::string knob::to_str() const { std::stringstream stream; stream << *m_ptr; return stream.str(); } /////////////////////////////////////////////////////////////////////////////// floaty_knob::floaty_knob(double* value, const std::string& metavar, const std::string& help) : consumer_base(metavar, help) , m_ptr(value) { AR_DEBUG_ASSERT(m_ptr); } size_t floaty_knob::consume(string_vec_citer start, const string_vec_citer& end) { if (start != end) { std::stringstream stream(*start); if (!(stream >> *m_ptr)) { return static_cast(-1); } // Failing on trailing, non-numerical values std::string trailing; if (stream >> trailing) { return static_cast(-1); } m_value_set = true; return 1; } return static_cast(-1); } std::string floaty_knob::to_str() const { if (std::isnan(*m_ptr)) { return ""; } else { std::stringstream stream; stream << *m_ptr; return stream.str(); } } } // namespace argparse } // namespace ar adapterremoval-2.3.1/src/argparse.hpp000066400000000000000000000325571350370616400176500ustar00rootroot00000000000000/*************************************************************************\ * AdapterRemoval - cleaning next-generation sequencing reads * * * * Copyright (C) 2011 by Stinus Lindgreen - stinus@binf.ku.dk * * Copyright (C) 2014 by Mikkel Schubert - mikkelsch@gmail.com * * * * If you use the program, please cite the paper: * * S. Lindgreen (2012): AdapterRemoval: Easy Cleaning of Next Generation * * Sequencing Reads, BMC Research Notes, 5:337 * * http://www.biomedcentral.com/1756-0500/5/337/ * * * * This program is free software: you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation, either version 3 of the License, or * * (at your option) any later version. * * * * This program is distributed in the hope that it will be useful, * * but WITHOUT ANY WARRANTY; without even the implied warranty of * * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * * GNU General Public License for more details. * * * * You should have received a copy of the GNU General Public License * * along with this program. If not, see . * \*************************************************************************/ #ifndef ARGPARSE_H #define ARGPARSE_H #include #include #include #include #include "commontypes.hpp" namespace ar { namespace argparse { class consumer_base; typedef consumer_base* consumer_ptr; typedef std::map consumer_map; //! Parse results for command-line arguments enum class parse_result { //! Terminate now (e.g. --version or --help used) exit, //! Error occurred parsing arguments / invalid combination of args error, //! No errors parsing commandline arguments ok }; /** * Simple type-safe parsing of command-line options. * * To handle a an argument, an object of type consumer_base is assigned * to the argparse::parser using the [] operator. For example, the parse and * save an integer value to a variable when the user supplies the argument * '--example', the following is done: * * int target = 0; // Must be initialized! * argparse::parser argparser(...); * argparser["--example"] = new argparse::knob(&target); * argparser.parse_args(argc, argv); * * Aliases can be created for command-line arguments simply by assigning the * same parser to multiple keys; for example, to alias '--example' as '-e': * * argparser["-e"] = argparser["--example"]; * * The class automatically handles the following arguments: * --help, --h, -help, -h: Displays the program help * --version, -v: Displays the program name and version string * * In both cases, the parse_args function returns false. * * The assigned consumer_ptrs are owned by and freed by the argparse::parser * upon destruction of the object. Pointers assigned multiple times (i.e. when * used with aliases) are only freed once. */ class parser { public: /** * Arguments: * name: Name of the program; used in --version and --help. * version: Version string (excluding the name); is used by the * arguments --help and --version. * help: General help string used by --help; should not include the * parameters themselves, as this is done automatically. */ parser(const std::string& name, const std::string& version, const std::string& help); /** Deletes all (unique) parsers assigned to the set. */ ~parser(); /** Parses a set of command-line options as passed to main(argc, argv). */ parse_result parse_args(int argc, char* argv[]); /** Returns true if the option with the given key has been set. */ bool is_set(const std::string& key) const; /** * Returns a reference to the pointer for the parser with the given key. * * If an entry does not exist for the given key, it is created upon access. */ consumer_ptr& operator[](const std::string& key); /** * Returns a reference to the pointer for the parser with the given key. * * If an entry does not exist for the given key, out_of_range is thrown. */ const consumer_ptr& at(const std::string& key) const; /** Add a blank line between the previous and the next command. */ void add_seperator(); /** Add a blank line and a header between the previous and next command. */ void add_header(const std::string& header); /** Create alias for key with name alias. */ void create_alias(const std::string& key, const std::string& alias); /** Helper function; prints the program name and version string. */ void print_version() const; /** Helper functions; prints the full set of help-text. */ void print_help() const; //! Copy construction not supported parser(const parser&) = delete; //! Assignment not supported parser& operator=(const parser&) = delete; private: typedef std::pair key_pair; typedef std::vector key_pair_vec; /** Pretty-print the listed arguments. */ void print_arguments(const key_pair_vec& keys) const; /** * Attempt to find argument by similarity. * * @param it If a match is found, is set to iterator of matching parser, otherwise it is set to m_parsers.end(). * @param str String containing expected argument. * @return True if a match is found, false otherwise. * * If an exact match or a single partial match is found, 'it' is set and * true is returned; otherwise it is set to m_parsers.end() and false is * returned. In the case of multiple partial matches, the help string for * each candidate is printed. */ bool find_argument(consumer_map::iterator& it, const std::string& str); /** Generate metavar from argument, namely uppercase without dashes. */ std::string get_metavar_str(const consumer_ptr, const std::string&) const; //! Vector of keys (command-line options), tracking the order of addition. key_pair_vec m_keys; //! Map of keys (command-line args) to parser pointers; multiple //! keys may be associated with the same pointer. consumer_map m_parsers; //! Name of the program std::string m_name; //! Version string for the program (excluding the name) std::string m_version; //! Help text for the program. std::string m_help; }; /** * Base class for argument parsers; * * Each consumer must implement the consume function, which takes iterators to * the arguments following the key for this parser (i.e. not including the * --option). These then consume zero or more values, returning the number * thus consumed, or (size_t)-1 if the values were missing or invalid. */ class consumer_base { public: /** * Base constructor; sets various values used when printing --help. * * metavar - Used to represent the input value; if empty, * argparse::parser will use the current key associated with * the parser to generate a metavar. * help - Help string; the value %default is replaced with the default * value. */ consumer_base(const std::string& metavar, const std::string& help); /* Destructor; does nothing in the base class. */ virtual ~consumer_base(); /** * Attempts to consume a value specified on the command-line; returns the * number of values consumed (if any), or -1 if parsing failed (e.g. due to * the specified value being of the wrong type). * * Parameters: * start - Iterator pointing to the value following the command-line * argument, if any remain to be consumed. * end - Iterator past-the-end of the list of command-line arguments. */ virtual size_t consume(string_vec_citer start, const string_vec_citer& end) = 0; /** Returns true if the consumer has consumed a value. **/ virtual bool is_set() const; /** Returns the metavariable associated with the consumer. **/ virtual const std::string& metavar() const; /** Returns the help string associated with the consumer. **/ virtual const std::string& help() const; /** Returns the value associated with the consumer as a string. **/ virtual std::string to_str() const = 0; //! Copy construction not supported consumer_base(const consumer_base&) = delete; //! Assignment not supported consumer_base& operator=(const consumer_base&) = delete; protected: //! Should be set to true if a value has been consumed in a derived class. bool m_value_set; //! Stores the metavar associated with the consumer std::string m_metavar; //! Stores the optional description of default behavior. std::string m_help; }; /** * Consumer for boolean values (i.e. flags). * * Unlike typical consumers, this consumer does not expected a value associated * with the command-line argument, but instead sets the associated value to * true if the command-line argument is specified one or more times. */ class flag : public consumer_base { public: /** * See consumer_base::consumer_base * * Unlike the base constructor, this class does not take a 'metavar', as * no values are consumed during parsing. */ flag(bool* sink = nullptr, const std::string& help = ""); /** See consumer_base::consume */ virtual size_t consume(string_vec_citer start, const string_vec_citer& end); /** See consumer_base::to_str */ virtual std::string to_str() const; //! Copy construction not supported flag(const flag&) = delete; //! Assignment not supported flag& operator=(const flag&) = delete; private: //! Optional pointer to storage for boolean value; if nullptr, m_value is used. bool* m_ptr; }; /** * Consumer for string values (filenames, etc.). */ class any : public consumer_base { public: /** * See consumer_base::consumer_base */ any(std::string* sink = nullptr, const std::string& metavar = "", const std::string& help = ""); /** See consumer_base::consume */ virtual size_t consume(string_vec_citer start, const string_vec_citer& end); /** See consumer_base::to_str */ virtual std::string to_str() const; //! Copy construction not supported any(const any&) = delete; //! Assignment not supported any& operator=(const any&) = delete; private: //! Optional pointer to storage for string value; if nullptr, m_value is used. std::string* m_ptr; //! Value sink used if a pointer to a sink is not provided. std::string m_sink; }; /** * Consumer for multiple string values; consumes values until another option * (value starting with '-') is encountered. */ class many : public consumer_base { public: /** * See consumer_base::consumer_base */ many(string_vec* sink, const std::string& metavar = "", const std::string& help = ""); /** See consumer_base::consume */ virtual size_t consume(string_vec_citer start, const string_vec_citer& end); /** See consumer_base::to_str */ virtual std::string to_str() const; //! Copy construction not supported many(const many&) = delete; //! Assignment not supported many& operator=(const many&) = delete; private: //! Pointer to storage for string value; if nullptr, m_value is used. string_vec* m_ptr; }; /** * Consumer for unsigned integer values. * * Signed values are rejected. On 32 bit systems, the range of values is * limited to 0 .. 2^31 - 1, on 64 bit systems the range is 0 .. 2^64 - 1. */ class knob : public consumer_base { public: /** * See consumer_base::consumer_base; a sink must be set. */ knob(unsigned* sink, const std::string& metavar = "", const std::string& help = ""); /** See consumer_base::consume */ virtual size_t consume(string_vec_citer start, const string_vec_citer& end); /** See consumer_base::to_str */ virtual std::string to_str() const; //! Copy construction not supported knob(const knob&) = delete; //! Assignment not supported knob& operator=(const knob&) = delete; private: //! Pointer to storage for unsigned value (required). unsigned* m_ptr; }; /** * Consumer for floating point values (doubles). */ class floaty_knob : public consumer_base { public: /** See consumer_base::consumer_base; a sink must be set. */ floaty_knob(double* sink, const std::string& metavar = "", const std::string& help = ""); /** See consumer_base::consume */ virtual size_t consume(string_vec_citer start, const string_vec_citer& end); /** See consumer_base::to_str */ virtual std::string to_str() const; //! Copy construction not supported floaty_knob(const floaty_knob&) = delete; //! Assignment not supported floaty_knob& operator=(const floaty_knob&) = delete; private: //! Pointer to storage for unsigned value (required). double* m_ptr; }; } // namespace argparse } // namespace ar #endif adapterremoval-2.3.1/src/barcode_table.cpp000066400000000000000000000301141350370616400205700ustar00rootroot00000000000000/*************************************************************************\ * AdapterRemoval - cleaning next-generation sequencing reads * * * * Copyright (C) 2011 by Stinus Lindgreen - stinus@binf.ku.dk * * Copyright (C) 2014 by Mikkel Schubert - mikkelsch@gmail.com * * * * If you use the program, please cite the paper: * * S. Lindgreen (2012): AdapterRemoval: Easy Cleaning of Next Generation * * Sequencing Reads, BMC Research Notes, 5:337 * * http://www.biomedcentral.com/1756-0500/5/337/ * * * * This program is free software: you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation, either version 3 of the License, or * * (at your option) any later version. * * * * This program is distributed in the hope that it will be useful, * * but WITHOUT ANY WARRANTY; without even the implied warranty of * * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * * GNU General Public License for more details. * * * * You should have received a copy of the GNU General Public License * * along with this program. If not, see . * \*************************************************************************/ #include #include #include "barcode_table.hpp" #include "commontypes.hpp" #include "debug.hpp" #include "fastq_io.hpp" #include "strutils.hpp" #include "userconfig.hpp" namespace ar { typedef std::pair barcode_pair; typedef std::vector barcode_vec; struct next_subsequence { explicit next_subsequence(const char* seq_, const size_t max_local_mismatches_) : seq(seq_) , max_local_mismatches(max_local_mismatches_) { } const char* seq; const size_t max_local_mismatches; }; /////////////////////////////////////////////////////////////////////////////// // barcode_error barcode_error::barcode_error(const std::string& message) : std::exception() , m_message(message) { } barcode_error::barcode_error(const barcode_error& error) : std::exception() , m_message(error.m_message) { } barcode_error::~barcode_error() noexcept { } const char* barcode_error::what() const noexcept { return m_message.c_str(); } /////////////////////////////////////////////////////////////////////////////// demultiplexer_node::demultiplexer_node() : children() , value(barcode_table::no_match) { children.fill(barcode_table::no_match); } barcode_table::candidate::candidate(int barcode_, size_t mismatches_) : barcode(barcode_) , mismatches(mismatches_) { } /////////////////////////////////////////////////////////////////////////////// /** * Returns a lexicographically sorted list of merged barcodes, each paired with * the 0-based index of corresponding barcode in the source vector. */ barcode_vec sort_barcodes(const fastq_pair_vec& barcodes) { AR_DEBUG_ASSERT(!barcodes.empty()); barcode_vec sorted_barcodes; const size_t max_key_1_len = barcodes.front().first.length(); const size_t max_key_2_len = barcodes.front().second.length(); for (auto it = barcodes.begin(); it != barcodes.end(); ++it) { if (it->first.length() != max_key_1_len) { throw barcode_error("mate 1 barcodes do not have the same length"); } else if (it->second.length() != max_key_2_len) { throw barcode_error("mate 2 barcodes do not have the same length"); } std::string barcode; barcode.reserve(max_key_1_len + max_key_2_len); barcode.append(it->first.sequence()); barcode.append(it->second.sequence()); sorted_barcodes.push_back(barcode_pair(barcode, it - barcodes.begin())); } std::sort(sorted_barcodes.begin(), sorted_barcodes.end()); return sorted_barcodes; } /** Adds a nucleotide sequence with a given ID to a quad-tree. */ void add_sequence_to_tree(demux_node_vec& tree, const std::string& sequence, const size_t barcode_id) { size_t node_idx = 0; bool added_last_node = false; for (auto nuc : sequence) { auto& node = tree.at(node_idx); // Indicate when PE barcodes can be unambigiously identified from SE // reads node.value = (node.value == barcode_table::no_match) ? barcode_id : barcode_table::ambigious; const auto nuc_idx = ACGT_TO_IDX(nuc); auto child = node.children[nuc_idx]; added_last_node = (child == barcode_table::no_match); if (added_last_node) { // New nodes are added to the end of the list; as barcodes are // added in lexicographic order, this helps ensure that a set of // similar barcodes will be placed in mostly contiguous runs // of the vector representation. child = node.children[nuc_idx] = tree.size(); tree.push_back(demultiplexer_node()); } node_idx = child; } if (!added_last_node) { throw barcode_error(std::string("duplicate barcode (pair): ") + sequence); } tree.at(node_idx).value = barcode_id; } /** * Builds a sparse quad tree using the first sequence in a set of unique * barcodes pairs; duplicate pairs will negatively impact the identification of * these, since all hits will be considered ambiguous. */ demux_node_vec build_demux_tree(const fastq_pair_vec& barcodes) { // Step 1: Construct list of merged, sorted barcodes barcodes; // this allows construction of the sparse tree in one pass. const barcode_vec sorted_barcodes = sort_barcodes(barcodes); // Step 2: Create empty tree containing just the root node; creating // the root here simplifies the 'add_sequence_to_tree' function. demux_node_vec tree; tree.push_back(demultiplexer_node()); // Step 3: Add each barcode to the tree, in sorted order for (auto& pair : sorted_barcodes) { add_sequence_to_tree(tree, pair.first, pair.second); } return tree; } /////////////////////////////////////////////////////////////////////////////// const int barcode_table::no_match; const int barcode_table::ambigious; barcode_table::barcode_table(const fastq_pair_vec& barcodes, size_t mismatches, size_t mm_r1, size_t mm_r2) : m_nodes() , m_max_mismatches() , m_max_mismatches_r1() , m_max_mismatches_r2() , m_barcode_1_len() , m_barcode_2_len() { m_max_mismatches = std::min(mismatches, mm_r1 + mm_r2); m_max_mismatches_r1 = std::min(m_max_mismatches, mm_r1); m_max_mismatches_r2 = std::min(m_max_mismatches, mm_r2); if (!barcodes.empty()) { m_nodes = build_demux_tree(barcodes); m_barcode_1_len = barcodes.front().first.length(); m_barcode_2_len = barcodes.front().second.length(); } } int barcode_table::identify(const fastq& read_r1) const { if (read_r1.length() < m_barcode_1_len) { return barcode_table::no_match; } const std::string barcode = read_r1.sequence().substr(0, m_barcode_1_len); auto match = lookup(barcode.c_str(), 0, 0, nullptr); if (match.barcode == no_match && m_max_mismatches) { match = lookup_with_mm(barcode.c_str(), 0, m_max_mismatches, m_max_mismatches_r1, nullptr); } return match.barcode; } int barcode_table::identify(const fastq& read_r1, const fastq& read_r2) const { if (read_r1.length() < m_barcode_1_len || read_r2.length() < m_barcode_2_len) { return no_match; } const auto barcode_1 = read_r1.sequence().substr(0, m_barcode_1_len); const auto barcode_2 = read_r2.sequence().substr(0, m_barcode_2_len); const auto combined_barcode = barcode_1 + barcode_2; auto match = lookup(combined_barcode.c_str(), 0, 0, nullptr); if (match.barcode == no_match && m_max_mismatches) { const next_subsequence next(barcode_2.c_str(), m_max_mismatches_r2); if (m_max_mismatches_r1) { match = lookup_with_mm(barcode_1.c_str(), 0, m_max_mismatches, m_max_mismatches_r1, &next); } else { match = lookup(barcode_1.c_str(), 0, m_max_mismatches, &next); } } return match.barcode; } barcode_table::candidate barcode_table::lookup(const char* seq, int parent, const size_t max_global_mismatches, const next_subsequence* next) const { for (; *seq && parent != no_match; ++seq) { if (*seq == 'N') { return candidate(no_match); } const auto encoded_nuc = ACGT_TO_IDX(*seq); const auto& node = m_nodes.at(parent); parent = node.children.at(encoded_nuc); } if (parent == no_match) { return candidate(no_match); } else if (next) { const auto max_local_mismatches = std::min(max_global_mismatches, next->max_local_mismatches); if (max_local_mismatches) { return lookup_with_mm(next->seq, parent, max_global_mismatches, max_local_mismatches, nullptr); } else { return lookup(next->seq, parent, max_global_mismatches, nullptr); } } else { const auto& node = m_nodes.at(parent); return candidate(node.value, m_max_mismatches - max_global_mismatches); } } barcode_table::candidate barcode_table::lookup_with_mm( const char* seq, int parent, const size_t max_global_mismatches, const size_t max_local_mismatches, const next_subsequence* next) const { const demultiplexer_node& node = m_nodes.at(parent); const auto nucleotide = *seq; if (nucleotide) { candidate best_candidate; for (size_t encoded_i = 0; encoded_i < 4; ++encoded_i) { const auto child = node.children.at(encoded_i); if (child != -1) { candidate current_candidate; if (nucleotide == IDX_TO_ACGT(encoded_i)) { current_candidate = lookup_with_mm(seq + 1, child, max_global_mismatches, max_local_mismatches, next); } else if (max_local_mismatches == 1) { current_candidate = lookup(seq + 1, child, max_global_mismatches - 1, next); } else if (max_local_mismatches) { current_candidate = lookup_with_mm( seq + 1, child, max_global_mismatches - 1, max_local_mismatches - 1, next); } if (current_candidate.mismatches < best_candidate.mismatches) { best_candidate = current_candidate; } else if (current_candidate.mismatches == best_candidate.mismatches) { if (current_candidate.barcode != no_match) { best_candidate.barcode = ambigious; } } } } return best_candidate; } else if (next) { const size_t next_max_local_mismatches = std::min(max_global_mismatches, next->max_local_mismatches); if (next_max_local_mismatches) { return lookup_with_mm(next->seq, parent, max_global_mismatches, next_max_local_mismatches, nullptr); } else { return lookup(next->seq, parent, max_global_mismatches, nullptr); } } else { return candidate(node.value, m_max_mismatches - max_global_mismatches); } } } // namespace ar adapterremoval-2.3.1/src/barcode_table.hpp000066400000000000000000000076751350370616400206150ustar00rootroot00000000000000/*************************************************************************\ * AdapterRemoval - cleaning next-generation sequencing reads * * * * Copyright (C) 2011 by Stinus Lindgreen - stinus@binf.ku.dk * * Copyright (C) 2014 by Mikkel Schubert - mikkelsch@gmail.com * * * * If you use the program, please cite the paper: * * S. Lindgreen (2012): AdapterRemoval: Easy Cleaning of Next Generation * * Sequencing Reads, BMC Research Notes, 5:337 * * http://www.biomedcentral.com/1756-0500/5/337/ * * * * This program is free software: you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation, either version 3 of the License, or * * (at your option) any later version. * * * * This program is distributed in the hope that it will be useful, * * but WITHOUT ANY WARRANTY; without even the implied warranty of * * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * * GNU General Public License for more details. * * * * You should have received a copy of the GNU General Public License * * along with this program. If not, see . * \*************************************************************************/ #ifndef BARCODE_TABLE_H #define BARCODE_TABLE_H #include #include "fastq.hpp" #include "fastq_io.hpp" #include "scheduler.hpp" #include "statistics.hpp" namespace ar { class userconfig; struct next_subsequence; /** Exception raised for FASTQ parsing and validation errors. */ class barcode_error : public std::exception { public: barcode_error(const std::string& message); barcode_error(const barcode_error& error); virtual ~barcode_error() noexcept; /** Returns error message; string is owned by exception. */ virtual const char* what() const noexcept; private: //! Error message associated with exception. std::string m_message; }; /** * Struct representing node in quad-tree; children are referenced using the * corresponding indice in the vector representing the tree; -1 is used to * represent unassigned children. */ struct demultiplexer_node { demultiplexer_node(); std::array children; int value; }; typedef std::vector demux_node_vec; /** * */ class barcode_table { public: barcode_table(const fastq_pair_vec& barcodes, size_t max_mm, size_t max_mm_r1, size_t max_mm_r2); int identify(const fastq& read_r1) const; int identify(const fastq& read_r1, const fastq& read_r2) const; static const int no_match = -1; static const int ambigious = -2; protected: struct candidate { explicit candidate(int barcode = barcode_table::no_match, size_t mismatches = -1); int barcode; size_t mismatches; }; candidate lookup(const char* seq, int parent, const size_t max_global_mismatches, const next_subsequence* next) const; candidate lookup_with_mm(const char* seq, int parent, const size_t max_global_mismatches, const size_t max_local_mismatches, const next_subsequence* next) const; demux_node_vec m_nodes; size_t m_max_mismatches; size_t m_max_mismatches_r1; size_t m_max_mismatches_r2; size_t m_barcode_1_len; size_t m_barcode_2_len; }; } // namespace ar #endif adapterremoval-2.3.1/src/commontypes.hpp000066400000000000000000000075541350370616400204200ustar00rootroot00000000000000/*************************************************************************\ * AdapterRemoval - cleaning next-generation sequencing reads * * * * Copyright (C) 2011 by Stinus Lindgreen - stinus@binf.ku.dk * * Copyright (C) 2014 by Mikkel Schubert - mikkelsch@gmail.com * * * * If you use the program, please cite the paper: * * S. Lindgreen (2012): AdapterRemoval: Easy Cleaning of Next Generation * * Sequencing Reads, BMC Research Notes, 5:337 * * http://www.biomedcentral.com/1756-0500/5/337/ * * * * This program is free software: you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation, either version 3 of the License, or * * (at your option) any later version. * * * * This program is distributed in the hope that it will be useful, * * but WITHOUT ANY WARRANTY; without even the implied warranty of * * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * * GNU General Public License for more details. * * * * You should have received a copy of the GNU General Public License * * along with this program. If not, see . * \*************************************************************************/ #ifndef COMMONTYPES_H #define COMMONTYPES_H #include #include namespace ar { class fastq; typedef std::vector string_vec; typedef string_vec::const_iterator string_vec_citer; typedef std::pair string_pair; typedef std::vector string_pair_vec; typedef std::vector fastq_vec; typedef fastq_vec::iterator fastq_vec_iter; /** Different file-types read / generated by AdapterRemoval. */ enum class read_type { /** Mate 1 reads, either read or written by AR. */ mate_1 = 0, /** Mate 2 reads, either read or written by AR. */ mate_2, /** PE reads for which the mate has been discarded. */ singleton, /** Overlapping PE reads merged into a single sequence. */ collapsed, /** Collapsed reads truncated due to trimming of low-quality bases. */ collapsed_truncated, /** Discarded reads; e.g. too short reads. */ discarded, //! End value; not to be used as an argument. max }; /** Unique IDs for analytical steps. */ enum analyses_id { //! Step for reading of SE or PE reads ai_read_fastq = 0, //! Step for demultiplexing SE or PE reads ai_demultiplex, //! Step for writing mate 1 reads which were not identified ai_write_unidentified_1, //! Step for writing mate 2 reads which were not identified ai_write_unidentified_2, //! Offset for post-demultiplexing analytical steps //! If enabled, the demultiplexing step will forward reads to the //! nth * ai_analyses_offset analytical step, corresponding to the //! barcode number. ai_analyses_offset = 20, //! Step for reading adapter identification ai_identify_adapters = 20, //! Step for trimming of PE reads ai_trim_pe = 20, //! Step for trimming of SE reads ai_trim_se = 20, //! Offset added to write steps when zipping ai_zip_offset = 10, //! Steps for writing of trimmed reads ai_write_mate_1 = 21, ai_write_mate_2 = 22, ai_write_singleton = 23, ai_write_collapsed = 24, ai_write_collapsed_truncated = 25, ai_write_discarded = 26 }; } // namespace ar #endif adapterremoval-2.3.1/src/debug.cpp000066400000000000000000000052671350370616400171230ustar00rootroot00000000000000/*************************************************************************\ * AdapterRemoval - cleaning next-generation sequencing reads * * * * Copyright (C) 2015 by Mikkel Schubert - mikkelsch@gmail.com * * * * If you use the program, please cite the paper: * * S. Lindgreen (2012): AdapterRemoval: Easy Cleaning of Next Generation * * Sequencing Reads, BMC Research Notes, 5:337 * * http://www.biomedcentral.com/1756-0500/5/337/ * * * * This program is free software: you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation, either version 3 of the License, or * * (at your option) any later version. * * * * This program is distributed in the hope that it will be useful, * * but WITHOUT ANY WARRANTY; without even the implied warranty of * * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * * GNU General Public License for more details. * * * * You should have received a copy of the GNU General Public License * * along with this program. If not, see . * \*************************************************************************/ #include "debug.hpp" #include #include #include namespace ar { #ifdef AR_TEST_BUILD assert_failed::assert_failed(const assert_failed& errror) : m_what(errror.m_what) { } assert_failed::assert_failed(const std::string& what) : m_what(what) { } assert_failed::~assert_failed() noexcept { } const char* assert_failed::what() const noexcept { return m_what.c_str(); } #endif void debug_raise_assert(const char* filename, size_t lineno, const char* what) { std::stringstream message; message << "Assertion failed in '" << filename << "', line " << lineno << ": " << what; #ifdef AR_TEST_BUILD throw assert_failed(message.str()); #else std::cerr << "\nFATAL ERROR:\n" << message.str() << "\n\n" << "This should not happen! Please file a bug-report at\n " << "https://github.com/MikkelSchubert/adapterremoval/issues/new" << std::endl; std::abort(); #endif } } // namespace ar adapterremoval-2.3.1/src/debug.hpp000066400000000000000000000064231350370616400171230ustar00rootroot00000000000000/*************************************************************************\ * AdapterRemoval - cleaning next-generation sequencing reads * * * * Copyright (C) 2015 by Mikkel Schubert - mikkelsch@gmail.com * * * * If you use the program, please cite the paper: * * S. Lindgreen (2012): AdapterRemoval: Easy Cleaning of Next Generation * * Sequencing Reads, BMC Research Notes, 5:337 * * http://www.biomedcentral.com/1756-0500/5/337/ * * * * This program is free software: you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation, either version 3 of the License, or * * (at your option) any later version. * * * * This program is distributed in the hope that it will be useful, * * but WITHOUT ANY WARRANTY; without even the implied warranty of * * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * * GNU General Public License for more details. * * * * You should have received a copy of the GNU General Public License * * along with this program. If not, see . * \*************************************************************************/ #ifndef AR_DEBUG_H #define AR_DEBUG_H #include #include namespace ar { #ifdef AR_TEST_BUILD /** Exception explaining 'abort' calls when running unit-tests. */ class assert_failed : public std::exception { public: /** Copy constructor. */ assert_failed(const assert_failed& errror); /** Creates exception with the specified error message. */ assert_failed(const std::string& what); /** Does nothing. */ virtual ~assert_failed() noexcept; /** Returns user supplied error message; owned by object. */ virtual const char* what() const noexcept; private: //! User supplied error message const std::string m_what; }; #endif /** * Aborts after printing the filename, line-number, and message, plus * instructions for how to report the problem. */ [[noreturn]] void debug_raise_assert(const char* filename, size_t lineno, const char* what); /** Custom assert which prints various information on failure; always enabled. */ #define AR_DEBUG_ASSERT(test) \ do { \ if (!(test)) { \ debug_raise_assert(__FILE__, __LINE__, #test); \ } \ } while (0) /** Raise an assert failure with a user-specified message. */ #define AR_DEBUG_FAIL(msg) \ debug_raise_assert(__FILE__, __LINE__, msg) /** Raise a failure if a scope is accessed more than once at the same time. */ #define AR_DEBUG_LOCK(lock) \ std::unique_lock locker(lock, std::defer_lock); \ if (!locker.try_lock()) { \ AR_DEBUG_FAIL("race condition detected"); \ }; } // namespace ar #endif adapterremoval-2.3.1/src/demultiplex.cpp000066400000000000000000000151571350370616400203700ustar00rootroot00000000000000/*************************************************************************\ * AdapterRemoval - cleaning next-generation sequencing reads * * * * Copyright (C) 2011 by Stinus Lindgreen - stinus@binf.ku.dk * * Copyright (C) 2014 by Mikkel Schubert - mikkelsch@gmail.com * * * * If you use the program, please cite the paper: * * S. Lindgreen (2012): AdapterRemoval: Easy Cleaning of Next Generation * * Sequencing Reads, BMC Research Notes, 5:337 * * http://www.biomedcentral.com/1756-0500/5/337/ * * * * This program is free software: you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation, either version 3 of the License, or * * (at your option) any later version. * * * * This program is distributed in the hope that it will be useful, * * but WITHOUT ANY WARRANTY; without even the implied warranty of * * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * * GNU General Public License for more details. * * * * You should have received a copy of the GNU General Public License * * along with this program. If not, see . * \*************************************************************************/ #include #include #include "debug.hpp" #include "demultiplex.hpp" #include "commontypes.hpp" #include "fastq_io.hpp" #include "userconfig.hpp" #include "strutils.hpp" namespace ar { /////////////////////////////////////////////////////////////////////////////// demultiplex_reads::demultiplex_reads(const userconfig* config) : analytical_step(analytical_step::ordering::ordered) , m_barcodes(config->adapters.get_barcodes()) , m_barcode_table(m_barcodes, config->barcode_mm, config->barcode_mm_r1, config->barcode_mm_r2) , m_config(config) , m_cache() , m_unidentified_1(new fastq_output_chunk()) , m_unidentified_2() , m_statistics(m_barcodes.size()) , m_lock() { AR_DEBUG_ASSERT(!m_barcodes.empty()); if (!config->interleaved_output) { m_unidentified_2.reset(new fastq_output_chunk()); } for (size_t i = 0; i < m_barcodes.size(); ++i) { m_cache.push_back(read_chunk_ptr(new fastq_read_chunk())); } } demultiplex_reads::~demultiplex_reads() { } chunk_vec demultiplex_reads::flush_cache(bool eof) { chunk_vec output; if (eof || m_unidentified_1->count >= FASTQ_CHUNK_SIZE) { m_unidentified_1->eof = eof; output.push_back(chunk_pair(ai_write_unidentified_1, std::move(m_unidentified_1))); m_unidentified_1 = output_chunk_ptr(new fastq_output_chunk()); } if (m_config->paired_ended_mode && !m_config->interleaved_output && (eof || m_unidentified_2->count >= FASTQ_CHUNK_SIZE)) { m_unidentified_2->eof = eof; output.push_back(chunk_pair(ai_write_unidentified_2, std::move(m_unidentified_2))); m_unidentified_2 = output_chunk_ptr(new fastq_output_chunk()); } for (size_t nth = 0; nth < m_cache.size(); ++nth) { read_chunk_ptr& chunk = m_cache.at(nth); if (eof || chunk->reads_1.size() >= FASTQ_CHUNK_SIZE) { chunk->eof = eof; const size_t step_id = (nth + 1) * ai_analyses_offset; output.push_back(chunk_pair(step_id, std::move(chunk))); chunk = read_chunk_ptr(new fastq_read_chunk()); } } return output; } demux_statistics demultiplex_reads::statistics() const { return m_statistics; } /////////////////////////////////////////////////////////////////////////////// demultiplex_se_reads::demultiplex_se_reads(const userconfig* config) : demultiplex_reads(config) { } chunk_vec demultiplex_se_reads::process(analytical_chunk* chunk) { AR_DEBUG_LOCK(m_lock); read_chunk_ptr read_chunk(dynamic_cast(chunk)); for (const auto& read : read_chunk->reads_1) { const int best_barcode = m_barcode_table.identify(read); if (best_barcode < 0) { m_unidentified_1->add(*m_config->quality_output_fmt, read); if (best_barcode == -1) { m_statistics.unidentified += 1; } else { m_statistics.ambiguous += 1; } } else { read_chunk_ptr& dst = m_cache.at(best_barcode); dst->reads_1.push_back(read); dst->reads_1.back().truncate(m_barcodes.at(best_barcode).first.length()); m_statistics.barcodes.at(best_barcode) += 1; } } return flush_cache(read_chunk->eof); } /////////////////////////////////////////////////////////////////////////////// demultiplex_pe_reads::demultiplex_pe_reads(const userconfig* config) : demultiplex_reads(config) { } chunk_vec demultiplex_pe_reads::process(analytical_chunk* chunk) { AR_DEBUG_LOCK(m_lock); read_chunk_ptr read_chunk(dynamic_cast(chunk)); AR_DEBUG_ASSERT(read_chunk->reads_1.size() == read_chunk->reads_2.size()); fastq_vec::iterator it_1 = read_chunk->reads_1.begin(); fastq_vec::iterator it_2 = read_chunk->reads_2.begin(); for (; it_1 != read_chunk->reads_1.end(); ++it_1, ++it_2) { const int best_barcode = m_barcode_table.identify(*it_1, *it_2); if (best_barcode < 0) { m_unidentified_1->add(*m_config->quality_output_fmt, *it_1); if (m_config->interleaved_output) { m_unidentified_1->add(*m_config->quality_output_fmt, *it_2); } else { m_unidentified_2->add(*m_config->quality_output_fmt, *it_2); } if (best_barcode == -1) { m_statistics.unidentified += 1; } else { m_statistics.ambiguous += 1; } } else { read_chunk_ptr& dst = m_cache.at(best_barcode); it_1->truncate(m_barcodes.at(best_barcode).first.length()); dst->reads_1.push_back(*it_1); it_2->truncate(m_barcodes.at(best_barcode).second.length()); dst->reads_2.push_back(*it_2); m_statistics.barcodes.at(best_barcode) += 1; } } return flush_cache(read_chunk->eof); } } // namespace ar adapterremoval-2.3.1/src/demultiplex.hpp000066400000000000000000000117431350370616400203720ustar00rootroot00000000000000/*************************************************************************\ * AdapterRemoval - cleaning next-generation sequencing reads * * * * Copyright (C) 2011 by Stinus Lindgreen - stinus@binf.ku.dk * * Copyright (C) 2014 by Mikkel Schubert - mikkelsch@gmail.com * * * * If you use the program, please cite the paper: * * S. Lindgreen (2012): AdapterRemoval: Easy Cleaning of Next Generation * * Sequencing Reads, BMC Research Notes, 5:337 * * http://www.biomedcentral.com/1756-0500/5/337/ * * * * This program is free software: you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation, either version 3 of the License, or * * (at your option) any later version. * * * * This program is distributed in the hope that it will be useful, * * but WITHOUT ANY WARRANTY; without even the implied warranty of * * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * * GNU General Public License for more details. * * * * You should have received a copy of the GNU General Public License * * along with this program. If not, see . * \*************************************************************************/ #ifndef DEMULTIPLEX_H #define DEMULTIPLEX_H #include "barcode_table.hpp" #include "fastq.hpp" #include "fastq_io.hpp" #include "scheduler.hpp" #include "statistics.hpp" namespace ar { class userconfig; /** * Baseclass for demultiplexing of reads; responsible for building the quad-tree * representing the set of adapter sequences, and for maintaining the cache of * demultiplexed reads. */ class demultiplex_reads : public analytical_step { public: /** Setup demultiplexer; keeps pointer to config object. */ demultiplex_reads(const userconfig* config); /** Frees any unflushed caches. */ virtual ~demultiplex_reads(); /** Returns a statistics object summarizing the results up till now. */ demux_statistics statistics() const; //! Copy construction not supported demultiplex_reads(const demultiplex_reads&) = delete; //! Assignment not supported demultiplex_reads& operator=(const demultiplex_reads&) = delete; protected: //! List of barcode (pairs) supplied by caller const fastq_pair_vec& m_barcodes; //! Quad-tree representing all mate 1 adapters; for search with n mismatches const barcode_table m_barcode_table; //! Pointer to user settings used for output format for unidentified reads const userconfig* m_config; //! Returns a chunk-list with any set of reads exceeding the max cache size //! If 'eof' is true, all chunks are returned, and the 'eof' values in the //! chunks are set to true. chunk_vec flush_cache(bool eof = false); typedef std::vector demultiplexed_cache; //! Cache of demultiplex reads; used to reduce the number of output chunks //! generated from each processed chunk, which would otherwise increase //! linearly with the number of barcodes. demultiplexed_cache m_cache; //! Cache of unidentified mate 1 reads output_chunk_ptr m_unidentified_1; //! Cache of unidentified mate 2 reads output_chunk_ptr m_unidentified_2; //! Sink for demultiplexing statistics; used by subclasses. demux_statistics m_statistics; //! Lock used to verify that the analytical_step is only run sequentially. std::mutex m_lock; }; /** Demultiplexer for single-end reads. */ class demultiplex_se_reads : public demultiplex_reads { public: /** See demultiplex_reads::demultiplex_reads. */ demultiplex_se_reads(const userconfig* config); /** * Processes a read chunk, and forwards chunks to downstream steps, with * the IDs corresponding to ai_analyses_offset * (nth + 1) for the nth * barcode (pair). Unidentified reads are sent to ai_write_unidentified_1. */ chunk_vec process(analytical_chunk* chunk); }; /** Demultiplexer for paired-end reads. */ class demultiplex_pe_reads : public demultiplex_reads { public: /** See demultiplex_reads::demultiplex_reads. */ demultiplex_pe_reads(const userconfig* config); /** * Processes a read chunk, and forwards chunks to downstream steps, with * the IDs corresponding to ai_analyses_offset * (nth + 1) for the nth * barcode (pair). Unidentified reads are sent to ai_write_unidentified_1 * and ai_write_unidentified_2. */ chunk_vec process(analytical_chunk* chunk); }; } // namespace ar #endif adapterremoval-2.3.1/src/fastq.cpp000066400000000000000000000331671350370616400171530ustar00rootroot00000000000000/*************************************************************************\ * AdapterRemoval - cleaning next-generation sequencing reads * * * * Copyright (C) 2011 by Stinus Lindgreen - stinus@binf.ku.dk * * Copyright (C) 2014 by Mikkel Schubert - mikkelsch@gmail.com * * * * If you use the program, please cite the paper: * * S. Lindgreen (2012): AdapterRemoval: Easy Cleaning of Next Generation * * Sequencing Reads, BMC Research Notes, 5:337 * * http://www.biomedcentral.com/1756-0500/5/337/ * * * * This program is free software: you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation, either version 3 of the License, or * * (at your option) any later version. * * * * This program is distributed in the hope that it will be useful, * * but WITHOUT ANY WARRANTY; without even the implied warranty of * * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * * GNU General Public License for more details. * * * * You should have received a copy of the GNU General Public License * * along with this program. If not, see . * \*************************************************************************/ #include #include #include #include #include #include "debug.hpp" #include "fastq.hpp" #include "linereader.hpp" namespace ar { enum class read_mate { unknown, mate_1, mate_2, }; struct mate_info { mate_info() : name() , mate(read_mate::unknown) {} std::string desc() const { switch (mate) { case read_mate::unknown: return "unknown"; case read_mate::mate_1: return "mate 1"; case read_mate::mate_2: return "mate 2"; default: AR_DEBUG_FAIL("Invalid mate in mate_info::desc"); } } std::string name; read_mate mate; }; inline mate_info get_and_fix_mate_info(fastq& read, char mate_separator) { mate_info info; std::string& header = read.m_header; size_t pos = header.find_first_of(' '); if (pos == std::string::npos) { pos = header.length(); } if (pos >= 2 && header.at(pos - 2) == mate_separator) { const char digit = header.at(pos - 1); if (digit == '1') { header[pos - 2] = MATE_SEPARATOR; info.mate = read_mate::mate_1; pos -= 2; } else if (digit == '2') { header[pos - 2] = MATE_SEPARATOR; info.mate = read_mate::mate_2; pos -= 2; } } info.name = header.substr(0, pos); return info; } /////////////////////////////////////////////////////////////////////////////// // fastq fastq::fastq() : m_header() , m_sequence() , m_qualities() { } fastq::fastq(const std::string& header, const std::string& sequence, const std::string& qualities, const fastq_encoding& encoding) : m_header(header) , m_sequence(sequence) , m_qualities(qualities) { process_record(encoding); } fastq::fastq(const std::string& header, const std::string& sequence) : m_header(header) , m_sequence(sequence) , m_qualities(std::string(sequence.length(), '!')) { process_record(FASTQ_ENCODING_33); } bool fastq::operator==(const fastq& other) const { return (m_header == other.m_header) && (m_sequence == other.m_sequence) && (m_qualities == other.m_qualities); } size_t fastq::count_ns() const { return static_cast(std::count(m_sequence.begin(), m_sequence.end(), 'N')); } fastq::ntrimmed fastq::trim_trailing_bases(const bool trim_ns, char low_quality, const bool preserve5p) { low_quality += PHRED_OFFSET_33; auto is_quality_base = [&] (size_t i) { return m_qualities.at(i) > low_quality && (!trim_ns || m_sequence.at(i) != 'N'); }; size_t right_exclusive = 0; for (size_t i = m_sequence.length(); i; --i) { if (is_quality_base(i - 1)) { right_exclusive = i; break; } } size_t left_inclusive = 0; for (size_t i = 0; !preserve5p && i < right_exclusive; ++i) { if (is_quality_base(i)) { left_inclusive = i; break; } } return trim_sequence_and_qualities(left_inclusive, right_exclusive); } //! Calculates the size of the sliding window for quality trimming given a //! read length and a user-defined window-size (fraction or whole number). size_t calculate_winlen(const size_t read_length, const double window_size) { size_t winlen; if (window_size >= 1.0) { winlen = static_cast(window_size); } else { winlen = static_cast(window_size * read_length); } if (winlen == 0 || winlen > read_length) { winlen = read_length; } return winlen; } fastq::ntrimmed fastq::trim_windowed_bases(const bool trim_ns, char low_quality, const double window_size, const bool preserve5p) { AR_DEBUG_ASSERT(window_size >= 0.0); if (m_sequence.empty()) { return ntrimmed(); } low_quality += PHRED_OFFSET_33; auto is_quality_base = [&] (size_t i) { return m_qualities.at(i) > low_quality && (!trim_ns || m_sequence.at(i) != 'N'); }; const size_t winlen = calculate_winlen(length(), window_size); long running_sum = std::accumulate(m_qualities.begin(), m_qualities.begin() + winlen, 0); size_t left_inclusive = std::string::npos; size_t right_exclusive = std::string::npos; for (size_t offset = 0; offset + winlen <= length(); ++offset) { const long running_avg = running_sum / static_cast(winlen); // We trim away low quality bases and Ns from the start of reads, // **before** we consider windows. if (left_inclusive == std::string::npos && is_quality_base(offset) && running_avg > low_quality) { left_inclusive = offset; } if (left_inclusive != std::string::npos && (running_avg <= low_quality || offset + winlen == length())) { right_exclusive = offset; while (right_exclusive < length() && is_quality_base(right_exclusive)) { right_exclusive++; } break; } running_sum -= m_qualities.at(offset); if (offset + winlen < length()) { running_sum += m_qualities.at(offset + winlen); } } if (left_inclusive == std::string::npos) { // No starting window found. Trim all bases starting from start. return trim_sequence_and_qualities(length(), length()); } else if (preserve5p) { left_inclusive = 0; } AR_DEBUG_ASSERT(right_exclusive != std::string::npos); return trim_sequence_and_qualities(left_inclusive, right_exclusive); } void fastq::truncate(size_t pos, size_t len) { AR_DEBUG_ASSERT(pos == 0 || pos <= length()); if (pos || len < length()) { m_sequence = m_sequence.substr(pos, len); m_qualities = m_qualities.substr(pos, len); } } void fastq::reverse_complement() { std::reverse(m_sequence.begin(), m_sequence.end()); std::reverse(m_qualities.begin(), m_qualities.end()); // Lookup table for complementary bases based only on the last 4 bits static const char complements[] = "-T-GA--C------N-"; for (auto& nuc : m_sequence) { nuc = complements[nuc & 0xf]; } } void fastq::add_prefix_to_header(const std::string& prefix) { m_header.insert(0, prefix); } void fastq::add_postfix_to_header(const std::string& postfix) { m_header += postfix; } void fastq::discard() { m_sequence = 'N'; m_qualities = '!'; } bool fastq::read(line_reader_base& reader, const fastq_encoding& encoding) { std::string line; if (!reader.getline(line)) { // End of file; terminate gracefully return false; } m_header = line.substr(1); if (m_header.empty() || line.at(0) != '@') { throw fastq_error("Malformed or empty FASTQ header"); } if (!reader.getline(m_sequence)) { throw fastq_error("partial FASTQ record; cut off after header"); } else if (m_sequence.empty()) { throw fastq_error("sequence is empty"); } if (!reader.getline(line)) { throw fastq_error("partial FASTQ record; cut off after sequence"); } else if (line.empty() || line.at(0) != '+') { throw fastq_error("FASTQ record lacks separator character (+)"); } if (!reader.getline(m_qualities)) { throw fastq_error("partial FASTQ record; cut off after separator"); } else if (m_qualities.empty()) { throw fastq_error("no qualities"); } process_record(encoding); return true; } std::string fastq::to_str(const fastq_encoding& encoding) const { std::string result; // Size of header, sequence, qualities, 4 new-lines, '@' and '+' result.reserve(m_header.size() + m_sequence.size() * 2 + 6); result.push_back('@'); result.append(m_header); result.push_back('\n'); result.append(m_sequence); result.append("\n+\n", 3); encoding.encode(m_qualities, result); result.push_back('\n'); return result; } /////////////////////////////////////////////////////////////////////////////// // Public helper functions void fastq::clean_sequence(std::string& sequence) { for (char& nuc : sequence) { switch (nuc) { case 'A': case 'C': case 'G': case 'T': case 'N': break; case 'a': case 'c': case 'g': case 't': case 'n': nuc += 'A' - 'a'; break; case '.': nuc = 'N'; break; default: throw fastq_error("invalid character in FASTQ sequence; " "only A, C, G, T and N are expected!"); } } } char fastq::p_to_phred_33(double p) { // Lowest possible error rate representable is '~' (~5e-10) const auto min_p = std::max(5e-10, p); const auto raw_score = static_cast(-10.0 * std::log10(min_p)); return std::min('~', raw_score + PHRED_OFFSET_33); } void fastq::validate_paired_reads(fastq& mate1, fastq& mate2, char mate_separator) { if (mate1.length() == 0 || mate2.length() == 0) { throw fastq_error("Pair contains empty reads"); } const mate_info info1 = get_and_fix_mate_info(mate1, mate_separator); const mate_info info2 = get_and_fix_mate_info(mate2, mate_separator); if (info1.name != info2.name) { std::stringstream error; error << "Pair contains reads with mismatching names:\n" << " - '" << info1.name << "'\n" << " - '" << info2.name << "'"; if (info1.mate == read_mate::unknown || info2.mate == read_mate::unknown) { error << "\n\nNote that AdapterRemoval by determines the mate " "numbers as the digit found at the end of the read name, " "if this is preceded by the character '" << mate_separator << "'; if these data makes use of a different character to " "separate the mate number from the read name, then you " "will need to set the --mate-separator command-line " "option to the appropriate character."; } throw fastq_error(error.str()); } if (info1.mate != read_mate::unknown || info2.mate != read_mate::unknown) { if (info1.mate != read_mate::mate_1 || info2.mate != read_mate::mate_2) { std::stringstream error; error << "Inconsistent mate numbering; please verify data:\n" << "\nRead 1 identified as " << info1.desc() << ": " << mate1.name() << "\nRead 2 identified as " << info2.desc() << ": " << mate2.name(); throw fastq_error(error.str()); } } } /////////////////////////////////////////////////////////////////////////////// // Private helper functions void fastq::process_record(const fastq_encoding& encoding) { if (m_qualities.length() != m_sequence.length()) { throw fastq_error("invalid FASTQ record; sequence/quality length does not match"); } clean_sequence(m_sequence); encoding.decode(m_qualities); } fastq::ntrimmed fastq::trim_sequence_and_qualities(const size_t left_inclusive, const size_t right_exclusive) { const ntrimmed summary(left_inclusive, length() - right_exclusive); if (summary.first || summary.second) { const size_t retained = right_exclusive - left_inclusive; m_sequence = m_sequence.substr(left_inclusive, retained); m_qualities = m_qualities.substr(left_inclusive, retained); } return summary; } } // namespace ar adapterremoval-2.3.1/src/fastq.hpp000066400000000000000000000237571350370616400171640ustar00rootroot00000000000000/*************************************************************************\ * AdapterRemoval - cleaning next-generation sequencing reads * * * * Copyright (C) 2011 by Stinus Lindgreen - stinus@binf.ku.dk * * Copyright (C) 2014 by Mikkel Schubert - mikkelsch@gmail.com * * * * If you use the program, please cite the paper: * * S. Lindgreen (2012): AdapterRemoval: Easy Cleaning of Next Generation * * Sequencing Reads, BMC Research Notes, 5:337 * * http://www.biomedcentral.com/1756-0500/5/337/ * * * * This program is free software: you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation, either version 3 of the License, or * * (at your option) any later version. * * * * This program is distributed in the hope that it will be useful, * * but WITHOUT ANY WARRANTY; without even the implied warranty of * * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * * GNU General Public License for more details. * * * * You should have received a copy of the GNU General Public License * * along with this program. If not, see . * \*************************************************************************/ #ifndef FASTQ_H #define FASTQ_H #include #include #include "commontypes.hpp" #include "fastq_enc.hpp" namespace ar { class line_reader_base; struct mate_info; /** * Represents a FASTQ record with Phred (offset=33) encoded quality scores. */ class fastq { public: /** Constructs a dummy FASTQ record for which all fields are empty. **/ fastq(); /** * Create a new FASTQ record. * * @param header FASTQ header, including read name and meta information. * @param sequence nucleotide sequence containing the letters "acgtnACGTN." * @param qualities phred or solexa encoded quality scores * @param encoding the encoding used for the quality scores. * * Nucleotides are converted to uppercase, and dots are replaced with N. * Phred scores are calculated from the encoded scores, in the case of * Solexa encoding re-encoded under this scheme, otherwise simply decoded * to Phred+33 scores, if not already in this format. * * The quality scores are expected to be in the range of 0 .. 40, unless * the format is Phred+33, in which case the range 0 .. 41 is accepted. */ fastq(const std::string& header, const std::string& sequence, const std::string& qualities, const fastq_encoding& encoding = FASTQ_ENCODING_33); /** * Create FASTQ record from a sequence alone. * * @param header FASTQ header, including read name and meta information. * @param sequence nucleotide sequence containing the letters "acgtnACGTN." * * Works like the full constructor, except that qualities are all 0 ('!'). */ fastq(const std::string& header, const std::string& sequence); /** Returns true IFF all fields are identical. **/ bool operator==(const fastq& other) const; /** Returns the header (excluding the @) of the record. **/ const std::string& header() const; /** Returns the nucleotide sequence (ACGTN only) of the record. **/ const std::string& sequence() const; /** Returns the Phred+33 encoded scores (0 .. 41) for each base. **/ const std::string& qualities() const; /** Returns the name (excluding the @ and other fields) of the header. **/ std::string name() const; /** Returns the length of the sequence. */ size_t length() const; /** Returns the number of ambiguous nucleotides in the sequence (N). **/ size_t count_ns() const; /** The number of bases trimmmed from the 5p and 3p end respectively. **/ typedef std::pair ntrimmed; /** * Trims consecutive low-quality bases from the 5'/3' ends of the sequence. * * @param trim_ns If true, ambiguous bases ('N') are trimmed. * @param low_quality Trim bases with a quality score at or below this value. * @param preserve5p Only trim from the 3p end if true. * @return A pair containing the number of 5' and 3' bases trimmed. */ ntrimmed trim_trailing_bases(const bool trim_ns = true, char low_quality = -1, const bool preserve5p = false); /** * Trims low-quality bases using a sliding window approach. * * @param trim_ns If true, ambiguous bases ('N') are trimmed. * @param low_quality Trim bases with a quality score at or below this value. * @param winlen The length of the sliding window. * @param preserve5p Only trim from the 3p end if true. * @return A pair containing the number of 5' and 3' bases trimmed. */ ntrimmed trim_windowed_bases(const bool trim_ns = true, char low_quality = -1, const double window_size = 0.1, const bool preserve5p = false); /** * Truncates the record in place. * * This function behaves like std::string::substr, except that the * substrings (sequence / qualities) are re-assigned to the record itself. */ void truncate(size_t pos = 0, size_t len = std::string::npos); /** Reverse complements the record in place. */ void reverse_complement(); /** Adds a prefix to the header. */ void add_prefix_to_header(const std::string& prefix); /** Adds a postfix to the header. */ void add_postfix_to_header(const std::string& postfix); /** * Discards read data; the sequence is replaced with a single 'N', and the * and the quality string is replaced with a single '!'. */ void discard(); /** * Reads a FASTQ record from a list of lines (without newlines). * * If a malformed or invalid FASTQ record is encountered, the fastq_error * exception is raised. Note that 'this' record is only valid if read * returned true. Unlike the constructor, this function does not accept * empty headers, or sequences / qualities, as this typically indicates * a problem with the source file. */ bool read(line_reader_base& reader, const fastq_encoding& encoding = FASTQ_ENCODING_33); /** * Converts a FASTQ record to a string ending with a newline. * * Only the phred_33 and phred_64 encodings are supported. For phred_64, * quality bases are truncated to 0 .. 40, while phred_33 supports quality * scores in the range 0 .. 41. */ std::string to_str(const fastq_encoding& encoding = FASTQ_ENCODING_33) const; /** Converts an error-probability to a Phred+33 encoded quality score. **/ static char p_to_phred_33(double p); /** * Validate that two reads form a valid pair. * * The mate separator character is the character expected as the second-to- * last character, if the last character (either '1' or '2') specify the * mate number. Non-standard mate-separators (not '/') are changed to '/'. */ static void validate_paired_reads(fastq& mate1, fastq& mate2, char mate_separator = MATE_SEPARATOR); private: /** * Converting lower-case nucleotides to uppercase, '.' to N. * * If the sequence contains letters other than "acgtnACGTN.", a fastq_error * is thrown. **/ static void clean_sequence(std::string& sequence); /** Initializes record; used by constructor and read function. **/ void process_record(const fastq_encoding& encoding); /** * Trims the read to the specified bases, and returns a pair specifying the * number of 5' and 3' bases removed. */ ntrimmed trim_sequence_and_qualities(const size_t left_inclusive, const size_t right_exclusive); /** Helper function to get mate numbering and fix the separator char. */ friend mate_info get_and_fix_mate_info(fastq& read, char mate_separator); //! Header excluding the @ sigil, but (possibly) including meta-info std::string m_header; //! Nucleotide sequence; contains only uppercase letters "ACGTN" std::string m_sequence; //! Phred+33 encoded quality scores std::string m_qualities; }; /////////////////////////////////////////////////////////////////////////////// /** * Simple hashing function for nucleotides 'A', 'C', 'G', 'T', returning * numbers in the range 0-3. Passing characters other than "ACGT" (uppercase * only) will result in hash collisions. */ inline size_t ACGT_TO_IDX(char nt) { return (nt >> 1) & 0x3; } /** * Inverse of ACGT_TO_IDX. Only values in the range 0 to 3 are allowed. */ inline char IDX_TO_ACGT(size_t idx) { return "ACTG"[idx]; } /////////////////////////////////////////////////////////////////////////////// typedef std::pair fastq_pair; typedef std::vector fastq_pair_vec; /////////////////////////////////////////////////////////////////////////////// inline const std::string& fastq::header() const { return m_header; } inline std::string fastq::name() const { const size_t pos = m_header.find_first_of(' '); if (pos != std::string::npos) { return m_header.substr(0, pos); } return m_header; } inline const std::string& fastq::sequence() const { return m_sequence; } inline const std::string& fastq::qualities() const { return m_qualities; } inline size_t fastq::length() const { return m_sequence.length(); } } // namespace ar #endif adapterremoval-2.3.1/src/fastq_enc.cpp000066400000000000000000000264141350370616400177750ustar00rootroot00000000000000/*************************************************************************\ * AdapterRemoval - cleaning next-generation sequencing reads * * * * Copyright (C) 2011 by Stinus Lindgreen - stinus@binf.ku.dk * * Copyright (C) 2014 by Mikkel Schubert - mikkelsch@gmail.com * * * * If you use the program, please cite the paper: * * S. Lindgreen (2012): AdapterRemoval: Easy Cleaning of Next Generation * * Sequencing Reads, BMC Research Notes, 5:337 * * http://www.biomedcentral.com/1756-0500/5/337/ * * * * This program is free software: you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation, either version 3 of the License, or * * (at your option) any later version. * * * * This program is distributed in the hope that it will be useful, * * but WITHOUT ANY WARRANTY; without even the implied warranty of * * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * * GNU General Public License for more details. * * * * You should have received a copy of the GNU General Public License * * along with this program. If not, see . * \*************************************************************************/ #include #include #include #include #include #include #include "debug.hpp" #include "fastq_enc.hpp" namespace ar { /////////////////////////////////////////////////////////////////////////////// // fastq_error fastq_error::fastq_error(const std::string& message) : std::exception() , m_message(message) { } fastq_error::fastq_error(const fastq_error& error) : std::exception() , m_message(error.m_message) { } fastq_error::~fastq_error() noexcept { } const char* fastq_error::what() const noexcept { return m_message.c_str(); } /////////////////////////////////////////////////////////////////////////////// // Pre-calculation of Solexa <-> Phred conversions std::string calc_solexa_to_phred() { std::string scores; scores.resize(MAX_PHRED_SCORE - MIN_SOLEXA_SCORE + 1); for (int i = MIN_SOLEXA_SCORE; i <= MAX_PHRED_SCORE; ++i) { const double score = round(10.0 * log10(1.0 + pow(10, (i / 10.0)))); const int transformed = std::max(MIN_PHRED_SCORE, std::min(MAX_PHRED_SCORE, score)); scores.at(i - MIN_SOLEXA_SCORE) = transformed; } return scores; } std::string calc_phred_to_solexa() { std::string scores; scores.resize(MAX_PHRED_SCORE - MIN_PHRED_SCORE + 1); for (int i = MIN_PHRED_SCORE; i <= MAX_PHRED_SCORE; ++i) { const auto min_i = std::max(1, i); const auto score = round(10.0 * log10(pow(10.0, min_i / 10.0) - 1.0)); const auto transformed = std::max(MIN_SOLEXA_SCORE, std::min(MAX_PHRED_SCORE, score)); scores.at(i) = transformed; } return scores; } const std::string g_solexa_to_phred = calc_solexa_to_phred(); const std::string g_phred_to_solexa = calc_phred_to_solexa(); /////////////////////////////////////////////////////////////////////////////// [[noreturn]] void invalid_phred(const char offset, const char max_score, const char raw) { if (raw < offset) { AR_DEBUG_ASSERT(offset == 33 || offset == 64); if (offset == 33) { throw fastq_error("ASCII value of quality score is less than 33 " "(ASCII < '!'); input is corrupt or not in " "FASTQ format!"); } else if (offset == 64) { if (raw < ';') { throw fastq_error("Phred+64 encoded quality score is less than 0 " "(ASCII < ';'); Are these FASTQ reads actually in " "Phred+33 format? If so, use the command-line " "option \"--qualitybase 33\"\n\n" "See README for more information."); } else if (raw < '@') { // Value not less than -5, which is the lowest Solexa score throw fastq_error("Phred+64 encoded quality score is less than 0 " "(ASCII < '@'); Are these FASTQ reads actually in " "Phred+33 or Solexa format? If so, use the " "command-line option \"--qualitybase 33\" or " "\"--qualitybase solexa\"\n\n" "See README for more information."); } else { AR_DEBUG_FAIL("TODO"); } } else { AR_DEBUG_FAIL("Unexpected offset in fastq_encoding::decode"); } } else if (raw > max_score) { if (raw > '~') { throw fastq_error("ASCII value of quality score is greater than " "126 (ASCII > '~'); input is corrupt or not in " "FASTQ format!"); } else if (offset == 33) { std::stringstream ss; ss << "Phred+33 encoded quality score is greater than the " << "expected maximum (" << max_score << " = " << static_cast(offset + max_score) << "). Please " << "verify the format of these files.\n\n" << "If the quality scores are actually Phred+64 encoded, then " << "use the '--qualitybase 64' command-line option.\n\n" << "If the quality scores are Phred+33 encoded, but includes " << "scores in a greater range than expected, then use the " << "'--qualitymax' option. Note that this option effects both " << "reading and writing of FASTQ files.\n\n" << "See README for more information."; throw fastq_error(ss.str()); } else if (offset == 64) { std::stringstream ss; ss << "Phred+64 encoded quality score is greater than the " << "expected maximum (" << max_score << " = " << static_cast(offset + max_score) << "). Please " << "verify the format of these files.\n\n" << "If the quality scores are Phred+64 encoded, but includes " << "scores in a greater range than expected, then use the " << "'--qualitymax' command-line option. Note that this option " << "effects both reading and writing of FASTQ files.\n\n" << "See README for more information."; throw fastq_error(ss.str()); } else { AR_DEBUG_FAIL("Unexpected offset in fastq_encoding::decode"); } } else { AR_DEBUG_FAIL("invalid_phred called on valid PHRED score"); } } [[noreturn]] void invalid_solexa(const char offset, const char max_score, const char raw) { if (raw < ';') { if (raw < '!') { throw fastq_error("ASCII value of quality score is less than 33 " "(ASCII < '!'); input is corrupt or not in " "FASTQ format!"); } else { throw fastq_error("Solexa score is less than -5 (ASCII = ';'); " "Is this actually Phred+33 data? If so, use " "the '--qualitybase 33' command-line option.\n\n" "See the README for more information."); } } else if (raw > '~') { throw fastq_error("ASCII value of quality score is greater than " "126 (ASCII > '~'); input is corrupt or not in " "FASTQ format!"); } else { std::stringstream ss; ss << "Solaxa encoded quality score is greater than the " << "expected maximum (" << max_score << " = " << static_cast(offset + max_score) << "). Please " << "verify the format of these files.\n\n" << "If the quality scores are Solexa encoded, but includes " << "scores in a greater range than expected, then use the " << "'--qualitymax' command-line option. Note that this option " << "effects both reading and writing of FASTQ files.\n\n" << "See README for more information."; throw fastq_error(ss.str()); } } /////////////////////////////////////////////////////////////////////////////// fastq_encoding::fastq_encoding(char offset, char max_score) : m_offset(offset) , m_max_score(std::min('~' - offset, max_score)) { if (offset != 33 && offset != 64) { throw std::invalid_argument("Phred offset must be 33 or 64"); } else if (max_score < 0) { throw std::invalid_argument("Max ASCII encoded Phred score less than 0"); } else if (max_score > '~' - PHRED_OFFSET_33) { throw std::invalid_argument("ASCII value cutoff for quality scores " "lies after printable characters"); } } fastq_encoding::~fastq_encoding() { } void fastq_encoding::encode(const std::string& qualities, std::string& dst) const { const char ascii_max = m_offset + m_max_score; const char offset = m_offset - '!'; for (const auto& quality : qualities) { dst.push_back(std::min(ascii_max, quality + offset)); } } void fastq_encoding::decode(std::string& qualities) const { const char max_score = m_offset + m_max_score; const char offset = PHRED_OFFSET_33 - m_offset; for (auto& quality : qualities) { if (quality < m_offset || quality > max_score) { invalid_phred(m_offset, m_max_score, quality); } quality += offset; } } const char* fastq_encoding::name() const { if (m_offset == 33) { return "Phred+33"; } else if (m_offset == 64) { return "Phred+64"; } else { AR_DEBUG_FAIL("Unexpected offset in fastq_encoding::name"); } } size_t fastq_encoding::max_score() const { return m_max_score; } fastq_encoding_solexa::fastq_encoding_solexa(unsigned max_score) : fastq_encoding(PHRED_OFFSET_64, max_score) { } void fastq_encoding_solexa::encode(const std::string& qualities, std::string& dst) const { const char ascii_max = m_offset + m_max_score; for (const auto& quality : qualities) { dst.push_back(std::min(ascii_max, g_phred_to_solexa.at(quality - '!') + '@')); } } void fastq_encoding_solexa::decode(std::string& qualities) const { const char max_score = m_offset + m_max_score; for (auto& quality : qualities) { if (quality < ';' || quality > max_score) { invalid_solexa(m_offset, m_max_score, quality); } quality = g_solexa_to_phred.at(quality - ';') + '!'; } } const char* fastq_encoding_solexa::name() const { return "Solexa"; } } // namespace ar adapterremoval-2.3.1/src/fastq_enc.hpp000066400000000000000000000134571350370616400200050ustar00rootroot00000000000000/*************************************************************************\ * AdapterRemoval - cleaning next-generation sequencing reads * * * * Copyright (C) 2011 by Stinus Lindgreen - stinus@binf.ku.dk * * Copyright (C) 2014 by Mikkel Schubert - mikkelsch@gmail.com * * * * If you use the program, please cite the paper: * * S. Lindgreen (2012): AdapterRemoval: Easy Cleaning of Next Generation * * Sequencing Reads, BMC Research Notes, 5:337 * * http://www.biomedcentral.com/1756-0500/5/337/ * * * * This program is free software: you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation, either version 3 of the License, or * * (at your option) any later version. * * * * This program is distributed in the hope that it will be useful, * * but WITHOUT ANY WARRANTY; without even the implied warranty of * * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * * GNU General Public License for more details. * * * * You should have received a copy of the GNU General Public License * * along with this program. If not, see . * \*************************************************************************/ #ifndef FASTQ_ENC_H #define FASTQ_ENC_H #include namespace ar { //! Offset used by Phred+33 and SAM encodings const int PHRED_OFFSET_33 = '!'; //! Offset used by Phred+64 and Solexa encodings const int PHRED_OFFSET_64 = '@'; //! Minimum Phred score allowed; encodes to '!' const int MIN_PHRED_SCORE = 0; //! Maximum Phred score allowed by default, to ensure backwards compatibility //! with AdapterRemoval v1.x. const int MAX_PHRED_SCORE_DEFAULT = 41; //! Maximum Phred score allowed, as this encodes to the last printable //! character '~', when using an offset of 33. const int MAX_PHRED_SCORE = 93; //! Minimum Solexa score allowed; encodes to ';' with an offset of 64 const int MIN_SOLEXA_SCORE = -5; //! Maximum Solexa score allowed; encodes to 'h' with an offset of 64 const int MAX_SOLEXA_SCORE = 40; //! Default character used to separate mate number const char MATE_SEPARATOR = '/'; /** Exception raised for FASTQ parsing and validation errors. */ class fastq_error : public std::exception { public: fastq_error(const std::string& message); fastq_error(const fastq_error& error); virtual ~fastq_error() noexcept; /** Returns error message; string is owned by exception. */ virtual const char* what() const noexcept; private: //! Error message associated with exception. std::string m_message; }; class fastq_encoding { public: /** * Create FASTQ encoding with a given offset (33 or 64), allowing for * quality-scores up to a given value (0 - N). Input with higher scores * is rejected, and output is truncated to this score. */ fastq_encoding(char offset = PHRED_OFFSET_33, char max_score = MAX_PHRED_SCORE_DEFAULT); virtual ~fastq_encoding(); /** Appends encoded Phred+33/66 quality-scores to dst. */ virtual void encode(const std::string& qualities, std::string& dst) const; /** Decodes a string of ASCII values in-place. */ virtual void decode(std::string& qualities) const; /** Returns the standard name for this encoding. */ virtual const char* name() const; /** * Returns the maximum allowed quality score for input, and the range to * range to which output scores are truncated. */ size_t max_score() const; //! Copy construction not supported fastq_encoding(const fastq_encoding&) = delete; //! Assignment not supported fastq_encoding& operator=(const fastq_encoding&) = delete; protected: //! Character offset for Phred encoded scores (33 or 64) const char m_offset; //! Maximum allowed score; used for checking input / truncating output const char m_max_score; }; /** * Solexa scores encoding by adding '@'; max score is 40. * * Solexa scores are defined as Q = -10 * log10(p / (1 - p)), and differ from * Phred scores for values less than 13. Lossless conversion between the * formats is not possible, and since the fastq class stores quality scores as * Phred+33 internally, this means that reading Solexa scores is a lossy * operation, even if the output is written using Solexa scores. */ class fastq_encoding_solexa : public fastq_encoding { public: /** * Create FASTQ Solexa encoding with offset 64, allowing for quality-scores * up to a given value (0 - N). Input with higher scores is rejected, and * output is truncated to this score. */ fastq_encoding_solexa(unsigned max_score = MAX_PHRED_SCORE_DEFAULT); /** Appends encoded Phred+33/66 quality-scores to dst. */ virtual void encode(const std::string& qualities, std::string& dst) const override; /** Decodes a string of ASCII values in-place. */ virtual void decode(std::string& qualities) const override; /** Returns the standard name for this encoding. */ virtual const char* name() const override; }; static const fastq_encoding FASTQ_ENCODING_33(PHRED_OFFSET_33); static const fastq_encoding FASTQ_ENCODING_64(PHRED_OFFSET_64); static const fastq_encoding FASTQ_ENCODING_SAM(PHRED_OFFSET_33, MAX_PHRED_SCORE); static const fastq_encoding_solexa FASTQ_ENCODING_SOLEXA; } // namespace ar #endif adapterremoval-2.3.1/src/fastq_io.cpp000066400000000000000000000513361350370616400176400ustar00rootroot00000000000000/*************************************************************************\ * AdapterRemoval - cleaning next-generation sequencing reads * * * * Copyright (C) 2015 by Mikkel Schubert - mikkelsch@gmail.com * * * * If you use the program, please cite the paper: * * S. Lindgreen (2012): AdapterRemoval: Easy Cleaning of Next Generation * * Sequencing Reads, BMC Research Notes, 5:337 * * http://www.biomedcentral.com/1756-0500/5/337/ * * * * This program is free software: you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation, either version 3 of the License, or * * (at your option) any later version. * * * * This program is distributed in the hope that it will be useful, * * but WITHOUT ANY WARRANTY; without even the implied warranty of * * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * * GNU General Public License for more details. * * * * You should have received a copy of the GNU General Public License * * along with this program. If not, see . * \*************************************************************************/ #include #include #include #include #include "debug.hpp" #include "fastq_io.hpp" #include "userconfig.hpp" namespace ar { size_t read_fastq_reads(fastq_vec& dst, joined_line_readers& reader, size_t offset, const fastq_encoding& encoding) { dst.reserve(FASTQ_CHUNK_SIZE); try { fastq record; for (size_t i = 0; i < FASTQ_CHUNK_SIZE; ++i) { if (record.read(reader, encoding)) { dst.push_back(record); } else { break; } } } catch (const fastq_error& error) { print_locker lock; std::cerr << "Error reading FASTQ record at line " << offset + dst.size() * 4 << "; aborting:\n" << cli_formatter::fmt(error.what()) << std::endl; throw thread_abort(); } return dst.size() * 4; } /////////////////////////////////////////////////////////////////////////////// // Implementations for 'fastq_read_chunk' fastq_read_chunk::fastq_read_chunk(bool eof_) : eof(eof_) , reads_1() , reads_2() { } /////////////////////////////////////////////////////////////////////////////// // Implementations for 'fastq_output_chunk' fastq_output_chunk::fastq_output_chunk(bool eof_) : eof(eof_) , count(0) , reads() , buffers() { reads.reserve(FASTQ_CHUNK_SIZE); } fastq_output_chunk::~fastq_output_chunk() { for (auto& buffer : buffers) { delete[] buffer.second; } } void fastq_output_chunk::add(const fastq_encoding& encoding, const fastq& read, size_t count_) { count += count_; reads.push_back(read.to_str(encoding)); } /////////////////////////////////////////////////////////////////////////////// // Implementations for 'read_single_fastq' read_single_fastq::read_single_fastq(const fastq_encoding* encoding, const string_vec& filenames, size_t next_step) : analytical_step(analytical_step::ordering::ordered, true) , m_encoding(encoding) , m_line_offset(1) , m_io_input(filenames) , m_next_step(next_step) , m_eof(false) , m_lock() { AR_DEBUG_ASSERT(!filenames.empty()); } chunk_vec read_single_fastq::process(analytical_chunk* chunk) { AR_DEBUG_LOCK(m_lock); AR_DEBUG_ASSERT(chunk == nullptr); if (m_eof) { return chunk_vec(); } read_chunk_ptr file_chunk(new fastq_read_chunk()); const size_t n_read = read_fastq_reads(file_chunk->reads_1, m_io_input, m_line_offset, *m_encoding); if (!n_read) { // EOF is detected by failure to read any lines, not line_reader::eof, // so that unbalanced files can be caught in all cases. file_chunk->eof = true; m_eof = true; } m_line_offset += n_read; chunk_vec chunks; chunks.push_back(chunk_pair(m_next_step, std::move(file_chunk))); return chunks; } void read_single_fastq::finalize() { AR_DEBUG_LOCK(m_lock); if (!m_eof) { throw thread_error("read_single_fastq::finalize: terminated before EOF"); } } /////////////////////////////////////////////////////////////////////////////// // Implementations for 'read_paired_fastq' read_paired_fastq::read_paired_fastq(const fastq_encoding* encoding, const string_vec& filenames_1, const string_vec& filenames_2, size_t next_step) : analytical_step(analytical_step::ordering::ordered, true) , m_encoding(encoding) , m_line_offset(1) , m_io_input_1(filenames_1) , m_io_input_2(filenames_2) , m_next_step(next_step) , m_eof(false) , m_lock() { AR_DEBUG_ASSERT(filenames_1.size() == filenames_2.size()); } chunk_vec read_paired_fastq::process(analytical_chunk* chunk) { AR_DEBUG_LOCK(m_lock); AR_DEBUG_ASSERT(chunk == nullptr); if (m_eof) { return chunk_vec(); } read_chunk_ptr file_chunk(new fastq_read_chunk()); const size_t n_read_1 = read_fastq_reads(file_chunk->reads_1, m_io_input_1, m_line_offset, *m_encoding); const size_t n_read_2 = read_fastq_reads(file_chunk->reads_2, m_io_input_2, m_line_offset, *m_encoding); if (n_read_1 != n_read_2) { print_locker lock; std::cerr << "ERROR: Input --file1 and --file2 contains different " << "numbers of lines; one or the other file may have been " << "truncated. Please correct before continuing!" << std::endl; throw thread_abort(); } else if (!n_read_1) { // EOF is detected by failure to read any lines, not line_reader::eof, // so that unbalanced files can be caught in all cases. file_chunk->eof = true; m_eof = true; } m_line_offset += n_read_1; chunk_vec chunks; chunks.push_back(chunk_pair(m_next_step, std::move(file_chunk))); return chunks; } void read_paired_fastq::finalize() { AR_DEBUG_LOCK(m_lock); if (!m_eof) { throw thread_error("read_paired_fastq::finalize: terminated before EOF"); } } /////////////////////////////////////////////////////////////////////////////// // Implementations for 'read_interleaved_fastq' read_interleaved_fastq::read_interleaved_fastq(const fastq_encoding* encoding, const string_vec& filenames, size_t next_step) : analytical_step(analytical_step::ordering::ordered, true) , m_encoding(encoding) , m_line_offset(1) , m_io_input(filenames) , m_next_step(next_step) , m_eof(false) , m_lock() { AR_DEBUG_ASSERT(!filenames.empty()); } chunk_vec read_interleaved_fastq::process(analytical_chunk* chunk) { AR_DEBUG_LOCK(m_lock); AR_DEBUG_ASSERT(chunk == nullptr); if (m_eof) { return chunk_vec(); } read_chunk_ptr file_chunk(new fastq_read_chunk()); file_chunk->reads_1.reserve(FASTQ_CHUNK_SIZE); file_chunk->reads_2.reserve(FASTQ_CHUNK_SIZE); try { fastq record; for (size_t i = 0; i < FASTQ_CHUNK_SIZE; ++i) { // Mate 1 reads if (record.read(m_io_input, *m_encoding)) { file_chunk->reads_1.push_back(record); } else { break; } // Mate 2 reads if (record.read(m_io_input, *m_encoding)) { file_chunk->reads_2.push_back(record); } else { break; } } } catch (const fastq_error& error) { const size_t offset = m_line_offset + file_chunk->reads_1.size() * 4 + file_chunk->reads_2.size() * 4; print_locker lock; std::cerr << "Error reading FASTQ record starting at line " << offset << ":\n" << cli_formatter::fmt(error.what()) << std::endl; throw thread_abort(); } const size_t n_read_1 = file_chunk->reads_1.size(); const size_t n_read_2 = file_chunk->reads_2.size(); if (n_read_1 != n_read_2) { print_locker lock; std::cerr << "ERROR: Interleaved FASTQ file contains uneven number of " << "reads; file may have been truncated! Please correct " << "before continuing!" << std::endl; throw thread_abort(); } else if (!n_read_1) { file_chunk->eof = true; m_eof = true; } m_line_offset += (n_read_1 + n_read_2) * 4; chunk_vec chunks; chunks.push_back(chunk_pair(m_next_step, std::move(file_chunk))); return chunks; } void read_interleaved_fastq::finalize() { AR_DEBUG_LOCK(m_lock); if (!m_eof) { throw thread_error("read_interleaved_fastq::finalize: terminated before EOF"); } } /////////////////////////////////////////////////////////////////////////////// // Utility function used by both gzip and bzip compression steps /** * Writes a set of lines into a buffer, and returns the size of the buffer and * the buffer itself as a pair. */ std::pair build_input_buffer(const string_vec& lines) { size_t buffer_size = 0; for (const auto& line : lines) { buffer_size += line.size(); } unsigned char* input_buffer = new unsigned char[buffer_size]; unsigned char* input_buffer_ptr = input_buffer; for (const auto& line : lines) { std::memcpy(input_buffer_ptr, line.data(), line.size()); input_buffer_ptr += line.size(); } return std::pair(buffer_size, input_buffer); } /////////////////////////////////////////////////////////////////////////////// // Implementations for 'gzip_fastq' bzip2_fastq::bzip2_fastq(const userconfig& config, size_t next_step) : analytical_step(analytical_step::ordering::ordered, false) , m_buffered_reads(0) , m_next_step(next_step) , m_stream() , m_eof(false) , m_lock() { m_stream.bzalloc = nullptr; m_stream.bzfree = nullptr; m_stream.opaque = nullptr; const int errorcode = BZ2_bzCompressInit(/* strm = */ &m_stream, /* blockSize100k = */ config.bzip2_level, /* verbosity = */ 0, /* workFactor = */ 0); switch (errorcode) { case BZ_OK: break; case BZ_MEM_ERROR: throw thread_error("bzip2_fastq: not enough memory"); case BZ_CONFIG_ERROR: throw thread_error("bzip2_fastq: miscompiled bzip2 library"); case BZ_PARAM_ERROR: throw thread_error("bzip2_fastq: invalid parameters"); default: throw thread_error("bzip2_fastq: unknown error"); } } void bzip2_fastq::finalize() { AR_DEBUG_LOCK(m_lock); if (!m_eof) { throw thread_error("bzip2_fastq::finalize: terminated before EOF"); } const int errorcode = BZ2_bzCompressEnd(&m_stream); if (errorcode != BZ_OK) { print_locker lock; switch (errorcode) { case BZ_PARAM_ERROR: throw thread_error("bzip2_fastq::finalize: parameter error"); default: throw thread_error("Unknown error in bzip2_fastq::finalize"); } } } chunk_vec bzip2_fastq::process(analytical_chunk* chunk) { AR_DEBUG_LOCK(m_lock); output_chunk_ptr file_chunk(dynamic_cast(chunk)); buffer_vec& buffers = file_chunk->buffers; if (m_eof) { throw thread_error("bzip2_fastq::process: received data after EOF"); } m_eof = file_chunk->eof; if (file_chunk->reads.empty() && !m_eof) { return chunk_vec(); } std::pair input_buffer; std::pair output_buffer; try { input_buffer = build_input_buffer(file_chunk->reads); file_chunk->reads.clear(); m_stream.avail_in = input_buffer.first; m_stream.next_in = reinterpret_cast(input_buffer.second); if (m_stream.avail_in || m_eof) { int errorcode = -1; do { output_buffer.first = FASTQ_COMPRESSED_CHUNK; output_buffer.second = new unsigned char[FASTQ_COMPRESSED_CHUNK]; m_stream.avail_out = output_buffer.first; m_stream.next_out = reinterpret_cast(output_buffer.second); errorcode = BZ2_bzCompress(&m_stream, m_eof ? BZ_FINISH : BZ_RUN); switch (errorcode) { case BZ_RUN_OK: case BZ_FINISH_OK: case BZ_STREAM_END: break; case BZ_FLUSH_OK: throw thread_error("bzip2_fastq::process: BZ_FLUSH_OK"); case BZ_PARAM_ERROR: throw thread_error("bzip2_fastq::process: BZ_PARAM_ERROR"); case BZ_SEQUENCE_ERROR: throw thread_error("bzip2_fastq::process: sequence error"); default: throw thread_error("bzip2_fastq::process: unknown error"); } output_buffer.first = FASTQ_COMPRESSED_CHUNK - m_stream.avail_out; if (output_buffer.first) { buffers.push_back(output_buffer); } else { delete[] output_buffer.second; } output_buffer.second = nullptr; } while (m_stream.avail_in || errorcode == BZ_FINISH_OK); } delete[] input_buffer.second; } catch (...) { delete[] input_buffer.second; delete[] output_buffer.second; throw; } chunk_vec chunks; if (!file_chunk->buffers.empty() || m_eof) { file_chunk->count += m_buffered_reads; chunks.push_back(chunk_pair(m_next_step, std::move(file_chunk))); m_buffered_reads = 0; } else { m_buffered_reads += file_chunk->count; } return chunks; } /////////////////////////////////////////////////////////////////////////////// // Implementations for 'gzip_fastq' gzip_fastq::gzip_fastq(const userconfig& config, size_t next_step) : analytical_step(analytical_step::ordering::ordered, false) , m_buffered_reads(0) , m_next_step(next_step) , m_stream() , m_eof(false) , m_lock() { m_stream.zalloc = nullptr; m_stream.zfree = nullptr; m_stream.opaque = nullptr; const int errorcode = deflateInit2(/* strm = */ &m_stream, /* level = */ config.gzip_level, /* method = */ Z_DEFLATED, /* windowBits = */ 15 + 16, /* memLevel = */ 8, /* strategy = */ Z_DEFAULT_STRATEGY); switch (errorcode) { case Z_OK: break; case Z_MEM_ERROR: throw thread_error("gzip_fastq: not enough memory"); case Z_STREAM_ERROR: throw thread_error("gzip_fastq: invalid parameters"); case Z_VERSION_ERROR: throw thread_error("gzip_fastq: incompatible zlib version"); default: throw thread_error("gzip_fastq: unknown error"); } } void gzip_fastq::finalize() { AR_DEBUG_LOCK(m_lock); if (!m_eof) { throw thread_error("gzip_fastq::finalize: terminated before EOF"); } const int errorcode = deflateEnd(&m_stream); if (errorcode != Z_OK) { print_locker lock; switch (errorcode) { case Z_STREAM_ERROR: throw thread_error("gzip_fastq::finalize: stream error"); case Z_DATA_ERROR: throw thread_error("gzip_fastq::finalize: data error"); default: throw thread_error("Unknown error in gzip_fastq::finalize"); } } } chunk_vec gzip_fastq::process(analytical_chunk* chunk) { AR_DEBUG_LOCK(m_lock); output_chunk_ptr file_chunk(dynamic_cast(chunk)); buffer_vec& buffers = file_chunk->buffers; if (m_eof) { throw thread_error("bzip2_fastq::process: received data after EOF"); } m_eof = file_chunk->eof; if (file_chunk->reads.empty() && !m_eof) { return chunk_vec(); } std::pair input_buffer; std::pair output_buffer; try { input_buffer = build_input_buffer(file_chunk->reads); file_chunk->reads.clear(); if (input_buffer.first || m_eof) { m_stream.avail_in = input_buffer.first; m_stream.next_in = input_buffer.second; int returncode = -1; do { output_buffer.first = FASTQ_COMPRESSED_CHUNK; output_buffer.second = new unsigned char[FASTQ_COMPRESSED_CHUNK]; m_stream.avail_out = output_buffer.first; m_stream.next_out = output_buffer.second; returncode = deflate(&m_stream, m_eof ? Z_FINISH : Z_NO_FLUSH); switch (returncode) { case Z_OK: case Z_STREAM_END: break; case Z_BUF_ERROR: throw thread_error("gzip_fastq::process: buf error"); case Z_STREAM_ERROR: throw thread_error("gzip_fastq::process: stream error"); default: throw thread_error("gzip_fastq::process: unknown error"); } output_buffer.first = FASTQ_COMPRESSED_CHUNK - m_stream.avail_out; if (output_buffer.first) { buffers.push_back(output_buffer); } else { delete[] output_buffer.second; } output_buffer.second = nullptr; } while (m_stream.avail_out == 0 || (m_eof && returncode != Z_STREAM_END)); } delete[] input_buffer.second; } catch (...) { delete[] input_buffer.second; delete[] output_buffer.second; throw; } chunk_vec chunks; if (!file_chunk->buffers.empty() || m_eof) { file_chunk->count += m_buffered_reads; chunks.push_back(chunk_pair(m_next_step, std::move(file_chunk))); m_buffered_reads = 0; } else { m_buffered_reads += file_chunk->count; } return chunks; } /////////////////////////////////////////////////////////////////////////////// // Implementations for 'write_fastq' //! Mutex used to control access to s_timer and s_finalized; static std::mutex s_timer_lock; //! Timer used to track trimming progress; accessed by all instances static timer s_timer = timer("reads"); //! Indicates if 'timer::finalize' has been called. static bool s_finalized = false; write_fastq::write_fastq(const std::string& filename) : analytical_step(analytical_step::ordering::ordered, true) , m_output(filename) , m_eof(false) , m_lock() { } chunk_vec write_fastq::process(analytical_chunk* chunk) { AR_DEBUG_LOCK(m_lock); output_chunk_ptr file_chunk(dynamic_cast(chunk)); if (m_eof) { throw thread_error("write_fastq::process: received data after EOF"); } m_eof = file_chunk->eof; if (file_chunk->buffers.empty()) { m_output.write_strings(file_chunk->reads, m_eof); } else { AR_DEBUG_ASSERT(file_chunk->reads.empty()); m_output.write_buffers(file_chunk->buffers, m_eof); } std::lock_guard lock(s_timer_lock); s_timer.increment(file_chunk->count); return chunk_vec(); } void write_fastq::finalize() { AR_DEBUG_LOCK(m_lock); std::lock_guard lock(s_timer_lock); if (!s_finalized) { s_timer.finalize(); s_finalized = true; } if (!m_eof) { throw thread_error("write_fastq::finalize: terminated before EOF"); } // Close file to trigger any exceptions due to badbit / failbit m_output.close(); } } // namespace ar adapterremoval-2.3.1/src/fastq_io.hpp000066400000000000000000000273361350370616400176500ustar00rootroot00000000000000/*************************************************************************\ * AdapterRemoval - cleaning next-generation sequencing reads * * * * Copyright (C) 2015 by Mikkel Schubert - mikkelsch@gmail.com * * * * If you use the program, please cite the paper: * * S. Lindgreen (2012): AdapterRemoval: Easy Cleaning of Next Generation * * Sequencing Reads, BMC Research Notes, 5:337 * * http://www.biomedcentral.com/1756-0500/5/337/ * * * * This program is free software: you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation, either version 3 of the License, or * * (at your option) any later version. * * * * This program is distributed in the hope that it will be useful, * * but WITHOUT ANY WARRANTY; without even the implied warranty of * * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * * GNU General Public License for more details. * * * * You should have received a copy of the GNU General Public License * * along with this program. If not, see . * \*************************************************************************/ #ifndef FASTQ_IO_H #define FASTQ_IO_H #include #include #include "commontypes.hpp" #include "fastq.hpp" #include "linereader_joined.hpp" #include "scheduler.hpp" #include "strutils.hpp" #include "timer.hpp" #include "managed_writer.hpp" namespace ar { class userconfig; class fastq_read_chunk; class fastq_output_chunk; typedef std::unique_ptr output_chunk_ptr; typedef std::unique_ptr read_chunk_ptr; //! Number of FASTQ records to read for each data-chunk const size_t FASTQ_CHUNK_SIZE = 2 * 1024; //! Size of compressed chunks used to transport compressed data const size_t FASTQ_COMPRESSED_CHUNK = 40 * 1024; /** * Container object for (demultiplexed) reads. */ class fastq_read_chunk : public analytical_chunk { public: /** Create chunk representing lines starting at line offset (1-based). */ fastq_read_chunk(bool eof_ = false); //! Indicates that EOF has been reached. bool eof; //! Lines read from the mate 1 files fastq_vec reads_1; //! Lines read from the mate 2 files fastq_vec reads_2; }; /** * Container object for processed reads. */ class fastq_output_chunk : public analytical_chunk { public: /** Constructor; does nothing. */ fastq_output_chunk(bool eof_ = false); /** Destructor; frees buffers. */ ~fastq_output_chunk(); /** Add FASTQ read, accounting for one or more input reads. */ void add(const fastq_encoding& encoding, const fastq& read, size_t count = 1); //! Indicates that EOF has been reached. bool eof; //! The number of reads used to generate this chunk; may differ from the //! the number of reads, in the case of collapsed reads. size_t count; private: friend class gzip_fastq; friend class bzip2_fastq; friend class write_fastq; //! Lines read from the mate 1 and mate 2 files string_vec reads; //! Buffers of compressed lines buffer_vec buffers; }; /** * Simple file reading step. * * Reads from a single FASTQ file, storing the reads in a fastq_file_chunk. * Once the EOF has been reached, a single empty chunk will be returned, * marked using the 'eof' property. */ class read_single_fastq : public analytical_step { public: /** * Constructor. * * @param encoding FASTQ encoding for reading quality scores. * @param filename Path to FASTQ file containing mate 1 / 2 reads. * @param next_step ID of analytical step to which data is forwarded. * * Opens the input file corresponding to the specified mate. */ read_single_fastq(const fastq_encoding* encoding, const string_vec& filenames, size_t next_step); /** Reads N lines from the input file and saves them in an fastq_read_chunk. */ virtual chunk_vec process(analytical_chunk* chunk); /** Finalizer; checks that all input has been processed. */ virtual void finalize(); //! Copy construction not supported read_single_fastq(const read_single_fastq&) = delete; //! Assignment not supported read_single_fastq& operator=(const read_single_fastq&) = delete; private: //! Encoding used to parse FASTQ reads. const fastq_encoding* m_encoding; //! Current line in the input file (1-based) size_t m_line_offset; //! Line reader used to read raw / gzip'd / bzip2'd FASTQ files. joined_line_readers m_io_input; //! The analytical step following this step const size_t m_next_step; //! Used to track whether an EOF block has been received. bool m_eof; //! Lock used to verify that the analytical_step is only run sequentially. std::mutex m_lock; }; /** * Simple file reading step. * * Reads from the mate 1 and the mate 2 files, storing the reads in a * fastq_file_chunk. Once the EOF has been reached, a single empty chunk will * be returned, marked using the 'eof' property. */ class read_paired_fastq : public analytical_step { public: /** * Constructor. */ read_paired_fastq(const fastq_encoding* encoding, const string_vec& filenames_1, const string_vec& filenames_2, size_t next_step); /** Reads N lines from the input file and saves them in an fastq_file_chunk. */ virtual chunk_vec process(analytical_chunk* chunk); /** Finalizer; checks that all input has been processed. */ virtual void finalize(); //! Copy construction not supported read_paired_fastq(const read_paired_fastq&) = delete; //! Assignment not supported read_paired_fastq& operator=(const read_paired_fastq&) = delete; private: //! Encoding used to parse FASTQ reads. const fastq_encoding* m_encoding; //! Current line in the input file (1-based) size_t m_line_offset; //! Line reader used to read raw / gzip'd / bzip2'd FASTQ files. joined_line_readers m_io_input_1; //! Line reader used to read raw / gzip'd / bzip2'd FASTQ files. joined_line_readers m_io_input_2; //! The analytical step following this step const size_t m_next_step; //! Used to track whether an EOF block has been received. bool m_eof; //! Lock used to verify that the analytical_step is only run sequentially. std::mutex m_lock; }; /** * Simple file reading step. * * Reads from an FASTQ file containing interleaved FASTQ reads, storing the * reads in a fastq_file_chunk. Once the EOF has been reached, a single empty * chunk will be returned, marked using the 'eof' property. */ class read_interleaved_fastq : public analytical_step { public: /** * Constructor. */ read_interleaved_fastq(const fastq_encoding* encoding, const string_vec& filenames, size_t next_step); /** Reads N lines from the input file and saves them in an fastq_file_chunk. */ virtual chunk_vec process(analytical_chunk* chunk); /** Finalizer; checks that all input has been processed. */ virtual void finalize(); //! Copy construction not supported read_interleaved_fastq(const read_interleaved_fastq&) = delete; //! Assignment not supported read_interleaved_fastq& operator=(const read_interleaved_fastq&) = delete; private: //! Encoding used to parse FASTQ reads. const fastq_encoding* m_encoding; //! Current line in the input file (1-based) size_t m_line_offset; //! Line reader used to read raw / gzip'd / bzip2'd FASTQ files. joined_line_readers m_io_input; //! The analytical step following this step const size_t m_next_step; //! Used to track whether an EOF block has been received. bool m_eof; //! Lock used to verify that the analytical_step is only run sequentially. std::mutex m_lock; }; /** * BZip2 compression step; takes any lines in the input chunk, compresses them, * and adds them to the buffer list of the chunk, before forwarding it. */ class bzip2_fastq : public analytical_step { public: /** Constructor; 'next_step' sets the destination of compressed chunks. */ bzip2_fastq(const userconfig& config, size_t next_step); /** Compresses input lines, saving compressed chunks to chunk->buffers. */ virtual chunk_vec process(analytical_chunk* chunk); /** Checks that all input has been processed and frees stream. */ virtual void finalize(); //! Copy construction not supported bzip2_fastq(const bzip2_fastq&) = delete; //! Assignment not supported bzip2_fastq& operator=(const bzip2_fastq&) = delete; private: //! N reads which did not result in an output chunk size_t m_buffered_reads; //! The analytical step following this step const size_t m_next_step; //! BZip2 stream object bz_stream m_stream; //! Used to track whether an EOF block has been received. bool m_eof; //! Lock used to verify that the analytical_step is only run sequentially. std::mutex m_lock; }; /** * GZip compression step; takes any lines in the input chunk, compresses them, * and adds them to the buffer list of the chunk, before forwarding it. */ class gzip_fastq : public analytical_step { public: /** Constructor; 'next_step' sets the destination of compressed chunks. */ gzip_fastq(const userconfig& config, size_t next_step); /** Compresses input lines, saving compressed chunks to chunk->buffers. */ virtual chunk_vec process(analytical_chunk* chunk); /** Checks that all input has been processed and frees stream. */ virtual void finalize(); //! Copy construction not supported gzip_fastq(const gzip_fastq&) = delete; //! Assignment not supported gzip_fastq& operator=(const gzip_fastq&) = delete; private: //! N reads which did not result in an output chunk size_t m_buffered_reads; //! The analytical step following this step const size_t m_next_step; //! GZip stream object z_stream m_stream; //! Used to track whether an EOF block has been received. bool m_eof; //! Lock used to verify that the analytical_step is only run sequentially. std::mutex m_lock; }; /** * Simple file reading step. * * The 'process' function takes a fastq_file_chunk object and writes the lines * at the offset corresponding to the 'type' argument to the corresponding * output file. The list of lines is cleared upon writing. */ class write_fastq : public analytical_step { public: /** * Constructor. * * @param filename Filename to which FASTQ reads are written. * * Based on the read-type specified, and SE / PE mode, the corresponding * output file is opened */ write_fastq(const std::string& filename); /** Writes the reads of the type specified in the constructor. */ virtual chunk_vec process(analytical_chunk* chunk); /** Flushes the output file and prints progress report (if enabled). */ virtual void finalize(); private: //! Lazily opened / automatically closed handle managed_writer m_output; //! Used to track whether an EOF block has been received. bool m_eof; //! Lock used to verify that the analytical_step is only run sequentially. std::mutex m_lock; }; } // namespace ar #endif adapterremoval-2.3.1/src/linereader.cpp000066400000000000000000000335551350370616400201500ustar00rootroot00000000000000/*************************************************************************\ * AdapterRemoval - cleaning next-generation sequencing reads * * * * Copyright (C) 2015 by Mikkel Schubert - mikkelsch@gmail.com * * * * If you use the program, please cite the paper: * * S. Lindgreen (2012): AdapterRemoval: Easy Cleaning of Next Generation * * Sequencing Reads, BMC Research Notes, 5:337 * * http://www.biomedcentral.com/1756-0500/5/337/ * * * * This program is free software: you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation, either version 3 of the License, or * * (at your option) any later version. * * * * This program is distributed in the hope that it will be useful, * * but WITHOUT ANY WARRANTY; without even the implied warranty of * * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * * GNU General Public License for more details. * * * * You should have received a copy of the GNU General Public License * * along with this program. If not, see . * \*************************************************************************/ #include #include #include #include #include #include #include "linereader.hpp" #include "managed_writer.hpp" #include "threads.hpp" namespace ar { //! Size of compressed and uncompressed buffers. const int BUF_SIZE = 10 * BUFSIZ; /////////////////////////////////////////////////////////////////////////////// // Implementations for 'io_error' std::string format_io_msg(const std::string& message, int error_number) { if (error_number) { std::stringstream stream; stream << message << " ('" << std::strerror(error_number) << "')"; return stream.str(); } else { return message; } } io_error::io_error(const std::string& message, int error_number) : std::ios_base::failure(format_io_msg(message, error_number)) { } /////////////////////////////////////////////////////////////////////////////// // Implementations for 'gzip_error' std::string format_gzip_msg(const std::string& message, const char* gzip_msg) { if (gzip_msg) { std::stringstream stream; stream << message << " ('" << gzip_msg << "')"; return stream.str(); } else { return message; } } gzip_error::gzip_error(const std::string& message, const char* gzip_msg) : io_error(format_gzip_msg(message, gzip_msg)) { } /////////////////////////////////////////////////////////////////////////////// // Implementations for 'gzip_error' bzip2_error::bzip2_error(const std::string& message) : io_error(message) { } /////////////////////////////////////////////////////////////////////////////// // Implementations for 'line_reader' line_reader::line_reader(const std::string& fpath) : m_file(managed_writer::fopen(fpath, "rb")) , m_gzip_stream(nullptr) , m_bzip2_stream(nullptr) , m_buffer(nullptr) , m_buffer_ptr(nullptr) , m_buffer_end(nullptr) , m_raw_buffer(new char[BUF_SIZE]) , m_raw_buffer_end(m_raw_buffer + BUF_SIZE) , m_eof(false) { if (!m_file) { throw io_error("line_reader::open: failed to open file", errno); } } line_reader::~line_reader() { try { close_buffers_gzip(); close_buffers_bzip2(); delete[] m_raw_buffer; m_raw_buffer = nullptr; if (fclose(m_file)) { throw io_error("line_reader::close: error closing file", errno); } } catch (const std::exception& error) { print_locker lock; std::cerr << "Error closing file: " << error.what() << std::endl; std::exit(1); } } bool line_reader::getline(std::string& dst) { dst.clear(); while (m_file && !m_eof) { const char* start = m_buffer_ptr; char* end = m_buffer_ptr; for (; end != m_buffer_end; ++end) { if (*end == '\n') { // Excluding terminal \n dst.append(start, end - start); if (!dst.empty() && dst.back() == '\r') { // Excluding terminal \r; dst is examined, since the \r may // have been added separately, if the \r was the last // character in the previous buffer fill (see below). dst.pop_back(); } m_buffer_ptr = end + 1; return true; } } // Can potentially introduce a \r; this is handled above. dst.append(start, end - start); refill_buffers(); } return !dst.empty(); } void line_reader::refill_buffers() { if (m_buffer) { if (m_gzip_stream) { refill_buffers_gzip(); } else if (m_bzip2_stream) { refill_buffers_bzip2(); } else { refill_raw_buffer(); refill_buffers_uncompressed(); } } else { refill_raw_buffer(); if (identify_gzip()) { initialize_buffers_gzip(); } else if (identify_bzip2()) { initialize_buffers_bzip2(); } else { refill_buffers_uncompressed(); } } } void line_reader::refill_buffers_uncompressed() { m_buffer = m_raw_buffer; m_buffer_ptr = m_raw_buffer; m_buffer_end = m_raw_buffer_end; } void line_reader::refill_raw_buffer() { const int nread = fread(m_raw_buffer, 1, BUF_SIZE, m_file); if (nread == BUF_SIZE) { m_raw_buffer_end = m_raw_buffer + BUF_SIZE; } else if (ferror(m_file)) { throw io_error("line_reader::refill_buffer: error reading file", errno); } else { // EOF set only once all data has been consumed m_eof = (nread == 0); m_raw_buffer_end = m_raw_buffer + nread; } } bool line_reader::identify_gzip() const { if (m_raw_buffer_end - m_raw_buffer < 2) { return false; } else if (m_raw_buffer[0] != '\x1f' || m_raw_buffer[1] != '\x8b') { return false; } return true; } void line_reader::initialize_buffers_gzip() { m_buffer = new char[BUF_SIZE]; m_buffer_ptr = m_buffer + BUF_SIZE; m_buffer_end = m_buffer + BUF_SIZE; m_gzip_stream = new z_stream(); m_gzip_stream->zalloc = nullptr; m_gzip_stream->zfree = nullptr; m_gzip_stream->opaque = nullptr; m_gzip_stream->avail_in = m_raw_buffer_end - m_raw_buffer; m_gzip_stream->next_in = reinterpret_cast(m_raw_buffer); switch (inflateInit2(m_gzip_stream, 15 + 16)) { case Z_OK: break; case Z_MEM_ERROR: throw gzip_error("line_reader::initialize_buffers_gzip: insufficient memory", m_gzip_stream ? m_gzip_stream->msg : nullptr); case Z_VERSION_ERROR: throw gzip_error("line_reader::initialize_buffers_gzip: incompatible zlib version", m_gzip_stream ? m_gzip_stream->msg : nullptr); case Z_STREAM_ERROR: throw gzip_error("line_reader::initialize_buffers_gzip: invalid parameters", m_gzip_stream ? m_gzip_stream->msg : nullptr); default: throw gzip_error("line_reader::initialize_buffers_gzip: unknown error", m_gzip_stream ? m_gzip_stream->msg : nullptr); } } void line_reader::refill_buffers_gzip() { if (!m_gzip_stream->avail_in) { refill_raw_buffer(); m_gzip_stream->avail_in = m_raw_buffer_end - m_raw_buffer; m_gzip_stream->next_in = reinterpret_cast(m_raw_buffer); } m_gzip_stream->avail_out = BUF_SIZE; m_gzip_stream->next_out = reinterpret_cast(m_buffer); switch (inflate(m_gzip_stream, Z_NO_FLUSH)) { case Z_OK: case Z_BUF_ERROR: /* input buffer empty or output buffer full */ break; case Z_STREAM_END: // Handle concatenated streams; causes unnecessary reset at EOF if (inflateReset(m_gzip_stream) != Z_OK) { throw gzip_error("line_reader::refill_buffers_gzip: failed to reset stream", m_gzip_stream ? m_gzip_stream->msg : nullptr); } break; case Z_STREAM_ERROR: throw gzip_error("line_reader::refill_buffers_gzip: inconsistent stream state", m_gzip_stream ? m_gzip_stream->msg : nullptr); default: throw gzip_error("line_reader::refill_buffers_gzip: unknown error", m_gzip_stream ? m_gzip_stream->msg : nullptr); } m_buffer_ptr = m_buffer; m_buffer_end = m_buffer + (BUF_SIZE - m_gzip_stream->avail_out); } void line_reader::close_buffers_gzip() { if (m_gzip_stream) { switch (inflateEnd(m_gzip_stream)) { case Z_OK: break; case Z_STREAM_ERROR: throw gzip_error("line_reader::close: stream error", m_gzip_stream ? m_gzip_stream->msg : nullptr); default: throw gzip_error("Unknown error in line_reader::close", m_gzip_stream ? m_gzip_stream->msg : nullptr); } delete m_gzip_stream; m_gzip_stream = nullptr; delete[] m_buffer; m_buffer = nullptr; } } void bzip2_initialize_stream(bz_stream* stream) { switch (BZ2_bzDecompressInit(stream, /* verbosity */ 0, /* small */ 0)) { case BZ_OK: break; case BZ_CONFIG_ERROR: throw bzip2_error("bzip2_initialize_buffer: " "bzip2 library is miscompiled"); case BZ_PARAM_ERROR: throw bzip2_error("bzip2_initialize_buffer: " "invalid parameters during initialization"); case BZ_MEM_ERROR: throw bzip2_error("bzip2_initialize_buffer: " "insufficient memory to initialize"); case BZ_SEQUENCE_ERROR: throw bzip2_error("bzip2_initialize_buffer: bzip2 sequence error"); default: throw bzip2_error("bzip2_initialize_buffer: unknown error"); } } void bzip2_close_stream(bz_stream* stream) { switch (BZ2_bzDecompressEnd(stream)) { case BZ_OK: break; case BZ_PARAM_ERROR: throw bzip2_error("bzip2_close_stream: invalid parameters"); case BZ_SEQUENCE_ERROR: throw bzip2_error("bzip2_close_stream: bzip2 sequence error"); default: throw bzip2_error("bzip2_close_stream: unknown bzip2 error"); } } bool line_reader::identify_bzip2() const { if (m_raw_buffer_end - m_raw_buffer < 4) { return false; } else if (m_raw_buffer[0] != 'B' || m_raw_buffer[1] != 'Z') { // Fixed magic header "BZ" return false; } else if (m_raw_buffer[2] != 'h' && m_raw_buffer[2] != '0') { // bzip2 or bzip1 (deprecated) return false; } else if (m_raw_buffer[3] < '1' || m_raw_buffer[3] > '9') { // Blocksizes; '1' - '9' return false; } return true; } void line_reader::initialize_buffers_bzip2() { m_buffer = new char[BUF_SIZE]; m_buffer_ptr = m_buffer + BUF_SIZE; m_buffer_end = m_buffer + BUF_SIZE; m_bzip2_stream = new bz_stream(); m_bzip2_stream->bzalloc = nullptr; m_bzip2_stream->bzfree = nullptr; m_bzip2_stream->opaque = nullptr; m_bzip2_stream->avail_in = m_raw_buffer_end - m_raw_buffer; m_bzip2_stream->next_in = m_raw_buffer; bzip2_initialize_stream(m_bzip2_stream); } void line_reader::refill_buffers_bzip2() { if (!m_bzip2_stream->avail_in) { refill_raw_buffer(); m_bzip2_stream->avail_in = m_raw_buffer_end - m_raw_buffer; m_bzip2_stream->next_in = m_raw_buffer; } m_bzip2_stream->avail_out = BUF_SIZE; m_bzip2_stream->next_out = m_buffer; if (m_bzip2_stream->avail_in) { switch (BZ2_bzDecompress(m_bzip2_stream)) { case BZ_OK: break; case BZ_STREAM_END: // Close an restart stream, to handle concatenated files bzip2_close_stream(m_bzip2_stream); bzip2_initialize_stream(m_bzip2_stream); break; case BZ_PARAM_ERROR: throw bzip2_error("line_reader::refill_buffers_bzip2: " "inconsistent bzip2 parameters"); case BZ_DATA_ERROR: case BZ_DATA_ERROR_MAGIC: throw bzip2_error("line_reader::refill_buffers_bzip2: " "malformed bzip2 file"); case BZ_MEM_ERROR: throw bzip2_error("line_reader::refill_buffers_bzip2: " "insufficient memory to deflate bzip2 stream"); case BZ_SEQUENCE_ERROR: throw bzip2_error("line_reader::refill_buffers_bzip2: " "bzip2 sequence error"); default: throw bzip2_error("line_reader::refill_buffers_bzip2: " "unknown bzip2 error"); } } m_buffer_ptr = m_buffer; m_buffer_end = m_buffer + (BUF_SIZE - m_bzip2_stream->avail_out); } void line_reader::close_buffers_bzip2() { if (m_bzip2_stream) { bzip2_close_stream(m_bzip2_stream); delete m_bzip2_stream; m_bzip2_stream = nullptr; delete[] m_buffer; m_buffer = nullptr; } } } // namespace ar adapterremoval-2.3.1/src/linereader.hpp000066400000000000000000000124601350370616400201450ustar00rootroot00000000000000/*************************************************************************\ * AdapterRemoval - cleaning next-generation sequencing reads * * * * Copyright (C) 2015 by Mikkel Schubert - mikkelsch@gmail.com * * * * If you use the program, please cite the paper: * * S. Lindgreen (2012): AdapterRemoval: Easy Cleaning of Next Generation * * Sequencing Reads, BMC Research Notes, 5:337 * * http://www.biomedcentral.com/1756-0500/5/337/ * * * * This program is free software: you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation, either version 3 of the License, or * * (at your option) any later version. * * * * This program is distributed in the hope that it will be useful, * * but WITHOUT ANY WARRANTY; without even the implied warranty of * * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * * GNU General Public License for more details. * * * * You should have received a copy of the GNU General Public License * * along with this program. If not, see . * \*************************************************************************/ #ifndef GZFILE_H #define GZFILE_H #include #include #include #include #include namespace ar { /** Represents errors during basic IO. */ class io_error : public std::ios_base::failure { public: io_error(const std::string& message, int error_number = 0); }; /** Represents errors during GZip (de)compression. */ class gzip_error : public io_error { public: gzip_error(const std::string& message, const char* gzip_msg = nullptr); }; /** Represents errors during BZip2 (de)compression. */ class bzip2_error : public io_error { public: bzip2_error(const std::string& message); }; /** Base-class for line reading; used by receivers. */ class line_reader_base { public: /** Does nothing. */ line_reader_base(); /** Closes the file, if still open. */ virtual ~line_reader_base(); /** Reads a lien into dst, returning false on EOF. */ virtual bool getline(std::string& dst) = 0; }; /** * Simple line reader. * * Currently reads * - uncompressed files * - gzip compressed files * - bzip2 compressed files * * Errors are reported using either 'io_error' or 'gzip_error'. */ class line_reader : public line_reader_base { public: /** Constructor; opens file and throws on errors. */ line_reader(const std::string& fpath); /** Closes the file, if still open. */ ~line_reader(); /** Reads a lien into dst, returning false on EOF. */ bool getline(std::string& dst); //! Copy construction not supported line_reader(const line_reader&) = delete; //! Assignment not supported line_reader& operator=(const line_reader&) = delete; private: //! Refills 'm_buffer' and sets 'm_buffer_ptr' and 'm_buffer_end'. void refill_buffers(); //! Raw file used to read input. FILE* m_file; /** Refills 'm_raw_buffer'; sets 'm_raw_buffer_ptr' and 'm_raw_buffer_end'. */ void refill_raw_buffer(); /** Points 'm_buffer' and other points to corresponding 'm_raw_buffer's. */ void refill_buffers_uncompressed(); //! GZip stream pointer; used if input it detected to be gzip compressed. z_stream* m_gzip_stream; /** Returns true if the raw buffer contains gzip'd data. */ bool identify_gzip() const; /** Initializes gzip stream and output buffers. */ void initialize_buffers_gzip(); /** Refills 'm_buffer' from compressed data; may refill raw buffers. */ void refill_buffers_gzip(); /** Closes gzip buffers and frees associated memory. */ void close_buffers_gzip(); //! GZip stream pointer; used if input it detected to be gzip compressed. bz_stream* m_bzip2_stream; /** Returns true if the raw buffer contains bzip2'd data. */ bool identify_bzip2() const; /** Initializes bzip2 stream and output buffers. */ void initialize_buffers_bzip2(); /** Refills 'm_buffer' from compressed data; may refill raw buffers. */ void refill_buffers_bzip2(); /** Closes gzip2 buffers and frees associated memory. */ void close_buffers_bzip2(); //! Pointer to buffer of decompressed data. char* m_buffer; //! Pointer to current location in input buffer. char* m_buffer_ptr; //! Pointer to end of current buffer. char* m_buffer_end; //! Pointer to buffer of raw data. char* m_raw_buffer; //! Pointer to end of current raw buffer. char* m_raw_buffer_end; //! Indicates if a read across the EOF has been attempted. bool m_eof; }; /////////////////////////////////////////////////////////////////////////////// inline line_reader_base::line_reader_base() { } inline line_reader_base::~line_reader_base() { } } // namespace ar #endif adapterremoval-2.3.1/src/linereader_joined.cpp000066400000000000000000000055431350370616400214740ustar00rootroot00000000000000/*************************************************************************\ * AdapterRemoval - cleaning next-generation sequencing reads * * * * Copyright (C) 2015 by Mikkel Schubert - mikkelsch@gmail.com * * * * If you use the program, please cite the paper: * * S. Lindgreen (2012): AdapterRemoval: Easy Cleaning of Next Generation * * Sequencing Reads, BMC Research Notes, 5:337 * * http://www.biomedcentral.com/1756-0500/5/337/ * * * * This program is free software: you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation, either version 3 of the License, or * * (at your option) any later version. * * * * This program is distributed in the hope that it will be useful, * * but WITHOUT ANY WARRANTY; without even the implied warranty of * * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * * GNU General Public License for more details. * * * * You should have received a copy of the GNU General Public License * * along with this program. If not, see . * \*************************************************************************/ #include #include #include #include #include #include #include #include "debug.hpp" #include "linereader_joined.hpp" #include "threads.hpp" namespace ar { joined_line_readers::joined_line_readers(const string_vec& filenames) : m_filenames(filenames.rbegin(), filenames.rend()) , m_reader() , m_current_line(1) { } joined_line_readers::~joined_line_readers() { } bool joined_line_readers::getline(std::string& dst) { dst.clear(); while (dst.empty()) { if (m_reader && m_reader->getline(dst)) { m_current_line++; break; } else if (!open_next_file()) { break; } } return !dst.empty(); } bool joined_line_readers::open_next_file() { if (m_filenames.empty()) { return false; } auto filename = m_filenames.back(); { print_locker lock; std::cerr << "Opening FASTQ file '" << filename << "', line numbers start at " << m_current_line << std::endl; } m_reader.reset(new line_reader(filename)); m_filenames.pop_back(); return true; } } adapterremoval-2.3.1/src/linereader_joined.hpp000066400000000000000000000063551350370616400215030ustar00rootroot00000000000000/*************************************************************************\ * AdapterRemoval - cleaning next-generation sequencing reads * * * * Copyright (C) 2017 by Mikkel Schubert - mikkelsch@gmail.com * * * * If you use the program, please cite the paper: * * S. Lindgreen (2012): AdapterRemoval: Easy Cleaning of Next Generation * * Sequencing Reads, BMC Research Notes, 5:337 * * http://www.biomedcentral.com/1756-0500/5/337/ * * * * This program is free software: you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation, either version 3 of the License, or * * (at your option) any later version. * * * * This program is distributed in the hope that it will be useful, * * but WITHOUT ANY WARRANTY; without even the implied warranty of * * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * * GNU General Public License for more details. * * * * You should have received a copy of the GNU General Public License * * along with this program. If not, see . * \*************************************************************************/ #ifndef LINEREADER_JOINED_H #define LINEREADER_JOINED_H #include #include "commontypes.hpp" #include "linereader.hpp" namespace ar { /** * Multi-file line-reader * * Wrapper around line_reader that automatically reads through one or more * files, returning the content as a contiguous stream of lines. No assumptions * are made about the format of the individual files. */ class joined_line_readers : public line_reader_base { public: /** Creates line-reader over multiple files in the specified order. */ joined_line_readers(const string_vec& filenames); /** Closes any still open files. */ ~joined_line_readers(); /** * Reads a line from the currently open file; if EOF is encountered, the * currently open file is closed and the next file is opened. Returns true * if a line was successfully read, or false if no files remain. */ bool getline(std::string& dst); //! Copy construction not supported joined_line_readers(const joined_line_readers&) = delete; //! Assignment not supported joined_line_readers& operator=(const joined_line_readers&) = delete; private: /** * Open the next file, removes it from the queue, and returns true; returns * false if no files remain to be processed. */ bool open_next_file(); //! Files left to read; stored in reverse order. string_vec m_filenames; //! Currently open file, if any. std::unique_ptr m_reader; //! Current line across all files. size_t m_current_line; }; } // namespace ar #endif adapterremoval-2.3.1/src/main.cpp000066400000000000000000000066711350370616400167610ustar00rootroot00000000000000/*************************************************************************\ * AdapterRemoval - cleaning next-generation sequencing reads * * * * Copyright (C) 2011 by Stinus Lindgreen - stinus@binf.ku.dk * * Copyright (C) 2014 by Mikkel Schubert - mikkelsch@gmail.com * * * * If you use the program, please cite the paper: * * S. Lindgreen (2012): AdapterRemoval: Easy Cleaning of Next Generation * * Sequencing Reads, BMC Research Notes, 5:337 * * http://www.biomedcentral.com/1756-0500/5/337/ * * * * This program is free software: you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation, either version 3 of the License, or * * (at your option) any later version. * * * * This program is distributed in the hope that it will be useful, * * but WITHOUT ANY WARRANTY; without even the implied warranty of * * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * * GNU General Public License for more details. * * * * You should have received a copy of the GNU General Public License * * along with this program. If not, see . * \*************************************************************************/ #include #include "debug.hpp" #include "main.hpp" #include "userconfig.hpp" namespace ar { // See main_adapter_rm.cpp int remove_adapter_sequences(const userconfig& config); // See main_adapter_id.cpp int identify_adapter_sequences(const userconfig& config); // See main_demultiplex.cpp int demultiplex_sequences(const userconfig& config); } // namespace ar int main(int argc, char *argv[]) { using namespace ar; std::ios_base::sync_with_stdio(false); userconfig config(NAME, VERSION, HELPTEXT); switch (config.parse_args(argc, argv)) { case argparse::parse_result::error: { return 1; } case argparse::parse_result::exit: { // --version, --help, or similar used. return 0; } default: { // Ok } } auto returncode = 0; switch (config.run_type) { case ar_command::trim_adapters: { returncode = remove_adapter_sequences(config); break; } case ar_command::demultiplex_sequences: { returncode = demultiplex_sequences(config); break; } case ar_command::identify_adapters: { return identify_adapter_sequences(config); } default: { std::cerr << "ERROR: Unknown run-type: " << static_cast(config.run_type) << std::endl; return 1; } } if (returncode) { std::cerr << "ERROR: AdapterRemoval did not run to completion;\n" << " do NOT make use of resulting trimmed reads!" << std::endl; } return returncode; } adapterremoval-2.3.1/src/main.hpp000066400000000000000000000052721350370616400167620ustar00rootroot00000000000000/*************************************************************************\ * AdapterRemoval - cleaning next-generation sequencing reads * * * * Copyright (C) 2011 by Stinus Lindgreen - stinus@binf.ku.dk * * Copyright (C) 2014 by Mikkel Schubert - mikkelsch@gmail.com * * * * If you use the program, please cite the paper: * * S. Lindgreen (2012): AdapterRemoval: Easy Cleaning of Next Generation * * Sequencing Reads, BMC Research Notes, 5:337 * * http://www.biomedcentral.com/1756-0500/5/337/ * * * * This program is free software: you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation, either version 3 of the License, or * * (at your option) any later version. * * * * This program is distributed in the hope that it will be useful, * * but WITHOUT ANY WARRANTY; without even the implied warranty of * * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * * GNU General Public License for more details. * * * * You should have received a copy of the GNU General Public License * * along with this program. If not, see . * \*************************************************************************/ #ifndef MAIN_H #define MAIN_H #include namespace ar { const std::string NAME = "AdapterRemoval"; const std::string VERSION = "ver. 2.3.0"; const std::string HELPTEXT = \ "This program searches for and removes remnant adapter sequences from\n" "your read data. The program can analyze both single end and paired end\n" "data. For detailed explanation of the parameters, please refer to the\n" "man page. For comments, suggestions and feedback please contact Stinus\n" "Lindgreen (stinus@binf.ku.dk) and Mikkel Schubert (MikkelSch@gmail.com).\n" "\n" "If you use the program, please cite the paper:\n" " Schubert, Lindgreen, and Orlando (2016). AdapterRemoval v2: rapid\n" " adapter trimming, identification, and read merging.\n" " BMC Research Notes, 12;9(1):88.\n\n" " http://bmcresnotes.biomedcentral.com/articles/10.1186/s13104-016-1900-2\n"; } // namespace ar #endif adapterremoval-2.3.1/src/main_adapter_id.cpp000066400000000000000000000402431350370616400211260ustar00rootroot00000000000000/*************************************************************************\ * AdapterRemoval - cleaning next-generation sequencing reads * * * * Copyright (C) 2015 by Mikkel Schubert - mikkelsch@gmail.com * * * * If you use the program, please cite the paper: * * S. Lindgreen (2012): AdapterRemoval: Easy Cleaning of Next Generation * * Sequencing Reads, BMC Research Notes, 5:337 * * http://www.biomedcentral.com/1756-0500/5/337/ * * * * This program is free software: you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation, either version 3 of the License, or * * (at your option) any later version. * * * * This program is distributed in the hope that it will be useful, * * but WITHOUT ANY WARRANTY; without even the implied warranty of * * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * * GNU General Public License for more details. * * * * You should have received a copy of the GNU General Public License * * along with this program. If not, see . * \*************************************************************************/ #include #include #include #include #include #include #include #include #include "alignment.hpp" #include "debug.hpp" #include "fastq_io.hpp" #include "scheduler.hpp" #include "strutils.hpp" #include "timer.hpp" #include "userconfig.hpp" namespace ar { /////////////////////////////////////////////////////////////////////////////// // KMer related functions and constants //! Length of kmers to collect to find common kmers const size_t KMER_LENGTH = 9; //! Size of vector needed for kmer counts const size_t N_KMERS = 2 << (2 * KMER_LENGTH); //! The N most common kmers to print const size_t TOP_N_KMERS = 5; /** * Hashing function for string consisting of the chars "ACGT" (uppercase only). * Will return a unique number in the range 0 to 4^N - 1 for a given nucleotide * sequence. Passing characters other than "ACGT" (uppercase only) will result * in hash collisions. */ inline size_t kmer_to_size_t(const std::string& kmer) { size_t index = 0; for (size_t i = 0; i < kmer.length(); ++i) { index = (index << 2) | ACGT_TO_IDX(kmer.at(i)); } return index; } /** Translates a hash generated using kmer_to_size_t into a NT sequence. */ inline std::string size_t_to_kmer(size_t kmer) { std::string kmer_s(KMER_LENGTH, 'N'); for (size_t i = 1; i <= KMER_LENGTH; ++i) { kmer_s.at(KMER_LENGTH - i) = "ACTG"[kmer & 0x3]; kmer = kmer >> 2; } return kmer_s; } /** Simple structure for counting the frequency of A, C, G, and Ts. */ struct nt_counts { nt_counts() : counts(4, 0) { } /** Increment count of a nucleotide A, C, G, or T (uppercase only). */ void increment(char nt) { if (nt != 'N') { ++counts.at(ACGT_TO_IDX(nt)); } } /** Merge count objects. */ nt_counts& operator+=(const nt_counts& other) { merge_vectors(counts, other.counts); return *this; } //! Fixed sized vector (4) std::vector counts; }; typedef std::vector nt_count_vec; typedef std::vector kmer_map; typedef std::pair nt_count; /** Functor for sorting kmers by frequency. */ struct cmp_nt_count { bool operator()(const nt_count& a, const nt_count& b) const { return (a.second > b.second); } }; typedef std::priority_queue, cmp_nt_count> kmer_queue; typedef std::vector kmer_vector; /** Prints the N top kmers in a kmer_map, including sequence and frequency. */ void print_most_common_kmers(const kmer_map& kmers, size_t print_n = TOP_N_KMERS) { size_t total = 0; kmer_queue queue; for (size_t i = 0; i < kmers.size(); ++i) { nt_count value(i, kmers.at(i)); total += value.second; if (queue.size() >= print_n) { // The top value will be the currently lowest value in the queue if (queue.top().second < value.second) { queue.pop(); queue.push(value); } } else if (value.second) { queue.push(value); } } kmer_vector top_n_kmers; while (!queue.empty()) { top_n_kmers.push_back(queue.top()); queue.pop(); } std::cout.precision(2); std::cout << std::fixed; std::cout << " Top 5 most common " << KMER_LENGTH << "-bp 5'-kmers:\n"; std::reverse(top_n_kmers.begin(), top_n_kmers.end()); for (size_t i = 0; i < top_n_kmers.size(); ++i) { const nt_count& count = top_n_kmers.at(i); std::string kmer_s = size_t_to_kmer(count.first); std::cout << std::string(12, ' '); std::cout << i + 1<< ": " << kmer_s << " = " << std::right << std::setw(5) << (100.0 * count.second) / total << "% (" << count.second << ")" << "\n"; } } /////////////////////////////////////////////////////////////////////////////// // Consensus adapter related functions and constants /** * Build representation of identity between an adapter and a consensus sequence. * * The resulting string represents N with wildcards ('*'), matching bases with * pipes ('|') and mismatches with spaces (' '). Only overlapping bases are * compared. */ std::string compare_consensus_with_ref(const std::string& ref, const std::string& consensus) { std::stringstream identity; for (size_t i = 0, size = std::min(consensus.size(), ref.size()); i < size; ++i) { if (ref.at(i) == 'N' || consensus.at(i) == 'N') { identity << '*'; } else { identity << (ref.at(i) == consensus.at(i) ? '|' : ' '); } } return identity.str(); } /** * Takes a nt_counts object, and returns a pair containing the majority nt and * the Phred encoded quality score of the consensus, defined as the proportion * of the bases which match the majority nucleotide (p = m / (N + 1)). If no * majority nucleotide can be found, 'N' is returned instead. */ std::pair get_consensus_nt(const nt_counts& nts) { // Always assume one non-consensus observation; this is more reasonable // than allowing an error-rate of 0, especially for few observations. size_t total_count = 1; char best_nt_i = -1; size_t best_count = 0; for (char nt_i = 0; nt_i < 4; ++nt_i) { const size_t cur_count = nts.counts.at(nt_i); total_count += cur_count; if (cur_count > best_count) { best_nt_i = nt_i; best_count = cur_count; } else if (cur_count == best_count) { best_nt_i = -1; } } const double pvalue = 1.0 - best_count / static_cast(total_count); const char phred = fastq::p_to_phred_33(pvalue); const char best_nt = (best_nt_i == -1) ? 'N' : IDX_TO_ACGT(best_nt_i); return std::pair(best_nt, phred); } /** * Prints description of consensus adapter sequence. * * @param counts Observed nucleotide frequencies. * @param kmers Observed kmer frequencies. * @param name Argument name for adapter (--adapter1 / adapter2) * @param ref Default sequence for the inferred adapter */ void print_consensus_adapter(const nt_count_vec& counts, const kmer_map& kmers, const std::string& name, const std::string& ref) { std::stringstream sequence; std::stringstream qualities; for(nt_count_vec::const_iterator it = counts.begin(); it != counts.end(); ++it) { const std::pair consensus = get_consensus_nt(*it); sequence << consensus.first; qualities << consensus.second; } const std::string consensus = sequence.str(); const std::string identity = compare_consensus_with_ref(ref, consensus); std::cout << " " << name << ": " << ref << "\n" << " " << identity << "\n" << " Consensus: " << consensus << "\n" << " Quality: " << qualities.str() << "\n\n"; print_most_common_kmers(kmers); } /////////////////////////////////////////////////////////////////////////////// // /** Struct for collecting adapter fragments, kmer frequencies, and read stats. */ struct adapter_stats { public: adapter_stats(const userconfig& config) : pcr1_counts() , pcr2_counts() , pcr1_kmers(N_KMERS, 0) , pcr2_kmers(N_KMERS, 0) , stats(config.create_stats()) { } /** Merge overall statistics, consensus, and k-mer counts. */ adapter_stats& operator+=(const adapter_stats& other) { *stats += *other.stats; merge_vectors(pcr1_counts, other.pcr1_counts); merge_vectors(pcr2_counts, other.pcr2_counts); merge_vectors(pcr1_kmers, other.pcr1_kmers); merge_vectors(pcr2_kmers, other.pcr2_kmers); return *this; } //! Nucleotide frequencies of putative adapter 1 fragments nt_count_vec pcr1_counts; //! Nucleotide frequencies of putative adapter 2 fragments nt_count_vec pcr2_counts; //! 5' KMer frequencies of putative adapter 1 fragments kmer_map pcr1_kmers; //! 5' KMer frequencies of putative adapter 2 fragments kmer_map pcr2_kmers; //! Statistics object for (number of) processed reads statistics_ptr stats; //! Copy construction not supported adapter_stats(const adapter_stats&) = delete; //! Assignment not supported adapter_stats& operator=(const adapter_stats&) = delete; }; /** Class for building (and merging) adapter_stats objects on demand. */ class adapter_sink : public statistics_sink { public: adapter_sink(const userconfig& config) : m_config(config) { } protected: virtual pointer new_sink() const { return pointer(new adapter_stats(m_config)); } virtual void reduce(pointer& dst, const pointer& src) const { (*dst) += (*src); } //! Copy construction not supported adapter_sink(const adapter_sink&) = delete; //! Assignment not supported adapter_sink& operator=(const adapter_sink&) = delete; private: const userconfig& m_config; }; /////////////////////////////////////////////////////////////////////////////// // Threaded adapter identification step class adapter_identification : public analytical_step { public: adapter_identification(const userconfig& config) : analytical_step(analytical_step::ordering::unordered) , m_config(config) , m_timer("reads") , m_sinks(config) { } chunk_vec process(analytical_chunk* chunk) { if (!chunk) { throw std::invalid_argument("sink received nullptr chunk"); } const fastq empty_adapter("dummy", "", ""); fastq_pair_vec adapters; adapters.push_back(fastq_pair(empty_adapter, empty_adapter)); read_chunk_ptr file_chunk(dynamic_cast(chunk)); adapter_sink::pointer sink = m_sinks.get_sink(); statistics& stats = *sink->stats; AR_DEBUG_ASSERT(file_chunk->reads_1.size() == file_chunk->reads_2.size()); fastq_vec::iterator read_1 = file_chunk->reads_1.begin(); fastq_vec::iterator read_2 = file_chunk->reads_2.begin(); while (read_1 != file_chunk->reads_1.end()) { process_reads(adapters, stats, *sink, *read_1++, *read_2++); } m_sinks.return_sink(std::move(sink)); m_timer.increment(file_chunk->reads_1.size() * 2); return chunk_vec(); } /** Prints summary of inferred consensus sequences. */ void finalize() { m_timer.finalize(); std::unique_ptr sink(m_sinks.finalize()); std::cout << " Found " << sink->stats->well_aligned_reads << " overlapping pairs ...\n" << " Of which " << sink->stats->number_of_reads_with_adapter.at(0) << " contained adapter sequence(s) ...\n\n" << "Printing adapter sequences, including poly-A tails:" << std::endl; print_consensus_adapter(sink->pcr1_counts, sink->pcr1_kmers, "--adapter1", m_config.adapters.get_raw_adapters().front().first.sequence()); std::cout << "\n\n"; fastq adapter2 = m_config.adapters.get_raw_adapters().front().second; adapter2.reverse_complement(); print_consensus_adapter(sink->pcr2_counts, sink->pcr2_kmers, "--adapter2", adapter2.sequence()); } private: void process_reads(const fastq_pair_vec& adapters, statistics& stats, adapter_stats& sink, fastq& read1, fastq& read2) { // Throws if read-names or mate numbering does not match fastq::validate_paired_reads(read1, read2, m_config.mate_separator); // Reverse complement to match the orientation of read1 read2.reverse_complement(); const alignment_info alignment = align_paired_ended_sequences(read1, read2, adapters, m_config.shift); if (m_config.is_good_alignment(alignment)) { stats.well_aligned_reads++; if (m_config.is_alignment_collapsible(alignment)) { if (extract_adapter_sequences(alignment, read1, read2)) { stats.number_of_reads_with_adapter.at(0)++; process_adapter(read1.sequence(), sink.pcr1_counts, sink.pcr1_kmers); read2.reverse_complement(); process_adapter(read2.sequence(), sink.pcr2_counts, sink.pcr2_kmers); } } } else { stats.unaligned_reads++; } } void process_adapter(const std::string& sequence, nt_count_vec& counts, kmer_map& kmers) { if (counts.size() < sequence.length()) { counts.resize(sequence.length()); } for (size_t i = 0; i < std::min(counts.size(), sequence.length()); ++i) { counts.at(i).increment(sequence.at(i)); } if (sequence.length() >= KMER_LENGTH) { const std::string kmer = sequence.substr(0, KMER_LENGTH); if (!std::count(kmer.begin(), kmer.end(), 'N')) { kmers.at(kmer_to_size_t(kmer)) += 1; } } } const userconfig& m_config; timer m_timer; adapter_sink m_sinks; }; int identify_adapter_sequences(const userconfig& config) { std::cout << "Attempting to identify adapter sequences ..." << std::endl; scheduler sch; try { if (config.interleaved_input) { sch.add_step(ai_read_fastq, "read_interleaved_fastq", new read_interleaved_fastq(config.quality_input_fmt.get(), config.input_files_1, ai_identify_adapters)); } else { sch.add_step(ai_read_fastq, "read_paired_fastq", new read_paired_fastq(config.quality_input_fmt.get(), config.input_files_1, config.input_files_2, ai_identify_adapters)); } } catch (const std::ios_base::failure& error) { std::cerr << "IO error opening file; aborting:\n" << cli_formatter::fmt(error.what()) << std::endl; return 1; } sch.add_step(ai_identify_adapters, "identify_adapters", new adapter_identification(config)); if (!sch.run(config.max_threads)) { return 1; } return 0; } } // namespace ar adapterremoval-2.3.1/src/main_adapter_rm.cpp000066400000000000000000001022461350370616400211520ustar00rootroot00000000000000/*************************************************************************\ * AdapterRemoval - cleaning next-generation sequencing reads * * * * Copyright (C) 2011 by Stinus Lindgreen - stinus@binf.ku.dk * * Copyright (C) 2014 by Mikkel Schubert - mikkelsch@gmail.com * * * * If you use the program, please cite the paper: * * S. Lindgreen (2012): AdapterRemoval: Easy Cleaning of Next Generation * * Sequencing Reads, BMC Research Notes, 5:337 * * http://www.biomedcentral.com/1756-0500/5/337/ * * * * This program is free software: you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation, either version 3 of the License, or * * (at your option) any later version. * * * * This program is distributed in the hope that it will be useful, * * but WITHOUT ANY WARRANTY; without even the implied warranty of * * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * * GNU General Public License for more details. * * * * You should have received a copy of the GNU General Public License * * along with this program. If not, see . * \*************************************************************************/ #include #include #include #include #include #include #include #include #include "alignment.hpp" #include "debug.hpp" #include "demultiplex.hpp" #include "fastq.hpp" #include "fastq_io.hpp" #include "main.hpp" #include "strutils.hpp" #include "trimmed_reads.hpp" #include "userconfig.hpp" namespace ar { typedef std::unique_ptr mt19937_ptr; std::ostream& operator<<(std::ostream& stream, const fastq::ntrimmed& ntrim) { stream << ntrim.first; if (ntrim.first != ntrim.second) { stream << " " << ntrim.second; } return stream; } void write_settings(const userconfig& config, std::ostream& output, int nth) { output << NAME << " " << VERSION << "\nTrimming of "; if (config.adapters.barcode_count()) { if (config.adapters.get_barcodes().front().second.length()) { output << "double-indexed "; } else { output << "single-indexed "; } } if (config.paired_ended_mode) { if (config.interleaved_input) { output << "interleaved "; } output << "paired-end reads\n"; } else { output << "single-end reads\n"; } if (config.adapters.barcode_count()) { output << "\n\n[Demultiplexing]" << "\nMaximum mismatches (total): " << config.barcode_mm; if (config.paired_ended_mode) { output << "\nMaximum mate 1 mismatches: " << config.barcode_mm_r1; output << "\nMaximum mate 2 mismatches: " << config.barcode_mm_r2; } output << "\n\n\n[Demultiplexing samples]" << "\nName\tBarcode_1\tBarcode_2\n"; const fastq_pair_vec barcodes = config.adapters.get_barcodes(); for (size_t idx = 0; idx < barcodes.size(); ++idx) { output << config.adapters.get_sample_name(idx); if (static_cast(idx) == nth) { output << "*"; } const fastq_pair& current = barcodes.at(idx); output << "\t" << current.first.sequence(); if (current.second.length()) { output << "\t" << current.second.sequence() << "\n"; } else { output << "\t*\n"; } } } output << "\n\n[Adapter sequences]"; if (nth == -1) { const fastq_pair_vec adapters = config.adapters.get_raw_adapters(); size_t adapter_id = 0; for (auto it = adapters.cbegin(); it != adapters.cend(); ++it, ++adapter_id) { output << "\nAdapter1[" << adapter_id + 1 << "]: " << it->first.sequence(); fastq adapter_2 = it->second; adapter_2.reverse_complement(); output << "\nAdapter2[" << adapter_id + 1 << "]: " << adapter_2.sequence() << "\n"; } } else { const string_pair_vec adapters = config.adapters.get_pretty_adapter_set(nth); size_t adapter_id = 0; for (auto it = adapters.cbegin(); it != adapters.cend(); ++it, ++adapter_id) { output << "\nAdapter1[" << adapter_id + 1 << "]: " << it->first; output << "\nAdapter2[" << adapter_id + 1 << "]: " << it->second << "\n"; } } output << "\n\n[Adapter trimming]"; if (config.max_threads > 1 || config.deterministic) { output << "\nRNG seed: NA"; } else { output << "\nRNG seed: " << config.seed; } output << "\nAlignment shift value: " << config.shift << "\nGlobal mismatch threshold: " << config.mismatch_threshold << "\nQuality format (input): " << config.quality_input_fmt->name() << "\nQuality score max (input): " << config.quality_input_fmt->max_score() << "\nQuality format (output): " << config.quality_output_fmt->name() << "\nQuality score max (output): " << config.quality_output_fmt->max_score() << "\nMate-number separator (input): '" << config.mate_separator << "'" << "\nTrimming 5p: " << config.trim_fixed_5p << "\nTrimming 3p: " << config.trim_fixed_3p << "\nTrimming Ns: " << ((config.trim_ambiguous_bases) ? "Yes" : "No") << "\nTrimming Phred scores <= " << config.low_quality_score << ": " << (config.trim_by_quality ? "Yes" : "No") << "\nTrimming using sliding windows: "; if (config.trim_window_length >= 1) { output << static_cast(config.trim_window_length); } else if (config.trim_window_length >= 0) { output << config.trim_window_length; } else { output << "No"; } output << "\nMinimum genomic length: " << config.min_genomic_length << "\nMaximum genomic length: " << config.max_genomic_length << "\nCollapse overlapping reads: " << ((config.collapse) ? "Yes" : "No") << "\nMinimum overlap (in case of collapse): " << config.min_alignment_length; if (!config.paired_ended_mode) { output << "\nMinimum adapter overlap: " << config.min_adapter_overlap; } } void write_trimming_settings(const userconfig& config, const statistics& stats, size_t nth, std::ostream& settings) { write_settings(config, settings, nth); const std::string reads_type = (config.paired_ended_mode ? "read pairs: " : "reads: "); settings << "\n\n\n[Trimming statistics]" << "\nTotal number of " << reads_type << stats.records << "\nNumber of unaligned " << reads_type << stats.unaligned_reads << "\nNumber of well aligned " << reads_type << stats.well_aligned_reads << "\nNumber of discarded mate 1 reads: " << stats.discard1 << "\nNumber of singleton mate 1 reads: " << stats.keep1; if (config.paired_ended_mode) { settings << "\nNumber of discarded mate 2 reads: " << stats.discard2 << "\nNumber of singleton mate 2 reads: " << stats.keep2; } for (size_t adapter_id = 0; adapter_id < stats.number_of_reads_with_adapter.size(); ++adapter_id) { const size_t count = stats.number_of_reads_with_adapter.at(adapter_id); // Value between 0 and stats.records for SE, and 0 and 2*stats.records // for N PE pairs. For PE reads, mate 1 and mate 2 reads being of // unequal length can cause uneven numbers. settings << "\nNumber of reads with adapters[" << adapter_id + 1 << "]: " << count; } if (config.collapse) { settings << "\nNumber of full-length collapsed pairs: " << stats.number_of_full_length_collapsed << "\nNumber of truncated collapsed pairs: " << stats.number_of_truncated_collapsed; } settings << "\nNumber of retained reads: " << stats.total_number_of_good_reads << "\nNumber of retained nucleotides: " << stats.total_number_of_nucleotides << "\nAverage length of retained reads: " << (stats.total_number_of_good_reads ? ( static_cast(stats.total_number_of_nucleotides) / stats.total_number_of_good_reads) : 0); settings << "\n\n\n[Length distribution]" << "\nLength\tMate1\t"; if (config.paired_ended_mode) { settings << "Mate2\tSingleton\t"; } if (config.collapse) { settings << "Collapsed\tCollapsedTruncated\t"; } settings << "Discarded\tAll\n"; for (size_t length = 0; length < stats.read_lengths.size(); ++length) { const std::vector& lengths = stats.read_lengths.at(length); const size_t total = std::accumulate(lengths.begin(), lengths.end(), 0); settings << length << '\t' << lengths.at(static_cast(read_type::mate_1)); if (config.paired_ended_mode) { settings << '\t' << lengths.at(static_cast(read_type::mate_2)) << '\t' << lengths.at(static_cast(read_type::singleton)); } if (config.collapse) { settings << '\t' << lengths.at(static_cast(read_type::collapsed)) << '\t' << lengths.at(static_cast(read_type::collapsed_truncated)); } settings << '\t' << lengths.at(static_cast(read_type::discarded)) << '\t' << total << '\n'; } settings.flush(); } //! Implemented in main_demultiplex.cpp void write_demultiplex_statistics(std::ofstream& output, const userconfig& config, const demultiplex_reads* step); bool write_demux_settings(const userconfig& config, const demultiplex_reads* step) { if (!step) { // Demultiplexing not enabled; nothing to do return true; } const std::string filename = config.get_output_filename("demux_stats"); try { std::ofstream output(filename.c_str(), std::ofstream::out); if (!output.is_open()) { std::string message = std::string("Failed to open file '") + filename + "': "; throw std::ofstream::failure(message + std::strerror(errno)); } output.exceptions(std::ofstream::failbit | std::ofstream::badbit); write_settings(config, output, -1); output << "\n"; write_demultiplex_statistics(output, config, step); } catch (const std::ios_base::failure& error) { std::cerr << "IO error writing demultiplexing statistics; aborting:\n" << cli_formatter::fmt(error.what()) << std::endl; return false; } return true; } /** Trims fixed numbers of bases from the 5' and/or 3' termini of reads. **/ void trim_read_termini_if_enabled(const userconfig& config, fastq& read, read_type type) { size_t trim_5p = 0; size_t trim_3p = 0; switch (type) { case read_type::mate_1: trim_5p = config.trim_fixed_5p.first; trim_3p = config.trim_fixed_3p.first; break; case read_type::mate_2: trim_5p = config.trim_fixed_5p.second; trim_3p = config.trim_fixed_3p.second; break; case read_type::collapsed: if (config.paired_ended_mode) { trim_5p = config.trim_fixed_5p.first; trim_3p = config.trim_fixed_5p.second; } else { trim_5p = config.trim_fixed_5p.first; trim_3p = config.trim_fixed_3p.first; } break; default: throw std::invalid_argument("Invalid read type in trim_read_termini_if_enabled"); } if (trim_5p || trim_3p) { if (trim_5p + trim_3p < read.length()) { read.truncate(trim_5p, read.length() - std::min(read.length(), trim_5p + trim_3p)); } else { read.truncate(0, 0); } } } /** Trims a read if enabled, returning the #bases removed from each end. */ fastq::ntrimmed trim_sequence_by_quality_if_enabled(const userconfig& config, fastq& read) { if (config.trim_window_length >= 0) { return read.trim_windowed_bases(config.trim_ambiguous_bases, config.low_quality_score, config.trim_window_length, config.preserve5p); } else if (config.trim_ambiguous_bases || config.trim_by_quality) { const char quality_score = config.trim_by_quality ? config.low_quality_score : -1; return read.trim_trailing_bases(config.trim_ambiguous_bases, quality_score, config.preserve5p); } return fastq::ntrimmed(); } void process_collapsed_read(const userconfig& config, statistics& stats, fastq& collapsed_read, fastq* mate_read, trimmed_reads& chunks) { trim_read_termini_if_enabled(config, collapsed_read, read_type::collapsed); fastq::ntrimmed trimmed; if (!config.preserve5p) { // A collapsed read essentially consists of two 5p termini, both // informative for PCR duplicate removal. trimmed = trim_sequence_by_quality_if_enabled(config, collapsed_read); } // If trimmed, the external coordinates are no longer reliable // for determining the size of the original template. const bool was_trimmed = trimmed.first || trimmed.second; collapsed_read.add_prefix_to_header(was_trimmed ? "MT_" : "M_"); if (mate_read) { mate_read->add_prefix_to_header(was_trimmed ? "MT_" : "M_"); } const size_t read_count = config.paired_ended_mode ? 2 : 1; if (config.is_acceptable_read(collapsed_read)) { stats.total_number_of_nucleotides += collapsed_read.length(); stats.total_number_of_good_reads++; stats.inc_length_count(was_trimmed ? read_type::collapsed_truncated : read_type::collapsed, collapsed_read.length()); if (was_trimmed) { chunks.add_collapsed_truncated_read(collapsed_read, read_status::passed, read_count); stats.number_of_truncated_collapsed++; } else { chunks.add_collapsed_read(collapsed_read, read_status::passed, read_count); stats.number_of_full_length_collapsed++; } } else { stats.discard1++; stats.discard2++; stats.inc_length_count(read_type::discarded, collapsed_read.length()); if (was_trimmed) { chunks.add_collapsed_truncated_read(collapsed_read, read_status::failed, read_count); } else { chunks.add_collapsed_read(collapsed_read, read_status::failed, read_count); } } } class reads_processor : public analytical_step { public: reads_processor(const userconfig& config, size_t nth) : analytical_step(analytical_step::ordering::unordered) , m_config(config) , m_adapters(config.adapters.get_adapter_set(nth)) , m_stats(config) , m_nth(nth) { } statistics_ptr get_final_statistics() { return m_stats.finalize(); } protected: class stats_sink : public statistics_sink { public: stats_sink(const userconfig& config) : m_config(config) { } protected: virtual pointer new_sink() const { return m_config.create_stats(); } virtual void reduce(pointer& dst, const pointer& src) const { (*dst) += (*src); } const userconfig& m_config; }; const userconfig& m_config; const fastq_pair_vec m_adapters; stats_sink m_stats; const size_t m_nth; }; class se_reads_processor : public reads_processor { public: se_reads_processor(const userconfig& config, size_t nth = 0) : reads_processor(config, nth) { } chunk_vec process(analytical_chunk* chunk) { const size_t offset = m_nth * ai_analyses_offset; read_chunk_ptr read_chunk(dynamic_cast(chunk)); trimmed_reads chunks(m_config, offset, read_chunk->eof); stats_sink::pointer stats = m_stats.get_sink(); for (auto& read : read_chunk->reads_1) { const alignment_info alignment = align_single_ended_sequence(read, m_adapters, m_config.shift); if (m_config.is_good_alignment(alignment)) { truncate_single_ended_sequence(alignment, read); stats->number_of_reads_with_adapter.at(alignment.adapter_id)++; stats->well_aligned_reads++; if (m_config.is_alignment_collapsible(alignment)) { process_collapsed_read(m_config, *stats, read, nullptr, chunks); continue; } } else { stats->unaligned_reads++; } trim_read_termini_if_enabled(m_config, read, read_type::mate_1); trim_sequence_by_quality_if_enabled(m_config, read); if (m_config.is_acceptable_read(read)) { stats->keep1++; stats->total_number_of_good_reads++; stats->total_number_of_nucleotides += read.length(); chunks.add_mate_1_read(read, read_status::passed); stats->inc_length_count(read_type::mate_1, read.length()); } else { stats->discard1++; stats->inc_length_count(read_type::discarded, read.length()); chunks.add_mate_1_read(read, read_status::failed); } } stats->records += read_chunk->reads_1.size(); m_stats.return_sink(std::move(stats)); return chunks.finalize(); } }; /** Class for building RNGs on demand. */ class rng_sink : public statistics_sink { public: rng_sink(unsigned seed) : m_seed(seed) { } protected: virtual pointer new_sink() const { return pointer(new std::mt19937(m_seed())); } virtual void reduce(pointer&, const pointer&) const { // Intentionally left empty } //! Copy construction not supported rng_sink(const rng_sink&) = delete; //! Assignment not supported rng_sink& operator=(const rng_sink&) = delete; private: mutable std::mt19937 m_seed; }; class pe_reads_processor : public reads_processor { public: pe_reads_processor(const userconfig& config, size_t nth) : reads_processor(config, nth) , m_rngs(config.seed) { } chunk_vec process(analytical_chunk* chunk) { const size_t offset = m_nth * ai_analyses_offset; const char mate_separator = m_config.combined_output ? '\0' : m_config.mate_separator; mt19937_ptr rng; if (!m_config.deterministic) { rng = m_rngs.get_sink(); } read_chunk_ptr read_chunk(dynamic_cast(chunk)); trimmed_reads chunks(m_config, offset, read_chunk->eof); statistics_ptr stats = m_stats.get_sink(); AR_DEBUG_ASSERT(read_chunk->reads_1.size() == read_chunk->reads_2.size()); auto it_1 = read_chunk->reads_1.begin(); auto it_2 = read_chunk->reads_2.begin(); while (it_1 != read_chunk->reads_1.end()) { fastq read_1 = *it_1++; fastq read_2 = *it_2++; // Throws if read-names or mate numbering does not match fastq::validate_paired_reads(read_1, read_2, m_config.mate_separator); // Reverse complement to match the orientation of read_1 read_2.reverse_complement(); const alignment_info alignment = align_paired_ended_sequences(read_1, read_2, m_adapters, m_config.shift); if (m_config.is_good_alignment(alignment)) { stats->well_aligned_reads++; const size_t n_adapters = truncate_paired_ended_sequences(alignment, read_1, read_2); stats->number_of_reads_with_adapter.at(alignment.adapter_id) += n_adapters; if (m_config.is_alignment_collapsible(alignment)) { fastq collapsed_read = collapse_paired_ended_sequences(alignment, read_1, read_2, rng.get(), mate_separator); process_collapsed_read(m_config, *stats, collapsed_read, // Make sure read_2 header is updated, if needed m_config.combined_output ? &read_2 : nullptr, chunks); if (m_config.combined_output) { // Dummy read with read-count of zero; both mates have // already been accounted for in process_collapsed_read chunks.add_mate_2_read(read_2, read_status::failed, 0); } continue; } } else { stats->unaligned_reads++; } // Reads were not aligned or collapsing is not enabled // Undo reverse complementation (post truncation of adapters) read_2.reverse_complement(); // Trim fixed number of bases from 5' and/or 3' termini trim_read_termini_if_enabled(m_config, read_1, read_type::mate_1); trim_read_termini_if_enabled(m_config, read_2, read_type::mate_2); // Sliding window trimming or single-base trimming trim_sequence_by_quality_if_enabled(m_config, read_1); trim_sequence_by_quality_if_enabled(m_config, read_2); // Are the reads good enough? Not too many Ns? const bool read_1_acceptable = m_config.is_acceptable_read(read_1); const bool read_2_acceptable = m_config.is_acceptable_read(read_2); stats->total_number_of_nucleotides += read_1_acceptable ? read_1.length() : 0u; stats->total_number_of_nucleotides += read_2_acceptable ? read_2.length() : 0u; stats->total_number_of_good_reads += read_1_acceptable; stats->total_number_of_good_reads += read_2_acceptable; const read_status state_1 = read_1_acceptable ? read_status::passed : read_status::failed; const read_status state_2 = read_2_acceptable ? read_status::passed : read_status::failed; if (read_1_acceptable && read_2_acceptable) { stats->inc_length_count(read_type::mate_1, read_1.length()); stats->inc_length_count(read_type::mate_2, read_2.length()); } else { // Count singleton reads stats->keep1 += read_1_acceptable && !read_2_acceptable; stats->keep2 += read_2_acceptable && !read_1_acceptable; stats->discard1 += !read_1_acceptable; stats->discard2 += !read_2_acceptable; stats->inc_length_count(read_1_acceptable ? read_type::singleton : read_type::discarded, read_1.length()); stats->inc_length_count(read_2_acceptable ? read_type::singleton : read_type::discarded, read_2.length()); } // Queue reads last, since this result in modifications to lengths chunks.add_pe_reads(read_1, state_1, read_2, state_2); } stats->records += read_chunk->reads_1.size(); m_stats.return_sink(std::move(stats)); m_rngs.return_sink(std::move(rng)); return chunks.finalize(); } private: rng_sink m_rngs; }; bool write_settings(const userconfig& config, const std::vector& processors) { for (size_t nth = 0; nth < processors.size(); ++nth) { const std::string filename = config.get_output_filename("--settings", nth); const statistics_ptr stats = processors.at(nth)->get_final_statistics(); try { std::ofstream output(filename.c_str(), std::ofstream::out); if (!output.is_open()) { std::string message = std::string("Failed to open file '") + filename + "': "; throw std::ofstream::failure(message + std::strerror(errno)); } output.exceptions(std::ofstream::failbit | std::ofstream::badbit); write_trimming_settings(config, *stats, nth, output); } catch (const std::ios_base::failure& error) { std::cerr << "IO error writing settings file; aborting:\n" << cli_formatter::fmt(error.what()) << std::endl; return false; } } return true; } void add_write_step(const userconfig& config, scheduler& sch, size_t offset, const std::string& name, analytical_step* step) { if (config.gzip) { sch.add_step(offset + ai_zip_offset, "write_gzip_" + name, step); sch.add_step(offset, "gzip_" + name, new gzip_fastq(config, offset + ai_zip_offset)); } else if (config.bzip2) { sch.add_step(offset + ai_zip_offset, "write_bzip2_" + name, step); sch.add_step(offset, "bzip2_" + name, new bzip2_fastq(config, offset + ai_zip_offset)); } else { sch.add_step(offset, "write_" + name, step); } } int remove_adapter_sequences_se(const userconfig& config) { std::cerr << "Trimming single ended reads ..." << std::endl; scheduler sch; std::vector processors; demultiplex_reads* demultiplexer = nullptr; try { if (config.adapters.barcode_count()) { // Step 1: Read input file sch.add_step(ai_read_fastq, "read_fastq", new read_single_fastq(config.quality_input_fmt.get(), config.input_files_1, ai_demultiplex)); // Step 2: Parse and demultiplex reads based on single or double indices sch.add_step(ai_demultiplex, "demultiplex_se", demultiplexer = new demultiplex_se_reads(&config)); add_write_step(config, sch, ai_write_unidentified_1, "unidentified", new write_fastq(config.get_output_filename("demux_unknown"))); } else { sch.add_step(ai_read_fastq, "read_fastq", new read_single_fastq(config.quality_input_fmt.get(), config.input_files_1, ai_analyses_offset)); } // Step 3 - N: Trim and write demultiplexed reads for (size_t nth = 0; nth < config.adapters.adapter_set_count(); ++nth) { const size_t offset = nth * ai_analyses_offset; const std::string& sample = config.adapters.get_sample_name(nth); processors.push_back(new se_reads_processor(config, nth)); sch.add_step(offset + ai_trim_se, "trim_se_" + sample, processors.back()); add_write_step(config, sch, offset + ai_write_mate_1, sample + "_fastq", new write_fastq(config.get_output_filename("--output1", nth))); if (!config.combined_output) { add_write_step(config, sch, offset + ai_write_discarded, sample + "_discarded", new write_fastq(config.get_output_filename("--discarded", nth))); if (config.collapse) { add_write_step(config, sch, offset + ai_write_collapsed, sample + "_collapsed", new write_fastq(config.get_output_filename("--outputcollapsed", nth))); if (!config.preserve5p) { add_write_step(config, sch, offset + ai_write_collapsed_truncated, sample + "_collapsed_truncated", new write_fastq(config.get_output_filename("--outputcollapsedtruncated", nth))); } } } } } catch (const std::ios_base::failure& error) { std::cerr << "IO error opening file; aborting:\n" << cli_formatter::fmt(error.what()) << std::endl; return 1; } if (!sch.run(config.max_threads)) { return 1; } else if (!write_settings(config, processors)) { return 1; } else if (!write_demux_settings(config, demultiplexer)) { return 1; } return 0; } int remove_adapter_sequences_pe(const userconfig& config) { std::cerr << "Trimming paired end reads ..." << std::endl; scheduler sch; std::vector processors; demultiplex_reads* demultiplexer = nullptr; try { // Step 1: Read input file const size_t next_step = config.adapters.barcode_count() ? ai_demultiplex : ai_analyses_offset; if (config.interleaved_input) { sch.add_step(ai_read_fastq, "read_interleaved_fastq", new read_interleaved_fastq(config.quality_input_fmt.get(), config.input_files_1, next_step)); } else { sch.add_step(ai_read_fastq, "read_paired_fastq", new read_paired_fastq(config.quality_input_fmt.get(), config.input_files_1, config.input_files_2, next_step)); } if (config.adapters.barcode_count()) { // Step 2: Parse and demultiplex reads based on single or double indices sch.add_step(ai_demultiplex, "demultiplex_pe", demultiplexer = new demultiplex_pe_reads(&config)); add_write_step(config, sch, ai_write_unidentified_1, "unidentified_mate_1", new write_fastq(config.get_output_filename("demux_unknown", 1))); if (!config.interleaved_output) { add_write_step(config, sch, ai_write_unidentified_2, "unidentified_mate_2", new write_fastq(config.get_output_filename("demux_unknown", 2))); } } // Step 3 - N: Trim and write demultiplexed reads for (size_t nth = 0; nth < config.adapters.adapter_set_count(); ++nth) { const size_t offset = nth * ai_analyses_offset; const std::string& sample = config.adapters.get_sample_name(nth); processors.push_back(new pe_reads_processor(config, nth)); sch.add_step(offset + ai_trim_pe, "trim_pe_" + sample, processors.back()); add_write_step(config, sch, offset + ai_write_mate_1, sample + "_mate_1", new write_fastq(config.get_output_filename("--output1", nth))); if (!config.interleaved_output) { add_write_step(config, sch, offset + ai_write_mate_2, sample + "_mate_2", new write_fastq(config.get_output_filename("--output2", nth))); } if (!config.combined_output) { add_write_step(config, sch, offset + ai_write_discarded, sample + "_discarded", new write_fastq(config.get_output_filename("--discarded", nth))); add_write_step(config, sch, offset + ai_write_singleton, sample + "_singleton", new write_fastq(config.get_output_filename("--singleton", nth))); if (config.collapse) { add_write_step(config, sch, offset + ai_write_collapsed, sample + "_collapsed", new write_fastq(config.get_output_filename("--outputcollapsed", nth))); if (!config.preserve5p) { add_write_step(config, sch, offset + ai_write_collapsed_truncated, sample + "_collapsed_truncated", new write_fastq(config.get_output_filename("--outputcollapsedtruncated", nth))); } } } } } catch (const std::ios_base::failure& error) { std::cerr << "IO error opening file; aborting:\n" << cli_formatter::fmt(error.what()) << std::endl; return 1; } if (!sch.run(config.max_threads)) { return 1; } else if (!write_settings(config, processors)) { return 1; } else if (!write_demux_settings(config, demultiplexer)) { return 1; } return 0; } int remove_adapter_sequences(const userconfig& config) { if (config.paired_ended_mode) { return remove_adapter_sequences_pe(config); } else { return remove_adapter_sequences_se(config); } } } // namespace ar adapterremoval-2.3.1/src/main_demultiplex.cpp000066400000000000000000000354641350370616400213770ustar00rootroot00000000000000/*************************************************************************\ * AdapterRemoval - cleaning next-generation sequencing reads * * * * Copyright (C) 2011 by Stinus Lindgreen - stinus@binf.ku.dk * * Copyright (C) 2016 by Mikkel Schubert - mikkelsch@gmail.com * * * * If you use the program, please cite the paper: * * S. Lindgreen (2012): AdapterRemoval: Easy Cleaning of Next Generation * * Sequencing Reads, BMC Research Notes, 5:337 * * http://www.biomedcentral.com/1756-0500/5/337/ * * * * This program is free software: you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation, either version 3 of the License, or * * (at your option) any later version. * * * * This program is distributed in the hope that it will be useful, * * but WITHOUT ANY WARRANTY; without even the implied warranty of * * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * * GNU General Public License for more details. * * * * You should have received a copy of the GNU General Public License * * along with this program. If not, see . * \*************************************************************************/ #include #include #include #include #include #include "debug.hpp" #include "demultiplex.hpp" #include "fastq.hpp" #include "fastq_io.hpp" #include "main.hpp" //#include "strutils.hpp" #include "userconfig.hpp" namespace ar { //! Implemented in main_adapter_rm.cpp void add_write_step(const userconfig& config, scheduler& sch, size_t offset, const std::string& name, analytical_step* step); void write_demultiplex_statistics(std::ofstream& output, const userconfig& config, const demultiplex_reads* step) { const demux_statistics stats = step->statistics(); const size_t total = stats.total(); output.precision(3); output << std::fixed << std::setw(3) << "\n\n[Demultiplexing statistics]" << "\nName\tBarcode_1\tBarcode_2\tHits\tFraction\n" << "unidentified\tNA\tNA\t" << stats.unidentified << "\t" << stats.unidentified / static_cast(total) << "\n" << "ambiguous\tNA\tNA\t" << stats.ambiguous << "\t" << stats.ambiguous / static_cast(total) << "\n"; const fastq_pair_vec barcodes = config.adapters.get_barcodes(); for (size_t nth = 0; nth < barcodes.size(); ++nth) { const fastq_pair& current = barcodes.at(nth); output << config.adapters.get_sample_name(nth) << "\t" << current.first.sequence() << "\t"; if (current.second.length()) { output << current.second.sequence() << "\t"; } else { output << "*\t"; } output << stats.barcodes.at(nth) << "\t" << stats.barcodes.at(nth) / static_cast(total) << "\n"; } output << "*\t*\t*\t" << total << "\t" << 1.0 << std::endl; } bool write_demultiplex_settings(const userconfig& config, const demultiplex_reads* step, int nth = -1) { const std::string filename \ = config.get_output_filename(nth == -1 ? "demux_stats" : "--settings", nth); try { std::ofstream output(filename.c_str(), std::ofstream::out); if (!output.is_open()) { std::string message = std::string("Failed to open file '") + filename + "': "; throw std::ofstream::failure(message + std::strerror(errno)); } output.exceptions(std::ofstream::failbit | std::ofstream::badbit); output << NAME << " " << VERSION << "\nDemultiplexing of "; if (config.adapters.barcode_count()) { if (config.adapters.get_barcodes().front().second.length()) { output << "double-indexed "; } else { output << "single-indexed "; } } if (config.paired_ended_mode) { if (config.interleaved_input) { output << "interleaved "; } output << "paired-end reads"; } else { output << "single-end reads"; } output << "\n\n\n[Demultiplexing]" << "\nMaximum mismatches (total): " << config.barcode_mm; if (config.paired_ended_mode) { output << "\nMaximum mate 1 mismatches: " << config.barcode_mm_r1; output << "\nMaximum mate 2 mismatches: " << config.barcode_mm_r2; } output << "\n\n\n[Demultiplexing samples]" << "\nName\tBarcode_1\tBarcode_2\n"; const fastq_pair_vec barcodes = config.adapters.get_barcodes(); for (size_t idx = 0; idx < barcodes.size(); ++idx) { output << config.adapters.get_sample_name(idx); if (static_cast(nth) == idx) { output << "*"; } const fastq_pair& current = barcodes.at(idx); output << "\t" << current.first.sequence(); if (current.second.length()) { output << "\t" << current.second.sequence() << "\n"; } else { output << "\t*\n"; } } output << "\n\n[Adapter sequences]"; if (nth == -1) { const fastq_pair_vec adapters = config.adapters.get_raw_adapters(); size_t adapter_id = 0; for (fastq_pair_vec::const_iterator it = adapters.begin(); it != adapters.end(); ++it, ++adapter_id) { output << "\nAdapter1[" << adapter_id + 1 << "]: " << it->first.sequence(); fastq adapter_2 = it->second; adapter_2.reverse_complement(); output << "\nAdapter2[" << adapter_id + 1 << "]: " << adapter_2.sequence() << "\n"; } write_demultiplex_statistics(output, config, step); } else { const string_pair_vec adapters = config.adapters.get_pretty_adapter_set(nth); size_t adapter_id = 0; for (string_pair_vec::const_iterator it = adapters.begin(); it != adapters.end(); ++it, ++adapter_id) { output << "\nAdapter1[" << adapter_id + 1 << "]: " << it->first; output << "\nAdapter2[" << adapter_id + 1 << "]: " << it->second << "\n"; } } } catch (const std::ios_base::failure& error) { std::cerr << "IO error writing settings file; aborting:\n" << cli_formatter::fmt(error.what()) << std::endl; return false; } return true; } class se_demultiplexed_reads_processor : public analytical_step { public: se_demultiplexed_reads_processor(const userconfig& config, size_t nth) : analytical_step(analytical_step::ordering::unordered) , m_config(config) , m_nth(nth) { } chunk_vec process(analytical_chunk* chunk) { const size_t offset = m_nth * ai_analyses_offset; read_chunk_ptr read_chunk(dynamic_cast(chunk)); output_chunk_ptr encoded_reads(new fastq_output_chunk(read_chunk->eof)); for (const auto& read : read_chunk->reads_1) { encoded_reads->add(*m_config.quality_output_fmt, read); } chunk_vec chunks; chunks.push_back(chunk_pair(offset + ai_write_mate_1, std::move(encoded_reads))); return chunks; } private: const userconfig& m_config; const size_t m_nth; }; class pe_demultiplexed_reads_processor : public analytical_step { public: pe_demultiplexed_reads_processor(const userconfig& config, size_t nth) : analytical_step(analytical_step::ordering::unordered) , m_config(config) , m_nth(nth) { } chunk_vec process(analytical_chunk* chunk) { const size_t offset = m_nth * ai_analyses_offset; read_chunk_ptr read_chunk(dynamic_cast(chunk)); AR_DEBUG_ASSERT(read_chunk->reads_1.size() == read_chunk->reads_2.size()); output_chunk_ptr encoded_reads_1(new fastq_output_chunk(read_chunk->eof)); output_chunk_ptr encoded_reads_2; if (!m_config.interleaved_output) { encoded_reads_2.reset(new fastq_output_chunk(read_chunk->eof)); } fastq_vec::iterator it_1 = read_chunk->reads_1.begin(); fastq_vec::iterator it_2 = read_chunk->reads_2.begin(); while (it_1 != read_chunk->reads_1.end()) { fastq read_1 = *it_1++; fastq read_2 = *it_2++; encoded_reads_1->add(*m_config.quality_output_fmt, read_1); if (m_config.interleaved_output) { encoded_reads_1->add(*m_config.quality_output_fmt, read_2); } else { encoded_reads_2->add(*m_config.quality_output_fmt, read_2); } } chunk_vec chunks; chunks.push_back(chunk_pair(offset + ai_write_mate_1, std::move(encoded_reads_1))); if (!m_config.interleaved_output) { chunks.push_back(chunk_pair(offset + ai_write_mate_2, std::move(encoded_reads_2))); } return chunks; } private: const userconfig& m_config; const size_t m_nth; }; int demultiplex_sequences_se(const userconfig& config) { std::cerr << "Demultiplexing single ended reads ..." << std::endl; scheduler sch; demultiplex_reads* demultiplexer = nullptr; try { // Step 1: Read input file sch.add_step(ai_read_fastq, "read_fastq", new read_single_fastq(config.quality_input_fmt.get(), config.input_files_1, ai_demultiplex)); // Step 2: Parse and demultiplex reads based on single or double indices sch.add_step(ai_demultiplex, "demultiplex_se", demultiplexer = new demultiplex_se_reads(&config)); add_write_step(config, sch, ai_write_unidentified_1, "unidentified", new write_fastq(config.get_output_filename("demux_unknown"))); // Step 3 - N: Trim and write demultiplexed reads for (size_t nth = 0; nth < config.adapters.adapter_set_count(); ++nth) { const size_t offset = nth * ai_analyses_offset; const std::string& sample = config.adapters.get_sample_name(nth); sch.add_step(offset + ai_trim_se, "process_se_" + sample, new se_demultiplexed_reads_processor(config, nth)); add_write_step(config, sch, offset + ai_write_mate_1, sample + "_fastq", new write_fastq(config.get_output_filename("--output1", nth))); } } catch (const std::ios_base::failure& error) { std::cerr << "IO error opening file; aborting:\n" << cli_formatter::fmt(error.what()) << std::endl; return 1; } if (!sch.run(config.max_threads)) { return 1; } else if (!write_demultiplex_settings(config, demultiplexer)) { return 1; } for (size_t nth = 0; nth < config.adapters.adapter_set_count(); ++nth) { if (!write_demultiplex_settings(config, demultiplexer, nth)) { return 1; } } return 0; } int demultiplex_sequences_pe(const userconfig& config) { std::cerr << "Demultiplexing paired end reads ..." << std::endl; scheduler sch; demultiplex_reads* demultiplexer = nullptr; try { // Step 1: Read input file if (config.interleaved_input) { sch.add_step(ai_read_fastq, "read_interleaved_fastq", new read_interleaved_fastq(config.quality_input_fmt.get(), config.input_files_1, ai_demultiplex)); } else { sch.add_step(ai_read_fastq, "read_paired_fastq", new read_paired_fastq(config.quality_input_fmt.get(), config.input_files_1, config.input_files_2, ai_demultiplex)); } // Step 2: Parse and demultiplex reads based on single or double indices sch.add_step(ai_demultiplex, "demultiplex_pe", demultiplexer = new demultiplex_pe_reads(&config)); add_write_step(config, sch, ai_write_unidentified_1, "unidentified_mate_1", new write_fastq(config.get_output_filename("demux_unknown", 1))); if (!config.interleaved_output) { add_write_step(config, sch, ai_write_unidentified_2, "unidentified_mate_2", new write_fastq(config.get_output_filename("demux_unknown", 2))); } // Step 3 - N: Write demultiplexed reads for (size_t nth = 0; nth < config.adapters.adapter_set_count(); ++nth) { const size_t offset = nth * ai_analyses_offset; const std::string& sample = config.adapters.get_sample_name(nth); sch.add_step(offset + ai_trim_pe, "process_pe_" + sample, new pe_demultiplexed_reads_processor(config, nth)); add_write_step(config, sch, offset + ai_write_mate_1, sample + "_mate_1", new write_fastq(config.get_output_filename("--output1", nth))); if (!config.interleaved_output) { add_write_step(config, sch, offset + ai_write_mate_2, sample + "_mate_2", new write_fastq(config.get_output_filename("--output2", nth))); } } } catch (const std::ios_base::failure& error) { std::cerr << "IO error opening file; aborting:\n" << cli_formatter::fmt(error.what()) << std::endl; return 1; } if (!sch.run(config.max_threads)) { return 1; } else if (!write_demultiplex_settings(config, demultiplexer)) { return 1; } for (size_t nth = 0; nth < config.adapters.adapter_set_count(); ++nth) { if (!write_demultiplex_settings(config, demultiplexer, nth)) { return 1; } } return 0; } int demultiplex_sequences(const userconfig& config) { if (config.paired_ended_mode) { return demultiplex_sequences_pe(config); } else { return demultiplex_sequences_se(config); } } } // namespace ar adapterremoval-2.3.1/src/managed_writer.cpp000066400000000000000000000147301350370616400210200ustar00rootroot00000000000000/*************************************************************************\ * AdapterRemoval - cleaning next-generation sequencing reads * * * * Copyright (C) 2015 by Mikkel Schubert - mikkelsch@gmail.com * * * * If you use the program, please cite the paper: * * S. Lindgreen (2012): AdapterRemoval: Easy Cleaning of Next Generation * * Sequencing Reads, BMC Research Notes, 5:337 * * http://www.biomedcentral.com/1756-0500/5/337/ * * * * This program is free software: you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation, either version 3 of the License, or * * (at your option) any later version. * * * * This program is distributed in the hope that it will be useful, * * but WITHOUT ANY WARRANTY; without even the implied warranty of * * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * * GNU General Public License for more details. * * * * You should have received a copy of the GNU General Public License * * along with this program. If not, see . * \*************************************************************************/ #include #include #include #include #include "debug.hpp" #include "threads.hpp" #include "managed_writer.hpp" #include namespace ar { static std::mutex g_writer_lock; managed_writer* managed_writer::s_head = nullptr; managed_writer* managed_writer::s_tail = nullptr; bool managed_writer::s_warning_printed = false; managed_writer::managed_writer(const std::string& filename) : m_filename(filename) , m_stream() , m_created(false) , m_prev(nullptr) , m_next(nullptr) { m_stream.exceptions(std::ofstream::failbit | std::ofstream::badbit); } managed_writer::~managed_writer() { close(); } FILE* managed_writer::fopen(const std::string& filename, const char* mode) { AR_DEBUG_ASSERT(mode); while (true) { FILE* handle = ::fopen(filename.c_str(), mode); if (handle) { return handle; } else if (errno == EMFILE) { std::lock_guard lock(g_writer_lock); managed_writer::close_tail_writer(); } else { return nullptr; } } } void managed_writer::write_buffers(const buffer_vec& buffers, bool flush) { std::lock_guard lock(g_writer_lock); if (buffers.size() || flush) { managed_writer::open_writer(this); for (auto& buf : buffers) { if (buf.first) { m_stream.write(reinterpret_cast(buf.second), buf.first); } } if (flush) { m_stream.flush(); } } } void managed_writer::write_strings(const string_vec& strings, bool flush) { std::lock_guard lock(g_writer_lock); if (strings.size() || flush) { managed_writer::open_writer(this); for (const auto& str : strings) { m_stream.write(str.data(), str.length()); } if (flush) { m_stream.flush(); } } } void managed_writer::close() { std::lock_guard lock(g_writer_lock); managed_writer::remove_writer(this); if (m_stream.is_open()) { m_stream.close(); } } void managed_writer::open_writer(managed_writer* ptr) { const std::ios_base::openmode mode = ptr->m_created ? std::ofstream::app : std::ofstream::trunc; while (!ptr->m_stream.is_open()) { try { ptr->m_stream.open(ptr->m_filename, std::ofstream::binary | mode); break; } catch (const std::ofstream::failure&) { if (errno != int(std::errc::too_many_files_open)) { throw; } } managed_writer::close_tail_writer(); } if (ptr != s_head) { managed_writer::remove_writer(ptr); managed_writer::add_head_writer(ptr); } ptr->m_created = true; } void managed_writer::remove_writer(managed_writer* ptr) { AR_DEBUG_ASSERT(!s_head == !s_tail); AR_DEBUG_ASSERT(!s_head || !s_head->m_prev); AR_DEBUG_ASSERT(!s_tail || !s_tail->m_next); if (ptr == s_head) { s_head = ptr->m_next; } if (ptr == s_tail) { s_tail = ptr->m_prev; } AR_DEBUG_ASSERT(!s_head == !s_tail); if (ptr->m_prev) { ptr->m_prev->m_next = ptr->m_next; } if (ptr->m_next) { ptr->m_next->m_prev = ptr->m_prev; } ptr->m_prev = nullptr; ptr->m_next = nullptr; AR_DEBUG_ASSERT(ptr != s_head); AR_DEBUG_ASSERT(ptr != s_tail); AR_DEBUG_ASSERT(!ptr->m_prev); AR_DEBUG_ASSERT(!ptr->m_next); AR_DEBUG_ASSERT(!s_head || !s_head->m_prev); AR_DEBUG_ASSERT(!s_tail || !s_tail->m_next); } void managed_writer::add_head_writer(managed_writer* ptr) { AR_DEBUG_ASSERT(!ptr->m_prev); AR_DEBUG_ASSERT(!ptr->m_next); AR_DEBUG_ASSERT(!s_head == !s_tail); if (s_head) { ptr->m_next = s_head; s_head->m_prev = ptr; } s_head = ptr; if (!s_tail) { s_tail = ptr; } AR_DEBUG_ASSERT(s_head && s_tail); AR_DEBUG_ASSERT(!s_head->m_prev); AR_DEBUG_ASSERT(!s_tail->m_next); } void managed_writer::close_tail_writer() { AR_DEBUG_ASSERT(!s_head == !s_tail); if (!s_warning_printed) { print_locker lock; std::cerr << "\n" << "WARNING: Number of available file-handles (ulimit -n) is too low.\n" << " AdapterRemoval will dynamically close/re-open files as required,\n" << " but performance may suffer as a result.\n" << std::endl; s_warning_printed = true; } if (s_tail) { AR_DEBUG_ASSERT(s_tail->m_stream.is_open()); s_tail->m_stream.close(); managed_writer::remove_writer(s_tail); return; } throw std::runtime_error( "available number of file-handles too low; could not open any files"); } } // namespace ar adapterremoval-2.3.1/src/managed_writer.hpp000066400000000000000000000076621350370616400210330ustar00rootroot00000000000000/*************************************************************************\ * AdapterRemoval - cleaning next-generation sequencing reads * * * * Copyright (C) 2015 by Mikkel Schubert - mikkelsch@gmail.com * * * * If you use the program, please cite the paper: * * S. Lindgreen (2012): AdapterRemoval: Easy Cleaning of Next Generation * * Sequencing Reads, BMC Research Notes, 5:337 * * http://www.biomedcentral.com/1756-0500/5/337/ * * * * This program is free software: you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation, either version 3 of the License, or * * (at your option) any later version. * * * * This program is distributed in the hope that it will be useful, * * but WITHOUT ANY WARRANTY; without even the implied warranty of * * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * * GNU General Public License for more details. * * * * You should have received a copy of the GNU General Public License * * along with this program. If not, see . * \*************************************************************************/ #ifndef WRITER_HPP #define WRITER_HPP #include #include #include "commontypes.hpp" namespace ar { typedef std::pair buffer_pair; typedef std::vector buffer_vec; /** * Writer that manages open handles if open files exceeds ulimits. * * The file is lazily opened the first time a write is performed; * if the file cannot be opened due to the number of already open * files, the writer will close the least recently used handle and * retry. */ class managed_writer { public: managed_writer(const std::string& filename); ~managed_writer(); /** * Opens a file using fopen and returns the handle. * * If too many handles are used, this funtion will close writers until * the file can be succesfully opened. */ static FILE* fopen(const std::string& filename, const char* mode); void write_buffers(const buffer_vec& buffers, bool flush); void write_strings(const string_vec& strings, bool flush); void close(); managed_writer(const managed_writer&) = delete; managed_writer& operator=(const managed_writer&) = delete; private: /* Ensure that the writer is open, closing existing files if nessesary. */ static void open_writer(managed_writer* ptr); /* Removes the writer from the list of open writers. */ static void remove_writer(managed_writer* ptr); /* Sets the writer as the most recently used writer. */ static void add_head_writer(managed_writer* ptr); /* Close the least recently used writer. */ static void close_tail_writer(); //! Destination filename; is created lazily. std::string m_filename; //! Lazily opened, managed handle; may be closed to free up handles. std::ofstream m_stream; //! Indicates if the file has been created bool m_created; //! Previous managed_writer; used more recently than this. managed_writer* m_prev; //! Next managed_writer; used before this. managed_writer* m_next; //! Most recently used managed_writer static managed_writer* s_head; //! Least recently used managed_writer static managed_writer* s_tail; //! Indicates if a performance warning has been printed static bool s_warning_printed; }; } // namespace ar #endif adapterremoval-2.3.1/src/scheduler.cpp000066400000000000000000000273251350370616400200120ustar00rootroot00000000000000/*************************************************************************\ * AdapterRemoval - cleaning next-generation sequencing reads * * * * Copyright (C) 2015 by Mikkel Schubert - mikkelsch@gmail.com * * * * If you use the program, please cite the paper: * * S. Lindgreen (2012): AdapterRemoval: Easy Cleaning of Next Generation * * Sequencing Reads, BMC Research Notes, 5:337 * * http://www.biomedcentral.com/1756-0500/5/337/ * * * * This program is free software: you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation, either version 3 of the License, or * * (at your option) any later version. * * * * This program is distributed in the hope that it will be useful, * * but WITHOUT ANY WARRANTY; without even the implied warranty of * * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * * GNU General Public License for more details. * * * * You should have received a copy of the GNU General Public License * * along with this program. If not, see . * \*************************************************************************/ #include #include #include #include #include #include #include "debug.hpp" #include "scheduler.hpp" #include "strutils.hpp" namespace ar { /////////////////////////////////////////////////////////////////////////////// // analytical_chunk analytical_chunk::analytical_chunk() { } analytical_chunk::~analytical_chunk() { } /////////////////////////////////////////////////////////////////////////////// // analytical_step analytical_step::analytical_step(ordering step_order, bool file_io) : m_step_order(step_order) , m_file_io(file_io) { } analytical_step::~analytical_step() { } /////////////////////////////////////////////////////////////////////////////// // scheduler struct data_chunk { explicit data_chunk(size_t chunk_id_ = 0) : chunk_id(chunk_id_) , data() , counter(new bool()) { } explicit data_chunk(const data_chunk& parent, chunk_ptr data_) : chunk_id(parent.chunk_id) , data(std::move(data_)) , counter(parent.counter) { } /** Sorts by counter, data, type, in that order. **/ bool operator<(const data_chunk& other) const { if (chunk_id != other.chunk_id) { return chunk_id > other.chunk_id; } else if (data != other.data) { return data > other.data; } else if (counter != other.counter) { return counter > other.counter; } return false; } bool unique() const { return counter.unique(); } //! Strictly increasing counter; used to sort chunks for 'ordered' tasks size_t chunk_id; //! Use generated data; is normally not freed by this struct chunk_ptr data; private: //! Reference counts std::shared_ptr counter; }; /** Simple priority queue; needed to allow moving values out of queue. */ class chunk_queue { public: chunk_queue() : m_chunks() { } void push(data_chunk value) { m_chunks.push_back(std::move(value)); std::push_heap(m_chunks.begin(), m_chunks.end()); } data_chunk pop() { std::pop_heap(m_chunks.begin(), m_chunks.end()); data_chunk value = std::move(m_chunks.back()); m_chunks.pop_back(); return value; } const data_chunk& top() const { return m_chunks.front(); } bool empty() const { return m_chunks.empty(); } size_t size() const { return m_chunks.size(); } private: typedef std::vector chunk_vec; chunk_vec m_chunks; }; struct scheduler_step { scheduler_step(analytical_step* value, const std::string& name_) : lock() , ptr(value) , current_chunk(0) , last_chunk(0) , queue() , name(name_) { } bool can_run(size_t next_chunk) { if (ptr->get_ordering() == analytical_step::ordering::ordered) { return (current_chunk == next_chunk); } return true; } //! Mutex used to control access to step std::mutex lock; //! Analytical step implementation std::unique_ptr ptr; //! The current chunk to be processed size_t current_chunk; //! The last chunk queued to the step; //! Used to correct numbering for sparse output from sequential steps size_t last_chunk; //! (Ordered) vector of chunks to be processed chunk_queue queue; //! Short name for step used for error reporting std::string name; //! Copy construction not supported scheduler_step(const scheduler_step&) = delete; //! Assignment not supported scheduler_step& operator=(const scheduler_step&) = delete; }; scheduler::scheduler() : m_steps() , m_condition() , m_chunk_counter(0) , m_live_chunks(0) , m_queue_lock() , m_queue_calc() , m_queue_io() , m_io_active(false) , m_errors(false) { } scheduler::~scheduler() { } void scheduler::add_step(size_t step_id, const std::string& name, analytical_step* step) { if (m_steps.size() <= step_id) { m_steps.resize(step_id + 1); } AR_DEBUG_ASSERT(step); AR_DEBUG_ASSERT(!m_steps.at(step_id)); m_steps.at(step_id) = step_ptr(new scheduler_step(step, name)); } bool scheduler::run(int nthreads) { AR_DEBUG_ASSERT(!m_steps.empty()); AR_DEBUG_ASSERT(m_steps.front()); AR_DEBUG_ASSERT(nthreads >= 1); AR_DEBUG_ASSERT(!m_chunk_counter); for (size_t task = 3 * static_cast(nthreads); task; --task) { m_steps.front()->queue.push(data_chunk(m_chunk_counter++)); } queue_analytical_step(m_steps.front(), 0); std::vector threads; try { for (int i = 0; i < nthreads - 1; ++i) { threads.emplace_back(run_wrapper, this); } } catch (const std::system_error& error) { print_locker lock; std::cerr << "ERROR: Failed to create threads:\n" << cli_formatter::fmt(error.what()) << std::endl; set_errors_occured(); } // Run the main thread (the only thread in case of non-threaded mode) run_wrapper(this); for (auto& thread: threads) { try { thread.join(); } catch (const std::system_error& error) { std::cerr << "ERROR: Failed to join thread: " << error.what() << std::endl; set_errors_occured(); } } if (errors_occured()) { return false; } for (auto& step: m_steps) { if (step && !step->queue.empty()) { print_locker lock; std::cerr << "ERROR: Not all parts run for step " << step->name << "; " << step->queue.size() << " left ..." << std::endl; set_errors_occured(); } } if (errors_occured()) { return false; } for (auto step: m_steps) { if (step) { try { step->ptr->finalize(); } catch (const std::exception&) { std::cerr << "ERROR: Failed to finalizing task " << step->name << ":\n"; throw; } } } return true; } void scheduler::run_wrapper(scheduler* sch) { try { return sch->do_run(); } catch (const thread_abort&) { print_locker lock; std::cerr << "Aborting thread due to error." << std::endl; } catch (const std::exception& error) { print_locker lock; std::cerr << "ERROR: Unhandled exception in thread:\n" << cli_formatter::fmt(error.what()) << std::endl; } catch (...) { print_locker lock; std::cerr << "ERROR: Unhandled, non-standard exception in thread" << std::endl; } sch->set_errors_occured(); sch->m_condition.notify_all(); } void scheduler::do_run() { std::unique_lock lock(m_queue_lock); while (!errors_occured()) { // Try to keep the disk busy by preferring IO chunks step_ptr current_step; if (m_io_active || m_queue_io.empty()) { if (!m_queue_calc.empty()) { current_step = m_queue_calc.front(); m_queue_calc.pop(); } else if (!m_live_chunks) { // Nothing left to do at all break; } } else { current_step = m_queue_io.front(); m_queue_io.pop(); m_io_active = true; } if (current_step) { lock.unlock(); execute_analytical_step(current_step); lock.lock(); } else { m_condition.wait(lock); } } // Signal any waiting threads m_condition.notify_all(); } void scheduler::execute_analytical_step(const step_ptr& step) { data_chunk chunk; { std::lock_guard lock(step->lock); chunk = step->queue.pop(); } chunk_vec chunks = step->ptr->process(chunk.data.release()); std::lock_guard lock(m_queue_lock); // Schedule each of the resulting blocks for (auto& result: chunks) { step_ptr& other_step = m_steps.at(result.first); AR_DEBUG_ASSERT(other_step != nullptr); std::lock_guard step_lock(other_step->lock); // Inherit reference count from source chunk data_chunk next_chunk(chunk, std::move(result.second)); if (step->ptr->get_ordering() == analytical_step::ordering::ordered) { // Ordered steps are allowed to not return results, so the chunk // numbering is remembered for down-stream steps next_chunk.chunk_id = other_step->last_chunk++; } other_step->queue.push(std::move(next_chunk)); queue_analytical_step(other_step, next_chunk.chunk_id); } // Unlock use of IO steps after finishing processing if (step->ptr->file_io()) { m_io_active = false; if (!m_queue_io.empty()) { m_condition.notify_all(); } } // Reschedule current step if ordered and next chunk is available if (step->ptr->get_ordering() == analytical_step::ordering::ordered) { std::lock_guard step_lock(step->lock); step->current_chunk++; if (!step->queue.empty()) { queue_analytical_step(step, step->queue.top().chunk_id); } } // End of the line for this chunk; re-schedule first step if (chunks.empty() && chunk.unique() && step != m_steps.front()) { step_ptr other_step = m_steps.front(); std::lock_guard step_lock(other_step->lock); other_step->queue.push(data_chunk(m_chunk_counter)); queue_analytical_step(other_step, m_chunk_counter); m_chunk_counter++; } // Decrement counters before releasing lock chunk = data_chunk(0); m_live_chunks--; } void scheduler::queue_analytical_step(const step_ptr& step, size_t current) { if (step->can_run(current)) { if (step->ptr->file_io()) { m_queue_io.push(step); } else { m_queue_calc.push(step); } m_live_chunks++; m_condition.notify_one(); } } } // namespace ar adapterremoval-2.3.1/src/scheduler.hpp000066400000000000000000000257571350370616400200260ustar00rootroot00000000000000/*************************************************************************\ * AdapterRemoval - cleaning next-generation sequencing reads * * * * Copyright (C) 2015 by Mikkel Schubert - mikkelsch@gmail.com * * * * If you use the program, please cite the paper: * * S. Lindgreen (2012): AdapterRemoval: Easy Cleaning of Next Generation * * Sequencing Reads, BMC Research Notes, 5:337 * * http://www.biomedcentral.com/1756-0500/5/337/ * * * * This program is free software: you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation, either version 3 of the License, or * * (at your option) any later version. * * * * This program is distributed in the hope that it will be useful, * * but WITHOUT ANY WARRANTY; without even the implied warranty of * * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * * GNU General Public License for more details. * * * * You should have received a copy of the GNU General Public License * * along with this program. If not, see . * \*************************************************************************/ #ifndef SCHEDULER_H #define SCHEDULER_H #include #include #include #include #include #include #include #include "threads.hpp" namespace ar { struct data_chunk; struct scheduler_step; /** * Base-class for data-chunks produced, processed and consumed by a pipeline. */ class analytical_chunk { public: /** Constructor; does nothing. */ analytical_chunk(); /** Destructor; does nothing. */ virtual ~analytical_chunk(); }; typedef std::unique_ptr chunk_ptr; typedef std::pair chunk_pair; typedef std::vector chunk_vec; /** * Sink for generating in-memory data-sinks of type T on demand, and reducing * these to a single result upon completion of analyses. Using this class * allows multiple threads to collect summary statistics, while the final * consumer sees only a single statistics object. * * The class T must implement the += operator, to allow the reduction of sinks. */ template class statistics_sink { public: typedef std::unique_ptr pointer; /** Constructor; does nothing. */ statistics_sink(); /** Destructor; deletes any remaining sinks. */ virtual ~statistics_sink(); /** Returns unused sink, or a new sink if no unused sinks are available. */ virtual pointer get_sink(); /** Return a sink after it has been used. */ virtual void return_sink(pointer ptr); /** * Return a single sink that is the sum of all sink objects, consuming (and * freeing) all sink objects generated by and returned to the sink. */ virtual pointer finalize(); protected: /** Returns a new sink object; to be implemented in subclasses. */ virtual pointer new_sink() const = 0; /** Called to reduce objects during finalization. */ virtual void reduce(pointer& dst, const pointer& src) const = 0; private: typedef std::queue sink_list; //! Lock used to control access to sink lists std::mutex m_sinks_lock; //! List of inactive sinks sink_list m_sinks; }; /** * Base class for analytical steps in a pipeline. * * Each step must implement the 'process' function as described below; note * that this function may be called simultaneously by multiple threads, and that * thread-safe storage (e.g. statistics_sink) must be used for writable * resources used by the step. */ class analytical_step { public: enum class ordering { //! Data must be consumed in the input order ordered, //! Data may be consumed in any order unordered }; /** * @param step_order Indicates the expected ordering of chunks; processing * steps are typically unordered, while IO is typically * ordered in order to ensure that output order matches * input order. * @param file_io Indicates if the step involves the use of file IO. */ analytical_step(ordering step_order, bool file_io = false); /** Destructor; does nothing in base class. **/ virtual ~analytical_step(); /** * Function called by pipeline to generate / process / consume data chunks. * * Initially, the first step in the pipeline will receive nullptr; during * subsequent cycles, the pipeline will return the value output from the * last step to the initial step, which may re-use it to avoid allocations; * if this is not done, the chunk must be freed by the first step. * * Best performance is therefore obtained if the chunk contains buffers * for all steps, and these can be re-used across cycles, thereby reducing * the number of (de)allocations that must be performed. * * To terminate the pipeline, the first step must cease to return chunks; * however, any other step MUST return valid chunks, even if no input data * was provided. This is to ensure that tracking of chunk ordering can be * maintained across steps. * * The only exceptions to this rule are steps which ONLY has unordered * downstream steps (that is, no chunk generated by this step will be * processed by an ordered step later in the pipeline). */ virtual chunk_vec process(analytical_chunk* chunk) = 0; /** * Called once the pipeline has been run to completion; this function is * called on nodes in the same order as the pipeline. */ virtual void finalize(); /** Returns the expected ordering (ordered / unordered) for input data. **/ ordering get_ordering() const; /** Returns true if the step involves file IO. */ bool file_io() const; //! Copy construction not supported analytical_step(const analytical_step&) = delete; //! Assignment not supported analytical_step& operator=(const analytical_step&) = delete; private: //! Stores the ordering of data chunks expected by the step const ordering m_step_order; //! True if the step involves file IO (read and / or writes) const bool m_file_io; }; /** * Multithreaded scheduler. * * See 'analytical_step' for information on implementing analyses. */ class scheduler { public: /** Constructor. */ scheduler(); /** Frees any object passed via 'add_step'. **/ ~scheduler(); /** * Adds a step to the pipeline. * * @param step_id Unique ID of current step; cannot be used twice. * @param name Textual name for the (type) of step being added. * @param step A analytical step; is deleted when scheduler is destroyed. * * The ID specified here is specified as the first value of 'chunk_pair's * in order to determine to which analytical step a chunk is assigned. **/ void add_step(size_t step_id, const std::string& name, analytical_step* step); /** Runs the pipeline with n threads; return false on error. */ bool run(int nthreads); //! Copy construction not supported scheduler(const scheduler&) = delete; //! Assignment not supported scheduler& operator=(const scheduler&) = delete; private: typedef std::shared_ptr step_ptr; typedef std::queue runables; typedef std::vector pipeline; /** Wrapper function which calls do_run on the provided thread. */ static void run_wrapper(scheduler*); /** Work function; invoked by each thread. */ void do_run(); /** Executes an analytical step. */ void execute_analytical_step(const step_ptr& step); /** Attempts to queue an analytical step given a current chunk. */ void queue_analytical_step(const step_ptr& step, size_t current); /** Returns true if an error has occurred, and the run should terminate. */ bool errors_occured(); /** Mark that an error has occurred, and that the run should terminate. */ void set_errors_occured(); //! Analytical steps pipeline m_steps; //! Condition used to signal the (potential) availability of work std::condition_variable m_condition; //! Counter used for sequential processing of data size_t m_chunk_counter; //! Count of currently live chunks size_t m_live_chunks; //! Lock used to control access to chunks std::mutex m_queue_lock; //! Queue used for currently runnable steps involving only calculations runables m_queue_calc; //! Queue used for currently runnable steps involving IO runables m_queue_io; //! Indicates if a thread is doing IO; access control through 'm_queue_lock' bool m_io_active; //! Set to indicate if errors have occurred std::atomic_bool m_errors; }; /////////////////////////////////////////////////////////////////////////////// // Implementations for 'statistics_sink' template statistics_sink::statistics_sink() : m_sinks_lock() , m_sinks() { } template statistics_sink::~statistics_sink() { } template typename statistics_sink::pointer statistics_sink::get_sink() { std::lock_guard lock(m_sinks_lock); if (m_sinks.empty()) { return new_sink(); } pointer ptr = std::move(m_sinks.front()); m_sinks.pop(); return ptr; } template void statistics_sink::return_sink(pointer ptr) { std::lock_guard lock(m_sinks_lock); m_sinks.push(std::move(ptr)); } template typename statistics_sink::pointer statistics_sink::finalize() { std::lock_guard lock(m_sinks_lock); if (m_sinks.empty()) { return new_sink(); } pointer result(std::move(m_sinks.front())); m_sinks.pop(); while (!m_sinks.empty()) { reduce(result, m_sinks.front()); m_sinks.pop(); } return std::move(result); } /////////////////////////////////////////////////////////////////////////////// // Implementations for 'analytical_step' inline void analytical_step::finalize() { } inline analytical_step::ordering analytical_step::get_ordering() const { return m_step_order; } inline bool analytical_step::file_io() const { return m_file_io; } /////////////////////////////////////////////////////////////////////////////// // Implementations for 'scheduler' inline bool scheduler::errors_occured() { return m_errors.load(); } inline void scheduler::set_errors_occured() { m_errors.store(true); } } // namespace ar #endif adapterremoval-2.3.1/src/statistics.hpp000066400000000000000000000133241350370616400202250ustar00rootroot00000000000000/*************************************************************************\ * AdapterRemoval - cleaning next-generation sequencing reads * * * * Copyright (C) 2011 by Stinus Lindgreen - stinus@binf.ku.dk * * Copyright (C) 2014 by Mikkel Schubert - mikkelsch@gmail.com * * * * If you use the program, please cite the paper: * * S. Lindgreen (2012): AdapterRemoval: Easy Cleaning of Next Generation * * Sequencing Reads, BMC Research Notes, 5:337 * * http://www.biomedcentral.com/1756-0500/5/337/ * * * * This program is free software: you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation, either version 3 of the License, or * * (at your option) any later version. * * * * This program is distributed in the hope that it will be useful, * * but WITHOUT ANY WARRANTY; without even the implied warranty of * * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * * GNU General Public License for more details. * * * * You should have received a copy of the GNU General Public License * * along with this program. If not, see . * \*************************************************************************/ #ifndef STATISTICS_H #define STATISTICS_H #include #include #include "commontypes.hpp" #include "vecutils.hpp" namespace ar { /** Object used to collect summary statistics for trimming and other tasks. */ struct statistics { statistics() : number_of_full_length_collapsed(0) , number_of_truncated_collapsed(0) , total_number_of_nucleotides(0) , total_number_of_good_reads(0) , number_of_reads_with_adapter() , unaligned_reads(0) , well_aligned_reads(0) , poorly_aligned_reads(0) , keep1(0) , discard1(0) , keep2(0) , discard2(0) , records(0) , read_lengths() { } //! Number of collapsed reads which (likely) represent full inserts size_t number_of_full_length_collapsed; //! Number of collapsed reads which were truncated due to low-quality bases size_t number_of_truncated_collapsed; //! Total number of nucleotides left after trimming, collapsing, filtering size_t total_number_of_nucleotides; //! Total number of reads left after trimming, collapsing, filtering size_t total_number_of_good_reads; //! Number of reads / pairs with adapters trimmed std::vector number_of_reads_with_adapter; //! Number of unaligned reads; not enough bases, too many mismatches, etc. size_t unaligned_reads; //! Number of alignments with enough aligned bases, not too many mismatches size_t well_aligned_reads; //! Number of alignments with a zero or lower score size_t poorly_aligned_reads; //! Number of retained mate 1 reads size_t keep1; //! Number of discarded mate 1 reads size_t discard1; //! Number of retained mate 2 reads size_t keep2; //! Number of discarded mate 2 reads size_t discard2; //! Total number of reads / pairs processed size_t records; /** Increment the number of reads with of a given type / length. */ void inc_length_count(read_type type, size_t length) { if (length >= read_lengths.size()) { read_lengths.resize(length + 1, std::vector(static_cast(read_type::max))); } ++read_lengths.at(length).at(static_cast(type)); } //! Per read-type length distributions of reads std::vector > read_lengths; /** Combine statistics objects, e.g. those used by different threads. */ statistics& operator+=(const statistics& other) { number_of_full_length_collapsed += other.number_of_full_length_collapsed; number_of_truncated_collapsed += other.number_of_truncated_collapsed; total_number_of_nucleotides += other.total_number_of_nucleotides; total_number_of_good_reads += other.total_number_of_good_reads; unaligned_reads += other.unaligned_reads; well_aligned_reads += other.well_aligned_reads; poorly_aligned_reads += other.poorly_aligned_reads; keep1 += other.keep1; discard1 += other.discard1; keep2 += other.keep2; discard2 += other.discard2; records += other.records; merge_vectors(number_of_reads_with_adapter, other.number_of_reads_with_adapter); merge_sub_vectors(read_lengths, other.read_lengths); return *this; } }; /** Object used to collect summary statistics for demultiplexing. */ struct demux_statistics { demux_statistics(const size_t n_barcodes) : barcodes(n_barcodes) , unidentified(0) , ambiguous(0) { } size_t total() const { size_t total = unidentified + ambiguous; for (size_t i = 0; i < barcodes.size(); ++i) { total += barcodes.at(i); } return total; } //! Number of reads / pairs identified for a given barcode / pair of barcodes std::vector barcodes; //! Number of reads / pairs with no hits size_t unidentified; //! Number of reads / pairs with no single best hit size_t ambiguous; }; } // namespace ar #endif adapterremoval-2.3.1/src/strutils.cpp000066400000000000000000000147341350370616400177250ustar00rootroot00000000000000/*************************************************************************\ * AdapterRemoval - cleaning next-generation sequencing reads * * * * Copyright (C) 2015 by Mikkel Schubert - mikkelsch@gmail.com * * * * If you use the program, please cite the paper: * * S. Lindgreen (2012): AdapterRemoval: Easy Cleaning of Next Generation * * Sequencing Reads, BMC Research Notes, 5:337 * * http://www.biomedcentral.com/1756-0500/5/337/ * * * * This program is free software: you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation, either version 3 of the License, or * * (at your option) any later version. * * * * This program is distributed in the hope that it will be useful, * * but WITHOUT ANY WARRANTY; without even the implied warranty of * * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * * GNU General Public License for more details. * * * * You should have received a copy of the GNU General Public License * * along with this program. If not, see . * \*************************************************************************/ #include #include #include #include #include #include #include "strutils.hpp" namespace ar { unsigned str_to_unsigned(const std::string& s) { std::stringstream stream(s); int64_t temp = 0; if (!(stream >> temp)) { throw std::invalid_argument("value is not a valid number"); } // Failing on trailing, non-numerical values std::string trailing; if (stream >> trailing) { throw std::invalid_argument("value contains trailing text"); } if (temp < 0 || temp > std::numeric_limits::max()) { throw std::invalid_argument("numerical value overflows"); } return static_cast(temp); } std::string toupper(const std::string& str) { std::string uppercased = str; for (auto& current : uppercased) { if (current >= 'a' && current <= 'z') { current -= 32; } }; return uppercased; } std::string indent_lines(const std::string& lines, size_t n_indent) { std::string line; std::stringstream lines_out; const std::string indentation = std::string(n_indent, ' '); size_t last_pos = 0; while (true) { const size_t next_pos = lines.find('\n', last_pos); if (next_pos == std::string::npos) { if (lines.size() - last_pos) { lines_out << indentation; } lines_out << lines.substr(last_pos); break; } else { if (next_pos - last_pos) { lines_out << indentation; } lines_out << lines.substr(last_pos, next_pos - last_pos + 1); last_pos = next_pos + 1; } } return lines_out.str(); } std::string columnize_text(const std::string& value, size_t max_width, size_t ljust) { size_t current_width = 0; size_t current_ljust = 0; std::stringstream lines_out; std::stringstream lines_in(value); std::string substr; while (lines_in >> substr) { if (current_width) { if (current_ljust + current_width + 1 + substr.length() > max_width) { current_ljust = ljust; lines_out << "\n" << std::left << std::setw(current_ljust) << "" << substr; current_width = substr.length(); } else { lines_out << " " << substr; current_width += substr.length() + 1; } } else { lines_out << substr; current_width += substr.length(); } } return lines_out.str(); } /////////////////////////////////////////////////////////////////////////////// // Implementations for 'cli_formatter' cli_formatter::cli_formatter() : m_indent_first(true) , m_ljust(0) , m_columns(DEFAULT_MAX_COLUMNS) , m_indentation(4) { struct winsize size; if (!ioctl(STDOUT_FILENO, TIOCGWINSZ, &size)) { m_columns = size.ws_col; } } cli_formatter& cli_formatter::set_column_width(size_t value) { m_columns = value; return *this; } cli_formatter& cli_formatter::set_ljust(size_t value) { m_ljust = value; return *this; } cli_formatter& cli_formatter::set_indent(size_t value) { m_indentation = value; return *this; } cli_formatter& cli_formatter::set_indent_first_line(bool value) { m_indent_first = value; return *this; } std::string cli_formatter::format(const std::string& lines) const { std::string line; std::stringstream lines_out; size_t last_pos = 0; while (true) { const size_t next_pos = lines.find('\n', last_pos); // Current line, excluding terminal newline const size_t end_pos = (next_pos == std::string::npos) ? next_pos : (next_pos - last_pos); line = lines.substr(last_pos, end_pos), // Format into fixed width columns, indenting by ljust after first line line = columnize_text(line, m_columns, m_ljust); // Add fixed width indentation if (m_indentation) { line = indent_lines(line, m_indentation); } lines_out << line; if (next_pos == std::string::npos) { break; } else if (lines.at(next_pos) == '\n') { lines_out << '\n'; last_pos = next_pos + 1; } } line = lines_out.str(); if (!m_indent_first) { line = line.substr(m_indentation); } return line; } std::string cli_formatter::fmt(const std::string& value) { cli_formatter formatter; return formatter.format(value); } std::string cli_formatter::fmt(const std::string& prefix, const std::string& value) { cli_formatter formatter; formatter.set_indent(prefix.size()); formatter.set_indent_first_line(false); return prefix + value; } } // namespace ar adapterremoval-2.3.1/src/strutils.hpp000066400000000000000000000112721350370616400177240ustar00rootroot00000000000000/*************************************************************************\ * AdapterRemoval - cleaning next-generation sequencing reads * * * * Copyright (C) 2015 by Mikkel Schubert - mikkelsch@gmail.com * * * * If you use the program, please cite the paper: * * S. Lindgreen (2012): AdapterRemoval: Easy Cleaning of Next Generation * * Sequencing Reads, BMC Research Notes, 5:337 * * http://www.biomedcentral.com/1756-0500/5/337/ * * * * This program is free software: you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation, either version 3 of the License, or * * (at your option) any later version. * * * * This program is distributed in the hope that it will be useful, * * but WITHOUT ANY WARRANTY; without even the implied warranty of * * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * * GNU General Public License for more details. * * * * You should have received a copy of the GNU General Public License * * along with this program. If not, see . * \*************************************************************************/ #ifndef STRUTILS_H #define STRUTILS_H #include #include #include namespace ar { const size_t DEFAULT_MAX_COLUMNS = 78; const size_t DEFAULT_INDENTATION = 4; /** * Convert a string to an unsigned integer. * * Throws std::invalid_argument if the string does not contain a proper number, * if it contains more than just a number, or if the number overflows a * unsigned integer. */ unsigned str_to_unsigned(const std::string& s); /** Uppercases letters in the range a-z */ std::string toupper(const std::string& str); /** Split text by newlines and add fixed indentation following newlines. */ std::string indent_lines(const std::string& lines, size_t identation = DEFAULT_INDENTATION); /** * Formats text into fixed-width columns. * * @param value Text representing a single paragraph to be formatted. * @param max_width Maximum width of output lines in characters. * @param ljust Indent lines after the first line by this amount of characters. * * Note that all whitespace in the input string is consumed; output words are * seperated by a single space, and the terminal line does not end with a * newline. */ std::string columnize_text(const std::string& value, size_t max_width = DEFAULT_MAX_COLUMNS, size_t ljust = 0); /** * Wrapper around 'indent_lines' and 'columnize_text'. * * Defaults to 78 character columns, with 4 character indentation, and * no ljust, corresponding to function defaults. Unlike simply combining * 'indent_lines' and 'columnize_text', the 'format' function preserves * newlines, allowing paragraphs to be printed easily. */ class cli_formatter { public: /** Creates formatter using default parameters (see above). */ cli_formatter(); /** Include (or not) indentation on the first line of output. */ cli_formatter& set_indent_first_line(bool value); /** Maximum number of columns in each line in output. */ cli_formatter& set_column_width(size_t value); /** Number of spaces to indent line 2+ in each paragraph. */ cli_formatter& set_ljust(size_t value); /** Fixed indentation for each line (see also set_indent_first_line). */ cli_formatter& set_indent(size_t value); /** Formats string using the current settings. */ std::string format(const std::string& value) const; /** Format string using default parameters. */ static std::string fmt(const std::string& value); /** * Format string using default parameters, but include prefix on first line * and indent subsequent lines using the width of the prefix. */ static std::string fmt(const std::string& prefix, const std::string& value); private: //! Specifices whether or not to indent the first line of output. bool m_indent_first; //! Number of spaces to indent the 2+ lines in each paragraph. size_t m_ljust; //! The maximum number of columns (in characters). size_t m_columns; //! The number of spaces to indent each line (see also m_indent_first_line) size_t m_indentation; }; } // namespace ar #endif adapterremoval-2.3.1/src/threads.cpp000066400000000000000000000057371350370616400174710ustar00rootroot00000000000000/*************************************************************************\ * AdapterRemoval - cleaning next-generation sequencing reads * * * * Copyright (C) 2015 by Mikkel Schubert - mikkelsch@gmail.com * * * * If you use the program, please cite the paper: * * S. Lindgreen (2012): AdapterRemoval: Easy Cleaning of Next Generation * * Sequencing Reads, BMC Research Notes, 5:337 * * http://www.biomedcentral.com/1756-0500/5/337/ * * * * This program is free software: you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation, either version 3 of the License, or * * (at your option) any later version. * * * * This program is distributed in the hope that it will be useful, * * but WITHOUT ANY WARRANTY; without even the implied warranty of * * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * * GNU General Public License for more details. * * * * You should have received a copy of the GNU General Public License * * along with this program. If not, see . * \*************************************************************************/ #include #include #include #include #include #include #include "threads.hpp" #include namespace ar { /////////////////////////////////////////////////////////////////////////////// // exceptions thread_error::thread_error(const std::string& message) : std::exception() , m_message(message) { } thread_error::thread_error(const thread_error& error) : std::exception() , m_message(error.m_message) { } thread_error::~thread_error() noexcept { } const char* thread_error::what() const noexcept { return m_message.c_str(); } thread_abort::thread_abort() : thread_error("abort thread") { } /////////////////////////////////////////////////////////////////////////////// // print_locker //! Shared mutex for STDOUT / STDERR static std::mutex s_print_mutex; //! Shared bool indicating if STDERR contains a partial line. static bool s_stderr_is_incomplete = false; print_locker::print_locker(bool flush_stderr) : m_lock(s_print_mutex) { if (flush_stderr && s_stderr_is_incomplete) { s_stderr_is_incomplete = false; std::cerr << std::endl; } } print_locker::~print_locker() { } void print_locker::partial_stderr_output() { s_stderr_is_incomplete = true; } } // namespace ar adapterremoval-2.3.1/src/threads.hpp000066400000000000000000000071021350370616400174620ustar00rootroot00000000000000/*************************************************************************\ * AdapterRemoval - cleaning next-generation sequencing reads * * * * Copyright (C) 2015 by Mikkel Schubert - mikkelsch@gmail.com * * * * If you use the program, please cite the paper: * * S. Lindgreen (2012): AdapterRemoval: Easy Cleaning of Next Generation * * Sequencing Reads, BMC Research Notes, 5:337 * * http://www.biomedcentral.com/1756-0500/5/337/ * * * * This program is free software: you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation, either version 3 of the License, or * * (at your option) any later version. * * * * This program is distributed in the hope that it will be useful, * * but WITHOUT ANY WARRANTY; without even the implied warranty of * * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * * GNU General Public License for more details. * * * * You should have received a copy of the GNU General Public License * * along with this program. If not, see . * \*************************************************************************/ #ifndef THREADS_H #define THREADS_H #include #include #include namespace ar { /** * Exception thrown for threading related errors, including errors with * threads, mutexes, and conditionals. */ class thread_error : public std::exception { public: /** Constructor; takes an error-message. */ thread_error(const std::string& message); /** Copy-constructor; takes an exiting error. */ thread_error(const thread_error& error); /** Destructor; does nothing. */ ~thread_error() noexcept; /** Returns error message; lifetime is the same as the object. */ virtual const char* what() const noexcept; private: //! User provided error message std::string m_message; }; /** * This exception may be thrown by a task to abort the thread; error-messages * are assumed to have already been printed by the thrower, and no further * messages are printed. */ class thread_abort : public thread_error { public: thread_abort(); }; /** * Locker for using stdout / stderr. * * Any useage of stdout and / or stderr should be preceded by creating a * print_locker object. This ensures that output from different threads is * not interleaved, regardless of the destination of these pipes. */ class print_locker { public: /* * Locks the mutex (blocking). If flush_stderr is true, and * partial_stderr_output has been called, then a newline is first * written to stderr. */ print_locker(bool flush_stderr=true); //! Unlocks the mutex ~print_locker(); //! Call to indicate that a partial line has been written to STDERR. void partial_stderr_output(); //! Copy construction not supported print_locker(const print_locker&) = delete; //! Assignment not supported print_locker& operator=(const print_locker&) = delete; private: std::lock_guard m_lock; }; } // namespace ar #endif adapterremoval-2.3.1/src/timer.cpp000066400000000000000000000121321350370616400171420ustar00rootroot00000000000000/*************************************************************************\ * AdapterRemoval - cleaning next-generation sequencing reads * * * * Copyright (C) 2011 by Stinus Lindgreen - stinus@binf.ku.dk * * Copyright (C) 2014 by Mikkel Schubert - mikkelsch@gmail.com * * * * If you use the program, please cite the paper: * * S. Lindgreen (2012): AdapterRemoval: Easy Cleaning of Next Generation * * Sequencing Reads, BMC Research Notes, 5:337 * * http://www.biomedcentral.com/1756-0500/5/337/ * * * * This program is free software: you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation, either version 3 of the License, or * * (at your option) any later version. * * * * This program is distributed in the hope that it will be useful, * * but WITHOUT ANY WARRANTY; without even the implied warranty of * * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * * GNU General Public License for more details. * * * * You should have received a copy of the GNU General Public License * * along with this program. If not, see . * \*************************************************************************/ #include #include #include #include #include #include #include "timer.hpp" #include "threads.hpp" namespace ar { //! Print progress report every N items const size_t REPORT_EVERY = 1e6; //! Number of blocks to store for calculating mean rate const size_t AVG_BLOCKS = 10; double get_current_time() { struct timeval timestamp; gettimeofday(×tamp, nullptr); return timestamp.tv_sec + timestamp.tv_usec / 1e6; } std::string thousands_sep(size_t number) { if (!number) { return std::string(1, '0'); } static const std::locale locale; static const std::numpunct& facet = std::use_facet >(locale); std::string str; for (size_t i = 1; number; ++i) { str.append(1, '0' + number % 10); number /= 10; if (number && (i % 3 == 0)) { str.append(1, facet.thousands_sep()); } } return std::string(str.rbegin(), str.rend()); } std::string format_time(double seconds) { std::stringstream stream; stream.precision(1); stream << std::setfill('0'); if (seconds > 60 * 60) { stream << static_cast(seconds) / (60 * 60) << ":"; stream << std::setw(2); } if (seconds > 60) { stream << (static_cast(seconds) % (60 * 60)) / 60 << ":"; stream << std::setw(4) << std::setfill('0'); } stream << std::fixed << (static_cast(seconds * 100) % 6000) / 100.0 << "s"; return stream.str(); } timer::timer(const std::string& what) : m_what(what) , m_total(0) , m_first_time(get_current_time()) , m_counts() { m_counts.push_back(time_count_pair(get_current_time(), 0)); } void timer::increment(size_t inc) { m_total += inc; m_counts.back().second += inc; if (m_counts.back().second >= REPORT_EVERY) { const double current_time = get_current_time(); // Number of seconds since oldest block was created const double seconds = current_time - m_counts.front().first; size_t current_total = 0; for (const auto& time_block : m_counts) { current_total += time_block.second; } do_print(static_cast(current_total / seconds), current_time); m_counts.push_back(time_count_pair(current_time, 0)); while (m_counts.size() > AVG_BLOCKS) { m_counts.pop_front(); } } } void timer::finalize() const { const double current_time = get_current_time(); const double seconds = current_time - m_first_time; do_print(static_cast(m_total / seconds), current_time, true); } void timer::do_print(size_t rate, double current_time, bool finalize) const { print_locker lock(false); if (finalize) { std::cerr << "\rProcessed a total of "; } else { std::cerr << "\rProcessed "; } if (rate > 10000) { rate = (rate / 1000) * 1000; } std::cerr << thousands_sep(m_total) << " " << m_what << " in " << format_time(current_time - m_first_time) << "; " << thousands_sep(rate) << " " << m_what << " per second "; if (finalize) { std::cerr << "on average ..." << std::endl; } else { std::cerr << "..."; std::cerr.flush(); lock.partial_stderr_output(); } } } // namespace ar adapterremoval-2.3.1/src/timer.hpp000066400000000000000000000063431350370616400171560ustar00rootroot00000000000000/*************************************************************************\ * AdapterRemoval - cleaning next-generation sequencing reads * * * * Copyright (C) 2011 by Stinus Lindgreen - stinus@binf.ku.dk * * Copyright (C) 2014 by Mikkel Schubert - mikkelsch@gmail.com * * * * If you use the program, please cite the paper: * * S. Lindgreen (2012): AdapterRemoval: Easy Cleaning of Next Generation * * Sequencing Reads, BMC Research Notes, 5:337 * * http://www.biomedcentral.com/1756-0500/5/337/ * * * * This program is free software: you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation, either version 3 of the License, or * * (at your option) any later version. * * * * This program is distributed in the hope that it will be useful, * * but WITHOUT ANY WARRANTY; without even the implied warranty of * * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * * GNU General Public License for more details. * * * * You should have received a copy of the GNU General Public License * * along with this program. If not, see . * \*************************************************************************/ #ifndef TIMER_H #define TIMER_H #include #include namespace ar { /** * Simply class for reporting current progress of a run. * * Every 1 million records / reads / etc processed, when the counter is * incremented using the 'increment' function, a progress report is printed: * "Processed last 1,000,000 pairs in 14.1s; 2,000,000 pairs in 28.9s ..." * * A final summary is printed using the 'finalize' function: * "Processed a total of 4,000,000 reads in 31.9s ..." */ class timer { public: /* Constructor. * * @param what Short name of what is being processed, for use in reports. */ timer(const std::string& what); /** Increment the progress, and (possibly) print a status report. */ void increment(size_t inc = 1); /** Print final summary based on the number of increments. */ void finalize() const; private: typedef std::pair time_count_pair; typedef std::deque time_count_deque; /** Print summary based on current rate; finalize to end with newline. */ void do_print(size_t rate, double current_time, bool finalize = false) const; //! Description of what is being processed. std::string m_what; //! Total number of items processed size_t m_total; //! Starting time (in seconds) of the timer. double m_first_time; //! Counts for last N updates, for calculating running mean rate. time_count_deque m_counts; }; } // namespace ar #endif adapterremoval-2.3.1/src/trimmed_reads.cpp000066400000000000000000000143771350370616400206560ustar00rootroot00000000000000/*************************************************************************\ * AdapterRemoval - cleaning next-generation sequencing reads * * * * Copyright (C) 2011 by Stinus Lindgreen - stinus@binf.ku.dk * * Copyright (C) 2014 by Mikkel Schubert - mikkelsch@gmail.com * * * * If you use the program, please cite the paper: * * S. Lindgreen (2012): AdapterRemoval: Easy Cleaning of Next Generation * * Sequencing Reads, BMC Research Notes, 5:337 * * http://www.biomedcentral.com/1756-0500/5/337/ * * * * This program is free software: you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation, either version 3 of the License, or * * (at your option) any later version. * * * * This program is distributed in the hope that it will be useful, * * but WITHOUT ANY WARRANTY; without even the implied warranty of * * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * * GNU General Public License for more details. * * * * You should have received a copy of the GNU General Public License * * along with this program. If not, see . * \*************************************************************************/ #include "trimmed_reads.hpp" #include "userconfig.hpp" namespace ar { inline void add_chunk(chunk_vec& chunks, size_t target, output_chunk_ptr chunk) { if (chunk.get()) { chunks.push_back(chunk_pair(target, std::move(chunk))); } } trimmed_reads::trimmed_reads(const userconfig& config, size_t offset, bool eof) : m_config(config) , m_encoding(*config.quality_output_fmt) , m_offset(offset) , m_mate_1() , m_mate_2() , m_singleton() , m_collapsed() , m_collapsed_truncated() , m_discarded() { m_mate_1.reset(new fastq_output_chunk(eof)); if (config.paired_ended_mode && !config.interleaved_output) { m_mate_2.reset(new fastq_output_chunk(eof)); } if (!config.combined_output) { m_discarded.reset(new fastq_output_chunk(eof)); if (config.paired_ended_mode) { m_singleton.reset(new fastq_output_chunk(eof)); } if (config.collapse) { m_collapsed.reset(new fastq_output_chunk(eof)); if (!config.preserve5p) { m_collapsed_truncated.reset(new fastq_output_chunk(eof)); } } } } void trimmed_reads::add_mate_1_read(fastq& read, read_status state, size_t read_count) { // Single end reads always go into the mate 1 file or the discarded file distribute_read(m_mate_1, m_mate_1, read, state, read_status::passed, read_count); } void trimmed_reads::add_mate_2_read(fastq& read, read_status state, size_t read_count) { // Single end reads always go into the mate 2 file or the discarded file distribute_read(m_mate_2, m_mate_1, read, state, read_status::passed, read_count); } void trimmed_reads::add_pe_reads(fastq& read_1, read_status state_1, fastq& read_2, read_status state_2) { distribute_read(m_mate_1, m_mate_1, read_1, state_1, state_2); distribute_read(m_mate_2, m_mate_1, read_2, state_2, state_1); } void trimmed_reads::add_collapsed_read(fastq& read, read_status state, size_t read_count) { output_chunk_ptr& destination = m_config.combined_output ? m_mate_1 : m_collapsed; // Collapsed reads may go into the mate 1, mate 2, or discard file distribute_read(destination, destination, read, state, read_status::passed, read_count); } void trimmed_reads::add_collapsed_truncated_read(fastq& read, read_status state, size_t read_count) { output_chunk_ptr& destination = m_config.combined_output ? m_mate_1 : m_collapsed_truncated; // Collapsed tr. reads may go into the mate 1, mate 2, or discard file distribute_read(destination, destination, read, state, read_status::passed, read_count); } chunk_vec trimmed_reads::finalize() { chunk_vec chunks; add_chunk(chunks, m_offset + ai_write_mate_1, std::move(m_mate_1)); add_chunk(chunks, m_offset + ai_write_mate_2, std::move(m_mate_2)); add_chunk(chunks, m_offset + ai_write_singleton, std::move(m_singleton)); add_chunk(chunks, m_offset + ai_write_collapsed, std::move(m_collapsed)); add_chunk(chunks, m_offset + ai_write_collapsed_truncated, std::move(m_collapsed_truncated)); add_chunk(chunks, m_offset + ai_write_discarded, std::move(m_discarded)); return chunks; } void trimmed_reads::distribute_read(output_chunk_ptr& regular, output_chunk_ptr& interleaved, fastq& read, read_status state_1, read_status state_2, size_t read_count) { if (state_1 == read_status::passed) { if (state_2 == read_status::passed || m_config.combined_output) { if (m_config.interleaved_output) { interleaved->add(m_encoding, read, read_count); } else { regular->add(m_encoding, read, read_count); } } else { m_singleton->add(m_encoding, read, read_count); } } else if (m_config.combined_output) { read.discard(); if (m_config.interleaved_output) { interleaved->add(m_encoding, read, read_count); } else { regular->add(m_encoding, read, read_count); } } else { m_discarded->add(m_encoding, read, read_count); } } } // namespace ar adapterremoval-2.3.1/src/trimmed_reads.hpp000066400000000000000000000155661350370616400206640ustar00rootroot00000000000000/*************************************************************************\ * AdapterRemoval - cleaning next-generation sequencing reads * * * * Copyright (C) 2011 by Stinus Lindgreen - stinus@binf.ku.dk * * Copyright (C) 2014 by Mikkel Schubert - mikkelsch@gmail.com * * * * If you use the program, please cite the paper: * * S. Lindgreen (2012): AdapterRemoval: Easy Cleaning of Next Generation * * Sequencing Reads, BMC Research Notes, 5:337 * * http://www.biomedcentral.com/1756-0500/5/337/ * * * * This program is free software: you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation, either version 3 of the License, or * * (at your option) any later version. * * * * This program is distributed in the hope that it will be useful, * * but WITHOUT ANY WARRANTY; without even the implied warranty of * * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * * GNU General Public License for more details. * * * * You should have received a copy of the GNU General Public License * * along with this program. If not, see . * \*************************************************************************/ #ifndef TRIMMED_READS_H #define TRIMMED_READS_H #include #include "fastq_io.hpp" #include "scheduler.hpp" #include "statistics.hpp" class fastq; class userconfig; namespace ar { //! Enum representing the possible states of read processing enum class read_status { //! Read passed all checks, and should be written to the main output file passed, //! Read failed one or more checks, and should be discarded; this may //! include stripping the sequence and qualities, and flagging the read failed, }; /** * Helper-class for directing trimmed reads to the next step in the pipeline. */ class trimmed_reads { public: /** * Constructor. * * @param config Global User-config instance; must outlive instance. * @param config offset The file-offset for the reads being processed. * @param config eof If true, this chunk of reads are at the EOF. */ trimmed_reads(const userconfig& config, size_t offset, bool eof); /** * Encodes and caches the specified mate 1 read. * * @param read Processed FASTQ read. * @param state FAILED or PASSED; determines destination file. * @param read_count Number of actual reads represented by 'read'; for * merged sequences this may be > 1. * * Note that 'read' may be modified (truncated) depending on user options. */ void add_mate_1_read(fastq& read, read_status state, size_t read_count = 1); /** * Encodes and caches the specified mate 2 read. * * @param read Processed FASTQ read. * @param state FAILED or PASSED; determines destination file. * @param read_count Number of actual reads represented by 'read'; for * merged sequences this may be > 1. * * Note that 'read' may be modified (truncated) depending on user options. */ void add_mate_2_read(fastq& read, read_status state, size_t read_count = 1); /** * Encodes and caches the specified pair of reads. * * @param read_1 Processed mate 1 FASTQ read. * @param state_1 FAILED or PASSED; determines destination file for mate 1. * @param read_2 Processed mate 2 FASTQ read. * @param state_2 FAILED or PASSED; determines destination file for mate 2. * * Note that 'read' may be modified (truncated) depending on user options. */ void add_pe_reads(fastq& read_1, read_status state_1, fastq& read_2, read_status state_2); /** * Encodes and caches the specified collapsed read. * * @param read Processed FASTQ read. * @param state FAILED or PASSED; determines destination file. * @param read_count Number of actual reads represented by 'read'; for * merged sequences this may be > 1. * * Note that 'read' may be modified (truncated) depending on user options. */ void add_collapsed_read(fastq& read, read_status, size_t read_count = 1); /** * Encodes and caches the specified collapsed, truncated read. * * @param read Processed FASTQ read. * @param state FAILED or PASSED; determines destination file. * @param read_count Number of actual reads represented by 'read'; for * merged sequences this may be > 1. * * Note that 'read' may be modified (truncated) depending on user options. */ void add_collapsed_truncated_read(fastq& read, read_status state, size_t read_count = 1); /** Returns vector of chunks from all cached reads. */ chunk_vec finalize(); //! Copy construction not supported trimmed_reads(const trimmed_reads&) = delete; //! Assignment not supported trimmed_reads& operator=(const trimmed_reads&) = delete; private: /* * Helper function; assigns a given read to a cache depending on state and * user settings, it's state (state_1) and the state of its mate (state_2). * * If interleaved output is enabled, reads are typically (depending on * state, etc.) written to 'regular', and are otherwise written to * 'interleaved'. */ void distribute_read(output_chunk_ptr& regular, output_chunk_ptr& interleaved, fastq& read, read_status state_1, read_status state_2, size_t read_count = 1); //! User configuration; must outlive instance. const userconfig& m_config; //! Output-encoding used to write reads. const fastq_encoding& m_encoding; //! The offset of this chunk of reads. size_t m_offset; //! Pointer to cached mate 1 reads. output_chunk_ptr m_mate_1; //! Pointer to cached mate 2 reads; may be nullptr. output_chunk_ptr m_mate_2; //! Pointer to cached singleton reads; may be nullptr. output_chunk_ptr m_singleton; //! Pointer to cached collapsed reads; may be nullptr. output_chunk_ptr m_collapsed; //! Pointer to cached collapsed, truncated reads; may be nullptr. output_chunk_ptr m_collapsed_truncated; //! Pointer to cached discarded reads; may be nullptr. output_chunk_ptr m_discarded; }; } // namespace ar #endif adapterremoval-2.3.1/src/userconfig.cpp000066400000000000000000001060531350370616400201740ustar00rootroot00000000000000/*************************************************************************\ * AdapterRemoval - cleaning next-generation sequencing reads * * * * Copyright (C) 2011 by Stinus Lindgreen - stinus@binf.ku.dk * * Copyright (C) 2014 by Mikkel Schubert - mikkelsch@gmail.com * * * * If you use the program, please cite the paper: * * S. Lindgreen (2012): AdapterRemoval: Easy Cleaning of Next Generation * * Sequencing Reads, BMC Research Notes, 5:337 * * http://www.biomedcentral.com/1756-0500/5/337/ * * * * This program is free software: you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation, either version 3 of the License, or * * (at your option) any later version. * * * * This program is distributed in the hope that it will be useful, * * but WITHOUT ANY WARRANTY; without even the implied warranty of * * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * * GNU General Public License for more details. * * * * You should have received a copy of the GNU General Public License * * along with this program. If not, see . * \*************************************************************************/ #include #include #include #include #include #include #include #include "alignment.hpp" #include "debug.hpp" #include "fastq.hpp" #include "strutils.hpp" #include "userconfig.hpp" namespace ar { size_t get_seed() { struct timeval timestamp; gettimeofday(×tamp, nullptr); return (timestamp.tv_sec << 20) | timestamp.tv_usec; } fastq_encoding_ptr select_encoding(const std::string& name, const std::string& value, size_t quality_max = MAX_PHRED_SCORE_DEFAULT) { fastq_encoding_ptr ptr; const std::string uppercase_value = toupper(value); if (uppercase_value == "33") { ptr.reset(new fastq_encoding(PHRED_OFFSET_33, quality_max)); } else if (uppercase_value == "64") { ptr.reset(new fastq_encoding(PHRED_OFFSET_64, quality_max)); } else if (uppercase_value == "SOLEXA") { ptr.reset(new fastq_encoding_solexa(quality_max)); } else { std::cerr << "Error: Invalid value for " << name << ": '" << value << "'\n" << " expected values 33, 64, or solexa." << std::endl; } return ptr; } std::pair parse_trim_argument(const string_vec& values) { unsigned mate_1 = 0; unsigned mate_2 = 0; switch (values.size()) { case 1: mate_1 = str_to_unsigned(values.front()); mate_2 = mate_1; break; case 2: mate_1 = str_to_unsigned(values.front()); mate_2 = str_to_unsigned(values.back()); break; default: throw std::invalid_argument("please specify exactly one or two values"); } return std::pair(mate_1, mate_2); } userconfig::userconfig(const std::string& name, const std::string& version, const std::string& help) : run_type(ar_command::trim_adapters) , basename("your_output") , input_files_1() , input_files_2() , paired_ended_mode(false) , interleaved_input(false) , interleaved_output(false) , combined_output(false) , mate_separator(MATE_SEPARATOR) , min_genomic_length(15) , max_genomic_length(std::numeric_limits::max()) , min_adapter_overlap(0) , min_alignment_length(11) , mismatch_threshold(-1.0) , quality_input_fmt() , quality_output_fmt() , trim_fixed_5p(0, 0) , trim_fixed_3p(0, 0) , trim_by_quality(false) , trim_window_length(std::numeric_limits::quiet_NaN()) , low_quality_score(2) , trim_ambiguous_bases(false) , max_ambiguous_bases(1000) , preserve5p(false) , collapse(false) , deterministic(false) , shift(2) , seed(get_seed()) , max_threads(1) , gzip(false) , gzip_level(6) , bzip2(false) , bzip2_level(9) , barcode_mm(0) , barcode_mm_r1(0) , barcode_mm_r2(0) , adapters() , argparser(name, version, help) , adapter_1("AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG") , adapter_2("AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT") , adapter_list() , barcode_list() , quality_input_base("33") , quality_output_base("33") , quality_max(MAX_PHRED_SCORE_DEFAULT) , mate_separator_str(1, MATE_SEPARATOR) , interleaved(false) , identify_adapters(false) , demultiplex_sequences(false) , trim5p() , trim3p() { argparser.add_header("OPTIONS:"); argparser["--file1"] = new argparse::many(&input_files_1, "FILE [FILE ...]", "Input files containing mate 1 reads or single-ended reads; " "one or more files may be listed [REQUIRED]."); argparser["--file2"] = new argparse::many(&input_files_2, "[FILE ...]", "Input files containing mate 2 reads; if used, then the same " "number of files as --file1 must be listed [OPTIONAL]."); argparser["--identify-adapters"] = new argparse::flag(&identify_adapters, "Attempt to identify the adapter pair of PE reads, by searching " "for overlapping mate reads [default: %default]."); argparser["--threads"] = new argparse::knob(&max_threads, "THREADS", "Maximum number of threads [default: %default]"); argparser.add_header("FASTQ OPTIONS:"); argparser["--qualitybase"] = new argparse::any(&quality_input_base, "BASE", "Quality base used to encode Phred scores in input; either 33, " "64, or solexa [default: %default]."); argparser["--qualitybase-output"] = new argparse::any(&quality_output_base, "BASE", "Quality base used to encode Phred scores in output; either 33, " "64, or solexa. By default, reads will be written in the same " "format as the that specified using --qualitybase."); argparser["--qualitymax"] = new argparse::knob(&quality_max, "BASE", "Specifies the maximum Phred score expected in input files, and " "used when writing output. ASCII encoded values are limited to " "the characters '!' (ASCII = 33) to '~' (ASCII = 126), meaning " "that possible scores are 0 - 93 with offset 33, and 0 - 62 " "for offset 64 and Solexa scores [default: %default]."); argparser["--mate-separator"] = new argparse::any(&mate_separator_str, "CHAR", "Character separating the mate number (1 or 2) from the read name " "in FASTQ records [default: '%default']."); argparser["--interleaved"] = new argparse::flag(&interleaved, "This option enables both the --interleaved-input option and the " "--interleaved-output option [default: %default]."); argparser["--interleaved-input"] = new argparse::flag(&interleaved_input, "The (single) input file provided contains both the mate 1 and " "mate 2 reads, one pair after the other, with one mate 1 reads " "followed by one mate 2 read. This option is implied by the " "--interleaved option [default: %default]."); argparser["--interleaved-output"] = new argparse::flag(&interleaved_output, "If set, trimmed paired-end reads are written to a single file " "containing mate 1 and mate 2 reads, one pair after the other. " "This option is implied by the --interleaved option [default: " "%default]."); argparser["--combined-output"] = new argparse::flag(&combined_output, "If set, all reads are written to the same file(s), specified by " "--output1 and --output2 (--output1 only if --interleaved-output " "is not set). Discarded reads are replaced with a single 'N' with " "Phred score 0 [default: %default]."); argparser.add_header("OUTPUT FILES:"); argparser["--basename"] = new argparse::any(&basename, "BASENAME", "Default prefix for all output files for which no filename was " "explicitly set [default: %default]."); argparser["--settings"] = new argparse::any(nullptr, "FILE", "Output file containing information on the parameters used in the " "run as well as overall statistics on the reads after trimming " "[default: BASENAME.settings]"); argparser["--output1"] = new argparse::any(nullptr, "FILE", "Output file containing trimmed mate1 reads [default: " "BASENAME.pair1.truncated (PE), BASENAME.truncated (SE), or " "BASENAME.paired.truncated (interleaved PE)]"); argparser["--output2"] = new argparse::any(nullptr, "FILE", "Output file containing trimmed mate 2 reads [default: " "BASENAME.pair2.truncated (only used in PE mode, but not if " "--interleaved-output is enabled)]"); argparser["--singleton"] = new argparse::any(nullptr, "FILE", "Output file to which containing paired reads for which the mate " "has been discarded [default: BASENAME.singleton.truncated]"); argparser["--outputcollapsed"] = new argparse::any(nullptr, "FILE", "If --collapsed is set, contains overlapping mate-pairs which " "have been merged into a single read (PE mode) or reads for which " "the adapter was identified by a minimum overlap, indicating that " "the entire template molecule is present. This does not include " "which have subsequently been trimmed due to low-quality or " "ambiguous nucleotides [default: BASENAME.collapsed]"); argparser["--outputcollapsedtruncated"] = new argparse::any(nullptr, "FILE", "Collapsed reads (see --outputcollapsed) which were trimmed due " "the presence of low-quality or ambiguous nucleotides " "[default: BASENAME.collapsed.truncated]"); argparser["--discarded"] = new argparse::any(nullptr, "FILE", "Contains reads discarded due to the --minlength, --maxlength or " "--maxns options [default: BASENAME.discarded]"); argparser.add_header("OUTPUT COMPRESSION:"); argparser["--gzip"] = new argparse::flag(&gzip, "Enable gzip compression [default: %default]"); argparser["--gzip-level"] = new argparse::knob(&gzip_level, "LEVEL", "Compression level, 0 - 9 [default: %default]"); argparser["--bzip2"] = new argparse::flag(&bzip2, "Enable bzip2 compression [default: %default]"); argparser["--bzip2-level"] = new argparse::knob(&bzip2_level, "LEVEL", "Compression level, 0 - 9 [default: %default]"); argparser.add_header("TRIMMING SETTINGS:"); // Backwards compatibility with AdapterRemoval v1; not recommended due to // schematicts that differ from most other adapter trimming programs, // namely requiring that the --pcr2 sequence is that which is observed in // the reverse complement of mate 2, rather than in the raw reads. argparser["--pcr1"] = new argparse::any(&adapter_1, "SEQUENCE", "HIDDEN"); argparser["--pcr2"] = new argparse::any(&adapter_2, "SEQUENCE", "HIDDEN"); argparser["--adapter1"] = new argparse::any(&adapter_1, "SEQUENCE", "Adapter sequence expected to be found in mate 1 reads " "[default: %default]."); argparser["--adapter2"] = new argparse::any(&adapter_2, "SEQUENCE", "Adapter sequence expected to be found in mate 2 reads " "[default: %default]."); argparser["--adapter-list"] = new argparse::any(&adapter_list, "FILENAME", "Read table of white-space separated adapters pairs, used as if " "the first column was supplied to --adapter1, and the second " "column was supplied to --adapter2; only the first adapter in " "each pair is required SE trimming mode [default: %default]."); argparser.add_seperator(); argparser["--minadapteroverlap"] = new argparse::knob(&min_adapter_overlap, "LENGTH", "In single-end mode, reads are only trimmed if the overlap " "between read and the adapter is at least X bases long, not " "counting ambiguous nucleotides (N); this is independent of the " "--minalignmentlength when using --collapse, allowing a " "conservative selection of putative complete inserts while " "ensuring that all possible adapter contamination is trimmed " "[default: %default]."); argparser["--mm"] = new argparse::floaty_knob(&mismatch_threshold, "MISMATCH_RATE", "Max error-rate when aligning reads and/or adapters. If > 1, the " "max error-rate is set to 1 / MISMATCH_RATE; if < 0, the defaults " "are used, otherwise the user-supplied value is used directly " "[default: 1/3 for trimming; 1/10 when identifying adapters]."); argparser["--shift"] = new argparse::knob(&shift, "N", "Consider alignments where up to N nucleotides are missing from " "the 5' termini [default: %default]."); argparser.add_seperator(); argparser["--trim5p"] = new argparse::many(&trim5p, "N [N]", "Trim the 5' of reads by a fixed amount after removing adapters, " "but before carrying out quality based trimming. Specify one " "value to trim mate 1 and mate 2 reads the same amount, or two " "values separated by a space to trim each mate different amounts " "[default: no trimming]."); argparser["--trim3p"] = new argparse::many(&trim3p, "N [N]", "Trim the 3' of reads by a fixed amount. See --trim5p."); argparser["--trimns"] = new argparse::flag(&trim_ambiguous_bases, "If set, trim ambiguous bases (N) at 5'/3' termini " "[default: %default]"); argparser["--maxns"] = new argparse::knob(&max_ambiguous_bases, "MAX", "Reads containing more ambiguous bases (N) than this number after " "trimming are discarded [default: %default]."); argparser["--trimqualities"] = new argparse::flag(&trim_by_quality, "If set, trim bases at 5'/3' termini with quality scores <= to " "--minquality value [default: %default]"); argparser["--trimwindows"] = new argparse::floaty_knob(&trim_window_length, "INT", "If set, quality trimming will be carried out using window based " "approach, where windows with an average quality less than " "--minquality will be trimmed. If >= 1, this value will be used " "as the window size. If the value is < 1, the value will be " "multiplied with the read length to determine a window size per " "read. If the resulting window size is 0 or larger than the read " "length, the read length is used as the window size. This option " "implies --trimqualities [default: %default]."); argparser["--minquality"] = new argparse::knob(&low_quality_score, "PHRED", "Inclusive minimum; see --trimqualities for details " "[default: %default]"); argparser["--preserve5p"] = new argparse::flag(&preserve5p, "If set, bases at the 5p will not be trimmed by --trimns, " "--trimqualities, and --trimwindows. Collapsed reads will " "not be quality trimmed when this option is enabled " "[default: 5p bases are trimmed]"); argparser.add_seperator(); argparser["--minlength"] = new argparse::knob(&min_genomic_length, "LENGTH", "Reads shorter than this length are discarded " "following trimming [default: %default]."); argparser["--maxlength"] = new argparse::knob(&max_genomic_length, "LENGTH", "Reads longer than this length are discarded " "following trimming [default: %default]."); argparser.add_header("READ MERGING:"); argparser["--collapse"] = new argparse::flag(&collapse, "When set, paired ended read alignments of --minalignmentlength " "or more bases are combined into a single consensus sequence, " "representing the complete insert, and written to either " "basename.collapsed or basename.collapsed.truncated (if trimmed " "due to low-quality bases following collapse); for single-ended " "reads, putative complete inserts are identified as having at " "least --minalignmentlength bases overlap with the adapter " "sequence, and are written to the the same files " "[default: %default]."); argparser["--collapse-deterministic"] = new argparse::flag(&deterministic, "In standard --collapse mode, AdapterRemoval will randomly select " "one of two different overlapping bases if these have the same " "quality (otherwise it picks the highest quality base). With " "--collapse-deterministic, AdapterRemoval will instead set such " "bases to N. This option implies --collapse [default: %default]."); argparser["--minalignmentlength"] = new argparse::knob(&min_alignment_length, "LENGTH", "If --collapse is set, paired reads must overlap at least this " "number of bases to be collapsed, and single-ended reads must " "overlap at least this number of bases with the adapter to be " "considered complete template molecules [default: %default]."); argparser["--seed"] = new argparse::knob(&seed, "SEED", "Sets the RNG seed used when choosing between bases with equal " "Phred scores when --collapse is enabled. This option is not " "available if more than one thread is used. If not specified, a" "seed is generated using the current time."); argparser.add_header("DEMULTIPLEXING:"); argparser["--barcode-list"] = new argparse::any(&barcode_list, "FILENAME", "List of barcodes or barcode pairs for single or double-indexed " "demultiplexing. Note that both indexes should be specified for " "both single-end and paired-end trimming, if double-indexed " "multiplexing was used, in order to ensure that the demultiplexed " "reads can be trimmed correctly [default: %default]."); argparser["--barcode-mm"] = new argparse::knob(&barcode_mm, "N", "Maximum number of mismatches allowed when counting mismatches in " "both the mate 1 and the mate 2 barcode for paired reads."); argparser["--barcode-mm-r1"] = new argparse::knob(&barcode_mm_r1, "N", "Maximum number of mismatches allowed for the mate 1 barcode; " "if not set, this value is equal to the '--barcode-mm' value; " "cannot be higher than the '--barcode-mm value'."); argparser["--barcode-mm-r2"] = new argparse::knob(&barcode_mm_r2, "N", "Maximum number of mismatches allowed for the mate 2 barcode; " "if not set, this value is equal to the '--barcode-mm' value; " "cannot be higher than the '--barcode-mm value'."); argparser["--demultiplex-only"] = new argparse::flag(&demultiplex_sequences, "Only carry out demultiplexing using the list of barcodes " "supplied with --barcode-list. No other processing is done."); } argparse::parse_result userconfig::parse_args(int argc, char *argv[]) { if (argc <= 1) { argparser.print_help(); return argparse::parse_result::error; } const argparse::parse_result result = argparser.parse_args(argc, argv); if (result != argparse::parse_result::ok) { return result; } // --collapse-deterministic implies --collapse collapse |= deterministic; quality_input_fmt = select_encoding("--qualitybase", quality_input_base, quality_max); if (!quality_input_fmt.get()) { return argparse::parse_result::error; } if (argparser.is_set("--qualitybase-output")) { quality_output_fmt = select_encoding("--qualitybase-out", quality_output_base, quality_max); if (!quality_output_fmt.get()) { return argparse::parse_result::error; } } else { // Default to using the same output encoding as the input quality_output_fmt = select_encoding("--qualitybase", quality_input_base, quality_max); if (!quality_output_fmt.get()) { return argparse::parse_result::error; } } if (mate_separator_str.size() != 1) { std::cerr << "Error: The argument for --mate-separator must be " "exactly one character long, not " << mate_separator_str.size() << " characters!" << std::endl; return argparse::parse_result::error; } else { mate_separator = mate_separator_str.at(0); } // Previous settings are overwritten; this ensures that bad arguments are still caught if (identify_adapters) { // By default quality scores are ignored when inferring adapter // sequences. However, arguments are still checked above. quality_input_fmt.reset(new fastq_encoding(PHRED_OFFSET_33, MAX_PHRED_SCORE)); quality_output_fmt.reset(new fastq_encoding(PHRED_OFFSET_33, MAX_PHRED_SCORE)); run_type = ar_command::identify_adapters; } if (demultiplex_sequences) { if (identify_adapters) { std::cerr << "Error: Cannot use --identify-adapters and " << "--demultiplex-only at the same time!" << std::endl; return argparse::parse_result::error; } else if (!argparser.is_set("--barcode-list")) { std::cerr << "Error: Cannot use --demultiplex-only without specifying " << "a list of barcodes using --barcode-list!" << std::endl; return argparse::parse_result::error; } run_type = ar_command::demultiplex_sequences; } if (low_quality_score > static_cast(MAX_PHRED_SCORE)) { std::cerr << "Error: Invalid value for --minquality: " << low_quality_score << "\n" << " must be in the range 0 .. " << MAX_PHRED_SCORE << std::endl; return argparse::parse_result::error; } else if (trim_window_length >= 0) { trim_by_quality = true; } else if (trim_window_length < 0.0) { std::cerr << "Error: Invalid value for --trimwindows (" << trim_window_length << "); value must be >= 0." << std::endl; return argparse::parse_result::error; } // Check for invalid combinations of settings if (input_files_1.empty() && input_files_2.empty()) { std::cerr << "Error: No input files (--file1 / --file2) specified.\n" << "Please specify at least one input file using --file1 FILENAME." << std::endl; return argparse::parse_result::error; } else if (!input_files_2.empty() && (input_files_1.size() != input_files_2.size())) { std::cerr << "Error: Different number of files specified for --file1 and --file2." << std::endl; return argparse::parse_result::error; } else if (!input_files_2.empty()) { paired_ended_mode = true; min_adapter_overlap = 0; } interleaved_input |= interleaved; interleaved_output |= interleaved; if (interleaved_input) { if (!input_files_2.empty()) { std::cerr << "Error: The options --interleaved and " << "--interleaved-input cannot be used " << "together with the --file2 option; only --file1 must " << "be specified!" << std::endl; return argparse::parse_result::error; } // Enable paired end mode .. other than the FASTQ reader, all other // parts of the pipeline simply run in paired-end mode. paired_ended_mode = true; } if (identify_adapters && !paired_ended_mode) { std::cerr << "Error: Both input files (--file1 / --file2) must be " << "specified when using --identify-adapters, or input must " << "be interleaved FASTQ reads (requires --interleaved)." << std::endl; return argparse::parse_result::error; } // (Optionally) read adapters from file and validate if (!setup_adapter_sequences()) { return argparse::parse_result::error; } // Set mismatch threshold if (mismatch_threshold > 1) { mismatch_threshold = 1.0 / mismatch_threshold; } else if (mismatch_threshold < 0) { if (identify_adapters) { mismatch_threshold = 1.0 / 10.0; } else { // Defaults for PE / SE trimming (changed in v2) mismatch_threshold = 1.0 / 3.0; } } if (gzip_level > 9) { std::cerr << "Error: --gzip-level must be in the range 0 to 9, not " << gzip_level << std::endl; return argparse::parse_result::error; } if (bzip2_level < 1 || bzip2_level > 9) { std::cerr << "Error: --bzip2-level must be in the range 1 to 9, not " << bzip2_level << std::endl; return argparse::parse_result::error; } else if (bzip2 && gzip) { std::cerr << "Error: Cannot enable --gzip and --bzip2 at the same time!" << std::endl; return argparse::parse_result::error; } if (!max_threads) { std::cerr << "Error: --threads must be at least 1!" << std::endl; return argparse::parse_result::error; } else if (max_threads > 1 && argparser.is_set("--seed")) { std::cerr << "Warning: The option --seed should not be used when " << "using multiple threads; multi-threaded behavior is not " << "deterministic even with a fixed seed!" << std::endl; } try { if (argparser.is_set("--trim5p")) { trim_fixed_5p = parse_trim_argument(trim5p); } } catch (const std::invalid_argument& error) { std::cerr << "Error: Could not parse --trim5p argument(s): " << error.what() << std::endl; return argparse::parse_result::error; } try { if (argparser.is_set("--trim3p")) { trim_fixed_3p = parse_trim_argument(trim3p); } } catch (const std::invalid_argument& error) { std::cerr << "Error: Could not parse --trim3p argument(s): " << error.what() << std::endl; return argparse::parse_result::error; } return argparse::parse_result::ok; } statistics_ptr userconfig::create_stats() const { statistics_ptr stats(new statistics()); stats->number_of_reads_with_adapter.resize(adapters.adapter_count()); return stats; } bool userconfig::is_good_alignment(const alignment_info& alignment) const { if (!alignment.length || alignment.score <= 0) { return false; } // Only pairs of called bases are considered part of the alignment const size_t n_aligned = static_cast(alignment.length - alignment.n_ambiguous); size_t mm_threshold = static_cast(mismatch_threshold * n_aligned); if (n_aligned < min_adapter_overlap) { return false; } if (n_aligned < 6) { mm_threshold = 0; } else if (n_aligned < 10) { // --mm may imply fewer allowed mismatches than 1, so always compare mm_threshold = std::min(1, mm_threshold); } if (alignment.n_mismatches > mm_threshold) { return false; } return true; } bool userconfig::is_alignment_collapsible(const alignment_info& alignment) const { if (alignment.length < alignment.n_ambiguous) { throw std::invalid_argument("#ambiguous bases > read length"); } const size_t n_aligned = alignment.length - alignment.n_ambiguous; if (n_aligned < min_alignment_length) { return false; } return collapse || identify_adapters; } bool userconfig::is_acceptable_read(const fastq& seq) const { const size_t seq_len = seq.length(); return seq_len >= min_genomic_length && seq_len <= max_genomic_length && (max_ambiguous_bases >= seq_len || seq.count_ns() <= max_ambiguous_bases); } std::string userconfig::get_output_filename(const std::string& key, size_t nth) const { std::string filename = basename; if (filename.length() && filename.back() != '/') { filename.push_back('.'); } if (key == "demux_stats") { return filename += "settings"; } else if (key == "demux_unknown") { filename += "unidentified"; AR_DEBUG_ASSERT(nth <= 2); if (!interleaved_output) { if (nth) { filename.push_back('_'); filename.push_back('0' + nth); } } else { filename += ".paired"; } } else if (adapters.barcode_count()) { filename.append(adapters.get_sample_name(nth)); filename.push_back('.'); } else if (argparser.is_set(key)) { return argparser.at(key)->to_str(); } if (key == "--settings") { return filename + "settings"; } else if (key == "--outputcollapsed") { filename += "collapsed"; } else if (key == "--outputcollapsedtruncated") { filename += "collapsed.truncated"; } else if (key == "--discarded") { filename += "discarded"; } else if (paired_ended_mode) { if (key == "--output1") { if (interleaved_output) { filename += "paired"; } else { filename += "pair1"; } } else if (key == "--output2") { filename += "pair2"; } else if (key == "--singleton") { filename += "singleton"; } else if (key != "demux_unknown") { throw std::invalid_argument("invalid read-type in userconfig::get_output_filename constructor: " + key); } if (run_type != ar_command::demultiplex_sequences && key != "demux_unknown") { filename += ".truncated"; } } else if (key == "--output1") { if (run_type != ar_command::demultiplex_sequences) { filename += "truncated"; } } else if (key != "demux_unknown") { throw std::invalid_argument("invalid read-type in userconfig::get_output_filename constructor: " + key); } // Currently only when demultiplexing; for backwards compatibility if (run_type == ar_command::demultiplex_sequences) { if (filename.back() == '.') { filename += "fastq"; } else { filename += ".fastq"; } } if (gzip) { filename += ".gz"; } else if (bzip2) { filename += ".bz2"; } return filename; } bool check_and_set_barcode_mm(const argparse::parser& argparser, const std::string& key, unsigned barcode_mm, unsigned& dst) { if (!argparser.is_set(key)) { dst = barcode_mm; } else if (dst > barcode_mm) { std::cerr << "The maximum number of errors for " << key << " is set \n" "to a higher value than the total number of mismatches allowed\n" "for barcodes (--barcode-mm). Please correct these settings." << std::endl; return false; } return true; } bool userconfig::setup_adapter_sequences() { const bool pcr_is_set = argparser.is_set("--pcr1") || argparser.is_set("--pcr2"); const bool adapters_is_set = argparser.is_set("--adapter1") || argparser.is_set("--adapter2"); const bool adapter_list_is_set = argparser.is_set("--adapter-list"); if (pcr_is_set) { std::cerr << "WARNING: Command-line options --pcr1 and --pcr2 are deprecated.\n" << " Using --adapter1 and --adapter2 is recommended.\n" << " Please see documentation for more information.\n" << std::endl; } if (pcr_is_set && (adapters_is_set || adapter_list_is_set)) { std::cerr << "ERROR: " << "Either use --pcr1 and --pcr2, or use --adapter1 and " << "--adapter2 / --adapter-list, not both!\n\n" << std::endl; return false; } else if (adapters_is_set && adapter_list_is_set) { std::cerr << "ERROR: " << "Use either --adapter1 and --adapter2, or " << "--adapter-list, not both!" << std::endl; return false; } if (adapter_list_is_set) { if (!adapters.load_adapters(adapter_list, paired_ended_mode)) { return false; } else if (adapters.adapter_count()) { std::cerr << "Read " << adapters.adapter_count() << " adapters / adapter pairs from '" << adapter_list << "'..." << std::endl; } else { std::cerr << "Error: No adapter sequences found in table!" << std::endl; return false; } } else { try { adapters.add_adapters(adapter_1, adapter_2, !pcr_is_set); } catch (const fastq_error& error) { std::cerr << "Error parsing adapter sequence(s):\n" << " " << error.what() << std::endl; return false; } } if (!argparser.is_set("--barcode-mm")) { barcode_mm = barcode_mm_r1 + barcode_mm_r2; } if (!check_and_set_barcode_mm(argparser, "--barcode-mm-r1", barcode_mm, barcode_mm_r1)) { return false; } if (!check_and_set_barcode_mm(argparser, "--barcode-mm-r2", barcode_mm, barcode_mm_r2)) { return false; } if (argparser.is_set("--barcode-list")) { if (!adapters.load_barcodes(barcode_list, paired_ended_mode)) { return false; } else if (adapters.adapter_count()) { std::cerr << "Read " << adapters.barcode_count() << " barcodes / barcode pairs from '" << barcode_list << "' ..." << std::endl; } else { std::cerr << "Error: No barcodes sequences found in table!" << std::endl; return false; } } return true; } } // namespace ar adapterremoval-2.3.1/src/userconfig.hpp000066400000000000000000000213621350370616400202000ustar00rootroot00000000000000/*************************************************************************\ * AdapterRemoval - cleaning next-generation sequencing reads * * * * Copyright (C) 2011 by Stinus Lindgreen - stinus@binf.ku.dk * * Copyright (C) 2014 by Mikkel Schubert - mikkelsch@gmail.com * * * * If you use the program, please cite the paper: * * S. Lindgreen (2012): AdapterRemoval: Easy Cleaning of Next Generation * * Sequencing Reads, BMC Research Notes, 5:337 * * http://www.biomedcentral.com/1756-0500/5/337/ * * * * This program is free software: you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation, either version 3 of the License, or * * (at your option) any later version. * * * * This program is distributed in the hope that it will be useful, * * but WITHOUT ANY WARRANTY; without even the implied warranty of * * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * * GNU General Public License for more details. * * * * You should have received a copy of the GNU General Public License * * along with this program. If not, see . * \*************************************************************************/ #ifndef CONFIG_H #define CONFIG_H #include #include #include #include "adapterset.hpp" #include "argparse.hpp" #include "commontypes.hpp" #include "fastq.hpp" #include "alignment.hpp" #include "statistics.hpp" namespace ar { struct alignment_info; typedef std::unique_ptr fastq_encoding_ptr; typedef std::unique_ptr statistics_ptr; enum class ar_command { trim_adapters, identify_adapters, demultiplex_sequences, }; /** * Configuration store, containing all user-supplied options / default values, * as well as help-functions using these options. */ class userconfig { public: /** * @param name Name of program. * @param version Version string excluding program name. * @param help Help text describing program. */ userconfig(const std::string& name, const std::string& version, const std::string& help); /** Parses a set of commandline arguments. */ argparse::parse_result parse_args(int argc, char *argv[]); /** Returns new statistics object, initialized using usersettings. */ statistics_ptr create_stats() const; std::string get_output_filename(const std::string& key, size_t nth = 0) const; /** Characterize an alignment based on user settings. */ bool is_good_alignment(const alignment_info& alignment) const; /** Returns true if the alignment is sufficient for collapsing. */ bool is_alignment_collapsible(const alignment_info& alignment) const; /** Returns true if the read matches the quality criteria set by the user. **/ bool is_acceptable_read(const fastq& seq) const; //! Type of run to execute; see command ar_command run_type; //! Prefix used for output files for which no filename was explicitly set std::string basename; //! Path to input file containing mate 1 reads (required) string_vec input_files_1; //! Path to input file containing mate 2 reads (for PE reads) string_vec input_files_2; //! Set to true if both --input1 and --input2 are set, or if either of //! --interleaved or --interleaved-input are set. bool paired_ended_mode; //! Set to true if --interleaved or --interleaved-input is set. bool interleaved_input; //! Set to true if --interleaved or --interleaved-output is set. bool interleaved_output; //! Set to true if --combined-output is set. bool combined_output; //! Character separating the mate number from the read name in FASTQ reads. char mate_separator; //! The minimum length of trimmed reads (ie. genomic nts) to be retained unsigned min_genomic_length; //! The maximum length of trimmed reads (ie. genomic nts) to be retained unsigned max_genomic_length; //! The minimum required overlap before trimming single-end reads. unsigned min_adapter_overlap; //! The minimum required genomic overlap before collapsing reads into one. unsigned min_alignment_length; //! Rate of mismatches determining the threshold for a an acceptable //! alignment, depending on the length of the alignment. But see also the //! limits set in the function 'is_good_alignment'. double mismatch_threshold; //! Quality format expected in input files. fastq_encoding_ptr quality_input_fmt; //! Quality format to use when writing FASTQ records. fastq_encoding_ptr quality_output_fmt; //! Fixed number of bases to trim from 5' for mate 1 and mate 2 reads std::pair trim_fixed_5p; //! Fixed number of bases to trim from 3' for mate 1 and mate 2 reads std::pair trim_fixed_3p; //! If true, read termini are trimmed for low-quality bases. bool trim_by_quality; //! Window size for window trimming; a fraction, whole number, or negative. double trim_window_length; //! The highest quality score which is considered low-quality unsigned low_quality_score; //! If true, ambiguous bases (N) at read termini are trimmed. bool trim_ambiguous_bases; //! The maximum number of ambiguous bases (N) in an read; reads exceeding //! this number following trimming (optionally) are discarded. unsigned max_ambiguous_bases; //! If true, only the 3p is trimmed for low quality bases (if enabled) bool preserve5p; //! If true, PE reads overlapping at least 'min_alignment_length' are //! collapsed to generate a higher quality consensus sequence. bool collapse; //! Deterministic collapse; set equal-quality conflicting bases to N. bool deterministic; // Allow for slipping basepairs by allowing missing bases in adapter unsigned shift; //! RNG seed for randomly selecting between to bases with the same quality //! when collapsing overllapping PE reads. unsigned seed; //! The maximum number of threads used by the program unsigned max_threads; //! GZip compression enabled / disabled bool gzip; //! GZip compression level used for output reads unsigned int gzip_level; //! BZip2 compression enabled / disabled bool bzip2; //! BZip2 compression level used for output reads unsigned int bzip2_level; //! Maximum number of mismatches (considering both barcodes for PE) unsigned barcode_mm; //! Maximum number of mismatches (considering both barcodes for PE) unsigned barcode_mm_r1; //! Maximum number of mismatches (considering both barcodes for PE) unsigned barcode_mm_r2; adapter_set adapters; //! Copy construction not supported userconfig(const userconfig&) = delete; //! Assignment not supported userconfig& operator=(const userconfig&) = delete; private: /** Sets up adapter sequences based on user settings. * * @return True on success, false otherwise. */ bool setup_adapter_sequences(); //! Argument parser setup to parse the arguments expected by AR argparse::parser argparser; //! Sink for --adapter1, adapter sequence expected at 3' of mate 1 reads std::string adapter_1; //! Sink for --adapter2, adapter sequence expected at 3' of mate 2 reads std::string adapter_2; //! Sink for --adapter-list; list of adapter #1 and #2 sequences std::string adapter_list; //! Sink for --barcode-list; list of barcode #1 (and #2 sequences) std::string barcode_list; //! Sink for user-supplied quality score formats; use quality_input_fmt. std::string quality_input_base; //! Sink for user-supplied quality score formats; use quality_output_fmt. std::string quality_output_base; //! Sink for maximum quality score for input / output unsigned quality_max; //! Sink for the mate separator character; use mate separator std::string mate_separator_str; //! Sink for --interleaved bool interleaved; //! Sink for --identify-adapters bool identify_adapters; //! Sink for --demultiplex-sequences bool demultiplex_sequences; //! Sink for --trim5p string_vec trim5p; //! Sink for --trim3p string_vec trim3p; }; } // namespace ar #endif adapterremoval-2.3.1/src/vecutils.hpp000066400000000000000000000056041350370616400176730ustar00rootroot00000000000000/*************************************************************************\ * AdapterRemoval - cleaning next-generation sequencing reads * * * * Copyright (C) 2015 by Mikkel Schubert - mikkelsch@gmail.com * * * * If you use the program, please cite the paper: * * S. Lindgreen (2012): AdapterRemoval: Easy Cleaning of Next Generation * * Sequencing Reads, BMC Research Notes, 5:337 * * http://www.biomedcentral.com/1756-0500/5/337/ * * * * This program is free software: you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation, either version 3 of the License, or * * (at your option) any later version. * * * * This program is distributed in the hope that it will be useful, * * but WITHOUT ANY WARRANTY; without even the implied warranty of * * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * * GNU General Public License for more details. * * * * You should have received a copy of the GNU General Public License * * along with this program. If not, see . * \*************************************************************************/ #ifndef UTILS_H #define UTILS_H #include namespace ar { /** * Merge two vectors by adding each value in src to each value in 'dst'. * * If 'dst' is shorter than 'src', it is resized to the same length as 'src'. */ template void merge_vectors(std::vector& dst, const std::vector& src) { if (dst.size() < src.size()) { dst.resize(src.size()); } typename std::vector::iterator dst_it = dst.begin(); typename std::vector::const_iterator src_it = src.begin(); while (src_it != src.end()) { *dst_it++ += *src_it++; } } /** * Merge each pair of value in vectors of vectors using merge_vector. * * If 'dst' is shorter than 'src', it is resized to the same length as 'src'. */ template void merge_sub_vectors(std::vector >& dst, const std::vector >& src) { if (dst.size() < src.size()) { dst.resize(src.size()); } typename std::vector >::iterator dst_it = dst.begin(); typename std::vector >::const_iterator src_it = src.begin(); while (src_it != src.end()) { merge_vectors(*dst_it++, *src_it++); } } } // namespace ar #endif adapterremoval-2.3.1/tests/000077500000000000000000000000001350370616400156725ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/000077500000000000000000000000001350370616400200525ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/README000066400000000000000000000013221350370616400207300ustar00rootroot00000000000000Sequences: No adapter Short adapter Long adapter Complete adapter Filetypes: Unix Windows (\r\n) Automatic variants? - gzip - bzip - uncompressed Single end: x --collapse x --combined-output x --trimns x --trimqualities x --minlength x --maxlength Bad: --interleaved --interleaved-input --interleaved-output Possibilities: - adapter - overlap - collapse (yes, no, yes but too short) - lq trimming TODO: - Single-end - No adapter - No adapter, lq trimming - Single-end - No adapter - No adapter, lq trimming - No adapter, overlapping - No adapter, overlapping, lq trimming - No adapter, overlapping, too short - No adapter, overlapping, too short, lq trimming adapterremoval-2.3.1/tests/regression/demultiplexing/000077500000000000000000000000001350370616400231045ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/000077500000000000000000000000001350370616400260565ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/000077500000000000000000000000001350370616400264625ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/collapse/000077500000000000000000000000001350370616400302645ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/collapse/barcodes.txt000066400000000000000000000000661350370616400326110ustar00rootroot00000000000000sample_1 TGAGTCAT GTTAGTGG sample_2 GCAGAGAT CCTAGGGT adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/collapse/info.json000066400000000000000000000001051350370616400321060ustar00rootroot00000000000000{ "arguments": ["--collapse"], "return_code": 0, "stderr": [ ] } adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/collapse/input_1.fastq000066400000000000000000000033301350370616400327020ustar00rootroot00000000000000@read_s2_000/1 GCAGAGATACCCTAGGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_075/1 GCAGAGATCCTACAAAAGTTAAGTGCGCGTTTGGGCATCGTCCCGACGACTTCCGCTGAGTTGACTTAATGGCTTGTCGGTACACCCTAGGAGATCGGAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_000/1 TGAGTCATCCACTAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_075/1 TGAGTCATGCACAGTTACACTGCCGTTTGTCTGTCCATGTAATTGTCTAATCACTTTAGAATACGGCTCCTGATATCATCACCCCACTAACAGATCGGAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_200/1 TGAGTCATACATCCAAGTCGGGCAACCTCTCACATTACTTAGGCCAGGCACTTGCACATCGAAGCAAAGGAGAGATAATTGCCGTATCCTCTGTGCACGT + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_200/1 GCAGAGATGCCCATAAAATATTGCTCGCAACGGTATGCTAGACCCAGGACATCCGCTTTATCCGTGGTGATAGCAACTGGAGGCATCTAACGTTCACACG + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_150/1 TGAGTCATAGAATGAGCGGGGTCGACTCGTAACGATCTCTGCAGGGCGATGGTCTACATAGGCCCCACATCCAGATTATCTCGTAAAAGGAAAAACGGTT + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_150/1 GCAGAGATTAGCCCCCGGGGTGTGGGGTTTTGCTTCCGCCACAAAAATGGTGCGCTAAATGACCATTGCGTACACTCCAACGCGAAATGTAGGGCGCCGA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/collapse/input_2.fastq000066400000000000000000000033301350370616400327030ustar00rootroot00000000000000@read_s2_000/2 CCTAGGGTATCTCTGCAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_075/2 CCTAGGGTGTACCGACAAGCCATTAAGTCAACTCAGCGGAAGTCGTCGGGACGATGCCCAAACGCGCACTTAACTTTTGTAGGATCTCTGCAGATCGGAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_000/2 GTTAGTGGATGACTCAAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_075/2 GTTAGTGGGGTGATGATATCAGGAGCCGTATTCTAAAGTGATTAGACAATTACATGGACAGACAAACGGCAGTGTAACTGTGCATGACTCAAGATCGGAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_200/2 GTTAGTGGGATAATACGCTCTAGAGAAAAAGAGTGATAAGTGAATAACCGGGCTATAGTGACAAAGAATTCCGCGTTACTAAATCACCCAACCCACCTTC + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_200/2 CCTAGGGTTTACTTTTGATTCAACACCGACTTGGTCCCGCCTCCACGTGCAACACCCCCTTTTAATAGCAACGCGCTCACCGAGGCTCCTCCCATCCACA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_150/2 GTTAGTGGATGTGGTTATAGCAACCGCTCACTTCTCACGTACTGGTGATACTCCTTTGGTACTTTCAACCGTTTTTCCTTTTACGAGATAATCTGGATGT + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_150/2 CCTAGGGTCCTCTCGATTCGGCAGTACCCAATTGTTGACGATCAGCATATTATTATCTGATTGTGCTCGGCGCCCTACATTTCGCGTTGGAGTGTACGCA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 your_output.sample_1.collapsed000066400000000000000000000007501350370616400362150ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/collapse@M_read_s1_075 GCACAGTTACACTGCCGTTTGTCTGTCCATGTAATTGTCTAATCACTTTAGAATACGGCTCCTGATATCATCACC + JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ @M_read_s1_150 AGAATGAGCGGGGTCGACTCGTAACGATCTCTGCAGGGCGATGGTCTACATAGGCCCCACATCCAGATTATCTCGTAAAAGGAAAAACGGTTGAAAGTACCAAAGGAGTATCACCAGTACGTGAGAAGTGAGCGGTTGCTATAACCACAT + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ@@@AAAAAABBBBBBCCCCCCCDDDDDDDEEEEEEEEEFFFFFFFFFGGGGGGGGGGG your_output.sample_1.collapsed.truncated000066400000000000000000000000001350370616400401710ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/collapseyour_output.sample_1.discarded000066400000000000000000000000231350370616400361620ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/collapse@M_read_s1_000 + your_output.sample_1.pair1.truncated000066400000000000000000000003131350370616400372460ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/collapse@read_s1_200/1 ACATCCAAGTCGGGCAACCTCTCACATTACTTAGGCCAGGCACTTGCACATCGAAGCAAAGGAGAGATAATTGCCGTATCCTCTGTGCACGT + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 your_output.sample_1.pair2.truncated000066400000000000000000000003131350370616400372470ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/collapse@read_s1_200/2 GATAATACGCTCTAGAGAAAAAGAGTGATAAGTGAATAACCGGGCTATAGTGACAAAGAATTCCGCGTTACTAAATCACCCAACCCACCTTC + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 your_output.sample_1.settings000066400000000000000000000101261350370616400361050ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/collapseAdapterRemoval ver. 2.2.0 Trimming of double-indexed paired-end reads [Demultiplexing] Maximum mismatches (total): 0 Maximum mate 1 mismatches: 0 Maximum mate 2 mismatches: 0 [Demultiplexing samples] Name Barcode_1 Barcode_2 sample_1* TGAGTCAT GTTAGTGG sample_2 GCAGAGAT CCTAGGGT [Adapter sequences] Adapter1[1]: CCACTAAC_AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: ATGACTCA_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 4078236736 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: Yes Minimum overlap (in case of collapse): 11 [Trimming statistics] Total number of read pairs: 4 Number of unaligned read pairs: 1 Number of well aligned read pairs: 3 Number of discarded mate 1 reads: 1 Number of singleton mate 1 reads: 0 Number of discarded mate 2 reads: 1 Number of singleton mate 2 reads: 0 Number of reads with adapters[1]: 4 Number of full-length collapsed pairs: 2 Number of truncated collapsed pairs: 0 Number of retained reads: 4 Number of retained nucleotides: 409 Average length of retained reads: 102.25 [Length distribution] Length Mate1 Mate2 Singleton Collapsed CollapsedTruncated Discarded All 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 3 0 0 0 0 0 0 0 4 0 0 0 0 0 0 0 5 0 0 0 0 0 0 0 6 0 0 0 0 0 0 0 7 0 0 0 0 0 0 0 8 0 0 0 0 0 0 0 9 0 0 0 0 0 0 0 10 0 0 0 0 0 0 0 11 0 0 0 0 0 0 0 12 0 0 0 0 0 0 0 13 0 0 0 0 0 0 0 14 0 0 0 0 0 0 0 15 0 0 0 0 0 0 0 16 0 0 0 0 0 0 0 17 0 0 0 0 0 0 0 18 0 0 0 0 0 0 0 19 0 0 0 0 0 0 0 20 0 0 0 0 0 0 0 21 0 0 0 0 0 0 0 22 0 0 0 0 0 0 0 23 0 0 0 0 0 0 0 24 0 0 0 0 0 0 0 25 0 0 0 0 0 0 0 26 0 0 0 0 0 0 0 27 0 0 0 0 0 0 0 28 0 0 0 0 0 0 0 29 0 0 0 0 0 0 0 30 0 0 0 0 0 0 0 31 0 0 0 0 0 0 0 32 0 0 0 0 0 0 0 33 0 0 0 0 0 0 0 34 0 0 0 0 0 0 0 35 0 0 0 0 0 0 0 36 0 0 0 0 0 0 0 37 0 0 0 0 0 0 0 38 0 0 0 0 0 0 0 39 0 0 0 0 0 0 0 40 0 0 0 0 0 0 0 41 0 0 0 0 0 0 0 42 0 0 0 0 0 0 0 43 0 0 0 0 0 0 0 44 0 0 0 0 0 0 0 45 0 0 0 0 0 0 0 46 0 0 0 0 0 0 0 47 0 0 0 0 0 0 0 48 0 0 0 0 0 0 0 49 0 0 0 0 0 0 0 50 0 0 0 0 0 0 0 51 0 0 0 0 0 0 0 52 0 0 0 0 0 0 0 53 0 0 0 0 0 0 0 54 0 0 0 0 0 0 0 55 0 0 0 0 0 0 0 56 0 0 0 0 0 0 0 57 0 0 0 0 0 0 0 58 0 0 0 0 0 0 0 59 0 0 0 0 0 0 0 60 0 0 0 0 0 0 0 61 0 0 0 0 0 0 0 62 0 0 0 0 0 0 0 63 0 0 0 0 0 0 0 64 0 0 0 0 0 0 0 65 0 0 0 0 0 0 0 66 0 0 0 0 0 0 0 67 0 0 0 0 0 0 0 68 0 0 0 0 0 0 0 69 0 0 0 0 0 0 0 70 0 0 0 0 0 0 0 71 0 0 0 0 0 0 0 72 0 0 0 0 0 0 0 73 0 0 0 0 0 0 0 74 0 0 0 0 0 0 0 75 0 0 0 1 0 0 1 76 0 0 0 0 0 0 0 77 0 0 0 0 0 0 0 78 0 0 0 0 0 0 0 79 0 0 0 0 0 0 0 80 0 0 0 0 0 0 0 81 0 0 0 0 0 0 0 82 0 0 0 0 0 0 0 83 0 0 0 0 0 0 0 84 0 0 0 0 0 0 0 85 0 0 0 0 0 0 0 86 0 0 0 0 0 0 0 87 0 0 0 0 0 0 0 88 0 0 0 0 0 0 0 89 0 0 0 0 0 0 0 90 0 0 0 0 0 0 0 91 0 0 0 0 0 0 0 92 1 1 0 0 0 0 2 93 0 0 0 0 0 0 0 94 0 0 0 0 0 0 0 95 0 0 0 0 0 0 0 96 0 0 0 0 0 0 0 97 0 0 0 0 0 0 0 98 0 0 0 0 0 0 0 99 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 101 0 0 0 0 0 0 0 102 0 0 0 0 0 0 0 103 0 0 0 0 0 0 0 104 0 0 0 0 0 0 0 105 0 0 0 0 0 0 0 106 0 0 0 0 0 0 0 107 0 0 0 0 0 0 0 108 0 0 0 0 0 0 0 109 0 0 0 0 0 0 0 110 0 0 0 0 0 0 0 111 0 0 0 0 0 0 0 112 0 0 0 0 0 0 0 113 0 0 0 0 0 0 0 114 0 0 0 0 0 0 0 115 0 0 0 0 0 0 0 116 0 0 0 0 0 0 0 117 0 0 0 0 0 0 0 118 0 0 0 0 0 0 0 119 0 0 0 0 0 0 0 120 0 0 0 0 0 0 0 121 0 0 0 0 0 0 0 122 0 0 0 0 0 0 0 123 0 0 0 0 0 0 0 124 0 0 0 0 0 0 0 125 0 0 0 0 0 0 0 126 0 0 0 0 0 0 0 127 0 0 0 0 0 0 0 128 0 0 0 0 0 0 0 129 0 0 0 0 0 0 0 130 0 0 0 0 0 0 0 131 0 0 0 0 0 0 0 132 0 0 0 0 0 0 0 133 0 0 0 0 0 0 0 134 0 0 0 0 0 0 0 135 0 0 0 0 0 0 0 136 0 0 0 0 0 0 0 137 0 0 0 0 0 0 0 138 0 0 0 0 0 0 0 139 0 0 0 0 0 0 0 140 0 0 0 0 0 0 0 141 0 0 0 0 0 0 0 142 0 0 0 0 0 0 0 143 0 0 0 0 0 0 0 144 0 0 0 0 0 0 0 145 0 0 0 0 0 0 0 146 0 0 0 0 0 0 0 147 0 0 0 0 0 0 0 148 0 0 0 0 0 0 0 149 0 0 0 0 0 0 0 150 0 0 0 1 0 0 1 your_output.sample_1.singleton.truncated000066400000000000000000000000001350370616400402250ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/collapseyour_output.sample_2.collapsed000066400000000000000000000007501350370616400362160ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/collapse@M_read_s2_075 CCTACAAAAGTTAAGTGCGCGTTTGGGCATCGTCCCGACGACTTCCGCTGAGTTGACTTAATGGCTTGTCGGTAC + JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ @M_read_s2_150 TAGCCCCCGGGGTGTGGGGTTTTGCTTCCGCCACAAAAATGGTGCGCTAAATGACCATTGCGTACACTCCAACGCGAAATGTAGGGCGCCGAGCACAATCAGATAATAATATGCTGATCGTCAACAATTGGGTACTGCCGAATCGAGAGG + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ@@@AAAAAABBBBBBCCCCCCCDDDDDDDEEEEEEEEEFFFFFFFFFGGGGGGGGGGG your_output.sample_2.collapsed.truncated000066400000000000000000000000001350370616400401720ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/collapseyour_output.sample_2.discarded000066400000000000000000000000231350370616400361630ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/collapse@M_read_s2_000 + your_output.sample_2.pair1.truncated000066400000000000000000000003131350370616400372470ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/collapse@read_s2_200/1 GCCCATAAAATATTGCTCGCAACGGTATGCTAGACCCAGGACATCCGCTTTATCCGTGGTGATAGCAACTGGAGGCATCTAACGTTCACACG + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 your_output.sample_2.pair2.truncated000066400000000000000000000003131350370616400372500ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/collapse@read_s2_200/2 TTACTTTTGATTCAACACCGACTTGGTCCCGCCTCCACGTGCAACACCCCCTTTTAATAGCAACGCGCTCACCGAGGCTCCTCCCATCCACA + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 your_output.sample_2.settings000066400000000000000000000101261350370616400361060ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/collapseAdapterRemoval ver. 2.2.0 Trimming of double-indexed paired-end reads [Demultiplexing] Maximum mismatches (total): 0 Maximum mate 1 mismatches: 0 Maximum mate 2 mismatches: 0 [Demultiplexing samples] Name Barcode_1 Barcode_2 sample_1 TGAGTCAT GTTAGTGG sample_2* GCAGAGAT CCTAGGGT [Adapter sequences] Adapter1[1]: ACCCTAGG_AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: ATCTCTGC_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 4078236736 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: Yes Minimum overlap (in case of collapse): 11 [Trimming statistics] Total number of read pairs: 4 Number of unaligned read pairs: 1 Number of well aligned read pairs: 3 Number of discarded mate 1 reads: 1 Number of singleton mate 1 reads: 0 Number of discarded mate 2 reads: 1 Number of singleton mate 2 reads: 0 Number of reads with adapters[1]: 4 Number of full-length collapsed pairs: 2 Number of truncated collapsed pairs: 0 Number of retained reads: 4 Number of retained nucleotides: 409 Average length of retained reads: 102.25 [Length distribution] Length Mate1 Mate2 Singleton Collapsed CollapsedTruncated Discarded All 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 3 0 0 0 0 0 0 0 4 0 0 0 0 0 0 0 5 0 0 0 0 0 0 0 6 0 0 0 0 0 0 0 7 0 0 0 0 0 0 0 8 0 0 0 0 0 0 0 9 0 0 0 0 0 0 0 10 0 0 0 0 0 0 0 11 0 0 0 0 0 0 0 12 0 0 0 0 0 0 0 13 0 0 0 0 0 0 0 14 0 0 0 0 0 0 0 15 0 0 0 0 0 0 0 16 0 0 0 0 0 0 0 17 0 0 0 0 0 0 0 18 0 0 0 0 0 0 0 19 0 0 0 0 0 0 0 20 0 0 0 0 0 0 0 21 0 0 0 0 0 0 0 22 0 0 0 0 0 0 0 23 0 0 0 0 0 0 0 24 0 0 0 0 0 0 0 25 0 0 0 0 0 0 0 26 0 0 0 0 0 0 0 27 0 0 0 0 0 0 0 28 0 0 0 0 0 0 0 29 0 0 0 0 0 0 0 30 0 0 0 0 0 0 0 31 0 0 0 0 0 0 0 32 0 0 0 0 0 0 0 33 0 0 0 0 0 0 0 34 0 0 0 0 0 0 0 35 0 0 0 0 0 0 0 36 0 0 0 0 0 0 0 37 0 0 0 0 0 0 0 38 0 0 0 0 0 0 0 39 0 0 0 0 0 0 0 40 0 0 0 0 0 0 0 41 0 0 0 0 0 0 0 42 0 0 0 0 0 0 0 43 0 0 0 0 0 0 0 44 0 0 0 0 0 0 0 45 0 0 0 0 0 0 0 46 0 0 0 0 0 0 0 47 0 0 0 0 0 0 0 48 0 0 0 0 0 0 0 49 0 0 0 0 0 0 0 50 0 0 0 0 0 0 0 51 0 0 0 0 0 0 0 52 0 0 0 0 0 0 0 53 0 0 0 0 0 0 0 54 0 0 0 0 0 0 0 55 0 0 0 0 0 0 0 56 0 0 0 0 0 0 0 57 0 0 0 0 0 0 0 58 0 0 0 0 0 0 0 59 0 0 0 0 0 0 0 60 0 0 0 0 0 0 0 61 0 0 0 0 0 0 0 62 0 0 0 0 0 0 0 63 0 0 0 0 0 0 0 64 0 0 0 0 0 0 0 65 0 0 0 0 0 0 0 66 0 0 0 0 0 0 0 67 0 0 0 0 0 0 0 68 0 0 0 0 0 0 0 69 0 0 0 0 0 0 0 70 0 0 0 0 0 0 0 71 0 0 0 0 0 0 0 72 0 0 0 0 0 0 0 73 0 0 0 0 0 0 0 74 0 0 0 0 0 0 0 75 0 0 0 1 0 0 1 76 0 0 0 0 0 0 0 77 0 0 0 0 0 0 0 78 0 0 0 0 0 0 0 79 0 0 0 0 0 0 0 80 0 0 0 0 0 0 0 81 0 0 0 0 0 0 0 82 0 0 0 0 0 0 0 83 0 0 0 0 0 0 0 84 0 0 0 0 0 0 0 85 0 0 0 0 0 0 0 86 0 0 0 0 0 0 0 87 0 0 0 0 0 0 0 88 0 0 0 0 0 0 0 89 0 0 0 0 0 0 0 90 0 0 0 0 0 0 0 91 0 0 0 0 0 0 0 92 1 1 0 0 0 0 2 93 0 0 0 0 0 0 0 94 0 0 0 0 0 0 0 95 0 0 0 0 0 0 0 96 0 0 0 0 0 0 0 97 0 0 0 0 0 0 0 98 0 0 0 0 0 0 0 99 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 101 0 0 0 0 0 0 0 102 0 0 0 0 0 0 0 103 0 0 0 0 0 0 0 104 0 0 0 0 0 0 0 105 0 0 0 0 0 0 0 106 0 0 0 0 0 0 0 107 0 0 0 0 0 0 0 108 0 0 0 0 0 0 0 109 0 0 0 0 0 0 0 110 0 0 0 0 0 0 0 111 0 0 0 0 0 0 0 112 0 0 0 0 0 0 0 113 0 0 0 0 0 0 0 114 0 0 0 0 0 0 0 115 0 0 0 0 0 0 0 116 0 0 0 0 0 0 0 117 0 0 0 0 0 0 0 118 0 0 0 0 0 0 0 119 0 0 0 0 0 0 0 120 0 0 0 0 0 0 0 121 0 0 0 0 0 0 0 122 0 0 0 0 0 0 0 123 0 0 0 0 0 0 0 124 0 0 0 0 0 0 0 125 0 0 0 0 0 0 0 126 0 0 0 0 0 0 0 127 0 0 0 0 0 0 0 128 0 0 0 0 0 0 0 129 0 0 0 0 0 0 0 130 0 0 0 0 0 0 0 131 0 0 0 0 0 0 0 132 0 0 0 0 0 0 0 133 0 0 0 0 0 0 0 134 0 0 0 0 0 0 0 135 0 0 0 0 0 0 0 136 0 0 0 0 0 0 0 137 0 0 0 0 0 0 0 138 0 0 0 0 0 0 0 139 0 0 0 0 0 0 0 140 0 0 0 0 0 0 0 141 0 0 0 0 0 0 0 142 0 0 0 0 0 0 0 143 0 0 0 0 0 0 0 144 0 0 0 0 0 0 0 145 0 0 0 0 0 0 0 146 0 0 0 0 0 0 0 147 0 0 0 0 0 0 0 148 0 0 0 0 0 0 0 149 0 0 0 0 0 0 0 150 0 0 0 1 0 0 1 your_output.sample_2.singleton.truncated000066400000000000000000000000001350370616400402260ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/collapseadapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/collapse/your_output.settings000066400000000000000000000022251350370616400344650ustar00rootroot00000000000000AdapterRemoval ver. 2.1.7 Trimming of double-indexed paired-end reads [Demultiplexing] Maximum mismatches (total): 0 Maximum mate 1 mismatches: 0 Maximum mate 2 mismatches: 0 [Demultiplexing samples] Name Barcode_1 Barcode_2 sample_1 TGAGTCAT GTTAGTGG sample_2 GCAGAGAT CCTAGGGT [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 1157297082 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: Yes Minimum overlap (in case of collapse): 11 [Demultiplexing statistics] Name Barcode_1 Barcode_2 Hits Fraction unidentified NA NA 0 0.000 ambiguous NA NA 0 0.000 sample_1 TGAGTCAT GTTAGTGG 4 0.500 sample_2 GCAGAGAT CCTAGGGT 4 0.500 * * * 8 1.000 your_output.unidentified_1000066400000000000000000000000001350370616400354220ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/collapseyour_output.unidentified_2000066400000000000000000000000001350370616400354230ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/collapseadapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/combined_output/000077500000000000000000000000001350370616400316625ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/combined_output/barcodes.txt000066400000000000000000000000661350370616400342070ustar00rootroot00000000000000sample_1 CTTGCCCT ACGTTATT sample_2 CGCCGATG TGCACGGG adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/combined_output/info.json000066400000000000000000000001141350370616400335040ustar00rootroot00000000000000{ "arguments": ["--combined-output"], "return_code": 0, "stderr": [ ] } adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/combined_output/input_1.fastq000066400000000000000000000033301350370616400343000ustar00rootroot00000000000000@read_s2_000/1 CGCCGATGCCCGTGCAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_200/1 CGCCGATGGCGTAAGTTGACGTCAGCCTGCGAGGTGCCACGCCAGTGGTTGCGCTCACCCGGGGCGTAGTTGCTCCGCGCAATTTCTTGGCAGTTCGATC + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_075/1 CTTGCCCTGGTTCTACGTTCTCCATCAGGTGGACGAGGGGATCTTGGCCCCCGTTCCTGCATTGGTATAATTAGACAGGATGAAATAACGTAGATCGGAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_200/1 CTTGCCCTGTAGTGCAATAAAAGGATCCTCTTGTGGCCGATTGCAGACCAGCCTCGGGGCTAAACTGATAATCGTATGCTATAGACCCTGGTCGACGCCG + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_150/1 CTTGCCCTCAGATGTCAGCTCATGTGTTGATATACAGCTAACTAAGGCCCGGGGGTTTAGGCTCAACCCTCTACCTGGTATACCGGCCCAACGCACTCGC + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_075/1 CGCCGATGTCTTGGGAACGAGAGTGCCACCAATTAAAGTGATGGATATCGAGACGTCCCAAACCACCGCAATAGGACGGGACACCCGTGCAAGATCGGAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_150/1 CGCCGATGAGCCCCGAGTGTCCATCACAAGCCACCTCCACTAACCATCTCGGTCCATTATTTGTCACTCGTGGCTAGAAGGGAATAAAGACAACTCTCTC + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_000/1 CTTGCCCTAATAACGTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/combined_output/input_2.fastq000066400000000000000000000033301350370616400343010ustar00rootroot00000000000000@read_s2_000/2 TGCACGGGCATCGGCGAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_200/2 TGCACGGGTAAGGGACGAAGTCACCGGGGGCGTTTCACTTGCGCGATCCATTGTAGTACTGGTGTGTCAATCTTCATCGGCAAAAGGTGCCTATCAAAAT + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_075/2 ACGTTATTTCATCCTGTCTAATTATACCAATGCAGGAACGGGGGCCAAGATCCCCTCGTCCACCTGATGGAGAACGTAGAACCAGGGCAAGAGATCGGAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_200/2 ACGTTATTAAGGCCCGCCCATCAGGTAAGAGCATGCTCGGGAGCCAACCCCGTGGGGTGGCAGCGATACTCTCCAATCTGTCATGCGTGTCAACGTGCGT + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_150/2 ACGTTATTGTGCTGCGTGAGTTGGAAGGATTGGATCCGGAAAGGCTTGGCCTTTGTAAATTCGACTGCGAGTGCGTTGGGCCGGTATACCAGGTAGAGGG + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_075/2 TGCACGGGTGTCCCGTCCTATTGCGGTGGTTTGGGACGTCTCGATATCCATCACTTTAATTGGTGGCACTCTCGTTCCCAAGACATCGGCGAGATCGGAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_150/2 TGCACGGGAAGGCTGGGTATACGGGGTAAATGGTGCCGCCTTGTTACACGCGCCGAGGTTTCAGATGAGAGAGTTGTCTTTATTCCCTTCTAGCCACGAG + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_000/2 ACGTTATTAGGGCAAGAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 your_output.sample_1.pair1.truncated000066400000000000000000000011241350370616400406450ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/combined_output@read_s1_075/1 GGTTCTACGTTCTCCATCAGGTGGACGAGGGGATCTTGGCCCCCGTTCCTGCATTGGTATAATTAGACAGGATGA + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; @read_s1_200/1 GTAGTGCAATAAAAGGATCCTCTTGTGGCCGATTGCAGACCAGCCTCGGGGCTAAACTGATAATCGTATGCTATAGACCCTGGTCGACGCCG + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_150/1 CAGATGTCAGCTCATGTGTTGATATACAGCTAACTAAGGCCCGGGGGTTTAGGCTCAACCCTCTACCTGGTATACCGGCCCAACGCACTCGC + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_000/1 N + ! your_output.sample_1.pair2.truncated000066400000000000000000000011241350370616400406460ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/combined_output@read_s1_075/2 TCATCCTGTCTAATTATACCAATGCAGGAACGGGGGCCAAGATCCCCTCGTCCACCTGATGGAGAACGTAGAACC + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; @read_s1_200/2 AAGGCCCGCCCATCAGGTAAGAGCATGCTCGGGAGCCAACCCCGTGGGGTGGCAGCGATACTCTCCAATCTGTCATGCGTGTCAACGTGCGT + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_150/2 GTGCTGCGTGAGTTGGAAGGATTGGATCCGGAAAGGCTTGGCCTTTGTAAATTCGACTGCGAGTGCGTTGGGCCGGTATACCAGGTAGAGGG + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_000/2 N + ! your_output.sample_1.settings000066400000000000000000000051501350370616400375040ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/combined_outputAdapterRemoval ver. 2.1.7 Trimming of double-indexed paired-end reads [Demultiplexing] Maximum mismatches (total): 0 Maximum mate 1 mismatches: 0 Maximum mate 2 mismatches: 0 [Demultiplexing samples] Name Barcode_1 Barcode_2 sample_1* CTTGCCCT ACGTTATT sample_2 CGCCGATG TGCACGGG [Adapter sequences] Adapter1[1]: AATAACGT_AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGGGCAAG_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 1157297082 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 [Trimming statistics] Total number of read pairs: 4 Number of unaligned read pairs: 1 Number of well aligned read pairs: 3 Number of discarded mate 1 reads: 1 Number of singleton mate 1 reads: 0 Number of discarded mate 2 reads: 1 Number of singleton mate 2 reads: 0 Number of reads with adapters[1]: 4 Number of retained reads: 6 Number of retained nucleotides: 518 Average length of retained reads: 86.3333 [Length distribution] Length Mate1 Mate2 Singleton Discarded All 0 0 0 0 2 2 1 0 0 0 0 0 2 0 0 0 0 0 3 0 0 0 0 0 4 0 0 0 0 0 5 0 0 0 0 0 6 0 0 0 0 0 7 0 0 0 0 0 8 0 0 0 0 0 9 0 0 0 0 0 10 0 0 0 0 0 11 0 0 0 0 0 12 0 0 0 0 0 13 0 0 0 0 0 14 0 0 0 0 0 15 0 0 0 0 0 16 0 0 0 0 0 17 0 0 0 0 0 18 0 0 0 0 0 19 0 0 0 0 0 20 0 0 0 0 0 21 0 0 0 0 0 22 0 0 0 0 0 23 0 0 0 0 0 24 0 0 0 0 0 25 0 0 0 0 0 26 0 0 0 0 0 27 0 0 0 0 0 28 0 0 0 0 0 29 0 0 0 0 0 30 0 0 0 0 0 31 0 0 0 0 0 32 0 0 0 0 0 33 0 0 0 0 0 34 0 0 0 0 0 35 0 0 0 0 0 36 0 0 0 0 0 37 0 0 0 0 0 38 0 0 0 0 0 39 0 0 0 0 0 40 0 0 0 0 0 41 0 0 0 0 0 42 0 0 0 0 0 43 0 0 0 0 0 44 0 0 0 0 0 45 0 0 0 0 0 46 0 0 0 0 0 47 0 0 0 0 0 48 0 0 0 0 0 49 0 0 0 0 0 50 0 0 0 0 0 51 0 0 0 0 0 52 0 0 0 0 0 53 0 0 0 0 0 54 0 0 0 0 0 55 0 0 0 0 0 56 0 0 0 0 0 57 0 0 0 0 0 58 0 0 0 0 0 59 0 0 0 0 0 60 0 0 0 0 0 61 0 0 0 0 0 62 0 0 0 0 0 63 0 0 0 0 0 64 0 0 0 0 0 65 0 0 0 0 0 66 0 0 0 0 0 67 0 0 0 0 0 68 0 0 0 0 0 69 0 0 0 0 0 70 0 0 0 0 0 71 0 0 0 0 0 72 0 0 0 0 0 73 0 0 0 0 0 74 0 0 0 0 0 75 1 1 0 0 2 76 0 0 0 0 0 77 0 0 0 0 0 78 0 0 0 0 0 79 0 0 0 0 0 80 0 0 0 0 0 81 0 0 0 0 0 82 0 0 0 0 0 83 0 0 0 0 0 84 0 0 0 0 0 85 0 0 0 0 0 86 0 0 0 0 0 87 0 0 0 0 0 88 0 0 0 0 0 89 0 0 0 0 0 90 0 0 0 0 0 91 0 0 0 0 0 92 2 2 0 0 4 your_output.sample_2.pair1.truncated000066400000000000000000000011241350370616400406460ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/combined_output@read_s2_000/1 N + ! @read_s2_200/1 GCGTAAGTTGACGTCAGCCTGCGAGGTGCCACGCCAGTGGTTGCGCTCACCCGGGGCGTAGTTGCTCCGCGCAATTTCTTGGCAGTTCGATC + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_075/1 TCTTGGGAACGAGAGTGCCACCAATTAAAGTGATGGATATCGAGACGTCCCAAACCACCGCAATAGGACGGGACA + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; @read_s2_150/1 AGCCCCGAGTGTCCATCACAAGCCACCTCCACTAACCATCTCGGTCCATTATTTGTCACTCGTGGCTAGAAGGGAATAAAGACAACTCTCTC + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 your_output.sample_2.pair2.truncated000066400000000000000000000011241350370616400406470ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/combined_output@read_s2_000/2 N + ! @read_s2_200/2 TAAGGGACGAAGTCACCGGGGGCGTTTCACTTGCGCGATCCATTGTAGTACTGGTGTGTCAATCTTCATCGGCAAAAGGTGCCTATCAAAAT + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_075/2 TGTCCCGTCCTATTGCGGTGGTTTGGGACGTCTCGATATCCATCACTTTAATTGGTGGCACTCTCGTTCCCAAGA + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; @read_s2_150/2 AAGGCTGGGTATACGGGGTAAATGGTGCCGCCTTGTTACACGCGCCGAGGTTTCAGATGAGAGAGTTGTCTTTATTCCCTTCTAGCCACGAG + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 your_output.sample_2.settings000066400000000000000000000051501350370616400375050ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/combined_outputAdapterRemoval ver. 2.1.7 Trimming of double-indexed paired-end reads [Demultiplexing] Maximum mismatches (total): 0 Maximum mate 1 mismatches: 0 Maximum mate 2 mismatches: 0 [Demultiplexing samples] Name Barcode_1 Barcode_2 sample_1 CTTGCCCT ACGTTATT sample_2* CGCCGATG TGCACGGG [Adapter sequences] Adapter1[1]: CCCGTGCA_AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: CATCGGCG_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 1157297082 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 [Trimming statistics] Total number of read pairs: 4 Number of unaligned read pairs: 1 Number of well aligned read pairs: 3 Number of discarded mate 1 reads: 1 Number of singleton mate 1 reads: 0 Number of discarded mate 2 reads: 1 Number of singleton mate 2 reads: 0 Number of reads with adapters[1]: 4 Number of retained reads: 6 Number of retained nucleotides: 518 Average length of retained reads: 86.3333 [Length distribution] Length Mate1 Mate2 Singleton Discarded All 0 0 0 0 2 2 1 0 0 0 0 0 2 0 0 0 0 0 3 0 0 0 0 0 4 0 0 0 0 0 5 0 0 0 0 0 6 0 0 0 0 0 7 0 0 0 0 0 8 0 0 0 0 0 9 0 0 0 0 0 10 0 0 0 0 0 11 0 0 0 0 0 12 0 0 0 0 0 13 0 0 0 0 0 14 0 0 0 0 0 15 0 0 0 0 0 16 0 0 0 0 0 17 0 0 0 0 0 18 0 0 0 0 0 19 0 0 0 0 0 20 0 0 0 0 0 21 0 0 0 0 0 22 0 0 0 0 0 23 0 0 0 0 0 24 0 0 0 0 0 25 0 0 0 0 0 26 0 0 0 0 0 27 0 0 0 0 0 28 0 0 0 0 0 29 0 0 0 0 0 30 0 0 0 0 0 31 0 0 0 0 0 32 0 0 0 0 0 33 0 0 0 0 0 34 0 0 0 0 0 35 0 0 0 0 0 36 0 0 0 0 0 37 0 0 0 0 0 38 0 0 0 0 0 39 0 0 0 0 0 40 0 0 0 0 0 41 0 0 0 0 0 42 0 0 0 0 0 43 0 0 0 0 0 44 0 0 0 0 0 45 0 0 0 0 0 46 0 0 0 0 0 47 0 0 0 0 0 48 0 0 0 0 0 49 0 0 0 0 0 50 0 0 0 0 0 51 0 0 0 0 0 52 0 0 0 0 0 53 0 0 0 0 0 54 0 0 0 0 0 55 0 0 0 0 0 56 0 0 0 0 0 57 0 0 0 0 0 58 0 0 0 0 0 59 0 0 0 0 0 60 0 0 0 0 0 61 0 0 0 0 0 62 0 0 0 0 0 63 0 0 0 0 0 64 0 0 0 0 0 65 0 0 0 0 0 66 0 0 0 0 0 67 0 0 0 0 0 68 0 0 0 0 0 69 0 0 0 0 0 70 0 0 0 0 0 71 0 0 0 0 0 72 0 0 0 0 0 73 0 0 0 0 0 74 0 0 0 0 0 75 1 1 0 0 2 76 0 0 0 0 0 77 0 0 0 0 0 78 0 0 0 0 0 79 0 0 0 0 0 80 0 0 0 0 0 81 0 0 0 0 0 82 0 0 0 0 0 83 0 0 0 0 0 84 0 0 0 0 0 85 0 0 0 0 0 86 0 0 0 0 0 87 0 0 0 0 0 88 0 0 0 0 0 89 0 0 0 0 0 90 0 0 0 0 0 91 0 0 0 0 0 92 2 2 0 0 4 your_output.settings000066400000000000000000000022241350370616400360030ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/combined_outputAdapterRemoval ver. 2.1.7 Trimming of double-indexed paired-end reads [Demultiplexing] Maximum mismatches (total): 0 Maximum mate 1 mismatches: 0 Maximum mate 2 mismatches: 0 [Demultiplexing samples] Name Barcode_1 Barcode_2 sample_1 CTTGCCCT ACGTTATT sample_2 CGCCGATG TGCACGGG [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 1157297082 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 [Demultiplexing statistics] Name Barcode_1 Barcode_2 Hits Fraction unidentified NA NA 0 0.000 ambiguous NA NA 0 0.000 sample_1 CTTGCCCT ACGTTATT 4 0.500 sample_2 CGCCGATG TGCACGGG 4 0.500 * * * 8 1.000 your_output.unidentified_1000066400000000000000000000000001350370616400370200ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/combined_outputyour_output.unidentified_2000066400000000000000000000000001350370616400370210ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/combined_outputadapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/defaults/000077500000000000000000000000001350370616400302715ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/defaults/barcodes.txt000066400000000000000000000000661350370616400326160ustar00rootroot00000000000000sample_1 CTTGCCCT ACGTTATT sample_2 CGCCGATG TGCACGGG adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/defaults/info.json000066400000000000000000000000711350370616400321150ustar00rootroot00000000000000{ "arguments": [], "return_code": 0, "stderr": [ ] } adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/defaults/input_1.fastq000066400000000000000000000033301350370616400327070ustar00rootroot00000000000000@read_s2_000/1 CGCCGATGCCCGTGCAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_200/1 CGCCGATGGCGTAAGTTGACGTCAGCCTGCGAGGTGCCACGCCAGTGGTTGCGCTCACCCGGGGCGTAGTTGCTCCGCGCAATTTCTTGGCAGTTCGATC + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_075/1 CTTGCCCTGGTTCTACGTTCTCCATCAGGTGGACGAGGGGATCTTGGCCCCCGTTCCTGCATTGGTATAATTAGACAGGATGAAATAACGTAGATCGGAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_200/1 CTTGCCCTGTAGTGCAATAAAAGGATCCTCTTGTGGCCGATTGCAGACCAGCCTCGGGGCTAAACTGATAATCGTATGCTATAGACCCTGGTCGACGCCG + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_150/1 CTTGCCCTCAGATGTCAGCTCATGTGTTGATATACAGCTAACTAAGGCCCGGGGGTTTAGGCTCAACCCTCTACCTGGTATACCGGCCCAACGCACTCGC + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_075/1 CGCCGATGTCTTGGGAACGAGAGTGCCACCAATTAAAGTGATGGATATCGAGACGTCCCAAACCACCGCAATAGGACGGGACACCCGTGCAAGATCGGAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_150/1 CGCCGATGAGCCCCGAGTGTCCATCACAAGCCACCTCCACTAACCATCTCGGTCCATTATTTGTCACTCGTGGCTAGAAGGGAATAAAGACAACTCTCTC + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_000/1 CTTGCCCTAATAACGTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/defaults/input_2.fastq000066400000000000000000000033301350370616400327100ustar00rootroot00000000000000@read_s2_000/2 TGCACGGGCATCGGCGAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_200/2 TGCACGGGTAAGGGACGAAGTCACCGGGGGCGTTTCACTTGCGCGATCCATTGTAGTACTGGTGTGTCAATCTTCATCGGCAAAAGGTGCCTATCAAAAT + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_075/2 ACGTTATTTCATCCTGTCTAATTATACCAATGCAGGAACGGGGGCCAAGATCCCCTCGTCCACCTGATGGAGAACGTAGAACCAGGGCAAGAGATCGGAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_200/2 ACGTTATTAAGGCCCGCCCATCAGGTAAGAGCATGCTCGGGAGCCAACCCCGTGGGGTGGCAGCGATACTCTCCAATCTGTCATGCGTGTCAACGTGCGT + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_150/2 ACGTTATTGTGCTGCGTGAGTTGGAAGGATTGGATCCGGAAAGGCTTGGCCTTTGTAAATTCGACTGCGAGTGCGTTGGGCCGGTATACCAGGTAGAGGG + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_075/2 TGCACGGGTGTCCCGTCCTATTGCGGTGGTTTGGGACGTCTCGATATCCATCACTTTAATTGGTGGCACTCTCGTTCCCAAGACATCGGCGAGATCGGAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_150/2 TGCACGGGAAGGCTGGGTATACGGGGTAAATGGTGCCGCCTTGTTACACGCGCCGAGGTTTCAGATGAGAGAGTTGTCTTTATTCCCTTCTAGCCACGAG + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_000/2 ACGTTATTAGGGCAAGAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 your_output.sample_1.discarded000066400000000000000000000000461350370616400361740ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/defaults@read_s1_000/1 + @read_s1_000/2 + your_output.sample_1.pair1.truncated000066400000000000000000000010771350370616400372630ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/defaults@read_s1_075/1 GGTTCTACGTTCTCCATCAGGTGGACGAGGGGATCTTGGCCCCCGTTCCTGCATTGGTATAATTAGACAGGATGA + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; @read_s1_200/1 GTAGTGCAATAAAAGGATCCTCTTGTGGCCGATTGCAGACCAGCCTCGGGGCTAAACTGATAATCGTATGCTATAGACCCTGGTCGACGCCG + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_150/1 CAGATGTCAGCTCATGTGTTGATATACAGCTAACTAAGGCCCGGGGGTTTAGGCTCAACCCTCTACCTGGTATACCGGCCCAACGCACTCGC + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 your_output.sample_1.pair2.truncated000066400000000000000000000010771350370616400372640ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/defaults@read_s1_075/2 TCATCCTGTCTAATTATACCAATGCAGGAACGGGGGCCAAGATCCCCTCGTCCACCTGATGGAGAACGTAGAACC + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; @read_s1_200/2 AAGGCCCGCCCATCAGGTAAGAGCATGCTCGGGAGCCAACCCCGTGGGGTGGCAGCGATACTCTCCAATCTGTCATGCGTGTCAACGTGCGT + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_150/2 GTGCTGCGTGAGTTGGAAGGATTGGATCCGGAAAGGCTTGGCCTTTGTAAATTCGACTGCGAGTGCGTTGGGCCGGTATACCAGGTAGAGGG + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 your_output.sample_1.settings000066400000000000000000000051501350370616400361130ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/defaultsAdapterRemoval ver. 2.1.7 Trimming of double-indexed paired-end reads [Demultiplexing] Maximum mismatches (total): 0 Maximum mate 1 mismatches: 0 Maximum mate 2 mismatches: 0 [Demultiplexing samples] Name Barcode_1 Barcode_2 sample_1* CTTGCCCT ACGTTATT sample_2 CGCCGATG TGCACGGG [Adapter sequences] Adapter1[1]: AATAACGT_AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGGGCAAG_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 1157297082 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 [Trimming statistics] Total number of read pairs: 4 Number of unaligned read pairs: 1 Number of well aligned read pairs: 3 Number of discarded mate 1 reads: 1 Number of singleton mate 1 reads: 0 Number of discarded mate 2 reads: 1 Number of singleton mate 2 reads: 0 Number of reads with adapters[1]: 4 Number of retained reads: 6 Number of retained nucleotides: 518 Average length of retained reads: 86.3333 [Length distribution] Length Mate1 Mate2 Singleton Discarded All 0 0 0 0 2 2 1 0 0 0 0 0 2 0 0 0 0 0 3 0 0 0 0 0 4 0 0 0 0 0 5 0 0 0 0 0 6 0 0 0 0 0 7 0 0 0 0 0 8 0 0 0 0 0 9 0 0 0 0 0 10 0 0 0 0 0 11 0 0 0 0 0 12 0 0 0 0 0 13 0 0 0 0 0 14 0 0 0 0 0 15 0 0 0 0 0 16 0 0 0 0 0 17 0 0 0 0 0 18 0 0 0 0 0 19 0 0 0 0 0 20 0 0 0 0 0 21 0 0 0 0 0 22 0 0 0 0 0 23 0 0 0 0 0 24 0 0 0 0 0 25 0 0 0 0 0 26 0 0 0 0 0 27 0 0 0 0 0 28 0 0 0 0 0 29 0 0 0 0 0 30 0 0 0 0 0 31 0 0 0 0 0 32 0 0 0 0 0 33 0 0 0 0 0 34 0 0 0 0 0 35 0 0 0 0 0 36 0 0 0 0 0 37 0 0 0 0 0 38 0 0 0 0 0 39 0 0 0 0 0 40 0 0 0 0 0 41 0 0 0 0 0 42 0 0 0 0 0 43 0 0 0 0 0 44 0 0 0 0 0 45 0 0 0 0 0 46 0 0 0 0 0 47 0 0 0 0 0 48 0 0 0 0 0 49 0 0 0 0 0 50 0 0 0 0 0 51 0 0 0 0 0 52 0 0 0 0 0 53 0 0 0 0 0 54 0 0 0 0 0 55 0 0 0 0 0 56 0 0 0 0 0 57 0 0 0 0 0 58 0 0 0 0 0 59 0 0 0 0 0 60 0 0 0 0 0 61 0 0 0 0 0 62 0 0 0 0 0 63 0 0 0 0 0 64 0 0 0 0 0 65 0 0 0 0 0 66 0 0 0 0 0 67 0 0 0 0 0 68 0 0 0 0 0 69 0 0 0 0 0 70 0 0 0 0 0 71 0 0 0 0 0 72 0 0 0 0 0 73 0 0 0 0 0 74 0 0 0 0 0 75 1 1 0 0 2 76 0 0 0 0 0 77 0 0 0 0 0 78 0 0 0 0 0 79 0 0 0 0 0 80 0 0 0 0 0 81 0 0 0 0 0 82 0 0 0 0 0 83 0 0 0 0 0 84 0 0 0 0 0 85 0 0 0 0 0 86 0 0 0 0 0 87 0 0 0 0 0 88 0 0 0 0 0 89 0 0 0 0 0 90 0 0 0 0 0 91 0 0 0 0 0 92 2 2 0 0 4 your_output.sample_1.singleton.truncated000066400000000000000000000000001350370616400402320ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/defaultsyour_output.sample_2.discarded000066400000000000000000000000461350370616400361750ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/defaults@read_s2_000/1 + @read_s2_000/2 + your_output.sample_2.pair1.truncated000066400000000000000000000010771350370616400372640ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/defaults@read_s2_200/1 GCGTAAGTTGACGTCAGCCTGCGAGGTGCCACGCCAGTGGTTGCGCTCACCCGGGGCGTAGTTGCTCCGCGCAATTTCTTGGCAGTTCGATC + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_075/1 TCTTGGGAACGAGAGTGCCACCAATTAAAGTGATGGATATCGAGACGTCCCAAACCACCGCAATAGGACGGGACA + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; @read_s2_150/1 AGCCCCGAGTGTCCATCACAAGCCACCTCCACTAACCATCTCGGTCCATTATTTGTCACTCGTGGCTAGAAGGGAATAAAGACAACTCTCTC + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 your_output.sample_2.pair2.truncated000066400000000000000000000010771350370616400372650ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/defaults@read_s2_200/2 TAAGGGACGAAGTCACCGGGGGCGTTTCACTTGCGCGATCCATTGTAGTACTGGTGTGTCAATCTTCATCGGCAAAAGGTGCCTATCAAAAT + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_075/2 TGTCCCGTCCTATTGCGGTGGTTTGGGACGTCTCGATATCCATCACTTTAATTGGTGGCACTCTCGTTCCCAAGA + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; @read_s2_150/2 AAGGCTGGGTATACGGGGTAAATGGTGCCGCCTTGTTACACGCGCCGAGGTTTCAGATGAGAGAGTTGTCTTTATTCCCTTCTAGCCACGAG + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 your_output.sample_2.settings000066400000000000000000000051501350370616400361140ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/defaultsAdapterRemoval ver. 2.1.7 Trimming of double-indexed paired-end reads [Demultiplexing] Maximum mismatches (total): 0 Maximum mate 1 mismatches: 0 Maximum mate 2 mismatches: 0 [Demultiplexing samples] Name Barcode_1 Barcode_2 sample_1 CTTGCCCT ACGTTATT sample_2* CGCCGATG TGCACGGG [Adapter sequences] Adapter1[1]: CCCGTGCA_AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: CATCGGCG_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 1157297082 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 [Trimming statistics] Total number of read pairs: 4 Number of unaligned read pairs: 1 Number of well aligned read pairs: 3 Number of discarded mate 1 reads: 1 Number of singleton mate 1 reads: 0 Number of discarded mate 2 reads: 1 Number of singleton mate 2 reads: 0 Number of reads with adapters[1]: 4 Number of retained reads: 6 Number of retained nucleotides: 518 Average length of retained reads: 86.3333 [Length distribution] Length Mate1 Mate2 Singleton Discarded All 0 0 0 0 2 2 1 0 0 0 0 0 2 0 0 0 0 0 3 0 0 0 0 0 4 0 0 0 0 0 5 0 0 0 0 0 6 0 0 0 0 0 7 0 0 0 0 0 8 0 0 0 0 0 9 0 0 0 0 0 10 0 0 0 0 0 11 0 0 0 0 0 12 0 0 0 0 0 13 0 0 0 0 0 14 0 0 0 0 0 15 0 0 0 0 0 16 0 0 0 0 0 17 0 0 0 0 0 18 0 0 0 0 0 19 0 0 0 0 0 20 0 0 0 0 0 21 0 0 0 0 0 22 0 0 0 0 0 23 0 0 0 0 0 24 0 0 0 0 0 25 0 0 0 0 0 26 0 0 0 0 0 27 0 0 0 0 0 28 0 0 0 0 0 29 0 0 0 0 0 30 0 0 0 0 0 31 0 0 0 0 0 32 0 0 0 0 0 33 0 0 0 0 0 34 0 0 0 0 0 35 0 0 0 0 0 36 0 0 0 0 0 37 0 0 0 0 0 38 0 0 0 0 0 39 0 0 0 0 0 40 0 0 0 0 0 41 0 0 0 0 0 42 0 0 0 0 0 43 0 0 0 0 0 44 0 0 0 0 0 45 0 0 0 0 0 46 0 0 0 0 0 47 0 0 0 0 0 48 0 0 0 0 0 49 0 0 0 0 0 50 0 0 0 0 0 51 0 0 0 0 0 52 0 0 0 0 0 53 0 0 0 0 0 54 0 0 0 0 0 55 0 0 0 0 0 56 0 0 0 0 0 57 0 0 0 0 0 58 0 0 0 0 0 59 0 0 0 0 0 60 0 0 0 0 0 61 0 0 0 0 0 62 0 0 0 0 0 63 0 0 0 0 0 64 0 0 0 0 0 65 0 0 0 0 0 66 0 0 0 0 0 67 0 0 0 0 0 68 0 0 0 0 0 69 0 0 0 0 0 70 0 0 0 0 0 71 0 0 0 0 0 72 0 0 0 0 0 73 0 0 0 0 0 74 0 0 0 0 0 75 1 1 0 0 2 76 0 0 0 0 0 77 0 0 0 0 0 78 0 0 0 0 0 79 0 0 0 0 0 80 0 0 0 0 0 81 0 0 0 0 0 82 0 0 0 0 0 83 0 0 0 0 0 84 0 0 0 0 0 85 0 0 0 0 0 86 0 0 0 0 0 87 0 0 0 0 0 88 0 0 0 0 0 89 0 0 0 0 0 90 0 0 0 0 0 91 0 0 0 0 0 92 2 2 0 0 4 your_output.sample_2.singleton.truncated000066400000000000000000000000001350370616400402330ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/defaultsadapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/defaults/your_output.settings000066400000000000000000000022241350370616400344710ustar00rootroot00000000000000AdapterRemoval ver. 2.1.7 Trimming of double-indexed paired-end reads [Demultiplexing] Maximum mismatches (total): 0 Maximum mate 1 mismatches: 0 Maximum mate 2 mismatches: 0 [Demultiplexing samples] Name Barcode_1 Barcode_2 sample_1 CTTGCCCT ACGTTATT sample_2 CGCCGATG TGCACGGG [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 1157297082 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 [Demultiplexing statistics] Name Barcode_1 Barcode_2 Hits Fraction unidentified NA NA 0 0.000 ambiguous NA NA 0 0.000 sample_1 CTTGCCCT ACGTTATT 4 0.500 sample_2 CGCCGATG TGCACGGG 4 0.500 * * * 8 1.000 your_output.unidentified_1000066400000000000000000000000001350370616400354270ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/defaultsyour_output.unidentified_2000066400000000000000000000000001350370616400354300ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/defaultsadapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/demux_only/000077500000000000000000000000001350370616400306455ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/demux_only/interleaved/000077500000000000000000000000001350370616400331475ustar00rootroot00000000000000barcodes.txt000066400000000000000000000000661350370616400354150ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/demux_only/interleavedsample_1 GGCCCCTG CCAAAGCT sample_2 AATCCTAG GTCTAGTT info.json000066400000000000000000000001451350370616400347160ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/demux_only/interleaved{ "arguments": ["--demultiplex-only", "--interleaved-output"], "return_code": 0, "stderr": [ ] } input_1.fastq000066400000000000000000000033301350370616400355060ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/demux_only/interleaved@read_s2_000/1 AATCCTAGAACTAGACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_150/1 GGCCCCTGTTTCTGGACGACGCCCCTATAATGTATGATAATTATTCGATTGACATGGCGAACTTCAGCCATTAGCGCTTTCGCATAATGTCGTTGTATAT + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_200/1 GGCCCCTGAACCATCTGAGCGGTACTCGGGAAAACACGGACGAGGTGGGATATCTTTCCCTTCTCTTGCCATCGTGTATTTATCTGTATCTAATGCTACT + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_200/1 AATCCTAGTCGTACAATGCATCAGACACCGCTTTTGTGGCGTTTCGACCGTAATCTACATTTACATCTCGTTAATTCGCGACATTCATCGTGCCGTACTC + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_075/1 AATCCTAGATACGCTGTGCGTCCTGGAACTGCAACTCTCGGTGTACAGGCCATCGTAAATCGTACCCGATTGCGCTACGTTTCAACTAGACAGATCGGAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_150/1 AATCCTAGATACCCCGACACTCGACTTATATTTTCCTCAGCTAGTGCGAGAGTTAATGTAGCGACGAAACACTCCTGCCTCGGTACGAGCATCCCGGTAC + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_000/1 GGCCCCTGAGCTTTGGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_075/1 GGCCCCTGGGTGGCTATGTAGGGAAAAACTCCGCTAGAACAAAGAACAGCCTCCCTCAATCACCCATGTTCGTGCCTCGACGCAGCTTTGGAGATCGGAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 input_2.fastq000066400000000000000000000033301350370616400355070ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/demux_only/interleaved@read_s2_000/2 GTCTAGTTCTAGGATTAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_150/2 CCAAAGCTTTTAGACGGCAGACGCATCAACTTCCACATGACTGCTTGAACGACGATACACCTCTATATATACAACGACATTATGCGAAAGCGCTAATGGC + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_200/2 CCAAAGCTTACGGGTCCGTGCGCTTAGGTAAGAGCCCCGTTTTTTACGCGGAAAAGCGCCTGGAAGCTCAGAATTGAGGGAAGGGAAATGAGTCACGGGT + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_200/2 GTCTAGTTAAGCCAGTGCCCGCAAGTGGTACCTCCTTTATGGTACACCGAACACAGCGCTTCGCCTGGCTCAAACTGCAGCAGCAAGTACCTGCTCGATG + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_075/2 GTCTAGTTGAAACGTAGCGCAATCGGGTACGATTTACGATGGCCTGTACACCGAGAGTTGCAGTTCCAGGACGCACAGCGTATCTAGGATTAGATCGGAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_150/2 GTCTAGTTGACTGAGGGGCGCATTCTTAGTCGAGTCGTTTGTGGATAGTCAGGTCTGGTAAAGGATGTACCGGGATGCTCGTACCGAGGCAGGAGTGTTT + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_000/2 CCAAAGCTCAGGGGCCAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_075/2 CCAAAGCTGCGTCGAGGCACGAACATGGGTGATTGAGGGAGGCTGTTCTTTGTTCTAGCGGAGTTTTTCCCTACATAGCCACCCAGGGGCCAGATCGGAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 your_output.sample_1.paired.fastq000066400000000000000000000031301350370616400415060ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/demux_only/interleaved@read_s1_150/1 TTTCTGGACGACGCCCCTATAATGTATGATAATTATTCGATTGACATGGCGAACTTCAGCCATTAGCGCTTTCGCATAATGTCGTTGTATAT + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_150/2 TTTAGACGGCAGACGCATCAACTTCCACATGACTGCTTGAACGACGATACACCTCTATATATACAACGACATTATGCGAAAGCGCTAATGGC + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_200/1 AACCATCTGAGCGGTACTCGGGAAAACACGGACGAGGTGGGATATCTTTCCCTTCTCTTGCCATCGTGTATTTATCTGTATCTAATGCTACT + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_200/2 TACGGGTCCGTGCGCTTAGGTAAGAGCCCCGTTTTTTACGCGGAAAAGCGCCTGGAAGCTCAGAATTGAGGGAAGGGAAATGAGTCACGGGT + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_000/1 AGCTTTGGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAA + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_000/2 CAGGGGCCAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAA + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_075/1 GGTGGCTATGTAGGGAAAAACTCCGCTAGAACAAAGAACAGCCTCCCTCAATCACCCATGTTCGTGCCTCGACGCAGCTTTGGAGATCGGAA + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_075/2 GCGTCGAGGCACGAACATGGGTGATTGAGGGAGGCTGTTCTTTGTTCTAGCGGAGTTTTTCCCTACATAGCCACCCAGGGGCCAGATCGGAA + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 your_output.sample_1.settings000066400000000000000000000007401350370616400407710ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/demux_only/interleavedAdapterRemoval ver. 2.1.7 Demultiplexing of double-indexed paired-end reads [Demultiplexing] Maximum mismatches (total): 0 Maximum mate 1 mismatches: 0 Maximum mate 2 mismatches: 0 [Demultiplexing samples] Name Barcode_1 Barcode_2 sample_1* GGCCCCTG CCAAAGCT sample_2 AATCCTAG GTCTAGTT [Adapter sequences] Adapter1[1]: AGCTTTGG_AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: CAGGGGCC_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT your_output.sample_2.paired.fastq000066400000000000000000000031301350370616400415070ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/demux_only/interleaved@read_s2_000/1 AACTAGACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAA + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_000/2 CTAGGATTAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAA + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_200/1 TCGTACAATGCATCAGACACCGCTTTTGTGGCGTTTCGACCGTAATCTACATTTACATCTCGTTAATTCGCGACATTCATCGTGCCGTACTC + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_200/2 AAGCCAGTGCCCGCAAGTGGTACCTCCTTTATGGTACACCGAACACAGCGCTTCGCCTGGCTCAAACTGCAGCAGCAAGTACCTGCTCGATG + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_075/1 ATACGCTGTGCGTCCTGGAACTGCAACTCTCGGTGTACAGGCCATCGTAAATCGTACCCGATTGCGCTACGTTTCAACTAGACAGATCGGAA + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_075/2 GAAACGTAGCGCAATCGGGTACGATTTACGATGGCCTGTACACCGAGAGTTGCAGTTCCAGGACGCACAGCGTATCTAGGATTAGATCGGAA + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_150/1 ATACCCCGACACTCGACTTATATTTTCCTCAGCTAGTGCGAGAGTTAATGTAGCGACGAAACACTCCTGCCTCGGTACGAGCATCCCGGTAC + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_150/2 GACTGAGGGGCGCATTCTTAGTCGAGTCGTTTGTGGATAGTCAGGTCTGGTAAAGGATGTACCGGGATGCTCGTACCGAGGCAGGAGTGTTT + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 your_output.sample_2.settings000066400000000000000000000007401350370616400407720ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/demux_only/interleavedAdapterRemoval ver. 2.1.7 Demultiplexing of double-indexed paired-end reads [Demultiplexing] Maximum mismatches (total): 0 Maximum mate 1 mismatches: 0 Maximum mate 2 mismatches: 0 [Demultiplexing samples] Name Barcode_1 Barcode_2 sample_1 GGCCCCTG CCAAAGCT sample_2* AATCCTAG GTCTAGTT [Adapter sequences] Adapter1[1]: AACTAGAC_AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: CTAGGATT_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT your_output.settings000066400000000000000000000012311350370616400372650ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/demux_only/interleavedAdapterRemoval ver. 2.1.7 Demultiplexing of double-indexed paired-end reads [Demultiplexing] Maximum mismatches (total): 0 Maximum mate 1 mismatches: 0 Maximum mate 2 mismatches: 0 [Demultiplexing samples] Name Barcode_1 Barcode_2 sample_1 GGCCCCTG CCAAAGCT sample_2 AATCCTAG GTCTAGTT [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Demultiplexing statistics] Name Barcode_1 Barcode_2 Hits Fraction unidentified NA NA 0 0.000 ambiguous NA NA 0 0.000 sample_1 GGCCCCTG CCAAAGCT 4 0.500 sample_2 AATCCTAG GTCTAGTT 4 0.500 * * * 8 1.000 your_output.unidentified.paired.fastq000066400000000000000000000000001350370616400424450ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/demux_only/interleavedadapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/demux_only/regular/000077500000000000000000000000001350370616400323065ustar00rootroot00000000000000barcodes.txt000066400000000000000000000000661350370616400345540ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/demux_only/regularsample_1 GGCCCCTG CCAAAGCT sample_2 AATCCTAG GTCTAGTT adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/demux_only/regular/info.json000066400000000000000000000001151350370616400341310ustar00rootroot00000000000000{ "arguments": ["--demultiplex-only"], "return_code": 0, "stderr": [ ] } input_1.fastq000066400000000000000000000033301350370616400346450ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/demux_only/regular@read_s2_000/1 AATCCTAGAACTAGACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_150/1 GGCCCCTGTTTCTGGACGACGCCCCTATAATGTATGATAATTATTCGATTGACATGGCGAACTTCAGCCATTAGCGCTTTCGCATAATGTCGTTGTATAT + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_200/1 GGCCCCTGAACCATCTGAGCGGTACTCGGGAAAACACGGACGAGGTGGGATATCTTTCCCTTCTCTTGCCATCGTGTATTTATCTGTATCTAATGCTACT + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_200/1 AATCCTAGTCGTACAATGCATCAGACACCGCTTTTGTGGCGTTTCGACCGTAATCTACATTTACATCTCGTTAATTCGCGACATTCATCGTGCCGTACTC + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_075/1 AATCCTAGATACGCTGTGCGTCCTGGAACTGCAACTCTCGGTGTACAGGCCATCGTAAATCGTACCCGATTGCGCTACGTTTCAACTAGACAGATCGGAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_150/1 AATCCTAGATACCCCGACACTCGACTTATATTTTCCTCAGCTAGTGCGAGAGTTAATGTAGCGACGAAACACTCCTGCCTCGGTACGAGCATCCCGGTAC + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_000/1 GGCCCCTGAGCTTTGGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_075/1 GGCCCCTGGGTGGCTATGTAGGGAAAAACTCCGCTAGAACAAAGAACAGCCTCCCTCAATCACCCATGTTCGTGCCTCGACGCAGCTTTGGAGATCGGAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 input_2.fastq000066400000000000000000000033301350370616400346460ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/demux_only/regular@read_s2_000/2 GTCTAGTTCTAGGATTAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_150/2 CCAAAGCTTTTAGACGGCAGACGCATCAACTTCCACATGACTGCTTGAACGACGATACACCTCTATATATACAACGACATTATGCGAAAGCGCTAATGGC + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_200/2 CCAAAGCTTACGGGTCCGTGCGCTTAGGTAAGAGCCCCGTTTTTTACGCGGAAAAGCGCCTGGAAGCTCAGAATTGAGGGAAGGGAAATGAGTCACGGGT + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_200/2 GTCTAGTTAAGCCAGTGCCCGCAAGTGGTACCTCCTTTATGGTACACCGAACACAGCGCTTCGCCTGGCTCAAACTGCAGCAGCAAGTACCTGCTCGATG + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_075/2 GTCTAGTTGAAACGTAGCGCAATCGGGTACGATTTACGATGGCCTGTACACCGAGAGTTGCAGTTCCAGGACGCACAGCGTATCTAGGATTAGATCGGAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_150/2 GTCTAGTTGACTGAGGGGCGCATTCTTAGTCGAGTCGTTTGTGGATAGTCAGGTCTGGTAAAGGATGTACCGGGATGCTCGTACCGAGGCAGGAGTGTTT + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_000/2 CCAAAGCTCAGGGGCCAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_075/2 CCAAAGCTGCGTCGAGGCACGAACATGGGTGATTGAGGGAGGCTGTTCTTTGTTCTAGCGGAGTTTTTCCCTACATAGCCACCCAGGGGCCAGATCGGAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 your_output.sample_1.pair1.fastq000066400000000000000000000014541350370616400404240ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/demux_only/regular@read_s1_150/1 TTTCTGGACGACGCCCCTATAATGTATGATAATTATTCGATTGACATGGCGAACTTCAGCCATTAGCGCTTTCGCATAATGTCGTTGTATAT + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_200/1 AACCATCTGAGCGGTACTCGGGAAAACACGGACGAGGTGGGATATCTTTCCCTTCTCTTGCCATCGTGTATTTATCTGTATCTAATGCTACT + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_000/1 AGCTTTGGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAA + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_075/1 GGTGGCTATGTAGGGAAAAACTCCGCTAGAACAAAGAACAGCCTCCCTCAATCACCCATGTTCGTGCCTCGACGCAGCTTTGGAGATCGGAA + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 your_output.sample_1.pair2.fastq000066400000000000000000000014541350370616400404250ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/demux_only/regular@read_s1_150/2 TTTAGACGGCAGACGCATCAACTTCCACATGACTGCTTGAACGACGATACACCTCTATATATACAACGACATTATGCGAAAGCGCTAATGGC + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_200/2 TACGGGTCCGTGCGCTTAGGTAAGAGCCCCGTTTTTTACGCGGAAAAGCGCCTGGAAGCTCAGAATTGAGGGAAGGGAAATGAGTCACGGGT + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_000/2 CAGGGGCCAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAA + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_075/2 GCGTCGAGGCACGAACATGGGTGATTGAGGGAGGCTGTTCTTTGTTCTAGCGGAGTTTTTCCCTACATAGCCACCCAGGGGCCAGATCGGAA + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 your_output.sample_1.settings000066400000000000000000000007401350370616400401300ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/demux_only/regularAdapterRemoval ver. 2.1.7 Demultiplexing of double-indexed paired-end reads [Demultiplexing] Maximum mismatches (total): 0 Maximum mate 1 mismatches: 0 Maximum mate 2 mismatches: 0 [Demultiplexing samples] Name Barcode_1 Barcode_2 sample_1* GGCCCCTG CCAAAGCT sample_2 AATCCTAG GTCTAGTT [Adapter sequences] Adapter1[1]: AGCTTTGG_AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: CAGGGGCC_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT your_output.sample_2.pair1.fastq000066400000000000000000000014541350370616400404250ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/demux_only/regular@read_s2_000/1 AACTAGACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAA + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_200/1 TCGTACAATGCATCAGACACCGCTTTTGTGGCGTTTCGACCGTAATCTACATTTACATCTCGTTAATTCGCGACATTCATCGTGCCGTACTC + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_075/1 ATACGCTGTGCGTCCTGGAACTGCAACTCTCGGTGTACAGGCCATCGTAAATCGTACCCGATTGCGCTACGTTTCAACTAGACAGATCGGAA + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_150/1 ATACCCCGACACTCGACTTATATTTTCCTCAGCTAGTGCGAGAGTTAATGTAGCGACGAAACACTCCTGCCTCGGTACGAGCATCCCGGTAC + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 your_output.sample_2.pair2.fastq000066400000000000000000000014541350370616400404260ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/demux_only/regular@read_s2_000/2 CTAGGATTAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAA + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_200/2 AAGCCAGTGCCCGCAAGTGGTACCTCCTTTATGGTACACCGAACACAGCGCTTCGCCTGGCTCAAACTGCAGCAGCAAGTACCTGCTCGATG + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_075/2 GAAACGTAGCGCAATCGGGTACGATTTACGATGGCCTGTACACCGAGAGTTGCAGTTCCAGGACGCACAGCGTATCTAGGATTAGATCGGAA + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_150/2 GACTGAGGGGCGCATTCTTAGTCGAGTCGTTTGTGGATAGTCAGGTCTGGTAAAGGATGTACCGGGATGCTCGTACCGAGGCAGGAGTGTTT + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 your_output.sample_2.settings000066400000000000000000000007401350370616400401310ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/demux_only/regularAdapterRemoval ver. 2.1.7 Demultiplexing of double-indexed paired-end reads [Demultiplexing] Maximum mismatches (total): 0 Maximum mate 1 mismatches: 0 Maximum mate 2 mismatches: 0 [Demultiplexing samples] Name Barcode_1 Barcode_2 sample_1 GGCCCCTG CCAAAGCT sample_2* AATCCTAG GTCTAGTT [Adapter sequences] Adapter1[1]: AACTAGAC_AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: CTAGGATT_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT your_output.settings000066400000000000000000000012311350370616400364240ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/demux_only/regularAdapterRemoval ver. 2.1.7 Demultiplexing of double-indexed paired-end reads [Demultiplexing] Maximum mismatches (total): 0 Maximum mate 1 mismatches: 0 Maximum mate 2 mismatches: 0 [Demultiplexing samples] Name Barcode_1 Barcode_2 sample_1 GGCCCCTG CCAAAGCT sample_2 AATCCTAG GTCTAGTT [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Demultiplexing statistics] Name Barcode_1 Barcode_2 Hits Fraction unidentified NA NA 0 0.000 ambiguous NA NA 0 0.000 sample_1 GGCCCCTG CCAAAGCT 4 0.500 sample_2 AATCCTAG GTCTAGTT 4 0.500 * * * 8 1.000 your_output.unidentified_1.fastq000066400000000000000000000000001350370616400405610ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/demux_only/regularyour_output.unidentified_2.fastq000066400000000000000000000000001350370616400405620ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/demux_only/regularadapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/demux_only/unidentified/000077500000000000000000000000001350370616400333145ustar00rootroot00000000000000barcodes.txt000066400000000000000000000000661350370616400355620ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/demux_only/unidentifiedsample_1 GGCCCCTG CCAAAGCT sample_2 AATCCTAG GTCTAGTT info.json000066400000000000000000000001151350370616400350600ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/demux_only/unidentified{ "arguments": ["--demultiplex-only"], "return_code": 0, "stderr": [ ] } input_1.fastq000066400000000000000000000033301350370616400356530ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/demux_only/unidentified@read_s2_000/1 AATCCTAGAACTAGACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_150/1 GGCCCCTGTTTCTGGACGACGCCCCTATAATGTATGATAATTATTCGATTGACATGGCGAACTTCAGCCATTAGCGCTTTCGCATAATGTCGTTGTATAT + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_200/1 TGCCCCTGAACCATCTGAGCGGTACTCGGGAAAACACGGACGAGGTGGGATATCTTTCCCTTCTCTTGCCATCGTGTATTTATCTGTATCTAATGCTACT + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_200/1 AATCCTAGTCGTACAATGCATCAGACACCGCTTTTGTGGCGTTTCGACCGTAATCTACATTTACATCTCGTTAATTCGCGACATTCATCGTGCCGTACTC + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_075/1 AATCCTAGATACGCTGTGCGTCCTGGAACTGCAACTCTCGGTGTACAGGCCATCGTAAATCGTACCCGATTGCGCTACGTTTCAACTAGACAGATCGGAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_150/1 AATCCTAGATACCCCGACACTCGACTTATATTTTCCTCAGCTAGTGCGAGAGTTAATGTAGCGACGAAACACTCCTGCCTCGGTACGAGCATCCCGGTAC + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_000/1 GGCCCCTGAGCTTTGGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_075/1 GGCCCCTGGGTGGCTATGTAGGGAAAAACTCCGCTAGAACAAAGAACAGCCTCCCTCAATCACCCATGTTCGTGCCTCGACGCAGCTTTGGAGATCGGAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 input_2.fastq000066400000000000000000000033301350370616400356540ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/demux_only/unidentified@read_s2_000/2 GTCTAGTTCTAGGATTAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_150/2 CCAAAGCTTTTAGACGGCAGACGCATCAACTTCCACATGACTGCTTGAACGACGATACACCTCTATATATACAACGACATTATGCGAAAGCGCTAATGGC + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_200/2 CCAAAGCTTACGGGTCCGTGCGCTTAGGTAAGAGCCCCGTTTTTTACGCGGAAAAGCGCCTGGAAGCTCAGAATTGAGGGAAGGGAAATGAGTCACGGGT + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_200/2 GTCTAGTTAAGCCAGTGCCCGCAAGTGGTACCTCCTTTATGGTACACCGAACACAGCGCTTCGCCTGGCTCAAACTGCAGCAGCAAGTACCTGCTCGATG + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_075/2 ATCTAGTTGAAACGTAGCGCAATCGGGTACGATTTACGATGGCCTGTACACCGAGAGTTGCAGTTCCAGGACGCACAGCGTATCTAGGATTAGATCGGAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_150/2 GTCTAGTTGACTGAGGGGCGCATTCTTAGTCGAGTCGTTTGTGGATAGTCAGGTCTGGTAAAGGATGTACCGGGATGCTCGTACCGAGGCAGGAGTGTTT + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_000/2 CCAAAGCTCAGGGGCCAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_075/2 CCAAAGCTGCGTCGAGGCACGAACATGGGTGATTGAGGGAGGCTGTTCTTTGTTCTAGCGGAGTTTTTCCCTACATAGCCACCCAGGGGCCAGATCGGAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 your_output.sample_1.pair1.fastq000066400000000000000000000011411350370616400414230ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/demux_only/unidentified@read_s1_150/1 TTTCTGGACGACGCCCCTATAATGTATGATAATTATTCGATTGACATGGCGAACTTCAGCCATTAGCGCTTTCGCATAATGTCGTTGTATAT + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_000/1 AGCTTTGGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAA + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_075/1 GGTGGCTATGTAGGGAAAAACTCCGCTAGAACAAAGAACAGCCTCCCTCAATCACCCATGTTCGTGCCTCGACGCAGCTTTGGAGATCGGAA + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 your_output.sample_1.pair2.fastq000066400000000000000000000011411350370616400414240ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/demux_only/unidentified@read_s1_150/2 TTTAGACGGCAGACGCATCAACTTCCACATGACTGCTTGAACGACGATACACCTCTATATATACAACGACATTATGCGAAAGCGCTAATGGC + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_000/2 CAGGGGCCAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAA + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_075/2 GCGTCGAGGCACGAACATGGGTGATTGAGGGAGGCTGTTCTTTGTTCTAGCGGAGTTTTTCCCTACATAGCCACCCAGGGGCCAGATCGGAA + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 your_output.sample_1.settings000066400000000000000000000007401350370616400411360ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/demux_only/unidentifiedAdapterRemoval ver. 2.1.7 Demultiplexing of double-indexed paired-end reads [Demultiplexing] Maximum mismatches (total): 0 Maximum mate 1 mismatches: 0 Maximum mate 2 mismatches: 0 [Demultiplexing samples] Name Barcode_1 Barcode_2 sample_1* GGCCCCTG CCAAAGCT sample_2 AATCCTAG GTCTAGTT [Adapter sequences] Adapter1[1]: AGCTTTGG_AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: CAGGGGCC_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT your_output.sample_2.pair1.fastq000066400000000000000000000011411350370616400414240ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/demux_only/unidentified@read_s2_000/1 AACTAGACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAA + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_200/1 TCGTACAATGCATCAGACACCGCTTTTGTGGCGTTTCGACCGTAATCTACATTTACATCTCGTTAATTCGCGACATTCATCGTGCCGTACTC + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_150/1 ATACCCCGACACTCGACTTATATTTTCCTCAGCTAGTGCGAGAGTTAATGTAGCGACGAAACACTCCTGCCTCGGTACGAGCATCCCGGTAC + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 your_output.sample_2.pair2.fastq000066400000000000000000000011411350370616400414250ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/demux_only/unidentified@read_s2_000/2 CTAGGATTAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAA + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_200/2 AAGCCAGTGCCCGCAAGTGGTACCTCCTTTATGGTACACCGAACACAGCGCTTCGCCTGGCTCAAACTGCAGCAGCAAGTACCTGCTCGATG + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_150/2 GACTGAGGGGCGCATTCTTAGTCGAGTCGTTTGTGGATAGTCAGGTCTGGTAAAGGATGTACCGGGATGCTCGTACCGAGGCAGGAGTGTTT + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 your_output.sample_2.settings000066400000000000000000000007401350370616400411370ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/demux_only/unidentifiedAdapterRemoval ver. 2.1.7 Demultiplexing of double-indexed paired-end reads [Demultiplexing] Maximum mismatches (total): 0 Maximum mate 1 mismatches: 0 Maximum mate 2 mismatches: 0 [Demultiplexing samples] Name Barcode_1 Barcode_2 sample_1 GGCCCCTG CCAAAGCT sample_2* AATCCTAG GTCTAGTT [Adapter sequences] Adapter1[1]: AACTAGAC_AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: CTAGGATT_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT your_output.settings000066400000000000000000000012311350370616400374320ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/demux_only/unidentifiedAdapterRemoval ver. 2.1.7 Demultiplexing of double-indexed paired-end reads [Demultiplexing] Maximum mismatches (total): 0 Maximum mate 1 mismatches: 0 Maximum mate 2 mismatches: 0 [Demultiplexing samples] Name Barcode_1 Barcode_2 sample_1 GGCCCCTG CCAAAGCT sample_2 AATCCTAG GTCTAGTT [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Demultiplexing statistics] Name Barcode_1 Barcode_2 Hits Fraction unidentified NA NA 2 0.250 ambiguous NA NA 0 0.000 sample_1 GGCCCCTG CCAAAGCT 3 0.375 sample_2 AATCCTAG GTCTAGTT 3 0.375 * * * 8 1.000 your_output.unidentified_1.fastq000066400000000000000000000006661350370616400416110ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/demux_only/unidentified@read_s1_200/1 TGCCCCTGAACCATCTGAGCGGTACTCGGGAAAACACGGACGAGGTGGGATATCTTTCCCTTCTCTTGCCATCGTGTATTTATCTGTATCTAATGCTACT + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_075/1 AATCCTAGATACGCTGTGCGTCCTGGAACTGCAACTCTCGGTGTACAGGCCATCGTAAATCGTACCCGATTGCGCTACGTTTCAACTAGACAGATCGGAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 your_output.unidentified_2.fastq000066400000000000000000000006661350370616400416120ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/demux_only/unidentified@read_s1_200/2 CCAAAGCTTACGGGTCCGTGCGCTTAGGTAAGAGCCCCGTTTTTTACGCGGAAAAGCGCCTGGAAGCTCAGAATTGAGGGAAGGGAAATGAGTCACGGGT + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_075/2 ATCTAGTTGAAACGTAGCGCAATCGGGTACGATTTACGATGGCCTGTACACCGAGAGTTGCAGTTCCAGGACGCACAGCGTATCTAGGATTAGATCGGAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/interleaved/000077500000000000000000000000001350370616400307645ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/interleaved/both/000077500000000000000000000000001350370616400317205ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/interleaved/both/barcodes.txt000066400000000000000000000000661350370616400342450ustar00rootroot00000000000000sample_1 TTTTCAAC TAGATGGC sample_2 CTTTACAG GGGCTGCT adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/interleaved/both/info.json000066400000000000000000000001101350370616400335360ustar00rootroot00000000000000{ "arguments": ["--interleaved"], "return_code": 0, "stderr": [ ] } input_1.fastq000066400000000000000000000066601350370616400342700ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/interleaved/both@read_s2_000/1 CTTTACAGAGCAGCCCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_000/2 GGGCTGCTCTGTAAAGAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_150/1 TTTTCAACTTGACTTACACCCAGACGCTTCCGAACGAGGGGACGTGGCAAAGCGACAATCCTGTCAACACTATAATGCTTCCGAACGCAATATAAAGGAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_150/2 TAGATGGCGTACTTTACGAGATTGAGTGGATGAATCGGCGTTGCCCAAGCAGAGGCTCGGCTTTCGTTCCTTTATATTGCGTTCGGAAGCATTATAGTGT + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_200/1 CTTTACAGCCTAATAACTTGTTAATGACATCCTAAGCCCTTTGAAAAACTTTTCGTTGGATACGGTCCAGTCAGAAACTTTCAAAATCGGCCCGGGCGCG + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_200/2 GGGCTGCTAATACCCCTTAGTGTAGCTGGCGACTTCATCCAGACTGTATGTCTCTAGAGTTCATAACTCCGCGCACCGTCAACGTCTGATCATGCTGGGG + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_075/1 TTTTCAACTCGATATCTTTTGAGCAGGGATGCTTCCAGCACGTGAACCCAGGAAAATGCACGCGCGCGCACTGCACCCCCCCAGCCATCTAAGATCGGAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_075/2 TAGATGGCTGGGGGGGTGCAGTGCGCGCGCGTGCATTTTCCTGGGTTCACGTGCTGGAAGCATCCCTGCTCAAAAGATATCGAGTTGAAAAAGATCGGAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_075/1 CTTTACAGCCTGGAATCGCTGGTTACGGATGGTATTTAGATTATGGTACATCTAACAACATATGTCACACATTCCGGATCGGCAGCAGCCCAGATCGGAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_075/2 GGGCTGCTGCCGATCCGGAATGTGTGACATATGTTGTTAGATGTACCATAATCTAAATACCATCCGTAACCAGCGATTCCAGGCTGTAAAGAGATCGGAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_000/1 TTTTCAACGCCATCTAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_000/2 TAGATGGCGTTGAAAAAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_150/1 CTTTACAGTTAGCGCTTTTGCGCCGACTCATGAGTTTAGGGGAGGGATCTCACTCTACCCGACTACGGGCTCGAGTATCCGATACTTGCACAGATGAATA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_150/2 GGGCTGCTGTGGTTGGTCGAATATCCTGACTACCAACTCCTGGTACAATGGAGAATCTGACGGTGGTATTCATCTGTGCAAGTATCGGATACTCGAGCCC + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_200/1 TTTTCAACCAGGGTGGTGAACTACTCGTCCCATTCTTATCGCCGTCTTAACTCGGGACAGTAGTGCTCGAATCGCTCGCGGGGCTCCTCGGCCTTCAATG + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_200/2 TAGATGGCTAACTGGACGGTGACATTCTGCCGGTACCTAGACTGATCTTAAAACAGCCCGCACTCCGTATGTTCTAGGACAAGGTGGCATCTAGAACGAG + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 your_output.sample_1.discarded000066400000000000000000000000461350370616400376230ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/interleaved/both@read_s1_000/1 + @read_s1_000/2 + your_output.sample_1.paired.truncated000066400000000000000000000021761350370616400411430ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/interleaved/both@read_s1_150/1 TTGACTTACACCCAGACGCTTCCGAACGAGGGGACGTGGCAAAGCGACAATCCTGTCAACACTATAATGCTTCCGAACGCAATATAAAGGAA + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_150/2 GTACTTTACGAGATTGAGTGGATGAATCGGCGTTGCCCAAGCAGAGGCTCGGCTTTCGTTCCTTTATATTGCGTTCGGAAGCATTATAGTGT + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_075/1 TCGATATCTTTTGAGCAGGGATGCTTCCAGCACGTGAACCCAGGAAAATGCACGCGCGCGCACTGCACCCCCCCA + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; @read_s1_075/2 TGGGGGGGTGCAGTGCGCGCGCGTGCATTTTCCTGGGTTCACGTGCTGGAAGCATCCCTGCTCAAAAGATATCGA + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; @read_s1_200/1 CAGGGTGGTGAACTACTCGTCCCATTCTTATCGCCGTCTTAACTCGGGACAGTAGTGCTCGAATCGCTCGCGGGGCTCCTCGGCCTTCAATG + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_200/2 TAACTGGACGGTGACATTCTGCCGGTACCTAGACTGATCTTAAAACAGCCCGCACTCCGTATGTTCTAGGACAAGGTGGCATCTAGAACGAG + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 your_output.sample_1.settings000066400000000000000000000051501350370616400375420ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/interleaved/bothAdapterRemoval ver. 2.1.7 Trimming of double-indexed paired-end reads [Demultiplexing] Maximum mismatches (total): 0 Maximum mate 1 mismatches: 0 Maximum mate 2 mismatches: 0 [Demultiplexing samples] Name Barcode_1 Barcode_2 sample_1* TTTTCAAC TAGATGGC sample_2 CTTTACAG GGGCTGCT [Adapter sequences] Adapter1[1]: GCCATCTA_AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: GTTGAAAA_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 1157297082 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 [Trimming statistics] Total number of read pairs: 4 Number of unaligned read pairs: 1 Number of well aligned read pairs: 3 Number of discarded mate 1 reads: 1 Number of singleton mate 1 reads: 0 Number of discarded mate 2 reads: 1 Number of singleton mate 2 reads: 0 Number of reads with adapters[1]: 4 Number of retained reads: 6 Number of retained nucleotides: 518 Average length of retained reads: 86.3333 [Length distribution] Length Mate1 Mate2 Singleton Discarded All 0 0 0 0 2 2 1 0 0 0 0 0 2 0 0 0 0 0 3 0 0 0 0 0 4 0 0 0 0 0 5 0 0 0 0 0 6 0 0 0 0 0 7 0 0 0 0 0 8 0 0 0 0 0 9 0 0 0 0 0 10 0 0 0 0 0 11 0 0 0 0 0 12 0 0 0 0 0 13 0 0 0 0 0 14 0 0 0 0 0 15 0 0 0 0 0 16 0 0 0 0 0 17 0 0 0 0 0 18 0 0 0 0 0 19 0 0 0 0 0 20 0 0 0 0 0 21 0 0 0 0 0 22 0 0 0 0 0 23 0 0 0 0 0 24 0 0 0 0 0 25 0 0 0 0 0 26 0 0 0 0 0 27 0 0 0 0 0 28 0 0 0 0 0 29 0 0 0 0 0 30 0 0 0 0 0 31 0 0 0 0 0 32 0 0 0 0 0 33 0 0 0 0 0 34 0 0 0 0 0 35 0 0 0 0 0 36 0 0 0 0 0 37 0 0 0 0 0 38 0 0 0 0 0 39 0 0 0 0 0 40 0 0 0 0 0 41 0 0 0 0 0 42 0 0 0 0 0 43 0 0 0 0 0 44 0 0 0 0 0 45 0 0 0 0 0 46 0 0 0 0 0 47 0 0 0 0 0 48 0 0 0 0 0 49 0 0 0 0 0 50 0 0 0 0 0 51 0 0 0 0 0 52 0 0 0 0 0 53 0 0 0 0 0 54 0 0 0 0 0 55 0 0 0 0 0 56 0 0 0 0 0 57 0 0 0 0 0 58 0 0 0 0 0 59 0 0 0 0 0 60 0 0 0 0 0 61 0 0 0 0 0 62 0 0 0 0 0 63 0 0 0 0 0 64 0 0 0 0 0 65 0 0 0 0 0 66 0 0 0 0 0 67 0 0 0 0 0 68 0 0 0 0 0 69 0 0 0 0 0 70 0 0 0 0 0 71 0 0 0 0 0 72 0 0 0 0 0 73 0 0 0 0 0 74 0 0 0 0 0 75 1 1 0 0 2 76 0 0 0 0 0 77 0 0 0 0 0 78 0 0 0 0 0 79 0 0 0 0 0 80 0 0 0 0 0 81 0 0 0 0 0 82 0 0 0 0 0 83 0 0 0 0 0 84 0 0 0 0 0 85 0 0 0 0 0 86 0 0 0 0 0 87 0 0 0 0 0 88 0 0 0 0 0 89 0 0 0 0 0 90 0 0 0 0 0 91 0 0 0 0 0 92 2 2 0 0 4 your_output.sample_1.singleton.truncated000066400000000000000000000000001350370616400416610ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/interleaved/bothyour_output.sample_2.discarded000066400000000000000000000000461350370616400376240ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/interleaved/both@read_s2_000/1 + @read_s2_000/2 + your_output.sample_2.paired.truncated000066400000000000000000000021761350370616400411440ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/interleaved/both@read_s2_200/1 CCTAATAACTTGTTAATGACATCCTAAGCCCTTTGAAAAACTTTTCGTTGGATACGGTCCAGTCAGAAACTTTCAAAATCGGCCCGGGCGCG + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_200/2 AATACCCCTTAGTGTAGCTGGCGACTTCATCCAGACTGTATGTCTCTAGAGTTCATAACTCCGCGCACCGTCAACGTCTGATCATGCTGGGG + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_075/1 CCTGGAATCGCTGGTTACGGATGGTATTTAGATTATGGTACATCTAACAACATATGTCACACATTCCGGATCGGC + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; @read_s2_075/2 GCCGATCCGGAATGTGTGACATATGTTGTTAGATGTACCATAATCTAAATACCATCCGTAACCAGCGATTCCAGG + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; @read_s2_150/1 TTAGCGCTTTTGCGCCGACTCATGAGTTTAGGGGAGGGATCTCACTCTACCCGACTACGGGCTCGAGTATCCGATACTTGCACAGATGAATA + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_150/2 GTGGTTGGTCGAATATCCTGACTACCAACTCCTGGTACAATGGAGAATCTGACGGTGGTATTCATCTGTGCAAGTATCGGATACTCGAGCCC + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 your_output.sample_2.settings000066400000000000000000000051501350370616400375430ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/interleaved/bothAdapterRemoval ver. 2.1.7 Trimming of double-indexed paired-end reads [Demultiplexing] Maximum mismatches (total): 0 Maximum mate 1 mismatches: 0 Maximum mate 2 mismatches: 0 [Demultiplexing samples] Name Barcode_1 Barcode_2 sample_1 TTTTCAAC TAGATGGC sample_2* CTTTACAG GGGCTGCT [Adapter sequences] Adapter1[1]: AGCAGCCC_AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: CTGTAAAG_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 1157297082 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 [Trimming statistics] Total number of read pairs: 4 Number of unaligned read pairs: 1 Number of well aligned read pairs: 3 Number of discarded mate 1 reads: 1 Number of singleton mate 1 reads: 0 Number of discarded mate 2 reads: 1 Number of singleton mate 2 reads: 0 Number of reads with adapters[1]: 4 Number of retained reads: 6 Number of retained nucleotides: 518 Average length of retained reads: 86.3333 [Length distribution] Length Mate1 Mate2 Singleton Discarded All 0 0 0 0 2 2 1 0 0 0 0 0 2 0 0 0 0 0 3 0 0 0 0 0 4 0 0 0 0 0 5 0 0 0 0 0 6 0 0 0 0 0 7 0 0 0 0 0 8 0 0 0 0 0 9 0 0 0 0 0 10 0 0 0 0 0 11 0 0 0 0 0 12 0 0 0 0 0 13 0 0 0 0 0 14 0 0 0 0 0 15 0 0 0 0 0 16 0 0 0 0 0 17 0 0 0 0 0 18 0 0 0 0 0 19 0 0 0 0 0 20 0 0 0 0 0 21 0 0 0 0 0 22 0 0 0 0 0 23 0 0 0 0 0 24 0 0 0 0 0 25 0 0 0 0 0 26 0 0 0 0 0 27 0 0 0 0 0 28 0 0 0 0 0 29 0 0 0 0 0 30 0 0 0 0 0 31 0 0 0 0 0 32 0 0 0 0 0 33 0 0 0 0 0 34 0 0 0 0 0 35 0 0 0 0 0 36 0 0 0 0 0 37 0 0 0 0 0 38 0 0 0 0 0 39 0 0 0 0 0 40 0 0 0 0 0 41 0 0 0 0 0 42 0 0 0 0 0 43 0 0 0 0 0 44 0 0 0 0 0 45 0 0 0 0 0 46 0 0 0 0 0 47 0 0 0 0 0 48 0 0 0 0 0 49 0 0 0 0 0 50 0 0 0 0 0 51 0 0 0 0 0 52 0 0 0 0 0 53 0 0 0 0 0 54 0 0 0 0 0 55 0 0 0 0 0 56 0 0 0 0 0 57 0 0 0 0 0 58 0 0 0 0 0 59 0 0 0 0 0 60 0 0 0 0 0 61 0 0 0 0 0 62 0 0 0 0 0 63 0 0 0 0 0 64 0 0 0 0 0 65 0 0 0 0 0 66 0 0 0 0 0 67 0 0 0 0 0 68 0 0 0 0 0 69 0 0 0 0 0 70 0 0 0 0 0 71 0 0 0 0 0 72 0 0 0 0 0 73 0 0 0 0 0 74 0 0 0 0 0 75 1 1 0 0 2 76 0 0 0 0 0 77 0 0 0 0 0 78 0 0 0 0 0 79 0 0 0 0 0 80 0 0 0 0 0 81 0 0 0 0 0 82 0 0 0 0 0 83 0 0 0 0 0 84 0 0 0 0 0 85 0 0 0 0 0 86 0 0 0 0 0 87 0 0 0 0 0 88 0 0 0 0 0 89 0 0 0 0 0 90 0 0 0 0 0 91 0 0 0 0 0 92 2 2 0 0 4 your_output.sample_2.singleton.truncated000066400000000000000000000000001350370616400416620ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/interleaved/bothyour_output.settings000066400000000000000000000022241350370616400360410ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/interleaved/bothAdapterRemoval ver. 2.1.7 Trimming of double-indexed paired-end reads [Demultiplexing] Maximum mismatches (total): 0 Maximum mate 1 mismatches: 0 Maximum mate 2 mismatches: 0 [Demultiplexing samples] Name Barcode_1 Barcode_2 sample_1 TTTTCAAC TAGATGGC sample_2 CTTTACAG GGGCTGCT [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 1157297082 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 [Demultiplexing statistics] Name Barcode_1 Barcode_2 Hits Fraction unidentified NA NA 0 0.000 ambiguous NA NA 0 0.000 sample_1 TTTTCAAC TAGATGGC 4 0.500 sample_2 CTTTACAG GGGCTGCT 4 0.500 * * * 8 1.000 your_output.unidentified.paired000066400000000000000000000000001350370616400401010ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/interleaved/bothadapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/interleaved/output/000077500000000000000000000000001350370616400323245ustar00rootroot00000000000000barcodes.txt000066400000000000000000000000661350370616400345720ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/interleaved/outputsample_1 TGTAACGC CTCCTTAG sample_2 GGGGACTC GTATATGC adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/interleaved/output/info.json000066400000000000000000000001171350370616400341510ustar00rootroot00000000000000{ "arguments": ["--interleaved-output"], "return_code": 0, "stderr": [ ] } input_1.fastq000066400000000000000000000033301350370616400346630ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/interleaved/output@read_s1_150/1 TGTAACGCGAAAGCTTGCCAACTCTCAGATTACAGTTTAGCAATTCTCCGATAGACGTAGATAATAGTTGCGTTGACCGCTTTTCGGGGCACGGAAGTCA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_000/1 TGTAACGCCTAAGGAGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_075/1 GGGGACTCAAGAATCCGAGGCATAGCGAATCAATGTCACTTTGGTTCTGTCAGAACGACCTGCGAATCAAAACATGCCACGGGGCATATACAGATCGGAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_000/1 GGGGACTCGCATATACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_200/1 TGTAACGCCCAGCATCAAACATAACGTGATAGATACTCAACCATTTTCGGAGTAAACAATGAGAATAACCATGCGGCATGGGACGTGACACCAACGAACA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_075/1 TGTAACGCTGATGTGGCTCTAAAAGACCGGACGTTTCGCGTCCTTTGGAGCGGGTAGTGCGGTAGTAAAAATTTACACTAGCCCTAAGGAGAGATCGGAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_150/1 GGGGACTCCATTAGCCCACGCAACGGCTTAGGCGTCGAGGACATTAACAAGGGCGCGAGGGCCTTCACTTACATGGTATCTATCTCATCCAGTGCACGAC + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_200/1 GGGGACTCATCTCAAGCTCAAGATTAGCAGAAGGATTGTAGGCCCGGATCCGATAATCGATAAAGCCGTGATGTCAATACGGTCCCGGTCTGTCCAGCTA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 input_2.fastq000066400000000000000000000033301350370616400346640ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/interleaved/output@read_s1_150/2 CTCCTTAGTGGATGGGCAGAGAGATTCCCATTTGGCAGCGAGCGAGCCCCGTAGATAGCTGCTCTCTGACTTCCGTGCCCCGAAAAGCGGTCAACGCAAC + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_000/2 CTCCTTAGGCGTTACAAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_075/2 GTATATGCCCCGTGGCATGTTTTGATTCGCAGGTCGTTCTGACAGAACCAAAGTGACATTGATTCGCTATGCCTCGGATTCTTGAGTCCCCAGATCGGAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_000/2 GTATATGCGAGTCCCCAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_200/2 CTCCTTAGGTCCGAGCGCTAGGACCAGTCCCGTGTACCCAAATAGCGCGACCCCGTCCACGGTGTATGGGCAGTTACGGTAATCTTATGTTCAAAATGAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_075/2 CTCCTTAGGGCTAGTGTAAATTTTTACTACCGCACTACCCGCTCCAAAGGACGCGAAACGTCCGGTCTTTTAGAGCCACATCAGCGTTACAAGATCGGAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_150/2 GTATATGCCGAACTAGGTAGTCGCTTTACATAGGAGAGGTCGTTATGTATTACGTCACCGCGTTTCGTCGTGCACTGGATGAGATAGATACCATGTAAGT + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_200/2 GTATATGCAGATGCAGTACTGATTGAGAACTTTCAAATAACCCAAACAAGCGTACCAATGTATACTAGCCCACCGGCCTTCATCATCTAATTAATAGCAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 your_output.sample_1.discarded000066400000000000000000000000461350370616400402270ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/interleaved/output@read_s1_000/1 + @read_s1_000/2 + your_output.sample_1.paired.truncated000066400000000000000000000021761350370616400415470ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/interleaved/output@read_s1_150/1 GAAAGCTTGCCAACTCTCAGATTACAGTTTAGCAATTCTCCGATAGACGTAGATAATAGTTGCGTTGACCGCTTTTCGGGGCACGGAAGTCA + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_150/2 TGGATGGGCAGAGAGATTCCCATTTGGCAGCGAGCGAGCCCCGTAGATAGCTGCTCTCTGACTTCCGTGCCCCGAAAAGCGGTCAACGCAAC + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_200/1 CCAGCATCAAACATAACGTGATAGATACTCAACCATTTTCGGAGTAAACAATGAGAATAACCATGCGGCATGGGACGTGACACCAACGAACA + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_200/2 GTCCGAGCGCTAGGACCAGTCCCGTGTACCCAAATAGCGCGACCCCGTCCACGGTGTATGGGCAGTTACGGTAATCTTATGTTCAAAATGAA + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_075/1 TGATGTGGCTCTAAAAGACCGGACGTTTCGCGTCCTTTGGAGCGGGTAGTGCGGTAGTAAAAATTTACACTAGCC + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; @read_s1_075/2 GGCTAGTGTAAATTTTTACTACCGCACTACCCGCTCCAAAGGACGCGAAACGTCCGGTCTTTTAGAGCCACATCA + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; your_output.sample_1.settings000066400000000000000000000051501350370616400401460ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/interleaved/outputAdapterRemoval ver. 2.1.7 Trimming of double-indexed paired-end reads [Demultiplexing] Maximum mismatches (total): 0 Maximum mate 1 mismatches: 0 Maximum mate 2 mismatches: 0 [Demultiplexing samples] Name Barcode_1 Barcode_2 sample_1* TGTAACGC CTCCTTAG sample_2 GGGGACTC GTATATGC [Adapter sequences] Adapter1[1]: CTAAGGAG_AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: GCGTTACA_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 1157297082 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 [Trimming statistics] Total number of read pairs: 4 Number of unaligned read pairs: 1 Number of well aligned read pairs: 3 Number of discarded mate 1 reads: 1 Number of singleton mate 1 reads: 0 Number of discarded mate 2 reads: 1 Number of singleton mate 2 reads: 0 Number of reads with adapters[1]: 4 Number of retained reads: 6 Number of retained nucleotides: 518 Average length of retained reads: 86.3333 [Length distribution] Length Mate1 Mate2 Singleton Discarded All 0 0 0 0 2 2 1 0 0 0 0 0 2 0 0 0 0 0 3 0 0 0 0 0 4 0 0 0 0 0 5 0 0 0 0 0 6 0 0 0 0 0 7 0 0 0 0 0 8 0 0 0 0 0 9 0 0 0 0 0 10 0 0 0 0 0 11 0 0 0 0 0 12 0 0 0 0 0 13 0 0 0 0 0 14 0 0 0 0 0 15 0 0 0 0 0 16 0 0 0 0 0 17 0 0 0 0 0 18 0 0 0 0 0 19 0 0 0 0 0 20 0 0 0 0 0 21 0 0 0 0 0 22 0 0 0 0 0 23 0 0 0 0 0 24 0 0 0 0 0 25 0 0 0 0 0 26 0 0 0 0 0 27 0 0 0 0 0 28 0 0 0 0 0 29 0 0 0 0 0 30 0 0 0 0 0 31 0 0 0 0 0 32 0 0 0 0 0 33 0 0 0 0 0 34 0 0 0 0 0 35 0 0 0 0 0 36 0 0 0 0 0 37 0 0 0 0 0 38 0 0 0 0 0 39 0 0 0 0 0 40 0 0 0 0 0 41 0 0 0 0 0 42 0 0 0 0 0 43 0 0 0 0 0 44 0 0 0 0 0 45 0 0 0 0 0 46 0 0 0 0 0 47 0 0 0 0 0 48 0 0 0 0 0 49 0 0 0 0 0 50 0 0 0 0 0 51 0 0 0 0 0 52 0 0 0 0 0 53 0 0 0 0 0 54 0 0 0 0 0 55 0 0 0 0 0 56 0 0 0 0 0 57 0 0 0 0 0 58 0 0 0 0 0 59 0 0 0 0 0 60 0 0 0 0 0 61 0 0 0 0 0 62 0 0 0 0 0 63 0 0 0 0 0 64 0 0 0 0 0 65 0 0 0 0 0 66 0 0 0 0 0 67 0 0 0 0 0 68 0 0 0 0 0 69 0 0 0 0 0 70 0 0 0 0 0 71 0 0 0 0 0 72 0 0 0 0 0 73 0 0 0 0 0 74 0 0 0 0 0 75 1 1 0 0 2 76 0 0 0 0 0 77 0 0 0 0 0 78 0 0 0 0 0 79 0 0 0 0 0 80 0 0 0 0 0 81 0 0 0 0 0 82 0 0 0 0 0 83 0 0 0 0 0 84 0 0 0 0 0 85 0 0 0 0 0 86 0 0 0 0 0 87 0 0 0 0 0 88 0 0 0 0 0 89 0 0 0 0 0 90 0 0 0 0 0 91 0 0 0 0 0 92 2 2 0 0 4 your_output.sample_1.singleton.truncated000066400000000000000000000000001350370616400422650ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/interleaved/outputyour_output.sample_2.discarded000066400000000000000000000000461350370616400402300ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/interleaved/output@read_s2_000/1 + @read_s2_000/2 + your_output.sample_2.paired.truncated000066400000000000000000000021761350370616400415500ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/interleaved/output@read_s2_075/1 AAGAATCCGAGGCATAGCGAATCAATGTCACTTTGGTTCTGTCAGAACGACCTGCGAATCAAAACATGCCACGGG + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; @read_s2_075/2 CCCGTGGCATGTTTTGATTCGCAGGTCGTTCTGACAGAACCAAAGTGACATTGATTCGCTATGCCTCGGATTCTT + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; @read_s2_150/1 CATTAGCCCACGCAACGGCTTAGGCGTCGAGGACATTAACAAGGGCGCGAGGGCCTTCACTTACATGGTATCTATCTCATCCAGTGCACGAC + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_150/2 CGAACTAGGTAGTCGCTTTACATAGGAGAGGTCGTTATGTATTACGTCACCGCGTTTCGTCGTGCACTGGATGAGATAGATACCATGTAAGT + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_200/1 ATCTCAAGCTCAAGATTAGCAGAAGGATTGTAGGCCCGGATCCGATAATCGATAAAGCCGTGATGTCAATACGGTCCCGGTCTGTCCAGCTA + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_200/2 AGATGCAGTACTGATTGAGAACTTTCAAATAACCCAAACAAGCGTACCAATGTATACTAGCCCACCGGCCTTCATCATCTAATTAATAGCAA + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 your_output.sample_2.settings000066400000000000000000000051501350370616400401470ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/interleaved/outputAdapterRemoval ver. 2.1.7 Trimming of double-indexed paired-end reads [Demultiplexing] Maximum mismatches (total): 0 Maximum mate 1 mismatches: 0 Maximum mate 2 mismatches: 0 [Demultiplexing samples] Name Barcode_1 Barcode_2 sample_1 TGTAACGC CTCCTTAG sample_2* GGGGACTC GTATATGC [Adapter sequences] Adapter1[1]: GCATATAC_AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: GAGTCCCC_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 1157297082 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 [Trimming statistics] Total number of read pairs: 4 Number of unaligned read pairs: 1 Number of well aligned read pairs: 3 Number of discarded mate 1 reads: 1 Number of singleton mate 1 reads: 0 Number of discarded mate 2 reads: 1 Number of singleton mate 2 reads: 0 Number of reads with adapters[1]: 4 Number of retained reads: 6 Number of retained nucleotides: 518 Average length of retained reads: 86.3333 [Length distribution] Length Mate1 Mate2 Singleton Discarded All 0 0 0 0 2 2 1 0 0 0 0 0 2 0 0 0 0 0 3 0 0 0 0 0 4 0 0 0 0 0 5 0 0 0 0 0 6 0 0 0 0 0 7 0 0 0 0 0 8 0 0 0 0 0 9 0 0 0 0 0 10 0 0 0 0 0 11 0 0 0 0 0 12 0 0 0 0 0 13 0 0 0 0 0 14 0 0 0 0 0 15 0 0 0 0 0 16 0 0 0 0 0 17 0 0 0 0 0 18 0 0 0 0 0 19 0 0 0 0 0 20 0 0 0 0 0 21 0 0 0 0 0 22 0 0 0 0 0 23 0 0 0 0 0 24 0 0 0 0 0 25 0 0 0 0 0 26 0 0 0 0 0 27 0 0 0 0 0 28 0 0 0 0 0 29 0 0 0 0 0 30 0 0 0 0 0 31 0 0 0 0 0 32 0 0 0 0 0 33 0 0 0 0 0 34 0 0 0 0 0 35 0 0 0 0 0 36 0 0 0 0 0 37 0 0 0 0 0 38 0 0 0 0 0 39 0 0 0 0 0 40 0 0 0 0 0 41 0 0 0 0 0 42 0 0 0 0 0 43 0 0 0 0 0 44 0 0 0 0 0 45 0 0 0 0 0 46 0 0 0 0 0 47 0 0 0 0 0 48 0 0 0 0 0 49 0 0 0 0 0 50 0 0 0 0 0 51 0 0 0 0 0 52 0 0 0 0 0 53 0 0 0 0 0 54 0 0 0 0 0 55 0 0 0 0 0 56 0 0 0 0 0 57 0 0 0 0 0 58 0 0 0 0 0 59 0 0 0 0 0 60 0 0 0 0 0 61 0 0 0 0 0 62 0 0 0 0 0 63 0 0 0 0 0 64 0 0 0 0 0 65 0 0 0 0 0 66 0 0 0 0 0 67 0 0 0 0 0 68 0 0 0 0 0 69 0 0 0 0 0 70 0 0 0 0 0 71 0 0 0 0 0 72 0 0 0 0 0 73 0 0 0 0 0 74 0 0 0 0 0 75 1 1 0 0 2 76 0 0 0 0 0 77 0 0 0 0 0 78 0 0 0 0 0 79 0 0 0 0 0 80 0 0 0 0 0 81 0 0 0 0 0 82 0 0 0 0 0 83 0 0 0 0 0 84 0 0 0 0 0 85 0 0 0 0 0 86 0 0 0 0 0 87 0 0 0 0 0 88 0 0 0 0 0 89 0 0 0 0 0 90 0 0 0 0 0 91 0 0 0 0 0 92 2 2 0 0 4 your_output.sample_2.singleton.truncated000066400000000000000000000000001350370616400422660ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/interleaved/outputyour_output.settings000066400000000000000000000022241350370616400364450ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/interleaved/outputAdapterRemoval ver. 2.1.7 Trimming of double-indexed paired-end reads [Demultiplexing] Maximum mismatches (total): 0 Maximum mate 1 mismatches: 0 Maximum mate 2 mismatches: 0 [Demultiplexing samples] Name Barcode_1 Barcode_2 sample_1 TGTAACGC CTCCTTAG sample_2 GGGGACTC GTATATGC [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 1157297082 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 [Demultiplexing statistics] Name Barcode_1 Barcode_2 Hits Fraction unidentified NA NA 0 0.000 ambiguous NA NA 0 0.000 sample_1 TGTAACGC CTCCTTAG 4 0.500 sample_2 GGGGACTC GTATATGC 4 0.500 * * * 8 1.000 your_output.unidentified.paired000066400000000000000000000000001350370616400405050ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/interleaved/outputadapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/multiple_input/000077500000000000000000000000001350370616400315345ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/multiple_input/barcodes.txt000066400000000000000000000000661350370616400340610ustar00rootroot00000000000000sample_1 CTTGCCCT ACGTTATT sample_2 CGCCGATG TGCACGGG adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/multiple_input/info.json000066400000000000000000000000711350370616400333600ustar00rootroot00000000000000{ "arguments": [], "return_code": 0, "stderr": [ ] } adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/multiple_input/input_1a.fastq000066400000000000000000000012211350370616400343100ustar00rootroot00000000000000@read_s2_000/1 CGCCGATGCCCGTGCAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_200/1 CGCCGATGGCGTAAGTTGACGTCAGCCTGCGAGGTGCCACGCCAGTGGTTGCGCTCACCCGGGGCGTAGTTGCTCCGCGCAATTTCTTGGCAGTTCGATC + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_075/1 CTTGCCCTGGTTCTACGTTCTCCATCAGGTGGACGAGGGGATCTTGGCCCCCGTTCCTGCATTGGTATAATTAGACAGGATGAAATAACGTAGATCGGAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/multiple_input/input_1b.fastq000066400000000000000000000012211350370616400343110ustar00rootroot00000000000000@read_s1_200/1 CTTGCCCTGTAGTGCAATAAAAGGATCCTCTTGTGGCCGATTGCAGACCAGCCTCGGGGCTAAACTGATAATCGTATGCTATAGACCCTGGTCGACGCCG + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_150/1 CTTGCCCTCAGATGTCAGCTCATGTGTTGATATACAGCTAACTAAGGCCCGGGGGTTTAGGCTCAACCCTCTACCTGGTATACCGGCCCAACGCACTCGC + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_075/1 CGCCGATGTCTTGGGAACGAGAGTGCCACCAATTAAAGTGATGGATATCGAGACGTCCCAAACCACCGCAATAGGACGGGACACCCGTGCAAGATCGGAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/multiple_input/input_1c.fastq000066400000000000000000000006661350370616400343260ustar00rootroot00000000000000@read_s2_150/1 CGCCGATGAGCCCCGAGTGTCCATCACAAGCCACCTCCACTAACCATCTCGGTCCATTATTTGTCACTCGTGGCTAGAAGGGAATAAAGACAACTCTCTC + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_000/1 CTTGCCCTAATAACGTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/multiple_input/input_2a.fastq000066400000000000000000000012211350370616400343110ustar00rootroot00000000000000@read_s2_000/2 TGCACGGGCATCGGCGAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_200/2 TGCACGGGTAAGGGACGAAGTCACCGGGGGCGTTTCACTTGCGCGATCCATTGTAGTACTGGTGTGTCAATCTTCATCGGCAAAAGGTGCCTATCAAAAT + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_075/2 ACGTTATTTCATCCTGTCTAATTATACCAATGCAGGAACGGGGGCCAAGATCCCCTCGTCCACCTGATGGAGAACGTAGAACCAGGGCAAGAGATCGGAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/multiple_input/input_2b.fastq000066400000000000000000000012211350370616400343120ustar00rootroot00000000000000@read_s1_200/2 ACGTTATTAAGGCCCGCCCATCAGGTAAGAGCATGCTCGGGAGCCAACCCCGTGGGGTGGCAGCGATACTCTCCAATCTGTCATGCGTGTCAACGTGCGT + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_150/2 ACGTTATTGTGCTGCGTGAGTTGGAAGGATTGGATCCGGAAAGGCTTGGCCTTTGTAAATTCGACTGCGAGTGCGTTGGGCCGGTATACCAGGTAGAGGG + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_075/2 TGCACGGGTGTCCCGTCCTATTGCGGTGGTTTGGGACGTCTCGATATCCATCACTTTAATTGGTGGCACTCTCGTTCCCAAGACATCGGCGAGATCGGAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/multiple_input/input_2c.fastq000066400000000000000000000006661350370616400343270ustar00rootroot00000000000000@read_s2_150/2 TGCACGGGAAGGCTGGGTATACGGGGTAAATGGTGCCGCCTTGTTACACGCGCCGAGGTTTCAGATGAGAGAGTTGTCTTTATTCCCTTCTAGCCACGAG + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_000/2 ACGTTATTAGGGCAAGAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 your_output.sample_1.discarded000066400000000000000000000000461350370616400374370ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/multiple_input@read_s1_000/1 + @read_s1_000/2 + your_output.sample_1.pair1.truncated000066400000000000000000000010771350370616400405260ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/multiple_input@read_s1_075/1 GGTTCTACGTTCTCCATCAGGTGGACGAGGGGATCTTGGCCCCCGTTCCTGCATTGGTATAATTAGACAGGATGA + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; @read_s1_200/1 GTAGTGCAATAAAAGGATCCTCTTGTGGCCGATTGCAGACCAGCCTCGGGGCTAAACTGATAATCGTATGCTATAGACCCTGGTCGACGCCG + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_150/1 CAGATGTCAGCTCATGTGTTGATATACAGCTAACTAAGGCCCGGGGGTTTAGGCTCAACCCTCTACCTGGTATACCGGCCCAACGCACTCGC + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 your_output.sample_1.pair2.truncated000066400000000000000000000010771350370616400405270ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/multiple_input@read_s1_075/2 TCATCCTGTCTAATTATACCAATGCAGGAACGGGGGCCAAGATCCCCTCGTCCACCTGATGGAGAACGTAGAACC + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; @read_s1_200/2 AAGGCCCGCCCATCAGGTAAGAGCATGCTCGGGAGCCAACCCCGTGGGGTGGCAGCGATACTCTCCAATCTGTCATGCGTGTCAACGTGCGT + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_150/2 GTGCTGCGTGAGTTGGAAGGATTGGATCCGGAAAGGCTTGGCCTTTGTAAATTCGACTGCGAGTGCGTTGGGCCGGTATACCAGGTAGAGGG + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 your_output.sample_1.settings000066400000000000000000000051501350370616400373560ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/multiple_inputAdapterRemoval ver. 2.1.7 Trimming of double-indexed paired-end reads [Demultiplexing] Maximum mismatches (total): 0 Maximum mate 1 mismatches: 0 Maximum mate 2 mismatches: 0 [Demultiplexing samples] Name Barcode_1 Barcode_2 sample_1* CTTGCCCT ACGTTATT sample_2 CGCCGATG TGCACGGG [Adapter sequences] Adapter1[1]: AATAACGT_AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGGGCAAG_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 1157297082 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 [Trimming statistics] Total number of read pairs: 4 Number of unaligned read pairs: 1 Number of well aligned read pairs: 3 Number of discarded mate 1 reads: 1 Number of singleton mate 1 reads: 0 Number of discarded mate 2 reads: 1 Number of singleton mate 2 reads: 0 Number of reads with adapters[1]: 4 Number of retained reads: 6 Number of retained nucleotides: 518 Average length of retained reads: 86.3333 [Length distribution] Length Mate1 Mate2 Singleton Discarded All 0 0 0 0 2 2 1 0 0 0 0 0 2 0 0 0 0 0 3 0 0 0 0 0 4 0 0 0 0 0 5 0 0 0 0 0 6 0 0 0 0 0 7 0 0 0 0 0 8 0 0 0 0 0 9 0 0 0 0 0 10 0 0 0 0 0 11 0 0 0 0 0 12 0 0 0 0 0 13 0 0 0 0 0 14 0 0 0 0 0 15 0 0 0 0 0 16 0 0 0 0 0 17 0 0 0 0 0 18 0 0 0 0 0 19 0 0 0 0 0 20 0 0 0 0 0 21 0 0 0 0 0 22 0 0 0 0 0 23 0 0 0 0 0 24 0 0 0 0 0 25 0 0 0 0 0 26 0 0 0 0 0 27 0 0 0 0 0 28 0 0 0 0 0 29 0 0 0 0 0 30 0 0 0 0 0 31 0 0 0 0 0 32 0 0 0 0 0 33 0 0 0 0 0 34 0 0 0 0 0 35 0 0 0 0 0 36 0 0 0 0 0 37 0 0 0 0 0 38 0 0 0 0 0 39 0 0 0 0 0 40 0 0 0 0 0 41 0 0 0 0 0 42 0 0 0 0 0 43 0 0 0 0 0 44 0 0 0 0 0 45 0 0 0 0 0 46 0 0 0 0 0 47 0 0 0 0 0 48 0 0 0 0 0 49 0 0 0 0 0 50 0 0 0 0 0 51 0 0 0 0 0 52 0 0 0 0 0 53 0 0 0 0 0 54 0 0 0 0 0 55 0 0 0 0 0 56 0 0 0 0 0 57 0 0 0 0 0 58 0 0 0 0 0 59 0 0 0 0 0 60 0 0 0 0 0 61 0 0 0 0 0 62 0 0 0 0 0 63 0 0 0 0 0 64 0 0 0 0 0 65 0 0 0 0 0 66 0 0 0 0 0 67 0 0 0 0 0 68 0 0 0 0 0 69 0 0 0 0 0 70 0 0 0 0 0 71 0 0 0 0 0 72 0 0 0 0 0 73 0 0 0 0 0 74 0 0 0 0 0 75 1 1 0 0 2 76 0 0 0 0 0 77 0 0 0 0 0 78 0 0 0 0 0 79 0 0 0 0 0 80 0 0 0 0 0 81 0 0 0 0 0 82 0 0 0 0 0 83 0 0 0 0 0 84 0 0 0 0 0 85 0 0 0 0 0 86 0 0 0 0 0 87 0 0 0 0 0 88 0 0 0 0 0 89 0 0 0 0 0 90 0 0 0 0 0 91 0 0 0 0 0 92 2 2 0 0 4 your_output.sample_1.singleton.truncated000066400000000000000000000000001350370616400414750ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/multiple_inputyour_output.sample_2.discarded000066400000000000000000000000461350370616400374400ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/multiple_input@read_s2_000/1 + @read_s2_000/2 + your_output.sample_2.pair1.truncated000066400000000000000000000010771350370616400405270ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/multiple_input@read_s2_200/1 GCGTAAGTTGACGTCAGCCTGCGAGGTGCCACGCCAGTGGTTGCGCTCACCCGGGGCGTAGTTGCTCCGCGCAATTTCTTGGCAGTTCGATC + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_075/1 TCTTGGGAACGAGAGTGCCACCAATTAAAGTGATGGATATCGAGACGTCCCAAACCACCGCAATAGGACGGGACA + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; @read_s2_150/1 AGCCCCGAGTGTCCATCACAAGCCACCTCCACTAACCATCTCGGTCCATTATTTGTCACTCGTGGCTAGAAGGGAATAAAGACAACTCTCTC + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 your_output.sample_2.pair2.truncated000066400000000000000000000010771350370616400405300ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/multiple_input@read_s2_200/2 TAAGGGACGAAGTCACCGGGGGCGTTTCACTTGCGCGATCCATTGTAGTACTGGTGTGTCAATCTTCATCGGCAAAAGGTGCCTATCAAAAT + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_075/2 TGTCCCGTCCTATTGCGGTGGTTTGGGACGTCTCGATATCCATCACTTTAATTGGTGGCACTCTCGTTCCCAAGA + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; @read_s2_150/2 AAGGCTGGGTATACGGGGTAAATGGTGCCGCCTTGTTACACGCGCCGAGGTTTCAGATGAGAGAGTTGTCTTTATTCCCTTCTAGCCACGAG + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 your_output.sample_2.settings000066400000000000000000000051501350370616400373570ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/multiple_inputAdapterRemoval ver. 2.1.7 Trimming of double-indexed paired-end reads [Demultiplexing] Maximum mismatches (total): 0 Maximum mate 1 mismatches: 0 Maximum mate 2 mismatches: 0 [Demultiplexing samples] Name Barcode_1 Barcode_2 sample_1 CTTGCCCT ACGTTATT sample_2* CGCCGATG TGCACGGG [Adapter sequences] Adapter1[1]: CCCGTGCA_AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: CATCGGCG_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 1157297082 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 [Trimming statistics] Total number of read pairs: 4 Number of unaligned read pairs: 1 Number of well aligned read pairs: 3 Number of discarded mate 1 reads: 1 Number of singleton mate 1 reads: 0 Number of discarded mate 2 reads: 1 Number of singleton mate 2 reads: 0 Number of reads with adapters[1]: 4 Number of retained reads: 6 Number of retained nucleotides: 518 Average length of retained reads: 86.3333 [Length distribution] Length Mate1 Mate2 Singleton Discarded All 0 0 0 0 2 2 1 0 0 0 0 0 2 0 0 0 0 0 3 0 0 0 0 0 4 0 0 0 0 0 5 0 0 0 0 0 6 0 0 0 0 0 7 0 0 0 0 0 8 0 0 0 0 0 9 0 0 0 0 0 10 0 0 0 0 0 11 0 0 0 0 0 12 0 0 0 0 0 13 0 0 0 0 0 14 0 0 0 0 0 15 0 0 0 0 0 16 0 0 0 0 0 17 0 0 0 0 0 18 0 0 0 0 0 19 0 0 0 0 0 20 0 0 0 0 0 21 0 0 0 0 0 22 0 0 0 0 0 23 0 0 0 0 0 24 0 0 0 0 0 25 0 0 0 0 0 26 0 0 0 0 0 27 0 0 0 0 0 28 0 0 0 0 0 29 0 0 0 0 0 30 0 0 0 0 0 31 0 0 0 0 0 32 0 0 0 0 0 33 0 0 0 0 0 34 0 0 0 0 0 35 0 0 0 0 0 36 0 0 0 0 0 37 0 0 0 0 0 38 0 0 0 0 0 39 0 0 0 0 0 40 0 0 0 0 0 41 0 0 0 0 0 42 0 0 0 0 0 43 0 0 0 0 0 44 0 0 0 0 0 45 0 0 0 0 0 46 0 0 0 0 0 47 0 0 0 0 0 48 0 0 0 0 0 49 0 0 0 0 0 50 0 0 0 0 0 51 0 0 0 0 0 52 0 0 0 0 0 53 0 0 0 0 0 54 0 0 0 0 0 55 0 0 0 0 0 56 0 0 0 0 0 57 0 0 0 0 0 58 0 0 0 0 0 59 0 0 0 0 0 60 0 0 0 0 0 61 0 0 0 0 0 62 0 0 0 0 0 63 0 0 0 0 0 64 0 0 0 0 0 65 0 0 0 0 0 66 0 0 0 0 0 67 0 0 0 0 0 68 0 0 0 0 0 69 0 0 0 0 0 70 0 0 0 0 0 71 0 0 0 0 0 72 0 0 0 0 0 73 0 0 0 0 0 74 0 0 0 0 0 75 1 1 0 0 2 76 0 0 0 0 0 77 0 0 0 0 0 78 0 0 0 0 0 79 0 0 0 0 0 80 0 0 0 0 0 81 0 0 0 0 0 82 0 0 0 0 0 83 0 0 0 0 0 84 0 0 0 0 0 85 0 0 0 0 0 86 0 0 0 0 0 87 0 0 0 0 0 88 0 0 0 0 0 89 0 0 0 0 0 90 0 0 0 0 0 91 0 0 0 0 0 92 2 2 0 0 4 your_output.sample_2.singleton.truncated000066400000000000000000000000001350370616400414760ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/multiple_inputyour_output.settings000066400000000000000000000022241350370616400356550ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/multiple_inputAdapterRemoval ver. 2.1.7 Trimming of double-indexed paired-end reads [Demultiplexing] Maximum mismatches (total): 0 Maximum mate 1 mismatches: 0 Maximum mate 2 mismatches: 0 [Demultiplexing samples] Name Barcode_1 Barcode_2 sample_1 CTTGCCCT ACGTTATT sample_2 CGCCGATG TGCACGGG [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 1157297082 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 [Demultiplexing statistics] Name Barcode_1 Barcode_2 Hits Fraction unidentified NA NA 0 0.000 ambiguous NA NA 0 0.000 sample_1 CTTGCCCT ACGTTATT 4 0.500 sample_2 CGCCGATG TGCACGGG 4 0.500 * * * 8 1.000 your_output.unidentified_1000066400000000000000000000000001350370616400366720ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/multiple_inputyour_output.unidentified_2000066400000000000000000000000001350370616400366730ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/multiple_inputadapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/threads/000077500000000000000000000000001350370616400301145ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/threads/one/000077500000000000000000000000001350370616400306755ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/threads/one/barcodes.txt000066400000000000000000000000661350370616400332220ustar00rootroot00000000000000sample_1 CTTGCCCT ACGTTATT sample_2 CGCCGATG TGCACGGG adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/threads/one/info.json000066400000000000000000000001111350370616400325140ustar00rootroot00000000000000{ "arguments": ["--threads", "1"], "return_code": 0, "stderr": [ ] } adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/threads/one/input_1.fastq000066400000000000000000000033301350370616400333130ustar00rootroot00000000000000@read_s2_000/1 CGCCGATGCCCGTGCAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_200/1 CGCCGATGGCGTAAGTTGACGTCAGCCTGCGAGGTGCCACGCCAGTGGTTGCGCTCACCCGGGGCGTAGTTGCTCCGCGCAATTTCTTGGCAGTTCGATC + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_075/1 CTTGCCCTGGTTCTACGTTCTCCATCAGGTGGACGAGGGGATCTTGGCCCCCGTTCCTGCATTGGTATAATTAGACAGGATGAAATAACGTAGATCGGAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_200/1 CTTGCCCTGTAGTGCAATAAAAGGATCCTCTTGTGGCCGATTGCAGACCAGCCTCGGGGCTAAACTGATAATCGTATGCTATAGACCCTGGTCGACGCCG + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_150/1 CTTGCCCTCAGATGTCAGCTCATGTGTTGATATACAGCTAACTAAGGCCCGGGGGTTTAGGCTCAACCCTCTACCTGGTATACCGGCCCAACGCACTCGC + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_075/1 CGCCGATGTCTTGGGAACGAGAGTGCCACCAATTAAAGTGATGGATATCGAGACGTCCCAAACCACCGCAATAGGACGGGACACCCGTGCAAGATCGGAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_150/1 CGCCGATGAGCCCCGAGTGTCCATCACAAGCCACCTCCACTAACCATCTCGGTCCATTATTTGTCACTCGTGGCTAGAAGGGAATAAAGACAACTCTCTC + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_000/1 CTTGCCCTAATAACGTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/threads/one/input_2.fastq000066400000000000000000000033301350370616400333140ustar00rootroot00000000000000@read_s2_000/2 TGCACGGGCATCGGCGAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_200/2 TGCACGGGTAAGGGACGAAGTCACCGGGGGCGTTTCACTTGCGCGATCCATTGTAGTACTGGTGTGTCAATCTTCATCGGCAAAAGGTGCCTATCAAAAT + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_075/2 ACGTTATTTCATCCTGTCTAATTATACCAATGCAGGAACGGGGGCCAAGATCCCCTCGTCCACCTGATGGAGAACGTAGAACCAGGGCAAGAGATCGGAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_200/2 ACGTTATTAAGGCCCGCCCATCAGGTAAGAGCATGCTCGGGAGCCAACCCCGTGGGGTGGCAGCGATACTCTCCAATCTGTCATGCGTGTCAACGTGCGT + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_150/2 ACGTTATTGTGCTGCGTGAGTTGGAAGGATTGGATCCGGAAAGGCTTGGCCTTTGTAAATTCGACTGCGAGTGCGTTGGGCCGGTATACCAGGTAGAGGG + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_075/2 TGCACGGGTGTCCCGTCCTATTGCGGTGGTTTGGGACGTCTCGATATCCATCACTTTAATTGGTGGCACTCTCGTTCCCAAGACATCGGCGAGATCGGAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_150/2 TGCACGGGAAGGCTGGGTATACGGGGTAAATGGTGCCGCCTTGTTACACGCGCCGAGGTTTCAGATGAGAGAGTTGTCTTTATTCCCTTCTAGCCACGAG + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_000/2 ACGTTATTAGGGCAAGAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 your_output.sample_1.discarded000066400000000000000000000000461350370616400366000ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/threads/one@read_s1_000/1 + @read_s1_000/2 + your_output.sample_1.pair1.truncated000066400000000000000000000010771350370616400376670ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/threads/one@read_s1_075/1 GGTTCTACGTTCTCCATCAGGTGGACGAGGGGATCTTGGCCCCCGTTCCTGCATTGGTATAATTAGACAGGATGA + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; @read_s1_200/1 GTAGTGCAATAAAAGGATCCTCTTGTGGCCGATTGCAGACCAGCCTCGGGGCTAAACTGATAATCGTATGCTATAGACCCTGGTCGACGCCG + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_150/1 CAGATGTCAGCTCATGTGTTGATATACAGCTAACTAAGGCCCGGGGGTTTAGGCTCAACCCTCTACCTGGTATACCGGCCCAACGCACTCGC + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 your_output.sample_1.pair2.truncated000066400000000000000000000010771350370616400376700ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/threads/one@read_s1_075/2 TCATCCTGTCTAATTATACCAATGCAGGAACGGGGGCCAAGATCCCCTCGTCCACCTGATGGAGAACGTAGAACC + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; @read_s1_200/2 AAGGCCCGCCCATCAGGTAAGAGCATGCTCGGGAGCCAACCCCGTGGGGTGGCAGCGATACTCTCCAATCTGTCATGCGTGTCAACGTGCGT + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_150/2 GTGCTGCGTGAGTTGGAAGGATTGGATCCGGAAAGGCTTGGCCTTTGTAAATTCGACTGCGAGTGCGTTGGGCCGGTATACCAGGTAGAGGG + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 your_output.sample_1.settings000066400000000000000000000051501350370616400365170ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/threads/oneAdapterRemoval ver. 2.1.7 Trimming of double-indexed paired-end reads [Demultiplexing] Maximum mismatches (total): 0 Maximum mate 1 mismatches: 0 Maximum mate 2 mismatches: 0 [Demultiplexing samples] Name Barcode_1 Barcode_2 sample_1* CTTGCCCT ACGTTATT sample_2 CGCCGATG TGCACGGG [Adapter sequences] Adapter1[1]: AATAACGT_AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGGGCAAG_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 1157297082 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 [Trimming statistics] Total number of read pairs: 4 Number of unaligned read pairs: 1 Number of well aligned read pairs: 3 Number of discarded mate 1 reads: 1 Number of singleton mate 1 reads: 0 Number of discarded mate 2 reads: 1 Number of singleton mate 2 reads: 0 Number of reads with adapters[1]: 4 Number of retained reads: 6 Number of retained nucleotides: 518 Average length of retained reads: 86.3333 [Length distribution] Length Mate1 Mate2 Singleton Discarded All 0 0 0 0 2 2 1 0 0 0 0 0 2 0 0 0 0 0 3 0 0 0 0 0 4 0 0 0 0 0 5 0 0 0 0 0 6 0 0 0 0 0 7 0 0 0 0 0 8 0 0 0 0 0 9 0 0 0 0 0 10 0 0 0 0 0 11 0 0 0 0 0 12 0 0 0 0 0 13 0 0 0 0 0 14 0 0 0 0 0 15 0 0 0 0 0 16 0 0 0 0 0 17 0 0 0 0 0 18 0 0 0 0 0 19 0 0 0 0 0 20 0 0 0 0 0 21 0 0 0 0 0 22 0 0 0 0 0 23 0 0 0 0 0 24 0 0 0 0 0 25 0 0 0 0 0 26 0 0 0 0 0 27 0 0 0 0 0 28 0 0 0 0 0 29 0 0 0 0 0 30 0 0 0 0 0 31 0 0 0 0 0 32 0 0 0 0 0 33 0 0 0 0 0 34 0 0 0 0 0 35 0 0 0 0 0 36 0 0 0 0 0 37 0 0 0 0 0 38 0 0 0 0 0 39 0 0 0 0 0 40 0 0 0 0 0 41 0 0 0 0 0 42 0 0 0 0 0 43 0 0 0 0 0 44 0 0 0 0 0 45 0 0 0 0 0 46 0 0 0 0 0 47 0 0 0 0 0 48 0 0 0 0 0 49 0 0 0 0 0 50 0 0 0 0 0 51 0 0 0 0 0 52 0 0 0 0 0 53 0 0 0 0 0 54 0 0 0 0 0 55 0 0 0 0 0 56 0 0 0 0 0 57 0 0 0 0 0 58 0 0 0 0 0 59 0 0 0 0 0 60 0 0 0 0 0 61 0 0 0 0 0 62 0 0 0 0 0 63 0 0 0 0 0 64 0 0 0 0 0 65 0 0 0 0 0 66 0 0 0 0 0 67 0 0 0 0 0 68 0 0 0 0 0 69 0 0 0 0 0 70 0 0 0 0 0 71 0 0 0 0 0 72 0 0 0 0 0 73 0 0 0 0 0 74 0 0 0 0 0 75 1 1 0 0 2 76 0 0 0 0 0 77 0 0 0 0 0 78 0 0 0 0 0 79 0 0 0 0 0 80 0 0 0 0 0 81 0 0 0 0 0 82 0 0 0 0 0 83 0 0 0 0 0 84 0 0 0 0 0 85 0 0 0 0 0 86 0 0 0 0 0 87 0 0 0 0 0 88 0 0 0 0 0 89 0 0 0 0 0 90 0 0 0 0 0 91 0 0 0 0 0 92 2 2 0 0 4 your_output.sample_1.singleton.truncated000066400000000000000000000000001350370616400406360ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/threads/oneyour_output.sample_2.discarded000066400000000000000000000000461350370616400366010ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/threads/one@read_s2_000/1 + @read_s2_000/2 + your_output.sample_2.pair1.truncated000066400000000000000000000010771350370616400376700ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/threads/one@read_s2_200/1 GCGTAAGTTGACGTCAGCCTGCGAGGTGCCACGCCAGTGGTTGCGCTCACCCGGGGCGTAGTTGCTCCGCGCAATTTCTTGGCAGTTCGATC + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_075/1 TCTTGGGAACGAGAGTGCCACCAATTAAAGTGATGGATATCGAGACGTCCCAAACCACCGCAATAGGACGGGACA + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; @read_s2_150/1 AGCCCCGAGTGTCCATCACAAGCCACCTCCACTAACCATCTCGGTCCATTATTTGTCACTCGTGGCTAGAAGGGAATAAAGACAACTCTCTC + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 your_output.sample_2.pair2.truncated000066400000000000000000000010771350370616400376710ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/threads/one@read_s2_200/2 TAAGGGACGAAGTCACCGGGGGCGTTTCACTTGCGCGATCCATTGTAGTACTGGTGTGTCAATCTTCATCGGCAAAAGGTGCCTATCAAAAT + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_075/2 TGTCCCGTCCTATTGCGGTGGTTTGGGACGTCTCGATATCCATCACTTTAATTGGTGGCACTCTCGTTCCCAAGA + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; @read_s2_150/2 AAGGCTGGGTATACGGGGTAAATGGTGCCGCCTTGTTACACGCGCCGAGGTTTCAGATGAGAGAGTTGTCTTTATTCCCTTCTAGCCACGAG + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 your_output.sample_2.settings000066400000000000000000000051501350370616400365200ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/threads/oneAdapterRemoval ver. 2.1.7 Trimming of double-indexed paired-end reads [Demultiplexing] Maximum mismatches (total): 0 Maximum mate 1 mismatches: 0 Maximum mate 2 mismatches: 0 [Demultiplexing samples] Name Barcode_1 Barcode_2 sample_1 CTTGCCCT ACGTTATT sample_2* CGCCGATG TGCACGGG [Adapter sequences] Adapter1[1]: CCCGTGCA_AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: CATCGGCG_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 1157297082 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 [Trimming statistics] Total number of read pairs: 4 Number of unaligned read pairs: 1 Number of well aligned read pairs: 3 Number of discarded mate 1 reads: 1 Number of singleton mate 1 reads: 0 Number of discarded mate 2 reads: 1 Number of singleton mate 2 reads: 0 Number of reads with adapters[1]: 4 Number of retained reads: 6 Number of retained nucleotides: 518 Average length of retained reads: 86.3333 [Length distribution] Length Mate1 Mate2 Singleton Discarded All 0 0 0 0 2 2 1 0 0 0 0 0 2 0 0 0 0 0 3 0 0 0 0 0 4 0 0 0 0 0 5 0 0 0 0 0 6 0 0 0 0 0 7 0 0 0 0 0 8 0 0 0 0 0 9 0 0 0 0 0 10 0 0 0 0 0 11 0 0 0 0 0 12 0 0 0 0 0 13 0 0 0 0 0 14 0 0 0 0 0 15 0 0 0 0 0 16 0 0 0 0 0 17 0 0 0 0 0 18 0 0 0 0 0 19 0 0 0 0 0 20 0 0 0 0 0 21 0 0 0 0 0 22 0 0 0 0 0 23 0 0 0 0 0 24 0 0 0 0 0 25 0 0 0 0 0 26 0 0 0 0 0 27 0 0 0 0 0 28 0 0 0 0 0 29 0 0 0 0 0 30 0 0 0 0 0 31 0 0 0 0 0 32 0 0 0 0 0 33 0 0 0 0 0 34 0 0 0 0 0 35 0 0 0 0 0 36 0 0 0 0 0 37 0 0 0 0 0 38 0 0 0 0 0 39 0 0 0 0 0 40 0 0 0 0 0 41 0 0 0 0 0 42 0 0 0 0 0 43 0 0 0 0 0 44 0 0 0 0 0 45 0 0 0 0 0 46 0 0 0 0 0 47 0 0 0 0 0 48 0 0 0 0 0 49 0 0 0 0 0 50 0 0 0 0 0 51 0 0 0 0 0 52 0 0 0 0 0 53 0 0 0 0 0 54 0 0 0 0 0 55 0 0 0 0 0 56 0 0 0 0 0 57 0 0 0 0 0 58 0 0 0 0 0 59 0 0 0 0 0 60 0 0 0 0 0 61 0 0 0 0 0 62 0 0 0 0 0 63 0 0 0 0 0 64 0 0 0 0 0 65 0 0 0 0 0 66 0 0 0 0 0 67 0 0 0 0 0 68 0 0 0 0 0 69 0 0 0 0 0 70 0 0 0 0 0 71 0 0 0 0 0 72 0 0 0 0 0 73 0 0 0 0 0 74 0 0 0 0 0 75 1 1 0 0 2 76 0 0 0 0 0 77 0 0 0 0 0 78 0 0 0 0 0 79 0 0 0 0 0 80 0 0 0 0 0 81 0 0 0 0 0 82 0 0 0 0 0 83 0 0 0 0 0 84 0 0 0 0 0 85 0 0 0 0 0 86 0 0 0 0 0 87 0 0 0 0 0 88 0 0 0 0 0 89 0 0 0 0 0 90 0 0 0 0 0 91 0 0 0 0 0 92 2 2 0 0 4 your_output.sample_2.singleton.truncated000066400000000000000000000000001350370616400406370ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/threads/oneyour_output.settings000066400000000000000000000022241350370616400350160ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/threads/oneAdapterRemoval ver. 2.1.7 Trimming of double-indexed paired-end reads [Demultiplexing] Maximum mismatches (total): 0 Maximum mate 1 mismatches: 0 Maximum mate 2 mismatches: 0 [Demultiplexing samples] Name Barcode_1 Barcode_2 sample_1 CTTGCCCT ACGTTATT sample_2 CGCCGATG TGCACGGG [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 1157297082 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 [Demultiplexing statistics] Name Barcode_1 Barcode_2 Hits Fraction unidentified NA NA 0 0.000 ambiguous NA NA 0 0.000 sample_1 CTTGCCCT ACGTTATT 4 0.500 sample_2 CGCCGATG TGCACGGG 4 0.500 * * * 8 1.000 your_output.unidentified_1000066400000000000000000000000001350370616400360330ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/threads/oneyour_output.unidentified_2000066400000000000000000000000001350370616400360340ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/threads/oneadapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/threads/three/000077500000000000000000000000001350370616400312235ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/threads/three/barcodes.txt000066400000000000000000000000661350370616400335500ustar00rootroot00000000000000sample_1 CTTGCCCT ACGTTATT sample_2 CGCCGATG TGCACGGG adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/threads/three/info.json000066400000000000000000000001111350370616400330420ustar00rootroot00000000000000{ "arguments": ["--threads", "3"], "return_code": 0, "stderr": [ ] } adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/threads/three/input_1.fastq000066400000000000000000000033301350370616400336410ustar00rootroot00000000000000@read_s2_000/1 CGCCGATGCCCGTGCAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_200/1 CGCCGATGGCGTAAGTTGACGTCAGCCTGCGAGGTGCCACGCCAGTGGTTGCGCTCACCCGGGGCGTAGTTGCTCCGCGCAATTTCTTGGCAGTTCGATC + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_075/1 CTTGCCCTGGTTCTACGTTCTCCATCAGGTGGACGAGGGGATCTTGGCCCCCGTTCCTGCATTGGTATAATTAGACAGGATGAAATAACGTAGATCGGAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_200/1 CTTGCCCTGTAGTGCAATAAAAGGATCCTCTTGTGGCCGATTGCAGACCAGCCTCGGGGCTAAACTGATAATCGTATGCTATAGACCCTGGTCGACGCCG + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_150/1 CTTGCCCTCAGATGTCAGCTCATGTGTTGATATACAGCTAACTAAGGCCCGGGGGTTTAGGCTCAACCCTCTACCTGGTATACCGGCCCAACGCACTCGC + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_075/1 CGCCGATGTCTTGGGAACGAGAGTGCCACCAATTAAAGTGATGGATATCGAGACGTCCCAAACCACCGCAATAGGACGGGACACCCGTGCAAGATCGGAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_150/1 CGCCGATGAGCCCCGAGTGTCCATCACAAGCCACCTCCACTAACCATCTCGGTCCATTATTTGTCACTCGTGGCTAGAAGGGAATAAAGACAACTCTCTC + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_000/1 CTTGCCCTAATAACGTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/threads/three/input_2.fastq000066400000000000000000000033301350370616400336420ustar00rootroot00000000000000@read_s2_000/2 TGCACGGGCATCGGCGAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_200/2 TGCACGGGTAAGGGACGAAGTCACCGGGGGCGTTTCACTTGCGCGATCCATTGTAGTACTGGTGTGTCAATCTTCATCGGCAAAAGGTGCCTATCAAAAT + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_075/2 ACGTTATTTCATCCTGTCTAATTATACCAATGCAGGAACGGGGGCCAAGATCCCCTCGTCCACCTGATGGAGAACGTAGAACCAGGGCAAGAGATCGGAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_200/2 ACGTTATTAAGGCCCGCCCATCAGGTAAGAGCATGCTCGGGAGCCAACCCCGTGGGGTGGCAGCGATACTCTCCAATCTGTCATGCGTGTCAACGTGCGT + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_150/2 ACGTTATTGTGCTGCGTGAGTTGGAAGGATTGGATCCGGAAAGGCTTGGCCTTTGTAAATTCGACTGCGAGTGCGTTGGGCCGGTATACCAGGTAGAGGG + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_075/2 TGCACGGGTGTCCCGTCCTATTGCGGTGGTTTGGGACGTCTCGATATCCATCACTTTAATTGGTGGCACTCTCGTTCCCAAGACATCGGCGAGATCGGAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_150/2 TGCACGGGAAGGCTGGGTATACGGGGTAAATGGTGCCGCCTTGTTACACGCGCCGAGGTTTCAGATGAGAGAGTTGTCTTTATTCCCTTCTAGCCACGAG + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_000/2 ACGTTATTAGGGCAAGAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 your_output.sample_1.discarded000066400000000000000000000000461350370616400371260ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/threads/three@read_s1_000/1 + @read_s1_000/2 + your_output.sample_1.pair1.truncated000066400000000000000000000010771350370616400402150ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/threads/three@read_s1_075/1 GGTTCTACGTTCTCCATCAGGTGGACGAGGGGATCTTGGCCCCCGTTCCTGCATTGGTATAATTAGACAGGATGA + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; @read_s1_200/1 GTAGTGCAATAAAAGGATCCTCTTGTGGCCGATTGCAGACCAGCCTCGGGGCTAAACTGATAATCGTATGCTATAGACCCTGGTCGACGCCG + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_150/1 CAGATGTCAGCTCATGTGTTGATATACAGCTAACTAAGGCCCGGGGGTTTAGGCTCAACCCTCTACCTGGTATACCGGCCCAACGCACTCGC + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 your_output.sample_1.pair2.truncated000066400000000000000000000010771350370616400402160ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/threads/three@read_s1_075/2 TCATCCTGTCTAATTATACCAATGCAGGAACGGGGGCCAAGATCCCCTCGTCCACCTGATGGAGAACGTAGAACC + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; @read_s1_200/2 AAGGCCCGCCCATCAGGTAAGAGCATGCTCGGGAGCCAACCCCGTGGGGTGGCAGCGATACTCTCCAATCTGTCATGCGTGTCAACGTGCGT + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_150/2 GTGCTGCGTGAGTTGGAAGGATTGGATCCGGAAAGGCTTGGCCTTTGTAAATTCGACTGCGAGTGCGTTGGGCCGGTATACCAGGTAGAGGG + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 your_output.sample_1.settings000066400000000000000000000051401350370616400370440ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/threads/threeAdapterRemoval ver. 2.1.7 Trimming of double-indexed paired-end reads [Demultiplexing] Maximum mismatches (total): 0 Maximum mate 1 mismatches: 0 Maximum mate 2 mismatches: 0 [Demultiplexing samples] Name Barcode_1 Barcode_2 sample_1* CTTGCCCT ACGTTATT sample_2 CGCCGATG TGCACGGG [Adapter sequences] Adapter1[1]: AATAACGT_AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGGGCAAG_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: NA Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 [Trimming statistics] Total number of read pairs: 4 Number of unaligned read pairs: 1 Number of well aligned read pairs: 3 Number of discarded mate 1 reads: 1 Number of singleton mate 1 reads: 0 Number of discarded mate 2 reads: 1 Number of singleton mate 2 reads: 0 Number of reads with adapters[1]: 4 Number of retained reads: 6 Number of retained nucleotides: 518 Average length of retained reads: 86.3333 [Length distribution] Length Mate1 Mate2 Singleton Discarded All 0 0 0 0 2 2 1 0 0 0 0 0 2 0 0 0 0 0 3 0 0 0 0 0 4 0 0 0 0 0 5 0 0 0 0 0 6 0 0 0 0 0 7 0 0 0 0 0 8 0 0 0 0 0 9 0 0 0 0 0 10 0 0 0 0 0 11 0 0 0 0 0 12 0 0 0 0 0 13 0 0 0 0 0 14 0 0 0 0 0 15 0 0 0 0 0 16 0 0 0 0 0 17 0 0 0 0 0 18 0 0 0 0 0 19 0 0 0 0 0 20 0 0 0 0 0 21 0 0 0 0 0 22 0 0 0 0 0 23 0 0 0 0 0 24 0 0 0 0 0 25 0 0 0 0 0 26 0 0 0 0 0 27 0 0 0 0 0 28 0 0 0 0 0 29 0 0 0 0 0 30 0 0 0 0 0 31 0 0 0 0 0 32 0 0 0 0 0 33 0 0 0 0 0 34 0 0 0 0 0 35 0 0 0 0 0 36 0 0 0 0 0 37 0 0 0 0 0 38 0 0 0 0 0 39 0 0 0 0 0 40 0 0 0 0 0 41 0 0 0 0 0 42 0 0 0 0 0 43 0 0 0 0 0 44 0 0 0 0 0 45 0 0 0 0 0 46 0 0 0 0 0 47 0 0 0 0 0 48 0 0 0 0 0 49 0 0 0 0 0 50 0 0 0 0 0 51 0 0 0 0 0 52 0 0 0 0 0 53 0 0 0 0 0 54 0 0 0 0 0 55 0 0 0 0 0 56 0 0 0 0 0 57 0 0 0 0 0 58 0 0 0 0 0 59 0 0 0 0 0 60 0 0 0 0 0 61 0 0 0 0 0 62 0 0 0 0 0 63 0 0 0 0 0 64 0 0 0 0 0 65 0 0 0 0 0 66 0 0 0 0 0 67 0 0 0 0 0 68 0 0 0 0 0 69 0 0 0 0 0 70 0 0 0 0 0 71 0 0 0 0 0 72 0 0 0 0 0 73 0 0 0 0 0 74 0 0 0 0 0 75 1 1 0 0 2 76 0 0 0 0 0 77 0 0 0 0 0 78 0 0 0 0 0 79 0 0 0 0 0 80 0 0 0 0 0 81 0 0 0 0 0 82 0 0 0 0 0 83 0 0 0 0 0 84 0 0 0 0 0 85 0 0 0 0 0 86 0 0 0 0 0 87 0 0 0 0 0 88 0 0 0 0 0 89 0 0 0 0 0 90 0 0 0 0 0 91 0 0 0 0 0 92 2 2 0 0 4 your_output.sample_1.singleton.truncated000066400000000000000000000000001350370616400411640ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/threads/threeyour_output.sample_2.discarded000066400000000000000000000000461350370616400371270ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/threads/three@read_s2_000/1 + @read_s2_000/2 + your_output.sample_2.pair1.truncated000066400000000000000000000010771350370616400402160ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/threads/three@read_s2_200/1 GCGTAAGTTGACGTCAGCCTGCGAGGTGCCACGCCAGTGGTTGCGCTCACCCGGGGCGTAGTTGCTCCGCGCAATTTCTTGGCAGTTCGATC + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_075/1 TCTTGGGAACGAGAGTGCCACCAATTAAAGTGATGGATATCGAGACGTCCCAAACCACCGCAATAGGACGGGACA + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; @read_s2_150/1 AGCCCCGAGTGTCCATCACAAGCCACCTCCACTAACCATCTCGGTCCATTATTTGTCACTCGTGGCTAGAAGGGAATAAAGACAACTCTCTC + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 your_output.sample_2.pair2.truncated000066400000000000000000000010771350370616400402170ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/threads/three@read_s2_200/2 TAAGGGACGAAGTCACCGGGGGCGTTTCACTTGCGCGATCCATTGTAGTACTGGTGTGTCAATCTTCATCGGCAAAAGGTGCCTATCAAAAT + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_075/2 TGTCCCGTCCTATTGCGGTGGTTTGGGACGTCTCGATATCCATCACTTTAATTGGTGGCACTCTCGTTCCCAAGA + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; @read_s2_150/2 AAGGCTGGGTATACGGGGTAAATGGTGCCGCCTTGTTACACGCGCCGAGGTTTCAGATGAGAGAGTTGTCTTTATTCCCTTCTAGCCACGAG + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 your_output.sample_2.settings000066400000000000000000000051401350370616400370450ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/threads/threeAdapterRemoval ver. 2.1.7 Trimming of double-indexed paired-end reads [Demultiplexing] Maximum mismatches (total): 0 Maximum mate 1 mismatches: 0 Maximum mate 2 mismatches: 0 [Demultiplexing samples] Name Barcode_1 Barcode_2 sample_1 CTTGCCCT ACGTTATT sample_2* CGCCGATG TGCACGGG [Adapter sequences] Adapter1[1]: CCCGTGCA_AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: CATCGGCG_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: NA Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 [Trimming statistics] Total number of read pairs: 4 Number of unaligned read pairs: 1 Number of well aligned read pairs: 3 Number of discarded mate 1 reads: 1 Number of singleton mate 1 reads: 0 Number of discarded mate 2 reads: 1 Number of singleton mate 2 reads: 0 Number of reads with adapters[1]: 4 Number of retained reads: 6 Number of retained nucleotides: 518 Average length of retained reads: 86.3333 [Length distribution] Length Mate1 Mate2 Singleton Discarded All 0 0 0 0 2 2 1 0 0 0 0 0 2 0 0 0 0 0 3 0 0 0 0 0 4 0 0 0 0 0 5 0 0 0 0 0 6 0 0 0 0 0 7 0 0 0 0 0 8 0 0 0 0 0 9 0 0 0 0 0 10 0 0 0 0 0 11 0 0 0 0 0 12 0 0 0 0 0 13 0 0 0 0 0 14 0 0 0 0 0 15 0 0 0 0 0 16 0 0 0 0 0 17 0 0 0 0 0 18 0 0 0 0 0 19 0 0 0 0 0 20 0 0 0 0 0 21 0 0 0 0 0 22 0 0 0 0 0 23 0 0 0 0 0 24 0 0 0 0 0 25 0 0 0 0 0 26 0 0 0 0 0 27 0 0 0 0 0 28 0 0 0 0 0 29 0 0 0 0 0 30 0 0 0 0 0 31 0 0 0 0 0 32 0 0 0 0 0 33 0 0 0 0 0 34 0 0 0 0 0 35 0 0 0 0 0 36 0 0 0 0 0 37 0 0 0 0 0 38 0 0 0 0 0 39 0 0 0 0 0 40 0 0 0 0 0 41 0 0 0 0 0 42 0 0 0 0 0 43 0 0 0 0 0 44 0 0 0 0 0 45 0 0 0 0 0 46 0 0 0 0 0 47 0 0 0 0 0 48 0 0 0 0 0 49 0 0 0 0 0 50 0 0 0 0 0 51 0 0 0 0 0 52 0 0 0 0 0 53 0 0 0 0 0 54 0 0 0 0 0 55 0 0 0 0 0 56 0 0 0 0 0 57 0 0 0 0 0 58 0 0 0 0 0 59 0 0 0 0 0 60 0 0 0 0 0 61 0 0 0 0 0 62 0 0 0 0 0 63 0 0 0 0 0 64 0 0 0 0 0 65 0 0 0 0 0 66 0 0 0 0 0 67 0 0 0 0 0 68 0 0 0 0 0 69 0 0 0 0 0 70 0 0 0 0 0 71 0 0 0 0 0 72 0 0 0 0 0 73 0 0 0 0 0 74 0 0 0 0 0 75 1 1 0 0 2 76 0 0 0 0 0 77 0 0 0 0 0 78 0 0 0 0 0 79 0 0 0 0 0 80 0 0 0 0 0 81 0 0 0 0 0 82 0 0 0 0 0 83 0 0 0 0 0 84 0 0 0 0 0 85 0 0 0 0 0 86 0 0 0 0 0 87 0 0 0 0 0 88 0 0 0 0 0 89 0 0 0 0 0 90 0 0 0 0 0 91 0 0 0 0 0 92 2 2 0 0 4 your_output.sample_2.singleton.truncated000066400000000000000000000000001350370616400411650ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/threads/threeyour_output.settings000066400000000000000000000022141350370616400353430ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/threads/threeAdapterRemoval ver. 2.1.7 Trimming of double-indexed paired-end reads [Demultiplexing] Maximum mismatches (total): 0 Maximum mate 1 mismatches: 0 Maximum mate 2 mismatches: 0 [Demultiplexing samples] Name Barcode_1 Barcode_2 sample_1 CTTGCCCT ACGTTATT sample_2 CGCCGATG TGCACGGG [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: NA Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 [Demultiplexing statistics] Name Barcode_1 Barcode_2 Hits Fraction unidentified NA NA 0 0.000 ambiguous NA NA 0 0.000 sample_1 CTTGCCCT ACGTTATT 4 0.500 sample_2 CGCCGATG TGCACGGG 4 0.500 * * * 8 1.000 your_output.unidentified_1000066400000000000000000000000001350370616400363610ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/threads/threeyour_output.unidentified_2000066400000000000000000000000001350370616400363620ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/threads/threeadapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/threads/two/000077500000000000000000000000001350370616400307255ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/threads/two/barcodes.txt000066400000000000000000000000661350370616400332520ustar00rootroot00000000000000sample_1 CTTGCCCT ACGTTATT sample_2 CGCCGATG TGCACGGG adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/threads/two/info.json000066400000000000000000000001111350370616400325440ustar00rootroot00000000000000{ "arguments": ["--threads", "2"], "return_code": 0, "stderr": [ ] } adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/threads/two/input_1.fastq000066400000000000000000000033301350370616400333430ustar00rootroot00000000000000@read_s2_000/1 CGCCGATGCCCGTGCAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_200/1 CGCCGATGGCGTAAGTTGACGTCAGCCTGCGAGGTGCCACGCCAGTGGTTGCGCTCACCCGGGGCGTAGTTGCTCCGCGCAATTTCTTGGCAGTTCGATC + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_075/1 CTTGCCCTGGTTCTACGTTCTCCATCAGGTGGACGAGGGGATCTTGGCCCCCGTTCCTGCATTGGTATAATTAGACAGGATGAAATAACGTAGATCGGAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_200/1 CTTGCCCTGTAGTGCAATAAAAGGATCCTCTTGTGGCCGATTGCAGACCAGCCTCGGGGCTAAACTGATAATCGTATGCTATAGACCCTGGTCGACGCCG + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_150/1 CTTGCCCTCAGATGTCAGCTCATGTGTTGATATACAGCTAACTAAGGCCCGGGGGTTTAGGCTCAACCCTCTACCTGGTATACCGGCCCAACGCACTCGC + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_075/1 CGCCGATGTCTTGGGAACGAGAGTGCCACCAATTAAAGTGATGGATATCGAGACGTCCCAAACCACCGCAATAGGACGGGACACCCGTGCAAGATCGGAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_150/1 CGCCGATGAGCCCCGAGTGTCCATCACAAGCCACCTCCACTAACCATCTCGGTCCATTATTTGTCACTCGTGGCTAGAAGGGAATAAAGACAACTCTCTC + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_000/1 CTTGCCCTAATAACGTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/threads/two/input_2.fastq000066400000000000000000000033301350370616400333440ustar00rootroot00000000000000@read_s2_000/2 TGCACGGGCATCGGCGAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_200/2 TGCACGGGTAAGGGACGAAGTCACCGGGGGCGTTTCACTTGCGCGATCCATTGTAGTACTGGTGTGTCAATCTTCATCGGCAAAAGGTGCCTATCAAAAT + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_075/2 ACGTTATTTCATCCTGTCTAATTATACCAATGCAGGAACGGGGGCCAAGATCCCCTCGTCCACCTGATGGAGAACGTAGAACCAGGGCAAGAGATCGGAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_200/2 ACGTTATTAAGGCCCGCCCATCAGGTAAGAGCATGCTCGGGAGCCAACCCCGTGGGGTGGCAGCGATACTCTCCAATCTGTCATGCGTGTCAACGTGCGT + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_150/2 ACGTTATTGTGCTGCGTGAGTTGGAAGGATTGGATCCGGAAAGGCTTGGCCTTTGTAAATTCGACTGCGAGTGCGTTGGGCCGGTATACCAGGTAGAGGG + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_075/2 TGCACGGGTGTCCCGTCCTATTGCGGTGGTTTGGGACGTCTCGATATCCATCACTTTAATTGGTGGCACTCTCGTTCCCAAGACATCGGCGAGATCGGAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_150/2 TGCACGGGAAGGCTGGGTATACGGGGTAAATGGTGCCGCCTTGTTACACGCGCCGAGGTTTCAGATGAGAGAGTTGTCTTTATTCCCTTCTAGCCACGAG + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_000/2 ACGTTATTAGGGCAAGAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 your_output.sample_1.discarded000066400000000000000000000000461350370616400366300ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/threads/two@read_s1_000/1 + @read_s1_000/2 + your_output.sample_1.pair1.truncated000066400000000000000000000010771350370616400377170ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/threads/two@read_s1_075/1 GGTTCTACGTTCTCCATCAGGTGGACGAGGGGATCTTGGCCCCCGTTCCTGCATTGGTATAATTAGACAGGATGA + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; @read_s1_200/1 GTAGTGCAATAAAAGGATCCTCTTGTGGCCGATTGCAGACCAGCCTCGGGGCTAAACTGATAATCGTATGCTATAGACCCTGGTCGACGCCG + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_150/1 CAGATGTCAGCTCATGTGTTGATATACAGCTAACTAAGGCCCGGGGGTTTAGGCTCAACCCTCTACCTGGTATACCGGCCCAACGCACTCGC + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 your_output.sample_1.pair2.truncated000066400000000000000000000010771350370616400377200ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/threads/two@read_s1_075/2 TCATCCTGTCTAATTATACCAATGCAGGAACGGGGGCCAAGATCCCCTCGTCCACCTGATGGAGAACGTAGAACC + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; @read_s1_200/2 AAGGCCCGCCCATCAGGTAAGAGCATGCTCGGGAGCCAACCCCGTGGGGTGGCAGCGATACTCTCCAATCTGTCATGCGTGTCAACGTGCGT + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_150/2 GTGCTGCGTGAGTTGGAAGGATTGGATCCGGAAAGGCTTGGCCTTTGTAAATTCGACTGCGAGTGCGTTGGGCCGGTATACCAGGTAGAGGG + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 your_output.sample_1.settings000066400000000000000000000051401350370616400365460ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/threads/twoAdapterRemoval ver. 2.1.7 Trimming of double-indexed paired-end reads [Demultiplexing] Maximum mismatches (total): 0 Maximum mate 1 mismatches: 0 Maximum mate 2 mismatches: 0 [Demultiplexing samples] Name Barcode_1 Barcode_2 sample_1* CTTGCCCT ACGTTATT sample_2 CGCCGATG TGCACGGG [Adapter sequences] Adapter1[1]: AATAACGT_AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGGGCAAG_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: NA Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 [Trimming statistics] Total number of read pairs: 4 Number of unaligned read pairs: 1 Number of well aligned read pairs: 3 Number of discarded mate 1 reads: 1 Number of singleton mate 1 reads: 0 Number of discarded mate 2 reads: 1 Number of singleton mate 2 reads: 0 Number of reads with adapters[1]: 4 Number of retained reads: 6 Number of retained nucleotides: 518 Average length of retained reads: 86.3333 [Length distribution] Length Mate1 Mate2 Singleton Discarded All 0 0 0 0 2 2 1 0 0 0 0 0 2 0 0 0 0 0 3 0 0 0 0 0 4 0 0 0 0 0 5 0 0 0 0 0 6 0 0 0 0 0 7 0 0 0 0 0 8 0 0 0 0 0 9 0 0 0 0 0 10 0 0 0 0 0 11 0 0 0 0 0 12 0 0 0 0 0 13 0 0 0 0 0 14 0 0 0 0 0 15 0 0 0 0 0 16 0 0 0 0 0 17 0 0 0 0 0 18 0 0 0 0 0 19 0 0 0 0 0 20 0 0 0 0 0 21 0 0 0 0 0 22 0 0 0 0 0 23 0 0 0 0 0 24 0 0 0 0 0 25 0 0 0 0 0 26 0 0 0 0 0 27 0 0 0 0 0 28 0 0 0 0 0 29 0 0 0 0 0 30 0 0 0 0 0 31 0 0 0 0 0 32 0 0 0 0 0 33 0 0 0 0 0 34 0 0 0 0 0 35 0 0 0 0 0 36 0 0 0 0 0 37 0 0 0 0 0 38 0 0 0 0 0 39 0 0 0 0 0 40 0 0 0 0 0 41 0 0 0 0 0 42 0 0 0 0 0 43 0 0 0 0 0 44 0 0 0 0 0 45 0 0 0 0 0 46 0 0 0 0 0 47 0 0 0 0 0 48 0 0 0 0 0 49 0 0 0 0 0 50 0 0 0 0 0 51 0 0 0 0 0 52 0 0 0 0 0 53 0 0 0 0 0 54 0 0 0 0 0 55 0 0 0 0 0 56 0 0 0 0 0 57 0 0 0 0 0 58 0 0 0 0 0 59 0 0 0 0 0 60 0 0 0 0 0 61 0 0 0 0 0 62 0 0 0 0 0 63 0 0 0 0 0 64 0 0 0 0 0 65 0 0 0 0 0 66 0 0 0 0 0 67 0 0 0 0 0 68 0 0 0 0 0 69 0 0 0 0 0 70 0 0 0 0 0 71 0 0 0 0 0 72 0 0 0 0 0 73 0 0 0 0 0 74 0 0 0 0 0 75 1 1 0 0 2 76 0 0 0 0 0 77 0 0 0 0 0 78 0 0 0 0 0 79 0 0 0 0 0 80 0 0 0 0 0 81 0 0 0 0 0 82 0 0 0 0 0 83 0 0 0 0 0 84 0 0 0 0 0 85 0 0 0 0 0 86 0 0 0 0 0 87 0 0 0 0 0 88 0 0 0 0 0 89 0 0 0 0 0 90 0 0 0 0 0 91 0 0 0 0 0 92 2 2 0 0 4 your_output.sample_1.singleton.truncated000066400000000000000000000000001350370616400406660ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/threads/twoyour_output.sample_2.discarded000066400000000000000000000000461350370616400366310ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/threads/two@read_s2_000/1 + @read_s2_000/2 + your_output.sample_2.pair1.truncated000066400000000000000000000010771350370616400377200ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/threads/two@read_s2_200/1 GCGTAAGTTGACGTCAGCCTGCGAGGTGCCACGCCAGTGGTTGCGCTCACCCGGGGCGTAGTTGCTCCGCGCAATTTCTTGGCAGTTCGATC + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_075/1 TCTTGGGAACGAGAGTGCCACCAATTAAAGTGATGGATATCGAGACGTCCCAAACCACCGCAATAGGACGGGACA + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; @read_s2_150/1 AGCCCCGAGTGTCCATCACAAGCCACCTCCACTAACCATCTCGGTCCATTATTTGTCACTCGTGGCTAGAAGGGAATAAAGACAACTCTCTC + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 your_output.sample_2.pair2.truncated000066400000000000000000000010771350370616400377210ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/threads/two@read_s2_200/2 TAAGGGACGAAGTCACCGGGGGCGTTTCACTTGCGCGATCCATTGTAGTACTGGTGTGTCAATCTTCATCGGCAAAAGGTGCCTATCAAAAT + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_075/2 TGTCCCGTCCTATTGCGGTGGTTTGGGACGTCTCGATATCCATCACTTTAATTGGTGGCACTCTCGTTCCCAAGA + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; @read_s2_150/2 AAGGCTGGGTATACGGGGTAAATGGTGCCGCCTTGTTACACGCGCCGAGGTTTCAGATGAGAGAGTTGTCTTTATTCCCTTCTAGCCACGAG + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 your_output.sample_2.settings000066400000000000000000000051401350370616400365470ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/threads/twoAdapterRemoval ver. 2.1.7 Trimming of double-indexed paired-end reads [Demultiplexing] Maximum mismatches (total): 0 Maximum mate 1 mismatches: 0 Maximum mate 2 mismatches: 0 [Demultiplexing samples] Name Barcode_1 Barcode_2 sample_1 CTTGCCCT ACGTTATT sample_2* CGCCGATG TGCACGGG [Adapter sequences] Adapter1[1]: CCCGTGCA_AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: CATCGGCG_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: NA Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 [Trimming statistics] Total number of read pairs: 4 Number of unaligned read pairs: 1 Number of well aligned read pairs: 3 Number of discarded mate 1 reads: 1 Number of singleton mate 1 reads: 0 Number of discarded mate 2 reads: 1 Number of singleton mate 2 reads: 0 Number of reads with adapters[1]: 4 Number of retained reads: 6 Number of retained nucleotides: 518 Average length of retained reads: 86.3333 [Length distribution] Length Mate1 Mate2 Singleton Discarded All 0 0 0 0 2 2 1 0 0 0 0 0 2 0 0 0 0 0 3 0 0 0 0 0 4 0 0 0 0 0 5 0 0 0 0 0 6 0 0 0 0 0 7 0 0 0 0 0 8 0 0 0 0 0 9 0 0 0 0 0 10 0 0 0 0 0 11 0 0 0 0 0 12 0 0 0 0 0 13 0 0 0 0 0 14 0 0 0 0 0 15 0 0 0 0 0 16 0 0 0 0 0 17 0 0 0 0 0 18 0 0 0 0 0 19 0 0 0 0 0 20 0 0 0 0 0 21 0 0 0 0 0 22 0 0 0 0 0 23 0 0 0 0 0 24 0 0 0 0 0 25 0 0 0 0 0 26 0 0 0 0 0 27 0 0 0 0 0 28 0 0 0 0 0 29 0 0 0 0 0 30 0 0 0 0 0 31 0 0 0 0 0 32 0 0 0 0 0 33 0 0 0 0 0 34 0 0 0 0 0 35 0 0 0 0 0 36 0 0 0 0 0 37 0 0 0 0 0 38 0 0 0 0 0 39 0 0 0 0 0 40 0 0 0 0 0 41 0 0 0 0 0 42 0 0 0 0 0 43 0 0 0 0 0 44 0 0 0 0 0 45 0 0 0 0 0 46 0 0 0 0 0 47 0 0 0 0 0 48 0 0 0 0 0 49 0 0 0 0 0 50 0 0 0 0 0 51 0 0 0 0 0 52 0 0 0 0 0 53 0 0 0 0 0 54 0 0 0 0 0 55 0 0 0 0 0 56 0 0 0 0 0 57 0 0 0 0 0 58 0 0 0 0 0 59 0 0 0 0 0 60 0 0 0 0 0 61 0 0 0 0 0 62 0 0 0 0 0 63 0 0 0 0 0 64 0 0 0 0 0 65 0 0 0 0 0 66 0 0 0 0 0 67 0 0 0 0 0 68 0 0 0 0 0 69 0 0 0 0 0 70 0 0 0 0 0 71 0 0 0 0 0 72 0 0 0 0 0 73 0 0 0 0 0 74 0 0 0 0 0 75 1 1 0 0 2 76 0 0 0 0 0 77 0 0 0 0 0 78 0 0 0 0 0 79 0 0 0 0 0 80 0 0 0 0 0 81 0 0 0 0 0 82 0 0 0 0 0 83 0 0 0 0 0 84 0 0 0 0 0 85 0 0 0 0 0 86 0 0 0 0 0 87 0 0 0 0 0 88 0 0 0 0 0 89 0 0 0 0 0 90 0 0 0 0 0 91 0 0 0 0 0 92 2 2 0 0 4 your_output.sample_2.singleton.truncated000066400000000000000000000000001350370616400406670ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/threads/twoyour_output.settings000066400000000000000000000022141350370616400350450ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/threads/twoAdapterRemoval ver. 2.1.7 Trimming of double-indexed paired-end reads [Demultiplexing] Maximum mismatches (total): 0 Maximum mate 1 mismatches: 0 Maximum mate 2 mismatches: 0 [Demultiplexing samples] Name Barcode_1 Barcode_2 sample_1 CTTGCCCT ACGTTATT sample_2 CGCCGATG TGCACGGG [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: NA Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 [Demultiplexing statistics] Name Barcode_1 Barcode_2 Hits Fraction unidentified NA NA 0 0.000 ambiguous NA NA 0 0.000 sample_1 CTTGCCCT ACGTTATT 4 0.500 sample_2 CGCCGATG TGCACGGG 4 0.500 * * * 8 1.000 your_output.unidentified_1000066400000000000000000000000001350370616400360630ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/threads/twoyour_output.unidentified_2000066400000000000000000000000001350370616400360640ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/pe/threads/twoadapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/se/000077500000000000000000000000001350370616400264655ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/se/collapse/000077500000000000000000000000001350370616400302675ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/se/collapse/barcodes.txt000066400000000000000000000000661350370616400326140ustar00rootroot00000000000000sample_1 CTTGCCCT ACGTTATT sample_2 CGCCGATG TGCACGGG adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/se/collapse/info.json000066400000000000000000000001051350370616400321110ustar00rootroot00000000000000{ "arguments": ["--collapse"], "return_code": 0, "stderr": [ ] } adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/se/collapse/input_1.fastq000066400000000000000000000033301350370616400327050ustar00rootroot00000000000000@read_s2_000/1 CGCCGATGCCCGTGCAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_200/1 CGCCGATGGCGTAAGTTGACGTCAGCCTGCGAGGTGCCACGCCAGTGGTTGCGCTCACCCGGGGCGTAGTTGCTCCGCGCAATTTCTTGGCAGTTCGATC + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_075/1 CTTGCCCTGGTTCTACGTTCTCCATCAGGTGGACGAGGGGATCTTGGCCCCCGTTCCTGCATTGGTATAATTAGACAGGATGAAATAACGTAGATCGGAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_200/1 CTTGCCCTGTAGTGCAATAAAAGGATCCTCTTGTGGCCGATTGCAGACCAGCCTCGGGGCTAAACTGATAATCGTATGCTATAGACCCTGGTCGACGCCG + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_150/1 CTTGCCCTCAGATGTCAGCTCATGTGTTGATATACAGCTAACTAAGGCCCGGGGGTTTAGGCTCAACCCTCTACCTGGTATACCGGCCCAACGCACTCGC + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_075/1 CGCCGATGTCTTGGGAACGAGAGTGCCACCAATTAAAGTGATGGATATCGAGACGTCCCAAACCACCGCAATAGGACGGGACACCCGTGCAAGATCGGAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_150/1 CGCCGATGAGCCCCGAGTGTCCATCACAAGCCACCTCCACTAACCATCTCGGTCCATTATTTGTCACTCGTGGCTAGAAGGGAATAAAGACAACTCTCTC + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_000/1 CTTGCCCTAATAACGTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 your_output.sample_1.collapsed000066400000000000000000000002531350370616400362160ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/se/collapse@M_read_s1_075/1 GGTTCTACGTTCTCCATCAGGTGGACGAGGGGATCTTGGCCCCCGTTCCTGCATTGGTATAATTAGACAGGATGA + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; your_output.sample_1.collapsed.truncated000066400000000000000000000000001350370616400401740ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/se/collapseyour_output.sample_1.discarded000066400000000000000000000000251350370616400361670ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/se/collapse@M_read_s1_000/1 + your_output.sample_1.settings000066400000000000000000000051171350370616400361140ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/se/collapseAdapterRemoval ver. 2.2.0 Trimming of double-indexed single-end reads [Demultiplexing] Maximum mismatches (total): 0 [Demultiplexing samples] Name Barcode_1 Barcode_2 sample_1* CTTGCCCT ACGTTATT sample_2 CGCCGATG TGCACGGG [Adapter sequences] Adapter1[1]: AATAACGT_AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGGGCAAG_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 935224950 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: Yes Minimum overlap (in case of collapse): 11 Minimum adapter overlap: 0 [Trimming statistics] Total number of reads: 4 Number of unaligned reads: 2 Number of well aligned reads: 2 Number of discarded mate 1 reads: 1 Number of singleton mate 1 reads: 2 Number of reads with adapters[1]: 2 Number of full-length collapsed pairs: 1 Number of truncated collapsed pairs: 0 Number of retained reads: 3 Number of retained nucleotides: 259 Average length of retained reads: 86.3333 [Length distribution] Length Mate1 Collapsed CollapsedTruncated Discarded All 0 0 0 0 1 1 1 0 0 0 0 0 2 0 0 0 0 0 3 0 0 0 0 0 4 0 0 0 0 0 5 0 0 0 0 0 6 0 0 0 0 0 7 0 0 0 0 0 8 0 0 0 0 0 9 0 0 0 0 0 10 0 0 0 0 0 11 0 0 0 0 0 12 0 0 0 0 0 13 0 0 0 0 0 14 0 0 0 0 0 15 0 0 0 0 0 16 0 0 0 0 0 17 0 0 0 0 0 18 0 0 0 0 0 19 0 0 0 0 0 20 0 0 0 0 0 21 0 0 0 0 0 22 0 0 0 0 0 23 0 0 0 0 0 24 0 0 0 0 0 25 0 0 0 0 0 26 0 0 0 0 0 27 0 0 0 0 0 28 0 0 0 0 0 29 0 0 0 0 0 30 0 0 0 0 0 31 0 0 0 0 0 32 0 0 0 0 0 33 0 0 0 0 0 34 0 0 0 0 0 35 0 0 0 0 0 36 0 0 0 0 0 37 0 0 0 0 0 38 0 0 0 0 0 39 0 0 0 0 0 40 0 0 0 0 0 41 0 0 0 0 0 42 0 0 0 0 0 43 0 0 0 0 0 44 0 0 0 0 0 45 0 0 0 0 0 46 0 0 0 0 0 47 0 0 0 0 0 48 0 0 0 0 0 49 0 0 0 0 0 50 0 0 0 0 0 51 0 0 0 0 0 52 0 0 0 0 0 53 0 0 0 0 0 54 0 0 0 0 0 55 0 0 0 0 0 56 0 0 0 0 0 57 0 0 0 0 0 58 0 0 0 0 0 59 0 0 0 0 0 60 0 0 0 0 0 61 0 0 0 0 0 62 0 0 0 0 0 63 0 0 0 0 0 64 0 0 0 0 0 65 0 0 0 0 0 66 0 0 0 0 0 67 0 0 0 0 0 68 0 0 0 0 0 69 0 0 0 0 0 70 0 0 0 0 0 71 0 0 0 0 0 72 0 0 0 0 0 73 0 0 0 0 0 74 0 0 0 0 0 75 0 1 0 0 1 76 0 0 0 0 0 77 0 0 0 0 0 78 0 0 0 0 0 79 0 0 0 0 0 80 0 0 0 0 0 81 0 0 0 0 0 82 0 0 0 0 0 83 0 0 0 0 0 84 0 0 0 0 0 85 0 0 0 0 0 86 0 0 0 0 0 87 0 0 0 0 0 88 0 0 0 0 0 89 0 0 0 0 0 90 0 0 0 0 0 91 0 0 0 0 0 92 2 0 0 0 2 your_output.sample_1.truncated000066400000000000000000000006261350370616400362450ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/se/collapse@read_s1_200/1 GTAGTGCAATAAAAGGATCCTCTTGTGGCCGATTGCAGACCAGCCTCGGGGCTAAACTGATAATCGTATGCTATAGACCCTGGTCGACGCCG + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_150/1 CAGATGTCAGCTCATGTGTTGATATACAGCTAACTAAGGCCCGGGGGTTTAGGCTCAACCCTCTACCTGGTATACCGGCCCAACGCACTCGC + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 your_output.sample_2.collapsed000066400000000000000000000002531350370616400362170ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/se/collapse@M_read_s2_075/1 TCTTGGGAACGAGAGTGCCACCAATTAAAGTGATGGATATCGAGACGTCCCAAACCACCGCAATAGGACGGGACA + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; your_output.sample_2.collapsed.truncated000066400000000000000000000000001350370616400401750ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/se/collapseyour_output.sample_2.discarded000066400000000000000000000000251350370616400361700ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/se/collapse@M_read_s2_000/1 + your_output.sample_2.settings000066400000000000000000000051121350370616400361100ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/se/collapseAdapterRemoval ver. 2.2.0 Trimming of double-indexed single-end reads [Demultiplexing] Maximum mismatches (total): 0 [Demultiplexing samples] Name Barcode_1 Barcode_2 sample_1 CTTGCCCT ACGTTATT sample_2* CGCCGATG TGCACGGG [Adapter sequences] Adapter1[1]: CCCGTGCA_AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: CATCGGCG_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 935224950 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: Yes Minimum overlap (in case of collapse): 11 Minimum adapter overlap: 0 [Trimming statistics] Total number of reads: 4 Number of unaligned reads: 1 Number of well aligned reads: 3 Number of discarded mate 1 reads: 1 Number of singleton mate 1 reads: 2 Number of reads with adapters[1]: 3 Number of full-length collapsed pairs: 1 Number of truncated collapsed pairs: 0 Number of retained reads: 3 Number of retained nucleotides: 258 Average length of retained reads: 86 [Length distribution] Length Mate1 Collapsed CollapsedTruncated Discarded All 0 0 0 0 1 1 1 0 0 0 0 0 2 0 0 0 0 0 3 0 0 0 0 0 4 0 0 0 0 0 5 0 0 0 0 0 6 0 0 0 0 0 7 0 0 0 0 0 8 0 0 0 0 0 9 0 0 0 0 0 10 0 0 0 0 0 11 0 0 0 0 0 12 0 0 0 0 0 13 0 0 0 0 0 14 0 0 0 0 0 15 0 0 0 0 0 16 0 0 0 0 0 17 0 0 0 0 0 18 0 0 0 0 0 19 0 0 0 0 0 20 0 0 0 0 0 21 0 0 0 0 0 22 0 0 0 0 0 23 0 0 0 0 0 24 0 0 0 0 0 25 0 0 0 0 0 26 0 0 0 0 0 27 0 0 0 0 0 28 0 0 0 0 0 29 0 0 0 0 0 30 0 0 0 0 0 31 0 0 0 0 0 32 0 0 0 0 0 33 0 0 0 0 0 34 0 0 0 0 0 35 0 0 0 0 0 36 0 0 0 0 0 37 0 0 0 0 0 38 0 0 0 0 0 39 0 0 0 0 0 40 0 0 0 0 0 41 0 0 0 0 0 42 0 0 0 0 0 43 0 0 0 0 0 44 0 0 0 0 0 45 0 0 0 0 0 46 0 0 0 0 0 47 0 0 0 0 0 48 0 0 0 0 0 49 0 0 0 0 0 50 0 0 0 0 0 51 0 0 0 0 0 52 0 0 0 0 0 53 0 0 0 0 0 54 0 0 0 0 0 55 0 0 0 0 0 56 0 0 0 0 0 57 0 0 0 0 0 58 0 0 0 0 0 59 0 0 0 0 0 60 0 0 0 0 0 61 0 0 0 0 0 62 0 0 0 0 0 63 0 0 0 0 0 64 0 0 0 0 0 65 0 0 0 0 0 66 0 0 0 0 0 67 0 0 0 0 0 68 0 0 0 0 0 69 0 0 0 0 0 70 0 0 0 0 0 71 0 0 0 0 0 72 0 0 0 0 0 73 0 0 0 0 0 74 0 0 0 0 0 75 0 1 0 0 1 76 0 0 0 0 0 77 0 0 0 0 0 78 0 0 0 0 0 79 0 0 0 0 0 80 0 0 0 0 0 81 0 0 0 0 0 82 0 0 0 0 0 83 0 0 0 0 0 84 0 0 0 0 0 85 0 0 0 0 0 86 0 0 0 0 0 87 0 0 0 0 0 88 0 0 0 0 0 89 0 0 0 0 0 90 0 0 0 0 0 91 1 0 0 0 1 92 1 0 0 0 1 your_output.sample_2.truncated000066400000000000000000000006241350370616400362440ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/se/collapse@read_s2_200/1 GCGTAAGTTGACGTCAGCCTGCGAGGTGCCACGCCAGTGGTTGCGCTCACCCGGGGCGTAGTTGCTCCGCGCAATTTCTTGGCAGTTCGAT + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::998876654321 @read_s2_150/1 AGCCCCGAGTGTCCATCACAAGCCACCTCCACTAACCATCTCGGTCCATTATTTGTCACTCGTGGCTAGAAGGGAATAAAGACAACTCTCTC + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/se/collapse/your_output.settings000066400000000000000000000021661350370616400344740ustar00rootroot00000000000000AdapterRemoval ver. 2.1.7 Trimming of double-indexed single-end reads [Demultiplexing] Maximum mismatches (total): 0 [Demultiplexing samples] Name Barcode_1 Barcode_2 sample_1 CTTGCCCT ACGTTATT sample_2 CGCCGATG TGCACGGG [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 1157297082 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: Yes Minimum overlap (in case of collapse): 11 Minimum adapter overlap: 0 [Demultiplexing statistics] Name Barcode_1 Barcode_2 Hits Fraction unidentified NA NA 0 0.000 ambiguous NA NA 0 0.000 sample_1 CTTGCCCT ACGTTATT 4 0.500 sample_2 CGCCGATG TGCACGGG 4 0.500 * * * 8 1.000 your_output.unidentified000066400000000000000000000000001350370616400352050ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/se/collapseadapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/se/combined_output/000077500000000000000000000000001350370616400316655ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/se/combined_output/barcodes.txt000066400000000000000000000000661350370616400342120ustar00rootroot00000000000000sample_1 CTTGCCCT ACGTTATT sample_2 CGCCGATG TGCACGGG adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/se/combined_output/info.json000066400000000000000000000001141350370616400335070ustar00rootroot00000000000000{ "arguments": ["--combined-output"], "return_code": 0, "stderr": [ ] } adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/se/combined_output/input_1.fastq000066400000000000000000000033301350370616400343030ustar00rootroot00000000000000@read_s2_000/1 CGCCGATGCCCGTGCAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_200/1 CGCCGATGGCGTAAGTTGACGTCAGCCTGCGAGGTGCCACGCCAGTGGTTGCGCTCACCCGGGGCGTAGTTGCTCCGCGCAATTTCTTGGCAGTTCGATC + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_075/1 CTTGCCCTGGTTCTACGTTCTCCATCAGGTGGACGAGGGGATCTTGGCCCCCGTTCCTGCATTGGTATAATTAGACAGGATGAAATAACGTAGATCGGAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_200/1 CTTGCCCTGTAGTGCAATAAAAGGATCCTCTTGTGGCCGATTGCAGACCAGCCTCGGGGCTAAACTGATAATCGTATGCTATAGACCCTGGTCGACGCCG + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_150/1 CTTGCCCTCAGATGTCAGCTCATGTGTTGATATACAGCTAACTAAGGCCCGGGGGTTTAGGCTCAACCCTCTACCTGGTATACCGGCCCAACGCACTCGC + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_075/1 CGCCGATGTCTTGGGAACGAGAGTGCCACCAATTAAAGTGATGGATATCGAGACGTCCCAAACCACCGCAATAGGACGGGACACCCGTGCAAGATCGGAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_150/1 CGCCGATGAGCCCCGAGTGTCCATCACAAGCCACCTCCACTAACCATCTCGGTCCATTATTTGTCACTCGTGGCTAGAAGGGAATAAAGACAACTCTCTC + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_000/1 CTTGCCCTAATAACGTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 your_output.sample_1.settings000066400000000000000000000041561350370616400375140ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/se/combined_outputAdapterRemoval ver. 2.2.0 Trimming of double-indexed single-end reads [Demultiplexing] Maximum mismatches (total): 0 [Demultiplexing samples] Name Barcode_1 Barcode_2 sample_1* CTTGCCCT ACGTTATT sample_2 CGCCGATG TGCACGGG [Adapter sequences] Adapter1[1]: AATAACGT_AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGGGCAAG_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 4115144913 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 Minimum adapter overlap: 0 [Trimming statistics] Total number of reads: 4 Number of unaligned reads: 2 Number of well aligned reads: 2 Number of discarded mate 1 reads: 1 Number of singleton mate 1 reads: 3 Number of reads with adapters[1]: 2 Number of retained reads: 3 Number of retained nucleotides: 259 Average length of retained reads: 86.3333 [Length distribution] Length Mate1 Discarded All 0 0 1 1 1 0 0 0 2 0 0 0 3 0 0 0 4 0 0 0 5 0 0 0 6 0 0 0 7 0 0 0 8 0 0 0 9 0 0 0 10 0 0 0 11 0 0 0 12 0 0 0 13 0 0 0 14 0 0 0 15 0 0 0 16 0 0 0 17 0 0 0 18 0 0 0 19 0 0 0 20 0 0 0 21 0 0 0 22 0 0 0 23 0 0 0 24 0 0 0 25 0 0 0 26 0 0 0 27 0 0 0 28 0 0 0 29 0 0 0 30 0 0 0 31 0 0 0 32 0 0 0 33 0 0 0 34 0 0 0 35 0 0 0 36 0 0 0 37 0 0 0 38 0 0 0 39 0 0 0 40 0 0 0 41 0 0 0 42 0 0 0 43 0 0 0 44 0 0 0 45 0 0 0 46 0 0 0 47 0 0 0 48 0 0 0 49 0 0 0 50 0 0 0 51 0 0 0 52 0 0 0 53 0 0 0 54 0 0 0 55 0 0 0 56 0 0 0 57 0 0 0 58 0 0 0 59 0 0 0 60 0 0 0 61 0 0 0 62 0 0 0 63 0 0 0 64 0 0 0 65 0 0 0 66 0 0 0 67 0 0 0 68 0 0 0 69 0 0 0 70 0 0 0 71 0 0 0 72 0 0 0 73 0 0 0 74 0 0 0 75 1 0 1 76 0 0 0 77 0 0 0 78 0 0 0 79 0 0 0 80 0 0 0 81 0 0 0 82 0 0 0 83 0 0 0 84 0 0 0 85 0 0 0 86 0 0 0 87 0 0 0 88 0 0 0 89 0 0 0 90 0 0 0 91 0 0 0 92 2 0 2 your_output.sample_1.truncated000066400000000000000000000011241350370616400376350ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/se/combined_output@read_s1_075/1 GGTTCTACGTTCTCCATCAGGTGGACGAGGGGATCTTGGCCCCCGTTCCTGCATTGGTATAATTAGACAGGATGA + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; @read_s1_200/1 GTAGTGCAATAAAAGGATCCTCTTGTGGCCGATTGCAGACCAGCCTCGGGGCTAAACTGATAATCGTATGCTATAGACCCTGGTCGACGCCG + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_150/1 CAGATGTCAGCTCATGTGTTGATATACAGCTAACTAAGGCCCGGGGGTTTAGGCTCAACCCTCTACCTGGTATACCGGCCCAACGCACTCGC + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_000/1 N + ! your_output.sample_2.settings000066400000000000000000000041501350370616400375070ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/se/combined_outputAdapterRemoval ver. 2.2.0 Trimming of double-indexed single-end reads [Demultiplexing] Maximum mismatches (total): 0 [Demultiplexing samples] Name Barcode_1 Barcode_2 sample_1 CTTGCCCT ACGTTATT sample_2* CGCCGATG TGCACGGG [Adapter sequences] Adapter1[1]: CCCGTGCA_AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: CATCGGCG_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 356769071 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 Minimum adapter overlap: 0 [Trimming statistics] Total number of reads: 4 Number of unaligned reads: 1 Number of well aligned reads: 3 Number of discarded mate 1 reads: 1 Number of singleton mate 1 reads: 3 Number of reads with adapters[1]: 3 Number of retained reads: 3 Number of retained nucleotides: 258 Average length of retained reads: 86 [Length distribution] Length Mate1 Discarded All 0 0 1 1 1 0 0 0 2 0 0 0 3 0 0 0 4 0 0 0 5 0 0 0 6 0 0 0 7 0 0 0 8 0 0 0 9 0 0 0 10 0 0 0 11 0 0 0 12 0 0 0 13 0 0 0 14 0 0 0 15 0 0 0 16 0 0 0 17 0 0 0 18 0 0 0 19 0 0 0 20 0 0 0 21 0 0 0 22 0 0 0 23 0 0 0 24 0 0 0 25 0 0 0 26 0 0 0 27 0 0 0 28 0 0 0 29 0 0 0 30 0 0 0 31 0 0 0 32 0 0 0 33 0 0 0 34 0 0 0 35 0 0 0 36 0 0 0 37 0 0 0 38 0 0 0 39 0 0 0 40 0 0 0 41 0 0 0 42 0 0 0 43 0 0 0 44 0 0 0 45 0 0 0 46 0 0 0 47 0 0 0 48 0 0 0 49 0 0 0 50 0 0 0 51 0 0 0 52 0 0 0 53 0 0 0 54 0 0 0 55 0 0 0 56 0 0 0 57 0 0 0 58 0 0 0 59 0 0 0 60 0 0 0 61 0 0 0 62 0 0 0 63 0 0 0 64 0 0 0 65 0 0 0 66 0 0 0 67 0 0 0 68 0 0 0 69 0 0 0 70 0 0 0 71 0 0 0 72 0 0 0 73 0 0 0 74 0 0 0 75 1 0 1 76 0 0 0 77 0 0 0 78 0 0 0 79 0 0 0 80 0 0 0 81 0 0 0 82 0 0 0 83 0 0 0 84 0 0 0 85 0 0 0 86 0 0 0 87 0 0 0 88 0 0 0 89 0 0 0 90 0 0 0 91 1 0 1 92 1 0 1 your_output.sample_2.truncated000066400000000000000000000011221350370616400376340ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/se/combined_output@read_s2_000/1 N + ! @read_s2_200/1 GCGTAAGTTGACGTCAGCCTGCGAGGTGCCACGCCAGTGGTTGCGCTCACCCGGGGCGTAGTTGCTCCGCGCAATTTCTTGGCAGTTCGAT + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::998876654321 @read_s2_075/1 TCTTGGGAACGAGAGTGCCACCAATTAAAGTGATGGATATCGAGACGTCCCAAACCACCGCAATAGGACGGGACA + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; @read_s2_150/1 AGCCCCGAGTGTCCATCACAAGCCACCTCCACTAACCATCTCGGTCCATTATTTGTCACTCGTGGCTAGAAGGGAATAAAGACAACTCTCTC + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 your_output.settings000066400000000000000000000021651350370616400360120ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/se/combined_outputAdapterRemoval ver. 2.1.7 Trimming of double-indexed single-end reads [Demultiplexing] Maximum mismatches (total): 0 [Demultiplexing samples] Name Barcode_1 Barcode_2 sample_1 CTTGCCCT ACGTTATT sample_2 CGCCGATG TGCACGGG [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 1157297082 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 Minimum adapter overlap: 0 [Demultiplexing statistics] Name Barcode_1 Barcode_2 Hits Fraction unidentified NA NA 0 0.000 ambiguous NA NA 0 0.000 sample_1 CTTGCCCT ACGTTATT 4 0.500 sample_2 CGCCGATG TGCACGGG 4 0.500 * * * 8 1.000 your_output.unidentified000066400000000000000000000000001350370616400366030ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/se/combined_outputadapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/se/defaults/000077500000000000000000000000001350370616400302745ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/se/defaults/barcodes.txt000066400000000000000000000000661350370616400326210ustar00rootroot00000000000000sample_1 CTTGCCCT ACGTTATT sample_2 CGCCGATG TGCACGGG adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/se/defaults/info.json000066400000000000000000000000711350370616400321200ustar00rootroot00000000000000{ "arguments": [], "return_code": 0, "stderr": [ ] } adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/se/defaults/input_1.fastq000066400000000000000000000033301350370616400327120ustar00rootroot00000000000000@read_s2_000/1 CGCCGATGCCCGTGCAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_200/1 CGCCGATGGCGTAAGTTGACGTCAGCCTGCGAGGTGCCACGCCAGTGGTTGCGCTCACCCGGGGCGTAGTTGCTCCGCGCAATTTCTTGGCAGTTCGATC + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_075/1 CTTGCCCTGGTTCTACGTTCTCCATCAGGTGGACGAGGGGATCTTGGCCCCCGTTCCTGCATTGGTATAATTAGACAGGATGAAATAACGTAGATCGGAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_200/1 CTTGCCCTGTAGTGCAATAAAAGGATCCTCTTGTGGCCGATTGCAGACCAGCCTCGGGGCTAAACTGATAATCGTATGCTATAGACCCTGGTCGACGCCG + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_150/1 CTTGCCCTCAGATGTCAGCTCATGTGTTGATATACAGCTAACTAAGGCCCGGGGGTTTAGGCTCAACCCTCTACCTGGTATACCGGCCCAACGCACTCGC + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_075/1 CGCCGATGTCTTGGGAACGAGAGTGCCACCAATTAAAGTGATGGATATCGAGACGTCCCAAACCACCGCAATAGGACGGGACACCCGTGCAAGATCGGAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_150/1 CGCCGATGAGCCCCGAGTGTCCATCACAAGCCACCTCCACTAACCATCTCGGTCCATTATTTGTCACTCGTGGCTAGAAGGGAATAAAGACAACTCTCTC + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_000/1 CTTGCCCTAATAACGTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 your_output.sample_1.discarded000066400000000000000000000000231350370616400361720ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/se/defaults@read_s1_000/1 + your_output.sample_1.settings000066400000000000000000000041561350370616400361230ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/se/defaultsAdapterRemoval ver. 2.2.0 Trimming of double-indexed single-end reads [Demultiplexing] Maximum mismatches (total): 0 [Demultiplexing samples] Name Barcode_1 Barcode_2 sample_1* CTTGCCCT ACGTTATT sample_2 CGCCGATG TGCACGGG [Adapter sequences] Adapter1[1]: AATAACGT_AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGGGCAAG_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 4115144913 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 Minimum adapter overlap: 0 [Trimming statistics] Total number of reads: 4 Number of unaligned reads: 2 Number of well aligned reads: 2 Number of discarded mate 1 reads: 1 Number of singleton mate 1 reads: 3 Number of reads with adapters[1]: 2 Number of retained reads: 3 Number of retained nucleotides: 259 Average length of retained reads: 86.3333 [Length distribution] Length Mate1 Discarded All 0 0 1 1 1 0 0 0 2 0 0 0 3 0 0 0 4 0 0 0 5 0 0 0 6 0 0 0 7 0 0 0 8 0 0 0 9 0 0 0 10 0 0 0 11 0 0 0 12 0 0 0 13 0 0 0 14 0 0 0 15 0 0 0 16 0 0 0 17 0 0 0 18 0 0 0 19 0 0 0 20 0 0 0 21 0 0 0 22 0 0 0 23 0 0 0 24 0 0 0 25 0 0 0 26 0 0 0 27 0 0 0 28 0 0 0 29 0 0 0 30 0 0 0 31 0 0 0 32 0 0 0 33 0 0 0 34 0 0 0 35 0 0 0 36 0 0 0 37 0 0 0 38 0 0 0 39 0 0 0 40 0 0 0 41 0 0 0 42 0 0 0 43 0 0 0 44 0 0 0 45 0 0 0 46 0 0 0 47 0 0 0 48 0 0 0 49 0 0 0 50 0 0 0 51 0 0 0 52 0 0 0 53 0 0 0 54 0 0 0 55 0 0 0 56 0 0 0 57 0 0 0 58 0 0 0 59 0 0 0 60 0 0 0 61 0 0 0 62 0 0 0 63 0 0 0 64 0 0 0 65 0 0 0 66 0 0 0 67 0 0 0 68 0 0 0 69 0 0 0 70 0 0 0 71 0 0 0 72 0 0 0 73 0 0 0 74 0 0 0 75 1 0 1 76 0 0 0 77 0 0 0 78 0 0 0 79 0 0 0 80 0 0 0 81 0 0 0 82 0 0 0 83 0 0 0 84 0 0 0 85 0 0 0 86 0 0 0 87 0 0 0 88 0 0 0 89 0 0 0 90 0 0 0 91 0 0 0 92 2 0 2 your_output.sample_1.truncated000066400000000000000000000010771350370616400362530ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/se/defaults@read_s1_075/1 GGTTCTACGTTCTCCATCAGGTGGACGAGGGGATCTTGGCCCCCGTTCCTGCATTGGTATAATTAGACAGGATGA + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; @read_s1_200/1 GTAGTGCAATAAAAGGATCCTCTTGTGGCCGATTGCAGACCAGCCTCGGGGCTAAACTGATAATCGTATGCTATAGACCCTGGTCGACGCCG + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_150/1 CAGATGTCAGCTCATGTGTTGATATACAGCTAACTAAGGCCCGGGGGTTTAGGCTCAACCCTCTACCTGGTATACCGGCCCAACGCACTCGC + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 your_output.sample_2.discarded000066400000000000000000000000231350370616400361730ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/se/defaults@read_s2_000/1 + your_output.sample_2.settings000066400000000000000000000041501350370616400361160ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/se/defaultsAdapterRemoval ver. 2.2.0 Trimming of double-indexed single-end reads [Demultiplexing] Maximum mismatches (total): 0 [Demultiplexing samples] Name Barcode_1 Barcode_2 sample_1 CTTGCCCT ACGTTATT sample_2* CGCCGATG TGCACGGG [Adapter sequences] Adapter1[1]: CCCGTGCA_AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: CATCGGCG_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 356769071 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 Minimum adapter overlap: 0 [Trimming statistics] Total number of reads: 4 Number of unaligned reads: 1 Number of well aligned reads: 3 Number of discarded mate 1 reads: 1 Number of singleton mate 1 reads: 3 Number of reads with adapters[1]: 3 Number of retained reads: 3 Number of retained nucleotides: 258 Average length of retained reads: 86 [Length distribution] Length Mate1 Discarded All 0 0 1 1 1 0 0 0 2 0 0 0 3 0 0 0 4 0 0 0 5 0 0 0 6 0 0 0 7 0 0 0 8 0 0 0 9 0 0 0 10 0 0 0 11 0 0 0 12 0 0 0 13 0 0 0 14 0 0 0 15 0 0 0 16 0 0 0 17 0 0 0 18 0 0 0 19 0 0 0 20 0 0 0 21 0 0 0 22 0 0 0 23 0 0 0 24 0 0 0 25 0 0 0 26 0 0 0 27 0 0 0 28 0 0 0 29 0 0 0 30 0 0 0 31 0 0 0 32 0 0 0 33 0 0 0 34 0 0 0 35 0 0 0 36 0 0 0 37 0 0 0 38 0 0 0 39 0 0 0 40 0 0 0 41 0 0 0 42 0 0 0 43 0 0 0 44 0 0 0 45 0 0 0 46 0 0 0 47 0 0 0 48 0 0 0 49 0 0 0 50 0 0 0 51 0 0 0 52 0 0 0 53 0 0 0 54 0 0 0 55 0 0 0 56 0 0 0 57 0 0 0 58 0 0 0 59 0 0 0 60 0 0 0 61 0 0 0 62 0 0 0 63 0 0 0 64 0 0 0 65 0 0 0 66 0 0 0 67 0 0 0 68 0 0 0 69 0 0 0 70 0 0 0 71 0 0 0 72 0 0 0 73 0 0 0 74 0 0 0 75 1 0 1 76 0 0 0 77 0 0 0 78 0 0 0 79 0 0 0 80 0 0 0 81 0 0 0 82 0 0 0 83 0 0 0 84 0 0 0 85 0 0 0 86 0 0 0 87 0 0 0 88 0 0 0 89 0 0 0 90 0 0 0 91 1 0 1 92 1 0 1 your_output.sample_2.truncated000066400000000000000000000010751350370616400362520ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/se/defaults@read_s2_200/1 GCGTAAGTTGACGTCAGCCTGCGAGGTGCCACGCCAGTGGTTGCGCTCACCCGGGGCGTAGTTGCTCCGCGCAATTTCTTGGCAGTTCGAT + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::998876654321 @read_s2_075/1 TCTTGGGAACGAGAGTGCCACCAATTAAAGTGATGGATATCGAGACGTCCCAAACCACCGCAATAGGACGGGACA + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; @read_s2_150/1 AGCCCCGAGTGTCCATCACAAGCCACCTCCACTAACCATCTCGGTCCATTATTTGTCACTCGTGGCTAGAAGGGAATAAAGACAACTCTCTC + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/se/defaults/your_output.settings000066400000000000000000000021651350370616400345000ustar00rootroot00000000000000AdapterRemoval ver. 2.1.7 Trimming of double-indexed single-end reads [Demultiplexing] Maximum mismatches (total): 0 [Demultiplexing samples] Name Barcode_1 Barcode_2 sample_1 CTTGCCCT ACGTTATT sample_2 CGCCGATG TGCACGGG [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 1157297082 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 Minimum adapter overlap: 0 [Demultiplexing statistics] Name Barcode_1 Barcode_2 Hits Fraction unidentified NA NA 0 0.000 ambiguous NA NA 0 0.000 sample_1 CTTGCCCT ACGTTATT 4 0.500 sample_2 CGCCGATG TGCACGGG 4 0.500 * * * 8 1.000 your_output.unidentified000066400000000000000000000000001350370616400352120ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/se/defaultsadapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/se/demux_only/000077500000000000000000000000001350370616400306505ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/se/demux_only/regular/000077500000000000000000000000001350370616400323115ustar00rootroot00000000000000barcodes.txt000066400000000000000000000000661350370616400345570ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/se/demux_only/regularsample_1 GGCCCCTG CCAAAGCT sample_2 AATCCTAG GTCTAGTT adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/se/demux_only/regular/info.json000066400000000000000000000001151350370616400341340ustar00rootroot00000000000000{ "arguments": ["--demultiplex-only"], "return_code": 0, "stderr": [ ] } input_1.fastq000066400000000000000000000033301350370616400346500ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/se/demux_only/regular@read_s2_000/1 AATCCTAGAACTAGACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_150/1 GGCCCCTGTTTCTGGACGACGCCCCTATAATGTATGATAATTATTCGATTGACATGGCGAACTTCAGCCATTAGCGCTTTCGCATAATGTCGTTGTATAT + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_200/1 GGCCCCTGAACCATCTGAGCGGTACTCGGGAAAACACGGACGAGGTGGGATATCTTTCCCTTCTCTTGCCATCGTGTATTTATCTGTATCTAATGCTACT + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_200/1 AATCCTAGTCGTACAATGCATCAGACACCGCTTTTGTGGCGTTTCGACCGTAATCTACATTTACATCTCGTTAATTCGCGACATTCATCGTGCCGTACTC + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_075/1 AATCCTAGATACGCTGTGCGTCCTGGAACTGCAACTCTCGGTGTACAGGCCATCGTAAATCGTACCCGATTGCGCTACGTTTCAACTAGACAGATCGGAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_150/1 AATCCTAGATACCCCGACACTCGACTTATATTTTCCTCAGCTAGTGCGAGAGTTAATGTAGCGACGAAACACTCCTGCCTCGGTACGAGCATCCCGGTAC + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_000/1 GGCCCCTGAGCTTTGGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_075/1 GGCCCCTGGGTGGCTATGTAGGGAAAAACTCCGCTAGAACAAAGAACAGCCTCCCTCAATCACCCATGTTCGTGCCTCGACGCAGCTTTGGAGATCGGAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 your_output.sample_1.fastq000066400000000000000000000014541350370616400374140ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/se/demux_only/regular@read_s1_150/1 TTTCTGGACGACGCCCCTATAATGTATGATAATTATTCGATTGACATGGCGAACTTCAGCCATTAGCGCTTTCGCATAATGTCGTTGTATAT + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_200/1 AACCATCTGAGCGGTACTCGGGAAAACACGGACGAGGTGGGATATCTTTCCCTTCTCTTGCCATCGTGTATTTATCTGTATCTAATGCTACT + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_000/1 AGCTTTGGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAA + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_075/1 GGTGGCTATGTAGGGAAAAACTCCGCTAGAACAAAGAACAGCCTCCCTCAATCACCCATGTTCGTGCCTCGACGCAGCTTTGGAGATCGGAA + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 your_output.sample_1.settings000066400000000000000000000006461350370616400401400ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/se/demux_only/regularAdapterRemoval ver. 2.1.7 Demultiplexing of double-indexed single-end reads [Demultiplexing] Maximum mismatches (total): 0 [Demultiplexing samples] Name Barcode_1 Barcode_2 sample_1* GGCCCCTG CCAAAGCT sample_2 AATCCTAG GTCTAGTT [Adapter sequences] Adapter1[1]: AGCTTTGG_AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: CAGGGGCC_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT your_output.sample_2.fastq000066400000000000000000000014541350370616400374150ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/se/demux_only/regular@read_s2_000/1 AACTAGACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAA + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_200/1 TCGTACAATGCATCAGACACCGCTTTTGTGGCGTTTCGACCGTAATCTACATTTACATCTCGTTAATTCGCGACATTCATCGTGCCGTACTC + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_075/1 ATACGCTGTGCGTCCTGGAACTGCAACTCTCGGTGTACAGGCCATCGTAAATCGTACCCGATTGCGCTACGTTTCAACTAGACAGATCGGAA + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_150/1 ATACCCCGACACTCGACTTATATTTTCCTCAGCTAGTGCGAGAGTTAATGTAGCGACGAAACACTCCTGCCTCGGTACGAGCATCCCGGTAC + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 your_output.sample_2.settings000066400000000000000000000006461350370616400401410ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/se/demux_only/regularAdapterRemoval ver. 2.1.7 Demultiplexing of double-indexed single-end reads [Demultiplexing] Maximum mismatches (total): 0 [Demultiplexing samples] Name Barcode_1 Barcode_2 sample_1 GGCCCCTG CCAAAGCT sample_2* AATCCTAG GTCTAGTT [Adapter sequences] Adapter1[1]: AACTAGAC_AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: CTAGGATT_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT your_output.settings000066400000000000000000000011371350370616400364340ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/se/demux_only/regularAdapterRemoval ver. 2.1.7 Demultiplexing of double-indexed single-end reads [Demultiplexing] Maximum mismatches (total): 0 [Demultiplexing samples] Name Barcode_1 Barcode_2 sample_1 GGCCCCTG CCAAAGCT sample_2 AATCCTAG GTCTAGTT [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Demultiplexing statistics] Name Barcode_1 Barcode_2 Hits Fraction unidentified NA NA 0 0.000 ambiguous NA NA 0 0.000 sample_1 GGCCCCTG CCAAAGCT 4 0.500 sample_2 AATCCTAG GTCTAGTT 4 0.500 * * * 8 1.000 your_output.unidentified.fastq000066400000000000000000000000001350370616400403440ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/se/demux_only/regularadapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/se/demux_only/unidentified/000077500000000000000000000000001350370616400333175ustar00rootroot00000000000000barcodes.txt000066400000000000000000000000661350370616400355650ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/se/demux_only/unidentifiedsample_1 GGCCCCTG CCAAAGCT sample_2 AATCCTAG GTCTAGTT info.json000066400000000000000000000001151350370616400350630ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/se/demux_only/unidentified{ "arguments": ["--demultiplex-only"], "return_code": 0, "stderr": [ ] } input_1.fastq000066400000000000000000000033301350370616400356560ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/se/demux_only/unidentified@read_s2_000/1 AATCCTAGAACTAGACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_150/1 GGCCCCTGTTTCTGGACGACGCCCCTATAATGTATGATAATTATTCGATTGACATGGCGAACTTCAGCCATTAGCGCTTTCGCATAATGTCGTTGTATAT + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_200/1 TGCCCCTGAACCATCTGAGCGGTACTCGGGAAAACACGGACGAGGTGGGATATCTTTCCCTTCTCTTGCCATCGTGTATTTATCTGTATCTAATGCTACT + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_200/1 AATCCTAGTCGTACAATGCATCAGACACCGCTTTTGTGGCGTTTCGACCGTAATCTACATTTACATCTCGTTAATTCGCGACATTCATCGTGCCGTACTC + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_075/1 AATCCTAGATACGCTGTGCGTCCTGGAACTGCAACTCTCGGTGTACAGGCCATCGTAAATCGTACCCGATTGCGCTACGTTTCAACTAGACAGATCGGAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_150/1 AATCCTAGATACCCCGACACTCGACTTATATTTTCCTCAGCTAGTGCGAGAGTTAATGTAGCGACGAAACACTCCTGCCTCGGTACGAGCATCCCGGTAC + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_000/1 GGCCCCTGAGCTTTGGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_075/1 GGCCCCTGGGTGGCTATGTAGGGAAAAACTCCGCTAGAACAAAGAACAGCCTCCCTCAATCACCCATGTTCGTGCCTCGACGCAGCTTTGGAGATCGGAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 your_output.sample_1.fastq000066400000000000000000000011411350370616400404130ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/se/demux_only/unidentified@read_s1_150/1 TTTCTGGACGACGCCCCTATAATGTATGATAATTATTCGATTGACATGGCGAACTTCAGCCATTAGCGCTTTCGCATAATGTCGTTGTATAT + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_000/1 AGCTTTGGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAA + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_075/1 GGTGGCTATGTAGGGAAAAACTCCGCTAGAACAAAGAACAGCCTCCCTCAATCACCCATGTTCGTGCCTCGACGCAGCTTTGGAGATCGGAA + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 your_output.sample_1.settings000066400000000000000000000006461350370616400411460ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/se/demux_only/unidentifiedAdapterRemoval ver. 2.1.7 Demultiplexing of double-indexed single-end reads [Demultiplexing] Maximum mismatches (total): 0 [Demultiplexing samples] Name Barcode_1 Barcode_2 sample_1* GGCCCCTG CCAAAGCT sample_2 AATCCTAG GTCTAGTT [Adapter sequences] Adapter1[1]: AGCTTTGG_AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: CAGGGGCC_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT your_output.sample_2.fastq000066400000000000000000000014541350370616400404230ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/se/demux_only/unidentified@read_s2_000/1 AACTAGACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAA + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_200/1 TCGTACAATGCATCAGACACCGCTTTTGTGGCGTTTCGACCGTAATCTACATTTACATCTCGTTAATTCGCGACATTCATCGTGCCGTACTC + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_075/1 ATACGCTGTGCGTCCTGGAACTGCAACTCTCGGTGTACAGGCCATCGTAAATCGTACCCGATTGCGCTACGTTTCAACTAGACAGATCGGAA + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_150/1 ATACCCCGACACTCGACTTATATTTTCCTCAGCTAGTGCGAGAGTTAATGTAGCGACGAAACACTCCTGCCTCGGTACGAGCATCCCGGTAC + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 your_output.sample_2.settings000066400000000000000000000006461350370616400411470ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/se/demux_only/unidentifiedAdapterRemoval ver. 2.1.7 Demultiplexing of double-indexed single-end reads [Demultiplexing] Maximum mismatches (total): 0 [Demultiplexing samples] Name Barcode_1 Barcode_2 sample_1 GGCCCCTG CCAAAGCT sample_2* AATCCTAG GTCTAGTT [Adapter sequences] Adapter1[1]: AACTAGAC_AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: CTAGGATT_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT your_output.settings000066400000000000000000000011371350370616400374420ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/se/demux_only/unidentifiedAdapterRemoval ver. 2.1.7 Demultiplexing of double-indexed single-end reads [Demultiplexing] Maximum mismatches (total): 0 [Demultiplexing samples] Name Barcode_1 Barcode_2 sample_1 GGCCCCTG CCAAAGCT sample_2 AATCCTAG GTCTAGTT [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Demultiplexing statistics] Name Barcode_1 Barcode_2 Hits Fraction unidentified NA NA 1 0.125 ambiguous NA NA 0 0.000 sample_1 GGCCCCTG CCAAAGCT 3 0.375 sample_2 AATCCTAG GTCTAGTT 4 0.500 * * * 8 1.000 your_output.unidentified.fastq000066400000000000000000000003331350370616400413630ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/se/demux_only/unidentified@read_s1_200/1 TGCCCCTGAACCATCTGAGCGGTACTCGGGAAAACACGGACGAGGTGGGATATCTTTCCCTTCTCTTGCCATCGTGTATTTATCTGTATCTAATGCTACT + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/se/multiple_input/000077500000000000000000000000001350370616400315375ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/se/multiple_input/barcodes.txt000066400000000000000000000000661350370616400340640ustar00rootroot00000000000000sample_1 CTTGCCCT ACGTTATT sample_2 CGCCGATG TGCACGGG adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/se/multiple_input/info.json000066400000000000000000000000711350370616400333630ustar00rootroot00000000000000{ "arguments": [], "return_code": 0, "stderr": [ ] } adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/se/multiple_input/input_1a.fastq000066400000000000000000000012221350370616400343140ustar00rootroot00000000000000@read_s2_000/1 CGCCGATGCCCGTGCAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_200/1 CGCCGATGGCGTAAGTTGACGTCAGCCTGCGAGGTGCCACGCCAGTGGTTGCGCTCACCCGGGGCGTAGTTGCTCCGCGCAATTTCTTGGCAGTTCGATC + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_075/1 CTTGCCCTGGTTCTACGTTCTCCATCAGGTGGACGAGGGGATCTTGGCCCCCGTTCCTGCATTGGTATAATTAGACAGGATGAAATAACGTAGATCGGAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/se/multiple_input/input_1b.fastq000066400000000000000000000012211350370616400343140ustar00rootroot00000000000000@read_s1_200/1 CTTGCCCTGTAGTGCAATAAAAGGATCCTCTTGTGGCCGATTGCAGACCAGCCTCGGGGCTAAACTGATAATCGTATGCTATAGACCCTGGTCGACGCCG + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_150/1 CTTGCCCTCAGATGTCAGCTCATGTGTTGATATACAGCTAACTAAGGCCCGGGGGTTTAGGCTCAACCCTCTACCTGGTATACCGGCCCAACGCACTCGC + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_075/1 CGCCGATGTCTTGGGAACGAGAGTGCCACCAATTAAAGTGATGGATATCGAGACGTCCCAAACCACCGCAATAGGACGGGACACCCGTGCAAGATCGGAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/se/multiple_input/input_1c.fastq000066400000000000000000000006661350370616400343310ustar00rootroot00000000000000@read_s2_150/1 CGCCGATGAGCCCCGAGTGTCCATCACAAGCCACCTCCACTAACCATCTCGGTCCATTATTTGTCACTCGTGGCTAGAAGGGAATAAAGACAACTCTCTC + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_000/1 CTTGCCCTAATAACGTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 your_output.sample_1.discarded000066400000000000000000000000231350370616400374350ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/se/multiple_input@read_s1_000/1 + your_output.sample_1.settings000066400000000000000000000041561350370616400373660ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/se/multiple_inputAdapterRemoval ver. 2.2.0 Trimming of double-indexed single-end reads [Demultiplexing] Maximum mismatches (total): 0 [Demultiplexing samples] Name Barcode_1 Barcode_2 sample_1* CTTGCCCT ACGTTATT sample_2 CGCCGATG TGCACGGG [Adapter sequences] Adapter1[1]: AATAACGT_AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGGGCAAG_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 4115144913 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 Minimum adapter overlap: 0 [Trimming statistics] Total number of reads: 4 Number of unaligned reads: 2 Number of well aligned reads: 2 Number of discarded mate 1 reads: 1 Number of singleton mate 1 reads: 3 Number of reads with adapters[1]: 2 Number of retained reads: 3 Number of retained nucleotides: 259 Average length of retained reads: 86.3333 [Length distribution] Length Mate1 Discarded All 0 0 1 1 1 0 0 0 2 0 0 0 3 0 0 0 4 0 0 0 5 0 0 0 6 0 0 0 7 0 0 0 8 0 0 0 9 0 0 0 10 0 0 0 11 0 0 0 12 0 0 0 13 0 0 0 14 0 0 0 15 0 0 0 16 0 0 0 17 0 0 0 18 0 0 0 19 0 0 0 20 0 0 0 21 0 0 0 22 0 0 0 23 0 0 0 24 0 0 0 25 0 0 0 26 0 0 0 27 0 0 0 28 0 0 0 29 0 0 0 30 0 0 0 31 0 0 0 32 0 0 0 33 0 0 0 34 0 0 0 35 0 0 0 36 0 0 0 37 0 0 0 38 0 0 0 39 0 0 0 40 0 0 0 41 0 0 0 42 0 0 0 43 0 0 0 44 0 0 0 45 0 0 0 46 0 0 0 47 0 0 0 48 0 0 0 49 0 0 0 50 0 0 0 51 0 0 0 52 0 0 0 53 0 0 0 54 0 0 0 55 0 0 0 56 0 0 0 57 0 0 0 58 0 0 0 59 0 0 0 60 0 0 0 61 0 0 0 62 0 0 0 63 0 0 0 64 0 0 0 65 0 0 0 66 0 0 0 67 0 0 0 68 0 0 0 69 0 0 0 70 0 0 0 71 0 0 0 72 0 0 0 73 0 0 0 74 0 0 0 75 1 0 1 76 0 0 0 77 0 0 0 78 0 0 0 79 0 0 0 80 0 0 0 81 0 0 0 82 0 0 0 83 0 0 0 84 0 0 0 85 0 0 0 86 0 0 0 87 0 0 0 88 0 0 0 89 0 0 0 90 0 0 0 91 0 0 0 92 2 0 2 your_output.sample_1.truncated000066400000000000000000000010771350370616400375160ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/se/multiple_input@read_s1_075/1 GGTTCTACGTTCTCCATCAGGTGGACGAGGGGATCTTGGCCCCCGTTCCTGCATTGGTATAATTAGACAGGATGA + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; @read_s1_200/1 GTAGTGCAATAAAAGGATCCTCTTGTGGCCGATTGCAGACCAGCCTCGGGGCTAAACTGATAATCGTATGCTATAGACCCTGGTCGACGCCG + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_150/1 CAGATGTCAGCTCATGTGTTGATATACAGCTAACTAAGGCCCGGGGGTTTAGGCTCAACCCTCTACCTGGTATACCGGCCCAACGCACTCGC + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 your_output.sample_2.discarded000066400000000000000000000000231350370616400374360ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/se/multiple_input@read_s2_000/1 + your_output.sample_2.settings000066400000000000000000000041501350370616400373610ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/se/multiple_inputAdapterRemoval ver. 2.2.0 Trimming of double-indexed single-end reads [Demultiplexing] Maximum mismatches (total): 0 [Demultiplexing samples] Name Barcode_1 Barcode_2 sample_1 CTTGCCCT ACGTTATT sample_2* CGCCGATG TGCACGGG [Adapter sequences] Adapter1[1]: CCCGTGCA_AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: CATCGGCG_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 356769071 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 Minimum adapter overlap: 0 [Trimming statistics] Total number of reads: 4 Number of unaligned reads: 1 Number of well aligned reads: 3 Number of discarded mate 1 reads: 1 Number of singleton mate 1 reads: 3 Number of reads with adapters[1]: 3 Number of retained reads: 3 Number of retained nucleotides: 258 Average length of retained reads: 86 [Length distribution] Length Mate1 Discarded All 0 0 1 1 1 0 0 0 2 0 0 0 3 0 0 0 4 0 0 0 5 0 0 0 6 0 0 0 7 0 0 0 8 0 0 0 9 0 0 0 10 0 0 0 11 0 0 0 12 0 0 0 13 0 0 0 14 0 0 0 15 0 0 0 16 0 0 0 17 0 0 0 18 0 0 0 19 0 0 0 20 0 0 0 21 0 0 0 22 0 0 0 23 0 0 0 24 0 0 0 25 0 0 0 26 0 0 0 27 0 0 0 28 0 0 0 29 0 0 0 30 0 0 0 31 0 0 0 32 0 0 0 33 0 0 0 34 0 0 0 35 0 0 0 36 0 0 0 37 0 0 0 38 0 0 0 39 0 0 0 40 0 0 0 41 0 0 0 42 0 0 0 43 0 0 0 44 0 0 0 45 0 0 0 46 0 0 0 47 0 0 0 48 0 0 0 49 0 0 0 50 0 0 0 51 0 0 0 52 0 0 0 53 0 0 0 54 0 0 0 55 0 0 0 56 0 0 0 57 0 0 0 58 0 0 0 59 0 0 0 60 0 0 0 61 0 0 0 62 0 0 0 63 0 0 0 64 0 0 0 65 0 0 0 66 0 0 0 67 0 0 0 68 0 0 0 69 0 0 0 70 0 0 0 71 0 0 0 72 0 0 0 73 0 0 0 74 0 0 0 75 1 0 1 76 0 0 0 77 0 0 0 78 0 0 0 79 0 0 0 80 0 0 0 81 0 0 0 82 0 0 0 83 0 0 0 84 0 0 0 85 0 0 0 86 0 0 0 87 0 0 0 88 0 0 0 89 0 0 0 90 0 0 0 91 1 0 1 92 1 0 1 your_output.sample_2.truncated000066400000000000000000000010751350370616400375150ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/se/multiple_input@read_s2_200/1 GCGTAAGTTGACGTCAGCCTGCGAGGTGCCACGCCAGTGGTTGCGCTCACCCGGGGCGTAGTTGCTCCGCGCAATTTCTTGGCAGTTCGAT + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::998876654321 @read_s2_075/1 TCTTGGGAACGAGAGTGCCACCAATTAAAGTGATGGATATCGAGACGTCCCAAACCACCGCAATAGGACGGGACA + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; @read_s2_150/1 AGCCCCGAGTGTCCATCACAAGCCACCTCCACTAACCATCTCGGTCCATTATTTGTCACTCGTGGCTAGAAGGGAATAAAGACAACTCTCTC + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 your_output.settings000066400000000000000000000021651350370616400356640ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/se/multiple_inputAdapterRemoval ver. 2.1.7 Trimming of double-indexed single-end reads [Demultiplexing] Maximum mismatches (total): 0 [Demultiplexing samples] Name Barcode_1 Barcode_2 sample_1 CTTGCCCT ACGTTATT sample_2 CGCCGATG TGCACGGG [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 1157297082 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 Minimum adapter overlap: 0 [Demultiplexing statistics] Name Barcode_1 Barcode_2 Hits Fraction unidentified NA NA 0 0.000 ambiguous NA NA 0 0.000 sample_1 CTTGCCCT ACGTTATT 4 0.500 sample_2 CGCCGATG TGCACGGG 4 0.500 * * * 8 1.000 your_output.unidentified000066400000000000000000000000001350370616400364550ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/se/multiple_inputadapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/se/threads/000077500000000000000000000000001350370616400301175ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/se/threads/one/000077500000000000000000000000001350370616400307005ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/se/threads/one/barcodes.txt000066400000000000000000000000661350370616400332250ustar00rootroot00000000000000sample_1 CTTGCCCT ACGTTATT sample_2 CGCCGATG TGCACGGG adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/se/threads/one/info.json000066400000000000000000000001111350370616400325170ustar00rootroot00000000000000{ "arguments": ["--threads", "1"], "return_code": 0, "stderr": [ ] } adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/se/threads/one/input_1.fastq000066400000000000000000000033301350370616400333160ustar00rootroot00000000000000@read_s2_000/1 CGCCGATGCCCGTGCAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_200/1 CGCCGATGGCGTAAGTTGACGTCAGCCTGCGAGGTGCCACGCCAGTGGTTGCGCTCACCCGGGGCGTAGTTGCTCCGCGCAATTTCTTGGCAGTTCGATC + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_075/1 CTTGCCCTGGTTCTACGTTCTCCATCAGGTGGACGAGGGGATCTTGGCCCCCGTTCCTGCATTGGTATAATTAGACAGGATGAAATAACGTAGATCGGAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_200/1 CTTGCCCTGTAGTGCAATAAAAGGATCCTCTTGTGGCCGATTGCAGACCAGCCTCGGGGCTAAACTGATAATCGTATGCTATAGACCCTGGTCGACGCCG + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_150/1 CTTGCCCTCAGATGTCAGCTCATGTGTTGATATACAGCTAACTAAGGCCCGGGGGTTTAGGCTCAACCCTCTACCTGGTATACCGGCCCAACGCACTCGC + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_075/1 CGCCGATGTCTTGGGAACGAGAGTGCCACCAATTAAAGTGATGGATATCGAGACGTCCCAAACCACCGCAATAGGACGGGACACCCGTGCAAGATCGGAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_150/1 CGCCGATGAGCCCCGAGTGTCCATCACAAGCCACCTCCACTAACCATCTCGGTCCATTATTTGTCACTCGTGGCTAGAAGGGAATAAAGACAACTCTCTC + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_000/1 CTTGCCCTAATAACGTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 your_output.sample_1.discarded000066400000000000000000000000231350370616400365760ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/se/threads/one@read_s1_000/1 + your_output.sample_1.settings000066400000000000000000000041561350370616400365270ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/se/threads/oneAdapterRemoval ver. 2.2.0 Trimming of double-indexed single-end reads [Demultiplexing] Maximum mismatches (total): 0 [Demultiplexing samples] Name Barcode_1 Barcode_2 sample_1* CTTGCCCT ACGTTATT sample_2 CGCCGATG TGCACGGG [Adapter sequences] Adapter1[1]: AATAACGT_AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGGGCAAG_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 4115144913 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 Minimum adapter overlap: 0 [Trimming statistics] Total number of reads: 4 Number of unaligned reads: 2 Number of well aligned reads: 2 Number of discarded mate 1 reads: 1 Number of singleton mate 1 reads: 3 Number of reads with adapters[1]: 2 Number of retained reads: 3 Number of retained nucleotides: 259 Average length of retained reads: 86.3333 [Length distribution] Length Mate1 Discarded All 0 0 1 1 1 0 0 0 2 0 0 0 3 0 0 0 4 0 0 0 5 0 0 0 6 0 0 0 7 0 0 0 8 0 0 0 9 0 0 0 10 0 0 0 11 0 0 0 12 0 0 0 13 0 0 0 14 0 0 0 15 0 0 0 16 0 0 0 17 0 0 0 18 0 0 0 19 0 0 0 20 0 0 0 21 0 0 0 22 0 0 0 23 0 0 0 24 0 0 0 25 0 0 0 26 0 0 0 27 0 0 0 28 0 0 0 29 0 0 0 30 0 0 0 31 0 0 0 32 0 0 0 33 0 0 0 34 0 0 0 35 0 0 0 36 0 0 0 37 0 0 0 38 0 0 0 39 0 0 0 40 0 0 0 41 0 0 0 42 0 0 0 43 0 0 0 44 0 0 0 45 0 0 0 46 0 0 0 47 0 0 0 48 0 0 0 49 0 0 0 50 0 0 0 51 0 0 0 52 0 0 0 53 0 0 0 54 0 0 0 55 0 0 0 56 0 0 0 57 0 0 0 58 0 0 0 59 0 0 0 60 0 0 0 61 0 0 0 62 0 0 0 63 0 0 0 64 0 0 0 65 0 0 0 66 0 0 0 67 0 0 0 68 0 0 0 69 0 0 0 70 0 0 0 71 0 0 0 72 0 0 0 73 0 0 0 74 0 0 0 75 1 0 1 76 0 0 0 77 0 0 0 78 0 0 0 79 0 0 0 80 0 0 0 81 0 0 0 82 0 0 0 83 0 0 0 84 0 0 0 85 0 0 0 86 0 0 0 87 0 0 0 88 0 0 0 89 0 0 0 90 0 0 0 91 0 0 0 92 2 0 2 your_output.sample_1.truncated000066400000000000000000000010771350370616400366570ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/se/threads/one@read_s1_075/1 GGTTCTACGTTCTCCATCAGGTGGACGAGGGGATCTTGGCCCCCGTTCCTGCATTGGTATAATTAGACAGGATGA + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; @read_s1_200/1 GTAGTGCAATAAAAGGATCCTCTTGTGGCCGATTGCAGACCAGCCTCGGGGCTAAACTGATAATCGTATGCTATAGACCCTGGTCGACGCCG + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_150/1 CAGATGTCAGCTCATGTGTTGATATACAGCTAACTAAGGCCCGGGGGTTTAGGCTCAACCCTCTACCTGGTATACCGGCCCAACGCACTCGC + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 your_output.sample_2.discarded000066400000000000000000000000231350370616400365770ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/se/threads/one@read_s2_000/1 + your_output.sample_2.settings000066400000000000000000000041501350370616400365220ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/se/threads/oneAdapterRemoval ver. 2.2.0 Trimming of double-indexed single-end reads [Demultiplexing] Maximum mismatches (total): 0 [Demultiplexing samples] Name Barcode_1 Barcode_2 sample_1 CTTGCCCT ACGTTATT sample_2* CGCCGATG TGCACGGG [Adapter sequences] Adapter1[1]: CCCGTGCA_AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: CATCGGCG_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 356769071 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 Minimum adapter overlap: 0 [Trimming statistics] Total number of reads: 4 Number of unaligned reads: 1 Number of well aligned reads: 3 Number of discarded mate 1 reads: 1 Number of singleton mate 1 reads: 3 Number of reads with adapters[1]: 3 Number of retained reads: 3 Number of retained nucleotides: 258 Average length of retained reads: 86 [Length distribution] Length Mate1 Discarded All 0 0 1 1 1 0 0 0 2 0 0 0 3 0 0 0 4 0 0 0 5 0 0 0 6 0 0 0 7 0 0 0 8 0 0 0 9 0 0 0 10 0 0 0 11 0 0 0 12 0 0 0 13 0 0 0 14 0 0 0 15 0 0 0 16 0 0 0 17 0 0 0 18 0 0 0 19 0 0 0 20 0 0 0 21 0 0 0 22 0 0 0 23 0 0 0 24 0 0 0 25 0 0 0 26 0 0 0 27 0 0 0 28 0 0 0 29 0 0 0 30 0 0 0 31 0 0 0 32 0 0 0 33 0 0 0 34 0 0 0 35 0 0 0 36 0 0 0 37 0 0 0 38 0 0 0 39 0 0 0 40 0 0 0 41 0 0 0 42 0 0 0 43 0 0 0 44 0 0 0 45 0 0 0 46 0 0 0 47 0 0 0 48 0 0 0 49 0 0 0 50 0 0 0 51 0 0 0 52 0 0 0 53 0 0 0 54 0 0 0 55 0 0 0 56 0 0 0 57 0 0 0 58 0 0 0 59 0 0 0 60 0 0 0 61 0 0 0 62 0 0 0 63 0 0 0 64 0 0 0 65 0 0 0 66 0 0 0 67 0 0 0 68 0 0 0 69 0 0 0 70 0 0 0 71 0 0 0 72 0 0 0 73 0 0 0 74 0 0 0 75 1 0 1 76 0 0 0 77 0 0 0 78 0 0 0 79 0 0 0 80 0 0 0 81 0 0 0 82 0 0 0 83 0 0 0 84 0 0 0 85 0 0 0 86 0 0 0 87 0 0 0 88 0 0 0 89 0 0 0 90 0 0 0 91 1 0 1 92 1 0 1 your_output.sample_2.truncated000066400000000000000000000010751350370616400366560ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/se/threads/one@read_s2_200/1 GCGTAAGTTGACGTCAGCCTGCGAGGTGCCACGCCAGTGGTTGCGCTCACCCGGGGCGTAGTTGCTCCGCGCAATTTCTTGGCAGTTCGAT + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::998876654321 @read_s2_075/1 TCTTGGGAACGAGAGTGCCACCAATTAAAGTGATGGATATCGAGACGTCCCAAACCACCGCAATAGGACGGGACA + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; @read_s2_150/1 AGCCCCGAGTGTCCATCACAAGCCACCTCCACTAACCATCTCGGTCCATTATTTGTCACTCGTGGCTAGAAGGGAATAAAGACAACTCTCTC + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 your_output.settings000066400000000000000000000021651350370616400350250ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/se/threads/oneAdapterRemoval ver. 2.1.7 Trimming of double-indexed single-end reads [Demultiplexing] Maximum mismatches (total): 0 [Demultiplexing samples] Name Barcode_1 Barcode_2 sample_1 CTTGCCCT ACGTTATT sample_2 CGCCGATG TGCACGGG [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 1157297082 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 Minimum adapter overlap: 0 [Demultiplexing statistics] Name Barcode_1 Barcode_2 Hits Fraction unidentified NA NA 0 0.000 ambiguous NA NA 0 0.000 sample_1 CTTGCCCT ACGTTATT 4 0.500 sample_2 CGCCGATG TGCACGGG 4 0.500 * * * 8 1.000 your_output.unidentified000066400000000000000000000000001350370616400356160ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/se/threads/oneadapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/se/threads/three/000077500000000000000000000000001350370616400312265ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/se/threads/three/barcodes.txt000066400000000000000000000000661350370616400335530ustar00rootroot00000000000000sample_1 CTTGCCCT ACGTTATT sample_2 CGCCGATG TGCACGGG adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/se/threads/three/info.json000066400000000000000000000001111350370616400330450ustar00rootroot00000000000000{ "arguments": ["--threads", "3"], "return_code": 0, "stderr": [ ] } adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/se/threads/three/input_1.fastq000066400000000000000000000033301350370616400336440ustar00rootroot00000000000000@read_s2_000/1 CGCCGATGCCCGTGCAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_200/1 CGCCGATGGCGTAAGTTGACGTCAGCCTGCGAGGTGCCACGCCAGTGGTTGCGCTCACCCGGGGCGTAGTTGCTCCGCGCAATTTCTTGGCAGTTCGATC + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_075/1 CTTGCCCTGGTTCTACGTTCTCCATCAGGTGGACGAGGGGATCTTGGCCCCCGTTCCTGCATTGGTATAATTAGACAGGATGAAATAACGTAGATCGGAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_200/1 CTTGCCCTGTAGTGCAATAAAAGGATCCTCTTGTGGCCGATTGCAGACCAGCCTCGGGGCTAAACTGATAATCGTATGCTATAGACCCTGGTCGACGCCG + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_150/1 CTTGCCCTCAGATGTCAGCTCATGTGTTGATATACAGCTAACTAAGGCCCGGGGGTTTAGGCTCAACCCTCTACCTGGTATACCGGCCCAACGCACTCGC + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_075/1 CGCCGATGTCTTGGGAACGAGAGTGCCACCAATTAAAGTGATGGATATCGAGACGTCCCAAACCACCGCAATAGGACGGGACACCCGTGCAAGATCGGAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_150/1 CGCCGATGAGCCCCGAGTGTCCATCACAAGCCACCTCCACTAACCATCTCGGTCCATTATTTGTCACTCGTGGCTAGAAGGGAATAAAGACAACTCTCTC + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_000/1 CTTGCCCTAATAACGTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 your_output.sample_1.discarded000066400000000000000000000000231350370616400371240ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/se/threads/three@read_s1_000/1 + your_output.sample_1.settings000066400000000000000000000041461350370616400370540ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/se/threads/threeAdapterRemoval ver. 2.2.0 Trimming of double-indexed single-end reads [Demultiplexing] Maximum mismatches (total): 0 [Demultiplexing samples] Name Barcode_1 Barcode_2 sample_1* CTTGCCCT ACGTTATT sample_2 CGCCGATG TGCACGGG [Adapter sequences] Adapter1[1]: AATAACGT_AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGGGCAAG_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: NA Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 Minimum adapter overlap: 0 [Trimming statistics] Total number of reads: 4 Number of unaligned reads: 2 Number of well aligned reads: 2 Number of discarded mate 1 reads: 1 Number of singleton mate 1 reads: 3 Number of reads with adapters[1]: 2 Number of retained reads: 3 Number of retained nucleotides: 259 Average length of retained reads: 86.3333 [Length distribution] Length Mate1 Discarded All 0 0 1 1 1 0 0 0 2 0 0 0 3 0 0 0 4 0 0 0 5 0 0 0 6 0 0 0 7 0 0 0 8 0 0 0 9 0 0 0 10 0 0 0 11 0 0 0 12 0 0 0 13 0 0 0 14 0 0 0 15 0 0 0 16 0 0 0 17 0 0 0 18 0 0 0 19 0 0 0 20 0 0 0 21 0 0 0 22 0 0 0 23 0 0 0 24 0 0 0 25 0 0 0 26 0 0 0 27 0 0 0 28 0 0 0 29 0 0 0 30 0 0 0 31 0 0 0 32 0 0 0 33 0 0 0 34 0 0 0 35 0 0 0 36 0 0 0 37 0 0 0 38 0 0 0 39 0 0 0 40 0 0 0 41 0 0 0 42 0 0 0 43 0 0 0 44 0 0 0 45 0 0 0 46 0 0 0 47 0 0 0 48 0 0 0 49 0 0 0 50 0 0 0 51 0 0 0 52 0 0 0 53 0 0 0 54 0 0 0 55 0 0 0 56 0 0 0 57 0 0 0 58 0 0 0 59 0 0 0 60 0 0 0 61 0 0 0 62 0 0 0 63 0 0 0 64 0 0 0 65 0 0 0 66 0 0 0 67 0 0 0 68 0 0 0 69 0 0 0 70 0 0 0 71 0 0 0 72 0 0 0 73 0 0 0 74 0 0 0 75 1 0 1 76 0 0 0 77 0 0 0 78 0 0 0 79 0 0 0 80 0 0 0 81 0 0 0 82 0 0 0 83 0 0 0 84 0 0 0 85 0 0 0 86 0 0 0 87 0 0 0 88 0 0 0 89 0 0 0 90 0 0 0 91 0 0 0 92 2 0 2 your_output.sample_1.truncated000066400000000000000000000010771350370616400372050ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/se/threads/three@read_s1_075/1 GGTTCTACGTTCTCCATCAGGTGGACGAGGGGATCTTGGCCCCCGTTCCTGCATTGGTATAATTAGACAGGATGA + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; @read_s1_200/1 GTAGTGCAATAAAAGGATCCTCTTGTGGCCGATTGCAGACCAGCCTCGGGGCTAAACTGATAATCGTATGCTATAGACCCTGGTCGACGCCG + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_150/1 CAGATGTCAGCTCATGTGTTGATATACAGCTAACTAAGGCCCGGGGGTTTAGGCTCAACCCTCTACCTGGTATACCGGCCCAACGCACTCGC + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 your_output.sample_2.discarded000066400000000000000000000000231350370616400371250ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/se/threads/three@read_s2_000/1 + your_output.sample_2.settings000066400000000000000000000041411350370616400370500ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/se/threads/threeAdapterRemoval ver. 2.2.0 Trimming of double-indexed single-end reads [Demultiplexing] Maximum mismatches (total): 0 [Demultiplexing samples] Name Barcode_1 Barcode_2 sample_1 CTTGCCCT ACGTTATT sample_2* CGCCGATG TGCACGGG [Adapter sequences] Adapter1[1]: CCCGTGCA_AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: CATCGGCG_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: NA Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 Minimum adapter overlap: 0 [Trimming statistics] Total number of reads: 4 Number of unaligned reads: 1 Number of well aligned reads: 3 Number of discarded mate 1 reads: 1 Number of singleton mate 1 reads: 3 Number of reads with adapters[1]: 3 Number of retained reads: 3 Number of retained nucleotides: 258 Average length of retained reads: 86 [Length distribution] Length Mate1 Discarded All 0 0 1 1 1 0 0 0 2 0 0 0 3 0 0 0 4 0 0 0 5 0 0 0 6 0 0 0 7 0 0 0 8 0 0 0 9 0 0 0 10 0 0 0 11 0 0 0 12 0 0 0 13 0 0 0 14 0 0 0 15 0 0 0 16 0 0 0 17 0 0 0 18 0 0 0 19 0 0 0 20 0 0 0 21 0 0 0 22 0 0 0 23 0 0 0 24 0 0 0 25 0 0 0 26 0 0 0 27 0 0 0 28 0 0 0 29 0 0 0 30 0 0 0 31 0 0 0 32 0 0 0 33 0 0 0 34 0 0 0 35 0 0 0 36 0 0 0 37 0 0 0 38 0 0 0 39 0 0 0 40 0 0 0 41 0 0 0 42 0 0 0 43 0 0 0 44 0 0 0 45 0 0 0 46 0 0 0 47 0 0 0 48 0 0 0 49 0 0 0 50 0 0 0 51 0 0 0 52 0 0 0 53 0 0 0 54 0 0 0 55 0 0 0 56 0 0 0 57 0 0 0 58 0 0 0 59 0 0 0 60 0 0 0 61 0 0 0 62 0 0 0 63 0 0 0 64 0 0 0 65 0 0 0 66 0 0 0 67 0 0 0 68 0 0 0 69 0 0 0 70 0 0 0 71 0 0 0 72 0 0 0 73 0 0 0 74 0 0 0 75 1 0 1 76 0 0 0 77 0 0 0 78 0 0 0 79 0 0 0 80 0 0 0 81 0 0 0 82 0 0 0 83 0 0 0 84 0 0 0 85 0 0 0 86 0 0 0 87 0 0 0 88 0 0 0 89 0 0 0 90 0 0 0 91 1 0 1 92 1 0 1 your_output.sample_2.truncated000066400000000000000000000010751350370616400372040ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/se/threads/three@read_s2_200/1 GCGTAAGTTGACGTCAGCCTGCGAGGTGCCACGCCAGTGGTTGCGCTCACCCGGGGCGTAGTTGCTCCGCGCAATTTCTTGGCAGTTCGAT + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::998876654321 @read_s2_075/1 TCTTGGGAACGAGAGTGCCACCAATTAAAGTGATGGATATCGAGACGTCCCAAACCACCGCAATAGGACGGGACA + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; @read_s2_150/1 AGCCCCGAGTGTCCATCACAAGCCACCTCCACTAACCATCTCGGTCCATTATTTGTCACTCGTGGCTAGAAGGGAATAAAGACAACTCTCTC + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 your_output.settings000066400000000000000000000021551350370616400353520ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/se/threads/threeAdapterRemoval ver. 2.1.7 Trimming of double-indexed single-end reads [Demultiplexing] Maximum mismatches (total): 0 [Demultiplexing samples] Name Barcode_1 Barcode_2 sample_1 CTTGCCCT ACGTTATT sample_2 CGCCGATG TGCACGGG [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: NA Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 Minimum adapter overlap: 0 [Demultiplexing statistics] Name Barcode_1 Barcode_2 Hits Fraction unidentified NA NA 0 0.000 ambiguous NA NA 0 0.000 sample_1 CTTGCCCT ACGTTATT 4 0.500 sample_2 CGCCGATG TGCACGGG 4 0.500 * * * 8 1.000 your_output.unidentified000066400000000000000000000000001350370616400361440ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/se/threads/threeadapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/se/threads/two/000077500000000000000000000000001350370616400307305ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/se/threads/two/barcodes.txt000066400000000000000000000000661350370616400332550ustar00rootroot00000000000000sample_1 CTTGCCCT ACGTTATT sample_2 CGCCGATG TGCACGGG adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/se/threads/two/info.json000066400000000000000000000001111350370616400325470ustar00rootroot00000000000000{ "arguments": ["--threads", "2"], "return_code": 0, "stderr": [ ] } adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/se/threads/two/input_1.fastq000066400000000000000000000033301350370616400333460ustar00rootroot00000000000000@read_s2_000/1 CGCCGATGCCCGTGCAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_200/1 CGCCGATGGCGTAAGTTGACGTCAGCCTGCGAGGTGCCACGCCAGTGGTTGCGCTCACCCGGGGCGTAGTTGCTCCGCGCAATTTCTTGGCAGTTCGATC + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_075/1 CTTGCCCTGGTTCTACGTTCTCCATCAGGTGGACGAGGGGATCTTGGCCCCCGTTCCTGCATTGGTATAATTAGACAGGATGAAATAACGTAGATCGGAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_200/1 CTTGCCCTGTAGTGCAATAAAAGGATCCTCTTGTGGCCGATTGCAGACCAGCCTCGGGGCTAAACTGATAATCGTATGCTATAGACCCTGGTCGACGCCG + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_150/1 CTTGCCCTCAGATGTCAGCTCATGTGTTGATATACAGCTAACTAAGGCCCGGGGGTTTAGGCTCAACCCTCTACCTGGTATACCGGCCCAACGCACTCGC + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_075/1 CGCCGATGTCTTGGGAACGAGAGTGCCACCAATTAAAGTGATGGATATCGAGACGTCCCAAACCACCGCAATAGGACGGGACACCCGTGCAAGATCGGAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_150/1 CGCCGATGAGCCCCGAGTGTCCATCACAAGCCACCTCCACTAACCATCTCGGTCCATTATTTGTCACTCGTGGCTAGAAGGGAATAAAGACAACTCTCTC + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_000/1 CTTGCCCTAATAACGTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 your_output.sample_1.discarded000066400000000000000000000000231350370616400366260ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/se/threads/two@read_s1_000/1 + your_output.sample_1.settings000066400000000000000000000041461350370616400365560ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/se/threads/twoAdapterRemoval ver. 2.2.0 Trimming of double-indexed single-end reads [Demultiplexing] Maximum mismatches (total): 0 [Demultiplexing samples] Name Barcode_1 Barcode_2 sample_1* CTTGCCCT ACGTTATT sample_2 CGCCGATG TGCACGGG [Adapter sequences] Adapter1[1]: AATAACGT_AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGGGCAAG_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: NA Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 Minimum adapter overlap: 0 [Trimming statistics] Total number of reads: 4 Number of unaligned reads: 2 Number of well aligned reads: 2 Number of discarded mate 1 reads: 1 Number of singleton mate 1 reads: 3 Number of reads with adapters[1]: 2 Number of retained reads: 3 Number of retained nucleotides: 259 Average length of retained reads: 86.3333 [Length distribution] Length Mate1 Discarded All 0 0 1 1 1 0 0 0 2 0 0 0 3 0 0 0 4 0 0 0 5 0 0 0 6 0 0 0 7 0 0 0 8 0 0 0 9 0 0 0 10 0 0 0 11 0 0 0 12 0 0 0 13 0 0 0 14 0 0 0 15 0 0 0 16 0 0 0 17 0 0 0 18 0 0 0 19 0 0 0 20 0 0 0 21 0 0 0 22 0 0 0 23 0 0 0 24 0 0 0 25 0 0 0 26 0 0 0 27 0 0 0 28 0 0 0 29 0 0 0 30 0 0 0 31 0 0 0 32 0 0 0 33 0 0 0 34 0 0 0 35 0 0 0 36 0 0 0 37 0 0 0 38 0 0 0 39 0 0 0 40 0 0 0 41 0 0 0 42 0 0 0 43 0 0 0 44 0 0 0 45 0 0 0 46 0 0 0 47 0 0 0 48 0 0 0 49 0 0 0 50 0 0 0 51 0 0 0 52 0 0 0 53 0 0 0 54 0 0 0 55 0 0 0 56 0 0 0 57 0 0 0 58 0 0 0 59 0 0 0 60 0 0 0 61 0 0 0 62 0 0 0 63 0 0 0 64 0 0 0 65 0 0 0 66 0 0 0 67 0 0 0 68 0 0 0 69 0 0 0 70 0 0 0 71 0 0 0 72 0 0 0 73 0 0 0 74 0 0 0 75 1 0 1 76 0 0 0 77 0 0 0 78 0 0 0 79 0 0 0 80 0 0 0 81 0 0 0 82 0 0 0 83 0 0 0 84 0 0 0 85 0 0 0 86 0 0 0 87 0 0 0 88 0 0 0 89 0 0 0 90 0 0 0 91 0 0 0 92 2 0 2 your_output.sample_1.truncated000066400000000000000000000010771350370616400367070ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/se/threads/two@read_s1_075/1 GGTTCTACGTTCTCCATCAGGTGGACGAGGGGATCTTGGCCCCCGTTCCTGCATTGGTATAATTAGACAGGATGA + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; @read_s1_200/1 GTAGTGCAATAAAAGGATCCTCTTGTGGCCGATTGCAGACCAGCCTCGGGGCTAAACTGATAATCGTATGCTATAGACCCTGGTCGACGCCG + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_150/1 CAGATGTCAGCTCATGTGTTGATATACAGCTAACTAAGGCCCGGGGGTTTAGGCTCAACCCTCTACCTGGTATACCGGCCCAACGCACTCGC + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 your_output.sample_2.discarded000066400000000000000000000000231350370616400366270ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/se/threads/two@read_s2_000/1 + your_output.sample_2.settings000066400000000000000000000041411350370616400365520ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/se/threads/twoAdapterRemoval ver. 2.2.0 Trimming of double-indexed single-end reads [Demultiplexing] Maximum mismatches (total): 0 [Demultiplexing samples] Name Barcode_1 Barcode_2 sample_1 CTTGCCCT ACGTTATT sample_2* CGCCGATG TGCACGGG [Adapter sequences] Adapter1[1]: CCCGTGCA_AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: CATCGGCG_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: NA Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 Minimum adapter overlap: 0 [Trimming statistics] Total number of reads: 4 Number of unaligned reads: 1 Number of well aligned reads: 3 Number of discarded mate 1 reads: 1 Number of singleton mate 1 reads: 3 Number of reads with adapters[1]: 3 Number of retained reads: 3 Number of retained nucleotides: 258 Average length of retained reads: 86 [Length distribution] Length Mate1 Discarded All 0 0 1 1 1 0 0 0 2 0 0 0 3 0 0 0 4 0 0 0 5 0 0 0 6 0 0 0 7 0 0 0 8 0 0 0 9 0 0 0 10 0 0 0 11 0 0 0 12 0 0 0 13 0 0 0 14 0 0 0 15 0 0 0 16 0 0 0 17 0 0 0 18 0 0 0 19 0 0 0 20 0 0 0 21 0 0 0 22 0 0 0 23 0 0 0 24 0 0 0 25 0 0 0 26 0 0 0 27 0 0 0 28 0 0 0 29 0 0 0 30 0 0 0 31 0 0 0 32 0 0 0 33 0 0 0 34 0 0 0 35 0 0 0 36 0 0 0 37 0 0 0 38 0 0 0 39 0 0 0 40 0 0 0 41 0 0 0 42 0 0 0 43 0 0 0 44 0 0 0 45 0 0 0 46 0 0 0 47 0 0 0 48 0 0 0 49 0 0 0 50 0 0 0 51 0 0 0 52 0 0 0 53 0 0 0 54 0 0 0 55 0 0 0 56 0 0 0 57 0 0 0 58 0 0 0 59 0 0 0 60 0 0 0 61 0 0 0 62 0 0 0 63 0 0 0 64 0 0 0 65 0 0 0 66 0 0 0 67 0 0 0 68 0 0 0 69 0 0 0 70 0 0 0 71 0 0 0 72 0 0 0 73 0 0 0 74 0 0 0 75 1 0 1 76 0 0 0 77 0 0 0 78 0 0 0 79 0 0 0 80 0 0 0 81 0 0 0 82 0 0 0 83 0 0 0 84 0 0 0 85 0 0 0 86 0 0 0 87 0 0 0 88 0 0 0 89 0 0 0 90 0 0 0 91 1 0 1 92 1 0 1 your_output.sample_2.truncated000066400000000000000000000010751350370616400367060ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/se/threads/two@read_s2_200/1 GCGTAAGTTGACGTCAGCCTGCGAGGTGCCACGCCAGTGGTTGCGCTCACCCGGGGCGTAGTTGCTCCGCGCAATTTCTTGGCAGTTCGAT + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::998876654321 @read_s2_075/1 TCTTGGGAACGAGAGTGCCACCAATTAAAGTGATGGATATCGAGACGTCCCAAACCACCGCAATAGGACGGGACA + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; @read_s2_150/1 AGCCCCGAGTGTCCATCACAAGCCACCTCCACTAACCATCTCGGTCCATTATTTGTCACTCGTGGCTAGAAGGGAATAAAGACAACTCTCTC + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 your_output.settings000066400000000000000000000021551350370616400350540ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/se/threads/twoAdapterRemoval ver. 2.1.7 Trimming of double-indexed single-end reads [Demultiplexing] Maximum mismatches (total): 0 [Demultiplexing samples] Name Barcode_1 Barcode_2 sample_1 CTTGCCCT ACGTTATT sample_2 CGCCGATG TGCACGGG [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: NA Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 Minimum adapter overlap: 0 [Demultiplexing statistics] Name Barcode_1 Barcode_2 Hits Fraction unidentified NA NA 0 0.000 ambiguous NA NA 0 0.000 sample_1 CTTGCCCT ACGTTATT 4 0.500 sample_2 CGCCGATG TGCACGGG 4 0.500 * * * 8 1.000 your_output.unidentified000066400000000000000000000000001350370616400356460ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/double_indexed/se/threads/twoadapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/000077500000000000000000000000001350370616400260655ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/000077500000000000000000000000001350370616400264715ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/collapse/000077500000000000000000000000001350370616400302735ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/collapse/barcodes.txt000066400000000000000000000000461350370616400326160ustar00rootroot00000000000000sample_1 CAAGCACG sample_2 ATTTTGAG adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/collapse/info.json000066400000000000000000000001051350370616400321150ustar00rootroot00000000000000{ "arguments": ["--collapse"], "return_code": 0, "stderr": [ ] } adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/collapse/input_1.fastq000066400000000000000000000033301350370616400327110ustar00rootroot00000000000000@read_s2_200/1 ATTTTGAGCTCAATAAGCTGTGCTAGAAGGAAGAGTCTAAGGCGACGACGACATTTGGCGTCGCCTCGCCGAGGCTAGTGATCTAGCTGGCAGTACCCCT + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_000/1 ATTTTGAGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAAAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_150/1 ATTTTGAGGATCTAACTGGATCGAGATAGGGCTGAGTGTGGCCGACGTTTTTGCCGCCCCTAAATAGTAGACAGTGACATCGTGAGGACCGCAGACTTAG + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_200/1 CAAGCACGAAGCGAGTCTCGGTTGCGTGTCTTAAAGACAAAGGGACTCCATACTGGCCGGAAGTCCGATATCGCTTAGTAACTCACTCTCGCAGTATTTA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_075/1 ATTTTGAGCTTGAAAAGACTTCCTCTTGGTCATTTTAGGGCATGCGTGACGGAATCTAATCGTGGTTCCCTGACACAACCCTTAGATCGGAAGAGCACAC + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_000/1 CAAGCACGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAAAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_150/1 CAAGCACGTCAATCCAAGGGATAAGCATGCGCCCATATAGTGGTAGCACAGCAATCTTCCGTCAATGCAGTGGGGCGCTCGGATCGCGGCTGTGCATGAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_075/1 CAAGCACGTCGTAGTCTCGGTGGGCAATTCCTACATGGTACCCGGCACGACAAAGTAGACAGCCCATGCCTAGCTCCCAACCGAGATCGGAAGAGCACAC + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/collapse/input_2.fastq000066400000000000000000000033301350370616400327120ustar00rootroot00000000000000@read_s2_200/2 ACCTAATGCAAGTTCCTTGTGATGTTAGAATATCCTAAGTCTATGGAATTCTTTTGCTTGGGAATTGTTGGCCTAAGTAGGTGGGTCGCCTTAGCGTGAT + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_000/2 CTCAAAATAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_150/2 ACTATGGTTGTCTGAATCACAAATGGCTAAACGGCTTCATAATAGTGTGGTATGCGTACTAAGTCTGCGGTCCTCACGATGTCACTGTCTACTATTTAGG + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_200/2 ATTTCACTGCCGGTTTGCTGTTCGGAATTTCTGTGAATTCGTGATTGCCATTGGGGAGGTTAAGGCAAACTATGAGATTGTTCCGGGTCAAGTAACTGGG + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_075/2 AAGGGTTGTGTCAGGGAACCACGATTAGATTCCGTCACGCATGCCCTAAAATGACCAAGAGGAAGTCTTTTCAAGCTCAAAATAGATCGGAAGAGCGTCG + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_000/2 CGTGCTTGAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_150/2 TCGCGCGAACGGCGCTGGGCCCCATGCGAAAAAGCGATACCATGAAGCGAGTATAATGTTCATGCACAGCCGCGATCCGAGCGCCCCACTGCATTGACGG + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_075/2 CGGTTGGGAGCTAGGCATGGGCTGTCTACTTTGTCGTGCCGGGTACCATGTAGGAATTGCCCACCGAGACTACGACGTGCTTGAGATCGGAAGAGCGTCG + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 your_output.sample_1.collapsed000066400000000000000000000007501350370616400362240ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/collapse@M_read_s1_150 TCAATCCAAGGGATAAGCATGCGCCCATATAGTGGTAGCACAGCAATCTTCCGTCAATGCAGTGGGGCGCTCGGATCGCGGCTGTGCATGAACATTATACTCGCTTCATGGTATCGCTTTTTCGCATGGGGCCCAGCGCCGTTCGCGCGA + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJABBBBBBCCCCCCCDDDDDDDEEEEEEEEEFFFFFFFFFGGGGGGGGGGGHHHHHHHH @M_read_s1_075 TCGTAGTCTCGGTGGGCAATTCCTACATGGTACCCGGCACGACAAAGTAGACAGCCCATGCCTAGCTCCCAACCG + JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ your_output.sample_1.collapsed.truncated000066400000000000000000000000001350370616400402000ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/collapseyour_output.sample_1.discarded000066400000000000000000000000231350370616400361710ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/collapse@M_read_s1_000 + your_output.sample_1.pair1.truncated000066400000000000000000000003131350370616400372550ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/collapse@read_s1_200/1 AAGCGAGTCTCGGTTGCGTGTCTTAAAGACAAAGGGACTCCATACTGGCCGGAAGTCCGATATCGCTTAGTAACTCACTCTCGCAGTATTTA + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 your_output.sample_1.pair2.truncated000066400000000000000000000003331350370616400372600ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/collapse@read_s1_200/2 ATTTCACTGCCGGTTTGCTGTTCGGAATTTCTGTGAATTCGTGATTGCCATTGGGGAGGTTAAGGCAAACTATGAGATTGTTCCGGGTCAAGTAACTGGG + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 your_output.sample_1.settings000066400000000000000000000100771350370616400361210ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/collapseAdapterRemoval ver. 2.2.0 Trimming of single-indexed paired-end reads [Demultiplexing] Maximum mismatches (total): 0 Maximum mate 1 mismatches: 0 Maximum mate 2 mismatches: 0 [Demultiplexing samples] Name Barcode_1 Barcode_2 sample_1* CAAGCACG * sample_2 ATTTTGAG * [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: CGTGCTTG_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 2769367494 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: Yes Minimum overlap (in case of collapse): 11 [Trimming statistics] Total number of read pairs: 4 Number of unaligned read pairs: 1 Number of well aligned read pairs: 3 Number of discarded mate 1 reads: 1 Number of singleton mate 1 reads: 0 Number of discarded mate 2 reads: 1 Number of singleton mate 2 reads: 0 Number of reads with adapters[1]: 4 Number of full-length collapsed pairs: 2 Number of truncated collapsed pairs: 0 Number of retained reads: 4 Number of retained nucleotides: 417 Average length of retained reads: 104.25 [Length distribution] Length Mate1 Mate2 Singleton Collapsed CollapsedTruncated Discarded All 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 3 0 0 0 0 0 0 0 4 0 0 0 0 0 0 0 5 0 0 0 0 0 0 0 6 0 0 0 0 0 0 0 7 0 0 0 0 0 0 0 8 0 0 0 0 0 0 0 9 0 0 0 0 0 0 0 10 0 0 0 0 0 0 0 11 0 0 0 0 0 0 0 12 0 0 0 0 0 0 0 13 0 0 0 0 0 0 0 14 0 0 0 0 0 0 0 15 0 0 0 0 0 0 0 16 0 0 0 0 0 0 0 17 0 0 0 0 0 0 0 18 0 0 0 0 0 0 0 19 0 0 0 0 0 0 0 20 0 0 0 0 0 0 0 21 0 0 0 0 0 0 0 22 0 0 0 0 0 0 0 23 0 0 0 0 0 0 0 24 0 0 0 0 0 0 0 25 0 0 0 0 0 0 0 26 0 0 0 0 0 0 0 27 0 0 0 0 0 0 0 28 0 0 0 0 0 0 0 29 0 0 0 0 0 0 0 30 0 0 0 0 0 0 0 31 0 0 0 0 0 0 0 32 0 0 0 0 0 0 0 33 0 0 0 0 0 0 0 34 0 0 0 0 0 0 0 35 0 0 0 0 0 0 0 36 0 0 0 0 0 0 0 37 0 0 0 0 0 0 0 38 0 0 0 0 0 0 0 39 0 0 0 0 0 0 0 40 0 0 0 0 0 0 0 41 0 0 0 0 0 0 0 42 0 0 0 0 0 0 0 43 0 0 0 0 0 0 0 44 0 0 0 0 0 0 0 45 0 0 0 0 0 0 0 46 0 0 0 0 0 0 0 47 0 0 0 0 0 0 0 48 0 0 0 0 0 0 0 49 0 0 0 0 0 0 0 50 0 0 0 0 0 0 0 51 0 0 0 0 0 0 0 52 0 0 0 0 0 0 0 53 0 0 0 0 0 0 0 54 0 0 0 0 0 0 0 55 0 0 0 0 0 0 0 56 0 0 0 0 0 0 0 57 0 0 0 0 0 0 0 58 0 0 0 0 0 0 0 59 0 0 0 0 0 0 0 60 0 0 0 0 0 0 0 61 0 0 0 0 0 0 0 62 0 0 0 0 0 0 0 63 0 0 0 0 0 0 0 64 0 0 0 0 0 0 0 65 0 0 0 0 0 0 0 66 0 0 0 0 0 0 0 67 0 0 0 0 0 0 0 68 0 0 0 0 0 0 0 69 0 0 0 0 0 0 0 70 0 0 0 0 0 0 0 71 0 0 0 0 0 0 0 72 0 0 0 0 0 0 0 73 0 0 0 0 0 0 0 74 0 0 0 0 0 0 0 75 0 0 0 1 0 0 1 76 0 0 0 0 0 0 0 77 0 0 0 0 0 0 0 78 0 0 0 0 0 0 0 79 0 0 0 0 0 0 0 80 0 0 0 0 0 0 0 81 0 0 0 0 0 0 0 82 0 0 0 0 0 0 0 83 0 0 0 0 0 0 0 84 0 0 0 0 0 0 0 85 0 0 0 0 0 0 0 86 0 0 0 0 0 0 0 87 0 0 0 0 0 0 0 88 0 0 0 0 0 0 0 89 0 0 0 0 0 0 0 90 0 0 0 0 0 0 0 91 0 0 0 0 0 0 0 92 1 0 0 0 0 0 1 93 0 0 0 0 0 0 0 94 0 0 0 0 0 0 0 95 0 0 0 0 0 0 0 96 0 0 0 0 0 0 0 97 0 0 0 0 0 0 0 98 0 0 0 0 0 0 0 99 0 0 0 0 0 0 0 100 0 1 0 0 0 0 1 101 0 0 0 0 0 0 0 102 0 0 0 0 0 0 0 103 0 0 0 0 0 0 0 104 0 0 0 0 0 0 0 105 0 0 0 0 0 0 0 106 0 0 0 0 0 0 0 107 0 0 0 0 0 0 0 108 0 0 0 0 0 0 0 109 0 0 0 0 0 0 0 110 0 0 0 0 0 0 0 111 0 0 0 0 0 0 0 112 0 0 0 0 0 0 0 113 0 0 0 0 0 0 0 114 0 0 0 0 0 0 0 115 0 0 0 0 0 0 0 116 0 0 0 0 0 0 0 117 0 0 0 0 0 0 0 118 0 0 0 0 0 0 0 119 0 0 0 0 0 0 0 120 0 0 0 0 0 0 0 121 0 0 0 0 0 0 0 122 0 0 0 0 0 0 0 123 0 0 0 0 0 0 0 124 0 0 0 0 0 0 0 125 0 0 0 0 0 0 0 126 0 0 0 0 0 0 0 127 0 0 0 0 0 0 0 128 0 0 0 0 0 0 0 129 0 0 0 0 0 0 0 130 0 0 0 0 0 0 0 131 0 0 0 0 0 0 0 132 0 0 0 0 0 0 0 133 0 0 0 0 0 0 0 134 0 0 0 0 0 0 0 135 0 0 0 0 0 0 0 136 0 0 0 0 0 0 0 137 0 0 0 0 0 0 0 138 0 0 0 0 0 0 0 139 0 0 0 0 0 0 0 140 0 0 0 0 0 0 0 141 0 0 0 0 0 0 0 142 0 0 0 0 0 0 0 143 0 0 0 0 0 0 0 144 0 0 0 0 0 0 0 145 0 0 0 0 0 0 0 146 0 0 0 0 0 0 0 147 0 0 0 0 0 0 0 148 0 0 0 0 0 0 0 149 0 0 0 0 0 0 0 150 0 0 0 1 0 0 1 your_output.sample_1.singleton.truncated000066400000000000000000000000001350370616400402340ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/collapseyour_output.sample_2.collapsed000066400000000000000000000007501350370616400362250ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/collapse@M_read_s2_150 GATCTAACTGGATCGAGATAGGGCTGAGTGTGGCCGACGTTTTTGCCGCCCCTAAATAGTAGACAGTGACATCGTGAGGACCGCAGACTTAGTACGCATACCACACTATTATGAAGCCGTTTAGCCATTTGTGATTCAGACAACCATAGT + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJABBBBBBCCCCCCCDDDDDDDEEEEEEEEEFFFFFFFFFGGGGGGGGGGGHHHHHHHH @M_read_s2_075 CTTGAAAAGACTTCCTCTTGGTCATTTTAGGGCATGCGTGACGGAATCTAATCGTGGTTCCCTGACACAACCCTT + JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ your_output.sample_2.collapsed.truncated000066400000000000000000000000001350370616400402010ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/collapseyour_output.sample_2.discarded000066400000000000000000000000231350370616400361720ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/collapse@M_read_s2_000 + your_output.sample_2.pair1.truncated000066400000000000000000000003131350370616400372560ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/collapse@read_s2_200/1 CTCAATAAGCTGTGCTAGAAGGAAGAGTCTAAGGCGACGACGACATTTGGCGTCGCCTCGCCGAGGCTAGTGATCTAGCTGGCAGTACCCCT + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 your_output.sample_2.pair2.truncated000066400000000000000000000003331350370616400372610ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/collapse@read_s2_200/2 ACCTAATGCAAGTTCCTTGTGATGTTAGAATATCCTAAGTCTATGGAATTCTTTTGCTTGGGAATTGTTGGCCTAAGTAGGTGGGTCGCCTTAGCGTGAT + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 your_output.sample_2.settings000066400000000000000000000100771350370616400361220ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/collapseAdapterRemoval ver. 2.2.0 Trimming of single-indexed paired-end reads [Demultiplexing] Maximum mismatches (total): 0 Maximum mate 1 mismatches: 0 Maximum mate 2 mismatches: 0 [Demultiplexing samples] Name Barcode_1 Barcode_2 sample_1 CAAGCACG * sample_2* ATTTTGAG * [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: CTCAAAAT_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 2769367494 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: Yes Minimum overlap (in case of collapse): 11 [Trimming statistics] Total number of read pairs: 4 Number of unaligned read pairs: 1 Number of well aligned read pairs: 3 Number of discarded mate 1 reads: 1 Number of singleton mate 1 reads: 0 Number of discarded mate 2 reads: 1 Number of singleton mate 2 reads: 0 Number of reads with adapters[1]: 4 Number of full-length collapsed pairs: 2 Number of truncated collapsed pairs: 0 Number of retained reads: 4 Number of retained nucleotides: 417 Average length of retained reads: 104.25 [Length distribution] Length Mate1 Mate2 Singleton Collapsed CollapsedTruncated Discarded All 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 3 0 0 0 0 0 0 0 4 0 0 0 0 0 0 0 5 0 0 0 0 0 0 0 6 0 0 0 0 0 0 0 7 0 0 0 0 0 0 0 8 0 0 0 0 0 0 0 9 0 0 0 0 0 0 0 10 0 0 0 0 0 0 0 11 0 0 0 0 0 0 0 12 0 0 0 0 0 0 0 13 0 0 0 0 0 0 0 14 0 0 0 0 0 0 0 15 0 0 0 0 0 0 0 16 0 0 0 0 0 0 0 17 0 0 0 0 0 0 0 18 0 0 0 0 0 0 0 19 0 0 0 0 0 0 0 20 0 0 0 0 0 0 0 21 0 0 0 0 0 0 0 22 0 0 0 0 0 0 0 23 0 0 0 0 0 0 0 24 0 0 0 0 0 0 0 25 0 0 0 0 0 0 0 26 0 0 0 0 0 0 0 27 0 0 0 0 0 0 0 28 0 0 0 0 0 0 0 29 0 0 0 0 0 0 0 30 0 0 0 0 0 0 0 31 0 0 0 0 0 0 0 32 0 0 0 0 0 0 0 33 0 0 0 0 0 0 0 34 0 0 0 0 0 0 0 35 0 0 0 0 0 0 0 36 0 0 0 0 0 0 0 37 0 0 0 0 0 0 0 38 0 0 0 0 0 0 0 39 0 0 0 0 0 0 0 40 0 0 0 0 0 0 0 41 0 0 0 0 0 0 0 42 0 0 0 0 0 0 0 43 0 0 0 0 0 0 0 44 0 0 0 0 0 0 0 45 0 0 0 0 0 0 0 46 0 0 0 0 0 0 0 47 0 0 0 0 0 0 0 48 0 0 0 0 0 0 0 49 0 0 0 0 0 0 0 50 0 0 0 0 0 0 0 51 0 0 0 0 0 0 0 52 0 0 0 0 0 0 0 53 0 0 0 0 0 0 0 54 0 0 0 0 0 0 0 55 0 0 0 0 0 0 0 56 0 0 0 0 0 0 0 57 0 0 0 0 0 0 0 58 0 0 0 0 0 0 0 59 0 0 0 0 0 0 0 60 0 0 0 0 0 0 0 61 0 0 0 0 0 0 0 62 0 0 0 0 0 0 0 63 0 0 0 0 0 0 0 64 0 0 0 0 0 0 0 65 0 0 0 0 0 0 0 66 0 0 0 0 0 0 0 67 0 0 0 0 0 0 0 68 0 0 0 0 0 0 0 69 0 0 0 0 0 0 0 70 0 0 0 0 0 0 0 71 0 0 0 0 0 0 0 72 0 0 0 0 0 0 0 73 0 0 0 0 0 0 0 74 0 0 0 0 0 0 0 75 0 0 0 1 0 0 1 76 0 0 0 0 0 0 0 77 0 0 0 0 0 0 0 78 0 0 0 0 0 0 0 79 0 0 0 0 0 0 0 80 0 0 0 0 0 0 0 81 0 0 0 0 0 0 0 82 0 0 0 0 0 0 0 83 0 0 0 0 0 0 0 84 0 0 0 0 0 0 0 85 0 0 0 0 0 0 0 86 0 0 0 0 0 0 0 87 0 0 0 0 0 0 0 88 0 0 0 0 0 0 0 89 0 0 0 0 0 0 0 90 0 0 0 0 0 0 0 91 0 0 0 0 0 0 0 92 1 0 0 0 0 0 1 93 0 0 0 0 0 0 0 94 0 0 0 0 0 0 0 95 0 0 0 0 0 0 0 96 0 0 0 0 0 0 0 97 0 0 0 0 0 0 0 98 0 0 0 0 0 0 0 99 0 0 0 0 0 0 0 100 0 1 0 0 0 0 1 101 0 0 0 0 0 0 0 102 0 0 0 0 0 0 0 103 0 0 0 0 0 0 0 104 0 0 0 0 0 0 0 105 0 0 0 0 0 0 0 106 0 0 0 0 0 0 0 107 0 0 0 0 0 0 0 108 0 0 0 0 0 0 0 109 0 0 0 0 0 0 0 110 0 0 0 0 0 0 0 111 0 0 0 0 0 0 0 112 0 0 0 0 0 0 0 113 0 0 0 0 0 0 0 114 0 0 0 0 0 0 0 115 0 0 0 0 0 0 0 116 0 0 0 0 0 0 0 117 0 0 0 0 0 0 0 118 0 0 0 0 0 0 0 119 0 0 0 0 0 0 0 120 0 0 0 0 0 0 0 121 0 0 0 0 0 0 0 122 0 0 0 0 0 0 0 123 0 0 0 0 0 0 0 124 0 0 0 0 0 0 0 125 0 0 0 0 0 0 0 126 0 0 0 0 0 0 0 127 0 0 0 0 0 0 0 128 0 0 0 0 0 0 0 129 0 0 0 0 0 0 0 130 0 0 0 0 0 0 0 131 0 0 0 0 0 0 0 132 0 0 0 0 0 0 0 133 0 0 0 0 0 0 0 134 0 0 0 0 0 0 0 135 0 0 0 0 0 0 0 136 0 0 0 0 0 0 0 137 0 0 0 0 0 0 0 138 0 0 0 0 0 0 0 139 0 0 0 0 0 0 0 140 0 0 0 0 0 0 0 141 0 0 0 0 0 0 0 142 0 0 0 0 0 0 0 143 0 0 0 0 0 0 0 144 0 0 0 0 0 0 0 145 0 0 0 0 0 0 0 146 0 0 0 0 0 0 0 147 0 0 0 0 0 0 0 148 0 0 0 0 0 0 0 149 0 0 0 0 0 0 0 150 0 0 0 1 0 0 1 your_output.sample_2.singleton.truncated000066400000000000000000000000001350370616400402350ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/collapseadapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/collapse/your_output.settings000066400000000000000000000021711350370616400344740ustar00rootroot00000000000000AdapterRemoval ver. 2.1.7 Trimming of single-indexed paired-end reads [Demultiplexing] Maximum mismatches (total): 0 Maximum mate 1 mismatches: 0 Maximum mate 2 mismatches: 0 [Demultiplexing samples] Name Barcode_1 Barcode_2 sample_1 CAAGCACG * sample_2 ATTTTGAG * [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 1157297082 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: Yes Minimum overlap (in case of collapse): 11 [Demultiplexing statistics] Name Barcode_1 Barcode_2 Hits Fraction unidentified NA NA 0 0.000 ambiguous NA NA 0 0.000 sample_1 CAAGCACG * 4 0.500 sample_2 ATTTTGAG * 4 0.500 * * * 8 1.000 your_output.unidentified_1000066400000000000000000000000001350370616400354310ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/collapseyour_output.unidentified_2000066400000000000000000000000001350370616400354320ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/collapseadapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/combined_output/000077500000000000000000000000001350370616400316715ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/combined_output/barcodes.txt000066400000000000000000000000461350370616400342140ustar00rootroot00000000000000sample_1 GCGCCGGA sample_2 CAGGACAT adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/combined_output/info.json000066400000000000000000000001141350370616400335130ustar00rootroot00000000000000{ "arguments": ["--combined-output"], "return_code": 0, "stderr": [ ] } adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/combined_output/input_1.fastq000066400000000000000000000033301350370616400343070ustar00rootroot00000000000000@read_s1_000/1 GCGCCGGAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAAAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_000/1 CAGGACATAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAAAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_075/1 GCGCCGGAGACGGTCCCATTAATGCACTATCGGATTTACACATTTGCGTGAATAAATCGACAGATGAATCATTAAGCTCCTACAGATCGGAAGAGCACAC + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_150/1 CAGGACATTGATCTCATACATTTAAACAAAGTATGCCTTACGCATGCCTTAATGATACGTAACCTAGGCAACAGAGTCTTTACTTGTACCTGCTACACAC + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_200/1 GCGCCGGATCCATCAGGATCGTATTATACTAAGCTAGGACTGTGCAGTGCACAGAGAGGAGATGACCATGATCCTCGAGCAAGTTGCCGCAGGCTCGGGC + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_150/1 GCGCCGGATGCACCGTAGCCATATGGGCTGTTGGGGACACAGGGCGTCGGCATTCCTTTATTACTGACGCCGCTAGAGTCTATGCAAGGTTATAACGTAT + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_075/1 CAGGACATTCGCTAGCCCAAGATCACGCTTTCCGCGACGTTTTAGAGCGTGCATACCGGGGCGTTTCTCAGATAGGTATTTCAAGATCGGAAGAGCACAC + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_200/1 CAGGACATACCCTCACGCTTGCACGACGACAGCGGTCCCCTATAAATGTATGTTGACGCAGCGAGAGGCCAGGACCCGGGCGTGTTACCACTAAGACCCT + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/combined_output/input_2.fastq000066400000000000000000000033301350370616400343100ustar00rootroot00000000000000@read_s1_000/2 TCCGGCGCAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_000/2 ATGTCCTGAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_075/2 GTAGGAGCTTAATGATTCATCTGTCGATTTATTCACGCAAATGTGTAAATCCGATAGTGCATTAATGGGACCGTCTCCGGCGCAGATCGGAAGAGCGTCG + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_150/2 AGAACAGGATACAATGAAAATGCATCGCGTTGGCAACTCTCACCTTGCTCTTGGACCCGTGTGTAGCAGGTACAAGTAAAGACTCTGTTGCCTAGGTTAC + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_200/2 CCTTCTTATGCTCGACTGGCTCTGTATAAGCCCAAGACATTATGAAAGGTCTCGCGTTTGTCTACCAGGCTCCGTTACGGATACAAGTGCCCTACTGTCA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_150/2 ATCAAGGGAGGTCACGTGAATTTTGCCTTCTAGACTAGCGTACATGACCGCGAATTAGATACGTTATAACCTTGCATAGACTCTAGCGGCGTCAGTAATA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_075/2 TGAAATACCTATCTGAGAAACGCCCCGGTATGCACGCTCTAAAACGTCGCGGAAAGCGTGATCTTGGGCTAGCGAATGTCCTGAGATCGGAAGAGCGTCG + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_200/2 ATGCTGATTAGATATGTCTTTCATCGGCTTGTGACCGAGGAGTGGTACGGCCGTTCCATATTGGGTGATTAGGAAGATGTCCCGGCTTGCTGCTTCTCGT + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 your_output.sample_1.pair1.truncated000066400000000000000000000011241350370616400406540ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/combined_output@read_s1_000/1 N + ! @read_s1_075/1 GACGGTCCCATTAATGCACTATCGGATTTACACATTTGCGTGAATAAATCGACAGATGAATCATTAAGCTCCTAC + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; @read_s1_200/1 TCCATCAGGATCGTATTATACTAAGCTAGGACTGTGCAGTGCACAGAGAGGAGATGACCATGATCCTCGAGCAAGTTGCCGCAGGCTCGGGC + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_150/1 TGCACCGTAGCCATATGGGCTGTTGGGGACACAGGGCGTCGGCATTCCTTTATTACTGACGCCGCTAGAGTCTATGCAAGGTTATAACGTAT + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 your_output.sample_1.pair2.truncated000066400000000000000000000011641350370616400406610ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/combined_output@read_s1_000/2 N + ! @read_s1_075/2 GTAGGAGCTTAATGATTCATCTGTCGATTTATTCACGCAAATGTGTAAATCCGATAGTGCATTAATGGGACCGTC + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>> @read_s1_200/2 CCTTCTTATGCTCGACTGGCTCTGTATAAGCCCAAGACATTATGAAAGGTCTCGCGTTTGTCTACCAGGCTCCGTTACGGATACAAGTGCCCTACTGTCA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_150/2 ATCAAGGGAGGTCACGTGAATTTTGCCTTCTAGACTAGCGTACATGACCGCGAATTAGATACGTTATAACCTTGCATAGACTCTAGCGGCGTCAGTAATA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 your_output.sample_1.settings000066400000000000000000000052651350370616400375220ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/combined_outputAdapterRemoval ver. 2.2.0 Trimming of single-indexed paired-end reads [Demultiplexing] Maximum mismatches (total): 0 Maximum mate 1 mismatches: 0 Maximum mate 2 mismatches: 0 [Demultiplexing samples] Name Barcode_1 Barcode_2 sample_1* GCGCCGGA * sample_2 CAGGACAT * [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: TCCGGCGC_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 2459456692 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 [Trimming statistics] Total number of read pairs: 4 Number of unaligned read pairs: 1 Number of well aligned read pairs: 3 Number of discarded mate 1 reads: 1 Number of singleton mate 1 reads: 0 Number of discarded mate 2 reads: 1 Number of singleton mate 2 reads: 0 Number of reads with adapters[1]: 4 Number of retained reads: 6 Number of retained nucleotides: 534 Average length of retained reads: 89 [Length distribution] Length Mate1 Mate2 Singleton Discarded All 0 0 0 0 2 2 1 0 0 0 0 0 2 0 0 0 0 0 3 0 0 0 0 0 4 0 0 0 0 0 5 0 0 0 0 0 6 0 0 0 0 0 7 0 0 0 0 0 8 0 0 0 0 0 9 0 0 0 0 0 10 0 0 0 0 0 11 0 0 0 0 0 12 0 0 0 0 0 13 0 0 0 0 0 14 0 0 0 0 0 15 0 0 0 0 0 16 0 0 0 0 0 17 0 0 0 0 0 18 0 0 0 0 0 19 0 0 0 0 0 20 0 0 0 0 0 21 0 0 0 0 0 22 0 0 0 0 0 23 0 0 0 0 0 24 0 0 0 0 0 25 0 0 0 0 0 26 0 0 0 0 0 27 0 0 0 0 0 28 0 0 0 0 0 29 0 0 0 0 0 30 0 0 0 0 0 31 0 0 0 0 0 32 0 0 0 0 0 33 0 0 0 0 0 34 0 0 0 0 0 35 0 0 0 0 0 36 0 0 0 0 0 37 0 0 0 0 0 38 0 0 0 0 0 39 0 0 0 0 0 40 0 0 0 0 0 41 0 0 0 0 0 42 0 0 0 0 0 43 0 0 0 0 0 44 0 0 0 0 0 45 0 0 0 0 0 46 0 0 0 0 0 47 0 0 0 0 0 48 0 0 0 0 0 49 0 0 0 0 0 50 0 0 0 0 0 51 0 0 0 0 0 52 0 0 0 0 0 53 0 0 0 0 0 54 0 0 0 0 0 55 0 0 0 0 0 56 0 0 0 0 0 57 0 0 0 0 0 58 0 0 0 0 0 59 0 0 0 0 0 60 0 0 0 0 0 61 0 0 0 0 0 62 0 0 0 0 0 63 0 0 0 0 0 64 0 0 0 0 0 65 0 0 0 0 0 66 0 0 0 0 0 67 0 0 0 0 0 68 0 0 0 0 0 69 0 0 0 0 0 70 0 0 0 0 0 71 0 0 0 0 0 72 0 0 0 0 0 73 0 0 0 0 0 74 0 0 0 0 0 75 1 1 0 0 2 76 0 0 0 0 0 77 0 0 0 0 0 78 0 0 0 0 0 79 0 0 0 0 0 80 0 0 0 0 0 81 0 0 0 0 0 82 0 0 0 0 0 83 0 0 0 0 0 84 0 0 0 0 0 85 0 0 0 0 0 86 0 0 0 0 0 87 0 0 0 0 0 88 0 0 0 0 0 89 0 0 0 0 0 90 0 0 0 0 0 91 0 0 0 0 0 92 2 0 0 0 2 93 0 0 0 0 0 94 0 0 0 0 0 95 0 0 0 0 0 96 0 0 0 0 0 97 0 0 0 0 0 98 0 0 0 0 0 99 0 0 0 0 0 100 0 2 0 0 2 your_output.sample_2.pair1.truncated000066400000000000000000000011241350370616400406550ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/combined_output@read_s2_000/1 N + ! @read_s2_150/1 TGATCTCATACATTTAAACAAAGTATGCCTTACGCATGCCTTAATGATACGTAACCTAGGCAACAGAGTCTTTACTTGTACCTGCTACACAC + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_075/1 TCGCTAGCCCAAGATCACGCTTTCCGCGACGTTTTAGAGCGTGCATACCGGGGCGTTTCTCAGATAGGTATTTCA + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; @read_s2_200/1 ACCCTCACGCTTGCACGACGACAGCGGTCCCCTATAAATGTATGTTGACGCAGCGAGAGGCCAGGACCCGGGCGTGTTACCACTAAGACCCT + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 your_output.sample_2.pair2.truncated000066400000000000000000000011641350370616400406620ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/combined_output@read_s2_000/2 N + ! @read_s2_150/2 AGAACAGGATACAATGAAAATGCATCGCGTTGGCAACTCTCACCTTGCTCTTGGACCCGTGTGTAGCAGGTACAAGTAAAGACTCTGTTGCCTAGGTTAC + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_075/2 TGAAATACCTATCTGAGAAACGCCCCGGTATGCACGCTCTAAAACGTCGCGGAAAGCGTGATCTTGGGCTAGCGA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>> @read_s2_200/2 ATGCTGATTAGATATGTCTTTCATCGGCTTGTGACCGAGGAGTGGTACGGCCGTTCCATATTGGGTGATTAGGAAGATGTCCCGGCTTGCTGCTTCTCGT + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 your_output.sample_2.settings000066400000000000000000000052651350370616400375230ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/combined_outputAdapterRemoval ver. 2.2.0 Trimming of single-indexed paired-end reads [Demultiplexing] Maximum mismatches (total): 0 Maximum mate 1 mismatches: 0 Maximum mate 2 mismatches: 0 [Demultiplexing samples] Name Barcode_1 Barcode_2 sample_1 GCGCCGGA * sample_2* CAGGACAT * [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: ATGTCCTG_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 2459456692 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 [Trimming statistics] Total number of read pairs: 4 Number of unaligned read pairs: 1 Number of well aligned read pairs: 3 Number of discarded mate 1 reads: 1 Number of singleton mate 1 reads: 0 Number of discarded mate 2 reads: 1 Number of singleton mate 2 reads: 0 Number of reads with adapters[1]: 4 Number of retained reads: 6 Number of retained nucleotides: 534 Average length of retained reads: 89 [Length distribution] Length Mate1 Mate2 Singleton Discarded All 0 0 0 0 2 2 1 0 0 0 0 0 2 0 0 0 0 0 3 0 0 0 0 0 4 0 0 0 0 0 5 0 0 0 0 0 6 0 0 0 0 0 7 0 0 0 0 0 8 0 0 0 0 0 9 0 0 0 0 0 10 0 0 0 0 0 11 0 0 0 0 0 12 0 0 0 0 0 13 0 0 0 0 0 14 0 0 0 0 0 15 0 0 0 0 0 16 0 0 0 0 0 17 0 0 0 0 0 18 0 0 0 0 0 19 0 0 0 0 0 20 0 0 0 0 0 21 0 0 0 0 0 22 0 0 0 0 0 23 0 0 0 0 0 24 0 0 0 0 0 25 0 0 0 0 0 26 0 0 0 0 0 27 0 0 0 0 0 28 0 0 0 0 0 29 0 0 0 0 0 30 0 0 0 0 0 31 0 0 0 0 0 32 0 0 0 0 0 33 0 0 0 0 0 34 0 0 0 0 0 35 0 0 0 0 0 36 0 0 0 0 0 37 0 0 0 0 0 38 0 0 0 0 0 39 0 0 0 0 0 40 0 0 0 0 0 41 0 0 0 0 0 42 0 0 0 0 0 43 0 0 0 0 0 44 0 0 0 0 0 45 0 0 0 0 0 46 0 0 0 0 0 47 0 0 0 0 0 48 0 0 0 0 0 49 0 0 0 0 0 50 0 0 0 0 0 51 0 0 0 0 0 52 0 0 0 0 0 53 0 0 0 0 0 54 0 0 0 0 0 55 0 0 0 0 0 56 0 0 0 0 0 57 0 0 0 0 0 58 0 0 0 0 0 59 0 0 0 0 0 60 0 0 0 0 0 61 0 0 0 0 0 62 0 0 0 0 0 63 0 0 0 0 0 64 0 0 0 0 0 65 0 0 0 0 0 66 0 0 0 0 0 67 0 0 0 0 0 68 0 0 0 0 0 69 0 0 0 0 0 70 0 0 0 0 0 71 0 0 0 0 0 72 0 0 0 0 0 73 0 0 0 0 0 74 0 0 0 0 0 75 1 1 0 0 2 76 0 0 0 0 0 77 0 0 0 0 0 78 0 0 0 0 0 79 0 0 0 0 0 80 0 0 0 0 0 81 0 0 0 0 0 82 0 0 0 0 0 83 0 0 0 0 0 84 0 0 0 0 0 85 0 0 0 0 0 86 0 0 0 0 0 87 0 0 0 0 0 88 0 0 0 0 0 89 0 0 0 0 0 90 0 0 0 0 0 91 0 0 0 0 0 92 2 0 0 0 2 93 0 0 0 0 0 94 0 0 0 0 0 95 0 0 0 0 0 96 0 0 0 0 0 97 0 0 0 0 0 98 0 0 0 0 0 99 0 0 0 0 0 100 0 2 0 0 2 your_output.settings000066400000000000000000000021701350370616400360120ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/combined_outputAdapterRemoval ver. 2.1.7 Trimming of single-indexed paired-end reads [Demultiplexing] Maximum mismatches (total): 0 Maximum mate 1 mismatches: 0 Maximum mate 2 mismatches: 0 [Demultiplexing samples] Name Barcode_1 Barcode_2 sample_1 GCGCCGGA * sample_2 CAGGACAT * [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 1157297082 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 [Demultiplexing statistics] Name Barcode_1 Barcode_2 Hits Fraction unidentified NA NA 0 0.000 ambiguous NA NA 0 0.000 sample_1 GCGCCGGA * 4 0.500 sample_2 CAGGACAT * 4 0.500 * * * 8 1.000 your_output.unidentified_1000066400000000000000000000000001350370616400370270ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/combined_outputyour_output.unidentified_2000066400000000000000000000000001350370616400370300ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/combined_outputadapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/defaults/000077500000000000000000000000001350370616400303005ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/defaults/barcodes.txt000066400000000000000000000000461350370616400326230ustar00rootroot00000000000000sample_1 GCGCCGGA sample_2 CAGGACAT adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/defaults/info.json000066400000000000000000000000711350370616400321240ustar00rootroot00000000000000{ "arguments": [], "return_code": 0, "stderr": [ ] } adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/defaults/input_1.fastq000066400000000000000000000033301350370616400327160ustar00rootroot00000000000000@read_s1_000/1 GCGCCGGAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAAAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_000/1 CAGGACATAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAAAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_075/1 GCGCCGGAGACGGTCCCATTAATGCACTATCGGATTTACACATTTGCGTGAATAAATCGACAGATGAATCATTAAGCTCCTACAGATCGGAAGAGCACAC + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_150/1 CAGGACATTGATCTCATACATTTAAACAAAGTATGCCTTACGCATGCCTTAATGATACGTAACCTAGGCAACAGAGTCTTTACTTGTACCTGCTACACAC + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_200/1 GCGCCGGATCCATCAGGATCGTATTATACTAAGCTAGGACTGTGCAGTGCACAGAGAGGAGATGACCATGATCCTCGAGCAAGTTGCCGCAGGCTCGGGC + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_150/1 GCGCCGGATGCACCGTAGCCATATGGGCTGTTGGGGACACAGGGCGTCGGCATTCCTTTATTACTGACGCCGCTAGAGTCTATGCAAGGTTATAACGTAT + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_075/1 CAGGACATTCGCTAGCCCAAGATCACGCTTTCCGCGACGTTTTAGAGCGTGCATACCGGGGCGTTTCTCAGATAGGTATTTCAAGATCGGAAGAGCACAC + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_200/1 CAGGACATACCCTCACGCTTGCACGACGACAGCGGTCCCCTATAAATGTATGTTGACGCAGCGAGAGGCCAGGACCCGGGCGTGTTACCACTAAGACCCT + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/defaults/input_2.fastq000066400000000000000000000033301350370616400327170ustar00rootroot00000000000000@read_s1_000/2 TCCGGCGCAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_000/2 ATGTCCTGAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_075/2 GTAGGAGCTTAATGATTCATCTGTCGATTTATTCACGCAAATGTGTAAATCCGATAGTGCATTAATGGGACCGTCTCCGGCGCAGATCGGAAGAGCGTCG + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_150/2 AGAACAGGATACAATGAAAATGCATCGCGTTGGCAACTCTCACCTTGCTCTTGGACCCGTGTGTAGCAGGTACAAGTAAAGACTCTGTTGCCTAGGTTAC + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_200/2 CCTTCTTATGCTCGACTGGCTCTGTATAAGCCCAAGACATTATGAAAGGTCTCGCGTTTGTCTACCAGGCTCCGTTACGGATACAAGTGCCCTACTGTCA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_150/2 ATCAAGGGAGGTCACGTGAATTTTGCCTTCTAGACTAGCGTACATGACCGCGAATTAGATACGTTATAACCTTGCATAGACTCTAGCGGCGTCAGTAATA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_075/2 TGAAATACCTATCTGAGAAACGCCCCGGTATGCACGCTCTAAAACGTCGCGGAAAGCGTGATCTTGGGCTAGCGAATGTCCTGAGATCGGAAGAGCGTCG + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_200/2 ATGCTGATTAGATATGTCTTTCATCGGCTTGTGACCGAGGAGTGGTACGGCCGTTCCATATTGGGTGATTAGGAAGATGTCCCGGCTTGCTGCTTCTCGT + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 your_output.sample_1.discarded000066400000000000000000000000461350370616400362030ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/defaults@read_s1_000/1 + @read_s1_000/2 + your_output.sample_1.pair1.truncated000066400000000000000000000010771350370616400372720ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/defaults@read_s1_075/1 GACGGTCCCATTAATGCACTATCGGATTTACACATTTGCGTGAATAAATCGACAGATGAATCATTAAGCTCCTAC + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; @read_s1_200/1 TCCATCAGGATCGTATTATACTAAGCTAGGACTGTGCAGTGCACAGAGAGGAGATGACCATGATCCTCGAGCAAGTTGCCGCAGGCTCGGGC + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_150/1 TGCACCGTAGCCATATGGGCTGTTGGGGACACAGGGCGTCGGCATTCCTTTATTACTGACGCCGCTAGAGTCTATGCAAGGTTATAACGTAT + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 your_output.sample_1.pair2.truncated000066400000000000000000000011371350370616400372700ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/defaults@read_s1_075/2 GTAGGAGCTTAATGATTCATCTGTCGATTTATTCACGCAAATGTGTAAATCCGATAGTGCATTAATGGGACCGTC + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>> @read_s1_200/2 CCTTCTTATGCTCGACTGGCTCTGTATAAGCCCAAGACATTATGAAAGGTCTCGCGTTTGTCTACCAGGCTCCGTTACGGATACAAGTGCCCTACTGTCA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_150/2 ATCAAGGGAGGTCACGTGAATTTTGCCTTCTAGACTAGCGTACATGACCGCGAATTAGATACGTTATAACCTTGCATAGACTCTAGCGGCGTCAGTAATA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 your_output.sample_1.settings000066400000000000000000000052651350370616400361310ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/defaultsAdapterRemoval ver. 2.2.0 Trimming of single-indexed paired-end reads [Demultiplexing] Maximum mismatches (total): 0 Maximum mate 1 mismatches: 0 Maximum mate 2 mismatches: 0 [Demultiplexing samples] Name Barcode_1 Barcode_2 sample_1* GCGCCGGA * sample_2 CAGGACAT * [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: TCCGGCGC_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 2459456692 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 [Trimming statistics] Total number of read pairs: 4 Number of unaligned read pairs: 1 Number of well aligned read pairs: 3 Number of discarded mate 1 reads: 1 Number of singleton mate 1 reads: 0 Number of discarded mate 2 reads: 1 Number of singleton mate 2 reads: 0 Number of reads with adapters[1]: 4 Number of retained reads: 6 Number of retained nucleotides: 534 Average length of retained reads: 89 [Length distribution] Length Mate1 Mate2 Singleton Discarded All 0 0 0 0 2 2 1 0 0 0 0 0 2 0 0 0 0 0 3 0 0 0 0 0 4 0 0 0 0 0 5 0 0 0 0 0 6 0 0 0 0 0 7 0 0 0 0 0 8 0 0 0 0 0 9 0 0 0 0 0 10 0 0 0 0 0 11 0 0 0 0 0 12 0 0 0 0 0 13 0 0 0 0 0 14 0 0 0 0 0 15 0 0 0 0 0 16 0 0 0 0 0 17 0 0 0 0 0 18 0 0 0 0 0 19 0 0 0 0 0 20 0 0 0 0 0 21 0 0 0 0 0 22 0 0 0 0 0 23 0 0 0 0 0 24 0 0 0 0 0 25 0 0 0 0 0 26 0 0 0 0 0 27 0 0 0 0 0 28 0 0 0 0 0 29 0 0 0 0 0 30 0 0 0 0 0 31 0 0 0 0 0 32 0 0 0 0 0 33 0 0 0 0 0 34 0 0 0 0 0 35 0 0 0 0 0 36 0 0 0 0 0 37 0 0 0 0 0 38 0 0 0 0 0 39 0 0 0 0 0 40 0 0 0 0 0 41 0 0 0 0 0 42 0 0 0 0 0 43 0 0 0 0 0 44 0 0 0 0 0 45 0 0 0 0 0 46 0 0 0 0 0 47 0 0 0 0 0 48 0 0 0 0 0 49 0 0 0 0 0 50 0 0 0 0 0 51 0 0 0 0 0 52 0 0 0 0 0 53 0 0 0 0 0 54 0 0 0 0 0 55 0 0 0 0 0 56 0 0 0 0 0 57 0 0 0 0 0 58 0 0 0 0 0 59 0 0 0 0 0 60 0 0 0 0 0 61 0 0 0 0 0 62 0 0 0 0 0 63 0 0 0 0 0 64 0 0 0 0 0 65 0 0 0 0 0 66 0 0 0 0 0 67 0 0 0 0 0 68 0 0 0 0 0 69 0 0 0 0 0 70 0 0 0 0 0 71 0 0 0 0 0 72 0 0 0 0 0 73 0 0 0 0 0 74 0 0 0 0 0 75 1 1 0 0 2 76 0 0 0 0 0 77 0 0 0 0 0 78 0 0 0 0 0 79 0 0 0 0 0 80 0 0 0 0 0 81 0 0 0 0 0 82 0 0 0 0 0 83 0 0 0 0 0 84 0 0 0 0 0 85 0 0 0 0 0 86 0 0 0 0 0 87 0 0 0 0 0 88 0 0 0 0 0 89 0 0 0 0 0 90 0 0 0 0 0 91 0 0 0 0 0 92 2 0 0 0 2 93 0 0 0 0 0 94 0 0 0 0 0 95 0 0 0 0 0 96 0 0 0 0 0 97 0 0 0 0 0 98 0 0 0 0 0 99 0 0 0 0 0 100 0 2 0 0 2 your_output.sample_1.singleton.truncated000066400000000000000000000000001350370616400402410ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/defaultsyour_output.sample_2.discarded000066400000000000000000000000461350370616400362040ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/defaults@read_s2_000/1 + @read_s2_000/2 + your_output.sample_2.pair1.truncated000066400000000000000000000010771350370616400372730ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/defaults@read_s2_150/1 TGATCTCATACATTTAAACAAAGTATGCCTTACGCATGCCTTAATGATACGTAACCTAGGCAACAGAGTCTTTACTTGTACCTGCTACACAC + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_075/1 TCGCTAGCCCAAGATCACGCTTTCCGCGACGTTTTAGAGCGTGCATACCGGGGCGTTTCTCAGATAGGTATTTCA + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; @read_s2_200/1 ACCCTCACGCTTGCACGACGACAGCGGTCCCCTATAAATGTATGTTGACGCAGCGAGAGGCCAGGACCCGGGCGTGTTACCACTAAGACCCT + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 your_output.sample_2.pair2.truncated000066400000000000000000000011371350370616400372710ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/defaults@read_s2_150/2 AGAACAGGATACAATGAAAATGCATCGCGTTGGCAACTCTCACCTTGCTCTTGGACCCGTGTGTAGCAGGTACAAGTAAAGACTCTGTTGCCTAGGTTAC + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_075/2 TGAAATACCTATCTGAGAAACGCCCCGGTATGCACGCTCTAAAACGTCGCGGAAAGCGTGATCTTGGGCTAGCGA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>> @read_s2_200/2 ATGCTGATTAGATATGTCTTTCATCGGCTTGTGACCGAGGAGTGGTACGGCCGTTCCATATTGGGTGATTAGGAAGATGTCCCGGCTTGCTGCTTCTCGT + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 your_output.sample_2.settings000066400000000000000000000052651350370616400361320ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/defaultsAdapterRemoval ver. 2.2.0 Trimming of single-indexed paired-end reads [Demultiplexing] Maximum mismatches (total): 0 Maximum mate 1 mismatches: 0 Maximum mate 2 mismatches: 0 [Demultiplexing samples] Name Barcode_1 Barcode_2 sample_1 GCGCCGGA * sample_2* CAGGACAT * [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: ATGTCCTG_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 2459456692 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 [Trimming statistics] Total number of read pairs: 4 Number of unaligned read pairs: 1 Number of well aligned read pairs: 3 Number of discarded mate 1 reads: 1 Number of singleton mate 1 reads: 0 Number of discarded mate 2 reads: 1 Number of singleton mate 2 reads: 0 Number of reads with adapters[1]: 4 Number of retained reads: 6 Number of retained nucleotides: 534 Average length of retained reads: 89 [Length distribution] Length Mate1 Mate2 Singleton Discarded All 0 0 0 0 2 2 1 0 0 0 0 0 2 0 0 0 0 0 3 0 0 0 0 0 4 0 0 0 0 0 5 0 0 0 0 0 6 0 0 0 0 0 7 0 0 0 0 0 8 0 0 0 0 0 9 0 0 0 0 0 10 0 0 0 0 0 11 0 0 0 0 0 12 0 0 0 0 0 13 0 0 0 0 0 14 0 0 0 0 0 15 0 0 0 0 0 16 0 0 0 0 0 17 0 0 0 0 0 18 0 0 0 0 0 19 0 0 0 0 0 20 0 0 0 0 0 21 0 0 0 0 0 22 0 0 0 0 0 23 0 0 0 0 0 24 0 0 0 0 0 25 0 0 0 0 0 26 0 0 0 0 0 27 0 0 0 0 0 28 0 0 0 0 0 29 0 0 0 0 0 30 0 0 0 0 0 31 0 0 0 0 0 32 0 0 0 0 0 33 0 0 0 0 0 34 0 0 0 0 0 35 0 0 0 0 0 36 0 0 0 0 0 37 0 0 0 0 0 38 0 0 0 0 0 39 0 0 0 0 0 40 0 0 0 0 0 41 0 0 0 0 0 42 0 0 0 0 0 43 0 0 0 0 0 44 0 0 0 0 0 45 0 0 0 0 0 46 0 0 0 0 0 47 0 0 0 0 0 48 0 0 0 0 0 49 0 0 0 0 0 50 0 0 0 0 0 51 0 0 0 0 0 52 0 0 0 0 0 53 0 0 0 0 0 54 0 0 0 0 0 55 0 0 0 0 0 56 0 0 0 0 0 57 0 0 0 0 0 58 0 0 0 0 0 59 0 0 0 0 0 60 0 0 0 0 0 61 0 0 0 0 0 62 0 0 0 0 0 63 0 0 0 0 0 64 0 0 0 0 0 65 0 0 0 0 0 66 0 0 0 0 0 67 0 0 0 0 0 68 0 0 0 0 0 69 0 0 0 0 0 70 0 0 0 0 0 71 0 0 0 0 0 72 0 0 0 0 0 73 0 0 0 0 0 74 0 0 0 0 0 75 1 1 0 0 2 76 0 0 0 0 0 77 0 0 0 0 0 78 0 0 0 0 0 79 0 0 0 0 0 80 0 0 0 0 0 81 0 0 0 0 0 82 0 0 0 0 0 83 0 0 0 0 0 84 0 0 0 0 0 85 0 0 0 0 0 86 0 0 0 0 0 87 0 0 0 0 0 88 0 0 0 0 0 89 0 0 0 0 0 90 0 0 0 0 0 91 0 0 0 0 0 92 2 0 0 0 2 93 0 0 0 0 0 94 0 0 0 0 0 95 0 0 0 0 0 96 0 0 0 0 0 97 0 0 0 0 0 98 0 0 0 0 0 99 0 0 0 0 0 100 0 2 0 0 2 your_output.sample_2.singleton.truncated000066400000000000000000000000001350370616400402420ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/defaultsadapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/defaults/your_output.settings000066400000000000000000000021701350370616400345000ustar00rootroot00000000000000AdapterRemoval ver. 2.1.7 Trimming of single-indexed paired-end reads [Demultiplexing] Maximum mismatches (total): 0 Maximum mate 1 mismatches: 0 Maximum mate 2 mismatches: 0 [Demultiplexing samples] Name Barcode_1 Barcode_2 sample_1 GCGCCGGA * sample_2 CAGGACAT * [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 1157297082 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 [Demultiplexing statistics] Name Barcode_1 Barcode_2 Hits Fraction unidentified NA NA 0 0.000 ambiguous NA NA 0 0.000 sample_1 GCGCCGGA * 4 0.500 sample_2 CAGGACAT * 4 0.500 * * * 8 1.000 your_output.unidentified_1000066400000000000000000000000001350370616400354360ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/defaultsyour_output.unidentified_2000066400000000000000000000000001350370616400354370ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/defaultsadapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/demux_only/000077500000000000000000000000001350370616400306545ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/demux_only/barcodes.txt000066400000000000000000000000461350370616400331770ustar00rootroot00000000000000sample_1 GCGCCGGA sample_2 CAGGACAT adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/demux_only/info.json000066400000000000000000000001151350370616400324770ustar00rootroot00000000000000{ "arguments": ["--demultiplex-only"], "return_code": 0, "stderr": [ ] } adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/demux_only/input_1.fastq000066400000000000000000000033301350370616400332720ustar00rootroot00000000000000@read_s1_000/1 GCGCCGGAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAAAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_000/1 CAGGACATAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAAAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_075/1 GCGCCGGAGACGGTCCCATTAATGCACTATCGGATTTACACATTTGCGTGAATAAATCGACAGATGAATCATTAAGCTCCTACAGATCGGAAGAGCACAC + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_150/1 CAGGACATTGATCTCATACATTTAAACAAAGTATGCCTTACGCATGCCTTAATGATACGTAACCTAGGCAACAGAGTCTTTACTTGTACCTGCTACACAC + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_200/1 GCGCCGGATCCATCAGGATCGTATTATACTAAGCTAGGACTGTGCAGTGCACAGAGAGGAGATGACCATGATCCTCGAGCAAGTTGCCGCAGGCTCGGGC + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_150/1 GCGCCGGATGCACCGTAGCCATATGGGCTGTTGGGGACACAGGGCGTCGGCATTCCTTTATTACTGACGCCGCTAGAGTCTATGCAAGGTTATAACGTAT + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_075/1 CAGGACATTCGCTAGCCCAAGATCACGCTTTCCGCGACGTTTTAGAGCGTGCATACCGGGGCGTTTCTCAGATAGGTATTTCAAGATCGGAAGAGCACAC + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_200/1 CAGGACATACCCTCACGCTTGCACGACGACAGCGGTCCCCTATAAATGTATGTTGACGCAGCGAGAGGCCAGGACCCGGGCGTGTTACCACTAAGACCCT + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/demux_only/input_2.fastq000066400000000000000000000033301350370616400332730ustar00rootroot00000000000000@read_s1_000/2 TCCGGCGCAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_000/2 ATGTCCTGAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_075/2 GTAGGAGCTTAATGATTCATCTGTCGATTTATTCACGCAAATGTGTAAATCCGATAGTGCATTAATGGGACCGTCTCCGGCGCAGATCGGAAGAGCGTCG + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_150/2 AGAACAGGATACAATGAAAATGCATCGCGTTGGCAACTCTCACCTTGCTCTTGGACCCGTGTGTAGCAGGTACAAGTAAAGACTCTGTTGCCTAGGTTAC + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_200/2 CCTTCTTATGCTCGACTGGCTCTGTATAAGCCCAAGACATTATGAAAGGTCTCGCGTTTGTCTACCAGGCTCCGTTACGGATACAAGTGCCCTACTGTCA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_150/2 ATCAAGGGAGGTCACGTGAATTTTGCCTTCTAGACTAGCGTACATGACCGCGAATTAGATACGTTATAACCTTGCATAGACTCTAGCGGCGTCAGTAATA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_075/2 TGAAATACCTATCTGAGAAACGCCCCGGTATGCACGCTCTAAAACGTCGCGGAAAGCGTGATCTTGGGCTAGCGAATGTCCTGAGATCGGAAGAGCGTCG + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_200/2 ATGCTGATTAGATATGTCTTTCATCGGCTTGTGACCGAGGAGTGGTACGGCCGTTCCATATTGGGTGATTAGGAAGATGTCCCGGCTTGCTGCTTCTCGT + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 your_output.sample_1.pair1.fastq000066400000000000000000000014541350370616400367720ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/demux_only@read_s1_000/1 AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAAAA + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_075/1 GACGGTCCCATTAATGCACTATCGGATTTACACATTTGCGTGAATAAATCGACAGATGAATCATTAAGCTCCTACAGATCGGAAGAGCACAC + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_200/1 TCCATCAGGATCGTATTATACTAAGCTAGGACTGTGCAGTGCACAGAGAGGAGATGACCATGATCCTCGAGCAAGTTGCCGCAGGCTCGGGC + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_150/1 TGCACCGTAGCCATATGGGCTGTTGGGGACACAGGGCGTCGGCATTCCTTTATTACTGACGCCGCTAGAGTCTATGCAAGGTTATAACGTAT + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 your_output.sample_1.pair2.fastq000066400000000000000000000015541350370616400367740ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/demux_only@read_s1_000/2 TCCGGCGCAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_075/2 GTAGGAGCTTAATGATTCATCTGTCGATTTATTCACGCAAATGTGTAAATCCGATAGTGCATTAATGGGACCGTCTCCGGCGCAGATCGGAAGAGCGTCG + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_200/2 CCTTCTTATGCTCGACTGGCTCTGTATAAGCCCAAGACATTATGAAAGGTCTCGCGTTTGTCTACCAGGCTCCGTTACGGATACAAGTGCCCTACTGTCA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_150/2 ATCAAGGGAGGTCACGTGAATTTTGCCTTCTAGACTAGCGTACATGACCGCGAATTAGATACGTTATAACCTTGCATAGACTCTAGCGGCGTCAGTAATA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 your_output.sample_1.settings000066400000000000000000000007111350370616400364740ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/demux_onlyAdapterRemoval ver. 2.2.0 Demultiplexing of single-indexed paired-end reads [Demultiplexing] Maximum mismatches (total): 0 Maximum mate 1 mismatches: 0 Maximum mate 2 mismatches: 0 [Demultiplexing samples] Name Barcode_1 Barcode_2 sample_1* GCGCCGGA * sample_2 CAGGACAT * [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: TCCGGCGC_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT your_output.sample_2.pair1.fastq000066400000000000000000000014541350370616400367730ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/demux_only@read_s2_000/1 AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAAAA + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_150/1 TGATCTCATACATTTAAACAAAGTATGCCTTACGCATGCCTTAATGATACGTAACCTAGGCAACAGAGTCTTTACTTGTACCTGCTACACAC + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_075/1 TCGCTAGCCCAAGATCACGCTTTCCGCGACGTTTTAGAGCGTGCATACCGGGGCGTTTCTCAGATAGGTATTTCAAGATCGGAAGAGCACAC + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_200/1 ACCCTCACGCTTGCACGACGACAGCGGTCCCCTATAAATGTATGTTGACGCAGCGAGAGGCCAGGACCCGGGCGTGTTACCACTAAGACCCT + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 your_output.sample_2.pair2.fastq000066400000000000000000000015541350370616400367750ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/demux_only@read_s2_000/2 ATGTCCTGAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_150/2 AGAACAGGATACAATGAAAATGCATCGCGTTGGCAACTCTCACCTTGCTCTTGGACCCGTGTGTAGCAGGTACAAGTAAAGACTCTGTTGCCTAGGTTAC + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_075/2 TGAAATACCTATCTGAGAAACGCCCCGGTATGCACGCTCTAAAACGTCGCGGAAAGCGTGATCTTGGGCTAGCGAATGTCCTGAGATCGGAAGAGCGTCG + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_200/2 ATGCTGATTAGATATGTCTTTCATCGGCTTGTGACCGAGGAGTGGTACGGCCGTTCCATATTGGGTGATTAGGAAGATGTCCCGGCTTGCTGCTTCTCGT + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 your_output.sample_2.settings000066400000000000000000000007111350370616400364750ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/demux_onlyAdapterRemoval ver. 2.2.0 Demultiplexing of single-indexed paired-end reads [Demultiplexing] Maximum mismatches (total): 0 Maximum mate 1 mismatches: 0 Maximum mate 2 mismatches: 0 [Demultiplexing samples] Name Barcode_1 Barcode_2 sample_1 GCGCCGGA * sample_2* CAGGACAT * [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: ATGTCCTG_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT your_output.settings000066400000000000000000000011751350370616400350010ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/demux_onlyAdapterRemoval ver. 2.2.0 Demultiplexing of single-indexed paired-end reads [Demultiplexing] Maximum mismatches (total): 0 Maximum mate 1 mismatches: 0 Maximum mate 2 mismatches: 0 [Demultiplexing samples] Name Barcode_1 Barcode_2 sample_1 GCGCCGGA * sample_2 CAGGACAT * [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Demultiplexing statistics] Name Barcode_1 Barcode_2 Hits Fraction unidentified NA NA 0 0.000 ambiguous NA NA 0 0.000 sample_1 GCGCCGGA * 4 0.500 sample_2 CAGGACAT * 4 0.500 * * * 8 1.000 your_output.unidentified_1.fastq000066400000000000000000000000001350370616400371270ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/demux_onlyyour_output.unidentified_2.fastq000066400000000000000000000000001350370616400371300ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/demux_onlyadapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/interleaved/000077500000000000000000000000001350370616400307735ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/interleaved/both/000077500000000000000000000000001350370616400317275ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/interleaved/both/barcodes.txt000066400000000000000000000000461350370616400342520ustar00rootroot00000000000000sample_1 GCGCCGGA sample_2 CAGGACAT adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/interleaved/both/info.json000066400000000000000000000001101350370616400335450ustar00rootroot00000000000000{ "arguments": ["--interleaved"], "return_code": 0, "stderr": [ ] } input_1.fastq000066400000000000000000000066601350370616400342770ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/interleaved/both@read_s1_000/1 GCGCCGGAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAAAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_000/2 TCCGGCGCAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_000/1 CAGGACATAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAAAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_000/2 ATGTCCTGAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_075/1 GCGCCGGAGACGGTCCCATTAATGCACTATCGGATTTACACATTTGCGTGAATAAATCGACAGATGAATCATTAAGCTCCTACAGATCGGAAGAGCACAC + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_075/2 GTAGGAGCTTAATGATTCATCTGTCGATTTATTCACGCAAATGTGTAAATCCGATAGTGCATTAATGGGACCGTCTCCGGCGCAGATCGGAAGAGCGTCG + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_150/1 CAGGACATTGATCTCATACATTTAAACAAAGTATGCCTTACGCATGCCTTAATGATACGTAACCTAGGCAACAGAGTCTTTACTTGTACCTGCTACACAC + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_150/2 AGAACAGGATACAATGAAAATGCATCGCGTTGGCAACTCTCACCTTGCTCTTGGACCCGTGTGTAGCAGGTACAAGTAAAGACTCTGTTGCCTAGGTTAC + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_200/1 GCGCCGGATCCATCAGGATCGTATTATACTAAGCTAGGACTGTGCAGTGCACAGAGAGGAGATGACCATGATCCTCGAGCAAGTTGCCGCAGGCTCGGGC + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_200/2 CCTTCTTATGCTCGACTGGCTCTGTATAAGCCCAAGACATTATGAAAGGTCTCGCGTTTGTCTACCAGGCTCCGTTACGGATACAAGTGCCCTACTGTCA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_150/1 GCGCCGGATGCACCGTAGCCATATGGGCTGTTGGGGACACAGGGCGTCGGCATTCCTTTATTACTGACGCCGCTAGAGTCTATGCAAGGTTATAACGTAT + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_150/2 ATCAAGGGAGGTCACGTGAATTTTGCCTTCTAGACTAGCGTACATGACCGCGAATTAGATACGTTATAACCTTGCATAGACTCTAGCGGCGTCAGTAATA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_075/1 CAGGACATTCGCTAGCCCAAGATCACGCTTTCCGCGACGTTTTAGAGCGTGCATACCGGGGCGTTTCTCAGATAGGTATTTCAAGATCGGAAGAGCACAC + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_075/2 TGAAATACCTATCTGAGAAACGCCCCGGTATGCACGCTCTAAAACGTCGCGGAAAGCGTGATCTTGGGCTAGCGAATGTCCTGAGATCGGAAGAGCGTCG + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_200/1 CAGGACATACCCTCACGCTTGCACGACGACAGCGGTCCCCTATAAATGTATGTTGACGCAGCGAGAGGCCAGGACCCGGGCGTGTTACCACTAAGACCCT + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_200/2 ATGCTGATTAGATATGTCTTTCATCGGCTTGTGACCGAGGAGTGGTACGGCCGTTCCATATTGGGTGATTAGGAAGATGTCCCGGCTTGCTGCTTCTCGT + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 your_output.sample_1.discarded000066400000000000000000000000461350370616400376320ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/interleaved/both@read_s1_000/1 + @read_s1_000/2 + your_output.sample_1.paired.truncated000066400000000000000000000022361350370616400411470ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/interleaved/both@read_s1_075/1 GACGGTCCCATTAATGCACTATCGGATTTACACATTTGCGTGAATAAATCGACAGATGAATCATTAAGCTCCTAC + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; @read_s1_075/2 GTAGGAGCTTAATGATTCATCTGTCGATTTATTCACGCAAATGTGTAAATCCGATAGTGCATTAATGGGACCGTC + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>> @read_s1_200/1 TCCATCAGGATCGTATTATACTAAGCTAGGACTGTGCAGTGCACAGAGAGGAGATGACCATGATCCTCGAGCAAGTTGCCGCAGGCTCGGGC + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_200/2 CCTTCTTATGCTCGACTGGCTCTGTATAAGCCCAAGACATTATGAAAGGTCTCGCGTTTGTCTACCAGGCTCCGTTACGGATACAAGTGCCCTACTGTCA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_150/1 TGCACCGTAGCCATATGGGCTGTTGGGGACACAGGGCGTCGGCATTCCTTTATTACTGACGCCGCTAGAGTCTATGCAAGGTTATAACGTAT + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_150/2 ATCAAGGGAGGTCACGTGAATTTTGCCTTCTAGACTAGCGTACATGACCGCGAATTAGATACGTTATAACCTTGCATAGACTCTAGCGGCGTCAGTAATA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 your_output.sample_1.settings000066400000000000000000000052651350370616400375600ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/interleaved/bothAdapterRemoval ver. 2.2.0 Trimming of single-indexed paired-end reads [Demultiplexing] Maximum mismatches (total): 0 Maximum mate 1 mismatches: 0 Maximum mate 2 mismatches: 0 [Demultiplexing samples] Name Barcode_1 Barcode_2 sample_1* GCGCCGGA * sample_2 CAGGACAT * [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: TCCGGCGC_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 2459456692 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 [Trimming statistics] Total number of read pairs: 4 Number of unaligned read pairs: 1 Number of well aligned read pairs: 3 Number of discarded mate 1 reads: 1 Number of singleton mate 1 reads: 0 Number of discarded mate 2 reads: 1 Number of singleton mate 2 reads: 0 Number of reads with adapters[1]: 4 Number of retained reads: 6 Number of retained nucleotides: 534 Average length of retained reads: 89 [Length distribution] Length Mate1 Mate2 Singleton Discarded All 0 0 0 0 2 2 1 0 0 0 0 0 2 0 0 0 0 0 3 0 0 0 0 0 4 0 0 0 0 0 5 0 0 0 0 0 6 0 0 0 0 0 7 0 0 0 0 0 8 0 0 0 0 0 9 0 0 0 0 0 10 0 0 0 0 0 11 0 0 0 0 0 12 0 0 0 0 0 13 0 0 0 0 0 14 0 0 0 0 0 15 0 0 0 0 0 16 0 0 0 0 0 17 0 0 0 0 0 18 0 0 0 0 0 19 0 0 0 0 0 20 0 0 0 0 0 21 0 0 0 0 0 22 0 0 0 0 0 23 0 0 0 0 0 24 0 0 0 0 0 25 0 0 0 0 0 26 0 0 0 0 0 27 0 0 0 0 0 28 0 0 0 0 0 29 0 0 0 0 0 30 0 0 0 0 0 31 0 0 0 0 0 32 0 0 0 0 0 33 0 0 0 0 0 34 0 0 0 0 0 35 0 0 0 0 0 36 0 0 0 0 0 37 0 0 0 0 0 38 0 0 0 0 0 39 0 0 0 0 0 40 0 0 0 0 0 41 0 0 0 0 0 42 0 0 0 0 0 43 0 0 0 0 0 44 0 0 0 0 0 45 0 0 0 0 0 46 0 0 0 0 0 47 0 0 0 0 0 48 0 0 0 0 0 49 0 0 0 0 0 50 0 0 0 0 0 51 0 0 0 0 0 52 0 0 0 0 0 53 0 0 0 0 0 54 0 0 0 0 0 55 0 0 0 0 0 56 0 0 0 0 0 57 0 0 0 0 0 58 0 0 0 0 0 59 0 0 0 0 0 60 0 0 0 0 0 61 0 0 0 0 0 62 0 0 0 0 0 63 0 0 0 0 0 64 0 0 0 0 0 65 0 0 0 0 0 66 0 0 0 0 0 67 0 0 0 0 0 68 0 0 0 0 0 69 0 0 0 0 0 70 0 0 0 0 0 71 0 0 0 0 0 72 0 0 0 0 0 73 0 0 0 0 0 74 0 0 0 0 0 75 1 1 0 0 2 76 0 0 0 0 0 77 0 0 0 0 0 78 0 0 0 0 0 79 0 0 0 0 0 80 0 0 0 0 0 81 0 0 0 0 0 82 0 0 0 0 0 83 0 0 0 0 0 84 0 0 0 0 0 85 0 0 0 0 0 86 0 0 0 0 0 87 0 0 0 0 0 88 0 0 0 0 0 89 0 0 0 0 0 90 0 0 0 0 0 91 0 0 0 0 0 92 2 0 0 0 2 93 0 0 0 0 0 94 0 0 0 0 0 95 0 0 0 0 0 96 0 0 0 0 0 97 0 0 0 0 0 98 0 0 0 0 0 99 0 0 0 0 0 100 0 2 0 0 2 your_output.sample_1.singleton.truncated000066400000000000000000000000001350370616400416700ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/interleaved/bothyour_output.sample_2.discarded000066400000000000000000000000461350370616400376330ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/interleaved/both@read_s2_000/1 + @read_s2_000/2 + your_output.sample_2.paired.truncated000066400000000000000000000022361350370616400411500ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/interleaved/both@read_s2_150/1 TGATCTCATACATTTAAACAAAGTATGCCTTACGCATGCCTTAATGATACGTAACCTAGGCAACAGAGTCTTTACTTGTACCTGCTACACAC + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_150/2 AGAACAGGATACAATGAAAATGCATCGCGTTGGCAACTCTCACCTTGCTCTTGGACCCGTGTGTAGCAGGTACAAGTAAAGACTCTGTTGCCTAGGTTAC + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_075/1 TCGCTAGCCCAAGATCACGCTTTCCGCGACGTTTTAGAGCGTGCATACCGGGGCGTTTCTCAGATAGGTATTTCA + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; @read_s2_075/2 TGAAATACCTATCTGAGAAACGCCCCGGTATGCACGCTCTAAAACGTCGCGGAAAGCGTGATCTTGGGCTAGCGA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>> @read_s2_200/1 ACCCTCACGCTTGCACGACGACAGCGGTCCCCTATAAATGTATGTTGACGCAGCGAGAGGCCAGGACCCGGGCGTGTTACCACTAAGACCCT + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_200/2 ATGCTGATTAGATATGTCTTTCATCGGCTTGTGACCGAGGAGTGGTACGGCCGTTCCATATTGGGTGATTAGGAAGATGTCCCGGCTTGCTGCTTCTCGT + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 your_output.sample_2.settings000066400000000000000000000052651350370616400375610ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/interleaved/bothAdapterRemoval ver. 2.2.0 Trimming of single-indexed paired-end reads [Demultiplexing] Maximum mismatches (total): 0 Maximum mate 1 mismatches: 0 Maximum mate 2 mismatches: 0 [Demultiplexing samples] Name Barcode_1 Barcode_2 sample_1 GCGCCGGA * sample_2* CAGGACAT * [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: ATGTCCTG_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 2459456692 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 [Trimming statistics] Total number of read pairs: 4 Number of unaligned read pairs: 1 Number of well aligned read pairs: 3 Number of discarded mate 1 reads: 1 Number of singleton mate 1 reads: 0 Number of discarded mate 2 reads: 1 Number of singleton mate 2 reads: 0 Number of reads with adapters[1]: 4 Number of retained reads: 6 Number of retained nucleotides: 534 Average length of retained reads: 89 [Length distribution] Length Mate1 Mate2 Singleton Discarded All 0 0 0 0 2 2 1 0 0 0 0 0 2 0 0 0 0 0 3 0 0 0 0 0 4 0 0 0 0 0 5 0 0 0 0 0 6 0 0 0 0 0 7 0 0 0 0 0 8 0 0 0 0 0 9 0 0 0 0 0 10 0 0 0 0 0 11 0 0 0 0 0 12 0 0 0 0 0 13 0 0 0 0 0 14 0 0 0 0 0 15 0 0 0 0 0 16 0 0 0 0 0 17 0 0 0 0 0 18 0 0 0 0 0 19 0 0 0 0 0 20 0 0 0 0 0 21 0 0 0 0 0 22 0 0 0 0 0 23 0 0 0 0 0 24 0 0 0 0 0 25 0 0 0 0 0 26 0 0 0 0 0 27 0 0 0 0 0 28 0 0 0 0 0 29 0 0 0 0 0 30 0 0 0 0 0 31 0 0 0 0 0 32 0 0 0 0 0 33 0 0 0 0 0 34 0 0 0 0 0 35 0 0 0 0 0 36 0 0 0 0 0 37 0 0 0 0 0 38 0 0 0 0 0 39 0 0 0 0 0 40 0 0 0 0 0 41 0 0 0 0 0 42 0 0 0 0 0 43 0 0 0 0 0 44 0 0 0 0 0 45 0 0 0 0 0 46 0 0 0 0 0 47 0 0 0 0 0 48 0 0 0 0 0 49 0 0 0 0 0 50 0 0 0 0 0 51 0 0 0 0 0 52 0 0 0 0 0 53 0 0 0 0 0 54 0 0 0 0 0 55 0 0 0 0 0 56 0 0 0 0 0 57 0 0 0 0 0 58 0 0 0 0 0 59 0 0 0 0 0 60 0 0 0 0 0 61 0 0 0 0 0 62 0 0 0 0 0 63 0 0 0 0 0 64 0 0 0 0 0 65 0 0 0 0 0 66 0 0 0 0 0 67 0 0 0 0 0 68 0 0 0 0 0 69 0 0 0 0 0 70 0 0 0 0 0 71 0 0 0 0 0 72 0 0 0 0 0 73 0 0 0 0 0 74 0 0 0 0 0 75 1 1 0 0 2 76 0 0 0 0 0 77 0 0 0 0 0 78 0 0 0 0 0 79 0 0 0 0 0 80 0 0 0 0 0 81 0 0 0 0 0 82 0 0 0 0 0 83 0 0 0 0 0 84 0 0 0 0 0 85 0 0 0 0 0 86 0 0 0 0 0 87 0 0 0 0 0 88 0 0 0 0 0 89 0 0 0 0 0 90 0 0 0 0 0 91 0 0 0 0 0 92 2 0 0 0 2 93 0 0 0 0 0 94 0 0 0 0 0 95 0 0 0 0 0 96 0 0 0 0 0 97 0 0 0 0 0 98 0 0 0 0 0 99 0 0 0 0 0 100 0 2 0 0 2 your_output.sample_2.singleton.truncated000066400000000000000000000000001350370616400416710ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/interleaved/bothyour_output.settings000066400000000000000000000021701350370616400360500ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/interleaved/bothAdapterRemoval ver. 2.1.7 Trimming of single-indexed paired-end reads [Demultiplexing] Maximum mismatches (total): 0 Maximum mate 1 mismatches: 0 Maximum mate 2 mismatches: 0 [Demultiplexing samples] Name Barcode_1 Barcode_2 sample_1 GCGCCGGA * sample_2 CAGGACAT * [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 1157297082 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 [Demultiplexing statistics] Name Barcode_1 Barcode_2 Hits Fraction unidentified NA NA 0 0.000 ambiguous NA NA 0 0.000 sample_1 GCGCCGGA * 4 0.500 sample_2 CAGGACAT * 4 0.500 * * * 8 1.000 your_output.unidentified.paired000066400000000000000000000000001350370616400401100ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/interleaved/bothadapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/interleaved/output/000077500000000000000000000000001350370616400323335ustar00rootroot00000000000000barcodes.txt000066400000000000000000000000461350370616400345770ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/interleaved/outputsample_1 GCGCCGGA sample_2 CAGGACAT adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/interleaved/output/info.json000066400000000000000000000001171350370616400341600ustar00rootroot00000000000000{ "arguments": ["--interleaved-output"], "return_code": 0, "stderr": [ ] } input_1.fastq000066400000000000000000000033301350370616400346720ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/interleaved/output@read_s1_000/1 GCGCCGGAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAAAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_000/1 CAGGACATAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAAAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_075/1 GCGCCGGAGACGGTCCCATTAATGCACTATCGGATTTACACATTTGCGTGAATAAATCGACAGATGAATCATTAAGCTCCTACAGATCGGAAGAGCACAC + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_150/1 CAGGACATTGATCTCATACATTTAAACAAAGTATGCCTTACGCATGCCTTAATGATACGTAACCTAGGCAACAGAGTCTTTACTTGTACCTGCTACACAC + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_200/1 GCGCCGGATCCATCAGGATCGTATTATACTAAGCTAGGACTGTGCAGTGCACAGAGAGGAGATGACCATGATCCTCGAGCAAGTTGCCGCAGGCTCGGGC + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_150/1 GCGCCGGATGCACCGTAGCCATATGGGCTGTTGGGGACACAGGGCGTCGGCATTCCTTTATTACTGACGCCGCTAGAGTCTATGCAAGGTTATAACGTAT + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_075/1 CAGGACATTCGCTAGCCCAAGATCACGCTTTCCGCGACGTTTTAGAGCGTGCATACCGGGGCGTTTCTCAGATAGGTATTTCAAGATCGGAAGAGCACAC + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_200/1 CAGGACATACCCTCACGCTTGCACGACGACAGCGGTCCCCTATAAATGTATGTTGACGCAGCGAGAGGCCAGGACCCGGGCGTGTTACCACTAAGACCCT + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 input_2.fastq000066400000000000000000000033301350370616400346730ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/interleaved/output@read_s1_000/2 TCCGGCGCAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_000/2 ATGTCCTGAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_075/2 GTAGGAGCTTAATGATTCATCTGTCGATTTATTCACGCAAATGTGTAAATCCGATAGTGCATTAATGGGACCGTCTCCGGCGCAGATCGGAAGAGCGTCG + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_150/2 AGAACAGGATACAATGAAAATGCATCGCGTTGGCAACTCTCACCTTGCTCTTGGACCCGTGTGTAGCAGGTACAAGTAAAGACTCTGTTGCCTAGGTTAC + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_200/2 CCTTCTTATGCTCGACTGGCTCTGTATAAGCCCAAGACATTATGAAAGGTCTCGCGTTTGTCTACCAGGCTCCGTTACGGATACAAGTGCCCTACTGTCA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_150/2 ATCAAGGGAGGTCACGTGAATTTTGCCTTCTAGACTAGCGTACATGACCGCGAATTAGATACGTTATAACCTTGCATAGACTCTAGCGGCGTCAGTAATA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_075/2 TGAAATACCTATCTGAGAAACGCCCCGGTATGCACGCTCTAAAACGTCGCGGAAAGCGTGATCTTGGGCTAGCGAATGTCCTGAGATCGGAAGAGCGTCG + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_200/2 ATGCTGATTAGATATGTCTTTCATCGGCTTGTGACCGAGGAGTGGTACGGCCGTTCCATATTGGGTGATTAGGAAGATGTCCCGGCTTGCTGCTTCTCGT + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 your_output.sample_1.discarded000066400000000000000000000000461350370616400402360ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/interleaved/output@read_s1_000/1 + @read_s1_000/2 + your_output.sample_1.paired.truncated000066400000000000000000000022361350370616400415530ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/interleaved/output@read_s1_075/1 GACGGTCCCATTAATGCACTATCGGATTTACACATTTGCGTGAATAAATCGACAGATGAATCATTAAGCTCCTAC + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; @read_s1_075/2 GTAGGAGCTTAATGATTCATCTGTCGATTTATTCACGCAAATGTGTAAATCCGATAGTGCATTAATGGGACCGTC + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>> @read_s1_200/1 TCCATCAGGATCGTATTATACTAAGCTAGGACTGTGCAGTGCACAGAGAGGAGATGACCATGATCCTCGAGCAAGTTGCCGCAGGCTCGGGC + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_200/2 CCTTCTTATGCTCGACTGGCTCTGTATAAGCCCAAGACATTATGAAAGGTCTCGCGTTTGTCTACCAGGCTCCGTTACGGATACAAGTGCCCTACTGTCA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_150/1 TGCACCGTAGCCATATGGGCTGTTGGGGACACAGGGCGTCGGCATTCCTTTATTACTGACGCCGCTAGAGTCTATGCAAGGTTATAACGTAT + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_150/2 ATCAAGGGAGGTCACGTGAATTTTGCCTTCTAGACTAGCGTACATGACCGCGAATTAGATACGTTATAACCTTGCATAGACTCTAGCGGCGTCAGTAATA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 your_output.sample_1.settings000066400000000000000000000052651350370616400401640ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/interleaved/outputAdapterRemoval ver. 2.2.0 Trimming of single-indexed paired-end reads [Demultiplexing] Maximum mismatches (total): 0 Maximum mate 1 mismatches: 0 Maximum mate 2 mismatches: 0 [Demultiplexing samples] Name Barcode_1 Barcode_2 sample_1* GCGCCGGA * sample_2 CAGGACAT * [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: TCCGGCGC_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 2459456692 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 [Trimming statistics] Total number of read pairs: 4 Number of unaligned read pairs: 1 Number of well aligned read pairs: 3 Number of discarded mate 1 reads: 1 Number of singleton mate 1 reads: 0 Number of discarded mate 2 reads: 1 Number of singleton mate 2 reads: 0 Number of reads with adapters[1]: 4 Number of retained reads: 6 Number of retained nucleotides: 534 Average length of retained reads: 89 [Length distribution] Length Mate1 Mate2 Singleton Discarded All 0 0 0 0 2 2 1 0 0 0 0 0 2 0 0 0 0 0 3 0 0 0 0 0 4 0 0 0 0 0 5 0 0 0 0 0 6 0 0 0 0 0 7 0 0 0 0 0 8 0 0 0 0 0 9 0 0 0 0 0 10 0 0 0 0 0 11 0 0 0 0 0 12 0 0 0 0 0 13 0 0 0 0 0 14 0 0 0 0 0 15 0 0 0 0 0 16 0 0 0 0 0 17 0 0 0 0 0 18 0 0 0 0 0 19 0 0 0 0 0 20 0 0 0 0 0 21 0 0 0 0 0 22 0 0 0 0 0 23 0 0 0 0 0 24 0 0 0 0 0 25 0 0 0 0 0 26 0 0 0 0 0 27 0 0 0 0 0 28 0 0 0 0 0 29 0 0 0 0 0 30 0 0 0 0 0 31 0 0 0 0 0 32 0 0 0 0 0 33 0 0 0 0 0 34 0 0 0 0 0 35 0 0 0 0 0 36 0 0 0 0 0 37 0 0 0 0 0 38 0 0 0 0 0 39 0 0 0 0 0 40 0 0 0 0 0 41 0 0 0 0 0 42 0 0 0 0 0 43 0 0 0 0 0 44 0 0 0 0 0 45 0 0 0 0 0 46 0 0 0 0 0 47 0 0 0 0 0 48 0 0 0 0 0 49 0 0 0 0 0 50 0 0 0 0 0 51 0 0 0 0 0 52 0 0 0 0 0 53 0 0 0 0 0 54 0 0 0 0 0 55 0 0 0 0 0 56 0 0 0 0 0 57 0 0 0 0 0 58 0 0 0 0 0 59 0 0 0 0 0 60 0 0 0 0 0 61 0 0 0 0 0 62 0 0 0 0 0 63 0 0 0 0 0 64 0 0 0 0 0 65 0 0 0 0 0 66 0 0 0 0 0 67 0 0 0 0 0 68 0 0 0 0 0 69 0 0 0 0 0 70 0 0 0 0 0 71 0 0 0 0 0 72 0 0 0 0 0 73 0 0 0 0 0 74 0 0 0 0 0 75 1 1 0 0 2 76 0 0 0 0 0 77 0 0 0 0 0 78 0 0 0 0 0 79 0 0 0 0 0 80 0 0 0 0 0 81 0 0 0 0 0 82 0 0 0 0 0 83 0 0 0 0 0 84 0 0 0 0 0 85 0 0 0 0 0 86 0 0 0 0 0 87 0 0 0 0 0 88 0 0 0 0 0 89 0 0 0 0 0 90 0 0 0 0 0 91 0 0 0 0 0 92 2 0 0 0 2 93 0 0 0 0 0 94 0 0 0 0 0 95 0 0 0 0 0 96 0 0 0 0 0 97 0 0 0 0 0 98 0 0 0 0 0 99 0 0 0 0 0 100 0 2 0 0 2 your_output.sample_1.singleton.truncated000066400000000000000000000000001350370616400422740ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/interleaved/outputyour_output.sample_2.discarded000066400000000000000000000000461350370616400402370ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/interleaved/output@read_s2_000/1 + @read_s2_000/2 + your_output.sample_2.paired.truncated000066400000000000000000000022361350370616400415540ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/interleaved/output@read_s2_150/1 TGATCTCATACATTTAAACAAAGTATGCCTTACGCATGCCTTAATGATACGTAACCTAGGCAACAGAGTCTTTACTTGTACCTGCTACACAC + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_150/2 AGAACAGGATACAATGAAAATGCATCGCGTTGGCAACTCTCACCTTGCTCTTGGACCCGTGTGTAGCAGGTACAAGTAAAGACTCTGTTGCCTAGGTTAC + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_075/1 TCGCTAGCCCAAGATCACGCTTTCCGCGACGTTTTAGAGCGTGCATACCGGGGCGTTTCTCAGATAGGTATTTCA + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; @read_s2_075/2 TGAAATACCTATCTGAGAAACGCCCCGGTATGCACGCTCTAAAACGTCGCGGAAAGCGTGATCTTGGGCTAGCGA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>> @read_s2_200/1 ACCCTCACGCTTGCACGACGACAGCGGTCCCCTATAAATGTATGTTGACGCAGCGAGAGGCCAGGACCCGGGCGTGTTACCACTAAGACCCT + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_200/2 ATGCTGATTAGATATGTCTTTCATCGGCTTGTGACCGAGGAGTGGTACGGCCGTTCCATATTGGGTGATTAGGAAGATGTCCCGGCTTGCTGCTTCTCGT + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 your_output.sample_2.settings000066400000000000000000000052651350370616400401650ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/interleaved/outputAdapterRemoval ver. 2.2.0 Trimming of single-indexed paired-end reads [Demultiplexing] Maximum mismatches (total): 0 Maximum mate 1 mismatches: 0 Maximum mate 2 mismatches: 0 [Demultiplexing samples] Name Barcode_1 Barcode_2 sample_1 GCGCCGGA * sample_2* CAGGACAT * [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: ATGTCCTG_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 2459456692 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 [Trimming statistics] Total number of read pairs: 4 Number of unaligned read pairs: 1 Number of well aligned read pairs: 3 Number of discarded mate 1 reads: 1 Number of singleton mate 1 reads: 0 Number of discarded mate 2 reads: 1 Number of singleton mate 2 reads: 0 Number of reads with adapters[1]: 4 Number of retained reads: 6 Number of retained nucleotides: 534 Average length of retained reads: 89 [Length distribution] Length Mate1 Mate2 Singleton Discarded All 0 0 0 0 2 2 1 0 0 0 0 0 2 0 0 0 0 0 3 0 0 0 0 0 4 0 0 0 0 0 5 0 0 0 0 0 6 0 0 0 0 0 7 0 0 0 0 0 8 0 0 0 0 0 9 0 0 0 0 0 10 0 0 0 0 0 11 0 0 0 0 0 12 0 0 0 0 0 13 0 0 0 0 0 14 0 0 0 0 0 15 0 0 0 0 0 16 0 0 0 0 0 17 0 0 0 0 0 18 0 0 0 0 0 19 0 0 0 0 0 20 0 0 0 0 0 21 0 0 0 0 0 22 0 0 0 0 0 23 0 0 0 0 0 24 0 0 0 0 0 25 0 0 0 0 0 26 0 0 0 0 0 27 0 0 0 0 0 28 0 0 0 0 0 29 0 0 0 0 0 30 0 0 0 0 0 31 0 0 0 0 0 32 0 0 0 0 0 33 0 0 0 0 0 34 0 0 0 0 0 35 0 0 0 0 0 36 0 0 0 0 0 37 0 0 0 0 0 38 0 0 0 0 0 39 0 0 0 0 0 40 0 0 0 0 0 41 0 0 0 0 0 42 0 0 0 0 0 43 0 0 0 0 0 44 0 0 0 0 0 45 0 0 0 0 0 46 0 0 0 0 0 47 0 0 0 0 0 48 0 0 0 0 0 49 0 0 0 0 0 50 0 0 0 0 0 51 0 0 0 0 0 52 0 0 0 0 0 53 0 0 0 0 0 54 0 0 0 0 0 55 0 0 0 0 0 56 0 0 0 0 0 57 0 0 0 0 0 58 0 0 0 0 0 59 0 0 0 0 0 60 0 0 0 0 0 61 0 0 0 0 0 62 0 0 0 0 0 63 0 0 0 0 0 64 0 0 0 0 0 65 0 0 0 0 0 66 0 0 0 0 0 67 0 0 0 0 0 68 0 0 0 0 0 69 0 0 0 0 0 70 0 0 0 0 0 71 0 0 0 0 0 72 0 0 0 0 0 73 0 0 0 0 0 74 0 0 0 0 0 75 1 1 0 0 2 76 0 0 0 0 0 77 0 0 0 0 0 78 0 0 0 0 0 79 0 0 0 0 0 80 0 0 0 0 0 81 0 0 0 0 0 82 0 0 0 0 0 83 0 0 0 0 0 84 0 0 0 0 0 85 0 0 0 0 0 86 0 0 0 0 0 87 0 0 0 0 0 88 0 0 0 0 0 89 0 0 0 0 0 90 0 0 0 0 0 91 0 0 0 0 0 92 2 0 0 0 2 93 0 0 0 0 0 94 0 0 0 0 0 95 0 0 0 0 0 96 0 0 0 0 0 97 0 0 0 0 0 98 0 0 0 0 0 99 0 0 0 0 0 100 0 2 0 0 2 your_output.sample_2.singleton.truncated000066400000000000000000000000001350370616400422750ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/interleaved/outputyour_output.settings000066400000000000000000000021701350370616400364540ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/interleaved/outputAdapterRemoval ver. 2.1.7 Trimming of single-indexed paired-end reads [Demultiplexing] Maximum mismatches (total): 0 Maximum mate 1 mismatches: 0 Maximum mate 2 mismatches: 0 [Demultiplexing samples] Name Barcode_1 Barcode_2 sample_1 GCGCCGGA * sample_2 CAGGACAT * [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 1157297082 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 [Demultiplexing statistics] Name Barcode_1 Barcode_2 Hits Fraction unidentified NA NA 0 0.000 ambiguous NA NA 0 0.000 sample_1 GCGCCGGA * 4 0.500 sample_2 CAGGACAT * 4 0.500 * * * 8 1.000 your_output.unidentified.paired000066400000000000000000000000001350370616400405140ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/interleaved/outputadapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/multiple_input/000077500000000000000000000000001350370616400315435ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/multiple_input/barcodes.txt000066400000000000000000000000461350370616400340660ustar00rootroot00000000000000sample_1 GCGCCGGA sample_2 CAGGACAT adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/multiple_input/info.json000066400000000000000000000000711350370616400333670ustar00rootroot00000000000000{ "arguments": [], "return_code": 0, "stderr": [ ] } adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/multiple_input/input_1a.fastq000066400000000000000000000012211350370616400343170ustar00rootroot00000000000000@read_s1_000/1 GCGCCGGAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAAAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_000/1 CAGGACATAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAAAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_075/1 GCGCCGGAGACGGTCCCATTAATGCACTATCGGATTTACACATTTGCGTGAATAAATCGACAGATGAATCATTAAGCTCCTACAGATCGGAAGAGCACAC + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/multiple_input/input_1b.fastq000066400000000000000000000012211350370616400343200ustar00rootroot00000000000000@read_s2_150/1 CAGGACATTGATCTCATACATTTAAACAAAGTATGCCTTACGCATGCCTTAATGATACGTAACCTAGGCAACAGAGTCTTTACTTGTACCTGCTACACAC + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_200/1 GCGCCGGATCCATCAGGATCGTATTATACTAAGCTAGGACTGTGCAGTGCACAGAGAGGAGATGACCATGATCCTCGAGCAAGTTGCCGCAGGCTCGGGC + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_150/1 GCGCCGGATGCACCGTAGCCATATGGGCTGTTGGGGACACAGGGCGTCGGCATTCCTTTATTACTGACGCCGCTAGAGTCTATGCAAGGTTATAACGTAT + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/multiple_input/input_1c.fastq000066400000000000000000000006661350370616400343350ustar00rootroot00000000000000@read_s2_075/1 CAGGACATTCGCTAGCCCAAGATCACGCTTTCCGCGACGTTTTAGAGCGTGCATACCGGGGCGTTTCTCAGATAGGTATTTCAAGATCGGAAGAGCACAC + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_200/1 CAGGACATACCCTCACGCTTGCACGACGACAGCGGTCCCCTATAAATGTATGTTGACGCAGCGAGAGGCCAGGACCCGGGCGTGTTACCACTAAGACCCT + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/multiple_input/input_2a.fastq000066400000000000000000000012211350370616400343200ustar00rootroot00000000000000@read_s1_000/2 TCCGGCGCAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_000/2 ATGTCCTGAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_075/2 GTAGGAGCTTAATGATTCATCTGTCGATTTATTCACGCAAATGTGTAAATCCGATAGTGCATTAATGGGACCGTCTCCGGCGCAGATCGGAAGAGCGTCG + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/multiple_input/input_2b.fastq000066400000000000000000000012211350370616400343210ustar00rootroot00000000000000@read_s2_150/2 AGAACAGGATACAATGAAAATGCATCGCGTTGGCAACTCTCACCTTGCTCTTGGACCCGTGTGTAGCAGGTACAAGTAAAGACTCTGTTGCCTAGGTTAC + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_200/2 CCTTCTTATGCTCGACTGGCTCTGTATAAGCCCAAGACATTATGAAAGGTCTCGCGTTTGTCTACCAGGCTCCGTTACGGATACAAGTGCCCTACTGTCA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_150/2 ATCAAGGGAGGTCACGTGAATTTTGCCTTCTAGACTAGCGTACATGACCGCGAATTAGATACGTTATAACCTTGCATAGACTCTAGCGGCGTCAGTAATA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/multiple_input/input_2c.fastq000066400000000000000000000006661350370616400343360ustar00rootroot00000000000000@read_s2_075/2 TGAAATACCTATCTGAGAAACGCCCCGGTATGCACGCTCTAAAACGTCGCGGAAAGCGTGATCTTGGGCTAGCGAATGTCCTGAGATCGGAAGAGCGTCG + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_200/2 ATGCTGATTAGATATGTCTTTCATCGGCTTGTGACCGAGGAGTGGTACGGCCGTTCCATATTGGGTGATTAGGAAGATGTCCCGGCTTGCTGCTTCTCGT + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 your_output.sample_1.discarded000066400000000000000000000000461350370616400374460ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/multiple_input@read_s1_000/1 + @read_s1_000/2 + your_output.sample_1.pair1.truncated000066400000000000000000000010771350370616400405350ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/multiple_input@read_s1_075/1 GACGGTCCCATTAATGCACTATCGGATTTACACATTTGCGTGAATAAATCGACAGATGAATCATTAAGCTCCTAC + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; @read_s1_200/1 TCCATCAGGATCGTATTATACTAAGCTAGGACTGTGCAGTGCACAGAGAGGAGATGACCATGATCCTCGAGCAAGTTGCCGCAGGCTCGGGC + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_150/1 TGCACCGTAGCCATATGGGCTGTTGGGGACACAGGGCGTCGGCATTCCTTTATTACTGACGCCGCTAGAGTCTATGCAAGGTTATAACGTAT + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 your_output.sample_1.pair2.truncated000066400000000000000000000011371350370616400405330ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/multiple_input@read_s1_075/2 GTAGGAGCTTAATGATTCATCTGTCGATTTATTCACGCAAATGTGTAAATCCGATAGTGCATTAATGGGACCGTC + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>> @read_s1_200/2 CCTTCTTATGCTCGACTGGCTCTGTATAAGCCCAAGACATTATGAAAGGTCTCGCGTTTGTCTACCAGGCTCCGTTACGGATACAAGTGCCCTACTGTCA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_150/2 ATCAAGGGAGGTCACGTGAATTTTGCCTTCTAGACTAGCGTACATGACCGCGAATTAGATACGTTATAACCTTGCATAGACTCTAGCGGCGTCAGTAATA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 your_output.sample_1.settings000066400000000000000000000052651350370616400373740ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/multiple_inputAdapterRemoval ver. 2.2.0 Trimming of single-indexed paired-end reads [Demultiplexing] Maximum mismatches (total): 0 Maximum mate 1 mismatches: 0 Maximum mate 2 mismatches: 0 [Demultiplexing samples] Name Barcode_1 Barcode_2 sample_1* GCGCCGGA * sample_2 CAGGACAT * [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: TCCGGCGC_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 2459456692 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 [Trimming statistics] Total number of read pairs: 4 Number of unaligned read pairs: 1 Number of well aligned read pairs: 3 Number of discarded mate 1 reads: 1 Number of singleton mate 1 reads: 0 Number of discarded mate 2 reads: 1 Number of singleton mate 2 reads: 0 Number of reads with adapters[1]: 4 Number of retained reads: 6 Number of retained nucleotides: 534 Average length of retained reads: 89 [Length distribution] Length Mate1 Mate2 Singleton Discarded All 0 0 0 0 2 2 1 0 0 0 0 0 2 0 0 0 0 0 3 0 0 0 0 0 4 0 0 0 0 0 5 0 0 0 0 0 6 0 0 0 0 0 7 0 0 0 0 0 8 0 0 0 0 0 9 0 0 0 0 0 10 0 0 0 0 0 11 0 0 0 0 0 12 0 0 0 0 0 13 0 0 0 0 0 14 0 0 0 0 0 15 0 0 0 0 0 16 0 0 0 0 0 17 0 0 0 0 0 18 0 0 0 0 0 19 0 0 0 0 0 20 0 0 0 0 0 21 0 0 0 0 0 22 0 0 0 0 0 23 0 0 0 0 0 24 0 0 0 0 0 25 0 0 0 0 0 26 0 0 0 0 0 27 0 0 0 0 0 28 0 0 0 0 0 29 0 0 0 0 0 30 0 0 0 0 0 31 0 0 0 0 0 32 0 0 0 0 0 33 0 0 0 0 0 34 0 0 0 0 0 35 0 0 0 0 0 36 0 0 0 0 0 37 0 0 0 0 0 38 0 0 0 0 0 39 0 0 0 0 0 40 0 0 0 0 0 41 0 0 0 0 0 42 0 0 0 0 0 43 0 0 0 0 0 44 0 0 0 0 0 45 0 0 0 0 0 46 0 0 0 0 0 47 0 0 0 0 0 48 0 0 0 0 0 49 0 0 0 0 0 50 0 0 0 0 0 51 0 0 0 0 0 52 0 0 0 0 0 53 0 0 0 0 0 54 0 0 0 0 0 55 0 0 0 0 0 56 0 0 0 0 0 57 0 0 0 0 0 58 0 0 0 0 0 59 0 0 0 0 0 60 0 0 0 0 0 61 0 0 0 0 0 62 0 0 0 0 0 63 0 0 0 0 0 64 0 0 0 0 0 65 0 0 0 0 0 66 0 0 0 0 0 67 0 0 0 0 0 68 0 0 0 0 0 69 0 0 0 0 0 70 0 0 0 0 0 71 0 0 0 0 0 72 0 0 0 0 0 73 0 0 0 0 0 74 0 0 0 0 0 75 1 1 0 0 2 76 0 0 0 0 0 77 0 0 0 0 0 78 0 0 0 0 0 79 0 0 0 0 0 80 0 0 0 0 0 81 0 0 0 0 0 82 0 0 0 0 0 83 0 0 0 0 0 84 0 0 0 0 0 85 0 0 0 0 0 86 0 0 0 0 0 87 0 0 0 0 0 88 0 0 0 0 0 89 0 0 0 0 0 90 0 0 0 0 0 91 0 0 0 0 0 92 2 0 0 0 2 93 0 0 0 0 0 94 0 0 0 0 0 95 0 0 0 0 0 96 0 0 0 0 0 97 0 0 0 0 0 98 0 0 0 0 0 99 0 0 0 0 0 100 0 2 0 0 2 your_output.sample_1.singleton.truncated000066400000000000000000000000001350370616400415040ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/multiple_inputyour_output.sample_2.discarded000066400000000000000000000000461350370616400374470ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/multiple_input@read_s2_000/1 + @read_s2_000/2 + your_output.sample_2.pair1.truncated000066400000000000000000000010771350370616400405360ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/multiple_input@read_s2_150/1 TGATCTCATACATTTAAACAAAGTATGCCTTACGCATGCCTTAATGATACGTAACCTAGGCAACAGAGTCTTTACTTGTACCTGCTACACAC + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_075/1 TCGCTAGCCCAAGATCACGCTTTCCGCGACGTTTTAGAGCGTGCATACCGGGGCGTTTCTCAGATAGGTATTTCA + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; @read_s2_200/1 ACCCTCACGCTTGCACGACGACAGCGGTCCCCTATAAATGTATGTTGACGCAGCGAGAGGCCAGGACCCGGGCGTGTTACCACTAAGACCCT + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 your_output.sample_2.pair2.truncated000066400000000000000000000011371350370616400405340ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/multiple_input@read_s2_150/2 AGAACAGGATACAATGAAAATGCATCGCGTTGGCAACTCTCACCTTGCTCTTGGACCCGTGTGTAGCAGGTACAAGTAAAGACTCTGTTGCCTAGGTTAC + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_075/2 TGAAATACCTATCTGAGAAACGCCCCGGTATGCACGCTCTAAAACGTCGCGGAAAGCGTGATCTTGGGCTAGCGA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>> @read_s2_200/2 ATGCTGATTAGATATGTCTTTCATCGGCTTGTGACCGAGGAGTGGTACGGCCGTTCCATATTGGGTGATTAGGAAGATGTCCCGGCTTGCTGCTTCTCGT + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 your_output.sample_2.settings000066400000000000000000000052651350370616400373750ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/multiple_inputAdapterRemoval ver. 2.2.0 Trimming of single-indexed paired-end reads [Demultiplexing] Maximum mismatches (total): 0 Maximum mate 1 mismatches: 0 Maximum mate 2 mismatches: 0 [Demultiplexing samples] Name Barcode_1 Barcode_2 sample_1 GCGCCGGA * sample_2* CAGGACAT * [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: ATGTCCTG_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 2459456692 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 [Trimming statistics] Total number of read pairs: 4 Number of unaligned read pairs: 1 Number of well aligned read pairs: 3 Number of discarded mate 1 reads: 1 Number of singleton mate 1 reads: 0 Number of discarded mate 2 reads: 1 Number of singleton mate 2 reads: 0 Number of reads with adapters[1]: 4 Number of retained reads: 6 Number of retained nucleotides: 534 Average length of retained reads: 89 [Length distribution] Length Mate1 Mate2 Singleton Discarded All 0 0 0 0 2 2 1 0 0 0 0 0 2 0 0 0 0 0 3 0 0 0 0 0 4 0 0 0 0 0 5 0 0 0 0 0 6 0 0 0 0 0 7 0 0 0 0 0 8 0 0 0 0 0 9 0 0 0 0 0 10 0 0 0 0 0 11 0 0 0 0 0 12 0 0 0 0 0 13 0 0 0 0 0 14 0 0 0 0 0 15 0 0 0 0 0 16 0 0 0 0 0 17 0 0 0 0 0 18 0 0 0 0 0 19 0 0 0 0 0 20 0 0 0 0 0 21 0 0 0 0 0 22 0 0 0 0 0 23 0 0 0 0 0 24 0 0 0 0 0 25 0 0 0 0 0 26 0 0 0 0 0 27 0 0 0 0 0 28 0 0 0 0 0 29 0 0 0 0 0 30 0 0 0 0 0 31 0 0 0 0 0 32 0 0 0 0 0 33 0 0 0 0 0 34 0 0 0 0 0 35 0 0 0 0 0 36 0 0 0 0 0 37 0 0 0 0 0 38 0 0 0 0 0 39 0 0 0 0 0 40 0 0 0 0 0 41 0 0 0 0 0 42 0 0 0 0 0 43 0 0 0 0 0 44 0 0 0 0 0 45 0 0 0 0 0 46 0 0 0 0 0 47 0 0 0 0 0 48 0 0 0 0 0 49 0 0 0 0 0 50 0 0 0 0 0 51 0 0 0 0 0 52 0 0 0 0 0 53 0 0 0 0 0 54 0 0 0 0 0 55 0 0 0 0 0 56 0 0 0 0 0 57 0 0 0 0 0 58 0 0 0 0 0 59 0 0 0 0 0 60 0 0 0 0 0 61 0 0 0 0 0 62 0 0 0 0 0 63 0 0 0 0 0 64 0 0 0 0 0 65 0 0 0 0 0 66 0 0 0 0 0 67 0 0 0 0 0 68 0 0 0 0 0 69 0 0 0 0 0 70 0 0 0 0 0 71 0 0 0 0 0 72 0 0 0 0 0 73 0 0 0 0 0 74 0 0 0 0 0 75 1 1 0 0 2 76 0 0 0 0 0 77 0 0 0 0 0 78 0 0 0 0 0 79 0 0 0 0 0 80 0 0 0 0 0 81 0 0 0 0 0 82 0 0 0 0 0 83 0 0 0 0 0 84 0 0 0 0 0 85 0 0 0 0 0 86 0 0 0 0 0 87 0 0 0 0 0 88 0 0 0 0 0 89 0 0 0 0 0 90 0 0 0 0 0 91 0 0 0 0 0 92 2 0 0 0 2 93 0 0 0 0 0 94 0 0 0 0 0 95 0 0 0 0 0 96 0 0 0 0 0 97 0 0 0 0 0 98 0 0 0 0 0 99 0 0 0 0 0 100 0 2 0 0 2 your_output.sample_2.singleton.truncated000066400000000000000000000000001350370616400415050ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/multiple_inputyour_output.settings000066400000000000000000000021701350370616400356640ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/multiple_inputAdapterRemoval ver. 2.1.7 Trimming of single-indexed paired-end reads [Demultiplexing] Maximum mismatches (total): 0 Maximum mate 1 mismatches: 0 Maximum mate 2 mismatches: 0 [Demultiplexing samples] Name Barcode_1 Barcode_2 sample_1 GCGCCGGA * sample_2 CAGGACAT * [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 1157297082 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 [Demultiplexing statistics] Name Barcode_1 Barcode_2 Hits Fraction unidentified NA NA 0 0.000 ambiguous NA NA 0 0.000 sample_1 GCGCCGGA * 4 0.500 sample_2 CAGGACAT * 4 0.500 * * * 8 1.000 your_output.unidentified_1000066400000000000000000000000001350370616400367010ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/multiple_inputyour_output.unidentified_2000066400000000000000000000000001350370616400367020ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/multiple_inputadapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/threads/000077500000000000000000000000001350370616400301235ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/threads/one/000077500000000000000000000000001350370616400307045ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/threads/one/barcodes.txt000066400000000000000000000000461350370616400332270ustar00rootroot00000000000000sample_1 GCGCCGGA sample_2 CAGGACAT adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/threads/one/info.json000066400000000000000000000001111350370616400325230ustar00rootroot00000000000000{ "arguments": ["--threads", "1"], "return_code": 0, "stderr": [ ] } adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/threads/one/input_1.fastq000066400000000000000000000033301350370616400333220ustar00rootroot00000000000000@read_s1_000/1 GCGCCGGAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAAAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_000/1 CAGGACATAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAAAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_075/1 GCGCCGGAGACGGTCCCATTAATGCACTATCGGATTTACACATTTGCGTGAATAAATCGACAGATGAATCATTAAGCTCCTACAGATCGGAAGAGCACAC + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_150/1 CAGGACATTGATCTCATACATTTAAACAAAGTATGCCTTACGCATGCCTTAATGATACGTAACCTAGGCAACAGAGTCTTTACTTGTACCTGCTACACAC + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_200/1 GCGCCGGATCCATCAGGATCGTATTATACTAAGCTAGGACTGTGCAGTGCACAGAGAGGAGATGACCATGATCCTCGAGCAAGTTGCCGCAGGCTCGGGC + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_150/1 GCGCCGGATGCACCGTAGCCATATGGGCTGTTGGGGACACAGGGCGTCGGCATTCCTTTATTACTGACGCCGCTAGAGTCTATGCAAGGTTATAACGTAT + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_075/1 CAGGACATTCGCTAGCCCAAGATCACGCTTTCCGCGACGTTTTAGAGCGTGCATACCGGGGCGTTTCTCAGATAGGTATTTCAAGATCGGAAGAGCACAC + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_200/1 CAGGACATACCCTCACGCTTGCACGACGACAGCGGTCCCCTATAAATGTATGTTGACGCAGCGAGAGGCCAGGACCCGGGCGTGTTACCACTAAGACCCT + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/threads/one/input_2.fastq000066400000000000000000000033301350370616400333230ustar00rootroot00000000000000@read_s1_000/2 TCCGGCGCAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_000/2 ATGTCCTGAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_075/2 GTAGGAGCTTAATGATTCATCTGTCGATTTATTCACGCAAATGTGTAAATCCGATAGTGCATTAATGGGACCGTCTCCGGCGCAGATCGGAAGAGCGTCG + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_150/2 AGAACAGGATACAATGAAAATGCATCGCGTTGGCAACTCTCACCTTGCTCTTGGACCCGTGTGTAGCAGGTACAAGTAAAGACTCTGTTGCCTAGGTTAC + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_200/2 CCTTCTTATGCTCGACTGGCTCTGTATAAGCCCAAGACATTATGAAAGGTCTCGCGTTTGTCTACCAGGCTCCGTTACGGATACAAGTGCCCTACTGTCA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_150/2 ATCAAGGGAGGTCACGTGAATTTTGCCTTCTAGACTAGCGTACATGACCGCGAATTAGATACGTTATAACCTTGCATAGACTCTAGCGGCGTCAGTAATA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_075/2 TGAAATACCTATCTGAGAAACGCCCCGGTATGCACGCTCTAAAACGTCGCGGAAAGCGTGATCTTGGGCTAGCGAATGTCCTGAGATCGGAAGAGCGTCG + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_200/2 ATGCTGATTAGATATGTCTTTCATCGGCTTGTGACCGAGGAGTGGTACGGCCGTTCCATATTGGGTGATTAGGAAGATGTCCCGGCTTGCTGCTTCTCGT + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 your_output.sample_1.discarded000066400000000000000000000000461350370616400366070ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/threads/one@read_s1_000/1 + @read_s1_000/2 + your_output.sample_1.pair1.truncated000066400000000000000000000010771350370616400376760ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/threads/one@read_s1_075/1 GACGGTCCCATTAATGCACTATCGGATTTACACATTTGCGTGAATAAATCGACAGATGAATCATTAAGCTCCTAC + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; @read_s1_200/1 TCCATCAGGATCGTATTATACTAAGCTAGGACTGTGCAGTGCACAGAGAGGAGATGACCATGATCCTCGAGCAAGTTGCCGCAGGCTCGGGC + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_150/1 TGCACCGTAGCCATATGGGCTGTTGGGGACACAGGGCGTCGGCATTCCTTTATTACTGACGCCGCTAGAGTCTATGCAAGGTTATAACGTAT + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 your_output.sample_1.pair2.truncated000066400000000000000000000011371350370616400376740ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/threads/one@read_s1_075/2 GTAGGAGCTTAATGATTCATCTGTCGATTTATTCACGCAAATGTGTAAATCCGATAGTGCATTAATGGGACCGTC + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>> @read_s1_200/2 CCTTCTTATGCTCGACTGGCTCTGTATAAGCCCAAGACATTATGAAAGGTCTCGCGTTTGTCTACCAGGCTCCGTTACGGATACAAGTGCCCTACTGTCA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_150/2 ATCAAGGGAGGTCACGTGAATTTTGCCTTCTAGACTAGCGTACATGACCGCGAATTAGATACGTTATAACCTTGCATAGACTCTAGCGGCGTCAGTAATA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 your_output.sample_1.settings000066400000000000000000000052651350370616400365350ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/threads/oneAdapterRemoval ver. 2.2.0 Trimming of single-indexed paired-end reads [Demultiplexing] Maximum mismatches (total): 0 Maximum mate 1 mismatches: 0 Maximum mate 2 mismatches: 0 [Demultiplexing samples] Name Barcode_1 Barcode_2 sample_1* GCGCCGGA * sample_2 CAGGACAT * [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: TCCGGCGC_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 2459456692 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 [Trimming statistics] Total number of read pairs: 4 Number of unaligned read pairs: 1 Number of well aligned read pairs: 3 Number of discarded mate 1 reads: 1 Number of singleton mate 1 reads: 0 Number of discarded mate 2 reads: 1 Number of singleton mate 2 reads: 0 Number of reads with adapters[1]: 4 Number of retained reads: 6 Number of retained nucleotides: 534 Average length of retained reads: 89 [Length distribution] Length Mate1 Mate2 Singleton Discarded All 0 0 0 0 2 2 1 0 0 0 0 0 2 0 0 0 0 0 3 0 0 0 0 0 4 0 0 0 0 0 5 0 0 0 0 0 6 0 0 0 0 0 7 0 0 0 0 0 8 0 0 0 0 0 9 0 0 0 0 0 10 0 0 0 0 0 11 0 0 0 0 0 12 0 0 0 0 0 13 0 0 0 0 0 14 0 0 0 0 0 15 0 0 0 0 0 16 0 0 0 0 0 17 0 0 0 0 0 18 0 0 0 0 0 19 0 0 0 0 0 20 0 0 0 0 0 21 0 0 0 0 0 22 0 0 0 0 0 23 0 0 0 0 0 24 0 0 0 0 0 25 0 0 0 0 0 26 0 0 0 0 0 27 0 0 0 0 0 28 0 0 0 0 0 29 0 0 0 0 0 30 0 0 0 0 0 31 0 0 0 0 0 32 0 0 0 0 0 33 0 0 0 0 0 34 0 0 0 0 0 35 0 0 0 0 0 36 0 0 0 0 0 37 0 0 0 0 0 38 0 0 0 0 0 39 0 0 0 0 0 40 0 0 0 0 0 41 0 0 0 0 0 42 0 0 0 0 0 43 0 0 0 0 0 44 0 0 0 0 0 45 0 0 0 0 0 46 0 0 0 0 0 47 0 0 0 0 0 48 0 0 0 0 0 49 0 0 0 0 0 50 0 0 0 0 0 51 0 0 0 0 0 52 0 0 0 0 0 53 0 0 0 0 0 54 0 0 0 0 0 55 0 0 0 0 0 56 0 0 0 0 0 57 0 0 0 0 0 58 0 0 0 0 0 59 0 0 0 0 0 60 0 0 0 0 0 61 0 0 0 0 0 62 0 0 0 0 0 63 0 0 0 0 0 64 0 0 0 0 0 65 0 0 0 0 0 66 0 0 0 0 0 67 0 0 0 0 0 68 0 0 0 0 0 69 0 0 0 0 0 70 0 0 0 0 0 71 0 0 0 0 0 72 0 0 0 0 0 73 0 0 0 0 0 74 0 0 0 0 0 75 1 1 0 0 2 76 0 0 0 0 0 77 0 0 0 0 0 78 0 0 0 0 0 79 0 0 0 0 0 80 0 0 0 0 0 81 0 0 0 0 0 82 0 0 0 0 0 83 0 0 0 0 0 84 0 0 0 0 0 85 0 0 0 0 0 86 0 0 0 0 0 87 0 0 0 0 0 88 0 0 0 0 0 89 0 0 0 0 0 90 0 0 0 0 0 91 0 0 0 0 0 92 2 0 0 0 2 93 0 0 0 0 0 94 0 0 0 0 0 95 0 0 0 0 0 96 0 0 0 0 0 97 0 0 0 0 0 98 0 0 0 0 0 99 0 0 0 0 0 100 0 2 0 0 2 your_output.sample_1.singleton.truncated000066400000000000000000000000001350370616400406450ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/threads/oneyour_output.sample_2.discarded000066400000000000000000000000461350370616400366100ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/threads/one@read_s2_000/1 + @read_s2_000/2 + your_output.sample_2.pair1.truncated000066400000000000000000000010771350370616400376770ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/threads/one@read_s2_150/1 TGATCTCATACATTTAAACAAAGTATGCCTTACGCATGCCTTAATGATACGTAACCTAGGCAACAGAGTCTTTACTTGTACCTGCTACACAC + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_075/1 TCGCTAGCCCAAGATCACGCTTTCCGCGACGTTTTAGAGCGTGCATACCGGGGCGTTTCTCAGATAGGTATTTCA + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; @read_s2_200/1 ACCCTCACGCTTGCACGACGACAGCGGTCCCCTATAAATGTATGTTGACGCAGCGAGAGGCCAGGACCCGGGCGTGTTACCACTAAGACCCT + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 your_output.sample_2.pair2.truncated000066400000000000000000000011371350370616400376750ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/threads/one@read_s2_150/2 AGAACAGGATACAATGAAAATGCATCGCGTTGGCAACTCTCACCTTGCTCTTGGACCCGTGTGTAGCAGGTACAAGTAAAGACTCTGTTGCCTAGGTTAC + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_075/2 TGAAATACCTATCTGAGAAACGCCCCGGTATGCACGCTCTAAAACGTCGCGGAAAGCGTGATCTTGGGCTAGCGA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>> @read_s2_200/2 ATGCTGATTAGATATGTCTTTCATCGGCTTGTGACCGAGGAGTGGTACGGCCGTTCCATATTGGGTGATTAGGAAGATGTCCCGGCTTGCTGCTTCTCGT + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 your_output.sample_2.settings000066400000000000000000000052651350370616400365360ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/threads/oneAdapterRemoval ver. 2.2.0 Trimming of single-indexed paired-end reads [Demultiplexing] Maximum mismatches (total): 0 Maximum mate 1 mismatches: 0 Maximum mate 2 mismatches: 0 [Demultiplexing samples] Name Barcode_1 Barcode_2 sample_1 GCGCCGGA * sample_2* CAGGACAT * [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: ATGTCCTG_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 2459456692 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 [Trimming statistics] Total number of read pairs: 4 Number of unaligned read pairs: 1 Number of well aligned read pairs: 3 Number of discarded mate 1 reads: 1 Number of singleton mate 1 reads: 0 Number of discarded mate 2 reads: 1 Number of singleton mate 2 reads: 0 Number of reads with adapters[1]: 4 Number of retained reads: 6 Number of retained nucleotides: 534 Average length of retained reads: 89 [Length distribution] Length Mate1 Mate2 Singleton Discarded All 0 0 0 0 2 2 1 0 0 0 0 0 2 0 0 0 0 0 3 0 0 0 0 0 4 0 0 0 0 0 5 0 0 0 0 0 6 0 0 0 0 0 7 0 0 0 0 0 8 0 0 0 0 0 9 0 0 0 0 0 10 0 0 0 0 0 11 0 0 0 0 0 12 0 0 0 0 0 13 0 0 0 0 0 14 0 0 0 0 0 15 0 0 0 0 0 16 0 0 0 0 0 17 0 0 0 0 0 18 0 0 0 0 0 19 0 0 0 0 0 20 0 0 0 0 0 21 0 0 0 0 0 22 0 0 0 0 0 23 0 0 0 0 0 24 0 0 0 0 0 25 0 0 0 0 0 26 0 0 0 0 0 27 0 0 0 0 0 28 0 0 0 0 0 29 0 0 0 0 0 30 0 0 0 0 0 31 0 0 0 0 0 32 0 0 0 0 0 33 0 0 0 0 0 34 0 0 0 0 0 35 0 0 0 0 0 36 0 0 0 0 0 37 0 0 0 0 0 38 0 0 0 0 0 39 0 0 0 0 0 40 0 0 0 0 0 41 0 0 0 0 0 42 0 0 0 0 0 43 0 0 0 0 0 44 0 0 0 0 0 45 0 0 0 0 0 46 0 0 0 0 0 47 0 0 0 0 0 48 0 0 0 0 0 49 0 0 0 0 0 50 0 0 0 0 0 51 0 0 0 0 0 52 0 0 0 0 0 53 0 0 0 0 0 54 0 0 0 0 0 55 0 0 0 0 0 56 0 0 0 0 0 57 0 0 0 0 0 58 0 0 0 0 0 59 0 0 0 0 0 60 0 0 0 0 0 61 0 0 0 0 0 62 0 0 0 0 0 63 0 0 0 0 0 64 0 0 0 0 0 65 0 0 0 0 0 66 0 0 0 0 0 67 0 0 0 0 0 68 0 0 0 0 0 69 0 0 0 0 0 70 0 0 0 0 0 71 0 0 0 0 0 72 0 0 0 0 0 73 0 0 0 0 0 74 0 0 0 0 0 75 1 1 0 0 2 76 0 0 0 0 0 77 0 0 0 0 0 78 0 0 0 0 0 79 0 0 0 0 0 80 0 0 0 0 0 81 0 0 0 0 0 82 0 0 0 0 0 83 0 0 0 0 0 84 0 0 0 0 0 85 0 0 0 0 0 86 0 0 0 0 0 87 0 0 0 0 0 88 0 0 0 0 0 89 0 0 0 0 0 90 0 0 0 0 0 91 0 0 0 0 0 92 2 0 0 0 2 93 0 0 0 0 0 94 0 0 0 0 0 95 0 0 0 0 0 96 0 0 0 0 0 97 0 0 0 0 0 98 0 0 0 0 0 99 0 0 0 0 0 100 0 2 0 0 2 your_output.sample_2.singleton.truncated000066400000000000000000000000001350370616400406460ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/threads/oneyour_output.settings000066400000000000000000000021701350370616400350250ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/threads/oneAdapterRemoval ver. 2.1.7 Trimming of single-indexed paired-end reads [Demultiplexing] Maximum mismatches (total): 0 Maximum mate 1 mismatches: 0 Maximum mate 2 mismatches: 0 [Demultiplexing samples] Name Barcode_1 Barcode_2 sample_1 GCGCCGGA * sample_2 CAGGACAT * [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 1157297082 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 [Demultiplexing statistics] Name Barcode_1 Barcode_2 Hits Fraction unidentified NA NA 0 0.000 ambiguous NA NA 0 0.000 sample_1 GCGCCGGA * 4 0.500 sample_2 CAGGACAT * 4 0.500 * * * 8 1.000 your_output.unidentified_1000066400000000000000000000000001350370616400360420ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/threads/oneyour_output.unidentified_2000066400000000000000000000000001350370616400360430ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/threads/oneadapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/threads/three/000077500000000000000000000000001350370616400312325ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/threads/three/barcodes.txt000066400000000000000000000000461350370616400335550ustar00rootroot00000000000000sample_1 GCGCCGGA sample_2 CAGGACAT adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/threads/three/info.json000066400000000000000000000001101350370616400330500ustar00rootroot00000000000000{ "arguments": ["--thread", "3"], "return_code": 0, "stderr": [ ] } adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/threads/three/input_1.fastq000066400000000000000000000033301350370616400336500ustar00rootroot00000000000000@read_s1_000/1 GCGCCGGAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAAAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_000/1 CAGGACATAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAAAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_075/1 GCGCCGGAGACGGTCCCATTAATGCACTATCGGATTTACACATTTGCGTGAATAAATCGACAGATGAATCATTAAGCTCCTACAGATCGGAAGAGCACAC + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_150/1 CAGGACATTGATCTCATACATTTAAACAAAGTATGCCTTACGCATGCCTTAATGATACGTAACCTAGGCAACAGAGTCTTTACTTGTACCTGCTACACAC + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_200/1 GCGCCGGATCCATCAGGATCGTATTATACTAAGCTAGGACTGTGCAGTGCACAGAGAGGAGATGACCATGATCCTCGAGCAAGTTGCCGCAGGCTCGGGC + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_150/1 GCGCCGGATGCACCGTAGCCATATGGGCTGTTGGGGACACAGGGCGTCGGCATTCCTTTATTACTGACGCCGCTAGAGTCTATGCAAGGTTATAACGTAT + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_075/1 CAGGACATTCGCTAGCCCAAGATCACGCTTTCCGCGACGTTTTAGAGCGTGCATACCGGGGCGTTTCTCAGATAGGTATTTCAAGATCGGAAGAGCACAC + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_200/1 CAGGACATACCCTCACGCTTGCACGACGACAGCGGTCCCCTATAAATGTATGTTGACGCAGCGAGAGGCCAGGACCCGGGCGTGTTACCACTAAGACCCT + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/threads/three/input_2.fastq000066400000000000000000000033301350370616400336510ustar00rootroot00000000000000@read_s1_000/2 TCCGGCGCAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_000/2 ATGTCCTGAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_075/2 GTAGGAGCTTAATGATTCATCTGTCGATTTATTCACGCAAATGTGTAAATCCGATAGTGCATTAATGGGACCGTCTCCGGCGCAGATCGGAAGAGCGTCG + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_150/2 AGAACAGGATACAATGAAAATGCATCGCGTTGGCAACTCTCACCTTGCTCTTGGACCCGTGTGTAGCAGGTACAAGTAAAGACTCTGTTGCCTAGGTTAC + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_200/2 CCTTCTTATGCTCGACTGGCTCTGTATAAGCCCAAGACATTATGAAAGGTCTCGCGTTTGTCTACCAGGCTCCGTTACGGATACAAGTGCCCTACTGTCA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_150/2 ATCAAGGGAGGTCACGTGAATTTTGCCTTCTAGACTAGCGTACATGACCGCGAATTAGATACGTTATAACCTTGCATAGACTCTAGCGGCGTCAGTAATA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_075/2 TGAAATACCTATCTGAGAAACGCCCCGGTATGCACGCTCTAAAACGTCGCGGAAAGCGTGATCTTGGGCTAGCGAATGTCCTGAGATCGGAAGAGCGTCG + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_200/2 ATGCTGATTAGATATGTCTTTCATCGGCTTGTGACCGAGGAGTGGTACGGCCGTTCCATATTGGGTGATTAGGAAGATGTCCCGGCTTGCTGCTTCTCGT + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 your_output.sample_1.discarded000066400000000000000000000000461350370616400371350ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/threads/three@read_s1_000/1 + @read_s1_000/2 + your_output.sample_1.pair1.truncated000066400000000000000000000010771350370616400402240ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/threads/three@read_s1_075/1 GACGGTCCCATTAATGCACTATCGGATTTACACATTTGCGTGAATAAATCGACAGATGAATCATTAAGCTCCTAC + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; @read_s1_200/1 TCCATCAGGATCGTATTATACTAAGCTAGGACTGTGCAGTGCACAGAGAGGAGATGACCATGATCCTCGAGCAAGTTGCCGCAGGCTCGGGC + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_150/1 TGCACCGTAGCCATATGGGCTGTTGGGGACACAGGGCGTCGGCATTCCTTTATTACTGACGCCGCTAGAGTCTATGCAAGGTTATAACGTAT + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 your_output.sample_1.pair2.truncated000066400000000000000000000011371350370616400402220ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/threads/three@read_s1_075/2 GTAGGAGCTTAATGATTCATCTGTCGATTTATTCACGCAAATGTGTAAATCCGATAGTGCATTAATGGGACCGTC + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>> @read_s1_200/2 CCTTCTTATGCTCGACTGGCTCTGTATAAGCCCAAGACATTATGAAAGGTCTCGCGTTTGTCTACCAGGCTCCGTTACGGATACAAGTGCCCTACTGTCA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_150/2 ATCAAGGGAGGTCACGTGAATTTTGCCTTCTAGACTAGCGTACATGACCGCGAATTAGATACGTTATAACCTTGCATAGACTCTAGCGGCGTCAGTAATA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 your_output.sample_1.settings000066400000000000000000000052551350370616400370620ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/threads/threeAdapterRemoval ver. 2.2.0 Trimming of single-indexed paired-end reads [Demultiplexing] Maximum mismatches (total): 0 Maximum mate 1 mismatches: 0 Maximum mate 2 mismatches: 0 [Demultiplexing samples] Name Barcode_1 Barcode_2 sample_1* GCGCCGGA * sample_2 CAGGACAT * [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: TCCGGCGC_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: NA Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 [Trimming statistics] Total number of read pairs: 4 Number of unaligned read pairs: 1 Number of well aligned read pairs: 3 Number of discarded mate 1 reads: 1 Number of singleton mate 1 reads: 0 Number of discarded mate 2 reads: 1 Number of singleton mate 2 reads: 0 Number of reads with adapters[1]: 4 Number of retained reads: 6 Number of retained nucleotides: 534 Average length of retained reads: 89 [Length distribution] Length Mate1 Mate2 Singleton Discarded All 0 0 0 0 2 2 1 0 0 0 0 0 2 0 0 0 0 0 3 0 0 0 0 0 4 0 0 0 0 0 5 0 0 0 0 0 6 0 0 0 0 0 7 0 0 0 0 0 8 0 0 0 0 0 9 0 0 0 0 0 10 0 0 0 0 0 11 0 0 0 0 0 12 0 0 0 0 0 13 0 0 0 0 0 14 0 0 0 0 0 15 0 0 0 0 0 16 0 0 0 0 0 17 0 0 0 0 0 18 0 0 0 0 0 19 0 0 0 0 0 20 0 0 0 0 0 21 0 0 0 0 0 22 0 0 0 0 0 23 0 0 0 0 0 24 0 0 0 0 0 25 0 0 0 0 0 26 0 0 0 0 0 27 0 0 0 0 0 28 0 0 0 0 0 29 0 0 0 0 0 30 0 0 0 0 0 31 0 0 0 0 0 32 0 0 0 0 0 33 0 0 0 0 0 34 0 0 0 0 0 35 0 0 0 0 0 36 0 0 0 0 0 37 0 0 0 0 0 38 0 0 0 0 0 39 0 0 0 0 0 40 0 0 0 0 0 41 0 0 0 0 0 42 0 0 0 0 0 43 0 0 0 0 0 44 0 0 0 0 0 45 0 0 0 0 0 46 0 0 0 0 0 47 0 0 0 0 0 48 0 0 0 0 0 49 0 0 0 0 0 50 0 0 0 0 0 51 0 0 0 0 0 52 0 0 0 0 0 53 0 0 0 0 0 54 0 0 0 0 0 55 0 0 0 0 0 56 0 0 0 0 0 57 0 0 0 0 0 58 0 0 0 0 0 59 0 0 0 0 0 60 0 0 0 0 0 61 0 0 0 0 0 62 0 0 0 0 0 63 0 0 0 0 0 64 0 0 0 0 0 65 0 0 0 0 0 66 0 0 0 0 0 67 0 0 0 0 0 68 0 0 0 0 0 69 0 0 0 0 0 70 0 0 0 0 0 71 0 0 0 0 0 72 0 0 0 0 0 73 0 0 0 0 0 74 0 0 0 0 0 75 1 1 0 0 2 76 0 0 0 0 0 77 0 0 0 0 0 78 0 0 0 0 0 79 0 0 0 0 0 80 0 0 0 0 0 81 0 0 0 0 0 82 0 0 0 0 0 83 0 0 0 0 0 84 0 0 0 0 0 85 0 0 0 0 0 86 0 0 0 0 0 87 0 0 0 0 0 88 0 0 0 0 0 89 0 0 0 0 0 90 0 0 0 0 0 91 0 0 0 0 0 92 2 0 0 0 2 93 0 0 0 0 0 94 0 0 0 0 0 95 0 0 0 0 0 96 0 0 0 0 0 97 0 0 0 0 0 98 0 0 0 0 0 99 0 0 0 0 0 100 0 2 0 0 2 your_output.sample_1.singleton.truncated000066400000000000000000000000001350370616400411730ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/threads/threeyour_output.sample_2.discarded000066400000000000000000000000461350370616400371360ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/threads/three@read_s2_000/1 + @read_s2_000/2 + your_output.sample_2.pair1.truncated000066400000000000000000000010771350370616400402250ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/threads/three@read_s2_150/1 TGATCTCATACATTTAAACAAAGTATGCCTTACGCATGCCTTAATGATACGTAACCTAGGCAACAGAGTCTTTACTTGTACCTGCTACACAC + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_075/1 TCGCTAGCCCAAGATCACGCTTTCCGCGACGTTTTAGAGCGTGCATACCGGGGCGTTTCTCAGATAGGTATTTCA + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; @read_s2_200/1 ACCCTCACGCTTGCACGACGACAGCGGTCCCCTATAAATGTATGTTGACGCAGCGAGAGGCCAGGACCCGGGCGTGTTACCACTAAGACCCT + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 your_output.sample_2.pair2.truncated000066400000000000000000000011371350370616400402230ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/threads/three@read_s2_150/2 AGAACAGGATACAATGAAAATGCATCGCGTTGGCAACTCTCACCTTGCTCTTGGACCCGTGTGTAGCAGGTACAAGTAAAGACTCTGTTGCCTAGGTTAC + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_075/2 TGAAATACCTATCTGAGAAACGCCCCGGTATGCACGCTCTAAAACGTCGCGGAAAGCGTGATCTTGGGCTAGCGA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>> @read_s2_200/2 ATGCTGATTAGATATGTCTTTCATCGGCTTGTGACCGAGGAGTGGTACGGCCGTTCCATATTGGGTGATTAGGAAGATGTCCCGGCTTGCTGCTTCTCGT + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 your_output.sample_2.settings000066400000000000000000000052551350370616400370630ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/threads/threeAdapterRemoval ver. 2.2.0 Trimming of single-indexed paired-end reads [Demultiplexing] Maximum mismatches (total): 0 Maximum mate 1 mismatches: 0 Maximum mate 2 mismatches: 0 [Demultiplexing samples] Name Barcode_1 Barcode_2 sample_1 GCGCCGGA * sample_2* CAGGACAT * [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: ATGTCCTG_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: NA Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 [Trimming statistics] Total number of read pairs: 4 Number of unaligned read pairs: 1 Number of well aligned read pairs: 3 Number of discarded mate 1 reads: 1 Number of singleton mate 1 reads: 0 Number of discarded mate 2 reads: 1 Number of singleton mate 2 reads: 0 Number of reads with adapters[1]: 4 Number of retained reads: 6 Number of retained nucleotides: 534 Average length of retained reads: 89 [Length distribution] Length Mate1 Mate2 Singleton Discarded All 0 0 0 0 2 2 1 0 0 0 0 0 2 0 0 0 0 0 3 0 0 0 0 0 4 0 0 0 0 0 5 0 0 0 0 0 6 0 0 0 0 0 7 0 0 0 0 0 8 0 0 0 0 0 9 0 0 0 0 0 10 0 0 0 0 0 11 0 0 0 0 0 12 0 0 0 0 0 13 0 0 0 0 0 14 0 0 0 0 0 15 0 0 0 0 0 16 0 0 0 0 0 17 0 0 0 0 0 18 0 0 0 0 0 19 0 0 0 0 0 20 0 0 0 0 0 21 0 0 0 0 0 22 0 0 0 0 0 23 0 0 0 0 0 24 0 0 0 0 0 25 0 0 0 0 0 26 0 0 0 0 0 27 0 0 0 0 0 28 0 0 0 0 0 29 0 0 0 0 0 30 0 0 0 0 0 31 0 0 0 0 0 32 0 0 0 0 0 33 0 0 0 0 0 34 0 0 0 0 0 35 0 0 0 0 0 36 0 0 0 0 0 37 0 0 0 0 0 38 0 0 0 0 0 39 0 0 0 0 0 40 0 0 0 0 0 41 0 0 0 0 0 42 0 0 0 0 0 43 0 0 0 0 0 44 0 0 0 0 0 45 0 0 0 0 0 46 0 0 0 0 0 47 0 0 0 0 0 48 0 0 0 0 0 49 0 0 0 0 0 50 0 0 0 0 0 51 0 0 0 0 0 52 0 0 0 0 0 53 0 0 0 0 0 54 0 0 0 0 0 55 0 0 0 0 0 56 0 0 0 0 0 57 0 0 0 0 0 58 0 0 0 0 0 59 0 0 0 0 0 60 0 0 0 0 0 61 0 0 0 0 0 62 0 0 0 0 0 63 0 0 0 0 0 64 0 0 0 0 0 65 0 0 0 0 0 66 0 0 0 0 0 67 0 0 0 0 0 68 0 0 0 0 0 69 0 0 0 0 0 70 0 0 0 0 0 71 0 0 0 0 0 72 0 0 0 0 0 73 0 0 0 0 0 74 0 0 0 0 0 75 1 1 0 0 2 76 0 0 0 0 0 77 0 0 0 0 0 78 0 0 0 0 0 79 0 0 0 0 0 80 0 0 0 0 0 81 0 0 0 0 0 82 0 0 0 0 0 83 0 0 0 0 0 84 0 0 0 0 0 85 0 0 0 0 0 86 0 0 0 0 0 87 0 0 0 0 0 88 0 0 0 0 0 89 0 0 0 0 0 90 0 0 0 0 0 91 0 0 0 0 0 92 2 0 0 0 2 93 0 0 0 0 0 94 0 0 0 0 0 95 0 0 0 0 0 96 0 0 0 0 0 97 0 0 0 0 0 98 0 0 0 0 0 99 0 0 0 0 0 100 0 2 0 0 2 your_output.sample_2.singleton.truncated000066400000000000000000000000001350370616400411740ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/threads/threeyour_output.settings000066400000000000000000000021601350370616400353520ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/threads/threeAdapterRemoval ver. 2.1.7 Trimming of single-indexed paired-end reads [Demultiplexing] Maximum mismatches (total): 0 Maximum mate 1 mismatches: 0 Maximum mate 2 mismatches: 0 [Demultiplexing samples] Name Barcode_1 Barcode_2 sample_1 GCGCCGGA * sample_2 CAGGACAT * [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: NA Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 [Demultiplexing statistics] Name Barcode_1 Barcode_2 Hits Fraction unidentified NA NA 0 0.000 ambiguous NA NA 0 0.000 sample_1 GCGCCGGA * 4 0.500 sample_2 CAGGACAT * 4 0.500 * * * 8 1.000 your_output.unidentified_1000066400000000000000000000000001350370616400363700ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/threads/threeyour_output.unidentified_2000066400000000000000000000000001350370616400363710ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/threads/threeadapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/threads/two/000077500000000000000000000000001350370616400307345ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/threads/two/barcodes.txt000066400000000000000000000000461350370616400332570ustar00rootroot00000000000000sample_1 GCGCCGGA sample_2 CAGGACAT adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/threads/two/info.json000066400000000000000000000001111350370616400325530ustar00rootroot00000000000000{ "arguments": ["--threads", "2"], "return_code": 0, "stderr": [ ] } adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/threads/two/input_1.fastq000066400000000000000000000033301350370616400333520ustar00rootroot00000000000000@read_s1_000/1 GCGCCGGAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAAAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_000/1 CAGGACATAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAAAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_075/1 GCGCCGGAGACGGTCCCATTAATGCACTATCGGATTTACACATTTGCGTGAATAAATCGACAGATGAATCATTAAGCTCCTACAGATCGGAAGAGCACAC + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_150/1 CAGGACATTGATCTCATACATTTAAACAAAGTATGCCTTACGCATGCCTTAATGATACGTAACCTAGGCAACAGAGTCTTTACTTGTACCTGCTACACAC + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_200/1 GCGCCGGATCCATCAGGATCGTATTATACTAAGCTAGGACTGTGCAGTGCACAGAGAGGAGATGACCATGATCCTCGAGCAAGTTGCCGCAGGCTCGGGC + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_150/1 GCGCCGGATGCACCGTAGCCATATGGGCTGTTGGGGACACAGGGCGTCGGCATTCCTTTATTACTGACGCCGCTAGAGTCTATGCAAGGTTATAACGTAT + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_075/1 CAGGACATTCGCTAGCCCAAGATCACGCTTTCCGCGACGTTTTAGAGCGTGCATACCGGGGCGTTTCTCAGATAGGTATTTCAAGATCGGAAGAGCACAC + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_200/1 CAGGACATACCCTCACGCTTGCACGACGACAGCGGTCCCCTATAAATGTATGTTGACGCAGCGAGAGGCCAGGACCCGGGCGTGTTACCACTAAGACCCT + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/threads/two/input_2.fastq000066400000000000000000000033301350370616400333530ustar00rootroot00000000000000@read_s1_000/2 TCCGGCGCAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_000/2 ATGTCCTGAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_075/2 GTAGGAGCTTAATGATTCATCTGTCGATTTATTCACGCAAATGTGTAAATCCGATAGTGCATTAATGGGACCGTCTCCGGCGCAGATCGGAAGAGCGTCG + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_150/2 AGAACAGGATACAATGAAAATGCATCGCGTTGGCAACTCTCACCTTGCTCTTGGACCCGTGTGTAGCAGGTACAAGTAAAGACTCTGTTGCCTAGGTTAC + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_200/2 CCTTCTTATGCTCGACTGGCTCTGTATAAGCCCAAGACATTATGAAAGGTCTCGCGTTTGTCTACCAGGCTCCGTTACGGATACAAGTGCCCTACTGTCA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_150/2 ATCAAGGGAGGTCACGTGAATTTTGCCTTCTAGACTAGCGTACATGACCGCGAATTAGATACGTTATAACCTTGCATAGACTCTAGCGGCGTCAGTAATA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_075/2 TGAAATACCTATCTGAGAAACGCCCCGGTATGCACGCTCTAAAACGTCGCGGAAAGCGTGATCTTGGGCTAGCGAATGTCCTGAGATCGGAAGAGCGTCG + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_200/2 ATGCTGATTAGATATGTCTTTCATCGGCTTGTGACCGAGGAGTGGTACGGCCGTTCCATATTGGGTGATTAGGAAGATGTCCCGGCTTGCTGCTTCTCGT + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 your_output.sample_1.discarded000066400000000000000000000000461350370616400366370ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/threads/two@read_s1_000/1 + @read_s1_000/2 + your_output.sample_1.pair1.truncated000066400000000000000000000010771350370616400377260ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/threads/two@read_s1_075/1 GACGGTCCCATTAATGCACTATCGGATTTACACATTTGCGTGAATAAATCGACAGATGAATCATTAAGCTCCTAC + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; @read_s1_200/1 TCCATCAGGATCGTATTATACTAAGCTAGGACTGTGCAGTGCACAGAGAGGAGATGACCATGATCCTCGAGCAAGTTGCCGCAGGCTCGGGC + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_150/1 TGCACCGTAGCCATATGGGCTGTTGGGGACACAGGGCGTCGGCATTCCTTTATTACTGACGCCGCTAGAGTCTATGCAAGGTTATAACGTAT + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 your_output.sample_1.pair2.truncated000066400000000000000000000011371350370616400377240ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/threads/two@read_s1_075/2 GTAGGAGCTTAATGATTCATCTGTCGATTTATTCACGCAAATGTGTAAATCCGATAGTGCATTAATGGGACCGTC + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>> @read_s1_200/2 CCTTCTTATGCTCGACTGGCTCTGTATAAGCCCAAGACATTATGAAAGGTCTCGCGTTTGTCTACCAGGCTCCGTTACGGATACAAGTGCCCTACTGTCA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_150/2 ATCAAGGGAGGTCACGTGAATTTTGCCTTCTAGACTAGCGTACATGACCGCGAATTAGATACGTTATAACCTTGCATAGACTCTAGCGGCGTCAGTAATA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 your_output.sample_1.settings000066400000000000000000000052551350370616400365640ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/threads/twoAdapterRemoval ver. 2.2.0 Trimming of single-indexed paired-end reads [Demultiplexing] Maximum mismatches (total): 0 Maximum mate 1 mismatches: 0 Maximum mate 2 mismatches: 0 [Demultiplexing samples] Name Barcode_1 Barcode_2 sample_1* GCGCCGGA * sample_2 CAGGACAT * [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: TCCGGCGC_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: NA Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 [Trimming statistics] Total number of read pairs: 4 Number of unaligned read pairs: 1 Number of well aligned read pairs: 3 Number of discarded mate 1 reads: 1 Number of singleton mate 1 reads: 0 Number of discarded mate 2 reads: 1 Number of singleton mate 2 reads: 0 Number of reads with adapters[1]: 4 Number of retained reads: 6 Number of retained nucleotides: 534 Average length of retained reads: 89 [Length distribution] Length Mate1 Mate2 Singleton Discarded All 0 0 0 0 2 2 1 0 0 0 0 0 2 0 0 0 0 0 3 0 0 0 0 0 4 0 0 0 0 0 5 0 0 0 0 0 6 0 0 0 0 0 7 0 0 0 0 0 8 0 0 0 0 0 9 0 0 0 0 0 10 0 0 0 0 0 11 0 0 0 0 0 12 0 0 0 0 0 13 0 0 0 0 0 14 0 0 0 0 0 15 0 0 0 0 0 16 0 0 0 0 0 17 0 0 0 0 0 18 0 0 0 0 0 19 0 0 0 0 0 20 0 0 0 0 0 21 0 0 0 0 0 22 0 0 0 0 0 23 0 0 0 0 0 24 0 0 0 0 0 25 0 0 0 0 0 26 0 0 0 0 0 27 0 0 0 0 0 28 0 0 0 0 0 29 0 0 0 0 0 30 0 0 0 0 0 31 0 0 0 0 0 32 0 0 0 0 0 33 0 0 0 0 0 34 0 0 0 0 0 35 0 0 0 0 0 36 0 0 0 0 0 37 0 0 0 0 0 38 0 0 0 0 0 39 0 0 0 0 0 40 0 0 0 0 0 41 0 0 0 0 0 42 0 0 0 0 0 43 0 0 0 0 0 44 0 0 0 0 0 45 0 0 0 0 0 46 0 0 0 0 0 47 0 0 0 0 0 48 0 0 0 0 0 49 0 0 0 0 0 50 0 0 0 0 0 51 0 0 0 0 0 52 0 0 0 0 0 53 0 0 0 0 0 54 0 0 0 0 0 55 0 0 0 0 0 56 0 0 0 0 0 57 0 0 0 0 0 58 0 0 0 0 0 59 0 0 0 0 0 60 0 0 0 0 0 61 0 0 0 0 0 62 0 0 0 0 0 63 0 0 0 0 0 64 0 0 0 0 0 65 0 0 0 0 0 66 0 0 0 0 0 67 0 0 0 0 0 68 0 0 0 0 0 69 0 0 0 0 0 70 0 0 0 0 0 71 0 0 0 0 0 72 0 0 0 0 0 73 0 0 0 0 0 74 0 0 0 0 0 75 1 1 0 0 2 76 0 0 0 0 0 77 0 0 0 0 0 78 0 0 0 0 0 79 0 0 0 0 0 80 0 0 0 0 0 81 0 0 0 0 0 82 0 0 0 0 0 83 0 0 0 0 0 84 0 0 0 0 0 85 0 0 0 0 0 86 0 0 0 0 0 87 0 0 0 0 0 88 0 0 0 0 0 89 0 0 0 0 0 90 0 0 0 0 0 91 0 0 0 0 0 92 2 0 0 0 2 93 0 0 0 0 0 94 0 0 0 0 0 95 0 0 0 0 0 96 0 0 0 0 0 97 0 0 0 0 0 98 0 0 0 0 0 99 0 0 0 0 0 100 0 2 0 0 2 your_output.sample_1.singleton.truncated000066400000000000000000000000001350370616400406750ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/threads/twoyour_output.sample_2.discarded000066400000000000000000000000461350370616400366400ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/threads/two@read_s2_000/1 + @read_s2_000/2 + your_output.sample_2.pair1.truncated000066400000000000000000000010771350370616400377270ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/threads/two@read_s2_150/1 TGATCTCATACATTTAAACAAAGTATGCCTTACGCATGCCTTAATGATACGTAACCTAGGCAACAGAGTCTTTACTTGTACCTGCTACACAC + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_075/1 TCGCTAGCCCAAGATCACGCTTTCCGCGACGTTTTAGAGCGTGCATACCGGGGCGTTTCTCAGATAGGTATTTCA + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; @read_s2_200/1 ACCCTCACGCTTGCACGACGACAGCGGTCCCCTATAAATGTATGTTGACGCAGCGAGAGGCCAGGACCCGGGCGTGTTACCACTAAGACCCT + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 your_output.sample_2.pair2.truncated000066400000000000000000000011371350370616400377250ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/threads/two@read_s2_150/2 AGAACAGGATACAATGAAAATGCATCGCGTTGGCAACTCTCACCTTGCTCTTGGACCCGTGTGTAGCAGGTACAAGTAAAGACTCTGTTGCCTAGGTTAC + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_075/2 TGAAATACCTATCTGAGAAACGCCCCGGTATGCACGCTCTAAAACGTCGCGGAAAGCGTGATCTTGGGCTAGCGA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>> @read_s2_200/2 ATGCTGATTAGATATGTCTTTCATCGGCTTGTGACCGAGGAGTGGTACGGCCGTTCCATATTGGGTGATTAGGAAGATGTCCCGGCTTGCTGCTTCTCGT + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 your_output.sample_2.settings000066400000000000000000000052551350370616400365650ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/threads/twoAdapterRemoval ver. 2.2.0 Trimming of single-indexed paired-end reads [Demultiplexing] Maximum mismatches (total): 0 Maximum mate 1 mismatches: 0 Maximum mate 2 mismatches: 0 [Demultiplexing samples] Name Barcode_1 Barcode_2 sample_1 GCGCCGGA * sample_2* CAGGACAT * [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: ATGTCCTG_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: NA Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 [Trimming statistics] Total number of read pairs: 4 Number of unaligned read pairs: 1 Number of well aligned read pairs: 3 Number of discarded mate 1 reads: 1 Number of singleton mate 1 reads: 0 Number of discarded mate 2 reads: 1 Number of singleton mate 2 reads: 0 Number of reads with adapters[1]: 4 Number of retained reads: 6 Number of retained nucleotides: 534 Average length of retained reads: 89 [Length distribution] Length Mate1 Mate2 Singleton Discarded All 0 0 0 0 2 2 1 0 0 0 0 0 2 0 0 0 0 0 3 0 0 0 0 0 4 0 0 0 0 0 5 0 0 0 0 0 6 0 0 0 0 0 7 0 0 0 0 0 8 0 0 0 0 0 9 0 0 0 0 0 10 0 0 0 0 0 11 0 0 0 0 0 12 0 0 0 0 0 13 0 0 0 0 0 14 0 0 0 0 0 15 0 0 0 0 0 16 0 0 0 0 0 17 0 0 0 0 0 18 0 0 0 0 0 19 0 0 0 0 0 20 0 0 0 0 0 21 0 0 0 0 0 22 0 0 0 0 0 23 0 0 0 0 0 24 0 0 0 0 0 25 0 0 0 0 0 26 0 0 0 0 0 27 0 0 0 0 0 28 0 0 0 0 0 29 0 0 0 0 0 30 0 0 0 0 0 31 0 0 0 0 0 32 0 0 0 0 0 33 0 0 0 0 0 34 0 0 0 0 0 35 0 0 0 0 0 36 0 0 0 0 0 37 0 0 0 0 0 38 0 0 0 0 0 39 0 0 0 0 0 40 0 0 0 0 0 41 0 0 0 0 0 42 0 0 0 0 0 43 0 0 0 0 0 44 0 0 0 0 0 45 0 0 0 0 0 46 0 0 0 0 0 47 0 0 0 0 0 48 0 0 0 0 0 49 0 0 0 0 0 50 0 0 0 0 0 51 0 0 0 0 0 52 0 0 0 0 0 53 0 0 0 0 0 54 0 0 0 0 0 55 0 0 0 0 0 56 0 0 0 0 0 57 0 0 0 0 0 58 0 0 0 0 0 59 0 0 0 0 0 60 0 0 0 0 0 61 0 0 0 0 0 62 0 0 0 0 0 63 0 0 0 0 0 64 0 0 0 0 0 65 0 0 0 0 0 66 0 0 0 0 0 67 0 0 0 0 0 68 0 0 0 0 0 69 0 0 0 0 0 70 0 0 0 0 0 71 0 0 0 0 0 72 0 0 0 0 0 73 0 0 0 0 0 74 0 0 0 0 0 75 1 1 0 0 2 76 0 0 0 0 0 77 0 0 0 0 0 78 0 0 0 0 0 79 0 0 0 0 0 80 0 0 0 0 0 81 0 0 0 0 0 82 0 0 0 0 0 83 0 0 0 0 0 84 0 0 0 0 0 85 0 0 0 0 0 86 0 0 0 0 0 87 0 0 0 0 0 88 0 0 0 0 0 89 0 0 0 0 0 90 0 0 0 0 0 91 0 0 0 0 0 92 2 0 0 0 2 93 0 0 0 0 0 94 0 0 0 0 0 95 0 0 0 0 0 96 0 0 0 0 0 97 0 0 0 0 0 98 0 0 0 0 0 99 0 0 0 0 0 100 0 2 0 0 2 your_output.sample_2.singleton.truncated000066400000000000000000000000001350370616400406760ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/threads/twoyour_output.settings000066400000000000000000000021601350370616400350540ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/threads/twoAdapterRemoval ver. 2.1.7 Trimming of single-indexed paired-end reads [Demultiplexing] Maximum mismatches (total): 0 Maximum mate 1 mismatches: 0 Maximum mate 2 mismatches: 0 [Demultiplexing samples] Name Barcode_1 Barcode_2 sample_1 GCGCCGGA * sample_2 CAGGACAT * [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: NA Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 [Demultiplexing statistics] Name Barcode_1 Barcode_2 Hits Fraction unidentified NA NA 0 0.000 ambiguous NA NA 0 0.000 sample_1 GCGCCGGA * 4 0.500 sample_2 CAGGACAT * 4 0.500 * * * 8 1.000 your_output.unidentified_1000066400000000000000000000000001350370616400360720ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/threads/twoyour_output.unidentified_2000066400000000000000000000000001350370616400360730ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/pe/threads/twoadapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/se/000077500000000000000000000000001350370616400264745ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/se/collapse/000077500000000000000000000000001350370616400302765ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/se/collapse/barcodes.txt000066400000000000000000000000461350370616400326210ustar00rootroot00000000000000sample_1 GCGCCGGA sample_2 CAGGACAT adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/se/collapse/info.json000066400000000000000000000001051350370616400321200ustar00rootroot00000000000000{ "arguments": ["--collapse"], "return_code": 0, "stderr": [ ] } adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/se/collapse/input_1.fastq000066400000000000000000000033301350370616400327140ustar00rootroot00000000000000@read_s1_000/1 GCGCCGGAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAAAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_000/1 CAGGACATAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAAAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_075/1 GCGCCGGAGACGGTCCCATTAATGCACTATCGGATTTACACATTTGCGTGAATAAATCGACAGATGAATCATTAAGCTCCTACAGATCGGAAGAGCACAC + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_150/1 CAGGACATTGATCTCATACATTTAAACAAAGTATGCCTTACGCATGCCTTAATGATACGTAACCTAGGCAACAGAGTCTTTACTTGTACCTGCTACACAC + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_200/1 GCGCCGGATCCATCAGGATCGTATTATACTAAGCTAGGACTGTGCAGTGCACAGAGAGGAGATGACCATGATCCTCGAGCAAGTTGCCGCAGGCTCGGGC + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_150/1 GCGCCGGATGCACCGTAGCCATATGGGCTGTTGGGGACACAGGGCGTCGGCATTCCTTTATTACTGACGCCGCTAGAGTCTATGCAAGGTTATAACGTAT + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_075/1 CAGGACATTCGCTAGCCCAAGATCACGCTTTCCGCGACGTTTTAGAGCGTGCATACCGGGGCGTTTCTCAGATAGGTATTTCAAGATCGGAAGAGCACAC + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_200/1 CAGGACATACCCTCACGCTTGCACGACGACAGCGGTCCCCTATAAATGTATGTTGACGCAGCGAGAGGCCAGGACCCGGGCGTGTTACCACTAAGACCCT + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 your_output.sample_1.collapsed000066400000000000000000000002531350370616400362250ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/se/collapse@M_read_s1_075/1 GACGGTCCCATTAATGCACTATCGGATTTACACATTTGCGTGAATAAATCGACAGATGAATCATTAAGCTCCTAC + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; your_output.sample_1.collapsed.truncated000066400000000000000000000000001350370616400402030ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/se/collapseyour_output.sample_1.discarded000066400000000000000000000000251350370616400361760ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/se/collapse@M_read_s1_000/1 + your_output.sample_1.settings000066400000000000000000000050711350370616400361220ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/se/collapseAdapterRemoval ver. 2.2.0 Trimming of single-indexed single-end reads [Demultiplexing] Maximum mismatches (total): 0 [Demultiplexing samples] Name Barcode_1 Barcode_2 sample_1* GCGCCGGA * sample_2 CAGGACAT * [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: TCCGGCGC_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 3843883243 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: Yes Minimum overlap (in case of collapse): 11 Minimum adapter overlap: 0 [Trimming statistics] Total number of reads: 4 Number of unaligned reads: 2 Number of well aligned reads: 2 Number of discarded mate 1 reads: 1 Number of singleton mate 1 reads: 2 Number of reads with adapters[1]: 2 Number of full-length collapsed pairs: 1 Number of truncated collapsed pairs: 0 Number of retained reads: 3 Number of retained nucleotides: 259 Average length of retained reads: 86.3333 [Length distribution] Length Mate1 Collapsed CollapsedTruncated Discarded All 0 0 0 0 1 1 1 0 0 0 0 0 2 0 0 0 0 0 3 0 0 0 0 0 4 0 0 0 0 0 5 0 0 0 0 0 6 0 0 0 0 0 7 0 0 0 0 0 8 0 0 0 0 0 9 0 0 0 0 0 10 0 0 0 0 0 11 0 0 0 0 0 12 0 0 0 0 0 13 0 0 0 0 0 14 0 0 0 0 0 15 0 0 0 0 0 16 0 0 0 0 0 17 0 0 0 0 0 18 0 0 0 0 0 19 0 0 0 0 0 20 0 0 0 0 0 21 0 0 0 0 0 22 0 0 0 0 0 23 0 0 0 0 0 24 0 0 0 0 0 25 0 0 0 0 0 26 0 0 0 0 0 27 0 0 0 0 0 28 0 0 0 0 0 29 0 0 0 0 0 30 0 0 0 0 0 31 0 0 0 0 0 32 0 0 0 0 0 33 0 0 0 0 0 34 0 0 0 0 0 35 0 0 0 0 0 36 0 0 0 0 0 37 0 0 0 0 0 38 0 0 0 0 0 39 0 0 0 0 0 40 0 0 0 0 0 41 0 0 0 0 0 42 0 0 0 0 0 43 0 0 0 0 0 44 0 0 0 0 0 45 0 0 0 0 0 46 0 0 0 0 0 47 0 0 0 0 0 48 0 0 0 0 0 49 0 0 0 0 0 50 0 0 0 0 0 51 0 0 0 0 0 52 0 0 0 0 0 53 0 0 0 0 0 54 0 0 0 0 0 55 0 0 0 0 0 56 0 0 0 0 0 57 0 0 0 0 0 58 0 0 0 0 0 59 0 0 0 0 0 60 0 0 0 0 0 61 0 0 0 0 0 62 0 0 0 0 0 63 0 0 0 0 0 64 0 0 0 0 0 65 0 0 0 0 0 66 0 0 0 0 0 67 0 0 0 0 0 68 0 0 0 0 0 69 0 0 0 0 0 70 0 0 0 0 0 71 0 0 0 0 0 72 0 0 0 0 0 73 0 0 0 0 0 74 0 0 0 0 0 75 0 1 0 0 1 76 0 0 0 0 0 77 0 0 0 0 0 78 0 0 0 0 0 79 0 0 0 0 0 80 0 0 0 0 0 81 0 0 0 0 0 82 0 0 0 0 0 83 0 0 0 0 0 84 0 0 0 0 0 85 0 0 0 0 0 86 0 0 0 0 0 87 0 0 0 0 0 88 0 0 0 0 0 89 0 0 0 0 0 90 0 0 0 0 0 91 0 0 0 0 0 92 2 0 0 0 2 your_output.sample_1.truncated000066400000000000000000000006261350370616400362540ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/se/collapse@read_s1_200/1 TCCATCAGGATCGTATTATACTAAGCTAGGACTGTGCAGTGCACAGAGAGGAGATGACCATGATCCTCGAGCAAGTTGCCGCAGGCTCGGGC + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_150/1 TGCACCGTAGCCATATGGGCTGTTGGGGACACAGGGCGTCGGCATTCCTTTATTACTGACGCCGCTAGAGTCTATGCAAGGTTATAACGTAT + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 your_output.sample_2.collapsed000066400000000000000000000002531350370616400362260ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/se/collapse@M_read_s2_075/1 TCGCTAGCCCAAGATCACGCTTTCCGCGACGTTTTAGAGCGTGCATACCGGGGCGTTTCTCAGATAGGTATTTCA + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; your_output.sample_2.collapsed.truncated000066400000000000000000000000001350370616400402040ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/se/collapseyour_output.sample_2.discarded000066400000000000000000000000251350370616400361770ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/se/collapse@M_read_s2_000/1 + your_output.sample_2.settings000066400000000000000000000050711350370616400361230ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/se/collapseAdapterRemoval ver. 2.2.0 Trimming of single-indexed single-end reads [Demultiplexing] Maximum mismatches (total): 0 [Demultiplexing samples] Name Barcode_1 Barcode_2 sample_1 GCGCCGGA * sample_2* CAGGACAT * [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: ATGTCCTG_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 3843883243 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: Yes Minimum overlap (in case of collapse): 11 Minimum adapter overlap: 0 [Trimming statistics] Total number of reads: 4 Number of unaligned reads: 2 Number of well aligned reads: 2 Number of discarded mate 1 reads: 1 Number of singleton mate 1 reads: 2 Number of reads with adapters[1]: 2 Number of full-length collapsed pairs: 1 Number of truncated collapsed pairs: 0 Number of retained reads: 3 Number of retained nucleotides: 259 Average length of retained reads: 86.3333 [Length distribution] Length Mate1 Collapsed CollapsedTruncated Discarded All 0 0 0 0 1 1 1 0 0 0 0 0 2 0 0 0 0 0 3 0 0 0 0 0 4 0 0 0 0 0 5 0 0 0 0 0 6 0 0 0 0 0 7 0 0 0 0 0 8 0 0 0 0 0 9 0 0 0 0 0 10 0 0 0 0 0 11 0 0 0 0 0 12 0 0 0 0 0 13 0 0 0 0 0 14 0 0 0 0 0 15 0 0 0 0 0 16 0 0 0 0 0 17 0 0 0 0 0 18 0 0 0 0 0 19 0 0 0 0 0 20 0 0 0 0 0 21 0 0 0 0 0 22 0 0 0 0 0 23 0 0 0 0 0 24 0 0 0 0 0 25 0 0 0 0 0 26 0 0 0 0 0 27 0 0 0 0 0 28 0 0 0 0 0 29 0 0 0 0 0 30 0 0 0 0 0 31 0 0 0 0 0 32 0 0 0 0 0 33 0 0 0 0 0 34 0 0 0 0 0 35 0 0 0 0 0 36 0 0 0 0 0 37 0 0 0 0 0 38 0 0 0 0 0 39 0 0 0 0 0 40 0 0 0 0 0 41 0 0 0 0 0 42 0 0 0 0 0 43 0 0 0 0 0 44 0 0 0 0 0 45 0 0 0 0 0 46 0 0 0 0 0 47 0 0 0 0 0 48 0 0 0 0 0 49 0 0 0 0 0 50 0 0 0 0 0 51 0 0 0 0 0 52 0 0 0 0 0 53 0 0 0 0 0 54 0 0 0 0 0 55 0 0 0 0 0 56 0 0 0 0 0 57 0 0 0 0 0 58 0 0 0 0 0 59 0 0 0 0 0 60 0 0 0 0 0 61 0 0 0 0 0 62 0 0 0 0 0 63 0 0 0 0 0 64 0 0 0 0 0 65 0 0 0 0 0 66 0 0 0 0 0 67 0 0 0 0 0 68 0 0 0 0 0 69 0 0 0 0 0 70 0 0 0 0 0 71 0 0 0 0 0 72 0 0 0 0 0 73 0 0 0 0 0 74 0 0 0 0 0 75 0 1 0 0 1 76 0 0 0 0 0 77 0 0 0 0 0 78 0 0 0 0 0 79 0 0 0 0 0 80 0 0 0 0 0 81 0 0 0 0 0 82 0 0 0 0 0 83 0 0 0 0 0 84 0 0 0 0 0 85 0 0 0 0 0 86 0 0 0 0 0 87 0 0 0 0 0 88 0 0 0 0 0 89 0 0 0 0 0 90 0 0 0 0 0 91 0 0 0 0 0 92 2 0 0 0 2 your_output.sample_2.truncated000066400000000000000000000006261350370616400362550ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/se/collapse@read_s2_150/1 TGATCTCATACATTTAAACAAAGTATGCCTTACGCATGCCTTAATGATACGTAACCTAGGCAACAGAGTCTTTACTTGTACCTGCTACACAC + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_200/1 ACCCTCACGCTTGCACGACGACAGCGGTCCCCTATAAATGTATGTTGACGCAGCGAGAGGCCAGGACCCGGGCGTGTTACCACTAAGACCCT + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/se/collapse/your_output.settings000066400000000000000000000021321350370616400344740ustar00rootroot00000000000000AdapterRemoval ver. 2.2.0 Trimming of single-indexed single-end reads [Demultiplexing] Maximum mismatches (total): 0 [Demultiplexing samples] Name Barcode_1 Barcode_2 sample_1 GCGCCGGA * sample_2 CAGGACAT * [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 3717807245 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: Yes Minimum overlap (in case of collapse): 11 Minimum adapter overlap: 0 [Demultiplexing statistics] Name Barcode_1 Barcode_2 Hits Fraction unidentified NA NA 0 0.000 ambiguous NA NA 0 0.000 sample_1 GCGCCGGA * 4 0.500 sample_2 CAGGACAT * 4 0.500 * * * 8 1.000 your_output.unidentified000066400000000000000000000000001350370616400352140ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/se/collapseadapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/se/combined_output/000077500000000000000000000000001350370616400316745ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/se/combined_output/barcodes.txt000066400000000000000000000000461350370616400342170ustar00rootroot00000000000000sample_1 GCGCCGGA sample_2 CAGGACAT adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/se/combined_output/info.json000066400000000000000000000001141350370616400335160ustar00rootroot00000000000000{ "arguments": ["--combined-output"], "return_code": 0, "stderr": [ ] } adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/se/combined_output/input_1.fastq000066400000000000000000000033301350370616400343120ustar00rootroot00000000000000@read_s1_000/1 GCGCCGGAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAAAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_000/1 CAGGACATAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAAAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_075/1 GCGCCGGAGACGGTCCCATTAATGCACTATCGGATTTACACATTTGCGTGAATAAATCGACAGATGAATCATTAAGCTCCTACAGATCGGAAGAGCACAC + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_150/1 CAGGACATTGATCTCATACATTTAAACAAAGTATGCCTTACGCATGCCTTAATGATACGTAACCTAGGCAACAGAGTCTTTACTTGTACCTGCTACACAC + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_200/1 GCGCCGGATCCATCAGGATCGTATTATACTAAGCTAGGACTGTGCAGTGCACAGAGAGGAGATGACCATGATCCTCGAGCAAGTTGCCGCAGGCTCGGGC + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_150/1 GCGCCGGATGCACCGTAGCCATATGGGCTGTTGGGGACACAGGGCGTCGGCATTCCTTTATTACTGACGCCGCTAGAGTCTATGCAAGGTTATAACGTAT + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_075/1 CAGGACATTCGCTAGCCCAAGATCACGCTTTCCGCGACGTTTTAGAGCGTGCATACCGGGGCGTTTCTCAGATAGGTATTTCAAGATCGGAAGAGCACAC + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_200/1 CAGGACATACCCTCACGCTTGCACGACGACAGCGGTCCCCTATAAATGTATGTTGACGCAGCGAGAGGCCAGGACCCGGGCGTGTTACCACTAAGACCCT + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 your_output.sample_1.settings000066400000000000000000000041271350370616400375210ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/se/combined_outputAdapterRemoval ver. 2.2.0 Trimming of single-indexed single-end reads [Demultiplexing] Maximum mismatches (total): 0 [Demultiplexing samples] Name Barcode_1 Barcode_2 sample_1* GCGCCGGA * sample_2 CAGGACAT * [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: TCCGGCGC_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 3717807245 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 Minimum adapter overlap: 0 [Trimming statistics] Total number of reads: 4 Number of unaligned reads: 2 Number of well aligned reads: 2 Number of discarded mate 1 reads: 1 Number of singleton mate 1 reads: 3 Number of reads with adapters[1]: 2 Number of retained reads: 3 Number of retained nucleotides: 259 Average length of retained reads: 86.3333 [Length distribution] Length Mate1 Discarded All 0 0 1 1 1 0 0 0 2 0 0 0 3 0 0 0 4 0 0 0 5 0 0 0 6 0 0 0 7 0 0 0 8 0 0 0 9 0 0 0 10 0 0 0 11 0 0 0 12 0 0 0 13 0 0 0 14 0 0 0 15 0 0 0 16 0 0 0 17 0 0 0 18 0 0 0 19 0 0 0 20 0 0 0 21 0 0 0 22 0 0 0 23 0 0 0 24 0 0 0 25 0 0 0 26 0 0 0 27 0 0 0 28 0 0 0 29 0 0 0 30 0 0 0 31 0 0 0 32 0 0 0 33 0 0 0 34 0 0 0 35 0 0 0 36 0 0 0 37 0 0 0 38 0 0 0 39 0 0 0 40 0 0 0 41 0 0 0 42 0 0 0 43 0 0 0 44 0 0 0 45 0 0 0 46 0 0 0 47 0 0 0 48 0 0 0 49 0 0 0 50 0 0 0 51 0 0 0 52 0 0 0 53 0 0 0 54 0 0 0 55 0 0 0 56 0 0 0 57 0 0 0 58 0 0 0 59 0 0 0 60 0 0 0 61 0 0 0 62 0 0 0 63 0 0 0 64 0 0 0 65 0 0 0 66 0 0 0 67 0 0 0 68 0 0 0 69 0 0 0 70 0 0 0 71 0 0 0 72 0 0 0 73 0 0 0 74 0 0 0 75 1 0 1 76 0 0 0 77 0 0 0 78 0 0 0 79 0 0 0 80 0 0 0 81 0 0 0 82 0 0 0 83 0 0 0 84 0 0 0 85 0 0 0 86 0 0 0 87 0 0 0 88 0 0 0 89 0 0 0 90 0 0 0 91 0 0 0 92 2 0 2 your_output.sample_1.truncated000066400000000000000000000011241350370616400376440ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/se/combined_output@read_s1_000/1 N + ! @read_s1_075/1 GACGGTCCCATTAATGCACTATCGGATTTACACATTTGCGTGAATAAATCGACAGATGAATCATTAAGCTCCTAC + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; @read_s1_200/1 TCCATCAGGATCGTATTATACTAAGCTAGGACTGTGCAGTGCACAGAGAGGAGATGACCATGATCCTCGAGCAAGTTGCCGCAGGCTCGGGC + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_150/1 TGCACCGTAGCCATATGGGCTGTTGGGGACACAGGGCGTCGGCATTCCTTTATTACTGACGCCGCTAGAGTCTATGCAAGGTTATAACGTAT + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 your_output.sample_2.settings000066400000000000000000000041271350370616400375220ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/se/combined_outputAdapterRemoval ver. 2.2.0 Trimming of single-indexed single-end reads [Demultiplexing] Maximum mismatches (total): 0 [Demultiplexing samples] Name Barcode_1 Barcode_2 sample_1 GCGCCGGA * sample_2* CAGGACAT * [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: ATGTCCTG_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 3717807245 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 Minimum adapter overlap: 0 [Trimming statistics] Total number of reads: 4 Number of unaligned reads: 2 Number of well aligned reads: 2 Number of discarded mate 1 reads: 1 Number of singleton mate 1 reads: 3 Number of reads with adapters[1]: 2 Number of retained reads: 3 Number of retained nucleotides: 259 Average length of retained reads: 86.3333 [Length distribution] Length Mate1 Discarded All 0 0 1 1 1 0 0 0 2 0 0 0 3 0 0 0 4 0 0 0 5 0 0 0 6 0 0 0 7 0 0 0 8 0 0 0 9 0 0 0 10 0 0 0 11 0 0 0 12 0 0 0 13 0 0 0 14 0 0 0 15 0 0 0 16 0 0 0 17 0 0 0 18 0 0 0 19 0 0 0 20 0 0 0 21 0 0 0 22 0 0 0 23 0 0 0 24 0 0 0 25 0 0 0 26 0 0 0 27 0 0 0 28 0 0 0 29 0 0 0 30 0 0 0 31 0 0 0 32 0 0 0 33 0 0 0 34 0 0 0 35 0 0 0 36 0 0 0 37 0 0 0 38 0 0 0 39 0 0 0 40 0 0 0 41 0 0 0 42 0 0 0 43 0 0 0 44 0 0 0 45 0 0 0 46 0 0 0 47 0 0 0 48 0 0 0 49 0 0 0 50 0 0 0 51 0 0 0 52 0 0 0 53 0 0 0 54 0 0 0 55 0 0 0 56 0 0 0 57 0 0 0 58 0 0 0 59 0 0 0 60 0 0 0 61 0 0 0 62 0 0 0 63 0 0 0 64 0 0 0 65 0 0 0 66 0 0 0 67 0 0 0 68 0 0 0 69 0 0 0 70 0 0 0 71 0 0 0 72 0 0 0 73 0 0 0 74 0 0 0 75 1 0 1 76 0 0 0 77 0 0 0 78 0 0 0 79 0 0 0 80 0 0 0 81 0 0 0 82 0 0 0 83 0 0 0 84 0 0 0 85 0 0 0 86 0 0 0 87 0 0 0 88 0 0 0 89 0 0 0 90 0 0 0 91 0 0 0 92 2 0 2 your_output.sample_2.truncated000066400000000000000000000011241350370616400376450ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/se/combined_output@read_s2_000/1 N + ! @read_s2_150/1 TGATCTCATACATTTAAACAAAGTATGCCTTACGCATGCCTTAATGATACGTAACCTAGGCAACAGAGTCTTTACTTGTACCTGCTACACAC + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_075/1 TCGCTAGCCCAAGATCACGCTTTCCGCGACGTTTTAGAGCGTGCATACCGGGGCGTTTCTCAGATAGGTATTTCA + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; @read_s2_200/1 ACCCTCACGCTTGCACGACGACAGCGGTCCCCTATAAATGTATGTTGACGCAGCGAGAGGCCAGGACCCGGGCGTGTTACCACTAAGACCCT + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 your_output.settings000066400000000000000000000021311350370616400360120ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/se/combined_outputAdapterRemoval ver. 2.2.0 Trimming of single-indexed single-end reads [Demultiplexing] Maximum mismatches (total): 0 [Demultiplexing samples] Name Barcode_1 Barcode_2 sample_1 GCGCCGGA * sample_2 CAGGACAT * [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 3717807245 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 Minimum adapter overlap: 0 [Demultiplexing statistics] Name Barcode_1 Barcode_2 Hits Fraction unidentified NA NA 0 0.000 ambiguous NA NA 0 0.000 sample_1 GCGCCGGA * 4 0.500 sample_2 CAGGACAT * 4 0.500 * * * 8 1.000 your_output.unidentified000066400000000000000000000000001350370616400366120ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/se/combined_outputadapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/se/defaults/000077500000000000000000000000001350370616400303035ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/se/defaults/barcodes.txt000066400000000000000000000000461350370616400326260ustar00rootroot00000000000000sample_1 GCGCCGGA sample_2 CAGGACAT adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/se/defaults/info.json000066400000000000000000000000711350370616400321270ustar00rootroot00000000000000{ "arguments": [], "return_code": 0, "stderr": [ ] } adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/se/defaults/input_1.fastq000066400000000000000000000033301350370616400327210ustar00rootroot00000000000000@read_s1_000/1 GCGCCGGAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAAAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_000/1 CAGGACATAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAAAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_075/1 GCGCCGGAGACGGTCCCATTAATGCACTATCGGATTTACACATTTGCGTGAATAAATCGACAGATGAATCATTAAGCTCCTACAGATCGGAAGAGCACAC + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_150/1 CAGGACATTGATCTCATACATTTAAACAAAGTATGCCTTACGCATGCCTTAATGATACGTAACCTAGGCAACAGAGTCTTTACTTGTACCTGCTACACAC + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_200/1 GCGCCGGATCCATCAGGATCGTATTATACTAAGCTAGGACTGTGCAGTGCACAGAGAGGAGATGACCATGATCCTCGAGCAAGTTGCCGCAGGCTCGGGC + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_150/1 GCGCCGGATGCACCGTAGCCATATGGGCTGTTGGGGACACAGGGCGTCGGCATTCCTTTATTACTGACGCCGCTAGAGTCTATGCAAGGTTATAACGTAT + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_075/1 CAGGACATTCGCTAGCCCAAGATCACGCTTTCCGCGACGTTTTAGAGCGTGCATACCGGGGCGTTTCTCAGATAGGTATTTCAAGATCGGAAGAGCACAC + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_200/1 CAGGACATACCCTCACGCTTGCACGACGACAGCGGTCCCCTATAAATGTATGTTGACGCAGCGAGAGGCCAGGACCCGGGCGTGTTACCACTAAGACCCT + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 your_output.sample_1.discarded000066400000000000000000000000231350370616400362010ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/se/defaults@read_s1_000/1 + your_output.sample_1.settings000066400000000000000000000041271350370616400361300ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/se/defaultsAdapterRemoval ver. 2.2.0 Trimming of single-indexed single-end reads [Demultiplexing] Maximum mismatches (total): 0 [Demultiplexing samples] Name Barcode_1 Barcode_2 sample_1* GCGCCGGA * sample_2 CAGGACAT * [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: TCCGGCGC_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 3717807245 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 Minimum adapter overlap: 0 [Trimming statistics] Total number of reads: 4 Number of unaligned reads: 2 Number of well aligned reads: 2 Number of discarded mate 1 reads: 1 Number of singleton mate 1 reads: 3 Number of reads with adapters[1]: 2 Number of retained reads: 3 Number of retained nucleotides: 259 Average length of retained reads: 86.3333 [Length distribution] Length Mate1 Discarded All 0 0 1 1 1 0 0 0 2 0 0 0 3 0 0 0 4 0 0 0 5 0 0 0 6 0 0 0 7 0 0 0 8 0 0 0 9 0 0 0 10 0 0 0 11 0 0 0 12 0 0 0 13 0 0 0 14 0 0 0 15 0 0 0 16 0 0 0 17 0 0 0 18 0 0 0 19 0 0 0 20 0 0 0 21 0 0 0 22 0 0 0 23 0 0 0 24 0 0 0 25 0 0 0 26 0 0 0 27 0 0 0 28 0 0 0 29 0 0 0 30 0 0 0 31 0 0 0 32 0 0 0 33 0 0 0 34 0 0 0 35 0 0 0 36 0 0 0 37 0 0 0 38 0 0 0 39 0 0 0 40 0 0 0 41 0 0 0 42 0 0 0 43 0 0 0 44 0 0 0 45 0 0 0 46 0 0 0 47 0 0 0 48 0 0 0 49 0 0 0 50 0 0 0 51 0 0 0 52 0 0 0 53 0 0 0 54 0 0 0 55 0 0 0 56 0 0 0 57 0 0 0 58 0 0 0 59 0 0 0 60 0 0 0 61 0 0 0 62 0 0 0 63 0 0 0 64 0 0 0 65 0 0 0 66 0 0 0 67 0 0 0 68 0 0 0 69 0 0 0 70 0 0 0 71 0 0 0 72 0 0 0 73 0 0 0 74 0 0 0 75 1 0 1 76 0 0 0 77 0 0 0 78 0 0 0 79 0 0 0 80 0 0 0 81 0 0 0 82 0 0 0 83 0 0 0 84 0 0 0 85 0 0 0 86 0 0 0 87 0 0 0 88 0 0 0 89 0 0 0 90 0 0 0 91 0 0 0 92 2 0 2 your_output.sample_1.truncated000066400000000000000000000010771350370616400362620ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/se/defaults@read_s1_075/1 GACGGTCCCATTAATGCACTATCGGATTTACACATTTGCGTGAATAAATCGACAGATGAATCATTAAGCTCCTAC + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; @read_s1_200/1 TCCATCAGGATCGTATTATACTAAGCTAGGACTGTGCAGTGCACAGAGAGGAGATGACCATGATCCTCGAGCAAGTTGCCGCAGGCTCGGGC + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_150/1 TGCACCGTAGCCATATGGGCTGTTGGGGACACAGGGCGTCGGCATTCCTTTATTACTGACGCCGCTAGAGTCTATGCAAGGTTATAACGTAT + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 your_output.sample_2.discarded000066400000000000000000000000231350370616400362020ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/se/defaults@read_s2_000/1 + your_output.sample_2.settings000066400000000000000000000041271350370616400361310ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/se/defaultsAdapterRemoval ver. 2.2.0 Trimming of single-indexed single-end reads [Demultiplexing] Maximum mismatches (total): 0 [Demultiplexing samples] Name Barcode_1 Barcode_2 sample_1 GCGCCGGA * sample_2* CAGGACAT * [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: ATGTCCTG_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 3717807245 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 Minimum adapter overlap: 0 [Trimming statistics] Total number of reads: 4 Number of unaligned reads: 2 Number of well aligned reads: 2 Number of discarded mate 1 reads: 1 Number of singleton mate 1 reads: 3 Number of reads with adapters[1]: 2 Number of retained reads: 3 Number of retained nucleotides: 259 Average length of retained reads: 86.3333 [Length distribution] Length Mate1 Discarded All 0 0 1 1 1 0 0 0 2 0 0 0 3 0 0 0 4 0 0 0 5 0 0 0 6 0 0 0 7 0 0 0 8 0 0 0 9 0 0 0 10 0 0 0 11 0 0 0 12 0 0 0 13 0 0 0 14 0 0 0 15 0 0 0 16 0 0 0 17 0 0 0 18 0 0 0 19 0 0 0 20 0 0 0 21 0 0 0 22 0 0 0 23 0 0 0 24 0 0 0 25 0 0 0 26 0 0 0 27 0 0 0 28 0 0 0 29 0 0 0 30 0 0 0 31 0 0 0 32 0 0 0 33 0 0 0 34 0 0 0 35 0 0 0 36 0 0 0 37 0 0 0 38 0 0 0 39 0 0 0 40 0 0 0 41 0 0 0 42 0 0 0 43 0 0 0 44 0 0 0 45 0 0 0 46 0 0 0 47 0 0 0 48 0 0 0 49 0 0 0 50 0 0 0 51 0 0 0 52 0 0 0 53 0 0 0 54 0 0 0 55 0 0 0 56 0 0 0 57 0 0 0 58 0 0 0 59 0 0 0 60 0 0 0 61 0 0 0 62 0 0 0 63 0 0 0 64 0 0 0 65 0 0 0 66 0 0 0 67 0 0 0 68 0 0 0 69 0 0 0 70 0 0 0 71 0 0 0 72 0 0 0 73 0 0 0 74 0 0 0 75 1 0 1 76 0 0 0 77 0 0 0 78 0 0 0 79 0 0 0 80 0 0 0 81 0 0 0 82 0 0 0 83 0 0 0 84 0 0 0 85 0 0 0 86 0 0 0 87 0 0 0 88 0 0 0 89 0 0 0 90 0 0 0 91 0 0 0 92 2 0 2 your_output.sample_2.truncated000066400000000000000000000010771350370616400362630ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/se/defaults@read_s2_150/1 TGATCTCATACATTTAAACAAAGTATGCCTTACGCATGCCTTAATGATACGTAACCTAGGCAACAGAGTCTTTACTTGTACCTGCTACACAC + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_075/1 TCGCTAGCCCAAGATCACGCTTTCCGCGACGTTTTAGAGCGTGCATACCGGGGCGTTTCTCAGATAGGTATTTCA + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; @read_s2_200/1 ACCCTCACGCTTGCACGACGACAGCGGTCCCCTATAAATGTATGTTGACGCAGCGAGAGGCCAGGACCCGGGCGTGTTACCACTAAGACCCT + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/se/defaults/your_output.settings000066400000000000000000000021311350370616400345000ustar00rootroot00000000000000AdapterRemoval ver. 2.2.0 Trimming of single-indexed single-end reads [Demultiplexing] Maximum mismatches (total): 0 [Demultiplexing samples] Name Barcode_1 Barcode_2 sample_1 GCGCCGGA * sample_2 CAGGACAT * [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 3717807245 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 Minimum adapter overlap: 0 [Demultiplexing statistics] Name Barcode_1 Barcode_2 Hits Fraction unidentified NA NA 0 0.000 ambiguous NA NA 0 0.000 sample_1 GCGCCGGA * 4 0.500 sample_2 CAGGACAT * 4 0.500 * * * 8 1.000 your_output.unidentified000066400000000000000000000000001350370616400352210ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/se/defaultsadapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/se/demux_only/000077500000000000000000000000001350370616400306575ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/se/demux_only/barcodes.txt000066400000000000000000000000461350370616400332020ustar00rootroot00000000000000sample_1 GCGCCGGA sample_2 CAGGACAT adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/se/demux_only/info.json000066400000000000000000000001151350370616400325020ustar00rootroot00000000000000{ "arguments": ["--demultiplex-only"], "return_code": 0, "stderr": [ ] } adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/se/demux_only/input_1.fastq000066400000000000000000000033301350370616400332750ustar00rootroot00000000000000@read_s1_000/1 GCGCCGGAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAAAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_000/1 CAGGACATAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAAAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_075/1 GCGCCGGAGACGGTCCCATTAATGCACTATCGGATTTACACATTTGCGTGAATAAATCGACAGATGAATCATTAAGCTCCTACAGATCGGAAGAGCACAC + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_150/1 CAGGACATTGATCTCATACATTTAAACAAAGTATGCCTTACGCATGCCTTAATGATACGTAACCTAGGCAACAGAGTCTTTACTTGTACCTGCTACACAC + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_200/1 GCGCCGGATCCATCAGGATCGTATTATACTAAGCTAGGACTGTGCAGTGCACAGAGAGGAGATGACCATGATCCTCGAGCAAGTTGCCGCAGGCTCGGGC + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_150/1 GCGCCGGATGCACCGTAGCCATATGGGCTGTTGGGGACACAGGGCGTCGGCATTCCTTTATTACTGACGCCGCTAGAGTCTATGCAAGGTTATAACGTAT + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_075/1 CAGGACATTCGCTAGCCCAAGATCACGCTTTCCGCGACGTTTTAGAGCGTGCATACCGGGGCGTTTCTCAGATAGGTATTTCAAGATCGGAAGAGCACAC + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_200/1 CAGGACATACCCTCACGCTTGCACGACGACAGCGGTCCCCTATAAATGTATGTTGACGCAGCGAGAGGCCAGGACCCGGGCGTGTTACCACTAAGACCCT + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 your_output.sample_1.fastq000066400000000000000000000014541350370616400357620ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/se/demux_only@read_s1_000/1 AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAAAA + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_075/1 GACGGTCCCATTAATGCACTATCGGATTTACACATTTGCGTGAATAAATCGACAGATGAATCATTAAGCTCCTACAGATCGGAAGAGCACAC + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_200/1 TCCATCAGGATCGTATTATACTAAGCTAGGACTGTGCAGTGCACAGAGAGGAGATGACCATGATCCTCGAGCAAGTTGCCGCAGGCTCGGGC + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_150/1 TGCACCGTAGCCATATGGGCTGTTGGGGACACAGGGCGTCGGCATTCCTTTATTACTGACGCCGCTAGAGTCTATGCAAGGTTATAACGTAT + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 your_output.sample_1.settings000066400000000000000000000006171350370616400365040ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/se/demux_onlyAdapterRemoval ver. 2.2.0 Demultiplexing of single-indexed single-end reads [Demultiplexing] Maximum mismatches (total): 0 [Demultiplexing samples] Name Barcode_1 Barcode_2 sample_1* GCGCCGGA * sample_2 CAGGACAT * [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: TCCGGCGC_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT your_output.sample_2.fastq000066400000000000000000000014541350370616400357630ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/se/demux_only@read_s2_000/1 AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAAAA + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_150/1 TGATCTCATACATTTAAACAAAGTATGCCTTACGCATGCCTTAATGATACGTAACCTAGGCAACAGAGTCTTTACTTGTACCTGCTACACAC + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_075/1 TCGCTAGCCCAAGATCACGCTTTCCGCGACGTTTTAGAGCGTGCATACCGGGGCGTTTCTCAGATAGGTATTTCAAGATCGGAAGAGCACAC + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_200/1 ACCCTCACGCTTGCACGACGACAGCGGTCCCCTATAAATGTATGTTGACGCAGCGAGAGGCCAGGACCCGGGCGTGTTACCACTAAGACCCT + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 your_output.sample_2.settings000066400000000000000000000006171350370616400365050ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/se/demux_onlyAdapterRemoval ver. 2.2.0 Demultiplexing of single-indexed single-end reads [Demultiplexing] Maximum mismatches (total): 0 [Demultiplexing samples] Name Barcode_1 Barcode_2 sample_1 GCGCCGGA * sample_2* CAGGACAT * [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: ATGTCCTG_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT your_output.settings000066400000000000000000000011031350370616400347730ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/se/demux_onlyAdapterRemoval ver. 2.2.0 Demultiplexing of single-indexed single-end reads [Demultiplexing] Maximum mismatches (total): 0 [Demultiplexing samples] Name Barcode_1 Barcode_2 sample_1 GCGCCGGA * sample_2 CAGGACAT * [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Demultiplexing statistics] Name Barcode_1 Barcode_2 Hits Fraction unidentified NA NA 0 0.000 ambiguous NA NA 0 0.000 sample_1 GCGCCGGA * 4 0.500 sample_2 CAGGACAT * 4 0.500 * * * 8 1.000 your_output.unidentified.fastq000066400000000000000000000000001350370616400367120ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/se/demux_onlyadapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/se/multiple_input/000077500000000000000000000000001350370616400315465ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/se/multiple_input/barcodes.txt000066400000000000000000000000461350370616400340710ustar00rootroot00000000000000sample_1 GCGCCGGA sample_2 CAGGACAT adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/se/multiple_input/info.json000066400000000000000000000000711350370616400333720ustar00rootroot00000000000000{ "arguments": [], "return_code": 0, "stderr": [ ] } adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/se/multiple_input/input_1a.fastq000066400000000000000000000006661350370616400343360ustar00rootroot00000000000000@read_s1_000/1 GCGCCGGAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAAAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_000/1 CAGGACATAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAAAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/se/multiple_input/input_1b.fastq000066400000000000000000000012211350370616400343230ustar00rootroot00000000000000@read_s1_075/1 GCGCCGGAGACGGTCCCATTAATGCACTATCGGATTTACACATTTGCGTGAATAAATCGACAGATGAATCATTAAGCTCCTACAGATCGGAAGAGCACAC + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_150/1 CAGGACATTGATCTCATACATTTAAACAAAGTATGCCTTACGCATGCCTTAATGATACGTAACCTAGGCAACAGAGTCTTTACTTGTACCTGCTACACAC + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_200/1 GCGCCGGATCCATCAGGATCGTATTATACTAAGCTAGGACTGTGCAGTGCACAGAGAGGAGATGACCATGATCCTCGAGCAAGTTGCCGCAGGCTCGGGC + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/se/multiple_input/input_1c.fastq000066400000000000000000000012211350370616400343240ustar00rootroot00000000000000@read_s1_150/1 GCGCCGGATGCACCGTAGCCATATGGGCTGTTGGGGACACAGGGCGTCGGCATTCCTTTATTACTGACGCCGCTAGAGTCTATGCAAGGTTATAACGTAT + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_075/1 CAGGACATTCGCTAGCCCAAGATCACGCTTTCCGCGACGTTTTAGAGCGTGCATACCGGGGCGTTTCTCAGATAGGTATTTCAAGATCGGAAGAGCACAC + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_200/1 CAGGACATACCCTCACGCTTGCACGACGACAGCGGTCCCCTATAAATGTATGTTGACGCAGCGAGAGGCCAGGACCCGGGCGTGTTACCACTAAGACCCT + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 your_output.sample_1.discarded000066400000000000000000000000231350370616400374440ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/se/multiple_input@read_s1_000/1 + your_output.sample_1.settings000066400000000000000000000041271350370616400373730ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/se/multiple_inputAdapterRemoval ver. 2.2.0 Trimming of single-indexed single-end reads [Demultiplexing] Maximum mismatches (total): 0 [Demultiplexing samples] Name Barcode_1 Barcode_2 sample_1* GCGCCGGA * sample_2 CAGGACAT * [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: TCCGGCGC_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 3717807245 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 Minimum adapter overlap: 0 [Trimming statistics] Total number of reads: 4 Number of unaligned reads: 2 Number of well aligned reads: 2 Number of discarded mate 1 reads: 1 Number of singleton mate 1 reads: 3 Number of reads with adapters[1]: 2 Number of retained reads: 3 Number of retained nucleotides: 259 Average length of retained reads: 86.3333 [Length distribution] Length Mate1 Discarded All 0 0 1 1 1 0 0 0 2 0 0 0 3 0 0 0 4 0 0 0 5 0 0 0 6 0 0 0 7 0 0 0 8 0 0 0 9 0 0 0 10 0 0 0 11 0 0 0 12 0 0 0 13 0 0 0 14 0 0 0 15 0 0 0 16 0 0 0 17 0 0 0 18 0 0 0 19 0 0 0 20 0 0 0 21 0 0 0 22 0 0 0 23 0 0 0 24 0 0 0 25 0 0 0 26 0 0 0 27 0 0 0 28 0 0 0 29 0 0 0 30 0 0 0 31 0 0 0 32 0 0 0 33 0 0 0 34 0 0 0 35 0 0 0 36 0 0 0 37 0 0 0 38 0 0 0 39 0 0 0 40 0 0 0 41 0 0 0 42 0 0 0 43 0 0 0 44 0 0 0 45 0 0 0 46 0 0 0 47 0 0 0 48 0 0 0 49 0 0 0 50 0 0 0 51 0 0 0 52 0 0 0 53 0 0 0 54 0 0 0 55 0 0 0 56 0 0 0 57 0 0 0 58 0 0 0 59 0 0 0 60 0 0 0 61 0 0 0 62 0 0 0 63 0 0 0 64 0 0 0 65 0 0 0 66 0 0 0 67 0 0 0 68 0 0 0 69 0 0 0 70 0 0 0 71 0 0 0 72 0 0 0 73 0 0 0 74 0 0 0 75 1 0 1 76 0 0 0 77 0 0 0 78 0 0 0 79 0 0 0 80 0 0 0 81 0 0 0 82 0 0 0 83 0 0 0 84 0 0 0 85 0 0 0 86 0 0 0 87 0 0 0 88 0 0 0 89 0 0 0 90 0 0 0 91 0 0 0 92 2 0 2 your_output.sample_1.truncated000066400000000000000000000010771350370616400375250ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/se/multiple_input@read_s1_075/1 GACGGTCCCATTAATGCACTATCGGATTTACACATTTGCGTGAATAAATCGACAGATGAATCATTAAGCTCCTAC + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; @read_s1_200/1 TCCATCAGGATCGTATTATACTAAGCTAGGACTGTGCAGTGCACAGAGAGGAGATGACCATGATCCTCGAGCAAGTTGCCGCAGGCTCGGGC + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_150/1 TGCACCGTAGCCATATGGGCTGTTGGGGACACAGGGCGTCGGCATTCCTTTATTACTGACGCCGCTAGAGTCTATGCAAGGTTATAACGTAT + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 your_output.sample_2.discarded000066400000000000000000000000231350370616400374450ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/se/multiple_input@read_s2_000/1 + your_output.sample_2.settings000066400000000000000000000041271350370616400373740ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/se/multiple_inputAdapterRemoval ver. 2.2.0 Trimming of single-indexed single-end reads [Demultiplexing] Maximum mismatches (total): 0 [Demultiplexing samples] Name Barcode_1 Barcode_2 sample_1 GCGCCGGA * sample_2* CAGGACAT * [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: ATGTCCTG_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 3717807245 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 Minimum adapter overlap: 0 [Trimming statistics] Total number of reads: 4 Number of unaligned reads: 2 Number of well aligned reads: 2 Number of discarded mate 1 reads: 1 Number of singleton mate 1 reads: 3 Number of reads with adapters[1]: 2 Number of retained reads: 3 Number of retained nucleotides: 259 Average length of retained reads: 86.3333 [Length distribution] Length Mate1 Discarded All 0 0 1 1 1 0 0 0 2 0 0 0 3 0 0 0 4 0 0 0 5 0 0 0 6 0 0 0 7 0 0 0 8 0 0 0 9 0 0 0 10 0 0 0 11 0 0 0 12 0 0 0 13 0 0 0 14 0 0 0 15 0 0 0 16 0 0 0 17 0 0 0 18 0 0 0 19 0 0 0 20 0 0 0 21 0 0 0 22 0 0 0 23 0 0 0 24 0 0 0 25 0 0 0 26 0 0 0 27 0 0 0 28 0 0 0 29 0 0 0 30 0 0 0 31 0 0 0 32 0 0 0 33 0 0 0 34 0 0 0 35 0 0 0 36 0 0 0 37 0 0 0 38 0 0 0 39 0 0 0 40 0 0 0 41 0 0 0 42 0 0 0 43 0 0 0 44 0 0 0 45 0 0 0 46 0 0 0 47 0 0 0 48 0 0 0 49 0 0 0 50 0 0 0 51 0 0 0 52 0 0 0 53 0 0 0 54 0 0 0 55 0 0 0 56 0 0 0 57 0 0 0 58 0 0 0 59 0 0 0 60 0 0 0 61 0 0 0 62 0 0 0 63 0 0 0 64 0 0 0 65 0 0 0 66 0 0 0 67 0 0 0 68 0 0 0 69 0 0 0 70 0 0 0 71 0 0 0 72 0 0 0 73 0 0 0 74 0 0 0 75 1 0 1 76 0 0 0 77 0 0 0 78 0 0 0 79 0 0 0 80 0 0 0 81 0 0 0 82 0 0 0 83 0 0 0 84 0 0 0 85 0 0 0 86 0 0 0 87 0 0 0 88 0 0 0 89 0 0 0 90 0 0 0 91 0 0 0 92 2 0 2 your_output.sample_2.truncated000066400000000000000000000010771350370616400375260ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/se/multiple_input@read_s2_150/1 TGATCTCATACATTTAAACAAAGTATGCCTTACGCATGCCTTAATGATACGTAACCTAGGCAACAGAGTCTTTACTTGTACCTGCTACACAC + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_075/1 TCGCTAGCCCAAGATCACGCTTTCCGCGACGTTTTAGAGCGTGCATACCGGGGCGTTTCTCAGATAGGTATTTCA + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; @read_s2_200/1 ACCCTCACGCTTGCACGACGACAGCGGTCCCCTATAAATGTATGTTGACGCAGCGAGAGGCCAGGACCCGGGCGTGTTACCACTAAGACCCT + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 your_output.settings000066400000000000000000000021311350370616400356640ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/se/multiple_inputAdapterRemoval ver. 2.2.0 Trimming of single-indexed single-end reads [Demultiplexing] Maximum mismatches (total): 0 [Demultiplexing samples] Name Barcode_1 Barcode_2 sample_1 GCGCCGGA * sample_2 CAGGACAT * [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 3717807245 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 Minimum adapter overlap: 0 [Demultiplexing statistics] Name Barcode_1 Barcode_2 Hits Fraction unidentified NA NA 0 0.000 ambiguous NA NA 0 0.000 sample_1 GCGCCGGA * 4 0.500 sample_2 CAGGACAT * 4 0.500 * * * 8 1.000 your_output.unidentified000066400000000000000000000000001350370616400364640ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/se/multiple_inputadapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/se/threads/000077500000000000000000000000001350370616400301265ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/se/threads/one/000077500000000000000000000000001350370616400307075ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/se/threads/one/barcodes.txt000066400000000000000000000000461350370616400332320ustar00rootroot00000000000000sample_1 GCGCCGGA sample_2 CAGGACAT adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/se/threads/one/info.json000066400000000000000000000001111350370616400325260ustar00rootroot00000000000000{ "arguments": ["--threads", "1"], "return_code": 0, "stderr": [ ] } adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/se/threads/one/input_1.fastq000066400000000000000000000033301350370616400333250ustar00rootroot00000000000000@read_s1_000/1 GCGCCGGAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAAAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_000/1 CAGGACATAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAAAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_075/1 GCGCCGGAGACGGTCCCATTAATGCACTATCGGATTTACACATTTGCGTGAATAAATCGACAGATGAATCATTAAGCTCCTACAGATCGGAAGAGCACAC + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_150/1 CAGGACATTGATCTCATACATTTAAACAAAGTATGCCTTACGCATGCCTTAATGATACGTAACCTAGGCAACAGAGTCTTTACTTGTACCTGCTACACAC + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_200/1 GCGCCGGATCCATCAGGATCGTATTATACTAAGCTAGGACTGTGCAGTGCACAGAGAGGAGATGACCATGATCCTCGAGCAAGTTGCCGCAGGCTCGGGC + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_150/1 GCGCCGGATGCACCGTAGCCATATGGGCTGTTGGGGACACAGGGCGTCGGCATTCCTTTATTACTGACGCCGCTAGAGTCTATGCAAGGTTATAACGTAT + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_075/1 CAGGACATTCGCTAGCCCAAGATCACGCTTTCCGCGACGTTTTAGAGCGTGCATACCGGGGCGTTTCTCAGATAGGTATTTCAAGATCGGAAGAGCACAC + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_200/1 CAGGACATACCCTCACGCTTGCACGACGACAGCGGTCCCCTATAAATGTATGTTGACGCAGCGAGAGGCCAGGACCCGGGCGTGTTACCACTAAGACCCT + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 your_output.sample_1.discarded000066400000000000000000000000231350370616400366050ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/se/threads/one@read_s1_000/1 + your_output.sample_1.settings000066400000000000000000000041271350370616400365340ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/se/threads/oneAdapterRemoval ver. 2.2.0 Trimming of single-indexed single-end reads [Demultiplexing] Maximum mismatches (total): 0 [Demultiplexing samples] Name Barcode_1 Barcode_2 sample_1* GCGCCGGA * sample_2 CAGGACAT * [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: TCCGGCGC_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 3717807245 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 Minimum adapter overlap: 0 [Trimming statistics] Total number of reads: 4 Number of unaligned reads: 2 Number of well aligned reads: 2 Number of discarded mate 1 reads: 1 Number of singleton mate 1 reads: 3 Number of reads with adapters[1]: 2 Number of retained reads: 3 Number of retained nucleotides: 259 Average length of retained reads: 86.3333 [Length distribution] Length Mate1 Discarded All 0 0 1 1 1 0 0 0 2 0 0 0 3 0 0 0 4 0 0 0 5 0 0 0 6 0 0 0 7 0 0 0 8 0 0 0 9 0 0 0 10 0 0 0 11 0 0 0 12 0 0 0 13 0 0 0 14 0 0 0 15 0 0 0 16 0 0 0 17 0 0 0 18 0 0 0 19 0 0 0 20 0 0 0 21 0 0 0 22 0 0 0 23 0 0 0 24 0 0 0 25 0 0 0 26 0 0 0 27 0 0 0 28 0 0 0 29 0 0 0 30 0 0 0 31 0 0 0 32 0 0 0 33 0 0 0 34 0 0 0 35 0 0 0 36 0 0 0 37 0 0 0 38 0 0 0 39 0 0 0 40 0 0 0 41 0 0 0 42 0 0 0 43 0 0 0 44 0 0 0 45 0 0 0 46 0 0 0 47 0 0 0 48 0 0 0 49 0 0 0 50 0 0 0 51 0 0 0 52 0 0 0 53 0 0 0 54 0 0 0 55 0 0 0 56 0 0 0 57 0 0 0 58 0 0 0 59 0 0 0 60 0 0 0 61 0 0 0 62 0 0 0 63 0 0 0 64 0 0 0 65 0 0 0 66 0 0 0 67 0 0 0 68 0 0 0 69 0 0 0 70 0 0 0 71 0 0 0 72 0 0 0 73 0 0 0 74 0 0 0 75 1 0 1 76 0 0 0 77 0 0 0 78 0 0 0 79 0 0 0 80 0 0 0 81 0 0 0 82 0 0 0 83 0 0 0 84 0 0 0 85 0 0 0 86 0 0 0 87 0 0 0 88 0 0 0 89 0 0 0 90 0 0 0 91 0 0 0 92 2 0 2 your_output.sample_1.truncated000066400000000000000000000010771350370616400366660ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/se/threads/one@read_s1_075/1 GACGGTCCCATTAATGCACTATCGGATTTACACATTTGCGTGAATAAATCGACAGATGAATCATTAAGCTCCTAC + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; @read_s1_200/1 TCCATCAGGATCGTATTATACTAAGCTAGGACTGTGCAGTGCACAGAGAGGAGATGACCATGATCCTCGAGCAAGTTGCCGCAGGCTCGGGC + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_150/1 TGCACCGTAGCCATATGGGCTGTTGGGGACACAGGGCGTCGGCATTCCTTTATTACTGACGCCGCTAGAGTCTATGCAAGGTTATAACGTAT + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 your_output.sample_2.discarded000066400000000000000000000000231350370616400366060ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/se/threads/one@read_s2_000/1 + your_output.sample_2.settings000066400000000000000000000041271350370616400365350ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/se/threads/oneAdapterRemoval ver. 2.2.0 Trimming of single-indexed single-end reads [Demultiplexing] Maximum mismatches (total): 0 [Demultiplexing samples] Name Barcode_1 Barcode_2 sample_1 GCGCCGGA * sample_2* CAGGACAT * [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: ATGTCCTG_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 3717807245 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 Minimum adapter overlap: 0 [Trimming statistics] Total number of reads: 4 Number of unaligned reads: 2 Number of well aligned reads: 2 Number of discarded mate 1 reads: 1 Number of singleton mate 1 reads: 3 Number of reads with adapters[1]: 2 Number of retained reads: 3 Number of retained nucleotides: 259 Average length of retained reads: 86.3333 [Length distribution] Length Mate1 Discarded All 0 0 1 1 1 0 0 0 2 0 0 0 3 0 0 0 4 0 0 0 5 0 0 0 6 0 0 0 7 0 0 0 8 0 0 0 9 0 0 0 10 0 0 0 11 0 0 0 12 0 0 0 13 0 0 0 14 0 0 0 15 0 0 0 16 0 0 0 17 0 0 0 18 0 0 0 19 0 0 0 20 0 0 0 21 0 0 0 22 0 0 0 23 0 0 0 24 0 0 0 25 0 0 0 26 0 0 0 27 0 0 0 28 0 0 0 29 0 0 0 30 0 0 0 31 0 0 0 32 0 0 0 33 0 0 0 34 0 0 0 35 0 0 0 36 0 0 0 37 0 0 0 38 0 0 0 39 0 0 0 40 0 0 0 41 0 0 0 42 0 0 0 43 0 0 0 44 0 0 0 45 0 0 0 46 0 0 0 47 0 0 0 48 0 0 0 49 0 0 0 50 0 0 0 51 0 0 0 52 0 0 0 53 0 0 0 54 0 0 0 55 0 0 0 56 0 0 0 57 0 0 0 58 0 0 0 59 0 0 0 60 0 0 0 61 0 0 0 62 0 0 0 63 0 0 0 64 0 0 0 65 0 0 0 66 0 0 0 67 0 0 0 68 0 0 0 69 0 0 0 70 0 0 0 71 0 0 0 72 0 0 0 73 0 0 0 74 0 0 0 75 1 0 1 76 0 0 0 77 0 0 0 78 0 0 0 79 0 0 0 80 0 0 0 81 0 0 0 82 0 0 0 83 0 0 0 84 0 0 0 85 0 0 0 86 0 0 0 87 0 0 0 88 0 0 0 89 0 0 0 90 0 0 0 91 0 0 0 92 2 0 2 your_output.sample_2.truncated000066400000000000000000000010771350370616400366670ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/se/threads/one@read_s2_150/1 TGATCTCATACATTTAAACAAAGTATGCCTTACGCATGCCTTAATGATACGTAACCTAGGCAACAGAGTCTTTACTTGTACCTGCTACACAC + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_075/1 TCGCTAGCCCAAGATCACGCTTTCCGCGACGTTTTAGAGCGTGCATACCGGGGCGTTTCTCAGATAGGTATTTCA + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; @read_s2_200/1 ACCCTCACGCTTGCACGACGACAGCGGTCCCCTATAAATGTATGTTGACGCAGCGAGAGGCCAGGACCCGGGCGTGTTACCACTAAGACCCT + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 your_output.settings000066400000000000000000000021311350370616400350250ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/se/threads/oneAdapterRemoval ver. 2.2.0 Trimming of single-indexed single-end reads [Demultiplexing] Maximum mismatches (total): 0 [Demultiplexing samples] Name Barcode_1 Barcode_2 sample_1 GCGCCGGA * sample_2 CAGGACAT * [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 3717807245 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 Minimum adapter overlap: 0 [Demultiplexing statistics] Name Barcode_1 Barcode_2 Hits Fraction unidentified NA NA 0 0.000 ambiguous NA NA 0 0.000 sample_1 GCGCCGGA * 4 0.500 sample_2 CAGGACAT * 4 0.500 * * * 8 1.000 your_output.unidentified000066400000000000000000000000001350370616400356250ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/se/threads/oneadapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/se/threads/three/000077500000000000000000000000001350370616400312355ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/se/threads/three/barcodes.txt000066400000000000000000000000461350370616400335600ustar00rootroot00000000000000sample_1 GCGCCGGA sample_2 CAGGACAT adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/se/threads/three/info.json000066400000000000000000000001111350370616400330540ustar00rootroot00000000000000{ "arguments": ["--threads", "3"], "return_code": 0, "stderr": [ ] } adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/se/threads/three/input_1.fastq000066400000000000000000000033301350370616400336530ustar00rootroot00000000000000@read_s1_000/1 GCGCCGGAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAAAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_000/1 CAGGACATAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAAAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_075/1 GCGCCGGAGACGGTCCCATTAATGCACTATCGGATTTACACATTTGCGTGAATAAATCGACAGATGAATCATTAAGCTCCTACAGATCGGAAGAGCACAC + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_150/1 CAGGACATTGATCTCATACATTTAAACAAAGTATGCCTTACGCATGCCTTAATGATACGTAACCTAGGCAACAGAGTCTTTACTTGTACCTGCTACACAC + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_200/1 GCGCCGGATCCATCAGGATCGTATTATACTAAGCTAGGACTGTGCAGTGCACAGAGAGGAGATGACCATGATCCTCGAGCAAGTTGCCGCAGGCTCGGGC + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_150/1 GCGCCGGATGCACCGTAGCCATATGGGCTGTTGGGGACACAGGGCGTCGGCATTCCTTTATTACTGACGCCGCTAGAGTCTATGCAAGGTTATAACGTAT + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_075/1 CAGGACATTCGCTAGCCCAAGATCACGCTTTCCGCGACGTTTTAGAGCGTGCATACCGGGGCGTTTCTCAGATAGGTATTTCAAGATCGGAAGAGCACAC + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_200/1 CAGGACATACCCTCACGCTTGCACGACGACAGCGGTCCCCTATAAATGTATGTTGACGCAGCGAGAGGCCAGGACCCGGGCGTGTTACCACTAAGACCCT + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 your_output.sample_1.discarded000066400000000000000000000000231350370616400371330ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/se/threads/three@read_s1_000/1 + your_output.sample_1.settings000066400000000000000000000041171350370616400370610ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/se/threads/threeAdapterRemoval ver. 2.2.0 Trimming of single-indexed single-end reads [Demultiplexing] Maximum mismatches (total): 0 [Demultiplexing samples] Name Barcode_1 Barcode_2 sample_1* GCGCCGGA * sample_2 CAGGACAT * [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: TCCGGCGC_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: NA Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 Minimum adapter overlap: 0 [Trimming statistics] Total number of reads: 4 Number of unaligned reads: 2 Number of well aligned reads: 2 Number of discarded mate 1 reads: 1 Number of singleton mate 1 reads: 3 Number of reads with adapters[1]: 2 Number of retained reads: 3 Number of retained nucleotides: 259 Average length of retained reads: 86.3333 [Length distribution] Length Mate1 Discarded All 0 0 1 1 1 0 0 0 2 0 0 0 3 0 0 0 4 0 0 0 5 0 0 0 6 0 0 0 7 0 0 0 8 0 0 0 9 0 0 0 10 0 0 0 11 0 0 0 12 0 0 0 13 0 0 0 14 0 0 0 15 0 0 0 16 0 0 0 17 0 0 0 18 0 0 0 19 0 0 0 20 0 0 0 21 0 0 0 22 0 0 0 23 0 0 0 24 0 0 0 25 0 0 0 26 0 0 0 27 0 0 0 28 0 0 0 29 0 0 0 30 0 0 0 31 0 0 0 32 0 0 0 33 0 0 0 34 0 0 0 35 0 0 0 36 0 0 0 37 0 0 0 38 0 0 0 39 0 0 0 40 0 0 0 41 0 0 0 42 0 0 0 43 0 0 0 44 0 0 0 45 0 0 0 46 0 0 0 47 0 0 0 48 0 0 0 49 0 0 0 50 0 0 0 51 0 0 0 52 0 0 0 53 0 0 0 54 0 0 0 55 0 0 0 56 0 0 0 57 0 0 0 58 0 0 0 59 0 0 0 60 0 0 0 61 0 0 0 62 0 0 0 63 0 0 0 64 0 0 0 65 0 0 0 66 0 0 0 67 0 0 0 68 0 0 0 69 0 0 0 70 0 0 0 71 0 0 0 72 0 0 0 73 0 0 0 74 0 0 0 75 1 0 1 76 0 0 0 77 0 0 0 78 0 0 0 79 0 0 0 80 0 0 0 81 0 0 0 82 0 0 0 83 0 0 0 84 0 0 0 85 0 0 0 86 0 0 0 87 0 0 0 88 0 0 0 89 0 0 0 90 0 0 0 91 0 0 0 92 2 0 2 your_output.sample_1.truncated000066400000000000000000000010771350370616400372140ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/se/threads/three@read_s1_075/1 GACGGTCCCATTAATGCACTATCGGATTTACACATTTGCGTGAATAAATCGACAGATGAATCATTAAGCTCCTAC + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; @read_s1_200/1 TCCATCAGGATCGTATTATACTAAGCTAGGACTGTGCAGTGCACAGAGAGGAGATGACCATGATCCTCGAGCAAGTTGCCGCAGGCTCGGGC + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_150/1 TGCACCGTAGCCATATGGGCTGTTGGGGACACAGGGCGTCGGCATTCCTTTATTACTGACGCCGCTAGAGTCTATGCAAGGTTATAACGTAT + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 your_output.sample_2.discarded000066400000000000000000000000231350370616400371340ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/se/threads/three@read_s2_000/1 + your_output.sample_2.settings000066400000000000000000000041171350370616400370620ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/se/threads/threeAdapterRemoval ver. 2.2.0 Trimming of single-indexed single-end reads [Demultiplexing] Maximum mismatches (total): 0 [Demultiplexing samples] Name Barcode_1 Barcode_2 sample_1 GCGCCGGA * sample_2* CAGGACAT * [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: ATGTCCTG_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: NA Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 Minimum adapter overlap: 0 [Trimming statistics] Total number of reads: 4 Number of unaligned reads: 2 Number of well aligned reads: 2 Number of discarded mate 1 reads: 1 Number of singleton mate 1 reads: 3 Number of reads with adapters[1]: 2 Number of retained reads: 3 Number of retained nucleotides: 259 Average length of retained reads: 86.3333 [Length distribution] Length Mate1 Discarded All 0 0 1 1 1 0 0 0 2 0 0 0 3 0 0 0 4 0 0 0 5 0 0 0 6 0 0 0 7 0 0 0 8 0 0 0 9 0 0 0 10 0 0 0 11 0 0 0 12 0 0 0 13 0 0 0 14 0 0 0 15 0 0 0 16 0 0 0 17 0 0 0 18 0 0 0 19 0 0 0 20 0 0 0 21 0 0 0 22 0 0 0 23 0 0 0 24 0 0 0 25 0 0 0 26 0 0 0 27 0 0 0 28 0 0 0 29 0 0 0 30 0 0 0 31 0 0 0 32 0 0 0 33 0 0 0 34 0 0 0 35 0 0 0 36 0 0 0 37 0 0 0 38 0 0 0 39 0 0 0 40 0 0 0 41 0 0 0 42 0 0 0 43 0 0 0 44 0 0 0 45 0 0 0 46 0 0 0 47 0 0 0 48 0 0 0 49 0 0 0 50 0 0 0 51 0 0 0 52 0 0 0 53 0 0 0 54 0 0 0 55 0 0 0 56 0 0 0 57 0 0 0 58 0 0 0 59 0 0 0 60 0 0 0 61 0 0 0 62 0 0 0 63 0 0 0 64 0 0 0 65 0 0 0 66 0 0 0 67 0 0 0 68 0 0 0 69 0 0 0 70 0 0 0 71 0 0 0 72 0 0 0 73 0 0 0 74 0 0 0 75 1 0 1 76 0 0 0 77 0 0 0 78 0 0 0 79 0 0 0 80 0 0 0 81 0 0 0 82 0 0 0 83 0 0 0 84 0 0 0 85 0 0 0 86 0 0 0 87 0 0 0 88 0 0 0 89 0 0 0 90 0 0 0 91 0 0 0 92 2 0 2 your_output.sample_2.truncated000066400000000000000000000010771350370616400372150ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/se/threads/three@read_s2_150/1 TGATCTCATACATTTAAACAAAGTATGCCTTACGCATGCCTTAATGATACGTAACCTAGGCAACAGAGTCTTTACTTGTACCTGCTACACAC + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_075/1 TCGCTAGCCCAAGATCACGCTTTCCGCGACGTTTTAGAGCGTGCATACCGGGGCGTTTCTCAGATAGGTATTTCA + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; @read_s2_200/1 ACCCTCACGCTTGCACGACGACAGCGGTCCCCTATAAATGTATGTTGACGCAGCGAGAGGCCAGGACCCGGGCGTGTTACCACTAAGACCCT + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 your_output.settings000066400000000000000000000021211350370616400353520ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/se/threads/threeAdapterRemoval ver. 2.2.0 Trimming of single-indexed single-end reads [Demultiplexing] Maximum mismatches (total): 0 [Demultiplexing samples] Name Barcode_1 Barcode_2 sample_1 GCGCCGGA * sample_2 CAGGACAT * [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: NA Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 Minimum adapter overlap: 0 [Demultiplexing statistics] Name Barcode_1 Barcode_2 Hits Fraction unidentified NA NA 0 0.000 ambiguous NA NA 0 0.000 sample_1 GCGCCGGA * 4 0.500 sample_2 CAGGACAT * 4 0.500 * * * 8 1.000 your_output.unidentified000066400000000000000000000000001350370616400361530ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/se/threads/threeadapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/se/threads/two/000077500000000000000000000000001350370616400307375ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/se/threads/two/barcodes.txt000066400000000000000000000000461350370616400332620ustar00rootroot00000000000000sample_1 GCGCCGGA sample_2 CAGGACAT adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/se/threads/two/info.json000066400000000000000000000001111350370616400325560ustar00rootroot00000000000000{ "arguments": ["--threads", "2"], "return_code": 0, "stderr": [ ] } adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/se/threads/two/input_1.fastq000066400000000000000000000033301350370616400333550ustar00rootroot00000000000000@read_s1_000/1 GCGCCGGAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAAAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_000/1 CAGGACATAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAAAA + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_075/1 GCGCCGGAGACGGTCCCATTAATGCACTATCGGATTTACACATTTGCGTGAATAAATCGACAGATGAATCATTAAGCTCCTACAGATCGGAAGAGCACAC + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_150/1 CAGGACATTGATCTCATACATTTAAACAAAGTATGCCTTACGCATGCCTTAATGATACGTAACCTAGGCAACAGAGTCTTTACTTGTACCTGCTACACAC + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_200/1 GCGCCGGATCCATCAGGATCGTATTATACTAAGCTAGGACTGTGCAGTGCACAGAGAGGAGATGACCATGATCCTCGAGCAAGTTGCCGCAGGCTCGGGC + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_150/1 GCGCCGGATGCACCGTAGCCATATGGGCTGTTGGGGACACAGGGCGTCGGCATTCCTTTATTACTGACGCCGCTAGAGTCTATGCAAGGTTATAACGTAT + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_075/1 CAGGACATTCGCTAGCCCAAGATCACGCTTTCCGCGACGTTTTAGAGCGTGCATACCGGGGCGTTTCTCAGATAGGTATTTCAAGATCGGAAGAGCACAC + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_200/1 CAGGACATACCCTCACGCTTGCACGACGACAGCGGTCCCCTATAAATGTATGTTGACGCAGCGAGAGGCCAGGACCCGGGCGTGTTACCACTAAGACCCT + HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 your_output.sample_1.discarded000066400000000000000000000000231350370616400366350ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/se/threads/two@read_s1_000/1 + your_output.sample_1.settings000066400000000000000000000041171350370616400365630ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/se/threads/twoAdapterRemoval ver. 2.2.0 Trimming of single-indexed single-end reads [Demultiplexing] Maximum mismatches (total): 0 [Demultiplexing samples] Name Barcode_1 Barcode_2 sample_1* GCGCCGGA * sample_2 CAGGACAT * [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: TCCGGCGC_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: NA Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 Minimum adapter overlap: 0 [Trimming statistics] Total number of reads: 4 Number of unaligned reads: 2 Number of well aligned reads: 2 Number of discarded mate 1 reads: 1 Number of singleton mate 1 reads: 3 Number of reads with adapters[1]: 2 Number of retained reads: 3 Number of retained nucleotides: 259 Average length of retained reads: 86.3333 [Length distribution] Length Mate1 Discarded All 0 0 1 1 1 0 0 0 2 0 0 0 3 0 0 0 4 0 0 0 5 0 0 0 6 0 0 0 7 0 0 0 8 0 0 0 9 0 0 0 10 0 0 0 11 0 0 0 12 0 0 0 13 0 0 0 14 0 0 0 15 0 0 0 16 0 0 0 17 0 0 0 18 0 0 0 19 0 0 0 20 0 0 0 21 0 0 0 22 0 0 0 23 0 0 0 24 0 0 0 25 0 0 0 26 0 0 0 27 0 0 0 28 0 0 0 29 0 0 0 30 0 0 0 31 0 0 0 32 0 0 0 33 0 0 0 34 0 0 0 35 0 0 0 36 0 0 0 37 0 0 0 38 0 0 0 39 0 0 0 40 0 0 0 41 0 0 0 42 0 0 0 43 0 0 0 44 0 0 0 45 0 0 0 46 0 0 0 47 0 0 0 48 0 0 0 49 0 0 0 50 0 0 0 51 0 0 0 52 0 0 0 53 0 0 0 54 0 0 0 55 0 0 0 56 0 0 0 57 0 0 0 58 0 0 0 59 0 0 0 60 0 0 0 61 0 0 0 62 0 0 0 63 0 0 0 64 0 0 0 65 0 0 0 66 0 0 0 67 0 0 0 68 0 0 0 69 0 0 0 70 0 0 0 71 0 0 0 72 0 0 0 73 0 0 0 74 0 0 0 75 1 0 1 76 0 0 0 77 0 0 0 78 0 0 0 79 0 0 0 80 0 0 0 81 0 0 0 82 0 0 0 83 0 0 0 84 0 0 0 85 0 0 0 86 0 0 0 87 0 0 0 88 0 0 0 89 0 0 0 90 0 0 0 91 0 0 0 92 2 0 2 your_output.sample_1.truncated000066400000000000000000000010771350370616400367160ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/se/threads/two@read_s1_075/1 GACGGTCCCATTAATGCACTATCGGATTTACACATTTGCGTGAATAAATCGACAGATGAATCATTAAGCTCCTAC + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; @read_s1_200/1 TCCATCAGGATCGTATTATACTAAGCTAGGACTGTGCAGTGCACAGAGAGGAGATGACCATGATCCTCGAGCAAGTTGCCGCAGGCTCGGGC + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s1_150/1 TGCACCGTAGCCATATGGGCTGTTGGGGACACAGGGCGTCGGCATTCCTTTATTACTGACGCCGCTAGAGTCTATGCAAGGTTATAACGTAT + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 your_output.sample_2.discarded000066400000000000000000000000231350370616400366360ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/se/threads/two@read_s2_000/1 + your_output.sample_2.settings000066400000000000000000000041171350370616400365640ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/se/threads/twoAdapterRemoval ver. 2.2.0 Trimming of single-indexed single-end reads [Demultiplexing] Maximum mismatches (total): 0 [Demultiplexing samples] Name Barcode_1 Barcode_2 sample_1 GCGCCGGA * sample_2* CAGGACAT * [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: ATGTCCTG_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: NA Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 Minimum adapter overlap: 0 [Trimming statistics] Total number of reads: 4 Number of unaligned reads: 2 Number of well aligned reads: 2 Number of discarded mate 1 reads: 1 Number of singleton mate 1 reads: 3 Number of reads with adapters[1]: 2 Number of retained reads: 3 Number of retained nucleotides: 259 Average length of retained reads: 86.3333 [Length distribution] Length Mate1 Discarded All 0 0 1 1 1 0 0 0 2 0 0 0 3 0 0 0 4 0 0 0 5 0 0 0 6 0 0 0 7 0 0 0 8 0 0 0 9 0 0 0 10 0 0 0 11 0 0 0 12 0 0 0 13 0 0 0 14 0 0 0 15 0 0 0 16 0 0 0 17 0 0 0 18 0 0 0 19 0 0 0 20 0 0 0 21 0 0 0 22 0 0 0 23 0 0 0 24 0 0 0 25 0 0 0 26 0 0 0 27 0 0 0 28 0 0 0 29 0 0 0 30 0 0 0 31 0 0 0 32 0 0 0 33 0 0 0 34 0 0 0 35 0 0 0 36 0 0 0 37 0 0 0 38 0 0 0 39 0 0 0 40 0 0 0 41 0 0 0 42 0 0 0 43 0 0 0 44 0 0 0 45 0 0 0 46 0 0 0 47 0 0 0 48 0 0 0 49 0 0 0 50 0 0 0 51 0 0 0 52 0 0 0 53 0 0 0 54 0 0 0 55 0 0 0 56 0 0 0 57 0 0 0 58 0 0 0 59 0 0 0 60 0 0 0 61 0 0 0 62 0 0 0 63 0 0 0 64 0 0 0 65 0 0 0 66 0 0 0 67 0 0 0 68 0 0 0 69 0 0 0 70 0 0 0 71 0 0 0 72 0 0 0 73 0 0 0 74 0 0 0 75 1 0 1 76 0 0 0 77 0 0 0 78 0 0 0 79 0 0 0 80 0 0 0 81 0 0 0 82 0 0 0 83 0 0 0 84 0 0 0 85 0 0 0 86 0 0 0 87 0 0 0 88 0 0 0 89 0 0 0 90 0 0 0 91 0 0 0 92 2 0 2 your_output.sample_2.truncated000066400000000000000000000010771350370616400367170ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/se/threads/two@read_s2_150/1 TGATCTCATACATTTAAACAAAGTATGCCTTACGCATGCCTTAATGATACGTAACCTAGGCAACAGAGTCTTTACTTGTACCTGCTACACAC + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 @read_s2_075/1 TCGCTAGCCCAAGATCACGCTTTCCGCGACGTTTTAGAGCGTGCATACCGGGGCGTTTCTCAGATAGGTATTTCA + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; @read_s2_200/1 ACCCTCACGCTTGCACGACGACAGCGGTCCCCTATAAATGTATGTTGACGCAGCGAGAGGCCAGGACCCGGGCGTGTTACCACTAAGACCCT + GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 your_output.settings000066400000000000000000000021211350370616400350540ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/se/threads/twoAdapterRemoval ver. 2.2.0 Trimming of single-indexed single-end reads [Demultiplexing] Maximum mismatches (total): 0 [Demultiplexing samples] Name Barcode_1 Barcode_2 sample_1 GCGCCGGA * sample_2 CAGGACAT * [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: NA Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 Minimum adapter overlap: 0 [Demultiplexing statistics] Name Barcode_1 Barcode_2 Hits Fraction unidentified NA NA 0 0.000 ambiguous NA NA 0 0.000 sample_1 GCGCCGGA * 4 0.500 sample_2 CAGGACAT * 4 0.500 * * * 8 1.000 your_output.unidentified000066400000000000000000000000001350370616400356550ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/demultiplexing/single_indexed/se/threads/twoadapterremoval-2.3.1/tests/regression/misc/000077500000000000000000000000001350370616400210055ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/misc/adapter_list/000077500000000000000000000000001350370616400234605ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/misc/adapter_list/adapters.txt000066400000000000000000000001741350370616400260260ustar00rootroot00000000000000AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT adapterremoval-2.3.1/tests/regression/misc/adapter_list/info.json000066400000000000000000000001311350370616400253010ustar00rootroot00000000000000{ "arguments": ["--adapter-list", "adapters.txt"], "return_code": 0, "stderr": [ ] } adapterremoval-2.3.1/tests/regression/misc/adapter_list/input_1.fastq000066400000000000000000000003551350370616400261020ustar00rootroot00000000000000@AAGGGCSeq_1_5180_50/1 meta data ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG + IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! adapterremoval-2.3.1/tests/regression/misc/adapter_list/input_2.fastq000066400000000000000000000003551350370616400261030ustar00rootroot00000000000000@AAGGGCSeq_1_5180_50/2 data meta AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGTAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCC + JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDEDBDBCBCCBBAA?ADAAA@@@>>>><=><<;<:<;87:78753420/,+)! adapterremoval-2.3.1/tests/regression/misc/adapter_list/your_output.discarded000066400000000000000000000000001350370616400277300ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/misc/adapter_list/your_output.pair1.truncated000066400000000000000000000002111350370616400310160ustar00rootroot00000000000000@AAGGGCSeq_1_5180_50/1 meta data ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCT + IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECC adapterremoval-2.3.1/tests/regression/misc/adapter_list/your_output.pair2.truncated000066400000000000000000000002111350370616400310170ustar00rootroot00000000000000@AAGGGCSeq_1_5180_50/2 data meta AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGT + JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDED adapterremoval-2.3.1/tests/regression/misc/adapter_list/your_output.settings000066400000000000000000000035111350370616400276600ustar00rootroot00000000000000AdapterRemoval ver. 2.1.7 Trimming of paired-end reads [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 372265332 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 [Trimming statistics] Total number of read pairs: 1 Number of unaligned read pairs: 0 Number of well aligned read pairs: 1 Number of discarded mate 1 reads: 0 Number of singleton mate 1 reads: 0 Number of discarded mate 2 reads: 0 Number of singleton mate 2 reads: 0 Number of reads with adapters[1]: 2 Number of retained reads: 2 Number of retained nucleotides: 100 Average length of retained reads: 50 [Length distribution] Length Mate1 Mate2 Singleton Discarded All 0 0 0 0 0 0 1 0 0 0 0 0 2 0 0 0 0 0 3 0 0 0 0 0 4 0 0 0 0 0 5 0 0 0 0 0 6 0 0 0 0 0 7 0 0 0 0 0 8 0 0 0 0 0 9 0 0 0 0 0 10 0 0 0 0 0 11 0 0 0 0 0 12 0 0 0 0 0 13 0 0 0 0 0 14 0 0 0 0 0 15 0 0 0 0 0 16 0 0 0 0 0 17 0 0 0 0 0 18 0 0 0 0 0 19 0 0 0 0 0 20 0 0 0 0 0 21 0 0 0 0 0 22 0 0 0 0 0 23 0 0 0 0 0 24 0 0 0 0 0 25 0 0 0 0 0 26 0 0 0 0 0 27 0 0 0 0 0 28 0 0 0 0 0 29 0 0 0 0 0 30 0 0 0 0 0 31 0 0 0 0 0 32 0 0 0 0 0 33 0 0 0 0 0 34 0 0 0 0 0 35 0 0 0 0 0 36 0 0 0 0 0 37 0 0 0 0 0 38 0 0 0 0 0 39 0 0 0 0 0 40 0 0 0 0 0 41 0 0 0 0 0 42 0 0 0 0 0 43 0 0 0 0 0 44 0 0 0 0 0 45 0 0 0 0 0 46 0 0 0 0 0 47 0 0 0 0 0 48 0 0 0 0 0 49 0 0 0 0 0 50 1 1 0 0 2 adapterremoval-2.3.1/tests/regression/misc/adapter_list/your_output.singleton.truncated000066400000000000000000000000001350370616400320000ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/misc/bad_args/000077500000000000000000000000001350370616400225475ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/misc/bad_args/demux_without_barcodes/000077500000000000000000000000001350370616400273165ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/misc/bad_args/demux_without_barcodes/info.json000066400000000000000000000003011350370616400311360ustar00rootroot00000000000000{ "arguments": ["--demultiplex-only"], "return_code": 1, "stderr": [ "Cannot use --demultiplex-only without specifying a list of barcodes using --barcode-list!" ], "exhaustive": false } adapterremoval-2.3.1/tests/regression/misc/bad_args/demux_without_barcodes/input_1.fastq000066400000000000000000000003551350370616400317400ustar00rootroot00000000000000@AAGGGCSeq_1_5180_50/1 meta data ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG + IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! adapterremoval-2.3.1/tests/regression/misc/bad_args/demux_without_barcodes/input_2.fastq000066400000000000000000000003551350370616400317410ustar00rootroot00000000000000@AAGGGCSeq_1_5180_50/2 data meta AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGTAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCC + JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDEDBDBCBCCBBAA?ADAAA@@@>>>><=><<;<:<;87:78753420/,+)! adapterremoval-2.3.1/tests/regression/misc/bad_args/fewer_file1/000077500000000000000000000000001350370616400247375ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/misc/bad_args/fewer_file1/info.json000066400000000000000000000002271350370616400265660ustar00rootroot00000000000000{ "arguments": [], "return_code": 1, "stderr": [ "Error: Different number of files specified for --file1 and --file2." ], "exhaustive": false } adapterremoval-2.3.1/tests/regression/misc/bad_args/fewer_file1/input_1a.fastq000066400000000000000000000015501350370616400275200ustar00rootroot00000000000000@read_150_1/1 CTTGGGTACTCAGCCTTAGGGTACCACATAGAGTTATCTTATATATTATAATTGCTCTTTTAACATAATTTTAAAAAATTTATATTAAACTTTCTCTGTT + HHHFFFFBBDGGGGGHHHHHGGFCDHGEE<@;+@C792A.CEEGGFFFFDEFGFHHHH@C2;@F;EDDHFDCCC@.DEEEG=BGEDC5>:=2@GFHHHFF @read_150_2/1 GAGTGGGCTTCATCCCTGGGATGCAAGGCTGGTTCAATATATGCAAATCAATAAATGTAATCCAGCATATAAACAGAACCAAAGAAGATCGGAAGAGCAC + HHHHHHHHHHHHHHHHHHHHHHHGC.@CFGHHHHHHHHFBFFHEHHHHFBGHFFFFFFHEDE@EBHHFHB<<>099BEB@=?*59/''.CCFHFHHHHHH @read_150_3/1 TATGTAATGACATAACTCTTATGGGCAACTTCACAAAAACACAGAAGAAAGCCCTCCTAAAGAATGAAATTCCAAAAAAAATCAGGTTACTGCTCACTGA + HHE=EE@DBBBGHGBFGGDDDDFFFHHHHHGHHHHHHGHHHE7BFHHHHHHG@4FEHHFHHHHFHHHHHHFFFE?EGCDE>CD:9=>+*;=37::ADDHF @read_150_4/1 CTCCTATATAAAGATAGCTCTGTAAAACAGGCCAAAAAGCAGAGTGGGGTGTGGGAAGGCAGGGAAAACTGTCCAGGAATAAAGGCATGAAATGAAACAA + HHHHHHHHHHHHHHHHEG@:EEB4DFHHEHFHHHHEGFFEEFCDHEFF:+1;?GFFCFHHHHHHHHHFHBB>>BEDGCDHHHHF adapterremoval-2.3.1/tests/regression/misc/bad_args/fewer_file1/input_1b.fastq000066400000000000000000000015501350370616400275210ustar00rootroot00000000000000@read_150_5/1 TACTCACGGACAAAGAATAAATATAGCTCCTCCAGGAGCTTAATAACTCAGTGCTGTCTAAACTCCTTACACCTGATGTTGATGCCATGGTTAGATAGTT + HHFFGGFDBHHEHHHHHHHHHHHHFHHHHFHHFEEDFD8=GHFFHHDHHHCHHFDHBHD:> @read_150_7/1 TAAGTAAGGTAGACAGCTAAGTCTAGTTTGTTCCCAGTGTTGTACCAGTCTCATCAGTGCCGTGTCTGGGTCTCACAGCCTCTGGTGTTCTATGCTGGAT + GFFEEDHHGHHHHHHHHB?GG77-/:>>@?6AC5GIB?BEBHHHHHHHHHHHHFGFHHHHHHEFEGF9?EHHHE@8BB12BEHHH @read_150_8/1 TAAAAACAAAAACCCTGATGAGAGTATTGATGTGTGCATAAACAAAGAAAAACATAATAGGAATAGAATGGTGAATTAAATTTTGTGAATTTTGGAAACC + HGGGGGHHHHHFHHGHHHHHHHEHHHHHHFHHEEHHHHHFE:/CGBHHHHHGFFGHHHHCEHEFECEFHHFEEE>E6,735@GG @read_150_3/2 GTCATTAACATTCACGAAGATAAATTTCTCCATTTTAAACAGAGACACTCAGTGAGCAGTAACCTGATTTTTTTTGGAATTTCATTCTTCAGGAGGGCTT + HHHHHHHHHHHHHHHHHH?GF5:@AFHHHGHFDDGGFFFHHFGHHHGGHHHHHHHHFGHFGEGC.18984>1BC=GFFAC<>E?..59&&-81:<<5.@ABCDBCE>:>@CDGHHHGEBFE/38@EEFBFGHHHHHHEGH?DHHHH>'9DEC**'*6 adapterremoval-2.3.1/tests/regression/misc/bad_args/fewer_file1/input_2b.fastq000066400000000000000000000015501350370616400275220ustar00rootroot00000000000000@read_150_5/2 TGGGGCCATCAGGAATTTTGCAGTGGTAATGGGGGACATTTTAGCTGAGACTTGGAAAAATGGTAGAATTTGCTCCAACATGAGGAAATATGAGCATTGA + HHHHGEGHHHHGEG;/FHHHHHHHHE;@==G=DC>DGFHHHHHHHHHHHHHHFD;>A5<(@<4 @read_150_7/2 ACTTGCACCTCTTCATCAGAGGAGCAGATCCAGGAACAGAAGTCCTGCATTTACAGGCTCTTCATATCTTGTGCCGGGTTTGGCTGCCAGGTGGCCAGCT + HHHHG=BDEDFFGGHHHHHHHHHHHHFHHFHHHCGHHHHHEBHHHHHHHHHHHHHHGEEE??6BCFHE624@7=1AFGBDHHHFFE<<.>,1349EEHHHHHHHGFHFHHHHHEHHD=:>-7@BC2BHHHHHHHGBHEFFHHGGHFGFHHEEFHFBEBEFHHFFBCA?B adapterremoval-2.3.1/tests/regression/misc/bad_args/fewer_file1/input_2c.fastq000066400000000000000000000006651350370616400275310ustar00rootroot00000000000000@read_150_9/2 GCCTTCCCTCTTCACTCCCTCCCTTATCCCAAACCTGCCTAGGTGGGGCTGATACAGACAGCAGGCCTGGCTCTACTTGTTTTGACAAAATATATGCCCT + GGGEBGHHHHHHHHHHHHHHHHHHHHFADHHHFHHHF?DEF@B>C;CDGEHGGHHHE@@DBFGHHHHGB>BBFEGEGHFHF8ADCFDEE4D?>H@:>DD= @read_150_10/2 TAGTCTTCTCTTTCCTGAGAATATTTTTATTGCAAATATGTAGTCATATATACGTAAGATAAGGATATTTTAAATACTACTTTAAAAGTTATTACTATAA + HHHHHHHHHHHHHHHHHHHHHHHHHHHHHFFFGHHHHHHHHHHHHEBDG>CCBB?FHFHHDEFHGDDGHHHHHH@BECHHEHGDHHHHHFHHHGEHHHHH adapterremoval-2.3.1/tests/regression/misc/bad_args/fewer_file2/000077500000000000000000000000001350370616400247405ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/misc/bad_args/fewer_file2/info.json000066400000000000000000000002271350370616400265670ustar00rootroot00000000000000{ "arguments": [], "return_code": 1, "stderr": [ "Error: Different number of files specified for --file1 and --file2." ], "exhaustive": false } adapterremoval-2.3.1/tests/regression/misc/bad_args/fewer_file2/input_1a.fastq000066400000000000000000000015501350370616400275210ustar00rootroot00000000000000@read_150_1/1 CTTGGGTACTCAGCCTTAGGGTACCACATAGAGTTATCTTATATATTATAATTGCTCTTTTAACATAATTTTAAAAAATTTATATTAAACTTTCTCTGTT + HHHFFFFBBDGGGGGHHHHHGGFCDHGEE<@;+@C792A.CEEGGFFFFDEFGFHHHH@C2;@F;EDDHFDCCC@.DEEEG=BGEDC5>:=2@GFHHHFF @read_150_2/1 GAGTGGGCTTCATCCCTGGGATGCAAGGCTGGTTCAATATATGCAAATCAATAAATGTAATCCAGCATATAAACAGAACCAAAGAAGATCGGAAGAGCAC + HHHHHHHHHHHHHHHHHHHHHHHGC.@CFGHHHHHHHHFBFFHEHHHHFBGHFFFFFFHEDE@EBHHFHB<<>099BEB@=?*59/''.CCFHFHHHHHH @read_150_3/1 TATGTAATGACATAACTCTTATGGGCAACTTCACAAAAACACAGAAGAAAGCCCTCCTAAAGAATGAAATTCCAAAAAAAATCAGGTTACTGCTCACTGA + HHE=EE@DBBBGHGBFGGDDDDFFFHHHHHGHHHHHHGHHHE7BFHHHHHHG@4FEHHFHHHHFHHHHHHFFFE?EGCDE>CD:9=>+*;=37::ADDHF @read_150_4/1 CTCCTATATAAAGATAGCTCTGTAAAACAGGCCAAAAAGCAGAGTGGGGTGTGGGAAGGCAGGGAAAACTGTCCAGGAATAAAGGCATGAAATGAAACAA + HHHHHHHHHHHHHHHHEG@:EEB4DFHHEHFHHHHEGFFEEFCDHEFF:+1;?GFFCFHHHHHHHHHFHBB>>BEDGCDHHHHF adapterremoval-2.3.1/tests/regression/misc/bad_args/fewer_file2/input_1b.fastq000066400000000000000000000015501350370616400275220ustar00rootroot00000000000000@read_150_5/1 TACTCACGGACAAAGAATAAATATAGCTCCTCCAGGAGCTTAATAACTCAGTGCTGTCTAAACTCCTTACACCTGATGTTGATGCCATGGTTAGATAGTT + HHFFGGFDBHHEHHHHHHHHHHHHFHHHHFHHFEEDFD8=GHFFHHDHHHCHHFDHBHD:> @read_150_7/1 TAAGTAAGGTAGACAGCTAAGTCTAGTTTGTTCCCAGTGTTGTACCAGTCTCATCAGTGCCGTGTCTGGGTCTCACAGCCTCTGGTGTTCTATGCTGGAT + GFFEEDHHGHHHHHHHHB?GG77-/:>>@?6AC5GIB?BEBHHHHHHHHHHHHFGFHHHHHHEFEGF9?EHHHE@8BB12BEHHH @read_150_8/1 TAAAAACAAAAACCCTGATGAGAGTATTGATGTGTGCATAAACAAAGAAAAACATAATAGGAATAGAATGGTGAATTAAATTTTGTGAATTTTGGAAACC + HGGGGGHHHHHFHHGHHHHHHHEHHHHHHFHHEEHHHHHFE:/CGBHHHHHGFFGHHHHCEHEFECEFHHFEEE>E6,735@GG @read_150_3/2 GTCATTAACATTCACGAAGATAAATTTCTCCATTTTAAACAGAGACACTCAGTGAGCAGTAACCTGATTTTTTTTGGAATTTCATTCTTCAGGAGGGCTT + HHHHHHHHHHHHHHHHHH?GF5:@AFHHHGHFDDGGFFFHHFGHHHGGHHHHHHHHFGHFGEGC.18984>1BC=GFFAC<>E?..59&&-81:<<5.@ABCDBCE>:>@CDGHHHGEBFE/38@EEFBFGHHHHHHEGH?DHHHH>'9DEC**'*6 adapterremoval-2.3.1/tests/regression/misc/bad_args/file2_only/000077500000000000000000000000001350370616400246115ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/misc/bad_args/file2_only/info.json000066400000000000000000000002271350370616400264400ustar00rootroot00000000000000{ "arguments": [], "return_code": 1, "stderr": [ "Error: Different number of files specified for --file1 and --file2." ], "exhaustive": false } adapterremoval-2.3.1/tests/regression/misc/bad_args/file2_only/input_2.fastq000066400000000000000000000000001350370616400272170ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/misc/bad_args/ident_and_demux/000077500000000000000000000000001350370616400256765ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/misc/bad_args/ident_and_demux/info.json000066400000000000000000000003061350370616400275230ustar00rootroot00000000000000{ "arguments": ["--identify-adapters", "--demultiplex-only"], "return_code": 1, "stderr": [ "Cannot use --identify-adapters and --demultiplex-only at the same time!" ], "exhaustive": false } adapterremoval-2.3.1/tests/regression/misc/bad_args/ident_and_demux/input_1.fastq000066400000000000000000000003551350370616400303200ustar00rootroot00000000000000@AAGGGCSeq_1_5180_50/1 meta data ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG + IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! adapterremoval-2.3.1/tests/regression/misc/bad_args/ident_and_demux/input_2.fastq000066400000000000000000000003551350370616400303210ustar00rootroot00000000000000@AAGGGCSeq_1_5180_50/2 data meta AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGTAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCC + JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDEDBDBCBCCBBAA?ADAAA@@@>>>><=><<;<:<;87:78753420/,+)! adapterremoval-2.3.1/tests/regression/misc/bad_args/negative_window/000077500000000000000000000000001350370616400257405ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/misc/bad_args/negative_window/info.json000066400000000000000000000002171350370616400275660ustar00rootroot00000000000000{ "arguments": ["--trimwindows", "-1"], "return_code": 1, "stderr": [ "Error: Invalid value for --trimwindows" ], "exhaustive": false } adapterremoval-2.3.1/tests/regression/misc/bad_args/negative_window/input_1.fastq000066400000000000000000000007341350370616400303630ustar00rootroot00000000000000@ATAGCCSeq_1_2959_500_1 meta data TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTG + JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! @ATAGCCSeq_1_2959_500_2 data meta GTCAGCGAAGGGTTGTAGTAGCCCGTAGGGGCCTACAACGTTGGGGCCTTTGCGTAGTTGTATATAGCCTAGAATTTTTCGTTCGGTAAGCATTAGGAAT + JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! adapterremoval-2.3.1/tests/regression/misc/bad_args/se_interleaved/000077500000000000000000000000001350370616400255405ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/misc/bad_args/se_interleaved/info.json000066400000000000000000000002161350370616400273650ustar00rootroot00000000000000{ "arguments": ["--interleaved"], "return_code": 1, "stderr": [ "Pair contains reads with mismatching names:" ], "exhaustive": false } adapterremoval-2.3.1/tests/regression/misc/bad_args/se_interleaved/input_1.fastq000066400000000000000000000007341350370616400301630ustar00rootroot00000000000000@ATAGCCSeq_1_2959_500_1 meta data TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTG + JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! @ATAGCCSeq_1_2959_500_2 data meta GTCAGCGAAGGGTTGTAGTAGCCCGTAGGGGCCTACAACGTTGGGGCCTTTGCGTAGTTGTATATAGCCTAGAATTTTTCGTTCGGTAAGCATTAGGAAT + JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! adapterremoval-2.3.1/tests/regression/misc/bad_args/se_interleaved_input/000077500000000000000000000000001350370616400267575ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/misc/bad_args/se_interleaved_input/info.json000066400000000000000000000002241350370616400306030ustar00rootroot00000000000000{ "arguments": ["--interleaved-input"], "return_code": 1, "stderr": [ "Pair contains reads with mismatching names:" ], "exhaustive": false } adapterremoval-2.3.1/tests/regression/misc/bad_args/se_interleaved_input/input_1.fastq000066400000000000000000000007341350370616400314020ustar00rootroot00000000000000@ATAGCCSeq_1_2959_500_1 meta data TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTG + JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! @ATAGCCSeq_1_2959_500_2 data meta GTCAGCGAAGGGTTGTAGTAGCCCGTAGGGGCCTACAACGTTGGGGCCTTTGCGTAGTTGTATATAGCCTAGAATTTTTCGTTCGGTAAGCATTAGGAAT + JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! adapterremoval-2.3.1/tests/regression/misc/basename/000077500000000000000000000000001350370616400225605ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/misc/basename/alt/000077500000000000000000000000001350370616400233405ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/misc/basename/alt/pe/000077500000000000000000000000001350370616400237445ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/misc/basename/alt/pe/alternative.collapsed000066400000000000000000000000001350370616400301400ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/misc/basename/alt/pe/alternative.collapsed.truncated000066400000000000000000000002101350370616400321330ustar00rootroot00000000000000@MT_AAGGGCSeq_1_5180_50 meta data CATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGGAGGCCT + JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ&JJJJJJ adapterremoval-2.3.1/tests/regression/misc/basename/alt/pe/alternative.discarded000066400000000000000000000000001350370616400301140ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/misc/basename/alt/pe/alternative.pair1.truncated000066400000000000000000000000001350370616400311760ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/misc/basename/alt/pe/alternative.pair2.truncated000066400000000000000000000000001350370616400311770ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/misc/basename/alt/pe/alternative.settings000066400000000000000000000041621350370616400300470ustar00rootroot00000000000000AdapterRemoval ver. 2.1.7 Trimming of paired-end reads [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 505768950 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: Yes Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: Yes Minimum overlap (in case of collapse): 11 [Trimming statistics] Total number of read pairs: 1 Number of unaligned read pairs: 0 Number of well aligned read pairs: 1 Number of discarded mate 1 reads: 0 Number of singleton mate 1 reads: 0 Number of discarded mate 2 reads: 0 Number of singleton mate 2 reads: 0 Number of reads with adapters[1]: 2 Number of full-length collapsed pairs: 0 Number of truncated collapsed pairs: 1 Number of retained reads: 1 Number of retained nucleotides: 49 Average length of retained reads: 49 [Length distribution] Length Mate1 Mate2 Singleton Collapsed CollapsedTruncated Discarded All 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 3 0 0 0 0 0 0 0 4 0 0 0 0 0 0 0 5 0 0 0 0 0 0 0 6 0 0 0 0 0 0 0 7 0 0 0 0 0 0 0 8 0 0 0 0 0 0 0 9 0 0 0 0 0 0 0 10 0 0 0 0 0 0 0 11 0 0 0 0 0 0 0 12 0 0 0 0 0 0 0 13 0 0 0 0 0 0 0 14 0 0 0 0 0 0 0 15 0 0 0 0 0 0 0 16 0 0 0 0 0 0 0 17 0 0 0 0 0 0 0 18 0 0 0 0 0 0 0 19 0 0 0 0 0 0 0 20 0 0 0 0 0 0 0 21 0 0 0 0 0 0 0 22 0 0 0 0 0 0 0 23 0 0 0 0 0 0 0 24 0 0 0 0 0 0 0 25 0 0 0 0 0 0 0 26 0 0 0 0 0 0 0 27 0 0 0 0 0 0 0 28 0 0 0 0 0 0 0 29 0 0 0 0 0 0 0 30 0 0 0 0 0 0 0 31 0 0 0 0 0 0 0 32 0 0 0 0 0 0 0 33 0 0 0 0 0 0 0 34 0 0 0 0 0 0 0 35 0 0 0 0 0 0 0 36 0 0 0 0 0 0 0 37 0 0 0 0 0 0 0 38 0 0 0 0 0 0 0 39 0 0 0 0 0 0 0 40 0 0 0 0 0 0 0 41 0 0 0 0 0 0 0 42 0 0 0 0 0 0 0 43 0 0 0 0 0 0 0 44 0 0 0 0 0 0 0 45 0 0 0 0 0 0 0 46 0 0 0 0 0 0 0 47 0 0 0 0 0 0 0 48 0 0 0 0 0 0 0 49 0 0 0 0 1 0 1 adapterremoval-2.3.1/tests/regression/misc/basename/alt/pe/alternative.singleton.truncated000066400000000000000000000000001350370616400321640ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/misc/basename/alt/pe/info.json000066400000000000000000000001561350370616400255740ustar00rootroot00000000000000{ "arguments": ["--collapse", "--trimns", "--basename", "alternative"], "return_code": 0, "stderr": [ ] } adapterremoval-2.3.1/tests/regression/misc/basename/alt/pe/input_1.fastq000066400000000000000000000003551350370616400263660ustar00rootroot00000000000000@AAGGGCSeq_1_5180_50/1 meta data NCATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG + IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! adapterremoval-2.3.1/tests/regression/misc/basename/alt/pe/input_2.fastq000066400000000000000000000003551350370616400263670ustar00rootroot00000000000000@AAGGGCSeq_1_5180_50/2 data meta AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGNAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCC + JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDEDBDBCBCCBBAA?ADAAA@@@>>>><=><<;<:<;87:78753420/,+)! adapterremoval-2.3.1/tests/regression/misc/basename/alt/se/000077500000000000000000000000001350370616400237475ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/misc/basename/alt/se/alternative.collapsed000066400000000000000000000000001350370616400301430ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/misc/basename/alt/se/alternative.collapsed.truncated000066400000000000000000000002121350370616400321400ustar00rootroot00000000000000@MT_AAGGGCSeq_1_5180_50/1 meta data ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCC + IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDEC adapterremoval-2.3.1/tests/regression/misc/basename/alt/se/alternative.discarded000066400000000000000000000000001350370616400301170ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/misc/basename/alt/se/alternative.settings000066400000000000000000000035361350370616400300560ustar00rootroot00000000000000AdapterRemoval ver. 2.1.7 Trimming of single-end reads [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 566778642 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: Yes Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: Yes Minimum overlap (in case of collapse): 11 Minimum adapter overlap: 0 [Trimming statistics] Total number of reads: 1 Number of unaligned reads: 0 Number of well aligned reads: 1 Number of discarded mate 1 reads: 0 Number of singleton mate 1 reads: 0 Number of reads with adapters[1]: 1 Number of full-length collapsed pairs: 0 Number of truncated collapsed pairs: 1 Number of retained reads: 1 Number of retained nucleotides: 49 Average length of retained reads: 49 [Length distribution] Length Mate1 Collapsed CollapsedTruncated Discarded All 0 0 0 0 0 0 1 0 0 0 0 0 2 0 0 0 0 0 3 0 0 0 0 0 4 0 0 0 0 0 5 0 0 0 0 0 6 0 0 0 0 0 7 0 0 0 0 0 8 0 0 0 0 0 9 0 0 0 0 0 10 0 0 0 0 0 11 0 0 0 0 0 12 0 0 0 0 0 13 0 0 0 0 0 14 0 0 0 0 0 15 0 0 0 0 0 16 0 0 0 0 0 17 0 0 0 0 0 18 0 0 0 0 0 19 0 0 0 0 0 20 0 0 0 0 0 21 0 0 0 0 0 22 0 0 0 0 0 23 0 0 0 0 0 24 0 0 0 0 0 25 0 0 0 0 0 26 0 0 0 0 0 27 0 0 0 0 0 28 0 0 0 0 0 29 0 0 0 0 0 30 0 0 0 0 0 31 0 0 0 0 0 32 0 0 0 0 0 33 0 0 0 0 0 34 0 0 0 0 0 35 0 0 0 0 0 36 0 0 0 0 0 37 0 0 0 0 0 38 0 0 0 0 0 39 0 0 0 0 0 40 0 0 0 0 0 41 0 0 0 0 0 42 0 0 0 0 0 43 0 0 0 0 0 44 0 0 0 0 0 45 0 0 0 0 0 46 0 0 0 0 0 47 0 0 0 0 0 48 0 0 0 0 0 49 0 0 1 0 1 adapterremoval-2.3.1/tests/regression/misc/basename/alt/se/alternative.truncated000066400000000000000000000000001350370616400301660ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/misc/basename/alt/se/info.json000066400000000000000000000001561350370616400255770ustar00rootroot00000000000000{ "arguments": ["--collapse", "--trimns", "--basename", "alternative"], "return_code": 0, "stderr": [ ] } adapterremoval-2.3.1/tests/regression/misc/basename/alt/se/input_1.fastq000066400000000000000000000003551350370616400263710ustar00rootroot00000000000000@AAGGGCSeq_1_5180_50/1 meta data ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCNAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG + IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! adapterremoval-2.3.1/tests/regression/misc/basename/none/000077500000000000000000000000001350370616400235175ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/misc/basename/none/pe/000077500000000000000000000000001350370616400241235ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/misc/basename/none/pe/collapsed000066400000000000000000000000001350370616400260020ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/misc/basename/none/pe/collapsed.truncated000066400000000000000000000002101350370616400277750ustar00rootroot00000000000000@MT_AAGGGCSeq_1_5180_50 meta data CATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGGAGGCCT + JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ&JJJJJJ adapterremoval-2.3.1/tests/regression/misc/basename/none/pe/discarded000066400000000000000000000000001350370616400257560ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/misc/basename/none/pe/info.json000066400000000000000000000001431350370616400257470ustar00rootroot00000000000000{ "arguments": ["--collapse", "--trimns", "--basename", ""], "return_code": 0, "stderr": [ ] } adapterremoval-2.3.1/tests/regression/misc/basename/none/pe/input_1.fastq000066400000000000000000000003551350370616400265450ustar00rootroot00000000000000@AAGGGCSeq_1_5180_50/1 meta data NCATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG + IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! adapterremoval-2.3.1/tests/regression/misc/basename/none/pe/input_2.fastq000066400000000000000000000003551350370616400265460ustar00rootroot00000000000000@AAGGGCSeq_1_5180_50/2 data meta AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGNAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCC + JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDEDBDBCBCCBBAA?ADAAA@@@>>>><=><<;<:<;87:78753420/,+)! adapterremoval-2.3.1/tests/regression/misc/basename/none/pe/pair1.truncated000066400000000000000000000000001350370616400270400ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/misc/basename/none/pe/pair2.truncated000066400000000000000000000000001350370616400270410ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/misc/basename/none/pe/settings000066400000000000000000000041621350370616400257110ustar00rootroot00000000000000AdapterRemoval ver. 2.1.7 Trimming of paired-end reads [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 505768950 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: Yes Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: Yes Minimum overlap (in case of collapse): 11 [Trimming statistics] Total number of read pairs: 1 Number of unaligned read pairs: 0 Number of well aligned read pairs: 1 Number of discarded mate 1 reads: 0 Number of singleton mate 1 reads: 0 Number of discarded mate 2 reads: 0 Number of singleton mate 2 reads: 0 Number of reads with adapters[1]: 2 Number of full-length collapsed pairs: 0 Number of truncated collapsed pairs: 1 Number of retained reads: 1 Number of retained nucleotides: 49 Average length of retained reads: 49 [Length distribution] Length Mate1 Mate2 Singleton Collapsed CollapsedTruncated Discarded All 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 3 0 0 0 0 0 0 0 4 0 0 0 0 0 0 0 5 0 0 0 0 0 0 0 6 0 0 0 0 0 0 0 7 0 0 0 0 0 0 0 8 0 0 0 0 0 0 0 9 0 0 0 0 0 0 0 10 0 0 0 0 0 0 0 11 0 0 0 0 0 0 0 12 0 0 0 0 0 0 0 13 0 0 0 0 0 0 0 14 0 0 0 0 0 0 0 15 0 0 0 0 0 0 0 16 0 0 0 0 0 0 0 17 0 0 0 0 0 0 0 18 0 0 0 0 0 0 0 19 0 0 0 0 0 0 0 20 0 0 0 0 0 0 0 21 0 0 0 0 0 0 0 22 0 0 0 0 0 0 0 23 0 0 0 0 0 0 0 24 0 0 0 0 0 0 0 25 0 0 0 0 0 0 0 26 0 0 0 0 0 0 0 27 0 0 0 0 0 0 0 28 0 0 0 0 0 0 0 29 0 0 0 0 0 0 0 30 0 0 0 0 0 0 0 31 0 0 0 0 0 0 0 32 0 0 0 0 0 0 0 33 0 0 0 0 0 0 0 34 0 0 0 0 0 0 0 35 0 0 0 0 0 0 0 36 0 0 0 0 0 0 0 37 0 0 0 0 0 0 0 38 0 0 0 0 0 0 0 39 0 0 0 0 0 0 0 40 0 0 0 0 0 0 0 41 0 0 0 0 0 0 0 42 0 0 0 0 0 0 0 43 0 0 0 0 0 0 0 44 0 0 0 0 0 0 0 45 0 0 0 0 0 0 0 46 0 0 0 0 0 0 0 47 0 0 0 0 0 0 0 48 0 0 0 0 0 0 0 49 0 0 0 0 1 0 1 adapterremoval-2.3.1/tests/regression/misc/basename/none/pe/singleton.truncated000066400000000000000000000000001350370616400300260ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/misc/basename/none/se/000077500000000000000000000000001350370616400241265ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/misc/basename/none/se/collapsed000066400000000000000000000000001350370616400260050ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/misc/basename/none/se/collapsed.truncated000066400000000000000000000002121350370616400300020ustar00rootroot00000000000000@MT_AAGGGCSeq_1_5180_50/1 meta data ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCC + IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDEC adapterremoval-2.3.1/tests/regression/misc/basename/none/se/discarded000066400000000000000000000000001350370616400257610ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/misc/basename/none/se/info.json000066400000000000000000000001431350370616400257520ustar00rootroot00000000000000{ "arguments": ["--collapse", "--trimns", "--basename", ""], "return_code": 0, "stderr": [ ] } adapterremoval-2.3.1/tests/regression/misc/basename/none/se/input_1.fastq000066400000000000000000000003551350370616400265500ustar00rootroot00000000000000@AAGGGCSeq_1_5180_50/1 meta data ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCNAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG + IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! adapterremoval-2.3.1/tests/regression/misc/basename/none/se/settings000066400000000000000000000035361350370616400257200ustar00rootroot00000000000000AdapterRemoval ver. 2.1.7 Trimming of single-end reads [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 566778642 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: Yes Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: Yes Minimum overlap (in case of collapse): 11 Minimum adapter overlap: 0 [Trimming statistics] Total number of reads: 1 Number of unaligned reads: 0 Number of well aligned reads: 1 Number of discarded mate 1 reads: 0 Number of singleton mate 1 reads: 0 Number of reads with adapters[1]: 1 Number of full-length collapsed pairs: 0 Number of truncated collapsed pairs: 1 Number of retained reads: 1 Number of retained nucleotides: 49 Average length of retained reads: 49 [Length distribution] Length Mate1 Collapsed CollapsedTruncated Discarded All 0 0 0 0 0 0 1 0 0 0 0 0 2 0 0 0 0 0 3 0 0 0 0 0 4 0 0 0 0 0 5 0 0 0 0 0 6 0 0 0 0 0 7 0 0 0 0 0 8 0 0 0 0 0 9 0 0 0 0 0 10 0 0 0 0 0 11 0 0 0 0 0 12 0 0 0 0 0 13 0 0 0 0 0 14 0 0 0 0 0 15 0 0 0 0 0 16 0 0 0 0 0 17 0 0 0 0 0 18 0 0 0 0 0 19 0 0 0 0 0 20 0 0 0 0 0 21 0 0 0 0 0 22 0 0 0 0 0 23 0 0 0 0 0 24 0 0 0 0 0 25 0 0 0 0 0 26 0 0 0 0 0 27 0 0 0 0 0 28 0 0 0 0 0 29 0 0 0 0 0 30 0 0 0 0 0 31 0 0 0 0 0 32 0 0 0 0 0 33 0 0 0 0 0 34 0 0 0 0 0 35 0 0 0 0 0 36 0 0 0 0 0 37 0 0 0 0 0 38 0 0 0 0 0 39 0 0 0 0 0 40 0 0 0 0 0 41 0 0 0 0 0 42 0 0 0 0 0 43 0 0 0 0 0 44 0 0 0 0 0 45 0 0 0 0 0 46 0 0 0 0 0 47 0 0 0 0 0 48 0 0 0 0 0 49 0 0 1 0 1 adapterremoval-2.3.1/tests/regression/misc/basename/none/se/truncated000066400000000000000000000000001350370616400260300ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/misc/basename/path/000077500000000000000000000000001350370616400235145ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/misc/basename/path/pe/000077500000000000000000000000001350370616400241205ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/misc/basename/path/pe/collapsed000066400000000000000000000000001350370616400257770ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/misc/basename/path/pe/collapsed.truncated000066400000000000000000000002101350370616400277720ustar00rootroot00000000000000@MT_AAGGGCSeq_1_5180_50 meta data CATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGGAGGCCT + JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ&JJJJJJ adapterremoval-2.3.1/tests/regression/misc/basename/path/pe/discarded000066400000000000000000000000001350370616400257530ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/misc/basename/path/pe/info.json000066400000000000000000000001451350370616400257460ustar00rootroot00000000000000{ "arguments": ["--collapse", "--trimns", "--basename", "./"], "return_code": 0, "stderr": [ ] } adapterremoval-2.3.1/tests/regression/misc/basename/path/pe/input_1.fastq000066400000000000000000000003551350370616400265420ustar00rootroot00000000000000@AAGGGCSeq_1_5180_50/1 meta data NCATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG + IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! adapterremoval-2.3.1/tests/regression/misc/basename/path/pe/input_2.fastq000066400000000000000000000003551350370616400265430ustar00rootroot00000000000000@AAGGGCSeq_1_5180_50/2 data meta AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGNAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCC + JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDEDBDBCBCCBBAA?ADAAA@@@>>>><=><<;<:<;87:78753420/,+)! adapterremoval-2.3.1/tests/regression/misc/basename/path/pe/pair1.truncated000066400000000000000000000000001350370616400270350ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/misc/basename/path/pe/pair2.truncated000066400000000000000000000000001350370616400270360ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/misc/basename/path/pe/settings000066400000000000000000000041621350370616400257060ustar00rootroot00000000000000AdapterRemoval ver. 2.1.7 Trimming of paired-end reads [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 505768950 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: Yes Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: Yes Minimum overlap (in case of collapse): 11 [Trimming statistics] Total number of read pairs: 1 Number of unaligned read pairs: 0 Number of well aligned read pairs: 1 Number of discarded mate 1 reads: 0 Number of singleton mate 1 reads: 0 Number of discarded mate 2 reads: 0 Number of singleton mate 2 reads: 0 Number of reads with adapters[1]: 2 Number of full-length collapsed pairs: 0 Number of truncated collapsed pairs: 1 Number of retained reads: 1 Number of retained nucleotides: 49 Average length of retained reads: 49 [Length distribution] Length Mate1 Mate2 Singleton Collapsed CollapsedTruncated Discarded All 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 3 0 0 0 0 0 0 0 4 0 0 0 0 0 0 0 5 0 0 0 0 0 0 0 6 0 0 0 0 0 0 0 7 0 0 0 0 0 0 0 8 0 0 0 0 0 0 0 9 0 0 0 0 0 0 0 10 0 0 0 0 0 0 0 11 0 0 0 0 0 0 0 12 0 0 0 0 0 0 0 13 0 0 0 0 0 0 0 14 0 0 0 0 0 0 0 15 0 0 0 0 0 0 0 16 0 0 0 0 0 0 0 17 0 0 0 0 0 0 0 18 0 0 0 0 0 0 0 19 0 0 0 0 0 0 0 20 0 0 0 0 0 0 0 21 0 0 0 0 0 0 0 22 0 0 0 0 0 0 0 23 0 0 0 0 0 0 0 24 0 0 0 0 0 0 0 25 0 0 0 0 0 0 0 26 0 0 0 0 0 0 0 27 0 0 0 0 0 0 0 28 0 0 0 0 0 0 0 29 0 0 0 0 0 0 0 30 0 0 0 0 0 0 0 31 0 0 0 0 0 0 0 32 0 0 0 0 0 0 0 33 0 0 0 0 0 0 0 34 0 0 0 0 0 0 0 35 0 0 0 0 0 0 0 36 0 0 0 0 0 0 0 37 0 0 0 0 0 0 0 38 0 0 0 0 0 0 0 39 0 0 0 0 0 0 0 40 0 0 0 0 0 0 0 41 0 0 0 0 0 0 0 42 0 0 0 0 0 0 0 43 0 0 0 0 0 0 0 44 0 0 0 0 0 0 0 45 0 0 0 0 0 0 0 46 0 0 0 0 0 0 0 47 0 0 0 0 0 0 0 48 0 0 0 0 0 0 0 49 0 0 0 0 1 0 1 adapterremoval-2.3.1/tests/regression/misc/basename/path/pe/singleton.truncated000066400000000000000000000000001350370616400300230ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/misc/basename/path/se/000077500000000000000000000000001350370616400241235ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/misc/basename/path/se/collapsed000066400000000000000000000000001350370616400260020ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/misc/basename/path/se/collapsed.truncated000066400000000000000000000002121350370616400277770ustar00rootroot00000000000000@MT_AAGGGCSeq_1_5180_50/1 meta data ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCC + IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDEC adapterremoval-2.3.1/tests/regression/misc/basename/path/se/discarded000066400000000000000000000000001350370616400257560ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/misc/basename/path/se/info.json000066400000000000000000000001451350370616400257510ustar00rootroot00000000000000{ "arguments": ["--collapse", "--trimns", "--basename", "./"], "return_code": 0, "stderr": [ ] } adapterremoval-2.3.1/tests/regression/misc/basename/path/se/input_1.fastq000066400000000000000000000003551350370616400265450ustar00rootroot00000000000000@AAGGGCSeq_1_5180_50/1 meta data ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCNAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG + IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! adapterremoval-2.3.1/tests/regression/misc/basename/path/se/settings000066400000000000000000000035361350370616400257150ustar00rootroot00000000000000AdapterRemoval ver. 2.1.7 Trimming of single-end reads [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 566778642 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: Yes Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: Yes Minimum overlap (in case of collapse): 11 Minimum adapter overlap: 0 [Trimming statistics] Total number of reads: 1 Number of unaligned reads: 0 Number of well aligned reads: 1 Number of discarded mate 1 reads: 0 Number of singleton mate 1 reads: 0 Number of reads with adapters[1]: 1 Number of full-length collapsed pairs: 0 Number of truncated collapsed pairs: 1 Number of retained reads: 1 Number of retained nucleotides: 49 Average length of retained reads: 49 [Length distribution] Length Mate1 Collapsed CollapsedTruncated Discarded All 0 0 0 0 0 0 1 0 0 0 0 0 2 0 0 0 0 0 3 0 0 0 0 0 4 0 0 0 0 0 5 0 0 0 0 0 6 0 0 0 0 0 7 0 0 0 0 0 8 0 0 0 0 0 9 0 0 0 0 0 10 0 0 0 0 0 11 0 0 0 0 0 12 0 0 0 0 0 13 0 0 0 0 0 14 0 0 0 0 0 15 0 0 0 0 0 16 0 0 0 0 0 17 0 0 0 0 0 18 0 0 0 0 0 19 0 0 0 0 0 20 0 0 0 0 0 21 0 0 0 0 0 22 0 0 0 0 0 23 0 0 0 0 0 24 0 0 0 0 0 25 0 0 0 0 0 26 0 0 0 0 0 27 0 0 0 0 0 28 0 0 0 0 0 29 0 0 0 0 0 30 0 0 0 0 0 31 0 0 0 0 0 32 0 0 0 0 0 33 0 0 0 0 0 34 0 0 0 0 0 35 0 0 0 0 0 36 0 0 0 0 0 37 0 0 0 0 0 38 0 0 0 0 0 39 0 0 0 0 0 40 0 0 0 0 0 41 0 0 0 0 0 42 0 0 0 0 0 43 0 0 0 0 0 44 0 0 0 0 0 45 0 0 0 0 0 46 0 0 0 0 0 47 0 0 0 0 0 48 0 0 0 0 0 49 0 0 1 0 1 adapterremoval-2.3.1/tests/regression/misc/basename/path/se/truncated000066400000000000000000000000001350370616400260250ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/misc/empty/000077500000000000000000000000001350370616400221435ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/misc/empty/pe/000077500000000000000000000000001350370616400225475ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/misc/empty/pe/info.json000066400000000000000000000000711350370616400243730ustar00rootroot00000000000000{ "arguments": [], "return_code": 0, "stderr": [ ] } adapterremoval-2.3.1/tests/regression/misc/empty/pe/input_1.fastq000066400000000000000000000000001350370616400251540ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/misc/empty/pe/input_2.fastq000066400000000000000000000000001350370616400251550ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/misc/empty/pe/your_output.discarded000066400000000000000000000000001350370616400270170ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/misc/empty/pe/your_output.pair1.truncated000066400000000000000000000000001350370616400301010ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/misc/empty/pe/your_output.pair2.truncated000066400000000000000000000000001350370616400301020ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/misc/empty/pe/your_output.settings000066400000000000000000000022711350370616400267510ustar00rootroot00000000000000AdapterRemoval ver. 2.1.7 Trimming of paired-end reads [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 220897227 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 [Trimming statistics] Total number of read pairs: 0 Number of unaligned read pairs: 0 Number of well aligned read pairs: 0 Number of discarded mate 1 reads: 0 Number of singleton mate 1 reads: 0 Number of discarded mate 2 reads: 0 Number of singleton mate 2 reads: 0 Number of reads with adapters[1]: 0 Number of retained reads: 0 Number of retained nucleotides: 0 Average length of retained reads: 0 [Length distribution] Length Mate1 Mate2 Singleton Discarded All adapterremoval-2.3.1/tests/regression/misc/empty/pe/your_output.singleton.truncated000066400000000000000000000000001350370616400310670ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/misc/empty/se/000077500000000000000000000000001350370616400225525ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/misc/empty/se/info.json000066400000000000000000000000711350370616400243760ustar00rootroot00000000000000{ "arguments": [], "return_code": 0, "stderr": [ ] } adapterremoval-2.3.1/tests/regression/misc/empty/se/input_1.fastq000066400000000000000000000000001350370616400251570ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/misc/empty/se/your_output.discarded000066400000000000000000000000001350370616400270220ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/misc/empty/se/your_output.settings000066400000000000000000000021561350370616400267560ustar00rootroot00000000000000AdapterRemoval ver. 2.1.7 Trimming of single-end reads [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 2121675954 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 Minimum adapter overlap: 0 [Trimming statistics] Total number of reads: 0 Number of unaligned reads: 0 Number of well aligned reads: 0 Number of discarded mate 1 reads: 0 Number of singleton mate 1 reads: 0 Number of reads with adapters[1]: 0 Number of retained reads: 0 Number of retained nucleotides: 0 Average length of retained reads: 0 [Length distribution] Length Mate1 Discarded All adapterremoval-2.3.1/tests/regression/misc/empty/se/your_output.truncated000066400000000000000000000000001350370616400270710ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/misc/no_arguments/000077500000000000000000000000001350370616400235065ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/misc/no_arguments/info.json000066400000000000000000000001551350370616400253350ustar00rootroot00000000000000{ "arguments": [], "return_code": 1, "stderr": [ "This program searches for" ], "exhaustive": false } adapterremoval-2.3.1/tests/regression/misc/output/000077500000000000000000000000001350370616400223455ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/misc/output/pe/000077500000000000000000000000001350370616400227515ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/misc/output/pe/disc000066400000000000000000000000001350370616400236040ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/misc/output/pe/info.json000066400000000000000000000004401350370616400245750ustar00rootroot00000000000000{ "arguments": ["--collapse", "--trimns", "--discarded", "disc", "--output1", "out1", "--output2", "out2", "--outputcollapsed", "oc", "--outputcollapsedtruncated", "oct", "--settings", "out_settings", "--singleton", "singles"], "return_code": 0, "stderr": [ ], "exhaustive": false } adapterremoval-2.3.1/tests/regression/misc/output/pe/input_1.fastq000066400000000000000000000003551350370616400253730ustar00rootroot00000000000000@AAGGGCSeq_1_5180_50/1 meta data NCATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG + IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! adapterremoval-2.3.1/tests/regression/misc/output/pe/input_2.fastq000066400000000000000000000003551350370616400253740ustar00rootroot00000000000000@AAGGGCSeq_1_5180_50/2 data meta AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGNAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCC + JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDEDBDBCBCCBBAA?ADAAA@@@>>>><=><<;<:<;87:78753420/,+)! adapterremoval-2.3.1/tests/regression/misc/output/pe/oc000066400000000000000000000000001350370616400232630ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/misc/output/pe/oct000066400000000000000000000002101350370616400234520ustar00rootroot00000000000000@MT_AAGGGCSeq_1_5180_50 meta data CATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGGAGGCCT + JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ&JJJJJJ adapterremoval-2.3.1/tests/regression/misc/output/pe/out1000066400000000000000000000000001350370616400235520ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/misc/output/pe/out2000066400000000000000000000000001350370616400235530ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/misc/output/pe/out_settings000066400000000000000000000041621350370616400254260ustar00rootroot00000000000000AdapterRemoval ver. 2.1.7 Trimming of paired-end reads [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 505768950 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: Yes Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: Yes Minimum overlap (in case of collapse): 11 [Trimming statistics] Total number of read pairs: 1 Number of unaligned read pairs: 0 Number of well aligned read pairs: 1 Number of discarded mate 1 reads: 0 Number of singleton mate 1 reads: 0 Number of discarded mate 2 reads: 0 Number of singleton mate 2 reads: 0 Number of reads with adapters[1]: 2 Number of full-length collapsed pairs: 0 Number of truncated collapsed pairs: 1 Number of retained reads: 1 Number of retained nucleotides: 49 Average length of retained reads: 49 [Length distribution] Length Mate1 Mate2 Singleton Collapsed CollapsedTruncated Discarded All 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 3 0 0 0 0 0 0 0 4 0 0 0 0 0 0 0 5 0 0 0 0 0 0 0 6 0 0 0 0 0 0 0 7 0 0 0 0 0 0 0 8 0 0 0 0 0 0 0 9 0 0 0 0 0 0 0 10 0 0 0 0 0 0 0 11 0 0 0 0 0 0 0 12 0 0 0 0 0 0 0 13 0 0 0 0 0 0 0 14 0 0 0 0 0 0 0 15 0 0 0 0 0 0 0 16 0 0 0 0 0 0 0 17 0 0 0 0 0 0 0 18 0 0 0 0 0 0 0 19 0 0 0 0 0 0 0 20 0 0 0 0 0 0 0 21 0 0 0 0 0 0 0 22 0 0 0 0 0 0 0 23 0 0 0 0 0 0 0 24 0 0 0 0 0 0 0 25 0 0 0 0 0 0 0 26 0 0 0 0 0 0 0 27 0 0 0 0 0 0 0 28 0 0 0 0 0 0 0 29 0 0 0 0 0 0 0 30 0 0 0 0 0 0 0 31 0 0 0 0 0 0 0 32 0 0 0 0 0 0 0 33 0 0 0 0 0 0 0 34 0 0 0 0 0 0 0 35 0 0 0 0 0 0 0 36 0 0 0 0 0 0 0 37 0 0 0 0 0 0 0 38 0 0 0 0 0 0 0 39 0 0 0 0 0 0 0 40 0 0 0 0 0 0 0 41 0 0 0 0 0 0 0 42 0 0 0 0 0 0 0 43 0 0 0 0 0 0 0 44 0 0 0 0 0 0 0 45 0 0 0 0 0 0 0 46 0 0 0 0 0 0 0 47 0 0 0 0 0 0 0 48 0 0 0 0 0 0 0 49 0 0 0 0 1 0 1 adapterremoval-2.3.1/tests/regression/misc/output/pe/singles000066400000000000000000000000001350370616400243260ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/misc/output/se/000077500000000000000000000000001350370616400227545ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/misc/output/se/disc000066400000000000000000000000001350370616400236070ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/misc/output/se/info.json000066400000000000000000000004131350370616400246000ustar00rootroot00000000000000{ "arguments": ["--collapse", "--trimns", "--discarded", "disc", "--output1", "out1", "--outputcollapsed", "oc", "--outputcollapsedtruncated", "oct", "--settings", "out_settings", "--singleton", "singles"], "return_code": 0, "stderr": [ ], "exhaustive": false } adapterremoval-2.3.1/tests/regression/misc/output/se/input_1.fastq000066400000000000000000000003551350370616400253760ustar00rootroot00000000000000@AAGGGCSeq_1_5180_50/1 meta data ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCNAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG + IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! adapterremoval-2.3.1/tests/regression/misc/output/se/oc000066400000000000000000000000001350370616400232660ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/misc/output/se/oct000066400000000000000000000002121350370616400234570ustar00rootroot00000000000000@MT_AAGGGCSeq_1_5180_50/1 meta data ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCC + IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDEC adapterremoval-2.3.1/tests/regression/misc/output/se/out1000066400000000000000000000000001350370616400235550ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/misc/output/se/out_settings000066400000000000000000000035361350370616400254350ustar00rootroot00000000000000AdapterRemoval ver. 2.1.7 Trimming of single-end reads [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 566778642 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: Yes Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: Yes Minimum overlap (in case of collapse): 11 Minimum adapter overlap: 0 [Trimming statistics] Total number of reads: 1 Number of unaligned reads: 0 Number of well aligned reads: 1 Number of discarded mate 1 reads: 0 Number of singleton mate 1 reads: 0 Number of reads with adapters[1]: 1 Number of full-length collapsed pairs: 0 Number of truncated collapsed pairs: 1 Number of retained reads: 1 Number of retained nucleotides: 49 Average length of retained reads: 49 [Length distribution] Length Mate1 Collapsed CollapsedTruncated Discarded All 0 0 0 0 0 0 1 0 0 0 0 0 2 0 0 0 0 0 3 0 0 0 0 0 4 0 0 0 0 0 5 0 0 0 0 0 6 0 0 0 0 0 7 0 0 0 0 0 8 0 0 0 0 0 9 0 0 0 0 0 10 0 0 0 0 0 11 0 0 0 0 0 12 0 0 0 0 0 13 0 0 0 0 0 14 0 0 0 0 0 15 0 0 0 0 0 16 0 0 0 0 0 17 0 0 0 0 0 18 0 0 0 0 0 19 0 0 0 0 0 20 0 0 0 0 0 21 0 0 0 0 0 22 0 0 0 0 0 23 0 0 0 0 0 24 0 0 0 0 0 25 0 0 0 0 0 26 0 0 0 0 0 27 0 0 0 0 0 28 0 0 0 0 0 29 0 0 0 0 0 30 0 0 0 0 0 31 0 0 0 0 0 32 0 0 0 0 0 33 0 0 0 0 0 34 0 0 0 0 0 35 0 0 0 0 0 36 0 0 0 0 0 37 0 0 0 0 0 38 0 0 0 0 0 39 0 0 0 0 0 40 0 0 0 0 0 41 0 0 0 0 0 42 0 0 0 0 0 43 0 0 0 0 0 44 0 0 0 0 0 45 0 0 0 0 0 46 0 0 0 0 0 47 0 0 0 0 0 48 0 0 0 0 0 49 0 0 1 0 1 adapterremoval-2.3.1/tests/regression/misc/trim5p_and_trim3p/000077500000000000000000000000001350370616400243455ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/misc/trim5p_and_trim3p/pe/000077500000000000000000000000001350370616400247515ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/misc/trim5p_and_trim3p/pe/trim3p/000077500000000000000000000000001350370616400261675ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/misc/trim5p_and_trim3p/pe/trim3p/info.json000066400000000000000000000001101350370616400300050ustar00rootroot00000000000000{ "arguments": ["--trim3p", "4"], "return_code": 0, "stderr": [ ] } adapterremoval-2.3.1/tests/regression/misc/trim5p_and_trim3p/pe/trim3p/input_1.fastq000066400000000000000000000003341350370616400306060ustar00rootroot00000000000000@read_150_158/1 ATGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCACCTAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAATAAAAAA + HHHHHHHHFGHHGGFHHDFF;CEEEEGC=@?19@A@5BBGBGEBDHHHHHHHHHHGGDDCDEHFHHFHHFFFGHHHHHHBG51?HDEEHHHBFHHHHFDEBEBGFH adapterremoval-2.3.1/tests/regression/misc/trim5p_and_trim3p/pe/trim3p/your_output.discarded000066400000000000000000000000501350370616400324440ustar00rootroot00000000000000@read_150_158/1 + @read_150_158/2 + adapterremoval-2.3.1/tests/regression/misc/trim5p_and_trim3p/pe/trim3p/your_output.pair1.truncated000066400000000000000000000000001350370616400335210ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/misc/trim5p_and_trim3p/pe/trim3p/your_output.pair2.truncated000066400000000000000000000000001350370616400335220ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/misc/trim5p_and_trim3p/pe/trim3p/your_output.settings000066400000000000000000000023061350370616400323700ustar00rootroot00000000000000AdapterRemoval ver. 2.2.3 Trimming of paired-end reads [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 1695835713 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 4 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 [Trimming statistics] Total number of read pairs: 1 Number of unaligned read pairs: 0 Number of well aligned read pairs: 1 Number of discarded mate 1 reads: 1 Number of singleton mate 1 reads: 0 Number of discarded mate 2 reads: 1 Number of singleton mate 2 reads: 0 Number of reads with adapters[1]: 2 Number of retained reads: 0 Number of retained nucleotides: 0 Average length of retained reads: 0 [Length distribution] Length Mate1 Mate2 Singleton Discarded All 0 0 0 0 2 2 your_output.singleton.truncated000066400000000000000000000000001350370616400344300ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/misc/trim5p_and_trim3p/pe/trim3padapterremoval-2.3.1/tests/regression/misc/trim5p_and_trim3p/pe/trim5p/000077500000000000000000000000001350370616400261715ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/misc/trim5p_and_trim3p/pe/trim5p/info.json000066400000000000000000000001101350370616400300070ustar00rootroot00000000000000{ "arguments": ["--trim5p", "4"], "return_code": 0, "stderr": [ ] } adapterremoval-2.3.1/tests/regression/misc/trim5p_and_trim3p/pe/trim5p/input_1.fastq000066400000000000000000000003341350370616400306100ustar00rootroot00000000000000@read_150_158/1 ATGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCACCTAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAATAAAAAA + HHHHHHHHFGHHGGFHHDFF;CEEEEGC=@?19@A@5BBGBGEBDHHHHHHHHHHGGDDCDEHFHHFHHFFFGHHHHHHBG51?HDEEHHHBFHHHHFDEBEBGFH adapterremoval-2.3.1/tests/regression/misc/trim5p_and_trim3p/pe/trim5p/your_output.discarded000066400000000000000000000000501350370616400324460ustar00rootroot00000000000000@read_150_158/1 + @read_150_158/2 + adapterremoval-2.3.1/tests/regression/misc/trim5p_and_trim3p/pe/trim5p/your_output.pair1.truncated000066400000000000000000000000001350370616400335230ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/misc/trim5p_and_trim3p/pe/trim5p/your_output.pair2.truncated000066400000000000000000000000001350370616400335240ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/misc/trim5p_and_trim3p/pe/trim5p/your_output.settings000066400000000000000000000023051350370616400323710ustar00rootroot00000000000000AdapterRemoval ver. 2.2.3 Trimming of paired-end reads [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 776875006 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 4 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 [Trimming statistics] Total number of read pairs: 1 Number of unaligned read pairs: 0 Number of well aligned read pairs: 1 Number of discarded mate 1 reads: 1 Number of singleton mate 1 reads: 0 Number of discarded mate 2 reads: 1 Number of singleton mate 2 reads: 0 Number of reads with adapters[1]: 2 Number of retained reads: 0 Number of retained nucleotides: 0 Average length of retained reads: 0 [Length distribution] Length Mate1 Mate2 Singleton Discarded All 0 0 0 0 2 2 your_output.singleton.truncated000066400000000000000000000000001350370616400344320ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/misc/trim5p_and_trim3p/pe/trim5padapterremoval-2.3.1/tests/regression/misc/trim5p_and_trim3p/pe/trim5p_and_trim3p/000077500000000000000000000000001350370616400303115ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/misc/trim5p_and_trim3p/pe/trim5p_and_trim3p/info.json000066400000000000000000000001311350370616400321320ustar00rootroot00000000000000{ "arguments": ["--trim5p", "4", "--trim3p", "4"], "return_code": 0, "stderr": [ ] } adapterremoval-2.3.1/tests/regression/misc/trim5p_and_trim3p/pe/trim5p_and_trim3p/input_1.fastq000066400000000000000000000003341350370616400327300ustar00rootroot00000000000000@read_150_158/1 ATGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCACCTAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAATAAAAAA + HHHHHHHHFGHHGGFHHDFF;CEEEEGC=@?19@A@5BBGBGEBDHHHHHHHHHHGGDDCDEHFHHFHHFFFGHHHHHHBG51?HDEEHHHBFHHHHFDEBEBGFH your_output.discarded000066400000000000000000000000501350370616400345070ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/misc/trim5p_and_trim3p/pe/trim5p_and_trim3p@read_150_158/1 + @read_150_158/2 + your_output.pair1.truncated000066400000000000000000000000001350370616400355640ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/misc/trim5p_and_trim3p/pe/trim5p_and_trim3pyour_output.pair2.truncated000066400000000000000000000000001350370616400355650ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/misc/trim5p_and_trim3p/pe/trim5p_and_trim3pyour_output.settings000066400000000000000000000023051350370616400344320ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/misc/trim5p_and_trim3p/pe/trim5p_and_trim3pAdapterRemoval ver. 2.2.3 Trimming of paired-end reads [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 796246708 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 4 Trimming 3p: 4 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 [Trimming statistics] Total number of read pairs: 1 Number of unaligned read pairs: 0 Number of well aligned read pairs: 1 Number of discarded mate 1 reads: 1 Number of singleton mate 1 reads: 0 Number of discarded mate 2 reads: 1 Number of singleton mate 2 reads: 0 Number of reads with adapters[1]: 2 Number of retained reads: 0 Number of retained nucleotides: 0 Average length of retained reads: 0 [Length distribution] Length Mate1 Mate2 Singleton Discarded All 0 0 0 0 2 2 your_output.singleton.truncated000066400000000000000000000000001350370616400365520ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/misc/trim5p_and_trim3p/pe/trim5p_and_trim3padapterremoval-2.3.1/tests/regression/misc/trim5p_and_trim3p/se/000077500000000000000000000000001350370616400247545ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/misc/trim5p_and_trim3p/se/trim3p/000077500000000000000000000000001350370616400261725ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/misc/trim5p_and_trim3p/se/trim3p/info.json000066400000000000000000000001101350370616400300100ustar00rootroot00000000000000{ "arguments": ["--trim3p", "4"], "return_code": 0, "stderr": [ ] } adapterremoval-2.3.1/tests/regression/misc/trim5p_and_trim3p/se/trim3p/input_1.fastq000066400000000000000000000003341350370616400306110ustar00rootroot00000000000000@read_150_158/1 ATGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCACCTAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAATAAAAAA + HHHHHHHHFGHHGGFHHDFF;CEEEEGC=@?19@A@>@==<=<;;;;<:9777755321/,)'! adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/collapse/input_2.fastq000066400000000000000000000003561350370616400325370ustar00rootroot00000000000000@ATAGCCSeq_1_2959_500/2 data meta GTCAGCGAAGGGTTGTAGTAGCCCGTAGGGGCCTACAACGTTGGGGCCTTTGCGTAGTTGTATATAGCCTAGAATTTTTCGTTCGGTAAGCATTAGGAAT + JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/collapse/your_output.collapsed000066400000000000000000000000001350370616400344070ustar00rootroot00000000000000your_output.collapsed.truncated000066400000000000000000000000001350370616400363200ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/collapseadapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/collapse/your_output.discarded000066400000000000000000000000001350370616400343630ustar00rootroot00000000000000your_output.pair1.truncated000066400000000000000000000003561350370616400354040ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/collapse@ATAGCCSeq_1_2959_500/1 meta data TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTG + JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! your_output.pair2.truncated000066400000000000000000000003561350370616400354050ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/collapse@ATAGCCSeq_1_2959_500/2 data meta GTCAGCGAAGGGTTGTAGTAGCCCGTAGGGGCCTACAACGTTGGGGCCTTTGCGTAGTTGTATATAGCCTAGAATTTTTCGTTCGGTAAGCATTAGGAAT + JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/collapse/your_output.settings000066400000000000000000000057301350370616400343200ustar00rootroot00000000000000AdapterRemoval ver. 2.1.7 Trimming of paired-end reads [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 1203911406 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: Yes Minimum overlap (in case of collapse): 11 [Trimming statistics] Total number of read pairs: 1 Number of unaligned read pairs: 1 Number of well aligned read pairs: 0 Number of discarded mate 1 reads: 0 Number of singleton mate 1 reads: 0 Number of discarded mate 2 reads: 0 Number of singleton mate 2 reads: 0 Number of reads with adapters[1]: 0 Number of full-length collapsed pairs: 0 Number of truncated collapsed pairs: 0 Number of retained reads: 2 Number of retained nucleotides: 200 Average length of retained reads: 100 [Length distribution] Length Mate1 Mate2 Singleton Collapsed CollapsedTruncated Discarded All 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 3 0 0 0 0 0 0 0 4 0 0 0 0 0 0 0 5 0 0 0 0 0 0 0 6 0 0 0 0 0 0 0 7 0 0 0 0 0 0 0 8 0 0 0 0 0 0 0 9 0 0 0 0 0 0 0 10 0 0 0 0 0 0 0 11 0 0 0 0 0 0 0 12 0 0 0 0 0 0 0 13 0 0 0 0 0 0 0 14 0 0 0 0 0 0 0 15 0 0 0 0 0 0 0 16 0 0 0 0 0 0 0 17 0 0 0 0 0 0 0 18 0 0 0 0 0 0 0 19 0 0 0 0 0 0 0 20 0 0 0 0 0 0 0 21 0 0 0 0 0 0 0 22 0 0 0 0 0 0 0 23 0 0 0 0 0 0 0 24 0 0 0 0 0 0 0 25 0 0 0 0 0 0 0 26 0 0 0 0 0 0 0 27 0 0 0 0 0 0 0 28 0 0 0 0 0 0 0 29 0 0 0 0 0 0 0 30 0 0 0 0 0 0 0 31 0 0 0 0 0 0 0 32 0 0 0 0 0 0 0 33 0 0 0 0 0 0 0 34 0 0 0 0 0 0 0 35 0 0 0 0 0 0 0 36 0 0 0 0 0 0 0 37 0 0 0 0 0 0 0 38 0 0 0 0 0 0 0 39 0 0 0 0 0 0 0 40 0 0 0 0 0 0 0 41 0 0 0 0 0 0 0 42 0 0 0 0 0 0 0 43 0 0 0 0 0 0 0 44 0 0 0 0 0 0 0 45 0 0 0 0 0 0 0 46 0 0 0 0 0 0 0 47 0 0 0 0 0 0 0 48 0 0 0 0 0 0 0 49 0 0 0 0 0 0 0 50 0 0 0 0 0 0 0 51 0 0 0 0 0 0 0 52 0 0 0 0 0 0 0 53 0 0 0 0 0 0 0 54 0 0 0 0 0 0 0 55 0 0 0 0 0 0 0 56 0 0 0 0 0 0 0 57 0 0 0 0 0 0 0 58 0 0 0 0 0 0 0 59 0 0 0 0 0 0 0 60 0 0 0 0 0 0 0 61 0 0 0 0 0 0 0 62 0 0 0 0 0 0 0 63 0 0 0 0 0 0 0 64 0 0 0 0 0 0 0 65 0 0 0 0 0 0 0 66 0 0 0 0 0 0 0 67 0 0 0 0 0 0 0 68 0 0 0 0 0 0 0 69 0 0 0 0 0 0 0 70 0 0 0 0 0 0 0 71 0 0 0 0 0 0 0 72 0 0 0 0 0 0 0 73 0 0 0 0 0 0 0 74 0 0 0 0 0 0 0 75 0 0 0 0 0 0 0 76 0 0 0 0 0 0 0 77 0 0 0 0 0 0 0 78 0 0 0 0 0 0 0 79 0 0 0 0 0 0 0 80 0 0 0 0 0 0 0 81 0 0 0 0 0 0 0 82 0 0 0 0 0 0 0 83 0 0 0 0 0 0 0 84 0 0 0 0 0 0 0 85 0 0 0 0 0 0 0 86 0 0 0 0 0 0 0 87 0 0 0 0 0 0 0 88 0 0 0 0 0 0 0 89 0 0 0 0 0 0 0 90 0 0 0 0 0 0 0 91 0 0 0 0 0 0 0 92 0 0 0 0 0 0 0 93 0 0 0 0 0 0 0 94 0 0 0 0 0 0 0 95 0 0 0 0 0 0 0 96 0 0 0 0 0 0 0 97 0 0 0 0 0 0 0 98 0 0 0 0 0 0 0 99 0 0 0 0 0 0 0 100 1 1 0 0 0 0 2 your_output.singleton.truncated000066400000000000000000000000001350370616400363540ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/collapseadapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/combined_output/000077500000000000000000000000001350370616400315115ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/combined_output/collapse/000077500000000000000000000000001350370616400333135ustar00rootroot00000000000000info.json000066400000000000000000000001321350370616400350560ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/combined_output/collapse{ "arguments": ["--combined-output", "--collapse"], "return_code": 0, "stderr": [ ] } input_1.fastq000066400000000000000000000003561350370616400356570ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/combined_output/collapse@ATAGCCSeq_1_2959_500/1 meta data TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTG + JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! input_2.fastq000066400000000000000000000003561350370616400356600ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/combined_output/collapse@ATAGCCSeq_1_2959_500/2 data meta GTCAGCGAAGGGTTGTAGTAGCCCGTAGGGGCCTACAACGTTGGGGCCTTTGCGTAGTTGTATATAGCCTAGAATTTTTCGTTCGGTAAGCATTAGGAAT + JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! your_output.pair1.truncated000066400000000000000000000003561350370616400406040ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/combined_output/collapse@ATAGCCSeq_1_2959_500/1 meta data TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTG + JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! your_output.pair2.truncated000066400000000000000000000003561350370616400406050ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/combined_output/collapse@ATAGCCSeq_1_2959_500/2 data meta GTCAGCGAAGGGTTGTAGTAGCCCGTAGGGGCCTACAACGTTGGGGCCTTTGCGTAGTTGTATATAGCCTAGAATTTTTCGTTCGGTAAGCATTAGGAAT + JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! your_output.settings000066400000000000000000000057301350370616400374410ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/combined_output/collapseAdapterRemoval ver. 2.1.7 Trimming of paired-end reads [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 2579970730 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: Yes Minimum overlap (in case of collapse): 11 [Trimming statistics] Total number of read pairs: 1 Number of unaligned read pairs: 1 Number of well aligned read pairs: 0 Number of discarded mate 1 reads: 0 Number of singleton mate 1 reads: 0 Number of discarded mate 2 reads: 0 Number of singleton mate 2 reads: 0 Number of reads with adapters[1]: 0 Number of full-length collapsed pairs: 0 Number of truncated collapsed pairs: 0 Number of retained reads: 2 Number of retained nucleotides: 200 Average length of retained reads: 100 [Length distribution] Length Mate1 Mate2 Singleton Collapsed CollapsedTruncated Discarded All 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 3 0 0 0 0 0 0 0 4 0 0 0 0 0 0 0 5 0 0 0 0 0 0 0 6 0 0 0 0 0 0 0 7 0 0 0 0 0 0 0 8 0 0 0 0 0 0 0 9 0 0 0 0 0 0 0 10 0 0 0 0 0 0 0 11 0 0 0 0 0 0 0 12 0 0 0 0 0 0 0 13 0 0 0 0 0 0 0 14 0 0 0 0 0 0 0 15 0 0 0 0 0 0 0 16 0 0 0 0 0 0 0 17 0 0 0 0 0 0 0 18 0 0 0 0 0 0 0 19 0 0 0 0 0 0 0 20 0 0 0 0 0 0 0 21 0 0 0 0 0 0 0 22 0 0 0 0 0 0 0 23 0 0 0 0 0 0 0 24 0 0 0 0 0 0 0 25 0 0 0 0 0 0 0 26 0 0 0 0 0 0 0 27 0 0 0 0 0 0 0 28 0 0 0 0 0 0 0 29 0 0 0 0 0 0 0 30 0 0 0 0 0 0 0 31 0 0 0 0 0 0 0 32 0 0 0 0 0 0 0 33 0 0 0 0 0 0 0 34 0 0 0 0 0 0 0 35 0 0 0 0 0 0 0 36 0 0 0 0 0 0 0 37 0 0 0 0 0 0 0 38 0 0 0 0 0 0 0 39 0 0 0 0 0 0 0 40 0 0 0 0 0 0 0 41 0 0 0 0 0 0 0 42 0 0 0 0 0 0 0 43 0 0 0 0 0 0 0 44 0 0 0 0 0 0 0 45 0 0 0 0 0 0 0 46 0 0 0 0 0 0 0 47 0 0 0 0 0 0 0 48 0 0 0 0 0 0 0 49 0 0 0 0 0 0 0 50 0 0 0 0 0 0 0 51 0 0 0 0 0 0 0 52 0 0 0 0 0 0 0 53 0 0 0 0 0 0 0 54 0 0 0 0 0 0 0 55 0 0 0 0 0 0 0 56 0 0 0 0 0 0 0 57 0 0 0 0 0 0 0 58 0 0 0 0 0 0 0 59 0 0 0 0 0 0 0 60 0 0 0 0 0 0 0 61 0 0 0 0 0 0 0 62 0 0 0 0 0 0 0 63 0 0 0 0 0 0 0 64 0 0 0 0 0 0 0 65 0 0 0 0 0 0 0 66 0 0 0 0 0 0 0 67 0 0 0 0 0 0 0 68 0 0 0 0 0 0 0 69 0 0 0 0 0 0 0 70 0 0 0 0 0 0 0 71 0 0 0 0 0 0 0 72 0 0 0 0 0 0 0 73 0 0 0 0 0 0 0 74 0 0 0 0 0 0 0 75 0 0 0 0 0 0 0 76 0 0 0 0 0 0 0 77 0 0 0 0 0 0 0 78 0 0 0 0 0 0 0 79 0 0 0 0 0 0 0 80 0 0 0 0 0 0 0 81 0 0 0 0 0 0 0 82 0 0 0 0 0 0 0 83 0 0 0 0 0 0 0 84 0 0 0 0 0 0 0 85 0 0 0 0 0 0 0 86 0 0 0 0 0 0 0 87 0 0 0 0 0 0 0 88 0 0 0 0 0 0 0 89 0 0 0 0 0 0 0 90 0 0 0 0 0 0 0 91 0 0 0 0 0 0 0 92 0 0 0 0 0 0 0 93 0 0 0 0 0 0 0 94 0 0 0 0 0 0 0 95 0 0 0 0 0 0 0 96 0 0 0 0 0 0 0 97 0 0 0 0 0 0 0 98 0 0 0 0 0 0 0 99 0 0 0 0 0 0 0 100 1 1 0 0 0 0 2 adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/combined_output/interleaved/000077500000000000000000000000001350370616400340135ustar00rootroot00000000000000collapse/000077500000000000000000000000001350370616400355365ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/combined_output/interleavedinfo.json000066400000000000000000000001621350370616400373630ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/combined_output/interleaved/collapse{ "arguments": ["--combined-output", "--collapse", "--interleaved-output"], "return_code": 0, "stderr": [ ] } input_1.fastq000066400000000000000000000003561350370616400401610ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/combined_output/interleaved/collapse@ATAGCCSeq_1_2959_500/1 meta data TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTG + JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! input_2.fastq000066400000000000000000000003561350370616400401620ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/combined_output/interleaved/collapse@ATAGCCSeq_1_2959_500/2 data meta GTCAGCGAAGGGTTGTAGTAGCCCGTAGGGGCCTACAACGTTGGGGCCTTTGCGTAGTTGTATATAGCCTAGAATTTTTCGTTCGGTAAGCATTAGGAAT + JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! your_output.paired.truncated000066400000000000000000000007341350370616400433360ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/combined_output/interleaved/collapse@ATAGCCSeq_1_2959_500/1 meta data TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTG + JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! @ATAGCCSeq_1_2959_500/2 data meta GTCAGCGAAGGGTTGTAGTAGCCCGTAGGGGCCTACAACGTTGGGGCCTTTGCGTAGTTGTATATAGCCTAGAATTTTTCGTTCGGTAAGCATTAGGAAT + JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! your_output.settings000066400000000000000000000057301350370616400417430ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/combined_output/interleaved/collapseAdapterRemoval ver. 2.1.7 Trimming of paired-end reads [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 2579970730 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: Yes Minimum overlap (in case of collapse): 11 [Trimming statistics] Total number of read pairs: 1 Number of unaligned read pairs: 1 Number of well aligned read pairs: 0 Number of discarded mate 1 reads: 0 Number of singleton mate 1 reads: 0 Number of discarded mate 2 reads: 0 Number of singleton mate 2 reads: 0 Number of reads with adapters[1]: 0 Number of full-length collapsed pairs: 0 Number of truncated collapsed pairs: 0 Number of retained reads: 2 Number of retained nucleotides: 200 Average length of retained reads: 100 [Length distribution] Length Mate1 Mate2 Singleton Collapsed CollapsedTruncated Discarded All 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 3 0 0 0 0 0 0 0 4 0 0 0 0 0 0 0 5 0 0 0 0 0 0 0 6 0 0 0 0 0 0 0 7 0 0 0 0 0 0 0 8 0 0 0 0 0 0 0 9 0 0 0 0 0 0 0 10 0 0 0 0 0 0 0 11 0 0 0 0 0 0 0 12 0 0 0 0 0 0 0 13 0 0 0 0 0 0 0 14 0 0 0 0 0 0 0 15 0 0 0 0 0 0 0 16 0 0 0 0 0 0 0 17 0 0 0 0 0 0 0 18 0 0 0 0 0 0 0 19 0 0 0 0 0 0 0 20 0 0 0 0 0 0 0 21 0 0 0 0 0 0 0 22 0 0 0 0 0 0 0 23 0 0 0 0 0 0 0 24 0 0 0 0 0 0 0 25 0 0 0 0 0 0 0 26 0 0 0 0 0 0 0 27 0 0 0 0 0 0 0 28 0 0 0 0 0 0 0 29 0 0 0 0 0 0 0 30 0 0 0 0 0 0 0 31 0 0 0 0 0 0 0 32 0 0 0 0 0 0 0 33 0 0 0 0 0 0 0 34 0 0 0 0 0 0 0 35 0 0 0 0 0 0 0 36 0 0 0 0 0 0 0 37 0 0 0 0 0 0 0 38 0 0 0 0 0 0 0 39 0 0 0 0 0 0 0 40 0 0 0 0 0 0 0 41 0 0 0 0 0 0 0 42 0 0 0 0 0 0 0 43 0 0 0 0 0 0 0 44 0 0 0 0 0 0 0 45 0 0 0 0 0 0 0 46 0 0 0 0 0 0 0 47 0 0 0 0 0 0 0 48 0 0 0 0 0 0 0 49 0 0 0 0 0 0 0 50 0 0 0 0 0 0 0 51 0 0 0 0 0 0 0 52 0 0 0 0 0 0 0 53 0 0 0 0 0 0 0 54 0 0 0 0 0 0 0 55 0 0 0 0 0 0 0 56 0 0 0 0 0 0 0 57 0 0 0 0 0 0 0 58 0 0 0 0 0 0 0 59 0 0 0 0 0 0 0 60 0 0 0 0 0 0 0 61 0 0 0 0 0 0 0 62 0 0 0 0 0 0 0 63 0 0 0 0 0 0 0 64 0 0 0 0 0 0 0 65 0 0 0 0 0 0 0 66 0 0 0 0 0 0 0 67 0 0 0 0 0 0 0 68 0 0 0 0 0 0 0 69 0 0 0 0 0 0 0 70 0 0 0 0 0 0 0 71 0 0 0 0 0 0 0 72 0 0 0 0 0 0 0 73 0 0 0 0 0 0 0 74 0 0 0 0 0 0 0 75 0 0 0 0 0 0 0 76 0 0 0 0 0 0 0 77 0 0 0 0 0 0 0 78 0 0 0 0 0 0 0 79 0 0 0 0 0 0 0 80 0 0 0 0 0 0 0 81 0 0 0 0 0 0 0 82 0 0 0 0 0 0 0 83 0 0 0 0 0 0 0 84 0 0 0 0 0 0 0 85 0 0 0 0 0 0 0 86 0 0 0 0 0 0 0 87 0 0 0 0 0 0 0 88 0 0 0 0 0 0 0 89 0 0 0 0 0 0 0 90 0 0 0 0 0 0 0 91 0 0 0 0 0 0 0 92 0 0 0 0 0 0 0 93 0 0 0 0 0 0 0 94 0 0 0 0 0 0 0 95 0 0 0 0 0 0 0 96 0 0 0 0 0 0 0 97 0 0 0 0 0 0 0 98 0 0 0 0 0 0 0 99 0 0 0 0 0 0 0 100 1 1 0 0 0 0 2 keep_both/000077500000000000000000000000001350370616400356745ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/combined_output/interleavedinfo.json000066400000000000000000000001441350370616400375210ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_both{ "arguments": ["--combined-output", "--interleaved-output"], "return_code": 0, "stderr": [ ] } input_1.fastq000066400000000000000000000003561350370616400403170ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_both@ATAGCCSeq_1_2959_500/1 meta data TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTG + JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! input_2.fastq000066400000000000000000000003561350370616400403200ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_both@ATAGCCSeq_1_2959_500/2 data meta GTCAGCGAAGGGTTGTAGTAGCCCGTAGGGGCCTACAACGTTGGGGCCTTTGCGTAGTTGTATATAGCCTAGAATTTTTCGTTCGGTAAGCATTAGGAAT + JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! your_output.paired.truncated000066400000000000000000000007341350370616400434740ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_both@ATAGCCSeq_1_2959_500/1 meta data TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTG + JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! @ATAGCCSeq_1_2959_500/2 data meta GTCAGCGAAGGGTTGTAGTAGCCCGTAGGGGCCTACAACGTTGGGGCCTTTGCGTAGTTGTATATAGCCTAGAATTTTTCGTTCGGTAAGCATTAGGAAT + JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! your_output.settings000066400000000000000000000047261350370616400421050ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_bothAdapterRemoval ver. 2.1.7 Trimming of paired-end reads [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 2644350168 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 [Trimming statistics] Total number of read pairs: 1 Number of unaligned read pairs: 1 Number of well aligned read pairs: 0 Number of discarded mate 1 reads: 0 Number of singleton mate 1 reads: 0 Number of discarded mate 2 reads: 0 Number of singleton mate 2 reads: 0 Number of reads with adapters[1]: 0 Number of retained reads: 2 Number of retained nucleotides: 200 Average length of retained reads: 100 [Length distribution] Length Mate1 Mate2 Singleton Discarded All 0 0 0 0 0 0 1 0 0 0 0 0 2 0 0 0 0 0 3 0 0 0 0 0 4 0 0 0 0 0 5 0 0 0 0 0 6 0 0 0 0 0 7 0 0 0 0 0 8 0 0 0 0 0 9 0 0 0 0 0 10 0 0 0 0 0 11 0 0 0 0 0 12 0 0 0 0 0 13 0 0 0 0 0 14 0 0 0 0 0 15 0 0 0 0 0 16 0 0 0 0 0 17 0 0 0 0 0 18 0 0 0 0 0 19 0 0 0 0 0 20 0 0 0 0 0 21 0 0 0 0 0 22 0 0 0 0 0 23 0 0 0 0 0 24 0 0 0 0 0 25 0 0 0 0 0 26 0 0 0 0 0 27 0 0 0 0 0 28 0 0 0 0 0 29 0 0 0 0 0 30 0 0 0 0 0 31 0 0 0 0 0 32 0 0 0 0 0 33 0 0 0 0 0 34 0 0 0 0 0 35 0 0 0 0 0 36 0 0 0 0 0 37 0 0 0 0 0 38 0 0 0 0 0 39 0 0 0 0 0 40 0 0 0 0 0 41 0 0 0 0 0 42 0 0 0 0 0 43 0 0 0 0 0 44 0 0 0 0 0 45 0 0 0 0 0 46 0 0 0 0 0 47 0 0 0 0 0 48 0 0 0 0 0 49 0 0 0 0 0 50 0 0 0 0 0 51 0 0 0 0 0 52 0 0 0 0 0 53 0 0 0 0 0 54 0 0 0 0 0 55 0 0 0 0 0 56 0 0 0 0 0 57 0 0 0 0 0 58 0 0 0 0 0 59 0 0 0 0 0 60 0 0 0 0 0 61 0 0 0 0 0 62 0 0 0 0 0 63 0 0 0 0 0 64 0 0 0 0 0 65 0 0 0 0 0 66 0 0 0 0 0 67 0 0 0 0 0 68 0 0 0 0 0 69 0 0 0 0 0 70 0 0 0 0 0 71 0 0 0 0 0 72 0 0 0 0 0 73 0 0 0 0 0 74 0 0 0 0 0 75 0 0 0 0 0 76 0 0 0 0 0 77 0 0 0 0 0 78 0 0 0 0 0 79 0 0 0 0 0 80 0 0 0 0 0 81 0 0 0 0 0 82 0 0 0 0 0 83 0 0 0 0 0 84 0 0 0 0 0 85 0 0 0 0 0 86 0 0 0 0 0 87 0 0 0 0 0 88 0 0 0 0 0 89 0 0 0 0 0 90 0 0 0 0 0 91 0 0 0 0 0 92 0 0 0 0 0 93 0 0 0 0 0 94 0 0 0 0 0 95 0 0 0 0 0 96 0 0 0 0 0 97 0 0 0 0 0 98 0 0 0 0 0 99 0 0 0 0 0 100 1 1 0 0 2 keep_mate1/000077500000000000000000000000001350370616400357475ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/combined_output/interleavedinfo.json000066400000000000000000000002061350370616400375730ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_mate1{ "arguments": ["--combined-output", "--minlength", "100", "--trimns", "--interleaved-output"], "return_code": 0, "stderr": [ ] } input_1.fastq000066400000000000000000000003561350370616400403720ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_mate1@ATAGCCSeq_1_2959_500/1 meta data TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTG + JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! input_2.fastq000066400000000000000000000003561350370616400403730ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_mate1@ATAGCCSeq_1_2959_500/2 data meta GTCAGCGAAGGGTTGTAGTAGCCCGTAGGGGCCTACAACGTTGGGGCCTTTGCGTAGTTGTATATAGCCTAGAATTTTTCGTTCGGTAAGCATTAGGAAN + JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! your_output.paired.truncated000066400000000000000000000004261350370616400435450ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_mate1@ATAGCCSeq_1_2959_500/1 meta data TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTG + JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! @ATAGCCSeq_1_2959_500/2 data meta N + ! your_output.settings000066400000000000000000000047301350370616400421530ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_mate1AdapterRemoval ver. 2.1.7 Trimming of paired-end reads [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 2806715714 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: Yes Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 100 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 [Trimming statistics] Total number of read pairs: 1 Number of unaligned read pairs: 1 Number of well aligned read pairs: 0 Number of discarded mate 1 reads: 0 Number of singleton mate 1 reads: 1 Number of discarded mate 2 reads: 1 Number of singleton mate 2 reads: 0 Number of reads with adapters[1]: 0 Number of retained reads: 1 Number of retained nucleotides: 100 Average length of retained reads: 100 [Length distribution] Length Mate1 Mate2 Singleton Discarded All 0 0 0 0 0 0 1 0 0 0 0 0 2 0 0 0 0 0 3 0 0 0 0 0 4 0 0 0 0 0 5 0 0 0 0 0 6 0 0 0 0 0 7 0 0 0 0 0 8 0 0 0 0 0 9 0 0 0 0 0 10 0 0 0 0 0 11 0 0 0 0 0 12 0 0 0 0 0 13 0 0 0 0 0 14 0 0 0 0 0 15 0 0 0 0 0 16 0 0 0 0 0 17 0 0 0 0 0 18 0 0 0 0 0 19 0 0 0 0 0 20 0 0 0 0 0 21 0 0 0 0 0 22 0 0 0 0 0 23 0 0 0 0 0 24 0 0 0 0 0 25 0 0 0 0 0 26 0 0 0 0 0 27 0 0 0 0 0 28 0 0 0 0 0 29 0 0 0 0 0 30 0 0 0 0 0 31 0 0 0 0 0 32 0 0 0 0 0 33 0 0 0 0 0 34 0 0 0 0 0 35 0 0 0 0 0 36 0 0 0 0 0 37 0 0 0 0 0 38 0 0 0 0 0 39 0 0 0 0 0 40 0 0 0 0 0 41 0 0 0 0 0 42 0 0 0 0 0 43 0 0 0 0 0 44 0 0 0 0 0 45 0 0 0 0 0 46 0 0 0 0 0 47 0 0 0 0 0 48 0 0 0 0 0 49 0 0 0 0 0 50 0 0 0 0 0 51 0 0 0 0 0 52 0 0 0 0 0 53 0 0 0 0 0 54 0 0 0 0 0 55 0 0 0 0 0 56 0 0 0 0 0 57 0 0 0 0 0 58 0 0 0 0 0 59 0 0 0 0 0 60 0 0 0 0 0 61 0 0 0 0 0 62 0 0 0 0 0 63 0 0 0 0 0 64 0 0 0 0 0 65 0 0 0 0 0 66 0 0 0 0 0 67 0 0 0 0 0 68 0 0 0 0 0 69 0 0 0 0 0 70 0 0 0 0 0 71 0 0 0 0 0 72 0 0 0 0 0 73 0 0 0 0 0 74 0 0 0 0 0 75 0 0 0 0 0 76 0 0 0 0 0 77 0 0 0 0 0 78 0 0 0 0 0 79 0 0 0 0 0 80 0 0 0 0 0 81 0 0 0 0 0 82 0 0 0 0 0 83 0 0 0 0 0 84 0 0 0 0 0 85 0 0 0 0 0 86 0 0 0 0 0 87 0 0 0 0 0 88 0 0 0 0 0 89 0 0 0 0 0 90 0 0 0 0 0 91 0 0 0 0 0 92 0 0 0 0 0 93 0 0 0 0 0 94 0 0 0 0 0 95 0 0 0 0 0 96 0 0 0 0 0 97 0 0 0 0 0 98 0 0 0 0 0 99 0 0 0 1 1 100 0 0 1 0 1 keep_mate2/000077500000000000000000000000001350370616400357505ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/combined_output/interleavedinfo.json000066400000000000000000000002061350370616400375740ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_mate2{ "arguments": ["--combined-output", "--minlength", "100", "--trimns", "--interleaved-output"], "return_code": 0, "stderr": [ ] } input_1.fastq000066400000000000000000000003561350370616400403730ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_mate2@ATAGCCSeq_1_2959_500/1 meta data TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTN + JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! input_2.fastq000066400000000000000000000003561350370616400403740ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_mate2@ATAGCCSeq_1_2959_500/2 data meta GTCAGCGAAGGGTTGTAGTAGCCCGTAGGGGCCTACAACGTTGGGGCCTTTGCGTAGTTGTATATAGCCTAGAATTTTTCGTTCGGTAAGCATTAGGAAT + JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! your_output.paired.truncated000066400000000000000000000004261350370616400435460ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_mate2@ATAGCCSeq_1_2959_500/1 meta data N + ! @ATAGCCSeq_1_2959_500/2 data meta GTCAGCGAAGGGTTGTAGTAGCCCGTAGGGGCCTACAACGTTGGGGCCTTTGCGTAGTTGTATATAGCCTAGAATTTTTCGTTCGGTAAGCATTAGGAAT + JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! your_output.settings000066400000000000000000000047301350370616400421540ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_mate2AdapterRemoval ver. 2.1.7 Trimming of paired-end reads [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 3115920885 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: Yes Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 100 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 [Trimming statistics] Total number of read pairs: 1 Number of unaligned read pairs: 0 Number of well aligned read pairs: 1 Number of discarded mate 1 reads: 1 Number of singleton mate 1 reads: 0 Number of discarded mate 2 reads: 0 Number of singleton mate 2 reads: 1 Number of reads with adapters[1]: 0 Number of retained reads: 1 Number of retained nucleotides: 100 Average length of retained reads: 100 [Length distribution] Length Mate1 Mate2 Singleton Discarded All 0 0 0 0 0 0 1 0 0 0 0 0 2 0 0 0 0 0 3 0 0 0 0 0 4 0 0 0 0 0 5 0 0 0 0 0 6 0 0 0 0 0 7 0 0 0 0 0 8 0 0 0 0 0 9 0 0 0 0 0 10 0 0 0 0 0 11 0 0 0 0 0 12 0 0 0 0 0 13 0 0 0 0 0 14 0 0 0 0 0 15 0 0 0 0 0 16 0 0 0 0 0 17 0 0 0 0 0 18 0 0 0 0 0 19 0 0 0 0 0 20 0 0 0 0 0 21 0 0 0 0 0 22 0 0 0 0 0 23 0 0 0 0 0 24 0 0 0 0 0 25 0 0 0 0 0 26 0 0 0 0 0 27 0 0 0 0 0 28 0 0 0 0 0 29 0 0 0 0 0 30 0 0 0 0 0 31 0 0 0 0 0 32 0 0 0 0 0 33 0 0 0 0 0 34 0 0 0 0 0 35 0 0 0 0 0 36 0 0 0 0 0 37 0 0 0 0 0 38 0 0 0 0 0 39 0 0 0 0 0 40 0 0 0 0 0 41 0 0 0 0 0 42 0 0 0 0 0 43 0 0 0 0 0 44 0 0 0 0 0 45 0 0 0 0 0 46 0 0 0 0 0 47 0 0 0 0 0 48 0 0 0 0 0 49 0 0 0 0 0 50 0 0 0 0 0 51 0 0 0 0 0 52 0 0 0 0 0 53 0 0 0 0 0 54 0 0 0 0 0 55 0 0 0 0 0 56 0 0 0 0 0 57 0 0 0 0 0 58 0 0 0 0 0 59 0 0 0 0 0 60 0 0 0 0 0 61 0 0 0 0 0 62 0 0 0 0 0 63 0 0 0 0 0 64 0 0 0 0 0 65 0 0 0 0 0 66 0 0 0 0 0 67 0 0 0 0 0 68 0 0 0 0 0 69 0 0 0 0 0 70 0 0 0 0 0 71 0 0 0 0 0 72 0 0 0 0 0 73 0 0 0 0 0 74 0 0 0 0 0 75 0 0 0 0 0 76 0 0 0 0 0 77 0 0 0 0 0 78 0 0 0 0 0 79 0 0 0 0 0 80 0 0 0 0 0 81 0 0 0 0 0 82 0 0 0 0 0 83 0 0 0 0 0 84 0 0 0 0 0 85 0 0 0 0 0 86 0 0 0 0 0 87 0 0 0 0 0 88 0 0 0 0 0 89 0 0 0 0 0 90 0 0 0 0 0 91 0 0 0 0 0 92 0 0 0 0 0 93 0 0 0 0 0 94 0 0 0 0 0 95 0 0 0 0 0 96 0 0 0 0 0 97 0 0 0 0 0 98 0 0 0 0 0 99 0 0 0 1 1 100 0 0 1 0 1 keep_neither/000077500000000000000000000000001350370616400363765ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/combined_output/interleavedinfo.json000066400000000000000000000002061350370616400402220ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_neither{ "arguments": ["--combined-output", "--minlength", "100", "--trimns", "--interleaved-output"], "return_code": 0, "stderr": [ ] } input_1.fastq000066400000000000000000000003561350370616400410210ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_neither@ATAGCCSeq_1_2959_500/1 meta data TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTN + JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! input_2.fastq000066400000000000000000000003561350370616400410220ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_neither@ATAGCCSeq_1_2959_500/2 data meta GTCAGCGAAGGGTTGTAGTAGCCCGTAGGGGCCTACAACGTTGGGGCCTTTGCGTAGTTGTATATAGCCTAGAATTTTTCGTTCGGTAAGCATTAGGAAN + JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! your_output.paired.truncated000066400000000000000000000001201350370616400441630ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_neither@ATAGCCSeq_1_2959_500/1 meta data N + ! @ATAGCCSeq_1_2959_500/2 data meta N + ! your_output.settings000066400000000000000000000047061350370616400426050ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_neitherAdapterRemoval ver. 2.1.7 Trimming of paired-end reads [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 2416745148 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: Yes Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 100 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 [Trimming statistics] Total number of read pairs: 1 Number of unaligned read pairs: 1 Number of well aligned read pairs: 0 Number of discarded mate 1 reads: 1 Number of singleton mate 1 reads: 0 Number of discarded mate 2 reads: 1 Number of singleton mate 2 reads: 0 Number of reads with adapters[1]: 0 Number of retained reads: 0 Number of retained nucleotides: 0 Average length of retained reads: 0 [Length distribution] Length Mate1 Mate2 Singleton Discarded All 0 0 0 0 0 0 1 0 0 0 0 0 2 0 0 0 0 0 3 0 0 0 0 0 4 0 0 0 0 0 5 0 0 0 0 0 6 0 0 0 0 0 7 0 0 0 0 0 8 0 0 0 0 0 9 0 0 0 0 0 10 0 0 0 0 0 11 0 0 0 0 0 12 0 0 0 0 0 13 0 0 0 0 0 14 0 0 0 0 0 15 0 0 0 0 0 16 0 0 0 0 0 17 0 0 0 0 0 18 0 0 0 0 0 19 0 0 0 0 0 20 0 0 0 0 0 21 0 0 0 0 0 22 0 0 0 0 0 23 0 0 0 0 0 24 0 0 0 0 0 25 0 0 0 0 0 26 0 0 0 0 0 27 0 0 0 0 0 28 0 0 0 0 0 29 0 0 0 0 0 30 0 0 0 0 0 31 0 0 0 0 0 32 0 0 0 0 0 33 0 0 0 0 0 34 0 0 0 0 0 35 0 0 0 0 0 36 0 0 0 0 0 37 0 0 0 0 0 38 0 0 0 0 0 39 0 0 0 0 0 40 0 0 0 0 0 41 0 0 0 0 0 42 0 0 0 0 0 43 0 0 0 0 0 44 0 0 0 0 0 45 0 0 0 0 0 46 0 0 0 0 0 47 0 0 0 0 0 48 0 0 0 0 0 49 0 0 0 0 0 50 0 0 0 0 0 51 0 0 0 0 0 52 0 0 0 0 0 53 0 0 0 0 0 54 0 0 0 0 0 55 0 0 0 0 0 56 0 0 0 0 0 57 0 0 0 0 0 58 0 0 0 0 0 59 0 0 0 0 0 60 0 0 0 0 0 61 0 0 0 0 0 62 0 0 0 0 0 63 0 0 0 0 0 64 0 0 0 0 0 65 0 0 0 0 0 66 0 0 0 0 0 67 0 0 0 0 0 68 0 0 0 0 0 69 0 0 0 0 0 70 0 0 0 0 0 71 0 0 0 0 0 72 0 0 0 0 0 73 0 0 0 0 0 74 0 0 0 0 0 75 0 0 0 0 0 76 0 0 0 0 0 77 0 0 0 0 0 78 0 0 0 0 0 79 0 0 0 0 0 80 0 0 0 0 0 81 0 0 0 0 0 82 0 0 0 0 0 83 0 0 0 0 0 84 0 0 0 0 0 85 0 0 0 0 0 86 0 0 0 0 0 87 0 0 0 0 0 88 0 0 0 0 0 89 0 0 0 0 0 90 0 0 0 0 0 91 0 0 0 0 0 92 0 0 0 0 0 93 0 0 0 0 0 94 0 0 0 0 0 95 0 0 0 0 0 96 0 0 0 0 0 97 0 0 0 0 0 98 0 0 0 0 0 99 0 0 0 2 2 adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/combined_output/keep_both/000077500000000000000000000000001350370616400334515ustar00rootroot00000000000000info.json000066400000000000000000000001141350370616400352140ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/combined_output/keep_both{ "arguments": ["--combined-output"], "return_code": 0, "stderr": [ ] } input_1.fastq000066400000000000000000000003561350370616400360150ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/combined_output/keep_both@ATAGCCSeq_1_2959_500/1 meta data TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTG + JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! input_2.fastq000066400000000000000000000003561350370616400360160ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/combined_output/keep_both@ATAGCCSeq_1_2959_500/2 data meta GTCAGCGAAGGGTTGTAGTAGCCCGTAGGGGCCTACAACGTTGGGGCCTTTGCGTAGTTGTATATAGCCTAGAATTTTTCGTTCGGTAAGCATTAGGAAT + JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! your_output.pair1.truncated000066400000000000000000000003561350370616400407420ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/combined_output/keep_both@ATAGCCSeq_1_2959_500/1 meta data TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTG + JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! your_output.pair2.truncated000066400000000000000000000003561350370616400407430ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/combined_output/keep_both@ATAGCCSeq_1_2959_500/2 data meta GTCAGCGAAGGGTTGTAGTAGCCCGTAGGGGCCTACAACGTTGGGGCCTTTGCGTAGTTGTATATAGCCTAGAATTTTTCGTTCGGTAAGCATTAGGAAT + JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! your_output.settings000066400000000000000000000047261350370616400376030ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/combined_output/keep_bothAdapterRemoval ver. 2.1.7 Trimming of paired-end reads [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 2644350168 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 [Trimming statistics] Total number of read pairs: 1 Number of unaligned read pairs: 1 Number of well aligned read pairs: 0 Number of discarded mate 1 reads: 0 Number of singleton mate 1 reads: 0 Number of discarded mate 2 reads: 0 Number of singleton mate 2 reads: 0 Number of reads with adapters[1]: 0 Number of retained reads: 2 Number of retained nucleotides: 200 Average length of retained reads: 100 [Length distribution] Length Mate1 Mate2 Singleton Discarded All 0 0 0 0 0 0 1 0 0 0 0 0 2 0 0 0 0 0 3 0 0 0 0 0 4 0 0 0 0 0 5 0 0 0 0 0 6 0 0 0 0 0 7 0 0 0 0 0 8 0 0 0 0 0 9 0 0 0 0 0 10 0 0 0 0 0 11 0 0 0 0 0 12 0 0 0 0 0 13 0 0 0 0 0 14 0 0 0 0 0 15 0 0 0 0 0 16 0 0 0 0 0 17 0 0 0 0 0 18 0 0 0 0 0 19 0 0 0 0 0 20 0 0 0 0 0 21 0 0 0 0 0 22 0 0 0 0 0 23 0 0 0 0 0 24 0 0 0 0 0 25 0 0 0 0 0 26 0 0 0 0 0 27 0 0 0 0 0 28 0 0 0 0 0 29 0 0 0 0 0 30 0 0 0 0 0 31 0 0 0 0 0 32 0 0 0 0 0 33 0 0 0 0 0 34 0 0 0 0 0 35 0 0 0 0 0 36 0 0 0 0 0 37 0 0 0 0 0 38 0 0 0 0 0 39 0 0 0 0 0 40 0 0 0 0 0 41 0 0 0 0 0 42 0 0 0 0 0 43 0 0 0 0 0 44 0 0 0 0 0 45 0 0 0 0 0 46 0 0 0 0 0 47 0 0 0 0 0 48 0 0 0 0 0 49 0 0 0 0 0 50 0 0 0 0 0 51 0 0 0 0 0 52 0 0 0 0 0 53 0 0 0 0 0 54 0 0 0 0 0 55 0 0 0 0 0 56 0 0 0 0 0 57 0 0 0 0 0 58 0 0 0 0 0 59 0 0 0 0 0 60 0 0 0 0 0 61 0 0 0 0 0 62 0 0 0 0 0 63 0 0 0 0 0 64 0 0 0 0 0 65 0 0 0 0 0 66 0 0 0 0 0 67 0 0 0 0 0 68 0 0 0 0 0 69 0 0 0 0 0 70 0 0 0 0 0 71 0 0 0 0 0 72 0 0 0 0 0 73 0 0 0 0 0 74 0 0 0 0 0 75 0 0 0 0 0 76 0 0 0 0 0 77 0 0 0 0 0 78 0 0 0 0 0 79 0 0 0 0 0 80 0 0 0 0 0 81 0 0 0 0 0 82 0 0 0 0 0 83 0 0 0 0 0 84 0 0 0 0 0 85 0 0 0 0 0 86 0 0 0 0 0 87 0 0 0 0 0 88 0 0 0 0 0 89 0 0 0 0 0 90 0 0 0 0 0 91 0 0 0 0 0 92 0 0 0 0 0 93 0 0 0 0 0 94 0 0 0 0 0 95 0 0 0 0 0 96 0 0 0 0 0 97 0 0 0 0 0 98 0 0 0 0 0 99 0 0 0 0 0 100 1 1 0 0 2 adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/combined_output/keep_mate1/000077500000000000000000000000001350370616400335245ustar00rootroot00000000000000info.json000066400000000000000000000001561350370616400352750ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/combined_output/keep_mate1{ "arguments": ["--combined-output", "--minlength", "100", "--trimns"], "return_code": 0, "stderr": [ ] } input_1.fastq000066400000000000000000000003561350370616400360700ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/combined_output/keep_mate1@ATAGCCSeq_1_2959_500/1 meta data TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTG + JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! input_2.fastq000066400000000000000000000003561350370616400360710ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/combined_output/keep_mate1@ATAGCCSeq_1_2959_500/2 data meta GTCAGCGAAGGGTTGTAGTAGCCCGTAGGGGCCTACAACGTTGGGGCCTTTGCGTAGTTGTATATAGCCTAGAATTTTTCGTTCGGTAAGCATTAGGAAN + JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! your_output.pair1.truncated000066400000000000000000000003561350370616400410150ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/combined_output/keep_mate1@ATAGCCSeq_1_2959_500/1 meta data TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTG + JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! your_output.pair2.truncated000066400000000000000000000000501350370616400410050ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/combined_output/keep_mate1@ATAGCCSeq_1_2959_500/2 data meta N + ! your_output.settings000066400000000000000000000047301350370616400376510ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/combined_output/keep_mate1AdapterRemoval ver. 2.1.7 Trimming of paired-end reads [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 2806715714 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: Yes Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 100 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 [Trimming statistics] Total number of read pairs: 1 Number of unaligned read pairs: 1 Number of well aligned read pairs: 0 Number of discarded mate 1 reads: 0 Number of singleton mate 1 reads: 1 Number of discarded mate 2 reads: 1 Number of singleton mate 2 reads: 0 Number of reads with adapters[1]: 0 Number of retained reads: 1 Number of retained nucleotides: 100 Average length of retained reads: 100 [Length distribution] Length Mate1 Mate2 Singleton Discarded All 0 0 0 0 0 0 1 0 0 0 0 0 2 0 0 0 0 0 3 0 0 0 0 0 4 0 0 0 0 0 5 0 0 0 0 0 6 0 0 0 0 0 7 0 0 0 0 0 8 0 0 0 0 0 9 0 0 0 0 0 10 0 0 0 0 0 11 0 0 0 0 0 12 0 0 0 0 0 13 0 0 0 0 0 14 0 0 0 0 0 15 0 0 0 0 0 16 0 0 0 0 0 17 0 0 0 0 0 18 0 0 0 0 0 19 0 0 0 0 0 20 0 0 0 0 0 21 0 0 0 0 0 22 0 0 0 0 0 23 0 0 0 0 0 24 0 0 0 0 0 25 0 0 0 0 0 26 0 0 0 0 0 27 0 0 0 0 0 28 0 0 0 0 0 29 0 0 0 0 0 30 0 0 0 0 0 31 0 0 0 0 0 32 0 0 0 0 0 33 0 0 0 0 0 34 0 0 0 0 0 35 0 0 0 0 0 36 0 0 0 0 0 37 0 0 0 0 0 38 0 0 0 0 0 39 0 0 0 0 0 40 0 0 0 0 0 41 0 0 0 0 0 42 0 0 0 0 0 43 0 0 0 0 0 44 0 0 0 0 0 45 0 0 0 0 0 46 0 0 0 0 0 47 0 0 0 0 0 48 0 0 0 0 0 49 0 0 0 0 0 50 0 0 0 0 0 51 0 0 0 0 0 52 0 0 0 0 0 53 0 0 0 0 0 54 0 0 0 0 0 55 0 0 0 0 0 56 0 0 0 0 0 57 0 0 0 0 0 58 0 0 0 0 0 59 0 0 0 0 0 60 0 0 0 0 0 61 0 0 0 0 0 62 0 0 0 0 0 63 0 0 0 0 0 64 0 0 0 0 0 65 0 0 0 0 0 66 0 0 0 0 0 67 0 0 0 0 0 68 0 0 0 0 0 69 0 0 0 0 0 70 0 0 0 0 0 71 0 0 0 0 0 72 0 0 0 0 0 73 0 0 0 0 0 74 0 0 0 0 0 75 0 0 0 0 0 76 0 0 0 0 0 77 0 0 0 0 0 78 0 0 0 0 0 79 0 0 0 0 0 80 0 0 0 0 0 81 0 0 0 0 0 82 0 0 0 0 0 83 0 0 0 0 0 84 0 0 0 0 0 85 0 0 0 0 0 86 0 0 0 0 0 87 0 0 0 0 0 88 0 0 0 0 0 89 0 0 0 0 0 90 0 0 0 0 0 91 0 0 0 0 0 92 0 0 0 0 0 93 0 0 0 0 0 94 0 0 0 0 0 95 0 0 0 0 0 96 0 0 0 0 0 97 0 0 0 0 0 98 0 0 0 0 0 99 0 0 0 1 1 100 0 0 1 0 1 adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/combined_output/keep_mate2/000077500000000000000000000000001350370616400335255ustar00rootroot00000000000000info.json000066400000000000000000000001561350370616400352760ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/combined_output/keep_mate2{ "arguments": ["--combined-output", "--minlength", "100", "--trimns"], "return_code": 0, "stderr": [ ] } input_1.fastq000066400000000000000000000003561350370616400360710ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/combined_output/keep_mate2@ATAGCCSeq_1_2959_500/1 meta data TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTN + JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! input_2.fastq000066400000000000000000000003561350370616400360720ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/combined_output/keep_mate2@ATAGCCSeq_1_2959_500/2 data meta GTCAGCGAAGGGTTGTAGTAGCCCGTAGGGGCCTACAACGTTGGGGCCTTTGCGTAGTTGTATATAGCCTAGAATTTTTCGTTCGGTAAGCATTAGGAAT + JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! your_output.pair1.truncated000066400000000000000000000000501350370616400410050ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/combined_output/keep_mate2@ATAGCCSeq_1_2959_500/1 meta data N + ! your_output.pair2.truncated000066400000000000000000000003561350370616400410170ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/combined_output/keep_mate2@ATAGCCSeq_1_2959_500/2 data meta GTCAGCGAAGGGTTGTAGTAGCCCGTAGGGGCCTACAACGTTGGGGCCTTTGCGTAGTTGTATATAGCCTAGAATTTTTCGTTCGGTAAGCATTAGGAAT + JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! your_output.settings000066400000000000000000000047301350370616400376520ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/combined_output/keep_mate2AdapterRemoval ver. 2.1.7 Trimming of paired-end reads [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 3115920885 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: Yes Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 100 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 [Trimming statistics] Total number of read pairs: 1 Number of unaligned read pairs: 0 Number of well aligned read pairs: 1 Number of discarded mate 1 reads: 1 Number of singleton mate 1 reads: 0 Number of discarded mate 2 reads: 0 Number of singleton mate 2 reads: 1 Number of reads with adapters[1]: 0 Number of retained reads: 1 Number of retained nucleotides: 100 Average length of retained reads: 100 [Length distribution] Length Mate1 Mate2 Singleton Discarded All 0 0 0 0 0 0 1 0 0 0 0 0 2 0 0 0 0 0 3 0 0 0 0 0 4 0 0 0 0 0 5 0 0 0 0 0 6 0 0 0 0 0 7 0 0 0 0 0 8 0 0 0 0 0 9 0 0 0 0 0 10 0 0 0 0 0 11 0 0 0 0 0 12 0 0 0 0 0 13 0 0 0 0 0 14 0 0 0 0 0 15 0 0 0 0 0 16 0 0 0 0 0 17 0 0 0 0 0 18 0 0 0 0 0 19 0 0 0 0 0 20 0 0 0 0 0 21 0 0 0 0 0 22 0 0 0 0 0 23 0 0 0 0 0 24 0 0 0 0 0 25 0 0 0 0 0 26 0 0 0 0 0 27 0 0 0 0 0 28 0 0 0 0 0 29 0 0 0 0 0 30 0 0 0 0 0 31 0 0 0 0 0 32 0 0 0 0 0 33 0 0 0 0 0 34 0 0 0 0 0 35 0 0 0 0 0 36 0 0 0 0 0 37 0 0 0 0 0 38 0 0 0 0 0 39 0 0 0 0 0 40 0 0 0 0 0 41 0 0 0 0 0 42 0 0 0 0 0 43 0 0 0 0 0 44 0 0 0 0 0 45 0 0 0 0 0 46 0 0 0 0 0 47 0 0 0 0 0 48 0 0 0 0 0 49 0 0 0 0 0 50 0 0 0 0 0 51 0 0 0 0 0 52 0 0 0 0 0 53 0 0 0 0 0 54 0 0 0 0 0 55 0 0 0 0 0 56 0 0 0 0 0 57 0 0 0 0 0 58 0 0 0 0 0 59 0 0 0 0 0 60 0 0 0 0 0 61 0 0 0 0 0 62 0 0 0 0 0 63 0 0 0 0 0 64 0 0 0 0 0 65 0 0 0 0 0 66 0 0 0 0 0 67 0 0 0 0 0 68 0 0 0 0 0 69 0 0 0 0 0 70 0 0 0 0 0 71 0 0 0 0 0 72 0 0 0 0 0 73 0 0 0 0 0 74 0 0 0 0 0 75 0 0 0 0 0 76 0 0 0 0 0 77 0 0 0 0 0 78 0 0 0 0 0 79 0 0 0 0 0 80 0 0 0 0 0 81 0 0 0 0 0 82 0 0 0 0 0 83 0 0 0 0 0 84 0 0 0 0 0 85 0 0 0 0 0 86 0 0 0 0 0 87 0 0 0 0 0 88 0 0 0 0 0 89 0 0 0 0 0 90 0 0 0 0 0 91 0 0 0 0 0 92 0 0 0 0 0 93 0 0 0 0 0 94 0 0 0 0 0 95 0 0 0 0 0 96 0 0 0 0 0 97 0 0 0 0 0 98 0 0 0 0 0 99 0 0 0 1 1 100 0 0 1 0 1 adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/combined_output/keep_neither/000077500000000000000000000000001350370616400341535ustar00rootroot00000000000000info.json000066400000000000000000000001561350370616400357240ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/combined_output/keep_neither{ "arguments": ["--combined-output", "--minlength", "100", "--trimns"], "return_code": 0, "stderr": [ ] } input_1.fastq000066400000000000000000000003561350370616400365170ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/combined_output/keep_neither@ATAGCCSeq_1_2959_500/1 meta data TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTN + JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! input_2.fastq000066400000000000000000000003561350370616400365200ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/combined_output/keep_neither@ATAGCCSeq_1_2959_500/2 data meta GTCAGCGAAGGGTTGTAGTAGCCCGTAGGGGCCTACAACGTTGGGGCCTTTGCGTAGTTGTATATAGCCTAGAATTTTTCGTTCGGTAAGCATTAGGAAN + JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! your_output.pair1.truncated000066400000000000000000000000501350370616400414330ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/combined_output/keep_neither@ATAGCCSeq_1_2959_500/1 meta data N + ! your_output.pair2.truncated000066400000000000000000000000501350370616400414340ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/combined_output/keep_neither@ATAGCCSeq_1_2959_500/2 data meta N + ! your_output.settings000066400000000000000000000047061350370616400403030ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/combined_output/keep_neitherAdapterRemoval ver. 2.1.7 Trimming of paired-end reads [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 2543753157 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: Yes Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 100 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 [Trimming statistics] Total number of read pairs: 1 Number of unaligned read pairs: 1 Number of well aligned read pairs: 0 Number of discarded mate 1 reads: 1 Number of singleton mate 1 reads: 0 Number of discarded mate 2 reads: 1 Number of singleton mate 2 reads: 0 Number of reads with adapters[1]: 0 Number of retained reads: 0 Number of retained nucleotides: 0 Average length of retained reads: 0 [Length distribution] Length Mate1 Mate2 Singleton Discarded All 0 0 0 0 0 0 1 0 0 0 0 0 2 0 0 0 0 0 3 0 0 0 0 0 4 0 0 0 0 0 5 0 0 0 0 0 6 0 0 0 0 0 7 0 0 0 0 0 8 0 0 0 0 0 9 0 0 0 0 0 10 0 0 0 0 0 11 0 0 0 0 0 12 0 0 0 0 0 13 0 0 0 0 0 14 0 0 0 0 0 15 0 0 0 0 0 16 0 0 0 0 0 17 0 0 0 0 0 18 0 0 0 0 0 19 0 0 0 0 0 20 0 0 0 0 0 21 0 0 0 0 0 22 0 0 0 0 0 23 0 0 0 0 0 24 0 0 0 0 0 25 0 0 0 0 0 26 0 0 0 0 0 27 0 0 0 0 0 28 0 0 0 0 0 29 0 0 0 0 0 30 0 0 0 0 0 31 0 0 0 0 0 32 0 0 0 0 0 33 0 0 0 0 0 34 0 0 0 0 0 35 0 0 0 0 0 36 0 0 0 0 0 37 0 0 0 0 0 38 0 0 0 0 0 39 0 0 0 0 0 40 0 0 0 0 0 41 0 0 0 0 0 42 0 0 0 0 0 43 0 0 0 0 0 44 0 0 0 0 0 45 0 0 0 0 0 46 0 0 0 0 0 47 0 0 0 0 0 48 0 0 0 0 0 49 0 0 0 0 0 50 0 0 0 0 0 51 0 0 0 0 0 52 0 0 0 0 0 53 0 0 0 0 0 54 0 0 0 0 0 55 0 0 0 0 0 56 0 0 0 0 0 57 0 0 0 0 0 58 0 0 0 0 0 59 0 0 0 0 0 60 0 0 0 0 0 61 0 0 0 0 0 62 0 0 0 0 0 63 0 0 0 0 0 64 0 0 0 0 0 65 0 0 0 0 0 66 0 0 0 0 0 67 0 0 0 0 0 68 0 0 0 0 0 69 0 0 0 0 0 70 0 0 0 0 0 71 0 0 0 0 0 72 0 0 0 0 0 73 0 0 0 0 0 74 0 0 0 0 0 75 0 0 0 0 0 76 0 0 0 0 0 77 0 0 0 0 0 78 0 0 0 0 0 79 0 0 0 0 0 80 0 0 0 0 0 81 0 0 0 0 0 82 0 0 0 0 0 83 0 0 0 0 0 84 0 0 0 0 0 85 0 0 0 0 0 86 0 0 0 0 0 87 0 0 0 0 0 88 0 0 0 0 0 89 0 0 0 0 0 90 0 0 0 0 0 91 0 0 0 0 0 92 0 0 0 0 0 93 0 0 0 0 0 94 0 0 0 0 0 95 0 0 0 0 0 96 0 0 0 0 0 97 0 0 0 0 0 98 0 0 0 0 0 99 0 0 0 2 2 adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/crlf_newlines/000077500000000000000000000000001350370616400311435ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/crlf_newlines/info.json000066400000000000000000000000711350370616400327670ustar00rootroot00000000000000{ "arguments": [], "return_code": 0, "stderr": [ ] } adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/crlf_newlines/input_1.fastq000066400000000000000000000003621350370616400335630ustar00rootroot00000000000000@ATAGCCSeq_1_2959_500/1 meta data TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTG + JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/crlf_newlines/input_2.fastq000066400000000000000000000003621350370616400335640ustar00rootroot00000000000000@ATAGCCSeq_1_2959_500/2 data meta GTCAGCGAAGGGTTGTAGTAGCCCGTAGGGGCCTACAACGTTGGGGCCTTTGCGTAGTTGTATATAGCCTAGAATTTTTCGTTCGGTAAGCATTAGGAAT + JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! your_output.discarded000066400000000000000000000000001350370616400353340ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/crlf_newlinesyour_output.pair1.truncated000066400000000000000000000003561350370616400364340ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/crlf_newlines@ATAGCCSeq_1_2959_500/1 meta data TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTG + JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! your_output.pair2.truncated000066400000000000000000000003561350370616400364350ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/crlf_newlines@ATAGCCSeq_1_2959_500/2 data meta GTCAGCGAAGGGTTGTAGTAGCCCGTAGGGGCCTACAACGTTGGGGCCTTTGCGTAGTTGTATATAGCCTAGAATTTTTCGTTCGGTAAGCATTAGGAAT + JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! your_output.settings000066400000000000000000000047251350370616400352740ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/crlf_newlinesAdapterRemoval ver. 2.1.7 Trimming of paired-end reads [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 981230521 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 [Trimming statistics] Total number of read pairs: 1 Number of unaligned read pairs: 1 Number of well aligned read pairs: 0 Number of discarded mate 1 reads: 0 Number of singleton mate 1 reads: 0 Number of discarded mate 2 reads: 0 Number of singleton mate 2 reads: 0 Number of reads with adapters[1]: 0 Number of retained reads: 2 Number of retained nucleotides: 200 Average length of retained reads: 100 [Length distribution] Length Mate1 Mate2 Singleton Discarded All 0 0 0 0 0 0 1 0 0 0 0 0 2 0 0 0 0 0 3 0 0 0 0 0 4 0 0 0 0 0 5 0 0 0 0 0 6 0 0 0 0 0 7 0 0 0 0 0 8 0 0 0 0 0 9 0 0 0 0 0 10 0 0 0 0 0 11 0 0 0 0 0 12 0 0 0 0 0 13 0 0 0 0 0 14 0 0 0 0 0 15 0 0 0 0 0 16 0 0 0 0 0 17 0 0 0 0 0 18 0 0 0 0 0 19 0 0 0 0 0 20 0 0 0 0 0 21 0 0 0 0 0 22 0 0 0 0 0 23 0 0 0 0 0 24 0 0 0 0 0 25 0 0 0 0 0 26 0 0 0 0 0 27 0 0 0 0 0 28 0 0 0 0 0 29 0 0 0 0 0 30 0 0 0 0 0 31 0 0 0 0 0 32 0 0 0 0 0 33 0 0 0 0 0 34 0 0 0 0 0 35 0 0 0 0 0 36 0 0 0 0 0 37 0 0 0 0 0 38 0 0 0 0 0 39 0 0 0 0 0 40 0 0 0 0 0 41 0 0 0 0 0 42 0 0 0 0 0 43 0 0 0 0 0 44 0 0 0 0 0 45 0 0 0 0 0 46 0 0 0 0 0 47 0 0 0 0 0 48 0 0 0 0 0 49 0 0 0 0 0 50 0 0 0 0 0 51 0 0 0 0 0 52 0 0 0 0 0 53 0 0 0 0 0 54 0 0 0 0 0 55 0 0 0 0 0 56 0 0 0 0 0 57 0 0 0 0 0 58 0 0 0 0 0 59 0 0 0 0 0 60 0 0 0 0 0 61 0 0 0 0 0 62 0 0 0 0 0 63 0 0 0 0 0 64 0 0 0 0 0 65 0 0 0 0 0 66 0 0 0 0 0 67 0 0 0 0 0 68 0 0 0 0 0 69 0 0 0 0 0 70 0 0 0 0 0 71 0 0 0 0 0 72 0 0 0 0 0 73 0 0 0 0 0 74 0 0 0 0 0 75 0 0 0 0 0 76 0 0 0 0 0 77 0 0 0 0 0 78 0 0 0 0 0 79 0 0 0 0 0 80 0 0 0 0 0 81 0 0 0 0 0 82 0 0 0 0 0 83 0 0 0 0 0 84 0 0 0 0 0 85 0 0 0 0 0 86 0 0 0 0 0 87 0 0 0 0 0 88 0 0 0 0 0 89 0 0 0 0 0 90 0 0 0 0 0 91 0 0 0 0 0 92 0 0 0 0 0 93 0 0 0 0 0 94 0 0 0 0 0 95 0 0 0 0 0 96 0 0 0 0 0 97 0 0 0 0 0 98 0 0 0 0 0 99 0 0 0 0 0 100 1 1 0 0 2 your_output.singleton.truncated000066400000000000000000000000001350370616400374040ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/crlf_newlinesadapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/defaults/000077500000000000000000000000001350370616400301205ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/defaults/info.json000066400000000000000000000000711350370616400317440ustar00rootroot00000000000000{ "arguments": [], "return_code": 0, "stderr": [ ] } adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/defaults/input_1.fastq000066400000000000000000000003561350370616400325430ustar00rootroot00000000000000@ATAGCCSeq_1_2959_500/1 meta data TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTG + JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/defaults/input_2.fastq000066400000000000000000000003561350370616400325440ustar00rootroot00000000000000@ATAGCCSeq_1_2959_500/2 data meta GTCAGCGAAGGGTTGTAGTAGCCCGTAGGGGCCTACAACGTTGGGGCCTTTGCGTAGTTGTATATAGCCTAGAATTTTTCGTTCGGTAAGCATTAGGAAT + JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/defaults/your_output.discarded000066400000000000000000000000001350370616400343700ustar00rootroot00000000000000your_output.pair1.truncated000066400000000000000000000003561350370616400354110ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/defaults@ATAGCCSeq_1_2959_500/1 meta data TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTG + JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! your_output.pair2.truncated000066400000000000000000000003561350370616400354120ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/defaults@ATAGCCSeq_1_2959_500/2 data meta GTCAGCGAAGGGTTGTAGTAGCCCGTAGGGGCCTACAACGTTGGGGCCTTTGCGTAGTTGTATATAGCCTAGAATTTTTCGTTCGGTAAGCATTAGGAAT + JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/defaults/your_output.settings000066400000000000000000000047251350370616400343300ustar00rootroot00000000000000AdapterRemoval ver. 2.1.7 Trimming of paired-end reads [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 981230521 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 [Trimming statistics] Total number of read pairs: 1 Number of unaligned read pairs: 1 Number of well aligned read pairs: 0 Number of discarded mate 1 reads: 0 Number of singleton mate 1 reads: 0 Number of discarded mate 2 reads: 0 Number of singleton mate 2 reads: 0 Number of reads with adapters[1]: 0 Number of retained reads: 2 Number of retained nucleotides: 200 Average length of retained reads: 100 [Length distribution] Length Mate1 Mate2 Singleton Discarded All 0 0 0 0 0 0 1 0 0 0 0 0 2 0 0 0 0 0 3 0 0 0 0 0 4 0 0 0 0 0 5 0 0 0 0 0 6 0 0 0 0 0 7 0 0 0 0 0 8 0 0 0 0 0 9 0 0 0 0 0 10 0 0 0 0 0 11 0 0 0 0 0 12 0 0 0 0 0 13 0 0 0 0 0 14 0 0 0 0 0 15 0 0 0 0 0 16 0 0 0 0 0 17 0 0 0 0 0 18 0 0 0 0 0 19 0 0 0 0 0 20 0 0 0 0 0 21 0 0 0 0 0 22 0 0 0 0 0 23 0 0 0 0 0 24 0 0 0 0 0 25 0 0 0 0 0 26 0 0 0 0 0 27 0 0 0 0 0 28 0 0 0 0 0 29 0 0 0 0 0 30 0 0 0 0 0 31 0 0 0 0 0 32 0 0 0 0 0 33 0 0 0 0 0 34 0 0 0 0 0 35 0 0 0 0 0 36 0 0 0 0 0 37 0 0 0 0 0 38 0 0 0 0 0 39 0 0 0 0 0 40 0 0 0 0 0 41 0 0 0 0 0 42 0 0 0 0 0 43 0 0 0 0 0 44 0 0 0 0 0 45 0 0 0 0 0 46 0 0 0 0 0 47 0 0 0 0 0 48 0 0 0 0 0 49 0 0 0 0 0 50 0 0 0 0 0 51 0 0 0 0 0 52 0 0 0 0 0 53 0 0 0 0 0 54 0 0 0 0 0 55 0 0 0 0 0 56 0 0 0 0 0 57 0 0 0 0 0 58 0 0 0 0 0 59 0 0 0 0 0 60 0 0 0 0 0 61 0 0 0 0 0 62 0 0 0 0 0 63 0 0 0 0 0 64 0 0 0 0 0 65 0 0 0 0 0 66 0 0 0 0 0 67 0 0 0 0 0 68 0 0 0 0 0 69 0 0 0 0 0 70 0 0 0 0 0 71 0 0 0 0 0 72 0 0 0 0 0 73 0 0 0 0 0 74 0 0 0 0 0 75 0 0 0 0 0 76 0 0 0 0 0 77 0 0 0 0 0 78 0 0 0 0 0 79 0 0 0 0 0 80 0 0 0 0 0 81 0 0 0 0 0 82 0 0 0 0 0 83 0 0 0 0 0 84 0 0 0 0 0 85 0 0 0 0 0 86 0 0 0 0 0 87 0 0 0 0 0 88 0 0 0 0 0 89 0 0 0 0 0 90 0 0 0 0 0 91 0 0 0 0 0 92 0 0 0 0 0 93 0 0 0 0 0 94 0 0 0 0 0 95 0 0 0 0 0 96 0 0 0 0 0 97 0 0 0 0 0 98 0 0 0 0 0 99 0 0 0 0 0 100 1 1 0 0 2 your_output.singleton.truncated000066400000000000000000000000001350370616400363610ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/defaultsadapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/interleaved/000077500000000000000000000000001350370616400306135ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/interleaved/both/000077500000000000000000000000001350370616400315475ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/interleaved/both/info.json000066400000000000000000000001101350370616400333650ustar00rootroot00000000000000{ "arguments": ["--interleaved"], "return_code": 0, "stderr": [ ] } adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/interleaved/both/input_1.fastq000066400000000000000000000007341350370616400341720ustar00rootroot00000000000000@ATAGCCSeq_1_2959_500/1 meta data TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTG + JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! @ATAGCCSeq_1_2959_500/2 data meta GTCAGCGAAGGGTTGTAGTAGCCCGTAGGGGCCTACAACGTTGGGGCCTTTGCGTAGTTGTATATAGCCTAGAATTTTTCGTTCGGTAAGCATTAGGAAT + JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! your_output.discarded000066400000000000000000000000001350370616400357400ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/interleaved/bothyour_output.paired.truncated000066400000000000000000000007341350370616400372700ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/interleaved/both@ATAGCCSeq_1_2959_500/1 meta data TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTG + JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! @ATAGCCSeq_1_2959_500/2 data meta GTCAGCGAAGGGTTGTAGTAGCCCGTAGGGGCCTACAACGTTGGGGCCTTTGCGTAGTTGTATATAGCCTAGAATTTTTCGTTCGGTAAGCATTAGGAAT + JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! your_output.settings000066400000000000000000000047251350370616400357000ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/interleaved/bothAdapterRemoval ver. 2.1.7 Trimming of paired-end reads [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 108917414 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 [Trimming statistics] Total number of read pairs: 1 Number of unaligned read pairs: 1 Number of well aligned read pairs: 0 Number of discarded mate 1 reads: 0 Number of singleton mate 1 reads: 0 Number of discarded mate 2 reads: 0 Number of singleton mate 2 reads: 0 Number of reads with adapters[1]: 0 Number of retained reads: 2 Number of retained nucleotides: 200 Average length of retained reads: 100 [Length distribution] Length Mate1 Mate2 Singleton Discarded All 0 0 0 0 0 0 1 0 0 0 0 0 2 0 0 0 0 0 3 0 0 0 0 0 4 0 0 0 0 0 5 0 0 0 0 0 6 0 0 0 0 0 7 0 0 0 0 0 8 0 0 0 0 0 9 0 0 0 0 0 10 0 0 0 0 0 11 0 0 0 0 0 12 0 0 0 0 0 13 0 0 0 0 0 14 0 0 0 0 0 15 0 0 0 0 0 16 0 0 0 0 0 17 0 0 0 0 0 18 0 0 0 0 0 19 0 0 0 0 0 20 0 0 0 0 0 21 0 0 0 0 0 22 0 0 0 0 0 23 0 0 0 0 0 24 0 0 0 0 0 25 0 0 0 0 0 26 0 0 0 0 0 27 0 0 0 0 0 28 0 0 0 0 0 29 0 0 0 0 0 30 0 0 0 0 0 31 0 0 0 0 0 32 0 0 0 0 0 33 0 0 0 0 0 34 0 0 0 0 0 35 0 0 0 0 0 36 0 0 0 0 0 37 0 0 0 0 0 38 0 0 0 0 0 39 0 0 0 0 0 40 0 0 0 0 0 41 0 0 0 0 0 42 0 0 0 0 0 43 0 0 0 0 0 44 0 0 0 0 0 45 0 0 0 0 0 46 0 0 0 0 0 47 0 0 0 0 0 48 0 0 0 0 0 49 0 0 0 0 0 50 0 0 0 0 0 51 0 0 0 0 0 52 0 0 0 0 0 53 0 0 0 0 0 54 0 0 0 0 0 55 0 0 0 0 0 56 0 0 0 0 0 57 0 0 0 0 0 58 0 0 0 0 0 59 0 0 0 0 0 60 0 0 0 0 0 61 0 0 0 0 0 62 0 0 0 0 0 63 0 0 0 0 0 64 0 0 0 0 0 65 0 0 0 0 0 66 0 0 0 0 0 67 0 0 0 0 0 68 0 0 0 0 0 69 0 0 0 0 0 70 0 0 0 0 0 71 0 0 0 0 0 72 0 0 0 0 0 73 0 0 0 0 0 74 0 0 0 0 0 75 0 0 0 0 0 76 0 0 0 0 0 77 0 0 0 0 0 78 0 0 0 0 0 79 0 0 0 0 0 80 0 0 0 0 0 81 0 0 0 0 0 82 0 0 0 0 0 83 0 0 0 0 0 84 0 0 0 0 0 85 0 0 0 0 0 86 0 0 0 0 0 87 0 0 0 0 0 88 0 0 0 0 0 89 0 0 0 0 0 90 0 0 0 0 0 91 0 0 0 0 0 92 0 0 0 0 0 93 0 0 0 0 0 94 0 0 0 0 0 95 0 0 0 0 0 96 0 0 0 0 0 97 0 0 0 0 0 98 0 0 0 0 0 99 0 0 0 0 0 100 1 1 0 0 2 your_output.singleton.truncated000066400000000000000000000000001350370616400400100ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/interleaved/bothadapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/interleaved/output/000077500000000000000000000000001350370616400321535ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/interleaved/output/info.json000066400000000000000000000001171350370616400340000ustar00rootroot00000000000000{ "arguments": ["--interleaved-output"], "return_code": 0, "stderr": [ ] } input_1.fastq000066400000000000000000000003561350370616400345170ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/interleaved/output@ATAGCCSeq_1_2959_500/1 meta data TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTG + JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! input_2.fastq000066400000000000000000000003561350370616400345200ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/interleaved/output@ATAGCCSeq_1_2959_500/2 data meta GTCAGCGAAGGGTTGTAGTAGCCCGTAGGGGCCTACAACGTTGGGGCCTTTGCGTAGTTGTATATAGCCTAGAATTTTTCGTTCGGTAAGCATTAGGAAT + JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! your_output.discarded000066400000000000000000000000001350370616400363440ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/interleaved/outputyour_output.paired.truncated000066400000000000000000000007341350370616400376740ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/interleaved/output@ATAGCCSeq_1_2959_500/1 meta data TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTG + JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! @ATAGCCSeq_1_2959_500/2 data meta GTCAGCGAAGGGTTGTAGTAGCCCGTAGGGGCCTACAACGTTGGGGCCTTTGCGTAGTTGTATATAGCCTAGAATTTTTCGTTCGGTAAGCATTAGGAAT + JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! your_output.settings000066400000000000000000000047251350370616400363040ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/interleaved/outputAdapterRemoval ver. 2.1.7 Trimming of paired-end reads [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 108917414 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 [Trimming statistics] Total number of read pairs: 1 Number of unaligned read pairs: 1 Number of well aligned read pairs: 0 Number of discarded mate 1 reads: 0 Number of singleton mate 1 reads: 0 Number of discarded mate 2 reads: 0 Number of singleton mate 2 reads: 0 Number of reads with adapters[1]: 0 Number of retained reads: 2 Number of retained nucleotides: 200 Average length of retained reads: 100 [Length distribution] Length Mate1 Mate2 Singleton Discarded All 0 0 0 0 0 0 1 0 0 0 0 0 2 0 0 0 0 0 3 0 0 0 0 0 4 0 0 0 0 0 5 0 0 0 0 0 6 0 0 0 0 0 7 0 0 0 0 0 8 0 0 0 0 0 9 0 0 0 0 0 10 0 0 0 0 0 11 0 0 0 0 0 12 0 0 0 0 0 13 0 0 0 0 0 14 0 0 0 0 0 15 0 0 0 0 0 16 0 0 0 0 0 17 0 0 0 0 0 18 0 0 0 0 0 19 0 0 0 0 0 20 0 0 0 0 0 21 0 0 0 0 0 22 0 0 0 0 0 23 0 0 0 0 0 24 0 0 0 0 0 25 0 0 0 0 0 26 0 0 0 0 0 27 0 0 0 0 0 28 0 0 0 0 0 29 0 0 0 0 0 30 0 0 0 0 0 31 0 0 0 0 0 32 0 0 0 0 0 33 0 0 0 0 0 34 0 0 0 0 0 35 0 0 0 0 0 36 0 0 0 0 0 37 0 0 0 0 0 38 0 0 0 0 0 39 0 0 0 0 0 40 0 0 0 0 0 41 0 0 0 0 0 42 0 0 0 0 0 43 0 0 0 0 0 44 0 0 0 0 0 45 0 0 0 0 0 46 0 0 0 0 0 47 0 0 0 0 0 48 0 0 0 0 0 49 0 0 0 0 0 50 0 0 0 0 0 51 0 0 0 0 0 52 0 0 0 0 0 53 0 0 0 0 0 54 0 0 0 0 0 55 0 0 0 0 0 56 0 0 0 0 0 57 0 0 0 0 0 58 0 0 0 0 0 59 0 0 0 0 0 60 0 0 0 0 0 61 0 0 0 0 0 62 0 0 0 0 0 63 0 0 0 0 0 64 0 0 0 0 0 65 0 0 0 0 0 66 0 0 0 0 0 67 0 0 0 0 0 68 0 0 0 0 0 69 0 0 0 0 0 70 0 0 0 0 0 71 0 0 0 0 0 72 0 0 0 0 0 73 0 0 0 0 0 74 0 0 0 0 0 75 0 0 0 0 0 76 0 0 0 0 0 77 0 0 0 0 0 78 0 0 0 0 0 79 0 0 0 0 0 80 0 0 0 0 0 81 0 0 0 0 0 82 0 0 0 0 0 83 0 0 0 0 0 84 0 0 0 0 0 85 0 0 0 0 0 86 0 0 0 0 0 87 0 0 0 0 0 88 0 0 0 0 0 89 0 0 0 0 0 90 0 0 0 0 0 91 0 0 0 0 0 92 0 0 0 0 0 93 0 0 0 0 0 94 0 0 0 0 0 95 0 0 0 0 0 96 0 0 0 0 0 97 0 0 0 0 0 98 0 0 0 0 0 99 0 0 0 0 0 100 1 1 0 0 2 your_output.singleton.truncated000066400000000000000000000000001350370616400404140ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/interleaved/outputadapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/maxlength/000077500000000000000000000000001350370616400303005ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/maxlength/both/000077500000000000000000000000001350370616400312345ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/maxlength/both/info.json000066400000000000000000000001301350370616400330540ustar00rootroot00000000000000{ "arguments": ["--maxlength", "99", "--trimns"], "return_code": 0, "stderr": [ ] } adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/maxlength/both/input_1.fastq000066400000000000000000000003561350370616400336570ustar00rootroot00000000000000@ATAGCCSeq_1_2959_500/1 meta data TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTG + JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/maxlength/both/input_2.fastq000066400000000000000000000003561350370616400336600ustar00rootroot00000000000000@ATAGCCSeq_1_2959_500/2 data meta GTCAGCGAAGGGTTGTAGTAGCCCGTAGGGGCCTACAACGTTGGGGCCTTTGCGTAGTTGTATATAGCCTAGAATTTTTCGTTCGGTAAGCATTAGGAAT + JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! your_output.discarded000066400000000000000000000007341350370616400354430ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/maxlength/both@ATAGCCSeq_1_2959_500/1 meta data TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTG + JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! @ATAGCCSeq_1_2959_500/2 data meta GTCAGCGAAGGGTTGTAGTAGCCCGTAGGGGCCTACAACGTTGGGGCCTTTGCGTAGTTGTATATAGCCTAGAATTTTTCGTTCGGTAAGCATTAGGAAT + JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! your_output.pair1.truncated000066400000000000000000000000001350370616400365070ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/maxlength/bothyour_output.pair2.truncated000066400000000000000000000000001350370616400365100ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/maxlength/bothyour_output.settings000066400000000000000000000047131350370616400353620ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/maxlength/bothAdapterRemoval ver. 2.1.7 Trimming of paired-end reads [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 2294078498 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: Yes Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 99 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 [Trimming statistics] Total number of read pairs: 1 Number of unaligned read pairs: 1 Number of well aligned read pairs: 0 Number of discarded mate 1 reads: 1 Number of singleton mate 1 reads: 0 Number of discarded mate 2 reads: 1 Number of singleton mate 2 reads: 0 Number of reads with adapters[1]: 0 Number of retained reads: 0 Number of retained nucleotides: 0 Average length of retained reads: 0 [Length distribution] Length Mate1 Mate2 Singleton Discarded All 0 0 0 0 0 0 1 0 0 0 0 0 2 0 0 0 0 0 3 0 0 0 0 0 4 0 0 0 0 0 5 0 0 0 0 0 6 0 0 0 0 0 7 0 0 0 0 0 8 0 0 0 0 0 9 0 0 0 0 0 10 0 0 0 0 0 11 0 0 0 0 0 12 0 0 0 0 0 13 0 0 0 0 0 14 0 0 0 0 0 15 0 0 0 0 0 16 0 0 0 0 0 17 0 0 0 0 0 18 0 0 0 0 0 19 0 0 0 0 0 20 0 0 0 0 0 21 0 0 0 0 0 22 0 0 0 0 0 23 0 0 0 0 0 24 0 0 0 0 0 25 0 0 0 0 0 26 0 0 0 0 0 27 0 0 0 0 0 28 0 0 0 0 0 29 0 0 0 0 0 30 0 0 0 0 0 31 0 0 0 0 0 32 0 0 0 0 0 33 0 0 0 0 0 34 0 0 0 0 0 35 0 0 0 0 0 36 0 0 0 0 0 37 0 0 0 0 0 38 0 0 0 0 0 39 0 0 0 0 0 40 0 0 0 0 0 41 0 0 0 0 0 42 0 0 0 0 0 43 0 0 0 0 0 44 0 0 0 0 0 45 0 0 0 0 0 46 0 0 0 0 0 47 0 0 0 0 0 48 0 0 0 0 0 49 0 0 0 0 0 50 0 0 0 0 0 51 0 0 0 0 0 52 0 0 0 0 0 53 0 0 0 0 0 54 0 0 0 0 0 55 0 0 0 0 0 56 0 0 0 0 0 57 0 0 0 0 0 58 0 0 0 0 0 59 0 0 0 0 0 60 0 0 0 0 0 61 0 0 0 0 0 62 0 0 0 0 0 63 0 0 0 0 0 64 0 0 0 0 0 65 0 0 0 0 0 66 0 0 0 0 0 67 0 0 0 0 0 68 0 0 0 0 0 69 0 0 0 0 0 70 0 0 0 0 0 71 0 0 0 0 0 72 0 0 0 0 0 73 0 0 0 0 0 74 0 0 0 0 0 75 0 0 0 0 0 76 0 0 0 0 0 77 0 0 0 0 0 78 0 0 0 0 0 79 0 0 0 0 0 80 0 0 0 0 0 81 0 0 0 0 0 82 0 0 0 0 0 83 0 0 0 0 0 84 0 0 0 0 0 85 0 0 0 0 0 86 0 0 0 0 0 87 0 0 0 0 0 88 0 0 0 0 0 89 0 0 0 0 0 90 0 0 0 0 0 91 0 0 0 0 0 92 0 0 0 0 0 93 0 0 0 0 0 94 0 0 0 0 0 95 0 0 0 0 0 96 0 0 0 0 0 97 0 0 0 0 0 98 0 0 0 0 0 99 0 0 0 0 0 100 0 0 0 2 2 your_output.singleton.truncated000066400000000000000000000000001350370616400374750ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/maxlength/bothadapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/maxlength/mate1/000077500000000000000000000000001350370616400313075ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/maxlength/mate1/info.json000066400000000000000000000001301350370616400331270ustar00rootroot00000000000000{ "arguments": ["--maxlength", "99", "--trimns"], "return_code": 0, "stderr": [ ] } adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/maxlength/mate1/input_1.fastq000066400000000000000000000003561350370616400337320ustar00rootroot00000000000000@ATAGCCSeq_1_2959_500/1 meta data TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTG + JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/maxlength/mate1/input_2.fastq000066400000000000000000000003541350370616400337310ustar00rootroot00000000000000@ATAGCCSeq_1_2959_500/2 data meta GTCAGCGAAGGGTTGTAGTAGCCCGTAGGGGCCTACAACGTTGGGGCCTTTGCGTAGTTGTATATAGCCTAGAATTTTTCGTTCGGTAAGCATTAGGAA + JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*& your_output.discarded000066400000000000000000000003561350370616400355160ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/maxlength/mate1@ATAGCCSeq_1_2959_500/1 meta data TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTG + JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! your_output.pair1.truncated000066400000000000000000000000001350370616400365620ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/maxlength/mate1your_output.pair2.truncated000066400000000000000000000000001350370616400365630ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/maxlength/mate1your_output.settings000066400000000000000000000047151350370616400354370ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/maxlength/mate1AdapterRemoval ver. 2.1.7 Trimming of paired-end reads [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 2378184469 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: Yes Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 99 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 [Trimming statistics] Total number of read pairs: 1 Number of unaligned read pairs: 1 Number of well aligned read pairs: 0 Number of discarded mate 1 reads: 1 Number of singleton mate 1 reads: 0 Number of discarded mate 2 reads: 0 Number of singleton mate 2 reads: 1 Number of reads with adapters[1]: 0 Number of retained reads: 1 Number of retained nucleotides: 99 Average length of retained reads: 99 [Length distribution] Length Mate1 Mate2 Singleton Discarded All 0 0 0 0 0 0 1 0 0 0 0 0 2 0 0 0 0 0 3 0 0 0 0 0 4 0 0 0 0 0 5 0 0 0 0 0 6 0 0 0 0 0 7 0 0 0 0 0 8 0 0 0 0 0 9 0 0 0 0 0 10 0 0 0 0 0 11 0 0 0 0 0 12 0 0 0 0 0 13 0 0 0 0 0 14 0 0 0 0 0 15 0 0 0 0 0 16 0 0 0 0 0 17 0 0 0 0 0 18 0 0 0 0 0 19 0 0 0 0 0 20 0 0 0 0 0 21 0 0 0 0 0 22 0 0 0 0 0 23 0 0 0 0 0 24 0 0 0 0 0 25 0 0 0 0 0 26 0 0 0 0 0 27 0 0 0 0 0 28 0 0 0 0 0 29 0 0 0 0 0 30 0 0 0 0 0 31 0 0 0 0 0 32 0 0 0 0 0 33 0 0 0 0 0 34 0 0 0 0 0 35 0 0 0 0 0 36 0 0 0 0 0 37 0 0 0 0 0 38 0 0 0 0 0 39 0 0 0 0 0 40 0 0 0 0 0 41 0 0 0 0 0 42 0 0 0 0 0 43 0 0 0 0 0 44 0 0 0 0 0 45 0 0 0 0 0 46 0 0 0 0 0 47 0 0 0 0 0 48 0 0 0 0 0 49 0 0 0 0 0 50 0 0 0 0 0 51 0 0 0 0 0 52 0 0 0 0 0 53 0 0 0 0 0 54 0 0 0 0 0 55 0 0 0 0 0 56 0 0 0 0 0 57 0 0 0 0 0 58 0 0 0 0 0 59 0 0 0 0 0 60 0 0 0 0 0 61 0 0 0 0 0 62 0 0 0 0 0 63 0 0 0 0 0 64 0 0 0 0 0 65 0 0 0 0 0 66 0 0 0 0 0 67 0 0 0 0 0 68 0 0 0 0 0 69 0 0 0 0 0 70 0 0 0 0 0 71 0 0 0 0 0 72 0 0 0 0 0 73 0 0 0 0 0 74 0 0 0 0 0 75 0 0 0 0 0 76 0 0 0 0 0 77 0 0 0 0 0 78 0 0 0 0 0 79 0 0 0 0 0 80 0 0 0 0 0 81 0 0 0 0 0 82 0 0 0 0 0 83 0 0 0 0 0 84 0 0 0 0 0 85 0 0 0 0 0 86 0 0 0 0 0 87 0 0 0 0 0 88 0 0 0 0 0 89 0 0 0 0 0 90 0 0 0 0 0 91 0 0 0 0 0 92 0 0 0 0 0 93 0 0 0 0 0 94 0 0 0 0 0 95 0 0 0 0 0 96 0 0 0 0 0 97 0 0 0 0 0 98 0 0 0 0 0 99 0 0 1 0 1 100 0 0 0 1 1 your_output.singleton.truncated000066400000000000000000000003541350370616400375640ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/maxlength/mate1@ATAGCCSeq_1_2959_500/2 data meta GTCAGCGAAGGGTTGTAGTAGCCCGTAGGGGCCTACAACGTTGGGGCCTTTGCGTAGTTGTATATAGCCTAGAATTTTTCGTTCGGTAAGCATTAGGAA + JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*& adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/maxlength/mate2/000077500000000000000000000000001350370616400313105ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/maxlength/mate2/info.json000066400000000000000000000001301350370616400331300ustar00rootroot00000000000000{ "arguments": ["--maxlength", "99", "--trimns"], "return_code": 0, "stderr": [ ] } adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/maxlength/mate2/input_1.fastq000066400000000000000000000003541350370616400337310ustar00rootroot00000000000000@ATAGCCSeq_1_2959_500/1 meta data TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCT + JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)' adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/maxlength/mate2/input_2.fastq000066400000000000000000000003561350370616400337340ustar00rootroot00000000000000@ATAGCCSeq_1_2959_500/2 data meta GTCAGCGAAGGGTTGTAGTAGCCCGTAGGGGCCTACAACGTTGGGGCCTTTGCGTAGTTGTATATAGCCTAGAATTTTTCGTTCGGTAAGCATTAGGAAT + JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! your_output.discarded000066400000000000000000000003561350370616400355170ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/maxlength/mate2@ATAGCCSeq_1_2959_500/2 data meta GTCAGCGAAGGGTTGTAGTAGCCCGTAGGGGCCTACAACGTTGGGGCCTTTGCGTAGTTGTATATAGCCTAGAATTTTTCGTTCGGTAAGCATTAGGAAT + JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! your_output.pair1.truncated000066400000000000000000000000001350370616400365630ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/maxlength/mate2your_output.pair2.truncated000066400000000000000000000000001350370616400365640ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/maxlength/mate2your_output.settings000066400000000000000000000047151350370616400354400ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/maxlength/mate2AdapterRemoval ver. 2.1.7 Trimming of paired-end reads [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 2394981856 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: Yes Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 99 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 [Trimming statistics] Total number of read pairs: 1 Number of unaligned read pairs: 0 Number of well aligned read pairs: 1 Number of discarded mate 1 reads: 0 Number of singleton mate 1 reads: 1 Number of discarded mate 2 reads: 1 Number of singleton mate 2 reads: 0 Number of reads with adapters[1]: 0 Number of retained reads: 1 Number of retained nucleotides: 99 Average length of retained reads: 99 [Length distribution] Length Mate1 Mate2 Singleton Discarded All 0 0 0 0 0 0 1 0 0 0 0 0 2 0 0 0 0 0 3 0 0 0 0 0 4 0 0 0 0 0 5 0 0 0 0 0 6 0 0 0 0 0 7 0 0 0 0 0 8 0 0 0 0 0 9 0 0 0 0 0 10 0 0 0 0 0 11 0 0 0 0 0 12 0 0 0 0 0 13 0 0 0 0 0 14 0 0 0 0 0 15 0 0 0 0 0 16 0 0 0 0 0 17 0 0 0 0 0 18 0 0 0 0 0 19 0 0 0 0 0 20 0 0 0 0 0 21 0 0 0 0 0 22 0 0 0 0 0 23 0 0 0 0 0 24 0 0 0 0 0 25 0 0 0 0 0 26 0 0 0 0 0 27 0 0 0 0 0 28 0 0 0 0 0 29 0 0 0 0 0 30 0 0 0 0 0 31 0 0 0 0 0 32 0 0 0 0 0 33 0 0 0 0 0 34 0 0 0 0 0 35 0 0 0 0 0 36 0 0 0 0 0 37 0 0 0 0 0 38 0 0 0 0 0 39 0 0 0 0 0 40 0 0 0 0 0 41 0 0 0 0 0 42 0 0 0 0 0 43 0 0 0 0 0 44 0 0 0 0 0 45 0 0 0 0 0 46 0 0 0 0 0 47 0 0 0 0 0 48 0 0 0 0 0 49 0 0 0 0 0 50 0 0 0 0 0 51 0 0 0 0 0 52 0 0 0 0 0 53 0 0 0 0 0 54 0 0 0 0 0 55 0 0 0 0 0 56 0 0 0 0 0 57 0 0 0 0 0 58 0 0 0 0 0 59 0 0 0 0 0 60 0 0 0 0 0 61 0 0 0 0 0 62 0 0 0 0 0 63 0 0 0 0 0 64 0 0 0 0 0 65 0 0 0 0 0 66 0 0 0 0 0 67 0 0 0 0 0 68 0 0 0 0 0 69 0 0 0 0 0 70 0 0 0 0 0 71 0 0 0 0 0 72 0 0 0 0 0 73 0 0 0 0 0 74 0 0 0 0 0 75 0 0 0 0 0 76 0 0 0 0 0 77 0 0 0 0 0 78 0 0 0 0 0 79 0 0 0 0 0 80 0 0 0 0 0 81 0 0 0 0 0 82 0 0 0 0 0 83 0 0 0 0 0 84 0 0 0 0 0 85 0 0 0 0 0 86 0 0 0 0 0 87 0 0 0 0 0 88 0 0 0 0 0 89 0 0 0 0 0 90 0 0 0 0 0 91 0 0 0 0 0 92 0 0 0 0 0 93 0 0 0 0 0 94 0 0 0 0 0 95 0 0 0 0 0 96 0 0 0 0 0 97 0 0 0 0 0 98 0 0 0 0 0 99 0 0 1 0 1 100 0 0 0 1 1 your_output.singleton.truncated000066400000000000000000000003541350370616400375650ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/maxlength/mate2@ATAGCCSeq_1_2959_500/1 meta data TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCT + JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)' adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/minlength/000077500000000000000000000000001350370616400302765ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/minlength/both/000077500000000000000000000000001350370616400312325ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/minlength/both/info.json000066400000000000000000000001301350370616400330520ustar00rootroot00000000000000{ "arguments": ["--minlength", "50", "--trimns"], "return_code": 0, "stderr": [ ] } adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/minlength/both/input_1.fastq000066400000000000000000000003561350370616400336550ustar00rootroot00000000000000@ATAGCCSeq_1_2959_500/1 meta data TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN + JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/minlength/both/input_2.fastq000066400000000000000000000003561350370616400336560ustar00rootroot00000000000000@ATAGCCSeq_1_2959_500/2 data meta GTCAGCGAAGGGTTGTAGTAGCCCGTAGGGGCCTACNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN + JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! your_output.discarded000066400000000000000000000003521350370616400354350ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/minlength/both@ATAGCCSeq_1_2959_500/1 meta data TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGG + JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEE @ATAGCCSeq_1_2959_500/2 data meta GTCAGCGAAGGGTTGTAGTAGCCCGTAGGGGCCTAC + JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEF your_output.pair1.truncated000066400000000000000000000000001350370616400365050ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/minlength/bothyour_output.pair2.truncated000066400000000000000000000000001350370616400365060ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/minlength/bothyour_output.settings000066400000000000000000000033551350370616400353610ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/minlength/bothAdapterRemoval ver. 2.1.7 Trimming of paired-end reads [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 2027572855 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: Yes Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 50 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 [Trimming statistics] Total number of read pairs: 1 Number of unaligned read pairs: 1 Number of well aligned read pairs: 0 Number of discarded mate 1 reads: 1 Number of singleton mate 1 reads: 0 Number of discarded mate 2 reads: 1 Number of singleton mate 2 reads: 0 Number of reads with adapters[1]: 0 Number of retained reads: 0 Number of retained nucleotides: 0 Average length of retained reads: 0 [Length distribution] Length Mate1 Mate2 Singleton Discarded All 0 0 0 0 0 0 1 0 0 0 0 0 2 0 0 0 0 0 3 0 0 0 0 0 4 0 0 0 0 0 5 0 0 0 0 0 6 0 0 0 0 0 7 0 0 0 0 0 8 0 0 0 0 0 9 0 0 0 0 0 10 0 0 0 0 0 11 0 0 0 0 0 12 0 0 0 0 0 13 0 0 0 0 0 14 0 0 0 0 0 15 0 0 0 0 0 16 0 0 0 0 0 17 0 0 0 0 0 18 0 0 0 0 0 19 0 0 0 0 0 20 0 0 0 0 0 21 0 0 0 0 0 22 0 0 0 0 0 23 0 0 0 0 0 24 0 0 0 0 0 25 0 0 0 0 0 26 0 0 0 0 0 27 0 0 0 0 0 28 0 0 0 0 0 29 0 0 0 0 0 30 0 0 0 0 0 31 0 0 0 0 0 32 0 0 0 0 0 33 0 0 0 0 0 34 0 0 0 0 0 35 0 0 0 0 0 36 0 0 0 1 1 37 0 0 0 0 0 38 0 0 0 0 0 39 0 0 0 0 0 40 0 0 0 0 0 41 0 0 0 0 0 42 0 0 0 0 0 43 0 0 0 1 1 your_output.singleton.truncated000066400000000000000000000000001350370616400374730ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/minlength/bothadapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/minlength/mate1/000077500000000000000000000000001350370616400313055ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/minlength/mate1/info.json000066400000000000000000000001301350370616400331250ustar00rootroot00000000000000{ "arguments": ["--minlength", "50", "--trimns"], "return_code": 0, "stderr": [ ] } adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/minlength/mate1/input_1.fastq000066400000000000000000000003561350370616400337300ustar00rootroot00000000000000@ATAGCCSeq_1_2959_500/1 meta data TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN + JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/minlength/mate1/input_2.fastq000066400000000000000000000003561350370616400337310ustar00rootroot00000000000000@ATAGCCSeq_1_2959_500/2 data meta GTCAGCGAAGGGTTGTAGTAGCCCGTAGGGGCCTACAACGTTGGGGCCTTTGCGTAGTTGTATATAGCCTAGAATTTTTCGTTCGGTAAGCATTAGGAAT + JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! your_output.discarded000066400000000000000000000001741350370616400355120ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/minlength/mate1@ATAGCCSeq_1_2959_500/1 meta data TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGG + JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEE your_output.pair1.truncated000066400000000000000000000000001350370616400365600ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/minlength/mate1your_output.pair2.truncated000066400000000000000000000000001350370616400365610ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/minlength/mate1your_output.settings000066400000000000000000000047271350370616400354400ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/minlength/mate1AdapterRemoval ver. 2.1.7 Trimming of paired-end reads [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 2010319782 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: Yes Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 50 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 [Trimming statistics] Total number of read pairs: 1 Number of unaligned read pairs: 1 Number of well aligned read pairs: 0 Number of discarded mate 1 reads: 1 Number of singleton mate 1 reads: 0 Number of discarded mate 2 reads: 0 Number of singleton mate 2 reads: 1 Number of reads with adapters[1]: 0 Number of retained reads: 1 Number of retained nucleotides: 100 Average length of retained reads: 100 [Length distribution] Length Mate1 Mate2 Singleton Discarded All 0 0 0 0 0 0 1 0 0 0 0 0 2 0 0 0 0 0 3 0 0 0 0 0 4 0 0 0 0 0 5 0 0 0 0 0 6 0 0 0 0 0 7 0 0 0 0 0 8 0 0 0 0 0 9 0 0 0 0 0 10 0 0 0 0 0 11 0 0 0 0 0 12 0 0 0 0 0 13 0 0 0 0 0 14 0 0 0 0 0 15 0 0 0 0 0 16 0 0 0 0 0 17 0 0 0 0 0 18 0 0 0 0 0 19 0 0 0 0 0 20 0 0 0 0 0 21 0 0 0 0 0 22 0 0 0 0 0 23 0 0 0 0 0 24 0 0 0 0 0 25 0 0 0 0 0 26 0 0 0 0 0 27 0 0 0 0 0 28 0 0 0 0 0 29 0 0 0 0 0 30 0 0 0 0 0 31 0 0 0 0 0 32 0 0 0 0 0 33 0 0 0 0 0 34 0 0 0 0 0 35 0 0 0 0 0 36 0 0 0 0 0 37 0 0 0 0 0 38 0 0 0 0 0 39 0 0 0 0 0 40 0 0 0 0 0 41 0 0 0 0 0 42 0 0 0 0 0 43 0 0 0 1 1 44 0 0 0 0 0 45 0 0 0 0 0 46 0 0 0 0 0 47 0 0 0 0 0 48 0 0 0 0 0 49 0 0 0 0 0 50 0 0 0 0 0 51 0 0 0 0 0 52 0 0 0 0 0 53 0 0 0 0 0 54 0 0 0 0 0 55 0 0 0 0 0 56 0 0 0 0 0 57 0 0 0 0 0 58 0 0 0 0 0 59 0 0 0 0 0 60 0 0 0 0 0 61 0 0 0 0 0 62 0 0 0 0 0 63 0 0 0 0 0 64 0 0 0 0 0 65 0 0 0 0 0 66 0 0 0 0 0 67 0 0 0 0 0 68 0 0 0 0 0 69 0 0 0 0 0 70 0 0 0 0 0 71 0 0 0 0 0 72 0 0 0 0 0 73 0 0 0 0 0 74 0 0 0 0 0 75 0 0 0 0 0 76 0 0 0 0 0 77 0 0 0 0 0 78 0 0 0 0 0 79 0 0 0 0 0 80 0 0 0 0 0 81 0 0 0 0 0 82 0 0 0 0 0 83 0 0 0 0 0 84 0 0 0 0 0 85 0 0 0 0 0 86 0 0 0 0 0 87 0 0 0 0 0 88 0 0 0 0 0 89 0 0 0 0 0 90 0 0 0 0 0 91 0 0 0 0 0 92 0 0 0 0 0 93 0 0 0 0 0 94 0 0 0 0 0 95 0 0 0 0 0 96 0 0 0 0 0 97 0 0 0 0 0 98 0 0 0 0 0 99 0 0 0 0 0 100 0 0 1 0 1 your_output.singleton.truncated000066400000000000000000000003561350370616400375640ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/minlength/mate1@ATAGCCSeq_1_2959_500/2 data meta GTCAGCGAAGGGTTGTAGTAGCCCGTAGGGGCCTACAACGTTGGGGCCTTTGCGTAGTTGTATATAGCCTAGAATTTTTCGTTCGGTAAGCATTAGGAAT + JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/minlength/mate2/000077500000000000000000000000001350370616400313065ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/minlength/mate2/info.json000066400000000000000000000001301350370616400331260ustar00rootroot00000000000000{ "arguments": ["--minlength", "50", "--trimns"], "return_code": 0, "stderr": [ ] } adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/minlength/mate2/input_1.fastq000066400000000000000000000003561350370616400337310ustar00rootroot00000000000000@ATAGCCSeq_1_2959_500/1 meta data TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTG + JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/minlength/mate2/input_2.fastq000066400000000000000000000003561350370616400337320ustar00rootroot00000000000000@ATAGCCSeq_1_2959_500/2 data meta GTCAGCGAAGGGTTGTAGTAGCCCGTAGGGGCCTACNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN + JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! your_output.discarded000066400000000000000000000001561350370616400355130ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/minlength/mate2@ATAGCCSeq_1_2959_500/2 data meta GTCAGCGAAGGGTTGTAGTAGCCCGTAGGGGCCTAC + JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEF your_output.pair1.truncated000066400000000000000000000000001350370616400365610ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/minlength/mate2your_output.pair2.truncated000066400000000000000000000000001350370616400365620ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/minlength/mate2your_output.settings000066400000000000000000000047271350370616400354410ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/minlength/mate2AdapterRemoval ver. 2.1.7 Trimming of paired-end reads [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 2024298981 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: Yes Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 50 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 [Trimming statistics] Total number of read pairs: 1 Number of unaligned read pairs: 0 Number of well aligned read pairs: 1 Number of discarded mate 1 reads: 0 Number of singleton mate 1 reads: 1 Number of discarded mate 2 reads: 1 Number of singleton mate 2 reads: 0 Number of reads with adapters[1]: 0 Number of retained reads: 1 Number of retained nucleotides: 100 Average length of retained reads: 100 [Length distribution] Length Mate1 Mate2 Singleton Discarded All 0 0 0 0 0 0 1 0 0 0 0 0 2 0 0 0 0 0 3 0 0 0 0 0 4 0 0 0 0 0 5 0 0 0 0 0 6 0 0 0 0 0 7 0 0 0 0 0 8 0 0 0 0 0 9 0 0 0 0 0 10 0 0 0 0 0 11 0 0 0 0 0 12 0 0 0 0 0 13 0 0 0 0 0 14 0 0 0 0 0 15 0 0 0 0 0 16 0 0 0 0 0 17 0 0 0 0 0 18 0 0 0 0 0 19 0 0 0 0 0 20 0 0 0 0 0 21 0 0 0 0 0 22 0 0 0 0 0 23 0 0 0 0 0 24 0 0 0 0 0 25 0 0 0 0 0 26 0 0 0 0 0 27 0 0 0 0 0 28 0 0 0 0 0 29 0 0 0 0 0 30 0 0 0 0 0 31 0 0 0 0 0 32 0 0 0 0 0 33 0 0 0 0 0 34 0 0 0 0 0 35 0 0 0 0 0 36 0 0 0 1 1 37 0 0 0 0 0 38 0 0 0 0 0 39 0 0 0 0 0 40 0 0 0 0 0 41 0 0 0 0 0 42 0 0 0 0 0 43 0 0 0 0 0 44 0 0 0 0 0 45 0 0 0 0 0 46 0 0 0 0 0 47 0 0 0 0 0 48 0 0 0 0 0 49 0 0 0 0 0 50 0 0 0 0 0 51 0 0 0 0 0 52 0 0 0 0 0 53 0 0 0 0 0 54 0 0 0 0 0 55 0 0 0 0 0 56 0 0 0 0 0 57 0 0 0 0 0 58 0 0 0 0 0 59 0 0 0 0 0 60 0 0 0 0 0 61 0 0 0 0 0 62 0 0 0 0 0 63 0 0 0 0 0 64 0 0 0 0 0 65 0 0 0 0 0 66 0 0 0 0 0 67 0 0 0 0 0 68 0 0 0 0 0 69 0 0 0 0 0 70 0 0 0 0 0 71 0 0 0 0 0 72 0 0 0 0 0 73 0 0 0 0 0 74 0 0 0 0 0 75 0 0 0 0 0 76 0 0 0 0 0 77 0 0 0 0 0 78 0 0 0 0 0 79 0 0 0 0 0 80 0 0 0 0 0 81 0 0 0 0 0 82 0 0 0 0 0 83 0 0 0 0 0 84 0 0 0 0 0 85 0 0 0 0 0 86 0 0 0 0 0 87 0 0 0 0 0 88 0 0 0 0 0 89 0 0 0 0 0 90 0 0 0 0 0 91 0 0 0 0 0 92 0 0 0 0 0 93 0 0 0 0 0 94 0 0 0 0 0 95 0 0 0 0 0 96 0 0 0 0 0 97 0 0 0 0 0 98 0 0 0 0 0 99 0 0 0 0 0 100 0 0 1 0 1 your_output.singleton.truncated000066400000000000000000000003561350370616400375650ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/minlength/mate2@ATAGCCSeq_1_2959_500/1 meta data TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTG + JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/trimns/000077500000000000000000000000001350370616400276255ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/trimns/excl_ns/000077500000000000000000000000001350370616400312605ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/trimns/excl_ns/info.json000066400000000000000000000001031350370616400331000ustar00rootroot00000000000000{ "arguments": ["--trimns"], "return_code": 0, "stderr": [ ] } adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/trimns/excl_ns/input_1.fastq000066400000000000000000000003561350370616400337030ustar00rootroot00000000000000@ATAGCCSeq_1_2959_500/1 meta data TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTG + JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/trimns/excl_ns/input_2.fastq000066400000000000000000000003561350370616400337040ustar00rootroot00000000000000@ATAGCCSeq_1_2959_500/2 data meta GTCAGCGAAGGGTTGTAGTAGCCCGTAGGGGCCTACAACGTTGGGGCCTTTGCGTAGTTGTATATAGCCTAGAATTTTTCGTTCGGTAAGCATTAGGAAT + JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! your_output.discarded000066400000000000000000000000001350370616400354510ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/trimns/excl_nsyour_output.pair1.truncated000066400000000000000000000003561350370616400365510ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/trimns/excl_ns@ATAGCCSeq_1_2959_500/1 meta data TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTG + JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! your_output.pair2.truncated000066400000000000000000000003561350370616400365520ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/trimns/excl_ns@ATAGCCSeq_1_2959_500/2 data meta GTCAGCGAAGGGTTGTAGTAGCCCGTAGGGGCCTACAACGTTGGGGCCTTTGCGTAGTTGTATATAGCCTAGAATTTTTCGTTCGGTAAGCATTAGGAAT + JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! your_output.settings000066400000000000000000000047261350370616400354120ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/trimns/excl_nsAdapterRemoval ver. 2.1.7 Trimming of paired-end reads [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 981230521 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: Yes Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 [Trimming statistics] Total number of read pairs: 1 Number of unaligned read pairs: 1 Number of well aligned read pairs: 0 Number of discarded mate 1 reads: 0 Number of singleton mate 1 reads: 0 Number of discarded mate 2 reads: 0 Number of singleton mate 2 reads: 0 Number of reads with adapters[1]: 0 Number of retained reads: 2 Number of retained nucleotides: 200 Average length of retained reads: 100 [Length distribution] Length Mate1 Mate2 Singleton Discarded All 0 0 0 0 0 0 1 0 0 0 0 0 2 0 0 0 0 0 3 0 0 0 0 0 4 0 0 0 0 0 5 0 0 0 0 0 6 0 0 0 0 0 7 0 0 0 0 0 8 0 0 0 0 0 9 0 0 0 0 0 10 0 0 0 0 0 11 0 0 0 0 0 12 0 0 0 0 0 13 0 0 0 0 0 14 0 0 0 0 0 15 0 0 0 0 0 16 0 0 0 0 0 17 0 0 0 0 0 18 0 0 0 0 0 19 0 0 0 0 0 20 0 0 0 0 0 21 0 0 0 0 0 22 0 0 0 0 0 23 0 0 0 0 0 24 0 0 0 0 0 25 0 0 0 0 0 26 0 0 0 0 0 27 0 0 0 0 0 28 0 0 0 0 0 29 0 0 0 0 0 30 0 0 0 0 0 31 0 0 0 0 0 32 0 0 0 0 0 33 0 0 0 0 0 34 0 0 0 0 0 35 0 0 0 0 0 36 0 0 0 0 0 37 0 0 0 0 0 38 0 0 0 0 0 39 0 0 0 0 0 40 0 0 0 0 0 41 0 0 0 0 0 42 0 0 0 0 0 43 0 0 0 0 0 44 0 0 0 0 0 45 0 0 0 0 0 46 0 0 0 0 0 47 0 0 0 0 0 48 0 0 0 0 0 49 0 0 0 0 0 50 0 0 0 0 0 51 0 0 0 0 0 52 0 0 0 0 0 53 0 0 0 0 0 54 0 0 0 0 0 55 0 0 0 0 0 56 0 0 0 0 0 57 0 0 0 0 0 58 0 0 0 0 0 59 0 0 0 0 0 60 0 0 0 0 0 61 0 0 0 0 0 62 0 0 0 0 0 63 0 0 0 0 0 64 0 0 0 0 0 65 0 0 0 0 0 66 0 0 0 0 0 67 0 0 0 0 0 68 0 0 0 0 0 69 0 0 0 0 0 70 0 0 0 0 0 71 0 0 0 0 0 72 0 0 0 0 0 73 0 0 0 0 0 74 0 0 0 0 0 75 0 0 0 0 0 76 0 0 0 0 0 77 0 0 0 0 0 78 0 0 0 0 0 79 0 0 0 0 0 80 0 0 0 0 0 81 0 0 0 0 0 82 0 0 0 0 0 83 0 0 0 0 0 84 0 0 0 0 0 85 0 0 0 0 0 86 0 0 0 0 0 87 0 0 0 0 0 88 0 0 0 0 0 89 0 0 0 0 0 90 0 0 0 0 0 91 0 0 0 0 0 92 0 0 0 0 0 93 0 0 0 0 0 94 0 0 0 0 0 95 0 0 0 0 0 96 0 0 0 0 0 97 0 0 0 0 0 98 0 0 0 0 0 99 0 0 0 0 0 100 1 1 0 0 2 your_output.singleton.truncated000066400000000000000000000000001350370616400375210ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/trimns/excl_nsadapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/trimns/incl_ns/000077500000000000000000000000001350370616400312525ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/trimns/incl_ns/info.json000066400000000000000000000001031350370616400330720ustar00rootroot00000000000000{ "arguments": ["--trimns"], "return_code": 0, "stderr": [ ] } adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/trimns/incl_ns/input_1.fastq000066400000000000000000000003561350370616400336750ustar00rootroot00000000000000@ATAGCCSeq_1_2959_500/1 meta data TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCATN + JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/trimns/incl_ns/input_2.fastq000066400000000000000000000003561350370616400336760ustar00rootroot00000000000000@ATAGCCSeq_1_2959_500/2 data meta GTCAGCGAAGGGTTGTAGTAGCCCGTAGGGGCCTACAACGTTGGGGCCTTTGCGTAGTTGTATATAGCCTAGAATTTTTCGTTCGGTAAGCATTAGGNNN + JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! your_output.discarded000066400000000000000000000000001350370616400354430ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/trimns/incl_nsyour_output.pair1.truncated000066400000000000000000000003541350370616400365410ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/trimns/incl_ns@ATAGCCSeq_1_2959_500/1 meta data TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCAT + JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)' your_output.pair2.truncated000066400000000000000000000003501350370616400365360ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/trimns/incl_ns@ATAGCCSeq_1_2959_500/2 data meta GTCAGCGAAGGGTTGTAGTAGCCCGTAGGGGCCTACAACGTTGGGGCCTTTGCGTAGTTGTATATAGCCTAGAATTTTTCGTTCGGTAAGCATTAGG + JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220. your_output.settings000066400000000000000000000047071350370616400354030ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/trimns/incl_nsAdapterRemoval ver. 2.1.7 Trimming of paired-end reads [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 981230521 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: Yes Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 [Trimming statistics] Total number of read pairs: 1 Number of unaligned read pairs: 1 Number of well aligned read pairs: 0 Number of discarded mate 1 reads: 0 Number of singleton mate 1 reads: 0 Number of discarded mate 2 reads: 0 Number of singleton mate 2 reads: 0 Number of reads with adapters[1]: 0 Number of retained reads: 2 Number of retained nucleotides: 196 Average length of retained reads: 98 [Length distribution] Length Mate1 Mate2 Singleton Discarded All 0 0 0 0 0 0 1 0 0 0 0 0 2 0 0 0 0 0 3 0 0 0 0 0 4 0 0 0 0 0 5 0 0 0 0 0 6 0 0 0 0 0 7 0 0 0 0 0 8 0 0 0 0 0 9 0 0 0 0 0 10 0 0 0 0 0 11 0 0 0 0 0 12 0 0 0 0 0 13 0 0 0 0 0 14 0 0 0 0 0 15 0 0 0 0 0 16 0 0 0 0 0 17 0 0 0 0 0 18 0 0 0 0 0 19 0 0 0 0 0 20 0 0 0 0 0 21 0 0 0 0 0 22 0 0 0 0 0 23 0 0 0 0 0 24 0 0 0 0 0 25 0 0 0 0 0 26 0 0 0 0 0 27 0 0 0 0 0 28 0 0 0 0 0 29 0 0 0 0 0 30 0 0 0 0 0 31 0 0 0 0 0 32 0 0 0 0 0 33 0 0 0 0 0 34 0 0 0 0 0 35 0 0 0 0 0 36 0 0 0 0 0 37 0 0 0 0 0 38 0 0 0 0 0 39 0 0 0 0 0 40 0 0 0 0 0 41 0 0 0 0 0 42 0 0 0 0 0 43 0 0 0 0 0 44 0 0 0 0 0 45 0 0 0 0 0 46 0 0 0 0 0 47 0 0 0 0 0 48 0 0 0 0 0 49 0 0 0 0 0 50 0 0 0 0 0 51 0 0 0 0 0 52 0 0 0 0 0 53 0 0 0 0 0 54 0 0 0 0 0 55 0 0 0 0 0 56 0 0 0 0 0 57 0 0 0 0 0 58 0 0 0 0 0 59 0 0 0 0 0 60 0 0 0 0 0 61 0 0 0 0 0 62 0 0 0 0 0 63 0 0 0 0 0 64 0 0 0 0 0 65 0 0 0 0 0 66 0 0 0 0 0 67 0 0 0 0 0 68 0 0 0 0 0 69 0 0 0 0 0 70 0 0 0 0 0 71 0 0 0 0 0 72 0 0 0 0 0 73 0 0 0 0 0 74 0 0 0 0 0 75 0 0 0 0 0 76 0 0 0 0 0 77 0 0 0 0 0 78 0 0 0 0 0 79 0 0 0 0 0 80 0 0 0 0 0 81 0 0 0 0 0 82 0 0 0 0 0 83 0 0 0 0 0 84 0 0 0 0 0 85 0 0 0 0 0 86 0 0 0 0 0 87 0 0 0 0 0 88 0 0 0 0 0 89 0 0 0 0 0 90 0 0 0 0 0 91 0 0 0 0 0 92 0 0 0 0 0 93 0 0 0 0 0 94 0 0 0 0 0 95 0 0 0 0 0 96 0 0 0 0 0 97 0 1 0 0 1 98 0 0 0 0 0 99 1 0 0 0 1 your_output.singleton.truncated000066400000000000000000000000001350370616400375130ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/trimns/incl_nsadapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/trimqualities/000077500000000000000000000000001350370616400312055ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/trimqualities/default/000077500000000000000000000000001350370616400326315ustar00rootroot00000000000000info.json000066400000000000000000000001121350370616400343720ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/trimqualities/default{ "arguments": ["--trimqualities"], "return_code": 0, "stderr": [ ] } input_1.fastq000066400000000000000000000003561350370616400351750ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/trimqualities/default@ATAGCCSeq_1_2959_500/1 meta data TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTG + JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! input_2.fastq000066400000000000000000000003561350370616400351760ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/trimqualities/default@ATAGCCSeq_1_2959_500/2 data meta GTCAGCGAAGGGTTGTAGTAGCCCGTAGGGGCCTACAACGTTGGGGCCTTTGCGTAGTTGTATATAGCCTAGAATTTTTCGTTCGGTAAGCATTAGGAAT + JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! your_output.discarded000066400000000000000000000000001350370616400370220ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/trimqualities/defaultyour_output.pair1.truncated000066400000000000000000000003541350370616400401200ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/trimqualities/default@ATAGCCSeq_1_2959_500/1 meta data TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCT + JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)' your_output.pair2.truncated000066400000000000000000000003541350370616400401210ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/trimqualities/default@ATAGCCSeq_1_2959_500/2 data meta GTCAGCGAAGGGTTGTAGTAGCCCGTAGGGGCCTACAACGTTGGGGCCTTTGCGTAGTTGTATATAGCCTAGAATTTTTCGTTCGGTAAGCATTAGGAA + JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*& your_output.settings000066400000000000000000000047101350370616400367540ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/trimqualities/defaultAdapterRemoval ver. 2.1.7 Trimming of paired-end reads [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 3198577441 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: Yes Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 [Trimming statistics] Total number of read pairs: 1 Number of unaligned read pairs: 1 Number of well aligned read pairs: 0 Number of discarded mate 1 reads: 0 Number of singleton mate 1 reads: 0 Number of discarded mate 2 reads: 0 Number of singleton mate 2 reads: 0 Number of reads with adapters[1]: 0 Number of retained reads: 2 Number of retained nucleotides: 198 Average length of retained reads: 99 [Length distribution] Length Mate1 Mate2 Singleton Discarded All 0 0 0 0 0 0 1 0 0 0 0 0 2 0 0 0 0 0 3 0 0 0 0 0 4 0 0 0 0 0 5 0 0 0 0 0 6 0 0 0 0 0 7 0 0 0 0 0 8 0 0 0 0 0 9 0 0 0 0 0 10 0 0 0 0 0 11 0 0 0 0 0 12 0 0 0 0 0 13 0 0 0 0 0 14 0 0 0 0 0 15 0 0 0 0 0 16 0 0 0 0 0 17 0 0 0 0 0 18 0 0 0 0 0 19 0 0 0 0 0 20 0 0 0 0 0 21 0 0 0 0 0 22 0 0 0 0 0 23 0 0 0 0 0 24 0 0 0 0 0 25 0 0 0 0 0 26 0 0 0 0 0 27 0 0 0 0 0 28 0 0 0 0 0 29 0 0 0 0 0 30 0 0 0 0 0 31 0 0 0 0 0 32 0 0 0 0 0 33 0 0 0 0 0 34 0 0 0 0 0 35 0 0 0 0 0 36 0 0 0 0 0 37 0 0 0 0 0 38 0 0 0 0 0 39 0 0 0 0 0 40 0 0 0 0 0 41 0 0 0 0 0 42 0 0 0 0 0 43 0 0 0 0 0 44 0 0 0 0 0 45 0 0 0 0 0 46 0 0 0 0 0 47 0 0 0 0 0 48 0 0 0 0 0 49 0 0 0 0 0 50 0 0 0 0 0 51 0 0 0 0 0 52 0 0 0 0 0 53 0 0 0 0 0 54 0 0 0 0 0 55 0 0 0 0 0 56 0 0 0 0 0 57 0 0 0 0 0 58 0 0 0 0 0 59 0 0 0 0 0 60 0 0 0 0 0 61 0 0 0 0 0 62 0 0 0 0 0 63 0 0 0 0 0 64 0 0 0 0 0 65 0 0 0 0 0 66 0 0 0 0 0 67 0 0 0 0 0 68 0 0 0 0 0 69 0 0 0 0 0 70 0 0 0 0 0 71 0 0 0 0 0 72 0 0 0 0 0 73 0 0 0 0 0 74 0 0 0 0 0 75 0 0 0 0 0 76 0 0 0 0 0 77 0 0 0 0 0 78 0 0 0 0 0 79 0 0 0 0 0 80 0 0 0 0 0 81 0 0 0 0 0 82 0 0 0 0 0 83 0 0 0 0 0 84 0 0 0 0 0 85 0 0 0 0 0 86 0 0 0 0 0 87 0 0 0 0 0 88 0 0 0 0 0 89 0 0 0 0 0 90 0 0 0 0 0 91 0 0 0 0 0 92 0 0 0 0 0 93 0 0 0 0 0 94 0 0 0 0 0 95 0 0 0 0 0 96 0 0 0 0 0 97 0 0 0 0 0 98 0 0 0 0 0 99 1 1 0 0 2 your_output.singleton.truncated000066400000000000000000000000001350370616400410720ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/trimqualities/defaultadapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/trimqualities/minq31/000077500000000000000000000000001350370616400323155ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/trimqualities/minq31/info.json000066400000000000000000000001401350370616400341360ustar00rootroot00000000000000{ "arguments": ["--trimqualities", "--minquality", "31"], "return_code": 0, "stderr": [ ] } input_1.fastq000066400000000000000000000003561350370616400346610ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/trimqualities/minq31@ATAGCCSeq_1_2959_500/1 meta data TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTG + JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! input_2.fastq000066400000000000000000000003561350370616400346620ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/trimqualities/minq31@ATAGCCSeq_1_2959_500/2 data meta GTCAGCGAAGGGTTGTAGTAGCCCGTAGGGGCCTACAACGTTGGGGCCTTTGCGTAGTTGTATATAGCCTAGAATTTTTCGTTCGGTAAGCATTAGGAAT + JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@BB?@>>?@@=>><=;:9:9:9866852220.*&! your_output.discarded000066400000000000000000000000001350370616400365060ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/trimqualities/minq31your_output.pair1.truncated000066400000000000000000000002541350370616400376030ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/trimqualities/minq31@ATAGCCSeq_1_2959_500/1 meta data TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTAT + JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A your_output.pair2.truncated000066400000000000000000000002561350370616400376060ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/trimqualities/minq31@ATAGCCSeq_1_2959_500/2 data meta GTCAGCGAAGGGTTGTAGTAGCCCGTAGGGGCCTACAACGTTGGGGCCTTTGCGTAGTTGTATATAGC + JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@BB your_output.settings000066400000000000000000000040701350370616400364370ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/trimqualities/minq31AdapterRemoval ver. 2.1.7 Trimming of paired-end reads [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 3418474566 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 31: Yes Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 [Trimming statistics] Total number of read pairs: 1 Number of unaligned read pairs: 1 Number of well aligned read pairs: 0 Number of discarded mate 1 reads: 0 Number of singleton mate 1 reads: 0 Number of discarded mate 2 reads: 0 Number of singleton mate 2 reads: 0 Number of reads with adapters[1]: 0 Number of retained reads: 2 Number of retained nucleotides: 135 Average length of retained reads: 67.5 [Length distribution] Length Mate1 Mate2 Singleton Discarded All 0 0 0 0 0 0 1 0 0 0 0 0 2 0 0 0 0 0 3 0 0 0 0 0 4 0 0 0 0 0 5 0 0 0 0 0 6 0 0 0 0 0 7 0 0 0 0 0 8 0 0 0 0 0 9 0 0 0 0 0 10 0 0 0 0 0 11 0 0 0 0 0 12 0 0 0 0 0 13 0 0 0 0 0 14 0 0 0 0 0 15 0 0 0 0 0 16 0 0 0 0 0 17 0 0 0 0 0 18 0 0 0 0 0 19 0 0 0 0 0 20 0 0 0 0 0 21 0 0 0 0 0 22 0 0 0 0 0 23 0 0 0 0 0 24 0 0 0 0 0 25 0 0 0 0 0 26 0 0 0 0 0 27 0 0 0 0 0 28 0 0 0 0 0 29 0 0 0 0 0 30 0 0 0 0 0 31 0 0 0 0 0 32 0 0 0 0 0 33 0 0 0 0 0 34 0 0 0 0 0 35 0 0 0 0 0 36 0 0 0 0 0 37 0 0 0 0 0 38 0 0 0 0 0 39 0 0 0 0 0 40 0 0 0 0 0 41 0 0 0 0 0 42 0 0 0 0 0 43 0 0 0 0 0 44 0 0 0 0 0 45 0 0 0 0 0 46 0 0 0 0 0 47 0 0 0 0 0 48 0 0 0 0 0 49 0 0 0 0 0 50 0 0 0 0 0 51 0 0 0 0 0 52 0 0 0 0 0 53 0 0 0 0 0 54 0 0 0 0 0 55 0 0 0 0 0 56 0 0 0 0 0 57 0 0 0 0 0 58 0 0 0 0 0 59 0 0 0 0 0 60 0 0 0 0 0 61 0 0 0 0 0 62 0 0 0 0 0 63 0 0 0 0 0 64 0 0 0 0 0 65 0 0 0 0 0 66 0 0 0 0 0 67 1 0 0 0 1 68 0 1 0 0 1 your_output.singleton.truncated000066400000000000000000000000001350370616400405560ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/non_overlapping/trimqualities/minq31adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/000077500000000000000000000000001350370616400254375ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/collapse/000077500000000000000000000000001350370616400272415ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/collapse/info.json000066400000000000000000000001051350370616400310630ustar00rootroot00000000000000{ "arguments": ["--collapse"], "return_code": 0, "stderr": [ ] } adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/collapse/input_1.fastq000066400000000000000000000003561350370616400316640ustar00rootroot00000000000000@ATAGCCSeq_1_2959_500/1 meta data TATCGAGCAACTCACCAAGTTCCTTTGATCCGAGGAACTACCCTTACGCCCATCGACGCTTGTTATTCCGGCCTCATATTGGAAGCTACACGCTAGACCA + JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/collapse/input_2.fastq000066400000000000000000000003561350370616400316650ustar00rootroot00000000000000@ATAGCCSeq_1_2959_500/2 data meta CATCTGGATTGTCGATCGCTGCCACCACTAGCCGGGTTTTTCTTTTGTAGTGGTCTAGCGTGTAGCTTCCAATATGAGGCCGGAATAACAAGCGTCGATG + JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/collapse/your_output.collapsed000066400000000000000000000005221350370616400335460ustar00rootroot00000000000000@M_ATAGCCSeq_1_2959_500 meta data TATCGAGCAACTCACCAAGTTCCTTTGATCCGAGGAACTACCCTTACGCCCATCGACGCTTGTTATTCCGGCCTCATATTGGAAGCTACACGCTAGACCACTACAAAAGAAAAACCCGGCTAGTGGTGGCAGCGATCGACAATCCAGATG + JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJCEBCEDECDEEEFFFFEFDGFIFFFHIIIGIHHGJGIGJJJIHJHJIIJHJ your_output.collapsed.truncated000066400000000000000000000000001350370616400354460ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/collapseadapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/collapse/your_output.discarded000066400000000000000000000000001350370616400335110ustar00rootroot00000000000000your_output.pair1.truncated000066400000000000000000000000001350370616400345140ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/collapseyour_output.pair2.truncated000066400000000000000000000000001350370616400345150ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/collapseadapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/collapse/your_output.settings000066400000000000000000000075331350370616400334510ustar00rootroot00000000000000AdapterRemoval ver. 2.1.7 Trimming of paired-end reads [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 664708214 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: Yes Minimum overlap (in case of collapse): 11 [Trimming statistics] Total number of read pairs: 1 Number of unaligned read pairs: 0 Number of well aligned read pairs: 1 Number of discarded mate 1 reads: 0 Number of singleton mate 1 reads: 0 Number of discarded mate 2 reads: 0 Number of singleton mate 2 reads: 0 Number of reads with adapters[1]: 0 Number of full-length collapsed pairs: 1 Number of truncated collapsed pairs: 0 Number of retained reads: 1 Number of retained nucleotides: 150 Average length of retained reads: 150 [Length distribution] Length Mate1 Mate2 Singleton Collapsed CollapsedTruncated Discarded All 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 3 0 0 0 0 0 0 0 4 0 0 0 0 0 0 0 5 0 0 0 0 0 0 0 6 0 0 0 0 0 0 0 7 0 0 0 0 0 0 0 8 0 0 0 0 0 0 0 9 0 0 0 0 0 0 0 10 0 0 0 0 0 0 0 11 0 0 0 0 0 0 0 12 0 0 0 0 0 0 0 13 0 0 0 0 0 0 0 14 0 0 0 0 0 0 0 15 0 0 0 0 0 0 0 16 0 0 0 0 0 0 0 17 0 0 0 0 0 0 0 18 0 0 0 0 0 0 0 19 0 0 0 0 0 0 0 20 0 0 0 0 0 0 0 21 0 0 0 0 0 0 0 22 0 0 0 0 0 0 0 23 0 0 0 0 0 0 0 24 0 0 0 0 0 0 0 25 0 0 0 0 0 0 0 26 0 0 0 0 0 0 0 27 0 0 0 0 0 0 0 28 0 0 0 0 0 0 0 29 0 0 0 0 0 0 0 30 0 0 0 0 0 0 0 31 0 0 0 0 0 0 0 32 0 0 0 0 0 0 0 33 0 0 0 0 0 0 0 34 0 0 0 0 0 0 0 35 0 0 0 0 0 0 0 36 0 0 0 0 0 0 0 37 0 0 0 0 0 0 0 38 0 0 0 0 0 0 0 39 0 0 0 0 0 0 0 40 0 0 0 0 0 0 0 41 0 0 0 0 0 0 0 42 0 0 0 0 0 0 0 43 0 0 0 0 0 0 0 44 0 0 0 0 0 0 0 45 0 0 0 0 0 0 0 46 0 0 0 0 0 0 0 47 0 0 0 0 0 0 0 48 0 0 0 0 0 0 0 49 0 0 0 0 0 0 0 50 0 0 0 0 0 0 0 51 0 0 0 0 0 0 0 52 0 0 0 0 0 0 0 53 0 0 0 0 0 0 0 54 0 0 0 0 0 0 0 55 0 0 0 0 0 0 0 56 0 0 0 0 0 0 0 57 0 0 0 0 0 0 0 58 0 0 0 0 0 0 0 59 0 0 0 0 0 0 0 60 0 0 0 0 0 0 0 61 0 0 0 0 0 0 0 62 0 0 0 0 0 0 0 63 0 0 0 0 0 0 0 64 0 0 0 0 0 0 0 65 0 0 0 0 0 0 0 66 0 0 0 0 0 0 0 67 0 0 0 0 0 0 0 68 0 0 0 0 0 0 0 69 0 0 0 0 0 0 0 70 0 0 0 0 0 0 0 71 0 0 0 0 0 0 0 72 0 0 0 0 0 0 0 73 0 0 0 0 0 0 0 74 0 0 0 0 0 0 0 75 0 0 0 0 0 0 0 76 0 0 0 0 0 0 0 77 0 0 0 0 0 0 0 78 0 0 0 0 0 0 0 79 0 0 0 0 0 0 0 80 0 0 0 0 0 0 0 81 0 0 0 0 0 0 0 82 0 0 0 0 0 0 0 83 0 0 0 0 0 0 0 84 0 0 0 0 0 0 0 85 0 0 0 0 0 0 0 86 0 0 0 0 0 0 0 87 0 0 0 0 0 0 0 88 0 0 0 0 0 0 0 89 0 0 0 0 0 0 0 90 0 0 0 0 0 0 0 91 0 0 0 0 0 0 0 92 0 0 0 0 0 0 0 93 0 0 0 0 0 0 0 94 0 0 0 0 0 0 0 95 0 0 0 0 0 0 0 96 0 0 0 0 0 0 0 97 0 0 0 0 0 0 0 98 0 0 0 0 0 0 0 99 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 101 0 0 0 0 0 0 0 102 0 0 0 0 0 0 0 103 0 0 0 0 0 0 0 104 0 0 0 0 0 0 0 105 0 0 0 0 0 0 0 106 0 0 0 0 0 0 0 107 0 0 0 0 0 0 0 108 0 0 0 0 0 0 0 109 0 0 0 0 0 0 0 110 0 0 0 0 0 0 0 111 0 0 0 0 0 0 0 112 0 0 0 0 0 0 0 113 0 0 0 0 0 0 0 114 0 0 0 0 0 0 0 115 0 0 0 0 0 0 0 116 0 0 0 0 0 0 0 117 0 0 0 0 0 0 0 118 0 0 0 0 0 0 0 119 0 0 0 0 0 0 0 120 0 0 0 0 0 0 0 121 0 0 0 0 0 0 0 122 0 0 0 0 0 0 0 123 0 0 0 0 0 0 0 124 0 0 0 0 0 0 0 125 0 0 0 0 0 0 0 126 0 0 0 0 0 0 0 127 0 0 0 0 0 0 0 128 0 0 0 0 0 0 0 129 0 0 0 0 0 0 0 130 0 0 0 0 0 0 0 131 0 0 0 0 0 0 0 132 0 0 0 0 0 0 0 133 0 0 0 0 0 0 0 134 0 0 0 0 0 0 0 135 0 0 0 0 0 0 0 136 0 0 0 0 0 0 0 137 0 0 0 0 0 0 0 138 0 0 0 0 0 0 0 139 0 0 0 0 0 0 0 140 0 0 0 0 0 0 0 141 0 0 0 0 0 0 0 142 0 0 0 0 0 0 0 143 0 0 0 0 0 0 0 144 0 0 0 0 0 0 0 145 0 0 0 0 0 0 0 146 0 0 0 0 0 0 0 147 0 0 0 0 0 0 0 148 0 0 0 0 0 0 0 149 0 0 0 0 0 0 0 150 0 0 0 1 0 0 1 your_output.singleton.truncated000066400000000000000000000000001350370616400355020ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/collapseadapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/collapse_deterministic/000077500000000000000000000000001350370616400321645ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/collapse_deterministic/info.json000066400000000000000000000001231350370616400340060ustar00rootroot00000000000000{ "arguments": ["--collapse-deterministic"], "return_code": 0, "stderr": [ ] } input_1.fastq000066400000000000000000000003551350370616400345270ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/collapse_deterministic@ATAGCCSeq_1_2959_500/1 meta data TATCGAGCAACTCACCAAGTTCCTTTGATCCGAGGAACTACCCTTACGCCCATCGACGCTTGTTATTCCGGCCTCATATCGGAAGCTACACGCTAGACCA + JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@C8AA@A@@@?>>@==<=<<;;;<:9777755321/D)'!input_2.fastq000066400000000000000000000003551350370616400345300ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/collapse_deterministic@ATAGCCSeq_1_2959_500/2 data meta CATCTGGATTGTCGATCGCTGCCACCACTAGCCGGGTTTTTCTTTTGTAGTGGACTAGCGTGTAGCTTCCAATATGAGGCCGGAATATCAAGCGTCGATG + JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@<>?@@=>><=;:9:9:9866852220.*&!your_output.collapsed000066400000000000000000000005221350370616400364120ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/collapse_deterministic@M_ATAGCCSeq_1_2959_500 meta data TATCGAGCAACTCACCAAGTTCCTTTGATCCGAGGAACTACCCTTACGCCCATCGACGCTTGNTATTCCGGCCTCATATNGGAAGCTACACGCTAGNCCACTACAAAAGAAAAACCCGGCTAGTGGTGGCAGCGATCGACAATCCAGATG + JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBJJJJJJJJJJJ!JJJJJJJJJJJJJJJJ!JJJJJJJJJJJJJJJJ!JJCEBCEDECDEEEFFFFEFDGFIFFFHIIIGIHHGJGIGJJJIHJHJIIJHJ your_output.collapsed.truncated000066400000000000000000000000001350370616400403710ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/collapse_deterministicyour_output.discarded000066400000000000000000000000001350370616400363550ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/collapse_deterministicyour_output.pair1.truncated000066400000000000000000000000001350370616400374370ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/collapse_deterministicyour_output.pair2.truncated000066400000000000000000000000001350370616400374400ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/collapse_deterministicyour_output.settings000066400000000000000000000075241350370616400363150ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/collapse_deterministicAdapterRemoval ver. 2.1.7 Trimming of paired-end reads [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: NA Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: Yes Minimum overlap (in case of collapse): 11 [Trimming statistics] Total number of read pairs: 1 Number of unaligned read pairs: 0 Number of well aligned read pairs: 1 Number of discarded mate 1 reads: 0 Number of singleton mate 1 reads: 0 Number of discarded mate 2 reads: 0 Number of singleton mate 2 reads: 0 Number of reads with adapters[1]: 0 Number of full-length collapsed pairs: 1 Number of truncated collapsed pairs: 0 Number of retained reads: 1 Number of retained nucleotides: 150 Average length of retained reads: 150 [Length distribution] Length Mate1 Mate2 Singleton Collapsed CollapsedTruncated Discarded All 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 3 0 0 0 0 0 0 0 4 0 0 0 0 0 0 0 5 0 0 0 0 0 0 0 6 0 0 0 0 0 0 0 7 0 0 0 0 0 0 0 8 0 0 0 0 0 0 0 9 0 0 0 0 0 0 0 10 0 0 0 0 0 0 0 11 0 0 0 0 0 0 0 12 0 0 0 0 0 0 0 13 0 0 0 0 0 0 0 14 0 0 0 0 0 0 0 15 0 0 0 0 0 0 0 16 0 0 0 0 0 0 0 17 0 0 0 0 0 0 0 18 0 0 0 0 0 0 0 19 0 0 0 0 0 0 0 20 0 0 0 0 0 0 0 21 0 0 0 0 0 0 0 22 0 0 0 0 0 0 0 23 0 0 0 0 0 0 0 24 0 0 0 0 0 0 0 25 0 0 0 0 0 0 0 26 0 0 0 0 0 0 0 27 0 0 0 0 0 0 0 28 0 0 0 0 0 0 0 29 0 0 0 0 0 0 0 30 0 0 0 0 0 0 0 31 0 0 0 0 0 0 0 32 0 0 0 0 0 0 0 33 0 0 0 0 0 0 0 34 0 0 0 0 0 0 0 35 0 0 0 0 0 0 0 36 0 0 0 0 0 0 0 37 0 0 0 0 0 0 0 38 0 0 0 0 0 0 0 39 0 0 0 0 0 0 0 40 0 0 0 0 0 0 0 41 0 0 0 0 0 0 0 42 0 0 0 0 0 0 0 43 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your_output.singleton.truncated000066400000000000000000000000001350370616400404250ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/collapse_deterministicadapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/combined_output/000077500000000000000000000000001350370616400306375ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/combined_output/collapse/000077500000000000000000000000001350370616400324415ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/combined_output/collapse/info.json000066400000000000000000000001321350370616400342630ustar00rootroot00000000000000{ "arguments": ["--combined-output", "--collapse"], "return_code": 0, "stderr": [ ] } input_1.fastq000066400000000000000000000003561350370616400350050ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/combined_output/collapse@ATAGCCSeq_1_2959_500/1 meta data TATCGAGCAACTCACCAAGTTCCTTTGATCCGAGGAACTACCCTTACGCCCATCGACGCTTGTTATTCCGGCCTCATATTGGAAGCTACACGCTAGACCA + JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! input_2.fastq000066400000000000000000000003561350370616400350060ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/combined_output/collapse@ATAGCCSeq_1_2959_500/2 data meta CATCTGGATTGTCGATCGCTGCCACCACTAGCCGGGTTTTTCTTTTGTAGTGGTCTAGCGTGTAGCTTCCAATATGAGGCCGGAATAACAAGCGTCGATG + JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! your_output.pair1.truncated000066400000000000000000000005241350370616400377270ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/combined_output/collapse@M_ATAGCCSeq_1_2959_500/1 meta data TATCGAGCAACTCACCAAGTTCCTTTGATCCGAGGAACTACCCTTACGCCCATCGACGCTTGTTATTCCGGCCTCATATTGGAAGCTACACGCTAGACCACTACAAAAGAAAAACCCGGCTAGTGGTGGCAGCGATCGACAATCCAGATG + JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJCEBCEDECDEEEFFFFEFDGFIFFFHIIIGIHHGJGIGJJJIHJHJIIJHJ your_output.pair2.truncated000066400000000000000000000000521350370616400377240ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/combined_output/collapse@M_ATAGCCSeq_1_2959_500/2 data meta N + ! your_output.settings000066400000000000000000000075341350370616400365730ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/combined_output/collapseAdapterRemoval ver. 2.1.7 Trimming of paired-end reads [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 1520646958 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: Yes Minimum overlap (in case of collapse): 11 [Trimming statistics] Total number of read pairs: 1 Number of unaligned read pairs: 0 Number of well aligned read pairs: 1 Number of discarded mate 1 reads: 0 Number of singleton mate 1 reads: 0 Number of discarded mate 2 reads: 0 Number of singleton mate 2 reads: 0 Number of reads with adapters[1]: 0 Number of full-length collapsed pairs: 1 Number of truncated collapsed pairs: 0 Number of retained reads: 1 Number of retained nucleotides: 150 Average length of retained reads: 150 [Length distribution] Length Mate1 Mate2 Singleton Collapsed CollapsedTruncated Discarded All 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 3 0 0 0 0 0 0 0 4 0 0 0 0 0 0 0 5 0 0 0 0 0 0 0 6 0 0 0 0 0 0 0 7 0 0 0 0 0 0 0 8 0 0 0 0 0 0 0 9 0 0 0 0 0 0 0 10 0 0 0 0 0 0 0 11 0 0 0 0 0 0 0 12 0 0 0 0 0 0 0 13 0 0 0 0 0 0 0 14 0 0 0 0 0 0 0 15 0 0 0 0 0 0 0 16 0 0 0 0 0 0 0 17 0 0 0 0 0 0 0 18 0 0 0 0 0 0 0 19 0 0 0 0 0 0 0 20 0 0 0 0 0 0 0 21 0 0 0 0 0 0 0 22 0 0 0 0 0 0 0 23 0 0 0 0 0 0 0 24 0 0 0 0 0 0 0 25 0 0 0 0 0 0 0 26 0 0 0 0 0 0 0 27 0 0 0 0 0 0 0 28 0 0 0 0 0 0 0 29 0 0 0 0 0 0 0 30 0 0 0 0 0 0 0 31 0 0 0 0 0 0 0 32 0 0 0 0 0 0 0 33 0 0 0 0 0 0 0 34 0 0 0 0 0 0 0 35 0 0 0 0 0 0 0 36 0 0 0 0 0 0 0 37 0 0 0 0 0 0 0 38 0 0 0 0 0 0 0 39 0 0 0 0 0 0 0 40 0 0 0 0 0 0 0 41 0 0 0 0 0 0 0 42 0 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adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/combined_output/interleaved/000077500000000000000000000000001350370616400331415ustar00rootroot00000000000000collapse/000077500000000000000000000000001350370616400346645ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/combined_output/interleavedinfo.json000066400000000000000000000001621350370616400365110ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/combined_output/interleaved/collapse{ "arguments": ["--combined-output", "--collapse", "--interleaved-output"], "return_code": 0, "stderr": [ ] } input_1.fastq000066400000000000000000000003561350370616400373070ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/combined_output/interleaved/collapse@ATAGCCSeq_1_2959_500/1 meta data TATCGAGCAACTCACCAAGTTCCTTTGATCCGAGGAACTACCCTTACGCCCATCGACGCTTGTTATTCCGGCCTCATATTGGAAGCTACACGCTAGACCA + JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! input_2.fastq000066400000000000000000000003561350370616400373100ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/combined_output/interleaved/collapse@ATAGCCSeq_1_2959_500/2 data meta CATCTGGATTGTCGATCGCTGCCACCACTAGCCGGGTTTTTCTTTTGTAGTGGTCTAGCGTGTAGCTTCCAATATGAGGCCGGAATAACAAGCGTCGATG + JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! your_output.paired.truncated000066400000000000000000000005761350370616400424700ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/combined_output/interleaved/collapse@M_ATAGCCSeq_1_2959_500/1 meta data TATCGAGCAACTCACCAAGTTCCTTTGATCCGAGGAACTACCCTTACGCCCATCGACGCTTGTTATTCCGGCCTCATATTGGAAGCTACACGCTAGACCACTACAAAAGAAAAACCCGGCTAGTGGTGGCAGCGATCGACAATCCAGATG + JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJCEBCEDECDEEEFFFFEFDGFIFFFHIIIGIHHGJGIGJJJIHJHJIIJHJ @M_ATAGCCSeq_1_2959_500/2 data meta N + ! your_output.settings000066400000000000000000000075341350370616400410750ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/combined_output/interleaved/collapseAdapterRemoval ver. 2.1.7 Trimming of paired-end reads [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 1520646958 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: Yes Minimum overlap (in case of collapse): 11 [Trimming statistics] Total number of read pairs: 1 Number of unaligned read pairs: 0 Number of well aligned read pairs: 1 Number of discarded mate 1 reads: 0 Number of singleton mate 1 reads: 0 Number of discarded mate 2 reads: 0 Number of singleton mate 2 reads: 0 Number of reads with adapters[1]: 0 Number of full-length collapsed pairs: 1 Number of truncated collapsed pairs: 0 Number of retained reads: 1 Number of retained nucleotides: 150 Average length of retained reads: 150 [Length distribution] Length Mate1 Mate2 Singleton Collapsed CollapsedTruncated Discarded All 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 3 0 0 0 0 0 0 0 4 0 0 0 0 0 0 0 5 0 0 0 0 0 0 0 6 0 0 0 0 0 0 0 7 0 0 0 0 0 0 0 8 0 0 0 0 0 0 0 9 0 0 0 0 0 0 0 10 0 0 0 0 0 0 0 11 0 0 0 0 0 0 0 12 0 0 0 0 0 0 0 13 0 0 0 0 0 0 0 14 0 0 0 0 0 0 0 15 0 0 0 0 0 0 0 16 0 0 0 0 0 0 0 17 0 0 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0 0 0 0 0 0 0 134 0 0 0 0 0 0 0 135 0 0 0 0 0 0 0 136 0 0 0 0 0 0 0 137 0 0 0 0 0 0 0 138 0 0 0 0 0 0 0 139 0 0 0 0 0 0 0 140 0 0 0 0 0 0 0 141 0 0 0 0 0 0 0 142 0 0 0 0 0 0 0 143 0 0 0 0 0 0 0 144 0 0 0 0 0 0 0 145 0 0 0 0 0 0 0 146 0 0 0 0 0 0 0 147 0 0 0 0 0 0 0 148 0 0 0 0 0 0 0 149 0 0 0 0 0 0 0 150 0 0 0 1 0 0 1 keep_both/000077500000000000000000000000001350370616400350225ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/combined_output/interleavedinfo.json000066400000000000000000000001441350370616400366470ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/combined_output/interleaved/keep_both{ "arguments": ["--combined-output", "--interleaved-output"], "return_code": 0, "stderr": [ ] } input_1.fastq000066400000000000000000000003561350370616400374450ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/combined_output/interleaved/keep_both@ATAGCCSeq_1_2959_500/1 meta data TATCGAGCAACTCACCAAGTTCCTTTGATCCGAGGAACTACCCTTACGCCCATCGACGCTTGTTATTCCGGCCTCATATTGGAAGCTACACGCTAGACCA + JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! input_2.fastq000066400000000000000000000003561350370616400374460ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/combined_output/interleaved/keep_both@ATAGCCSeq_1_2959_500/2 data meta CATCTGGATTGTCGATCGCTGCCACCACTAGCCGGGTTTTTCTTTTGTAGTGGTCTAGCGTGTAGCTTCCAATATGAGGCCGGAATAACAAGCGTCGATG + JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! your_output.paired.truncated000066400000000000000000000007341350370616400426220ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/combined_output/interleaved/keep_both@ATAGCCSeq_1_2959_500/1 meta data TATCGAGCAACTCACCAAGTTCCTTTGATCCGAGGAACTACCCTTACGCCCATCGACGCTTGTTATTCCGGCCTCATATTGGAAGCTACACGCTAGACCA + JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! @ATAGCCSeq_1_2959_500/2 data meta CATCTGGATTGTCGATCGCTGCCACCACTAGCCGGGTTTTTCTTTTGTAGTGGTCTAGCGTGTAGCTTCCAATATGAGGCCGGAATAACAAGCGTCGATG + JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! your_output.settings000066400000000000000000000047261350370616400412330ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/combined_output/interleaved/keep_bothAdapterRemoval ver. 2.1.7 Trimming of paired-end reads [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 1638235704 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 [Trimming statistics] Total number of read pairs: 1 Number of unaligned read pairs: 0 Number of well aligned read pairs: 1 Number of discarded mate 1 reads: 0 Number of singleton mate 1 reads: 0 Number of discarded mate 2 reads: 0 Number of singleton mate 2 reads: 0 Number of reads with adapters[1]: 0 Number of retained reads: 2 Number of retained nucleotides: 200 Average length of retained reads: 100 [Length distribution] Length Mate1 Mate2 Singleton Discarded All 0 0 0 0 0 0 1 0 0 0 0 0 2 0 0 0 0 0 3 0 0 0 0 0 4 0 0 0 0 0 5 0 0 0 0 0 6 0 0 0 0 0 7 0 0 0 0 0 8 0 0 0 0 0 9 0 0 0 0 0 10 0 0 0 0 0 11 0 0 0 0 0 12 0 0 0 0 0 13 0 0 0 0 0 14 0 0 0 0 0 15 0 0 0 0 0 16 0 0 0 0 0 17 0 0 0 0 0 18 0 0 0 0 0 19 0 0 0 0 0 20 0 0 0 0 0 21 0 0 0 0 0 22 0 0 0 0 0 23 0 0 0 0 0 24 0 0 0 0 0 25 0 0 0 0 0 26 0 0 0 0 0 27 0 0 0 0 0 28 0 0 0 0 0 29 0 0 0 0 0 30 0 0 0 0 0 31 0 0 0 0 0 32 0 0 0 0 0 33 0 0 0 0 0 34 0 0 0 0 0 35 0 0 0 0 0 36 0 0 0 0 0 37 0 0 0 0 0 38 0 0 0 0 0 39 0 0 0 0 0 40 0 0 0 0 0 41 0 0 0 0 0 42 0 0 0 0 0 43 0 0 0 0 0 44 0 0 0 0 0 45 0 0 0 0 0 46 0 0 0 0 0 47 0 0 0 0 0 48 0 0 0 0 0 49 0 0 0 0 0 50 0 0 0 0 0 51 0 0 0 0 0 52 0 0 0 0 0 53 0 0 0 0 0 54 0 0 0 0 0 55 0 0 0 0 0 56 0 0 0 0 0 57 0 0 0 0 0 58 0 0 0 0 0 59 0 0 0 0 0 60 0 0 0 0 0 61 0 0 0 0 0 62 0 0 0 0 0 63 0 0 0 0 0 64 0 0 0 0 0 65 0 0 0 0 0 66 0 0 0 0 0 67 0 0 0 0 0 68 0 0 0 0 0 69 0 0 0 0 0 70 0 0 0 0 0 71 0 0 0 0 0 72 0 0 0 0 0 73 0 0 0 0 0 74 0 0 0 0 0 75 0 0 0 0 0 76 0 0 0 0 0 77 0 0 0 0 0 78 0 0 0 0 0 79 0 0 0 0 0 80 0 0 0 0 0 81 0 0 0 0 0 82 0 0 0 0 0 83 0 0 0 0 0 84 0 0 0 0 0 85 0 0 0 0 0 86 0 0 0 0 0 87 0 0 0 0 0 88 0 0 0 0 0 89 0 0 0 0 0 90 0 0 0 0 0 91 0 0 0 0 0 92 0 0 0 0 0 93 0 0 0 0 0 94 0 0 0 0 0 95 0 0 0 0 0 96 0 0 0 0 0 97 0 0 0 0 0 98 0 0 0 0 0 99 0 0 0 0 0 100 1 1 0 0 2 keep_mate1/000077500000000000000000000000001350370616400350755ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/combined_output/interleavedinfo.json000066400000000000000000000002061350370616400367210ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/combined_output/interleaved/keep_mate1{ "arguments": ["--combined-output", "--minlength", "100", "--trimns", "--interleaved-output"], "return_code": 0, "stderr": [ ] } input_1.fastq000066400000000000000000000003561350370616400375200ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/combined_output/interleaved/keep_mate1@ATAGCCSeq_1_2959_500/1 meta data TATCGAGCAACTCACCAAGTTCCTTTGATCCGAGGAACTACCCTTACGCCCATCGACGCTTGTTATTCCGGCCTCATATTGGAAGCTACACGCTAGACCA + JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! input_2.fastq000066400000000000000000000003561350370616400375210ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/combined_output/interleaved/keep_mate1@ATAGCCSeq_1_2959_500/2 data meta CATCTGGATTGTCGATCGCTGCCACCACTAGCCGGGTTTTTCTTTTGTAGTGGTCTAGCGTGTAGCTTCCAATATGAGGCCGGAATAACAAGCGTCGATN + JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! your_output.paired.truncated000066400000000000000000000004261350370616400426730ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/combined_output/interleaved/keep_mate1@ATAGCCSeq_1_2959_500/1 meta data TATCGAGCAACTCACCAAGTTCCTTTGATCCGAGGAACTACCCTTACGCCCATCGACGCTTGTTATTCCGGCCTCATATTGGAAGCTACACGCTAGACCA + JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! @ATAGCCSeq_1_2959_500/2 data meta N + ! your_output.settings000066400000000000000000000047301350370616400413010ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/combined_output/interleaved/keep_mate1AdapterRemoval ver. 2.1.7 Trimming of paired-end reads [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 2898275634 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: Yes Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 100 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 [Trimming statistics] Total number of read pairs: 1 Number of unaligned read pairs: 0 Number of well aligned read pairs: 1 Number of discarded mate 1 reads: 0 Number of singleton mate 1 reads: 1 Number of discarded mate 2 reads: 1 Number of singleton mate 2 reads: 0 Number of reads with adapters[1]: 0 Number of retained reads: 1 Number of retained nucleotides: 100 Average length of retained reads: 100 [Length distribution] Length Mate1 Mate2 Singleton Discarded All 0 0 0 0 0 0 1 0 0 0 0 0 2 0 0 0 0 0 3 0 0 0 0 0 4 0 0 0 0 0 5 0 0 0 0 0 6 0 0 0 0 0 7 0 0 0 0 0 8 0 0 0 0 0 9 0 0 0 0 0 10 0 0 0 0 0 11 0 0 0 0 0 12 0 0 0 0 0 13 0 0 0 0 0 14 0 0 0 0 0 15 0 0 0 0 0 16 0 0 0 0 0 17 0 0 0 0 0 18 0 0 0 0 0 19 0 0 0 0 0 20 0 0 0 0 0 21 0 0 0 0 0 22 0 0 0 0 0 23 0 0 0 0 0 24 0 0 0 0 0 25 0 0 0 0 0 26 0 0 0 0 0 27 0 0 0 0 0 28 0 0 0 0 0 29 0 0 0 0 0 30 0 0 0 0 0 31 0 0 0 0 0 32 0 0 0 0 0 33 0 0 0 0 0 34 0 0 0 0 0 35 0 0 0 0 0 36 0 0 0 0 0 37 0 0 0 0 0 38 0 0 0 0 0 39 0 0 0 0 0 40 0 0 0 0 0 41 0 0 0 0 0 42 0 0 0 0 0 43 0 0 0 0 0 44 0 0 0 0 0 45 0 0 0 0 0 46 0 0 0 0 0 47 0 0 0 0 0 48 0 0 0 0 0 49 0 0 0 0 0 50 0 0 0 0 0 51 0 0 0 0 0 52 0 0 0 0 0 53 0 0 0 0 0 54 0 0 0 0 0 55 0 0 0 0 0 56 0 0 0 0 0 57 0 0 0 0 0 58 0 0 0 0 0 59 0 0 0 0 0 60 0 0 0 0 0 61 0 0 0 0 0 62 0 0 0 0 0 63 0 0 0 0 0 64 0 0 0 0 0 65 0 0 0 0 0 66 0 0 0 0 0 67 0 0 0 0 0 68 0 0 0 0 0 69 0 0 0 0 0 70 0 0 0 0 0 71 0 0 0 0 0 72 0 0 0 0 0 73 0 0 0 0 0 74 0 0 0 0 0 75 0 0 0 0 0 76 0 0 0 0 0 77 0 0 0 0 0 78 0 0 0 0 0 79 0 0 0 0 0 80 0 0 0 0 0 81 0 0 0 0 0 82 0 0 0 0 0 83 0 0 0 0 0 84 0 0 0 0 0 85 0 0 0 0 0 86 0 0 0 0 0 87 0 0 0 0 0 88 0 0 0 0 0 89 0 0 0 0 0 90 0 0 0 0 0 91 0 0 0 0 0 92 0 0 0 0 0 93 0 0 0 0 0 94 0 0 0 0 0 95 0 0 0 0 0 96 0 0 0 0 0 97 0 0 0 0 0 98 0 0 0 0 0 99 0 0 0 1 1 100 0 0 1 0 1 keep_mate2/000077500000000000000000000000001350370616400350765ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/combined_output/interleavedinfo.json000066400000000000000000000002061350370616400367220ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/combined_output/interleaved/keep_mate2{ "arguments": ["--combined-output", "--minlength", "100", "--trimns", "--interleaved-output"], "return_code": 0, "stderr": [ ] } input_1.fastq000066400000000000000000000003561350370616400375210ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/combined_output/interleaved/keep_mate2@ATAGCCSeq_1_2959_500/1 meta data TATCGAGCAACTCACCAAGTTCCTTTGATCCGAGGAACTACCCTTACGCCCATCGACGCTTGTTATTCCGGCCTCATATTGGAAGCTACACGCTAGACCN + JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! input_2.fastq000066400000000000000000000003561350370616400375220ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/combined_output/interleaved/keep_mate2@ATAGCCSeq_1_2959_500/2 data meta CATCTGGATTGTCGATCGCTGCCACCACTAGCCGGGTTTTTCTTTTGTAGTGGTCTAGCGTGTAGCTTCCAATATGAGGCCGGAATAACAAGCGTCGATG + JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! your_output.paired.truncated000066400000000000000000000004261350370616400426740ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/combined_output/interleaved/keep_mate2@ATAGCCSeq_1_2959_500/1 meta data N + ! @ATAGCCSeq_1_2959_500/2 data meta CATCTGGATTGTCGATCGCTGCCACCACTAGCCGGGTTTTTCTTTTGTAGTGGTCTAGCGTGTAGCTTCCAATATGAGGCCGGAATAACAAGCGTCGATG + JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! your_output.settings000066400000000000000000000047301350370616400413020ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/combined_output/interleaved/keep_mate2AdapterRemoval ver. 2.1.7 Trimming of paired-end reads [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 1902493234 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: Yes Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 100 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 [Trimming statistics] Total number of read pairs: 1 Number of unaligned read pairs: 0 Number of well aligned read pairs: 1 Number of discarded mate 1 reads: 1 Number of singleton mate 1 reads: 0 Number of discarded mate 2 reads: 0 Number of singleton mate 2 reads: 1 Number of reads with adapters[1]: 0 Number of retained reads: 1 Number of retained nucleotides: 100 Average length of retained reads: 100 [Length distribution] Length Mate1 Mate2 Singleton Discarded All 0 0 0 0 0 0 1 0 0 0 0 0 2 0 0 0 0 0 3 0 0 0 0 0 4 0 0 0 0 0 5 0 0 0 0 0 6 0 0 0 0 0 7 0 0 0 0 0 8 0 0 0 0 0 9 0 0 0 0 0 10 0 0 0 0 0 11 0 0 0 0 0 12 0 0 0 0 0 13 0 0 0 0 0 14 0 0 0 0 0 15 0 0 0 0 0 16 0 0 0 0 0 17 0 0 0 0 0 18 0 0 0 0 0 19 0 0 0 0 0 20 0 0 0 0 0 21 0 0 0 0 0 22 0 0 0 0 0 23 0 0 0 0 0 24 0 0 0 0 0 25 0 0 0 0 0 26 0 0 0 0 0 27 0 0 0 0 0 28 0 0 0 0 0 29 0 0 0 0 0 30 0 0 0 0 0 31 0 0 0 0 0 32 0 0 0 0 0 33 0 0 0 0 0 34 0 0 0 0 0 35 0 0 0 0 0 36 0 0 0 0 0 37 0 0 0 0 0 38 0 0 0 0 0 39 0 0 0 0 0 40 0 0 0 0 0 41 0 0 0 0 0 42 0 0 0 0 0 43 0 0 0 0 0 44 0 0 0 0 0 45 0 0 0 0 0 46 0 0 0 0 0 47 0 0 0 0 0 48 0 0 0 0 0 49 0 0 0 0 0 50 0 0 0 0 0 51 0 0 0 0 0 52 0 0 0 0 0 53 0 0 0 0 0 54 0 0 0 0 0 55 0 0 0 0 0 56 0 0 0 0 0 57 0 0 0 0 0 58 0 0 0 0 0 59 0 0 0 0 0 60 0 0 0 0 0 61 0 0 0 0 0 62 0 0 0 0 0 63 0 0 0 0 0 64 0 0 0 0 0 65 0 0 0 0 0 66 0 0 0 0 0 67 0 0 0 0 0 68 0 0 0 0 0 69 0 0 0 0 0 70 0 0 0 0 0 71 0 0 0 0 0 72 0 0 0 0 0 73 0 0 0 0 0 74 0 0 0 0 0 75 0 0 0 0 0 76 0 0 0 0 0 77 0 0 0 0 0 78 0 0 0 0 0 79 0 0 0 0 0 80 0 0 0 0 0 81 0 0 0 0 0 82 0 0 0 0 0 83 0 0 0 0 0 84 0 0 0 0 0 85 0 0 0 0 0 86 0 0 0 0 0 87 0 0 0 0 0 88 0 0 0 0 0 89 0 0 0 0 0 90 0 0 0 0 0 91 0 0 0 0 0 92 0 0 0 0 0 93 0 0 0 0 0 94 0 0 0 0 0 95 0 0 0 0 0 96 0 0 0 0 0 97 0 0 0 0 0 98 0 0 0 0 0 99 0 0 0 1 1 100 0 0 1 0 1 keep_neither/000077500000000000000000000000001350370616400355245ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/combined_output/interleavedinfo.json000066400000000000000000000002061350370616400373500ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/combined_output/interleaved/keep_neither{ "arguments": ["--combined-output", "--minlength", "100", "--trimns", "--interleaved-output"], "return_code": 0, "stderr": [ ] } input_1.fastq000066400000000000000000000003561350370616400401470ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/combined_output/interleaved/keep_neither@ATAGCCSeq_1_2959_500/1 meta data TATCGAGCAACTCACCAAGTTCCTTTGATCCGAGGAACTACCCTTACGCCCATCGACGCTTGTTATTCCGGCCTCATATTGGAAGCTACACGCTAGACCN + JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! input_2.fastq000066400000000000000000000003561350370616400401500ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/combined_output/interleaved/keep_neither@ATAGCCSeq_1_2959_500/2 data meta CATCTGGATTGTCGATCGCTGCCACCACTAGCCGGGTTTTTCTTTTGTAGTGGTCTAGCGTGTAGCTTCCAATATGAGGCCGGAATAACAAGCGTCGATN + JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! your_output.paired.truncated000066400000000000000000000001201350370616400433110ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/combined_output/interleaved/keep_neither@ATAGCCSeq_1_2959_500/1 meta data N + ! @ATAGCCSeq_1_2959_500/2 data meta N + ! your_output.settings000066400000000000000000000047061350370616400417330ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/combined_output/interleaved/keep_neitherAdapterRemoval ver. 2.1.7 Trimming of paired-end reads [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 4016683054 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: Yes Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 100 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 [Trimming statistics] Total number of read pairs: 1 Number of unaligned read pairs: 0 Number of well aligned read pairs: 1 Number of discarded mate 1 reads: 1 Number of singleton mate 1 reads: 0 Number of discarded mate 2 reads: 1 Number of singleton mate 2 reads: 0 Number of reads with adapters[1]: 0 Number of retained reads: 0 Number of retained nucleotides: 0 Average length of retained reads: 0 [Length distribution] Length Mate1 Mate2 Singleton Discarded All 0 0 0 0 0 0 1 0 0 0 0 0 2 0 0 0 0 0 3 0 0 0 0 0 4 0 0 0 0 0 5 0 0 0 0 0 6 0 0 0 0 0 7 0 0 0 0 0 8 0 0 0 0 0 9 0 0 0 0 0 10 0 0 0 0 0 11 0 0 0 0 0 12 0 0 0 0 0 13 0 0 0 0 0 14 0 0 0 0 0 15 0 0 0 0 0 16 0 0 0 0 0 17 0 0 0 0 0 18 0 0 0 0 0 19 0 0 0 0 0 20 0 0 0 0 0 21 0 0 0 0 0 22 0 0 0 0 0 23 0 0 0 0 0 24 0 0 0 0 0 25 0 0 0 0 0 26 0 0 0 0 0 27 0 0 0 0 0 28 0 0 0 0 0 29 0 0 0 0 0 30 0 0 0 0 0 31 0 0 0 0 0 32 0 0 0 0 0 33 0 0 0 0 0 34 0 0 0 0 0 35 0 0 0 0 0 36 0 0 0 0 0 37 0 0 0 0 0 38 0 0 0 0 0 39 0 0 0 0 0 40 0 0 0 0 0 41 0 0 0 0 0 42 0 0 0 0 0 43 0 0 0 0 0 44 0 0 0 0 0 45 0 0 0 0 0 46 0 0 0 0 0 47 0 0 0 0 0 48 0 0 0 0 0 49 0 0 0 0 0 50 0 0 0 0 0 51 0 0 0 0 0 52 0 0 0 0 0 53 0 0 0 0 0 54 0 0 0 0 0 55 0 0 0 0 0 56 0 0 0 0 0 57 0 0 0 0 0 58 0 0 0 0 0 59 0 0 0 0 0 60 0 0 0 0 0 61 0 0 0 0 0 62 0 0 0 0 0 63 0 0 0 0 0 64 0 0 0 0 0 65 0 0 0 0 0 66 0 0 0 0 0 67 0 0 0 0 0 68 0 0 0 0 0 69 0 0 0 0 0 70 0 0 0 0 0 71 0 0 0 0 0 72 0 0 0 0 0 73 0 0 0 0 0 74 0 0 0 0 0 75 0 0 0 0 0 76 0 0 0 0 0 77 0 0 0 0 0 78 0 0 0 0 0 79 0 0 0 0 0 80 0 0 0 0 0 81 0 0 0 0 0 82 0 0 0 0 0 83 0 0 0 0 0 84 0 0 0 0 0 85 0 0 0 0 0 86 0 0 0 0 0 87 0 0 0 0 0 88 0 0 0 0 0 89 0 0 0 0 0 90 0 0 0 0 0 91 0 0 0 0 0 92 0 0 0 0 0 93 0 0 0 0 0 94 0 0 0 0 0 95 0 0 0 0 0 96 0 0 0 0 0 97 0 0 0 0 0 98 0 0 0 0 0 99 0 0 0 2 2 adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/combined_output/keep_both/000077500000000000000000000000001350370616400325775ustar00rootroot00000000000000info.json000066400000000000000000000001141350370616400343420ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/combined_output/keep_both{ "arguments": ["--combined-output"], "return_code": 0, "stderr": [ ] } input_1.fastq000066400000000000000000000003561350370616400351430ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/combined_output/keep_both@ATAGCCSeq_1_2959_500/1 meta data TATCGAGCAACTCACCAAGTTCCTTTGATCCGAGGAACTACCCTTACGCCCATCGACGCTTGTTATTCCGGCCTCATATTGGAAGCTACACGCTAGACCA + JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! input_2.fastq000066400000000000000000000003561350370616400351440ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/combined_output/keep_both@ATAGCCSeq_1_2959_500/2 data meta CATCTGGATTGTCGATCGCTGCCACCACTAGCCGGGTTTTTCTTTTGTAGTGGTCTAGCGTGTAGCTTCCAATATGAGGCCGGAATAACAAGCGTCGATG + JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! your_output.pair1.truncated000066400000000000000000000003561350370616400400700ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/combined_output/keep_both@ATAGCCSeq_1_2959_500/1 meta data TATCGAGCAACTCACCAAGTTCCTTTGATCCGAGGAACTACCCTTACGCCCATCGACGCTTGTTATTCCGGCCTCATATTGGAAGCTACACGCTAGACCA + JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! your_output.pair2.truncated000066400000000000000000000003561350370616400400710ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/combined_output/keep_both@ATAGCCSeq_1_2959_500/2 data meta CATCTGGATTGTCGATCGCTGCCACCACTAGCCGGGTTTTTCTTTTGTAGTGGTCTAGCGTGTAGCTTCCAATATGAGGCCGGAATAACAAGCGTCGATG + JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! your_output.settings000066400000000000000000000047261350370616400367310ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/combined_output/keep_bothAdapterRemoval ver. 2.1.7 Trimming of paired-end reads [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 1638235704 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 [Trimming statistics] Total number of read pairs: 1 Number of unaligned read pairs: 0 Number of well aligned read pairs: 1 Number of discarded mate 1 reads: 0 Number of singleton mate 1 reads: 0 Number of discarded mate 2 reads: 0 Number of singleton mate 2 reads: 0 Number of reads with adapters[1]: 0 Number of retained reads: 2 Number of retained nucleotides: 200 Average length of retained reads: 100 [Length distribution] Length Mate1 Mate2 Singleton Discarded All 0 0 0 0 0 0 1 0 0 0 0 0 2 0 0 0 0 0 3 0 0 0 0 0 4 0 0 0 0 0 5 0 0 0 0 0 6 0 0 0 0 0 7 0 0 0 0 0 8 0 0 0 0 0 9 0 0 0 0 0 10 0 0 0 0 0 11 0 0 0 0 0 12 0 0 0 0 0 13 0 0 0 0 0 14 0 0 0 0 0 15 0 0 0 0 0 16 0 0 0 0 0 17 0 0 0 0 0 18 0 0 0 0 0 19 0 0 0 0 0 20 0 0 0 0 0 21 0 0 0 0 0 22 0 0 0 0 0 23 0 0 0 0 0 24 0 0 0 0 0 25 0 0 0 0 0 26 0 0 0 0 0 27 0 0 0 0 0 28 0 0 0 0 0 29 0 0 0 0 0 30 0 0 0 0 0 31 0 0 0 0 0 32 0 0 0 0 0 33 0 0 0 0 0 34 0 0 0 0 0 35 0 0 0 0 0 36 0 0 0 0 0 37 0 0 0 0 0 38 0 0 0 0 0 39 0 0 0 0 0 40 0 0 0 0 0 41 0 0 0 0 0 42 0 0 0 0 0 43 0 0 0 0 0 44 0 0 0 0 0 45 0 0 0 0 0 46 0 0 0 0 0 47 0 0 0 0 0 48 0 0 0 0 0 49 0 0 0 0 0 50 0 0 0 0 0 51 0 0 0 0 0 52 0 0 0 0 0 53 0 0 0 0 0 54 0 0 0 0 0 55 0 0 0 0 0 56 0 0 0 0 0 57 0 0 0 0 0 58 0 0 0 0 0 59 0 0 0 0 0 60 0 0 0 0 0 61 0 0 0 0 0 62 0 0 0 0 0 63 0 0 0 0 0 64 0 0 0 0 0 65 0 0 0 0 0 66 0 0 0 0 0 67 0 0 0 0 0 68 0 0 0 0 0 69 0 0 0 0 0 70 0 0 0 0 0 71 0 0 0 0 0 72 0 0 0 0 0 73 0 0 0 0 0 74 0 0 0 0 0 75 0 0 0 0 0 76 0 0 0 0 0 77 0 0 0 0 0 78 0 0 0 0 0 79 0 0 0 0 0 80 0 0 0 0 0 81 0 0 0 0 0 82 0 0 0 0 0 83 0 0 0 0 0 84 0 0 0 0 0 85 0 0 0 0 0 86 0 0 0 0 0 87 0 0 0 0 0 88 0 0 0 0 0 89 0 0 0 0 0 90 0 0 0 0 0 91 0 0 0 0 0 92 0 0 0 0 0 93 0 0 0 0 0 94 0 0 0 0 0 95 0 0 0 0 0 96 0 0 0 0 0 97 0 0 0 0 0 98 0 0 0 0 0 99 0 0 0 0 0 100 1 1 0 0 2 adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/combined_output/keep_mate1/000077500000000000000000000000001350370616400326525ustar00rootroot00000000000000info.json000066400000000000000000000001561350370616400344230ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/combined_output/keep_mate1{ "arguments": ["--combined-output", "--minlength", "100", "--trimns"], "return_code": 0, "stderr": [ ] } input_1.fastq000066400000000000000000000003561350370616400352160ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/combined_output/keep_mate1@ATAGCCSeq_1_2959_500/1 meta data TATCGAGCAACTCACCAAGTTCCTTTGATCCGAGGAACTACCCTTACGCCCATCGACGCTTGTTATTCCGGCCTCATATTGGAAGCTACACGCTAGACCA + JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! input_2.fastq000066400000000000000000000003561350370616400352170ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/combined_output/keep_mate1@ATAGCCSeq_1_2959_500/2 data meta CATCTGGATTGTCGATCGCTGCCACCACTAGCCGGGTTTTTCTTTTGTAGTGGTCTAGCGTGTAGCTTCCAATATGAGGCCGGAATAACAAGCGTCGATN + JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! your_output.pair1.truncated000066400000000000000000000003561350370616400401430ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/combined_output/keep_mate1@ATAGCCSeq_1_2959_500/1 meta data TATCGAGCAACTCACCAAGTTCCTTTGATCCGAGGAACTACCCTTACGCCCATCGACGCTTGTTATTCCGGCCTCATATTGGAAGCTACACGCTAGACCA + JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! your_output.pair2.truncated000066400000000000000000000000501350370616400401330ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/combined_output/keep_mate1@ATAGCCSeq_1_2959_500/2 data meta N + ! your_output.settings000066400000000000000000000047301350370616400367770ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/combined_output/keep_mate1AdapterRemoval ver. 2.1.7 Trimming of paired-end reads [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 2898275634 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: Yes Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 100 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 [Trimming statistics] Total number of read pairs: 1 Number of unaligned read pairs: 0 Number of well aligned read pairs: 1 Number of discarded mate 1 reads: 0 Number of singleton mate 1 reads: 1 Number of discarded mate 2 reads: 1 Number of singleton mate 2 reads: 0 Number of reads with adapters[1]: 0 Number of retained reads: 1 Number of retained nucleotides: 100 Average length of retained reads: 100 [Length distribution] Length Mate1 Mate2 Singleton Discarded All 0 0 0 0 0 0 1 0 0 0 0 0 2 0 0 0 0 0 3 0 0 0 0 0 4 0 0 0 0 0 5 0 0 0 0 0 6 0 0 0 0 0 7 0 0 0 0 0 8 0 0 0 0 0 9 0 0 0 0 0 10 0 0 0 0 0 11 0 0 0 0 0 12 0 0 0 0 0 13 0 0 0 0 0 14 0 0 0 0 0 15 0 0 0 0 0 16 0 0 0 0 0 17 0 0 0 0 0 18 0 0 0 0 0 19 0 0 0 0 0 20 0 0 0 0 0 21 0 0 0 0 0 22 0 0 0 0 0 23 0 0 0 0 0 24 0 0 0 0 0 25 0 0 0 0 0 26 0 0 0 0 0 27 0 0 0 0 0 28 0 0 0 0 0 29 0 0 0 0 0 30 0 0 0 0 0 31 0 0 0 0 0 32 0 0 0 0 0 33 0 0 0 0 0 34 0 0 0 0 0 35 0 0 0 0 0 36 0 0 0 0 0 37 0 0 0 0 0 38 0 0 0 0 0 39 0 0 0 0 0 40 0 0 0 0 0 41 0 0 0 0 0 42 0 0 0 0 0 43 0 0 0 0 0 44 0 0 0 0 0 45 0 0 0 0 0 46 0 0 0 0 0 47 0 0 0 0 0 48 0 0 0 0 0 49 0 0 0 0 0 50 0 0 0 0 0 51 0 0 0 0 0 52 0 0 0 0 0 53 0 0 0 0 0 54 0 0 0 0 0 55 0 0 0 0 0 56 0 0 0 0 0 57 0 0 0 0 0 58 0 0 0 0 0 59 0 0 0 0 0 60 0 0 0 0 0 61 0 0 0 0 0 62 0 0 0 0 0 63 0 0 0 0 0 64 0 0 0 0 0 65 0 0 0 0 0 66 0 0 0 0 0 67 0 0 0 0 0 68 0 0 0 0 0 69 0 0 0 0 0 70 0 0 0 0 0 71 0 0 0 0 0 72 0 0 0 0 0 73 0 0 0 0 0 74 0 0 0 0 0 75 0 0 0 0 0 76 0 0 0 0 0 77 0 0 0 0 0 78 0 0 0 0 0 79 0 0 0 0 0 80 0 0 0 0 0 81 0 0 0 0 0 82 0 0 0 0 0 83 0 0 0 0 0 84 0 0 0 0 0 85 0 0 0 0 0 86 0 0 0 0 0 87 0 0 0 0 0 88 0 0 0 0 0 89 0 0 0 0 0 90 0 0 0 0 0 91 0 0 0 0 0 92 0 0 0 0 0 93 0 0 0 0 0 94 0 0 0 0 0 95 0 0 0 0 0 96 0 0 0 0 0 97 0 0 0 0 0 98 0 0 0 0 0 99 0 0 0 1 1 100 0 0 1 0 1 adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/combined_output/keep_mate2/000077500000000000000000000000001350370616400326535ustar00rootroot00000000000000info.json000066400000000000000000000001561350370616400344240ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/combined_output/keep_mate2{ "arguments": ["--combined-output", "--minlength", "100", "--trimns"], "return_code": 0, "stderr": [ ] } input_1.fastq000066400000000000000000000003561350370616400352170ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/combined_output/keep_mate2@ATAGCCSeq_1_2959_500/1 meta data TATCGAGCAACTCACCAAGTTCCTTTGATCCGAGGAACTACCCTTACGCCCATCGACGCTTGTTATTCCGGCCTCATATTGGAAGCTACACGCTAGACCN + JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! input_2.fastq000066400000000000000000000003561350370616400352200ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/combined_output/keep_mate2@ATAGCCSeq_1_2959_500/2 data meta CATCTGGATTGTCGATCGCTGCCACCACTAGCCGGGTTTTTCTTTTGTAGTGGTCTAGCGTGTAGCTTCCAATATGAGGCCGGAATAACAAGCGTCGATG + JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! your_output.pair1.truncated000066400000000000000000000000501350370616400401330ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/combined_output/keep_mate2@ATAGCCSeq_1_2959_500/1 meta data N + ! your_output.pair2.truncated000066400000000000000000000003561350370616400401450ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/combined_output/keep_mate2@ATAGCCSeq_1_2959_500/2 data meta CATCTGGATTGTCGATCGCTGCCACCACTAGCCGGGTTTTTCTTTTGTAGTGGTCTAGCGTGTAGCTTCCAATATGAGGCCGGAATAACAAGCGTCGATG + JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! your_output.settings000066400000000000000000000047301350370616400370000ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/combined_output/keep_mate2AdapterRemoval ver. 2.1.7 Trimming of paired-end reads [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 1902493234 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: Yes Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 100 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 [Trimming statistics] Total number of read pairs: 1 Number of unaligned read pairs: 0 Number of well aligned read pairs: 1 Number of discarded mate 1 reads: 1 Number of singleton mate 1 reads: 0 Number of discarded mate 2 reads: 0 Number of singleton mate 2 reads: 1 Number of reads with adapters[1]: 0 Number of retained reads: 1 Number of retained nucleotides: 100 Average length of retained reads: 100 [Length distribution] Length Mate1 Mate2 Singleton Discarded All 0 0 0 0 0 0 1 0 0 0 0 0 2 0 0 0 0 0 3 0 0 0 0 0 4 0 0 0 0 0 5 0 0 0 0 0 6 0 0 0 0 0 7 0 0 0 0 0 8 0 0 0 0 0 9 0 0 0 0 0 10 0 0 0 0 0 11 0 0 0 0 0 12 0 0 0 0 0 13 0 0 0 0 0 14 0 0 0 0 0 15 0 0 0 0 0 16 0 0 0 0 0 17 0 0 0 0 0 18 0 0 0 0 0 19 0 0 0 0 0 20 0 0 0 0 0 21 0 0 0 0 0 22 0 0 0 0 0 23 0 0 0 0 0 24 0 0 0 0 0 25 0 0 0 0 0 26 0 0 0 0 0 27 0 0 0 0 0 28 0 0 0 0 0 29 0 0 0 0 0 30 0 0 0 0 0 31 0 0 0 0 0 32 0 0 0 0 0 33 0 0 0 0 0 34 0 0 0 0 0 35 0 0 0 0 0 36 0 0 0 0 0 37 0 0 0 0 0 38 0 0 0 0 0 39 0 0 0 0 0 40 0 0 0 0 0 41 0 0 0 0 0 42 0 0 0 0 0 43 0 0 0 0 0 44 0 0 0 0 0 45 0 0 0 0 0 46 0 0 0 0 0 47 0 0 0 0 0 48 0 0 0 0 0 49 0 0 0 0 0 50 0 0 0 0 0 51 0 0 0 0 0 52 0 0 0 0 0 53 0 0 0 0 0 54 0 0 0 0 0 55 0 0 0 0 0 56 0 0 0 0 0 57 0 0 0 0 0 58 0 0 0 0 0 59 0 0 0 0 0 60 0 0 0 0 0 61 0 0 0 0 0 62 0 0 0 0 0 63 0 0 0 0 0 64 0 0 0 0 0 65 0 0 0 0 0 66 0 0 0 0 0 67 0 0 0 0 0 68 0 0 0 0 0 69 0 0 0 0 0 70 0 0 0 0 0 71 0 0 0 0 0 72 0 0 0 0 0 73 0 0 0 0 0 74 0 0 0 0 0 75 0 0 0 0 0 76 0 0 0 0 0 77 0 0 0 0 0 78 0 0 0 0 0 79 0 0 0 0 0 80 0 0 0 0 0 81 0 0 0 0 0 82 0 0 0 0 0 83 0 0 0 0 0 84 0 0 0 0 0 85 0 0 0 0 0 86 0 0 0 0 0 87 0 0 0 0 0 88 0 0 0 0 0 89 0 0 0 0 0 90 0 0 0 0 0 91 0 0 0 0 0 92 0 0 0 0 0 93 0 0 0 0 0 94 0 0 0 0 0 95 0 0 0 0 0 96 0 0 0 0 0 97 0 0 0 0 0 98 0 0 0 0 0 99 0 0 0 1 1 100 0 0 1 0 1 adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/combined_output/keep_neither/000077500000000000000000000000001350370616400333015ustar00rootroot00000000000000info.json000066400000000000000000000001561350370616400350520ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/combined_output/keep_neither{ "arguments": ["--combined-output", "--minlength", "100", "--trimns"], "return_code": 0, "stderr": [ ] } input_1.fastq000066400000000000000000000003561350370616400356450ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/combined_output/keep_neither@ATAGCCSeq_1_2959_500/1 meta data TATCGAGCAACTCACCAAGTTCCTTTGATCCGAGGAACTACCCTTACGCCCATCGACGCTTGTTATTCCGGCCTCATATTGGAAGCTACACGCTAGACCN + JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! input_2.fastq000066400000000000000000000003561350370616400356460ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/combined_output/keep_neither@ATAGCCSeq_1_2959_500/2 data meta CATCTGGATTGTCGATCGCTGCCACCACTAGCCGGGTTTTTCTTTTGTAGTGGTCTAGCGTGTAGCTTCCAATATGAGGCCGGAATAACAAGCGTCGATN + JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! your_output.pair1.truncated000066400000000000000000000000501350370616400405610ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/combined_output/keep_neither@ATAGCCSeq_1_2959_500/1 meta data N + ! your_output.pair2.truncated000066400000000000000000000000501350370616400405620ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/combined_output/keep_neither@ATAGCCSeq_1_2959_500/2 data meta N + ! your_output.settings000066400000000000000000000047061350370616400374310ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/combined_output/keep_neitherAdapterRemoval ver. 2.1.7 Trimming of paired-end reads [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 4016683054 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: Yes Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 100 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 [Trimming statistics] Total number of read pairs: 1 Number of unaligned read pairs: 0 Number of well aligned read pairs: 1 Number of discarded mate 1 reads: 1 Number of singleton mate 1 reads: 0 Number of discarded mate 2 reads: 1 Number of singleton mate 2 reads: 0 Number of reads with adapters[1]: 0 Number of retained reads: 0 Number of retained nucleotides: 0 Average length of retained reads: 0 [Length distribution] Length Mate1 Mate2 Singleton Discarded All 0 0 0 0 0 0 1 0 0 0 0 0 2 0 0 0 0 0 3 0 0 0 0 0 4 0 0 0 0 0 5 0 0 0 0 0 6 0 0 0 0 0 7 0 0 0 0 0 8 0 0 0 0 0 9 0 0 0 0 0 10 0 0 0 0 0 11 0 0 0 0 0 12 0 0 0 0 0 13 0 0 0 0 0 14 0 0 0 0 0 15 0 0 0 0 0 16 0 0 0 0 0 17 0 0 0 0 0 18 0 0 0 0 0 19 0 0 0 0 0 20 0 0 0 0 0 21 0 0 0 0 0 22 0 0 0 0 0 23 0 0 0 0 0 24 0 0 0 0 0 25 0 0 0 0 0 26 0 0 0 0 0 27 0 0 0 0 0 28 0 0 0 0 0 29 0 0 0 0 0 30 0 0 0 0 0 31 0 0 0 0 0 32 0 0 0 0 0 33 0 0 0 0 0 34 0 0 0 0 0 35 0 0 0 0 0 36 0 0 0 0 0 37 0 0 0 0 0 38 0 0 0 0 0 39 0 0 0 0 0 40 0 0 0 0 0 41 0 0 0 0 0 42 0 0 0 0 0 43 0 0 0 0 0 44 0 0 0 0 0 45 0 0 0 0 0 46 0 0 0 0 0 47 0 0 0 0 0 48 0 0 0 0 0 49 0 0 0 0 0 50 0 0 0 0 0 51 0 0 0 0 0 52 0 0 0 0 0 53 0 0 0 0 0 54 0 0 0 0 0 55 0 0 0 0 0 56 0 0 0 0 0 57 0 0 0 0 0 58 0 0 0 0 0 59 0 0 0 0 0 60 0 0 0 0 0 61 0 0 0 0 0 62 0 0 0 0 0 63 0 0 0 0 0 64 0 0 0 0 0 65 0 0 0 0 0 66 0 0 0 0 0 67 0 0 0 0 0 68 0 0 0 0 0 69 0 0 0 0 0 70 0 0 0 0 0 71 0 0 0 0 0 72 0 0 0 0 0 73 0 0 0 0 0 74 0 0 0 0 0 75 0 0 0 0 0 76 0 0 0 0 0 77 0 0 0 0 0 78 0 0 0 0 0 79 0 0 0 0 0 80 0 0 0 0 0 81 0 0 0 0 0 82 0 0 0 0 0 83 0 0 0 0 0 84 0 0 0 0 0 85 0 0 0 0 0 86 0 0 0 0 0 87 0 0 0 0 0 88 0 0 0 0 0 89 0 0 0 0 0 90 0 0 0 0 0 91 0 0 0 0 0 92 0 0 0 0 0 93 0 0 0 0 0 94 0 0 0 0 0 95 0 0 0 0 0 96 0 0 0 0 0 97 0 0 0 0 0 98 0 0 0 0 0 99 0 0 0 2 2 adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/crlf_newlines/000077500000000000000000000000001350370616400302715ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/crlf_newlines/info.json000066400000000000000000000000711350370616400321150ustar00rootroot00000000000000{ "arguments": [], "return_code": 0, "stderr": [ ] } adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/crlf_newlines/input_1.fastq000066400000000000000000000003621350370616400327110ustar00rootroot00000000000000@ATAGCCSeq_1_2959_500/1 meta data TATCGAGCAACTCACCAAGTTCCTTTGATCCGAGGAACTACCCTTACGCCCATCGACGCTTGTTATTCCGGCCTCATATTGGAAGCTACACGCTAGACCA + JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/crlf_newlines/input_2.fastq000066400000000000000000000003621350370616400327120ustar00rootroot00000000000000@ATAGCCSeq_1_2959_500/2 data meta CATCTGGATTGTCGATCGCTGCCACCACTAGCCGGGTTTTTCTTTTGTAGTGGTCTAGCGTGTAGCTTCCAATATGAGGCCGGAATAACAAGCGTCGATG + JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! your_output.discarded000066400000000000000000000000001350370616400344620ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/crlf_newlinesyour_output.pair1.truncated000066400000000000000000000003561350370616400355620ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/crlf_newlines@ATAGCCSeq_1_2959_500/1 meta data TATCGAGCAACTCACCAAGTTCCTTTGATCCGAGGAACTACCCTTACGCCCATCGACGCTTGTTATTCCGGCCTCATATTGGAAGCTACACGCTAGACCA + JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! your_output.pair2.truncated000066400000000000000000000003561350370616400355630ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/crlf_newlines@ATAGCCSeq_1_2959_500/2 data meta CATCTGGATTGTCGATCGCTGCCACCACTAGCCGGGTTTTTCTTTTGTAGTGGTCTAGCGTGTAGCTTCCAATATGAGGCCGGAATAACAAGCGTCGATG + JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/crlf_newlines/your_output.settings000066400000000000000000000047241350370616400345000ustar00rootroot00000000000000AdapterRemoval ver. 2.1.7 Trimming of paired-end reads [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 11384421 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 [Trimming statistics] Total number of read pairs: 1 Number of unaligned read pairs: 0 Number of well aligned read pairs: 1 Number of discarded mate 1 reads: 0 Number of singleton mate 1 reads: 0 Number of discarded mate 2 reads: 0 Number of singleton mate 2 reads: 0 Number of reads with adapters[1]: 0 Number of retained reads: 2 Number of retained nucleotides: 200 Average length of retained reads: 100 [Length distribution] Length Mate1 Mate2 Singleton Discarded All 0 0 0 0 0 0 1 0 0 0 0 0 2 0 0 0 0 0 3 0 0 0 0 0 4 0 0 0 0 0 5 0 0 0 0 0 6 0 0 0 0 0 7 0 0 0 0 0 8 0 0 0 0 0 9 0 0 0 0 0 10 0 0 0 0 0 11 0 0 0 0 0 12 0 0 0 0 0 13 0 0 0 0 0 14 0 0 0 0 0 15 0 0 0 0 0 16 0 0 0 0 0 17 0 0 0 0 0 18 0 0 0 0 0 19 0 0 0 0 0 20 0 0 0 0 0 21 0 0 0 0 0 22 0 0 0 0 0 23 0 0 0 0 0 24 0 0 0 0 0 25 0 0 0 0 0 26 0 0 0 0 0 27 0 0 0 0 0 28 0 0 0 0 0 29 0 0 0 0 0 30 0 0 0 0 0 31 0 0 0 0 0 32 0 0 0 0 0 33 0 0 0 0 0 34 0 0 0 0 0 35 0 0 0 0 0 36 0 0 0 0 0 37 0 0 0 0 0 38 0 0 0 0 0 39 0 0 0 0 0 40 0 0 0 0 0 41 0 0 0 0 0 42 0 0 0 0 0 43 0 0 0 0 0 44 0 0 0 0 0 45 0 0 0 0 0 46 0 0 0 0 0 47 0 0 0 0 0 48 0 0 0 0 0 49 0 0 0 0 0 50 0 0 0 0 0 51 0 0 0 0 0 52 0 0 0 0 0 53 0 0 0 0 0 54 0 0 0 0 0 55 0 0 0 0 0 56 0 0 0 0 0 57 0 0 0 0 0 58 0 0 0 0 0 59 0 0 0 0 0 60 0 0 0 0 0 61 0 0 0 0 0 62 0 0 0 0 0 63 0 0 0 0 0 64 0 0 0 0 0 65 0 0 0 0 0 66 0 0 0 0 0 67 0 0 0 0 0 68 0 0 0 0 0 69 0 0 0 0 0 70 0 0 0 0 0 71 0 0 0 0 0 72 0 0 0 0 0 73 0 0 0 0 0 74 0 0 0 0 0 75 0 0 0 0 0 76 0 0 0 0 0 77 0 0 0 0 0 78 0 0 0 0 0 79 0 0 0 0 0 80 0 0 0 0 0 81 0 0 0 0 0 82 0 0 0 0 0 83 0 0 0 0 0 84 0 0 0 0 0 85 0 0 0 0 0 86 0 0 0 0 0 87 0 0 0 0 0 88 0 0 0 0 0 89 0 0 0 0 0 90 0 0 0 0 0 91 0 0 0 0 0 92 0 0 0 0 0 93 0 0 0 0 0 94 0 0 0 0 0 95 0 0 0 0 0 96 0 0 0 0 0 97 0 0 0 0 0 98 0 0 0 0 0 99 0 0 0 0 0 100 1 1 0 0 2 your_output.singleton.truncated000066400000000000000000000000001350370616400365320ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/crlf_newlinesadapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/defaults/000077500000000000000000000000001350370616400272465ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/defaults/info.json000066400000000000000000000000711350370616400310720ustar00rootroot00000000000000{ "arguments": [], "return_code": 0, "stderr": [ ] } adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/defaults/input_1.fastq000066400000000000000000000003561350370616400316710ustar00rootroot00000000000000@ATAGCCSeq_1_2959_500/1 meta data TATCGAGCAACTCACCAAGTTCCTTTGATCCGAGGAACTACCCTTACGCCCATCGACGCTTGTTATTCCGGCCTCATATTGGAAGCTACACGCTAGACCA + JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/defaults/input_2.fastq000066400000000000000000000003561350370616400316720ustar00rootroot00000000000000@ATAGCCSeq_1_2959_500/2 data meta CATCTGGATTGTCGATCGCTGCCACCACTAGCCGGGTTTTTCTTTTGTAGTGGTCTAGCGTGTAGCTTCCAATATGAGGCCGGAATAACAAGCGTCGATG + JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/defaults/your_output.discarded000066400000000000000000000000001350370616400335160ustar00rootroot00000000000000your_output.pair1.truncated000066400000000000000000000003561350370616400345370ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/defaults@ATAGCCSeq_1_2959_500/1 meta data TATCGAGCAACTCACCAAGTTCCTTTGATCCGAGGAACTACCCTTACGCCCATCGACGCTTGTTATTCCGGCCTCATATTGGAAGCTACACGCTAGACCA + JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! your_output.pair2.truncated000066400000000000000000000003561350370616400345400ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/defaults@ATAGCCSeq_1_2959_500/2 data meta CATCTGGATTGTCGATCGCTGCCACCACTAGCCGGGTTTTTCTTTTGTAGTGGTCTAGCGTGTAGCTTCCAATATGAGGCCGGAATAACAAGCGTCGATG + JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/defaults/your_output.settings000066400000000000000000000047241350370616400334550ustar00rootroot00000000000000AdapterRemoval ver. 2.1.7 Trimming of paired-end reads [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 11384421 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 [Trimming statistics] Total number of read pairs: 1 Number of unaligned read pairs: 0 Number of well aligned read pairs: 1 Number of discarded mate 1 reads: 0 Number of singleton mate 1 reads: 0 Number of discarded mate 2 reads: 0 Number of singleton mate 2 reads: 0 Number of reads with adapters[1]: 0 Number of retained reads: 2 Number of retained nucleotides: 200 Average length of retained reads: 100 [Length distribution] Length Mate1 Mate2 Singleton Discarded All 0 0 0 0 0 0 1 0 0 0 0 0 2 0 0 0 0 0 3 0 0 0 0 0 4 0 0 0 0 0 5 0 0 0 0 0 6 0 0 0 0 0 7 0 0 0 0 0 8 0 0 0 0 0 9 0 0 0 0 0 10 0 0 0 0 0 11 0 0 0 0 0 12 0 0 0 0 0 13 0 0 0 0 0 14 0 0 0 0 0 15 0 0 0 0 0 16 0 0 0 0 0 17 0 0 0 0 0 18 0 0 0 0 0 19 0 0 0 0 0 20 0 0 0 0 0 21 0 0 0 0 0 22 0 0 0 0 0 23 0 0 0 0 0 24 0 0 0 0 0 25 0 0 0 0 0 26 0 0 0 0 0 27 0 0 0 0 0 28 0 0 0 0 0 29 0 0 0 0 0 30 0 0 0 0 0 31 0 0 0 0 0 32 0 0 0 0 0 33 0 0 0 0 0 34 0 0 0 0 0 35 0 0 0 0 0 36 0 0 0 0 0 37 0 0 0 0 0 38 0 0 0 0 0 39 0 0 0 0 0 40 0 0 0 0 0 41 0 0 0 0 0 42 0 0 0 0 0 43 0 0 0 0 0 44 0 0 0 0 0 45 0 0 0 0 0 46 0 0 0 0 0 47 0 0 0 0 0 48 0 0 0 0 0 49 0 0 0 0 0 50 0 0 0 0 0 51 0 0 0 0 0 52 0 0 0 0 0 53 0 0 0 0 0 54 0 0 0 0 0 55 0 0 0 0 0 56 0 0 0 0 0 57 0 0 0 0 0 58 0 0 0 0 0 59 0 0 0 0 0 60 0 0 0 0 0 61 0 0 0 0 0 62 0 0 0 0 0 63 0 0 0 0 0 64 0 0 0 0 0 65 0 0 0 0 0 66 0 0 0 0 0 67 0 0 0 0 0 68 0 0 0 0 0 69 0 0 0 0 0 70 0 0 0 0 0 71 0 0 0 0 0 72 0 0 0 0 0 73 0 0 0 0 0 74 0 0 0 0 0 75 0 0 0 0 0 76 0 0 0 0 0 77 0 0 0 0 0 78 0 0 0 0 0 79 0 0 0 0 0 80 0 0 0 0 0 81 0 0 0 0 0 82 0 0 0 0 0 83 0 0 0 0 0 84 0 0 0 0 0 85 0 0 0 0 0 86 0 0 0 0 0 87 0 0 0 0 0 88 0 0 0 0 0 89 0 0 0 0 0 90 0 0 0 0 0 91 0 0 0 0 0 92 0 0 0 0 0 93 0 0 0 0 0 94 0 0 0 0 0 95 0 0 0 0 0 96 0 0 0 0 0 97 0 0 0 0 0 98 0 0 0 0 0 99 0 0 0 0 0 100 1 1 0 0 2 your_output.singleton.truncated000066400000000000000000000000001350370616400355070ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/defaultsadapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/interleaved/000077500000000000000000000000001350370616400277415ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/interleaved/both/000077500000000000000000000000001350370616400306755ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/interleaved/both/info.json000066400000000000000000000001101350370616400325130ustar00rootroot00000000000000{ "arguments": ["--interleaved"], "return_code": 0, "stderr": [ ] } adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/interleaved/both/input_1.fastq000066400000000000000000000007341350370616400333200ustar00rootroot00000000000000@ATAGCCSeq_1_2959_500/1 meta data TATCGAGCAACTCACCAAGTTCCTTTGATCCGAGGAACTACCCTTACGCCCATCGACGCTTGTTATTCCGGCCTCATATTGGAAGCTACACGCTAGACCA + JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! @ATAGCCSeq_1_2959_500/2 data meta CATCTGGATTGTCGATCGCTGCCACCACTAGCCGGGTTTTTCTTTTGTAGTGGTCTAGCGTGTAGCTTCCAATATGAGGCCGGAATAACAAGCGTCGATG + JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! your_output.discarded000066400000000000000000000000001350370616400350660ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/interleaved/bothyour_output.paired.truncated000066400000000000000000000007341350370616400364160ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/interleaved/both@ATAGCCSeq_1_2959_500/1 meta data TATCGAGCAACTCACCAAGTTCCTTTGATCCGAGGAACTACCCTTACGCCCATCGACGCTTGTTATTCCGGCCTCATATTGGAAGCTACACGCTAGACCA + JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! @ATAGCCSeq_1_2959_500/2 data meta CATCTGGATTGTCGATCGCTGCCACCACTAGCCGGGTTTTTCTTTTGTAGTGGTCTAGCGTGTAGCTTCCAATATGAGGCCGGAATAACAAGCGTCGATG + JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! your_output.settings000066400000000000000000000047401350370616400350230ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/interleaved/bothAdapterRemoval ver. 2.1.7 Trimming of interleaved paired-end reads [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 36753401 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 [Trimming statistics] Total number of read pairs: 1 Number of unaligned read pairs: 0 Number of well aligned read pairs: 1 Number of discarded mate 1 reads: 0 Number of singleton mate 1 reads: 0 Number of discarded mate 2 reads: 0 Number of singleton mate 2 reads: 0 Number of reads with adapters[1]: 0 Number of retained reads: 2 Number of retained nucleotides: 200 Average length of retained reads: 100 [Length distribution] Length Mate1 Mate2 Singleton Discarded All 0 0 0 0 0 0 1 0 0 0 0 0 2 0 0 0 0 0 3 0 0 0 0 0 4 0 0 0 0 0 5 0 0 0 0 0 6 0 0 0 0 0 7 0 0 0 0 0 8 0 0 0 0 0 9 0 0 0 0 0 10 0 0 0 0 0 11 0 0 0 0 0 12 0 0 0 0 0 13 0 0 0 0 0 14 0 0 0 0 0 15 0 0 0 0 0 16 0 0 0 0 0 17 0 0 0 0 0 18 0 0 0 0 0 19 0 0 0 0 0 20 0 0 0 0 0 21 0 0 0 0 0 22 0 0 0 0 0 23 0 0 0 0 0 24 0 0 0 0 0 25 0 0 0 0 0 26 0 0 0 0 0 27 0 0 0 0 0 28 0 0 0 0 0 29 0 0 0 0 0 30 0 0 0 0 0 31 0 0 0 0 0 32 0 0 0 0 0 33 0 0 0 0 0 34 0 0 0 0 0 35 0 0 0 0 0 36 0 0 0 0 0 37 0 0 0 0 0 38 0 0 0 0 0 39 0 0 0 0 0 40 0 0 0 0 0 41 0 0 0 0 0 42 0 0 0 0 0 43 0 0 0 0 0 44 0 0 0 0 0 45 0 0 0 0 0 46 0 0 0 0 0 47 0 0 0 0 0 48 0 0 0 0 0 49 0 0 0 0 0 50 0 0 0 0 0 51 0 0 0 0 0 52 0 0 0 0 0 53 0 0 0 0 0 54 0 0 0 0 0 55 0 0 0 0 0 56 0 0 0 0 0 57 0 0 0 0 0 58 0 0 0 0 0 59 0 0 0 0 0 60 0 0 0 0 0 61 0 0 0 0 0 62 0 0 0 0 0 63 0 0 0 0 0 64 0 0 0 0 0 65 0 0 0 0 0 66 0 0 0 0 0 67 0 0 0 0 0 68 0 0 0 0 0 69 0 0 0 0 0 70 0 0 0 0 0 71 0 0 0 0 0 72 0 0 0 0 0 73 0 0 0 0 0 74 0 0 0 0 0 75 0 0 0 0 0 76 0 0 0 0 0 77 0 0 0 0 0 78 0 0 0 0 0 79 0 0 0 0 0 80 0 0 0 0 0 81 0 0 0 0 0 82 0 0 0 0 0 83 0 0 0 0 0 84 0 0 0 0 0 85 0 0 0 0 0 86 0 0 0 0 0 87 0 0 0 0 0 88 0 0 0 0 0 89 0 0 0 0 0 90 0 0 0 0 0 91 0 0 0 0 0 92 0 0 0 0 0 93 0 0 0 0 0 94 0 0 0 0 0 95 0 0 0 0 0 96 0 0 0 0 0 97 0 0 0 0 0 98 0 0 0 0 0 99 0 0 0 0 0 100 1 1 0 0 2 your_output.singleton.truncated000066400000000000000000000000001350370616400371360ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/interleaved/bothadapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/interleaved/output/000077500000000000000000000000001350370616400313015ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/interleaved/output/info.json000066400000000000000000000001171350370616400331260ustar00rootroot00000000000000{ "arguments": ["--interleaved-output"], "return_code": 0, "stderr": [ ] } adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/interleaved/output/input_1.fastq000066400000000000000000000003561350370616400337240ustar00rootroot00000000000000@ATAGCCSeq_1_2959_500/1 meta data TATCGAGCAACTCACCAAGTTCCTTTGATCCGAGGAACTACCCTTACGCCCATCGACGCTTGTTATTCCGGCCTCATATTGGAAGCTACACGCTAGACCA + JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/interleaved/output/input_2.fastq000066400000000000000000000003561350370616400337250ustar00rootroot00000000000000@ATAGCCSeq_1_2959_500/2 data meta CATCTGGATTGTCGATCGCTGCCACCACTAGCCGGGTTTTTCTTTTGTAGTGGTCTAGCGTGTAGCTTCCAATATGAGGCCGGAATAACAAGCGTCGATG + JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! your_output.discarded000066400000000000000000000000001350370616400354720ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/interleaved/outputyour_output.paired.truncated000066400000000000000000000007341350370616400370220ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/interleaved/output@ATAGCCSeq_1_2959_500/1 meta data TATCGAGCAACTCACCAAGTTCCTTTGATCCGAGGAACTACCCTTACGCCCATCGACGCTTGTTATTCCGGCCTCATATTGGAAGCTACACGCTAGACCA + JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! @ATAGCCSeq_1_2959_500/2 data meta CATCTGGATTGTCGATCGCTGCCACCACTAGCCGGGTTTTTCTTTTGTAGTGGTCTAGCGTGTAGCTTCCAATATGAGGCCGGAATAACAAGCGTCGATG + JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! your_output.settings000066400000000000000000000047241350370616400354310ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/interleaved/outputAdapterRemoval ver. 2.1.7 Trimming of paired-end reads [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 32142888 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 [Trimming statistics] Total number of read pairs: 1 Number of unaligned read pairs: 0 Number of well aligned read pairs: 1 Number of discarded mate 1 reads: 0 Number of singleton mate 1 reads: 0 Number of discarded mate 2 reads: 0 Number of singleton mate 2 reads: 0 Number of reads with adapters[1]: 0 Number of retained reads: 2 Number of retained nucleotides: 200 Average length of retained reads: 100 [Length distribution] Length Mate1 Mate2 Singleton Discarded All 0 0 0 0 0 0 1 0 0 0 0 0 2 0 0 0 0 0 3 0 0 0 0 0 4 0 0 0 0 0 5 0 0 0 0 0 6 0 0 0 0 0 7 0 0 0 0 0 8 0 0 0 0 0 9 0 0 0 0 0 10 0 0 0 0 0 11 0 0 0 0 0 12 0 0 0 0 0 13 0 0 0 0 0 14 0 0 0 0 0 15 0 0 0 0 0 16 0 0 0 0 0 17 0 0 0 0 0 18 0 0 0 0 0 19 0 0 0 0 0 20 0 0 0 0 0 21 0 0 0 0 0 22 0 0 0 0 0 23 0 0 0 0 0 24 0 0 0 0 0 25 0 0 0 0 0 26 0 0 0 0 0 27 0 0 0 0 0 28 0 0 0 0 0 29 0 0 0 0 0 30 0 0 0 0 0 31 0 0 0 0 0 32 0 0 0 0 0 33 0 0 0 0 0 34 0 0 0 0 0 35 0 0 0 0 0 36 0 0 0 0 0 37 0 0 0 0 0 38 0 0 0 0 0 39 0 0 0 0 0 40 0 0 0 0 0 41 0 0 0 0 0 42 0 0 0 0 0 43 0 0 0 0 0 44 0 0 0 0 0 45 0 0 0 0 0 46 0 0 0 0 0 47 0 0 0 0 0 48 0 0 0 0 0 49 0 0 0 0 0 50 0 0 0 0 0 51 0 0 0 0 0 52 0 0 0 0 0 53 0 0 0 0 0 54 0 0 0 0 0 55 0 0 0 0 0 56 0 0 0 0 0 57 0 0 0 0 0 58 0 0 0 0 0 59 0 0 0 0 0 60 0 0 0 0 0 61 0 0 0 0 0 62 0 0 0 0 0 63 0 0 0 0 0 64 0 0 0 0 0 65 0 0 0 0 0 66 0 0 0 0 0 67 0 0 0 0 0 68 0 0 0 0 0 69 0 0 0 0 0 70 0 0 0 0 0 71 0 0 0 0 0 72 0 0 0 0 0 73 0 0 0 0 0 74 0 0 0 0 0 75 0 0 0 0 0 76 0 0 0 0 0 77 0 0 0 0 0 78 0 0 0 0 0 79 0 0 0 0 0 80 0 0 0 0 0 81 0 0 0 0 0 82 0 0 0 0 0 83 0 0 0 0 0 84 0 0 0 0 0 85 0 0 0 0 0 86 0 0 0 0 0 87 0 0 0 0 0 88 0 0 0 0 0 89 0 0 0 0 0 90 0 0 0 0 0 91 0 0 0 0 0 92 0 0 0 0 0 93 0 0 0 0 0 94 0 0 0 0 0 95 0 0 0 0 0 96 0 0 0 0 0 97 0 0 0 0 0 98 0 0 0 0 0 99 0 0 0 0 0 100 1 1 0 0 2 your_output.singleton.truncated000066400000000000000000000000001350370616400375420ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/interleaved/outputadapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/maxlength/000077500000000000000000000000001350370616400274265ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/maxlength/both/000077500000000000000000000000001350370616400303625ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/maxlength/both/info.json000066400000000000000000000001301350370616400322020ustar00rootroot00000000000000{ "arguments": ["--maxlength", "99", "--trimns"], "return_code": 0, "stderr": [ ] } adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/maxlength/both/input_1.fastq000066400000000000000000000003561350370616400330050ustar00rootroot00000000000000@ATAGCCSeq_1_2959_500/1 meta data TATCGAGCAACTCACCAAGTTCCTTTGATCCGAGGAACTACCCTTACGCCCATCGACGCTTGTTATTCCGGCCTCATATTGGAAGCTACACGCTAGACCA + JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/maxlength/both/input_2.fastq000066400000000000000000000003561350370616400330060ustar00rootroot00000000000000@ATAGCCSeq_1_2959_500/2 data meta CATCTGGATTGTCGATCGCTGCCACCACTAGCCGGGTTTTTCTTTTGTAGTGGTCTAGCGTGTAGCTTCCAATATGAGGCCGGAATAACAAGCGTCGATG + JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! your_output.discarded000066400000000000000000000007341350370616400345710ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/maxlength/both@ATAGCCSeq_1_2959_500/1 meta data TATCGAGCAACTCACCAAGTTCCTTTGATCCGAGGAACTACCCTTACGCCCATCGACGCTTGTTATTCCGGCCTCATATTGGAAGCTACACGCTAGACCA + JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! @ATAGCCSeq_1_2959_500/2 data meta CATCTGGATTGTCGATCGCTGCCACCACTAGCCGGGTTTTTCTTTTGTAGTGGTCTAGCGTGTAGCTTCCAATATGAGGCCGGAATAACAAGCGTCGATG + JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! your_output.pair1.truncated000066400000000000000000000000001350370616400356350ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/maxlength/bothyour_output.pair2.truncated000066400000000000000000000000001350370616400356360ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/maxlength/bothyour_output.settings000066400000000000000000000047131350370616400345100ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/maxlength/bothAdapterRemoval ver. 2.1.7 Trimming of paired-end reads [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 2714819290 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: Yes Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 99 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 [Trimming statistics] Total number of read pairs: 1 Number of unaligned read pairs: 0 Number of well aligned read pairs: 1 Number of discarded mate 1 reads: 1 Number of singleton mate 1 reads: 0 Number of discarded mate 2 reads: 1 Number of singleton mate 2 reads: 0 Number of reads with adapters[1]: 0 Number of retained reads: 0 Number of retained nucleotides: 0 Average length of retained reads: 0 [Length distribution] Length Mate1 Mate2 Singleton Discarded All 0 0 0 0 0 0 1 0 0 0 0 0 2 0 0 0 0 0 3 0 0 0 0 0 4 0 0 0 0 0 5 0 0 0 0 0 6 0 0 0 0 0 7 0 0 0 0 0 8 0 0 0 0 0 9 0 0 0 0 0 10 0 0 0 0 0 11 0 0 0 0 0 12 0 0 0 0 0 13 0 0 0 0 0 14 0 0 0 0 0 15 0 0 0 0 0 16 0 0 0 0 0 17 0 0 0 0 0 18 0 0 0 0 0 19 0 0 0 0 0 20 0 0 0 0 0 21 0 0 0 0 0 22 0 0 0 0 0 23 0 0 0 0 0 24 0 0 0 0 0 25 0 0 0 0 0 26 0 0 0 0 0 27 0 0 0 0 0 28 0 0 0 0 0 29 0 0 0 0 0 30 0 0 0 0 0 31 0 0 0 0 0 32 0 0 0 0 0 33 0 0 0 0 0 34 0 0 0 0 0 35 0 0 0 0 0 36 0 0 0 0 0 37 0 0 0 0 0 38 0 0 0 0 0 39 0 0 0 0 0 40 0 0 0 0 0 41 0 0 0 0 0 42 0 0 0 0 0 43 0 0 0 0 0 44 0 0 0 0 0 45 0 0 0 0 0 46 0 0 0 0 0 47 0 0 0 0 0 48 0 0 0 0 0 49 0 0 0 0 0 50 0 0 0 0 0 51 0 0 0 0 0 52 0 0 0 0 0 53 0 0 0 0 0 54 0 0 0 0 0 55 0 0 0 0 0 56 0 0 0 0 0 57 0 0 0 0 0 58 0 0 0 0 0 59 0 0 0 0 0 60 0 0 0 0 0 61 0 0 0 0 0 62 0 0 0 0 0 63 0 0 0 0 0 64 0 0 0 0 0 65 0 0 0 0 0 66 0 0 0 0 0 67 0 0 0 0 0 68 0 0 0 0 0 69 0 0 0 0 0 70 0 0 0 0 0 71 0 0 0 0 0 72 0 0 0 0 0 73 0 0 0 0 0 74 0 0 0 0 0 75 0 0 0 0 0 76 0 0 0 0 0 77 0 0 0 0 0 78 0 0 0 0 0 79 0 0 0 0 0 80 0 0 0 0 0 81 0 0 0 0 0 82 0 0 0 0 0 83 0 0 0 0 0 84 0 0 0 0 0 85 0 0 0 0 0 86 0 0 0 0 0 87 0 0 0 0 0 88 0 0 0 0 0 89 0 0 0 0 0 90 0 0 0 0 0 91 0 0 0 0 0 92 0 0 0 0 0 93 0 0 0 0 0 94 0 0 0 0 0 95 0 0 0 0 0 96 0 0 0 0 0 97 0 0 0 0 0 98 0 0 0 0 0 99 0 0 0 0 0 100 0 0 0 2 2 your_output.singleton.truncated000066400000000000000000000000001350370616400366230ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/maxlength/bothadapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/maxlength/mate1/000077500000000000000000000000001350370616400304355ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/maxlength/mate1/info.json000066400000000000000000000001301350370616400322550ustar00rootroot00000000000000{ "arguments": ["--maxlength", "99", "--trimns"], "return_code": 0, "stderr": [ ] } adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/maxlength/mate1/input_1.fastq000066400000000000000000000003561350370616400330600ustar00rootroot00000000000000@ATAGCCSeq_1_2959_500/1 meta data TATCGAGCAACTCACCAAGTTCCTTTGATCCGAGGAACTACCCTTACGCCCATCGACGCTTGTTATTCCGGCCTCATATTGGAAGCTACACGCTAGACCN + JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/maxlength/mate1/input_2.fastq000066400000000000000000000003561350370616400330610ustar00rootroot00000000000000@ATAGCCSeq_1_2959_500/2 data meta CATCTGGATTGTCGATCGCTGCCACCACTAGCCGGGTTTTTCTTTTGTAGTGGTCTAGCGTGTAGCTTCCAATATGAGGCCGGAATAACAAGCGTCGATG + JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! your_output.discarded000066400000000000000000000003561350370616400346440ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/maxlength/mate1@ATAGCCSeq_1_2959_500/2 data meta CATCTGGATTGTCGATCGCTGCCACCACTAGCCGGGTTTTTCTTTTGTAGTGGTCTAGCGTGTAGCTTCCAATATGAGGCCGGAATAACAAGCGTCGATG + JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! your_output.pair1.truncated000066400000000000000000000000001350370616400357100ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/maxlength/mate1your_output.pair2.truncated000066400000000000000000000000001350370616400357110ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/maxlength/mate1your_output.settings000066400000000000000000000047151350370616400345650ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/maxlength/mate1AdapterRemoval ver. 2.1.7 Trimming of paired-end reads [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 3802049955 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: Yes Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 99 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 [Trimming statistics] Total number of read pairs: 1 Number of unaligned read pairs: 0 Number of well aligned read pairs: 1 Number of discarded mate 1 reads: 0 Number of singleton mate 1 reads: 1 Number of discarded mate 2 reads: 1 Number of singleton mate 2 reads: 0 Number of reads with adapters[1]: 0 Number of retained reads: 1 Number of retained nucleotides: 99 Average length of retained reads: 99 [Length distribution] Length Mate1 Mate2 Singleton Discarded All 0 0 0 0 0 0 1 0 0 0 0 0 2 0 0 0 0 0 3 0 0 0 0 0 4 0 0 0 0 0 5 0 0 0 0 0 6 0 0 0 0 0 7 0 0 0 0 0 8 0 0 0 0 0 9 0 0 0 0 0 10 0 0 0 0 0 11 0 0 0 0 0 12 0 0 0 0 0 13 0 0 0 0 0 14 0 0 0 0 0 15 0 0 0 0 0 16 0 0 0 0 0 17 0 0 0 0 0 18 0 0 0 0 0 19 0 0 0 0 0 20 0 0 0 0 0 21 0 0 0 0 0 22 0 0 0 0 0 23 0 0 0 0 0 24 0 0 0 0 0 25 0 0 0 0 0 26 0 0 0 0 0 27 0 0 0 0 0 28 0 0 0 0 0 29 0 0 0 0 0 30 0 0 0 0 0 31 0 0 0 0 0 32 0 0 0 0 0 33 0 0 0 0 0 34 0 0 0 0 0 35 0 0 0 0 0 36 0 0 0 0 0 37 0 0 0 0 0 38 0 0 0 0 0 39 0 0 0 0 0 40 0 0 0 0 0 41 0 0 0 0 0 42 0 0 0 0 0 43 0 0 0 0 0 44 0 0 0 0 0 45 0 0 0 0 0 46 0 0 0 0 0 47 0 0 0 0 0 48 0 0 0 0 0 49 0 0 0 0 0 50 0 0 0 0 0 51 0 0 0 0 0 52 0 0 0 0 0 53 0 0 0 0 0 54 0 0 0 0 0 55 0 0 0 0 0 56 0 0 0 0 0 57 0 0 0 0 0 58 0 0 0 0 0 59 0 0 0 0 0 60 0 0 0 0 0 61 0 0 0 0 0 62 0 0 0 0 0 63 0 0 0 0 0 64 0 0 0 0 0 65 0 0 0 0 0 66 0 0 0 0 0 67 0 0 0 0 0 68 0 0 0 0 0 69 0 0 0 0 0 70 0 0 0 0 0 71 0 0 0 0 0 72 0 0 0 0 0 73 0 0 0 0 0 74 0 0 0 0 0 75 0 0 0 0 0 76 0 0 0 0 0 77 0 0 0 0 0 78 0 0 0 0 0 79 0 0 0 0 0 80 0 0 0 0 0 81 0 0 0 0 0 82 0 0 0 0 0 83 0 0 0 0 0 84 0 0 0 0 0 85 0 0 0 0 0 86 0 0 0 0 0 87 0 0 0 0 0 88 0 0 0 0 0 89 0 0 0 0 0 90 0 0 0 0 0 91 0 0 0 0 0 92 0 0 0 0 0 93 0 0 0 0 0 94 0 0 0 0 0 95 0 0 0 0 0 96 0 0 0 0 0 97 0 0 0 0 0 98 0 0 0 0 0 99 0 0 1 0 1 100 0 0 0 1 1 your_output.singleton.truncated000066400000000000000000000003541350370616400367120ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/maxlength/mate1@ATAGCCSeq_1_2959_500/1 meta data TATCGAGCAACTCACCAAGTTCCTTTGATCCGAGGAACTACCCTTACGCCCATCGACGCTTGTTATTCCGGCCTCATATTGGAAGCTACACGCTAGACC + JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)' adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/maxlength/mate2/000077500000000000000000000000001350370616400304365ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/maxlength/mate2/info.json000066400000000000000000000001301350370616400322560ustar00rootroot00000000000000{ "arguments": ["--maxlength", "99", "--trimns"], "return_code": 0, "stderr": [ ] } adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/maxlength/mate2/input_1.fastq000066400000000000000000000003561350370616400330610ustar00rootroot00000000000000@ATAGCCSeq_1_2959_500/1 meta data TATCGAGCAACTCACCAAGTTCCTTTGATCCGAGGAACTACCCTTACGCCCATCGACGCTTGTTATTCCGGCCTCATATTGGAAGCTACACGCTAGACCA + JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/maxlength/mate2/input_2.fastq000066400000000000000000000003561350370616400330620ustar00rootroot00000000000000@ATAGCCSeq_1_2959_500/2 data meta CATCTGGATTGTCGATCGCTGCCACCACTAGCCGGGTTTTTCTTTTGTAGTGGTCTAGCGTGTAGCTTCCAATATGAGGCCGGAATAACAAGCGTCGATN + JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! your_output.discarded000066400000000000000000000003561350370616400346450ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/maxlength/mate2@ATAGCCSeq_1_2959_500/1 meta data TATCGAGCAACTCACCAAGTTCCTTTGATCCGAGGAACTACCCTTACGCCCATCGACGCTTGTTATTCCGGCCTCATATTGGAAGCTACACGCTAGACCA + JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! your_output.pair1.truncated000066400000000000000000000000001350370616400357110ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/maxlength/mate2your_output.pair2.truncated000066400000000000000000000000001350370616400357120ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/maxlength/mate2your_output.settings000066400000000000000000000047151350370616400345660ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/maxlength/mate2AdapterRemoval ver. 2.1.7 Trimming of paired-end reads [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 3867243128 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: Yes Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 99 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 [Trimming statistics] Total number of read pairs: 1 Number of unaligned read pairs: 0 Number of well aligned read pairs: 1 Number of discarded mate 1 reads: 1 Number of singleton mate 1 reads: 0 Number of discarded mate 2 reads: 0 Number of singleton mate 2 reads: 1 Number of reads with adapters[1]: 0 Number of retained reads: 1 Number of retained nucleotides: 99 Average length of retained reads: 99 [Length distribution] Length Mate1 Mate2 Singleton Discarded All 0 0 0 0 0 0 1 0 0 0 0 0 2 0 0 0 0 0 3 0 0 0 0 0 4 0 0 0 0 0 5 0 0 0 0 0 6 0 0 0 0 0 7 0 0 0 0 0 8 0 0 0 0 0 9 0 0 0 0 0 10 0 0 0 0 0 11 0 0 0 0 0 12 0 0 0 0 0 13 0 0 0 0 0 14 0 0 0 0 0 15 0 0 0 0 0 16 0 0 0 0 0 17 0 0 0 0 0 18 0 0 0 0 0 19 0 0 0 0 0 20 0 0 0 0 0 21 0 0 0 0 0 22 0 0 0 0 0 23 0 0 0 0 0 24 0 0 0 0 0 25 0 0 0 0 0 26 0 0 0 0 0 27 0 0 0 0 0 28 0 0 0 0 0 29 0 0 0 0 0 30 0 0 0 0 0 31 0 0 0 0 0 32 0 0 0 0 0 33 0 0 0 0 0 34 0 0 0 0 0 35 0 0 0 0 0 36 0 0 0 0 0 37 0 0 0 0 0 38 0 0 0 0 0 39 0 0 0 0 0 40 0 0 0 0 0 41 0 0 0 0 0 42 0 0 0 0 0 43 0 0 0 0 0 44 0 0 0 0 0 45 0 0 0 0 0 46 0 0 0 0 0 47 0 0 0 0 0 48 0 0 0 0 0 49 0 0 0 0 0 50 0 0 0 0 0 51 0 0 0 0 0 52 0 0 0 0 0 53 0 0 0 0 0 54 0 0 0 0 0 55 0 0 0 0 0 56 0 0 0 0 0 57 0 0 0 0 0 58 0 0 0 0 0 59 0 0 0 0 0 60 0 0 0 0 0 61 0 0 0 0 0 62 0 0 0 0 0 63 0 0 0 0 0 64 0 0 0 0 0 65 0 0 0 0 0 66 0 0 0 0 0 67 0 0 0 0 0 68 0 0 0 0 0 69 0 0 0 0 0 70 0 0 0 0 0 71 0 0 0 0 0 72 0 0 0 0 0 73 0 0 0 0 0 74 0 0 0 0 0 75 0 0 0 0 0 76 0 0 0 0 0 77 0 0 0 0 0 78 0 0 0 0 0 79 0 0 0 0 0 80 0 0 0 0 0 81 0 0 0 0 0 82 0 0 0 0 0 83 0 0 0 0 0 84 0 0 0 0 0 85 0 0 0 0 0 86 0 0 0 0 0 87 0 0 0 0 0 88 0 0 0 0 0 89 0 0 0 0 0 90 0 0 0 0 0 91 0 0 0 0 0 92 0 0 0 0 0 93 0 0 0 0 0 94 0 0 0 0 0 95 0 0 0 0 0 96 0 0 0 0 0 97 0 0 0 0 0 98 0 0 0 0 0 99 0 0 1 0 1 100 0 0 0 1 1 your_output.singleton.truncated000066400000000000000000000003541350370616400367130ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/maxlength/mate2@ATAGCCSeq_1_2959_500/2 data meta CATCTGGATTGTCGATCGCTGCCACCACTAGCCGGGTTTTTCTTTTGTAGTGGTCTAGCGTGTAGCTTCCAATATGAGGCCGGAATAACAAGCGTCGAT + JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*& adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/minlength/000077500000000000000000000000001350370616400274245ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/minlength/both/000077500000000000000000000000001350370616400303605ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/minlength/both/info.json000066400000000000000000000001301350370616400322000ustar00rootroot00000000000000{ "arguments": ["--minlength", "90", "--trimns"], "return_code": 0, "stderr": [ ] } adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/minlength/both/input_1.fastq000066400000000000000000000003561350370616400330030ustar00rootroot00000000000000@ATAGCCSeq_1_2959_500/1 meta data TATCGAGCAACTCACCAAGTTCCTTTGATCCGAGGAACTACCCTTACGCCCATCGACGCTTGTTATTCCGGCCTCATATTGGAAGCTACNNNNNNNNNNN + JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/minlength/both/input_2.fastq000066400000000000000000000003561350370616400330040ustar00rootroot00000000000000@ATAGCCSeq_1_2959_500/2 data meta CATCTGGATTGTCGATCGCTGCCACCACTAGCCGGGTTTTTCTTTTGTAGTGGTCTAGCGTGTAGCTTCCAATATGAGGCCGGAATAANNNNNNNNNNNN + JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! your_output.discarded000066400000000000000000000006561350370616400345720ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/minlength/both@ATAGCCSeq_1_2959_500/1 meta data TATCGAGCAACTCACCAAGTTCCTTTGATCCGAGGAACTACCCTTACGCCCATCGACGCTTGTTATTCCGGCCTCATATTGGAAGCTAC + JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777 @ATAGCCSeq_1_2959_500/2 data meta CATCTGGATTGTCGATCGCTGCCACCACTAGCCGGGTTTTTCTTTTGTAGTGGTCTAGCGTGTAGCTTCCAATATGAGGCCGGAATAA + JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:98 your_output.pair1.truncated000066400000000000000000000000001350370616400356330ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/minlength/bothyour_output.pair2.truncated000066400000000000000000000000001350370616400356340ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/minlength/bothyour_output.settings000066400000000000000000000045031350370616400345030ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/minlength/bothAdapterRemoval ver. 2.1.7 Trimming of paired-end reads [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 4291984462 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: Yes Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 90 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 [Trimming statistics] Total number of read pairs: 1 Number of unaligned read pairs: 0 Number of well aligned read pairs: 1 Number of discarded mate 1 reads: 1 Number of singleton mate 1 reads: 0 Number of discarded mate 2 reads: 1 Number of singleton mate 2 reads: 0 Number of reads with adapters[1]: 0 Number of retained reads: 0 Number of retained nucleotides: 0 Average length of retained reads: 0 [Length distribution] Length Mate1 Mate2 Singleton Discarded All 0 0 0 0 0 0 1 0 0 0 0 0 2 0 0 0 0 0 3 0 0 0 0 0 4 0 0 0 0 0 5 0 0 0 0 0 6 0 0 0 0 0 7 0 0 0 0 0 8 0 0 0 0 0 9 0 0 0 0 0 10 0 0 0 0 0 11 0 0 0 0 0 12 0 0 0 0 0 13 0 0 0 0 0 14 0 0 0 0 0 15 0 0 0 0 0 16 0 0 0 0 0 17 0 0 0 0 0 18 0 0 0 0 0 19 0 0 0 0 0 20 0 0 0 0 0 21 0 0 0 0 0 22 0 0 0 0 0 23 0 0 0 0 0 24 0 0 0 0 0 25 0 0 0 0 0 26 0 0 0 0 0 27 0 0 0 0 0 28 0 0 0 0 0 29 0 0 0 0 0 30 0 0 0 0 0 31 0 0 0 0 0 32 0 0 0 0 0 33 0 0 0 0 0 34 0 0 0 0 0 35 0 0 0 0 0 36 0 0 0 0 0 37 0 0 0 0 0 38 0 0 0 0 0 39 0 0 0 0 0 40 0 0 0 0 0 41 0 0 0 0 0 42 0 0 0 0 0 43 0 0 0 0 0 44 0 0 0 0 0 45 0 0 0 0 0 46 0 0 0 0 0 47 0 0 0 0 0 48 0 0 0 0 0 49 0 0 0 0 0 50 0 0 0 0 0 51 0 0 0 0 0 52 0 0 0 0 0 53 0 0 0 0 0 54 0 0 0 0 0 55 0 0 0 0 0 56 0 0 0 0 0 57 0 0 0 0 0 58 0 0 0 0 0 59 0 0 0 0 0 60 0 0 0 0 0 61 0 0 0 0 0 62 0 0 0 0 0 63 0 0 0 0 0 64 0 0 0 0 0 65 0 0 0 0 0 66 0 0 0 0 0 67 0 0 0 0 0 68 0 0 0 0 0 69 0 0 0 0 0 70 0 0 0 0 0 71 0 0 0 0 0 72 0 0 0 0 0 73 0 0 0 0 0 74 0 0 0 0 0 75 0 0 0 0 0 76 0 0 0 0 0 77 0 0 0 0 0 78 0 0 0 0 0 79 0 0 0 0 0 80 0 0 0 0 0 81 0 0 0 0 0 82 0 0 0 0 0 83 0 0 0 0 0 84 0 0 0 0 0 85 0 0 0 0 0 86 0 0 0 0 0 87 0 0 0 0 0 88 0 0 0 1 1 89 0 0 0 1 1 your_output.singleton.truncated000066400000000000000000000000001350370616400366210ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/minlength/bothadapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/minlength/mate1/000077500000000000000000000000001350370616400304335ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/minlength/mate1/info.json000066400000000000000000000001301350370616400322530ustar00rootroot00000000000000{ "arguments": ["--minlength", "90", "--trimns"], "return_code": 0, "stderr": [ ] } adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/minlength/mate1/input_1.fastq000066400000000000000000000003561350370616400330560ustar00rootroot00000000000000@ATAGCCSeq_1_2959_500/1 meta data TATCGAGCAACTCACCAAGTTCCTTTGATCCGAGGAACTACCCTTACGCCCATCGACGCTTGTTATTCCGGCCTCATATTGGAAGCTACNNNNNNNNNNN + JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/minlength/mate1/input_2.fastq000066400000000000000000000003561350370616400330570ustar00rootroot00000000000000@ATAGCCSeq_1_2959_500/2 data meta CATCTGGATTGTCGATCGCTGCCACCACTAGCCGGGTTTTTCTTTTGTAGTGGTCTAGCGTGTAGCTTCCAATATGAGGCCGGAATAACAAGCGTCGATG + JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! your_output.discarded000066400000000000000000000003301350370616400346320ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/minlength/mate1@ATAGCCSeq_1_2959_500/1 meta data TATCGAGCAACTCACCAAGTTCCTTTGATCCGAGGAACTACCCTTACGCCCATCGACGCTTGTTATTCCGGCCTCATATTGGAAGCTAC + JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777 your_output.pair1.truncated000066400000000000000000000000001350370616400357060ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/minlength/mate1your_output.pair2.truncated000066400000000000000000000000001350370616400357070ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/minlength/mate1your_output.settings000066400000000000000000000047271350370616400345660ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/minlength/mate1AdapterRemoval ver. 2.1.7 Trimming of paired-end reads [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 4294353461 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: Yes Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 90 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 [Trimming statistics] Total number of read pairs: 1 Number of unaligned read pairs: 0 Number of well aligned read pairs: 1 Number of discarded mate 1 reads: 1 Number of singleton mate 1 reads: 0 Number of discarded mate 2 reads: 0 Number of singleton mate 2 reads: 1 Number of reads with adapters[1]: 0 Number of retained reads: 1 Number of retained nucleotides: 100 Average length of retained reads: 100 [Length distribution] Length Mate1 Mate2 Singleton Discarded All 0 0 0 0 0 0 1 0 0 0 0 0 2 0 0 0 0 0 3 0 0 0 0 0 4 0 0 0 0 0 5 0 0 0 0 0 6 0 0 0 0 0 7 0 0 0 0 0 8 0 0 0 0 0 9 0 0 0 0 0 10 0 0 0 0 0 11 0 0 0 0 0 12 0 0 0 0 0 13 0 0 0 0 0 14 0 0 0 0 0 15 0 0 0 0 0 16 0 0 0 0 0 17 0 0 0 0 0 18 0 0 0 0 0 19 0 0 0 0 0 20 0 0 0 0 0 21 0 0 0 0 0 22 0 0 0 0 0 23 0 0 0 0 0 24 0 0 0 0 0 25 0 0 0 0 0 26 0 0 0 0 0 27 0 0 0 0 0 28 0 0 0 0 0 29 0 0 0 0 0 30 0 0 0 0 0 31 0 0 0 0 0 32 0 0 0 0 0 33 0 0 0 0 0 34 0 0 0 0 0 35 0 0 0 0 0 36 0 0 0 0 0 37 0 0 0 0 0 38 0 0 0 0 0 39 0 0 0 0 0 40 0 0 0 0 0 41 0 0 0 0 0 42 0 0 0 0 0 43 0 0 0 0 0 44 0 0 0 0 0 45 0 0 0 0 0 46 0 0 0 0 0 47 0 0 0 0 0 48 0 0 0 0 0 49 0 0 0 0 0 50 0 0 0 0 0 51 0 0 0 0 0 52 0 0 0 0 0 53 0 0 0 0 0 54 0 0 0 0 0 55 0 0 0 0 0 56 0 0 0 0 0 57 0 0 0 0 0 58 0 0 0 0 0 59 0 0 0 0 0 60 0 0 0 0 0 61 0 0 0 0 0 62 0 0 0 0 0 63 0 0 0 0 0 64 0 0 0 0 0 65 0 0 0 0 0 66 0 0 0 0 0 67 0 0 0 0 0 68 0 0 0 0 0 69 0 0 0 0 0 70 0 0 0 0 0 71 0 0 0 0 0 72 0 0 0 0 0 73 0 0 0 0 0 74 0 0 0 0 0 75 0 0 0 0 0 76 0 0 0 0 0 77 0 0 0 0 0 78 0 0 0 0 0 79 0 0 0 0 0 80 0 0 0 0 0 81 0 0 0 0 0 82 0 0 0 0 0 83 0 0 0 0 0 84 0 0 0 0 0 85 0 0 0 0 0 86 0 0 0 0 0 87 0 0 0 0 0 88 0 0 0 0 0 89 0 0 0 1 1 90 0 0 0 0 0 91 0 0 0 0 0 92 0 0 0 0 0 93 0 0 0 0 0 94 0 0 0 0 0 95 0 0 0 0 0 96 0 0 0 0 0 97 0 0 0 0 0 98 0 0 0 0 0 99 0 0 0 0 0 100 0 0 1 0 1 your_output.singleton.truncated000066400000000000000000000003561350370616400367120ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/minlength/mate1@ATAGCCSeq_1_2959_500/2 data meta CATCTGGATTGTCGATCGCTGCCACCACTAGCCGGGTTTTTCTTTTGTAGTGGTCTAGCGTGTAGCTTCCAATATGAGGCCGGAATAACAAGCGTCGATG + JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/minlength/mate2/000077500000000000000000000000001350370616400304345ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/minlength/mate2/info.json000066400000000000000000000001301350370616400322540ustar00rootroot00000000000000{ "arguments": ["--minlength", "90", "--trimns"], "return_code": 0, "stderr": [ ] } adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/minlength/mate2/input_1.fastq000066400000000000000000000003561350370616400330570ustar00rootroot00000000000000@ATAGCCSeq_1_2959_500/1 meta data TATCGAGCAACTCACCAAGTTCCTTTGATCCGAGGAACTACCCTTACGCCCATCGACGCTTGTTATTCCGGCCTCATATTGGAAGCTACACGCTAGACCA + JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/minlength/mate2/input_2.fastq000066400000000000000000000003561350370616400330600ustar00rootroot00000000000000@ATAGCCSeq_1_2959_500/2 data meta CATCTGGATTGTCGATCGCTGCCACCACTAGCCGGGTTTTTCTTTTGTAGTGGTCTAGCGTGTAGCTTCCAATATGAGGCCGGAATAANNNNNNNNNNNN + JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! your_output.discarded000066400000000000000000000003261350370616400346400ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/minlength/mate2@ATAGCCSeq_1_2959_500/2 data meta CATCTGGATTGTCGATCGCTGCCACCACTAGCCGGGTTTTTCTTTTGTAGTGGTCTAGCGTGTAGCTTCCAATATGAGGCCGGAATAA + JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:98 your_output.pair1.truncated000066400000000000000000000000001350370616400357070ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/minlength/mate2your_output.pair2.truncated000066400000000000000000000000001350370616400357100ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/minlength/mate2your_output.settings000066400000000000000000000047241350370616400345640ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/minlength/mate2AdapterRemoval ver. 2.1.7 Trimming of paired-end reads [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 1485681 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: Yes Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 90 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 [Trimming statistics] Total number of read pairs: 1 Number of unaligned read pairs: 0 Number of well aligned read pairs: 1 Number of discarded mate 1 reads: 0 Number of singleton mate 1 reads: 1 Number of discarded mate 2 reads: 1 Number of singleton mate 2 reads: 0 Number of reads with adapters[1]: 0 Number of retained reads: 1 Number of retained nucleotides: 100 Average length of retained reads: 100 [Length distribution] Length Mate1 Mate2 Singleton Discarded All 0 0 0 0 0 0 1 0 0 0 0 0 2 0 0 0 0 0 3 0 0 0 0 0 4 0 0 0 0 0 5 0 0 0 0 0 6 0 0 0 0 0 7 0 0 0 0 0 8 0 0 0 0 0 9 0 0 0 0 0 10 0 0 0 0 0 11 0 0 0 0 0 12 0 0 0 0 0 13 0 0 0 0 0 14 0 0 0 0 0 15 0 0 0 0 0 16 0 0 0 0 0 17 0 0 0 0 0 18 0 0 0 0 0 19 0 0 0 0 0 20 0 0 0 0 0 21 0 0 0 0 0 22 0 0 0 0 0 23 0 0 0 0 0 24 0 0 0 0 0 25 0 0 0 0 0 26 0 0 0 0 0 27 0 0 0 0 0 28 0 0 0 0 0 29 0 0 0 0 0 30 0 0 0 0 0 31 0 0 0 0 0 32 0 0 0 0 0 33 0 0 0 0 0 34 0 0 0 0 0 35 0 0 0 0 0 36 0 0 0 0 0 37 0 0 0 0 0 38 0 0 0 0 0 39 0 0 0 0 0 40 0 0 0 0 0 41 0 0 0 0 0 42 0 0 0 0 0 43 0 0 0 0 0 44 0 0 0 0 0 45 0 0 0 0 0 46 0 0 0 0 0 47 0 0 0 0 0 48 0 0 0 0 0 49 0 0 0 0 0 50 0 0 0 0 0 51 0 0 0 0 0 52 0 0 0 0 0 53 0 0 0 0 0 54 0 0 0 0 0 55 0 0 0 0 0 56 0 0 0 0 0 57 0 0 0 0 0 58 0 0 0 0 0 59 0 0 0 0 0 60 0 0 0 0 0 61 0 0 0 0 0 62 0 0 0 0 0 63 0 0 0 0 0 64 0 0 0 0 0 65 0 0 0 0 0 66 0 0 0 0 0 67 0 0 0 0 0 68 0 0 0 0 0 69 0 0 0 0 0 70 0 0 0 0 0 71 0 0 0 0 0 72 0 0 0 0 0 73 0 0 0 0 0 74 0 0 0 0 0 75 0 0 0 0 0 76 0 0 0 0 0 77 0 0 0 0 0 78 0 0 0 0 0 79 0 0 0 0 0 80 0 0 0 0 0 81 0 0 0 0 0 82 0 0 0 0 0 83 0 0 0 0 0 84 0 0 0 0 0 85 0 0 0 0 0 86 0 0 0 0 0 87 0 0 0 0 0 88 0 0 0 1 1 89 0 0 0 0 0 90 0 0 0 0 0 91 0 0 0 0 0 92 0 0 0 0 0 93 0 0 0 0 0 94 0 0 0 0 0 95 0 0 0 0 0 96 0 0 0 0 0 97 0 0 0 0 0 98 0 0 0 0 0 99 0 0 0 0 0 100 0 0 1 0 1 your_output.singleton.truncated000066400000000000000000000003561350370616400367130ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/minlength/mate2@ATAGCCSeq_1_2959_500/1 meta data TATCGAGCAACTCACCAAGTTCCTTTGATCCGAGGAACTACCCTTACGCCCATCGACGCTTGTTATTCCGGCCTCATATTGGAAGCTACACGCTAGACCA + JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/trimns/000077500000000000000000000000001350370616400267535ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/trimns/excl_ns/000077500000000000000000000000001350370616400304065ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/trimns/excl_ns/info.json000066400000000000000000000001031350370616400322260ustar00rootroot00000000000000{ "arguments": ["--trimns"], "return_code": 0, "stderr": [ ] } adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/trimns/excl_ns/input_1.fastq000066400000000000000000000003561350370616400330310ustar00rootroot00000000000000@ATAGCCSeq_1_2959_500/1 meta data TATCGAGCAACTCACCAAGTTCCTTTGATCCGAGGAACTACCCTTACGCCCATCGACGCTTGTTATTCCGGCCTCATATTGGAAGCTACACGCTAGACCA + JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/trimns/excl_ns/input_2.fastq000066400000000000000000000003561350370616400330320ustar00rootroot00000000000000@ATAGCCSeq_1_2959_500/2 data meta CATCTGGATTGTCGATCGCTGCCACCACTAGCCGGGTTTTTCTTTTGTAGTGGTCTAGCGTGTAGCTTCCAATATGAGGCCGGAATAACAAGCGTCGATG + JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! your_output.discarded000066400000000000000000000000001350370616400345770ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/trimns/excl_nsyour_output.pair1.truncated000066400000000000000000000003561350370616400356770ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/trimns/excl_ns@ATAGCCSeq_1_2959_500/1 meta data TATCGAGCAACTCACCAAGTTCCTTTGATCCGAGGAACTACCCTTACGCCCATCGACGCTTGTTATTCCGGCCTCATATTGGAAGCTACACGCTAGACCA + JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! your_output.pair2.truncated000066400000000000000000000003561350370616400357000ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/trimns/excl_ns@ATAGCCSeq_1_2959_500/2 data meta CATCTGGATTGTCGATCGCTGCCACCACTAGCCGGGTTTTTCTTTTGTAGTGGTCTAGCGTGTAGCTTCCAATATGAGGCCGGAATAACAAGCGTCGATG + JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! your_output.settings000066400000000000000000000047261350370616400345400ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/trimns/excl_nsAdapterRemoval ver. 2.1.7 Trimming of paired-end reads [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 242897042 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: Yes Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 [Trimming statistics] Total number of read pairs: 1 Number of unaligned read pairs: 0 Number of well aligned read pairs: 1 Number of discarded mate 1 reads: 0 Number of singleton mate 1 reads: 0 Number of discarded mate 2 reads: 0 Number of singleton mate 2 reads: 0 Number of reads with adapters[1]: 0 Number of retained reads: 2 Number of retained nucleotides: 200 Average length of retained reads: 100 [Length distribution] Length Mate1 Mate2 Singleton Discarded All 0 0 0 0 0 0 1 0 0 0 0 0 2 0 0 0 0 0 3 0 0 0 0 0 4 0 0 0 0 0 5 0 0 0 0 0 6 0 0 0 0 0 7 0 0 0 0 0 8 0 0 0 0 0 9 0 0 0 0 0 10 0 0 0 0 0 11 0 0 0 0 0 12 0 0 0 0 0 13 0 0 0 0 0 14 0 0 0 0 0 15 0 0 0 0 0 16 0 0 0 0 0 17 0 0 0 0 0 18 0 0 0 0 0 19 0 0 0 0 0 20 0 0 0 0 0 21 0 0 0 0 0 22 0 0 0 0 0 23 0 0 0 0 0 24 0 0 0 0 0 25 0 0 0 0 0 26 0 0 0 0 0 27 0 0 0 0 0 28 0 0 0 0 0 29 0 0 0 0 0 30 0 0 0 0 0 31 0 0 0 0 0 32 0 0 0 0 0 33 0 0 0 0 0 34 0 0 0 0 0 35 0 0 0 0 0 36 0 0 0 0 0 37 0 0 0 0 0 38 0 0 0 0 0 39 0 0 0 0 0 40 0 0 0 0 0 41 0 0 0 0 0 42 0 0 0 0 0 43 0 0 0 0 0 44 0 0 0 0 0 45 0 0 0 0 0 46 0 0 0 0 0 47 0 0 0 0 0 48 0 0 0 0 0 49 0 0 0 0 0 50 0 0 0 0 0 51 0 0 0 0 0 52 0 0 0 0 0 53 0 0 0 0 0 54 0 0 0 0 0 55 0 0 0 0 0 56 0 0 0 0 0 57 0 0 0 0 0 58 0 0 0 0 0 59 0 0 0 0 0 60 0 0 0 0 0 61 0 0 0 0 0 62 0 0 0 0 0 63 0 0 0 0 0 64 0 0 0 0 0 65 0 0 0 0 0 66 0 0 0 0 0 67 0 0 0 0 0 68 0 0 0 0 0 69 0 0 0 0 0 70 0 0 0 0 0 71 0 0 0 0 0 72 0 0 0 0 0 73 0 0 0 0 0 74 0 0 0 0 0 75 0 0 0 0 0 76 0 0 0 0 0 77 0 0 0 0 0 78 0 0 0 0 0 79 0 0 0 0 0 80 0 0 0 0 0 81 0 0 0 0 0 82 0 0 0 0 0 83 0 0 0 0 0 84 0 0 0 0 0 85 0 0 0 0 0 86 0 0 0 0 0 87 0 0 0 0 0 88 0 0 0 0 0 89 0 0 0 0 0 90 0 0 0 0 0 91 0 0 0 0 0 92 0 0 0 0 0 93 0 0 0 0 0 94 0 0 0 0 0 95 0 0 0 0 0 96 0 0 0 0 0 97 0 0 0 0 0 98 0 0 0 0 0 99 0 0 0 0 0 100 1 1 0 0 2 your_output.singleton.truncated000066400000000000000000000000001350370616400366470ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/trimns/excl_nsadapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/trimns/incl_ns/000077500000000000000000000000001350370616400304005ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/trimns/incl_ns/info.json000066400000000000000000000001031350370616400322200ustar00rootroot00000000000000{ "arguments": ["--trimns"], "return_code": 0, "stderr": [ ] } adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/trimns/incl_ns/input_1.fastq000066400000000000000000000003561350370616400330230ustar00rootroot00000000000000@ATAGCCSeq_1_2959_500/1 meta data TATCGAGCAACTCACCAAGTTCCTTTGATCCGAGGAACTACCCTTACGCCCATCGACGCTTGTTATTCCGGCCTCATATTGGAAGNNNNNNNNNNNNNNN + JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/trimns/incl_ns/input_2.fastq000066400000000000000000000003561350370616400330240ustar00rootroot00000000000000@ATAGCCSeq_1_2959_500/2 data meta CATCTGGATTGTCGATCGCTGCCACCACTAGCCGGGTTTTTCTTTTGTAGTGGTCTAGCGTGTAGCTTCCAATATGAGGCCGGAATAACAAGCNNNNNNN + JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! your_output.discarded000066400000000000000000000000001350370616400345710ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/trimns/incl_nsyour_output.pair1.truncated000066400000000000000000000003201350370616400356600ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/trimns/incl_ns@ATAGCCSeq_1_2959_500/1 meta data TATCGAGCAACTCACCAAGTTCCTTTGATCCGAGGAACTACCCTTACGCCCATCGACGCTTGTTATTCCGGCCTCATATTGGAAG + JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<: your_output.pair2.truncated000066400000000000000000000003401350370616400356630ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/trimns/incl_ns@ATAGCCSeq_1_2959_500/2 data meta CATCTGGATTGTCGATCGCTGCCACCACTAGCCGGGTTTTTCTTTTGTAGTGGTCTAGCGTGTAGCTTCCAATATGAGGCCGGAATAACAAGC + JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852 your_output.settings000066400000000000000000000045711350370616400345300ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/trimns/incl_nsAdapterRemoval ver. 2.1.7 Trimming of paired-end reads [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 236123159 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: Yes Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 [Trimming statistics] Total number of read pairs: 1 Number of unaligned read pairs: 0 Number of well aligned read pairs: 1 Number of discarded mate 1 reads: 0 Number of singleton mate 1 reads: 0 Number of discarded mate 2 reads: 0 Number of singleton mate 2 reads: 0 Number of reads with adapters[1]: 0 Number of retained reads: 2 Number of retained nucleotides: 178 Average length of retained reads: 89 [Length distribution] Length Mate1 Mate2 Singleton Discarded All 0 0 0 0 0 0 1 0 0 0 0 0 2 0 0 0 0 0 3 0 0 0 0 0 4 0 0 0 0 0 5 0 0 0 0 0 6 0 0 0 0 0 7 0 0 0 0 0 8 0 0 0 0 0 9 0 0 0 0 0 10 0 0 0 0 0 11 0 0 0 0 0 12 0 0 0 0 0 13 0 0 0 0 0 14 0 0 0 0 0 15 0 0 0 0 0 16 0 0 0 0 0 17 0 0 0 0 0 18 0 0 0 0 0 19 0 0 0 0 0 20 0 0 0 0 0 21 0 0 0 0 0 22 0 0 0 0 0 23 0 0 0 0 0 24 0 0 0 0 0 25 0 0 0 0 0 26 0 0 0 0 0 27 0 0 0 0 0 28 0 0 0 0 0 29 0 0 0 0 0 30 0 0 0 0 0 31 0 0 0 0 0 32 0 0 0 0 0 33 0 0 0 0 0 34 0 0 0 0 0 35 0 0 0 0 0 36 0 0 0 0 0 37 0 0 0 0 0 38 0 0 0 0 0 39 0 0 0 0 0 40 0 0 0 0 0 41 0 0 0 0 0 42 0 0 0 0 0 43 0 0 0 0 0 44 0 0 0 0 0 45 0 0 0 0 0 46 0 0 0 0 0 47 0 0 0 0 0 48 0 0 0 0 0 49 0 0 0 0 0 50 0 0 0 0 0 51 0 0 0 0 0 52 0 0 0 0 0 53 0 0 0 0 0 54 0 0 0 0 0 55 0 0 0 0 0 56 0 0 0 0 0 57 0 0 0 0 0 58 0 0 0 0 0 59 0 0 0 0 0 60 0 0 0 0 0 61 0 0 0 0 0 62 0 0 0 0 0 63 0 0 0 0 0 64 0 0 0 0 0 65 0 0 0 0 0 66 0 0 0 0 0 67 0 0 0 0 0 68 0 0 0 0 0 69 0 0 0 0 0 70 0 0 0 0 0 71 0 0 0 0 0 72 0 0 0 0 0 73 0 0 0 0 0 74 0 0 0 0 0 75 0 0 0 0 0 76 0 0 0 0 0 77 0 0 0 0 0 78 0 0 0 0 0 79 0 0 0 0 0 80 0 0 0 0 0 81 0 0 0 0 0 82 0 0 0 0 0 83 0 0 0 0 0 84 0 0 0 0 0 85 1 0 0 0 1 86 0 0 0 0 0 87 0 0 0 0 0 88 0 0 0 0 0 89 0 0 0 0 0 90 0 0 0 0 0 91 0 0 0 0 0 92 0 0 0 0 0 93 0 1 0 0 1 your_output.singleton.truncated000066400000000000000000000000001350370616400366410ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/trimns/incl_nsadapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/trimqualities/000077500000000000000000000000001350370616400303335ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/trimqualities/default/000077500000000000000000000000001350370616400317575ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/trimqualities/default/info.json000066400000000000000000000001121350370616400335770ustar00rootroot00000000000000{ "arguments": ["--trimqualities"], "return_code": 0, "stderr": [ ] } input_1.fastq000066400000000000000000000003561350370616400343230ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/trimqualities/default@ATAGCCSeq_1_2959_500/1 meta data TATCGAGCAACTCACCAAGTTCCTTTGATCCGAGGAACTACCCTTACGCCCATCGACGCTTGTTATTCCGGCCTCATATTGGAAGCTACACGCTAGACCA + JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! input_2.fastq000066400000000000000000000003561350370616400343240ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/trimqualities/default@ATAGCCSeq_1_2959_500/2 data meta CATCTGGATTGTCGATCGCTGCCACCACTAGCCGGGTTTTTCTTTTGTAGTGGTCTAGCGTGTAGCTTCCAATATGAGGCCGGAATAACAAGCGTCGATG + JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! your_output.discarded000066400000000000000000000000001350370616400361500ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/trimqualities/defaultyour_output.pair1.truncated000066400000000000000000000003541350370616400372460ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/trimqualities/default@ATAGCCSeq_1_2959_500/1 meta data TATCGAGCAACTCACCAAGTTCCTTTGATCCGAGGAACTACCCTTACGCCCATCGACGCTTGTTATTCCGGCCTCATATTGGAAGCTACACGCTAGACC + JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)' your_output.pair2.truncated000066400000000000000000000003541350370616400372470ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/trimqualities/default@ATAGCCSeq_1_2959_500/2 data meta CATCTGGATTGTCGATCGCTGCCACCACTAGCCGGGTTTTTCTTTTGTAGTGGTCTAGCGTGTAGCTTCCAATATGAGGCCGGAATAACAAGCGTCGAT + JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*& your_output.settings000066400000000000000000000047071350370616400361100ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/trimqualities/defaultAdapterRemoval ver. 2.1.7 Trimming of paired-end reads [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 727785539 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: Yes Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 [Trimming statistics] Total number of read pairs: 1 Number of unaligned read pairs: 0 Number of well aligned read pairs: 1 Number of discarded mate 1 reads: 0 Number of singleton mate 1 reads: 0 Number of discarded mate 2 reads: 0 Number of singleton mate 2 reads: 0 Number of reads with adapters[1]: 0 Number of retained reads: 2 Number of retained nucleotides: 198 Average length of retained reads: 99 [Length distribution] Length Mate1 Mate2 Singleton Discarded All 0 0 0 0 0 0 1 0 0 0 0 0 2 0 0 0 0 0 3 0 0 0 0 0 4 0 0 0 0 0 5 0 0 0 0 0 6 0 0 0 0 0 7 0 0 0 0 0 8 0 0 0 0 0 9 0 0 0 0 0 10 0 0 0 0 0 11 0 0 0 0 0 12 0 0 0 0 0 13 0 0 0 0 0 14 0 0 0 0 0 15 0 0 0 0 0 16 0 0 0 0 0 17 0 0 0 0 0 18 0 0 0 0 0 19 0 0 0 0 0 20 0 0 0 0 0 21 0 0 0 0 0 22 0 0 0 0 0 23 0 0 0 0 0 24 0 0 0 0 0 25 0 0 0 0 0 26 0 0 0 0 0 27 0 0 0 0 0 28 0 0 0 0 0 29 0 0 0 0 0 30 0 0 0 0 0 31 0 0 0 0 0 32 0 0 0 0 0 33 0 0 0 0 0 34 0 0 0 0 0 35 0 0 0 0 0 36 0 0 0 0 0 37 0 0 0 0 0 38 0 0 0 0 0 39 0 0 0 0 0 40 0 0 0 0 0 41 0 0 0 0 0 42 0 0 0 0 0 43 0 0 0 0 0 44 0 0 0 0 0 45 0 0 0 0 0 46 0 0 0 0 0 47 0 0 0 0 0 48 0 0 0 0 0 49 0 0 0 0 0 50 0 0 0 0 0 51 0 0 0 0 0 52 0 0 0 0 0 53 0 0 0 0 0 54 0 0 0 0 0 55 0 0 0 0 0 56 0 0 0 0 0 57 0 0 0 0 0 58 0 0 0 0 0 59 0 0 0 0 0 60 0 0 0 0 0 61 0 0 0 0 0 62 0 0 0 0 0 63 0 0 0 0 0 64 0 0 0 0 0 65 0 0 0 0 0 66 0 0 0 0 0 67 0 0 0 0 0 68 0 0 0 0 0 69 0 0 0 0 0 70 0 0 0 0 0 71 0 0 0 0 0 72 0 0 0 0 0 73 0 0 0 0 0 74 0 0 0 0 0 75 0 0 0 0 0 76 0 0 0 0 0 77 0 0 0 0 0 78 0 0 0 0 0 79 0 0 0 0 0 80 0 0 0 0 0 81 0 0 0 0 0 82 0 0 0 0 0 83 0 0 0 0 0 84 0 0 0 0 0 85 0 0 0 0 0 86 0 0 0 0 0 87 0 0 0 0 0 88 0 0 0 0 0 89 0 0 0 0 0 90 0 0 0 0 0 91 0 0 0 0 0 92 0 0 0 0 0 93 0 0 0 0 0 94 0 0 0 0 0 95 0 0 0 0 0 96 0 0 0 0 0 97 0 0 0 0 0 98 0 0 0 0 0 99 1 1 0 0 2 your_output.singleton.truncated000066400000000000000000000000001350370616400402200ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/trimqualities/defaultadapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/trimqualities/minq31/000077500000000000000000000000001350370616400314435ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/trimqualities/minq31/info.json000066400000000000000000000001401350370616400332640ustar00rootroot00000000000000{ "arguments": ["--trimqualities", "--minquality", "31"], "return_code": 0, "stderr": [ ] } adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/trimqualities/minq31/input_1.fastq000066400000000000000000000003561350370616400340660ustar00rootroot00000000000000@ATAGCCSeq_1_2959_500/1 meta data TATCGAGCAACTCACCAAGTTCCTTTGATCCGAGGAACTACCCTTACGCCCATCGACGCTTGTTATTCCGGCCTCATATTGGAAGCTACACGCTAGACCA + JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/trimqualities/minq31/input_2.fastq000066400000000000000000000003561350370616400340670ustar00rootroot00000000000000@ATAGCCSeq_1_2959_500/2 data meta CATCTGGATTGTCGATCGCTGCCACCACTAGCCGGGTTTTTCTTTTGTAGTGGTCTAGCGTGTAGCTTCCAATATGAGGCCGGAATAACAAGCGTCGATG + JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! your_output.discarded000066400000000000000000000000001350370616400356340ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/trimqualities/minq31your_output.pair1.truncated000066400000000000000000000002541350370616400367310ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/trimqualities/minq31@ATAGCCSeq_1_2959_500/1 meta data TATCGAGCAACTCACCAAGTTCCTTTGATCCGAGGAACTACCCTTACGCCCATCGACGCTTGTTATT + JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A your_output.pair2.truncated000066400000000000000000000002541350370616400367320ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/trimqualities/minq31@ATAGCCSeq_1_2959_500/2 data meta CATCTGGATTGTCGATCGCTGCCACCACTAGCCGGGTTTTTCTTTTGTAGTGGTCTAGCGTGTAGCT + JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B your_output.settings000066400000000000000000000040501350370616400355630ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/trimqualities/minq31AdapterRemoval ver. 2.1.7 Trimming of paired-end reads [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 737094053 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 31: Yes Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 [Trimming statistics] Total number of read pairs: 1 Number of unaligned read pairs: 0 Number of well aligned read pairs: 1 Number of discarded mate 1 reads: 0 Number of singleton mate 1 reads: 0 Number of discarded mate 2 reads: 0 Number of singleton mate 2 reads: 0 Number of reads with adapters[1]: 0 Number of retained reads: 2 Number of retained nucleotides: 134 Average length of retained reads: 67 [Length distribution] Length Mate1 Mate2 Singleton Discarded All 0 0 0 0 0 0 1 0 0 0 0 0 2 0 0 0 0 0 3 0 0 0 0 0 4 0 0 0 0 0 5 0 0 0 0 0 6 0 0 0 0 0 7 0 0 0 0 0 8 0 0 0 0 0 9 0 0 0 0 0 10 0 0 0 0 0 11 0 0 0 0 0 12 0 0 0 0 0 13 0 0 0 0 0 14 0 0 0 0 0 15 0 0 0 0 0 16 0 0 0 0 0 17 0 0 0 0 0 18 0 0 0 0 0 19 0 0 0 0 0 20 0 0 0 0 0 21 0 0 0 0 0 22 0 0 0 0 0 23 0 0 0 0 0 24 0 0 0 0 0 25 0 0 0 0 0 26 0 0 0 0 0 27 0 0 0 0 0 28 0 0 0 0 0 29 0 0 0 0 0 30 0 0 0 0 0 31 0 0 0 0 0 32 0 0 0 0 0 33 0 0 0 0 0 34 0 0 0 0 0 35 0 0 0 0 0 36 0 0 0 0 0 37 0 0 0 0 0 38 0 0 0 0 0 39 0 0 0 0 0 40 0 0 0 0 0 41 0 0 0 0 0 42 0 0 0 0 0 43 0 0 0 0 0 44 0 0 0 0 0 45 0 0 0 0 0 46 0 0 0 0 0 47 0 0 0 0 0 48 0 0 0 0 0 49 0 0 0 0 0 50 0 0 0 0 0 51 0 0 0 0 0 52 0 0 0 0 0 53 0 0 0 0 0 54 0 0 0 0 0 55 0 0 0 0 0 56 0 0 0 0 0 57 0 0 0 0 0 58 0 0 0 0 0 59 0 0 0 0 0 60 0 0 0 0 0 61 0 0 0 0 0 62 0 0 0 0 0 63 0 0 0 0 0 64 0 0 0 0 0 65 0 0 0 0 0 66 0 0 0 0 0 67 1 1 0 0 2 your_output.singleton.truncated000066400000000000000000000000001350370616400377040ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/excl_adapter/overlapping/trimqualities/minq31adapterremoval-2.3.1/tests/regression/pe/incl_adapter/000077500000000000000000000000001350370616400231035ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/incl_adapter/collapse/000077500000000000000000000000001350370616400247055ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/incl_adapter/collapse/info.json000066400000000000000000000001051350370616400265270ustar00rootroot00000000000000{ "arguments": ["--collapse"], "return_code": 0, "stderr": [ ] } adapterremoval-2.3.1/tests/regression/pe/incl_adapter/collapse/input_1.fastq000066400000000000000000000003551350370616400273270ustar00rootroot00000000000000@AAGGGCSeq_1_5180_50/1 meta data ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG + IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! adapterremoval-2.3.1/tests/regression/pe/incl_adapter/collapse/input_2.fastq000066400000000000000000000003551350370616400273300ustar00rootroot00000000000000@AAGGGCSeq_1_5180_50/2 data meta AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGTAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCC + JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDEDBDBCBCCBBAA?ADAAA@@@>>>><=><<;<:<;87:78753420/,+)! adapterremoval-2.3.1/tests/regression/pe/incl_adapter/collapse/your_output.collapsed000066400000000000000000000002111350370616400312050ustar00rootroot00000000000000@M_AAGGGCSeq_1_5180_50 meta data ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGGAGGCCT + JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ&JJJJJJ adapterremoval-2.3.1/tests/regression/pe/incl_adapter/collapse/your_output.collapsed.truncated000066400000000000000000000000001350370616400331710ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/incl_adapter/collapse/your_output.discarded000066400000000000000000000000001350370616400311550ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/incl_adapter/collapse/your_output.pair1.truncated000066400000000000000000000000001350370616400322370ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/incl_adapter/collapse/your_output.pair2.truncated000066400000000000000000000000001350370616400322400ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/incl_adapter/collapse/your_output.settings000066400000000000000000000042021350370616400311030ustar00rootroot00000000000000AdapterRemoval ver. 2.1.7 Trimming of paired-end reads [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 429139444 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: Yes Minimum overlap (in case of collapse): 11 [Trimming statistics] Total number of read pairs: 1 Number of unaligned read pairs: 0 Number of well aligned read pairs: 1 Number of discarded mate 1 reads: 0 Number of singleton mate 1 reads: 0 Number of discarded mate 2 reads: 0 Number of singleton mate 2 reads: 0 Number of reads with adapters[1]: 2 Number of full-length collapsed pairs: 1 Number of truncated collapsed pairs: 0 Number of retained reads: 1 Number of retained nucleotides: 50 Average length of retained reads: 50 [Length distribution] Length Mate1 Mate2 Singleton Collapsed CollapsedTruncated Discarded All 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 3 0 0 0 0 0 0 0 4 0 0 0 0 0 0 0 5 0 0 0 0 0 0 0 6 0 0 0 0 0 0 0 7 0 0 0 0 0 0 0 8 0 0 0 0 0 0 0 9 0 0 0 0 0 0 0 10 0 0 0 0 0 0 0 11 0 0 0 0 0 0 0 12 0 0 0 0 0 0 0 13 0 0 0 0 0 0 0 14 0 0 0 0 0 0 0 15 0 0 0 0 0 0 0 16 0 0 0 0 0 0 0 17 0 0 0 0 0 0 0 18 0 0 0 0 0 0 0 19 0 0 0 0 0 0 0 20 0 0 0 0 0 0 0 21 0 0 0 0 0 0 0 22 0 0 0 0 0 0 0 23 0 0 0 0 0 0 0 24 0 0 0 0 0 0 0 25 0 0 0 0 0 0 0 26 0 0 0 0 0 0 0 27 0 0 0 0 0 0 0 28 0 0 0 0 0 0 0 29 0 0 0 0 0 0 0 30 0 0 0 0 0 0 0 31 0 0 0 0 0 0 0 32 0 0 0 0 0 0 0 33 0 0 0 0 0 0 0 34 0 0 0 0 0 0 0 35 0 0 0 0 0 0 0 36 0 0 0 0 0 0 0 37 0 0 0 0 0 0 0 38 0 0 0 0 0 0 0 39 0 0 0 0 0 0 0 40 0 0 0 0 0 0 0 41 0 0 0 0 0 0 0 42 0 0 0 0 0 0 0 43 0 0 0 0 0 0 0 44 0 0 0 0 0 0 0 45 0 0 0 0 0 0 0 46 0 0 0 0 0 0 0 47 0 0 0 0 0 0 0 48 0 0 0 0 0 0 0 49 0 0 0 0 0 0 0 50 0 0 0 1 0 0 1 adapterremoval-2.3.1/tests/regression/pe/incl_adapter/collapse/your_output.singleton.truncated000066400000000000000000000000001350370616400332250ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/incl_adapter/collapse_truncated/000077500000000000000000000000001350370616400267565ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/incl_adapter/collapse_truncated/info.json000066400000000000000000000001211350370616400305760ustar00rootroot00000000000000{ "arguments": ["--collapse", "--trimns"], "return_code": 0, "stderr": [ ] } adapterremoval-2.3.1/tests/regression/pe/incl_adapter/collapse_truncated/input_1.fastq000066400000000000000000000003551350370616400314000ustar00rootroot00000000000000@AAGGGCSeq_1_5180_50/1 meta data NCATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG + IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! adapterremoval-2.3.1/tests/regression/pe/incl_adapter/collapse_truncated/input_2.fastq000066400000000000000000000003551350370616400314010ustar00rootroot00000000000000@AAGGGCSeq_1_5180_50/2 data meta AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGNAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCC + JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDEDBDBCBCCBBAA?ADAAA@@@>>>><=><<;<:<;87:78753420/,+)! adapterremoval-2.3.1/tests/regression/pe/incl_adapter/collapse_truncated/your_output.collapsed000066400000000000000000000000001350370616400332520ustar00rootroot00000000000000your_output.collapsed.truncated000066400000000000000000000002101350370616400351660ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/incl_adapter/collapse_truncated@MT_AAGGGCSeq_1_5180_50 meta data CATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGGAGGCCT + JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ&JJJJJJ adapterremoval-2.3.1/tests/regression/pe/incl_adapter/collapse_truncated/your_output.discarded000066400000000000000000000000001350370616400332260ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/incl_adapter/collapse_truncated/your_output.pair1.truncated000066400000000000000000000000001350370616400343100ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/incl_adapter/collapse_truncated/your_output.pair2.truncated000066400000000000000000000000001350370616400343110ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/incl_adapter/collapse_truncated/your_output.settings000066400000000000000000000041621350370616400331610ustar00rootroot00000000000000AdapterRemoval ver. 2.1.7 Trimming of paired-end reads [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 505768950 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: Yes Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: Yes Minimum overlap (in case of collapse): 11 [Trimming statistics] Total number of read pairs: 1 Number of unaligned read pairs: 0 Number of well aligned read pairs: 1 Number of discarded mate 1 reads: 0 Number of singleton mate 1 reads: 0 Number of discarded mate 2 reads: 0 Number of singleton mate 2 reads: 0 Number of reads with adapters[1]: 2 Number of full-length collapsed pairs: 0 Number of truncated collapsed pairs: 1 Number of retained reads: 1 Number of retained nucleotides: 49 Average length of retained reads: 49 [Length distribution] Length Mate1 Mate2 Singleton Collapsed CollapsedTruncated Discarded All 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 3 0 0 0 0 0 0 0 4 0 0 0 0 0 0 0 5 0 0 0 0 0 0 0 6 0 0 0 0 0 0 0 7 0 0 0 0 0 0 0 8 0 0 0 0 0 0 0 9 0 0 0 0 0 0 0 10 0 0 0 0 0 0 0 11 0 0 0 0 0 0 0 12 0 0 0 0 0 0 0 13 0 0 0 0 0 0 0 14 0 0 0 0 0 0 0 15 0 0 0 0 0 0 0 16 0 0 0 0 0 0 0 17 0 0 0 0 0 0 0 18 0 0 0 0 0 0 0 19 0 0 0 0 0 0 0 20 0 0 0 0 0 0 0 21 0 0 0 0 0 0 0 22 0 0 0 0 0 0 0 23 0 0 0 0 0 0 0 24 0 0 0 0 0 0 0 25 0 0 0 0 0 0 0 26 0 0 0 0 0 0 0 27 0 0 0 0 0 0 0 28 0 0 0 0 0 0 0 29 0 0 0 0 0 0 0 30 0 0 0 0 0 0 0 31 0 0 0 0 0 0 0 32 0 0 0 0 0 0 0 33 0 0 0 0 0 0 0 34 0 0 0 0 0 0 0 35 0 0 0 0 0 0 0 36 0 0 0 0 0 0 0 37 0 0 0 0 0 0 0 38 0 0 0 0 0 0 0 39 0 0 0 0 0 0 0 40 0 0 0 0 0 0 0 41 0 0 0 0 0 0 0 42 0 0 0 0 0 0 0 43 0 0 0 0 0 0 0 44 0 0 0 0 0 0 0 45 0 0 0 0 0 0 0 46 0 0 0 0 0 0 0 47 0 0 0 0 0 0 0 48 0 0 0 0 0 0 0 49 0 0 0 0 1 0 1 your_output.singleton.truncated000066400000000000000000000000001350370616400352170ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/incl_adapter/collapse_truncatedadapterremoval-2.3.1/tests/regression/pe/incl_adapter/combined_output/000077500000000000000000000000001350370616400263035ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/incl_adapter/combined_output/collapse/000077500000000000000000000000001350370616400301055ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/incl_adapter/combined_output/collapse/info.json000066400000000000000000000001321350370616400317270ustar00rootroot00000000000000{ "arguments": ["--combined-output", "--collapse"], "return_code": 0, "stderr": [ ] } adapterremoval-2.3.1/tests/regression/pe/incl_adapter/combined_output/collapse/input_1.fastq000066400000000000000000000003551350370616400325270ustar00rootroot00000000000000@AAGGGCSeq_1_5180_50/1 meta data ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG + IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! adapterremoval-2.3.1/tests/regression/pe/incl_adapter/combined_output/collapse/input_2.fastq000066400000000000000000000003551350370616400325300ustar00rootroot00000000000000@AAGGGCSeq_1_5180_50/2 data meta AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGTAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCC + JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDEDBDBCBCCBBAA?ADAAA@@@>>>><=><<;<:<;87:78753420/,+)! your_output.pair1.truncated000066400000000000000000000002131350370616400353660ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/incl_adapter/combined_output/collapse@M_AAGGGCSeq_1_5180_50/1 meta data ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGGAGGCCT + JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ&JJJJJJ your_output.pair2.truncated000066400000000000000000000000511350370616400353670ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/incl_adapter/combined_output/collapse@M_AAGGGCSeq_1_5180_50/2 data meta N + ! adapterremoval-2.3.1/tests/regression/pe/incl_adapter/combined_output/collapse/your_output.settings000066400000000000000000000042021350370616400343030ustar00rootroot00000000000000AdapterRemoval ver. 2.1.7 Trimming of paired-end reads [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 429139444 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: Yes Minimum overlap (in case of collapse): 11 [Trimming statistics] Total number of read pairs: 1 Number of unaligned read pairs: 0 Number of well aligned read pairs: 1 Number of discarded mate 1 reads: 0 Number of singleton mate 1 reads: 0 Number of discarded mate 2 reads: 0 Number of singleton mate 2 reads: 0 Number of reads with adapters[1]: 2 Number of full-length collapsed pairs: 1 Number of truncated collapsed pairs: 0 Number of retained reads: 1 Number of retained nucleotides: 50 Average length of retained reads: 50 [Length distribution] Length Mate1 Mate2 Singleton Collapsed CollapsedTruncated Discarded All 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 3 0 0 0 0 0 0 0 4 0 0 0 0 0 0 0 5 0 0 0 0 0 0 0 6 0 0 0 0 0 0 0 7 0 0 0 0 0 0 0 8 0 0 0 0 0 0 0 9 0 0 0 0 0 0 0 10 0 0 0 0 0 0 0 11 0 0 0 0 0 0 0 12 0 0 0 0 0 0 0 13 0 0 0 0 0 0 0 14 0 0 0 0 0 0 0 15 0 0 0 0 0 0 0 16 0 0 0 0 0 0 0 17 0 0 0 0 0 0 0 18 0 0 0 0 0 0 0 19 0 0 0 0 0 0 0 20 0 0 0 0 0 0 0 21 0 0 0 0 0 0 0 22 0 0 0 0 0 0 0 23 0 0 0 0 0 0 0 24 0 0 0 0 0 0 0 25 0 0 0 0 0 0 0 26 0 0 0 0 0 0 0 27 0 0 0 0 0 0 0 28 0 0 0 0 0 0 0 29 0 0 0 0 0 0 0 30 0 0 0 0 0 0 0 31 0 0 0 0 0 0 0 32 0 0 0 0 0 0 0 33 0 0 0 0 0 0 0 34 0 0 0 0 0 0 0 35 0 0 0 0 0 0 0 36 0 0 0 0 0 0 0 37 0 0 0 0 0 0 0 38 0 0 0 0 0 0 0 39 0 0 0 0 0 0 0 40 0 0 0 0 0 0 0 41 0 0 0 0 0 0 0 42 0 0 0 0 0 0 0 43 0 0 0 0 0 0 0 44 0 0 0 0 0 0 0 45 0 0 0 0 0 0 0 46 0 0 0 0 0 0 0 47 0 0 0 0 0 0 0 48 0 0 0 0 0 0 0 49 0 0 0 0 0 0 0 50 0 0 0 1 0 0 1 adapterremoval-2.3.1/tests/regression/pe/incl_adapter/combined_output/collapse_truncated/000077500000000000000000000000001350370616400321565ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/incl_adapter/combined_output/collapse_truncated/info.json000066400000000000000000000001461350370616400340050ustar00rootroot00000000000000{ "arguments": ["--combined-output", "--collapse", "--trimns"], "return_code": 0, "stderr": [ ] } input_1.fastq000066400000000000000000000003551350370616400345210ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/incl_adapter/combined_output/collapse_truncated@AAGGGCSeq_1_5180_50/1 meta data NCATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG + IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! input_2.fastq000066400000000000000000000003551350370616400345220ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/incl_adapter/combined_output/collapse_truncated@AAGGGCSeq_1_5180_50/2 data meta AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGNAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCC + JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDEDBDBCBCCBBAA?ADAAA@@@>>>><=><<;<:<;87:78753420/,+)! your_output.pair1.truncated000066400000000000000000000002121350370616400374360ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/incl_adapter/combined_output/collapse_truncated@MT_AAGGGCSeq_1_5180_50/1 meta data CATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGGAGGCCT + JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ&JJJJJJ your_output.pair2.truncated000066400000000000000000000000521350370616400374410ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/incl_adapter/combined_output/collapse_truncated@MT_AAGGGCSeq_1_5180_50/2 data meta N + ! your_output.settings000066400000000000000000000041621350370616400363020ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/incl_adapter/combined_output/collapse_truncatedAdapterRemoval ver. 2.1.7 Trimming of paired-end reads [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 505768950 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: Yes Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: Yes Minimum overlap (in case of collapse): 11 [Trimming statistics] Total number of read pairs: 1 Number of unaligned read pairs: 0 Number of well aligned read pairs: 1 Number of discarded mate 1 reads: 0 Number of singleton mate 1 reads: 0 Number of discarded mate 2 reads: 0 Number of singleton mate 2 reads: 0 Number of reads with adapters[1]: 2 Number of full-length collapsed pairs: 0 Number of truncated collapsed pairs: 1 Number of retained reads: 1 Number of retained nucleotides: 49 Average length of retained reads: 49 [Length distribution] Length Mate1 Mate2 Singleton Collapsed CollapsedTruncated Discarded All 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 3 0 0 0 0 0 0 0 4 0 0 0 0 0 0 0 5 0 0 0 0 0 0 0 6 0 0 0 0 0 0 0 7 0 0 0 0 0 0 0 8 0 0 0 0 0 0 0 9 0 0 0 0 0 0 0 10 0 0 0 0 0 0 0 11 0 0 0 0 0 0 0 12 0 0 0 0 0 0 0 13 0 0 0 0 0 0 0 14 0 0 0 0 0 0 0 15 0 0 0 0 0 0 0 16 0 0 0 0 0 0 0 17 0 0 0 0 0 0 0 18 0 0 0 0 0 0 0 19 0 0 0 0 0 0 0 20 0 0 0 0 0 0 0 21 0 0 0 0 0 0 0 22 0 0 0 0 0 0 0 23 0 0 0 0 0 0 0 24 0 0 0 0 0 0 0 25 0 0 0 0 0 0 0 26 0 0 0 0 0 0 0 27 0 0 0 0 0 0 0 28 0 0 0 0 0 0 0 29 0 0 0 0 0 0 0 30 0 0 0 0 0 0 0 31 0 0 0 0 0 0 0 32 0 0 0 0 0 0 0 33 0 0 0 0 0 0 0 34 0 0 0 0 0 0 0 35 0 0 0 0 0 0 0 36 0 0 0 0 0 0 0 37 0 0 0 0 0 0 0 38 0 0 0 0 0 0 0 39 0 0 0 0 0 0 0 40 0 0 0 0 0 0 0 41 0 0 0 0 0 0 0 42 0 0 0 0 0 0 0 43 0 0 0 0 0 0 0 44 0 0 0 0 0 0 0 45 0 0 0 0 0 0 0 46 0 0 0 0 0 0 0 47 0 0 0 0 0 0 0 48 0 0 0 0 0 0 0 49 0 0 0 0 1 0 1 adapterremoval-2.3.1/tests/regression/pe/incl_adapter/combined_output/interleaved/000077500000000000000000000000001350370616400306055ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/incl_adapter/combined_output/interleaved/collapse/000077500000000000000000000000001350370616400324075ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/incl_adapter/combined_output/interleaved/collapse/info.json000066400000000000000000000001621350370616400342340ustar00rootroot00000000000000{ "arguments": ["--combined-output", "--collapse", "--interleaved-output"], "return_code": 0, "stderr": [ ] } input_1.fastq000066400000000000000000000003551350370616400347520ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/incl_adapter/combined_output/interleaved/collapse@AAGGGCSeq_1_5180_50/1 meta data ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG + IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! input_2.fastq000066400000000000000000000003551350370616400347530ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/incl_adapter/combined_output/interleaved/collapse@AAGGGCSeq_1_5180_50/2 data meta AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGTAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCC + JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDEDBDBCBCCBBAA?ADAAA@@@>>>><=><<;<:<;87:78753420/,+)! your_output.paired.truncated000066400000000000000000000002641350370616400401260ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/incl_adapter/combined_output/interleaved/collapse@M_AAGGGCSeq_1_5180_50/1 meta data ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGGAGGCCT + JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ&JJJJJJ @M_AAGGGCSeq_1_5180_50/2 data meta N + ! your_output.settings000066400000000000000000000042021350370616400365260ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/incl_adapter/combined_output/interleaved/collapseAdapterRemoval ver. 2.1.7 Trimming of paired-end reads [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 429139444 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: Yes Minimum overlap (in case of collapse): 11 [Trimming statistics] Total number of read pairs: 1 Number of unaligned read pairs: 0 Number of well aligned read pairs: 1 Number of discarded mate 1 reads: 0 Number of singleton mate 1 reads: 0 Number of discarded mate 2 reads: 0 Number of singleton mate 2 reads: 0 Number of reads with adapters[1]: 2 Number of full-length collapsed pairs: 1 Number of truncated collapsed pairs: 0 Number of retained reads: 1 Number of retained nucleotides: 50 Average length of retained reads: 50 [Length distribution] Length Mate1 Mate2 Singleton Collapsed CollapsedTruncated Discarded All 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 3 0 0 0 0 0 0 0 4 0 0 0 0 0 0 0 5 0 0 0 0 0 0 0 6 0 0 0 0 0 0 0 7 0 0 0 0 0 0 0 8 0 0 0 0 0 0 0 9 0 0 0 0 0 0 0 10 0 0 0 0 0 0 0 11 0 0 0 0 0 0 0 12 0 0 0 0 0 0 0 13 0 0 0 0 0 0 0 14 0 0 0 0 0 0 0 15 0 0 0 0 0 0 0 16 0 0 0 0 0 0 0 17 0 0 0 0 0 0 0 18 0 0 0 0 0 0 0 19 0 0 0 0 0 0 0 20 0 0 0 0 0 0 0 21 0 0 0 0 0 0 0 22 0 0 0 0 0 0 0 23 0 0 0 0 0 0 0 24 0 0 0 0 0 0 0 25 0 0 0 0 0 0 0 26 0 0 0 0 0 0 0 27 0 0 0 0 0 0 0 28 0 0 0 0 0 0 0 29 0 0 0 0 0 0 0 30 0 0 0 0 0 0 0 31 0 0 0 0 0 0 0 32 0 0 0 0 0 0 0 33 0 0 0 0 0 0 0 34 0 0 0 0 0 0 0 35 0 0 0 0 0 0 0 36 0 0 0 0 0 0 0 37 0 0 0 0 0 0 0 38 0 0 0 0 0 0 0 39 0 0 0 0 0 0 0 40 0 0 0 0 0 0 0 41 0 0 0 0 0 0 0 42 0 0 0 0 0 0 0 43 0 0 0 0 0 0 0 44 0 0 0 0 0 0 0 45 0 0 0 0 0 0 0 46 0 0 0 0 0 0 0 47 0 0 0 0 0 0 0 48 0 0 0 0 0 0 0 49 0 0 0 0 0 0 0 50 0 0 0 1 0 0 1 collapse_truncated/000077500000000000000000000000001350370616400344015ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/incl_adapter/combined_output/interleavedinfo.json000066400000000000000000000001761350370616400362330ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/incl_adapter/combined_output/interleaved/collapse_truncated{ "arguments": ["--combined-output", "--collapse", "--trimns", "--interleaved-output"], "return_code": 0, "stderr": [ ] } input_1.fastq000066400000000000000000000003551350370616400370230ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/incl_adapter/combined_output/interleaved/collapse_truncated@AAGGGCSeq_1_5180_50/1 meta data NCATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG + IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! input_2.fastq000066400000000000000000000003551350370616400370240ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/incl_adapter/combined_output/interleaved/collapse_truncated@AAGGGCSeq_1_5180_50/2 data meta AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGNAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCC + JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDEDBDBCBCCBBAA?ADAAA@@@>>>><=><<;<:<;87:78753420/,+)! your_output.paired.truncated000066400000000000000000000002641350370616400421770ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/incl_adapter/combined_output/interleaved/collapse_truncated@MT_AAGGGCSeq_1_5180_50/1 meta data CATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGGAGGCCT + JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ&JJJJJJ @MT_AAGGGCSeq_1_5180_50/2 data meta N + ! your_output.settings000066400000000000000000000041621350370616400406040ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/incl_adapter/combined_output/interleaved/collapse_truncatedAdapterRemoval ver. 2.1.7 Trimming of paired-end reads [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 505768950 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: Yes Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: Yes Minimum overlap (in case of collapse): 11 [Trimming statistics] Total number of read pairs: 1 Number of unaligned read pairs: 0 Number of well aligned read pairs: 1 Number of discarded mate 1 reads: 0 Number of singleton mate 1 reads: 0 Number of discarded mate 2 reads: 0 Number of singleton mate 2 reads: 0 Number of reads with adapters[1]: 2 Number of full-length collapsed pairs: 0 Number of truncated collapsed pairs: 1 Number of retained reads: 1 Number of retained nucleotides: 49 Average length of retained reads: 49 [Length distribution] Length Mate1 Mate2 Singleton Collapsed CollapsedTruncated Discarded All 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 3 0 0 0 0 0 0 0 4 0 0 0 0 0 0 0 5 0 0 0 0 0 0 0 6 0 0 0 0 0 0 0 7 0 0 0 0 0 0 0 8 0 0 0 0 0 0 0 9 0 0 0 0 0 0 0 10 0 0 0 0 0 0 0 11 0 0 0 0 0 0 0 12 0 0 0 0 0 0 0 13 0 0 0 0 0 0 0 14 0 0 0 0 0 0 0 15 0 0 0 0 0 0 0 16 0 0 0 0 0 0 0 17 0 0 0 0 0 0 0 18 0 0 0 0 0 0 0 19 0 0 0 0 0 0 0 20 0 0 0 0 0 0 0 21 0 0 0 0 0 0 0 22 0 0 0 0 0 0 0 23 0 0 0 0 0 0 0 24 0 0 0 0 0 0 0 25 0 0 0 0 0 0 0 26 0 0 0 0 0 0 0 27 0 0 0 0 0 0 0 28 0 0 0 0 0 0 0 29 0 0 0 0 0 0 0 30 0 0 0 0 0 0 0 31 0 0 0 0 0 0 0 32 0 0 0 0 0 0 0 33 0 0 0 0 0 0 0 34 0 0 0 0 0 0 0 35 0 0 0 0 0 0 0 36 0 0 0 0 0 0 0 37 0 0 0 0 0 0 0 38 0 0 0 0 0 0 0 39 0 0 0 0 0 0 0 40 0 0 0 0 0 0 0 41 0 0 0 0 0 0 0 42 0 0 0 0 0 0 0 43 0 0 0 0 0 0 0 44 0 0 0 0 0 0 0 45 0 0 0 0 0 0 0 46 0 0 0 0 0 0 0 47 0 0 0 0 0 0 0 48 0 0 0 0 0 0 0 49 0 0 0 0 1 0 1 adapterremoval-2.3.1/tests/regression/pe/incl_adapter/combined_output/interleaved/keep_both/000077500000000000000000000000001350370616400325455ustar00rootroot00000000000000info.json000066400000000000000000000001441350370616400343130ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/incl_adapter/combined_output/interleaved/keep_both{ "arguments": ["--combined-output", "--interleaved-output"], "return_code": 0, "stderr": [ ] } input_1.fastq000066400000000000000000000003551350370616400351100ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/incl_adapter/combined_output/interleaved/keep_both@AAGGGCSeq_1_5180_50/1 meta data ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG + IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! input_2.fastq000066400000000000000000000003551350370616400351110ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/incl_adapter/combined_output/interleaved/keep_both@AAGGGCSeq_1_5180_50/2 data meta AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGTAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCC + JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDEDBDBCBCCBBAA?ADAAA@@@>>>><=><<;<:<;87:78753420/,+)! your_output.paired.truncated000066400000000000000000000004221350370616400402600ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/incl_adapter/combined_output/interleaved/keep_both@AAGGGCSeq_1_5180_50/1 meta data ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCT + IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECC @AAGGGCSeq_1_5180_50/2 data meta AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGT + JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDED your_output.settings000066400000000000000000000035111350370616400366660ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/incl_adapter/combined_output/interleaved/keep_bothAdapterRemoval ver. 2.1.7 Trimming of paired-end reads [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 372265332 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 [Trimming statistics] Total number of read pairs: 1 Number of unaligned read pairs: 0 Number of well aligned read pairs: 1 Number of discarded mate 1 reads: 0 Number of singleton mate 1 reads: 0 Number of discarded mate 2 reads: 0 Number of singleton mate 2 reads: 0 Number of reads with adapters[1]: 2 Number of retained reads: 2 Number of retained nucleotides: 100 Average length of retained reads: 50 [Length distribution] Length Mate1 Mate2 Singleton Discarded All 0 0 0 0 0 0 1 0 0 0 0 0 2 0 0 0 0 0 3 0 0 0 0 0 4 0 0 0 0 0 5 0 0 0 0 0 6 0 0 0 0 0 7 0 0 0 0 0 8 0 0 0 0 0 9 0 0 0 0 0 10 0 0 0 0 0 11 0 0 0 0 0 12 0 0 0 0 0 13 0 0 0 0 0 14 0 0 0 0 0 15 0 0 0 0 0 16 0 0 0 0 0 17 0 0 0 0 0 18 0 0 0 0 0 19 0 0 0 0 0 20 0 0 0 0 0 21 0 0 0 0 0 22 0 0 0 0 0 23 0 0 0 0 0 24 0 0 0 0 0 25 0 0 0 0 0 26 0 0 0 0 0 27 0 0 0 0 0 28 0 0 0 0 0 29 0 0 0 0 0 30 0 0 0 0 0 31 0 0 0 0 0 32 0 0 0 0 0 33 0 0 0 0 0 34 0 0 0 0 0 35 0 0 0 0 0 36 0 0 0 0 0 37 0 0 0 0 0 38 0 0 0 0 0 39 0 0 0 0 0 40 0 0 0 0 0 41 0 0 0 0 0 42 0 0 0 0 0 43 0 0 0 0 0 44 0 0 0 0 0 45 0 0 0 0 0 46 0 0 0 0 0 47 0 0 0 0 0 48 0 0 0 0 0 49 0 0 0 0 0 50 1 1 0 0 2 adapterremoval-2.3.1/tests/regression/pe/incl_adapter/combined_output/interleaved/keep_mate1/000077500000000000000000000000001350370616400326205ustar00rootroot00000000000000info.json000066400000000000000000000002051350370616400343640ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/incl_adapter/combined_output/interleaved/keep_mate1{ "arguments": ["--combined-output", "--trimns", "--minlength", "50", "--interleaved-output"], "return_code": 0, "stderr": [ ] } input_1.fastq000066400000000000000000000003551350370616400351630ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/incl_adapter/combined_output/interleaved/keep_mate1@AAGGGCSeq_1_5180_50/1 meta data ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG + IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! input_2.fastq000066400000000000000000000003551350370616400351640ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/incl_adapter/combined_output/interleaved/keep_mate1@AAGGGCSeq_1_5180_50/2 data meta AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGNAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCC + JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDEDBDBCBCCBBAA?ADAAA@@@>>>><=><<;<:<;87:78753420/,+)! your_output.paired.truncated000066400000000000000000000002601350370616400403330ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/incl_adapter/combined_output/interleaved/keep_mate1@AAGGGCSeq_1_5180_50/1 meta data ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCT + IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECC @AAGGGCSeq_1_5180_50/2 data meta N + ! your_output.settings000066400000000000000000000035121350370616400367420ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/incl_adapter/combined_output/interleaved/keep_mate1AdapterRemoval ver. 2.1.7 Trimming of paired-end reads [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 3738807510 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: Yes Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 50 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 [Trimming statistics] Total number of read pairs: 1 Number of unaligned read pairs: 0 Number of well aligned read pairs: 1 Number of discarded mate 1 reads: 0 Number of singleton mate 1 reads: 1 Number of discarded mate 2 reads: 1 Number of singleton mate 2 reads: 0 Number of reads with adapters[1]: 2 Number of retained reads: 1 Number of retained nucleotides: 50 Average length of retained reads: 50 [Length distribution] Length Mate1 Mate2 Singleton Discarded All 0 0 0 0 0 0 1 0 0 0 0 0 2 0 0 0 0 0 3 0 0 0 0 0 4 0 0 0 0 0 5 0 0 0 0 0 6 0 0 0 0 0 7 0 0 0 0 0 8 0 0 0 0 0 9 0 0 0 0 0 10 0 0 0 0 0 11 0 0 0 0 0 12 0 0 0 0 0 13 0 0 0 0 0 14 0 0 0 0 0 15 0 0 0 0 0 16 0 0 0 0 0 17 0 0 0 0 0 18 0 0 0 0 0 19 0 0 0 0 0 20 0 0 0 0 0 21 0 0 0 0 0 22 0 0 0 0 0 23 0 0 0 0 0 24 0 0 0 0 0 25 0 0 0 0 0 26 0 0 0 0 0 27 0 0 0 0 0 28 0 0 0 0 0 29 0 0 0 0 0 30 0 0 0 0 0 31 0 0 0 0 0 32 0 0 0 0 0 33 0 0 0 0 0 34 0 0 0 0 0 35 0 0 0 0 0 36 0 0 0 0 0 37 0 0 0 0 0 38 0 0 0 0 0 39 0 0 0 0 0 40 0 0 0 0 0 41 0 0 0 0 0 42 0 0 0 0 0 43 0 0 0 0 0 44 0 0 0 0 0 45 0 0 0 0 0 46 0 0 0 0 0 47 0 0 0 0 0 48 0 0 0 0 0 49 0 0 0 1 1 50 0 0 1 0 1 adapterremoval-2.3.1/tests/regression/pe/incl_adapter/combined_output/interleaved/keep_mate2/000077500000000000000000000000001350370616400326215ustar00rootroot00000000000000info.json000066400000000000000000000002051350370616400343650ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/incl_adapter/combined_output/interleaved/keep_mate2{ "arguments": ["--combined-output", "--trimns", "--minlength", "50", "--interleaved-output"], "return_code": 0, "stderr": [ ] } input_1.fastq000066400000000000000000000003551350370616400351640ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/incl_adapter/combined_output/interleaved/keep_mate2@AAGGGCSeq_1_5180_50/1 meta data ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCNAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG + IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! input_2.fastq000066400000000000000000000003551350370616400351650ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/incl_adapter/combined_output/interleaved/keep_mate2@AAGGGCSeq_1_5180_50/2 data meta AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGTAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCC + JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDEDBDBCBCCBBAA?ADAAA@@@>>>><=><<;<:<;87:78753420/,+)! your_output.paired.truncated000066400000000000000000000002601350370616400403340ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/incl_adapter/combined_output/interleaved/keep_mate2@AAGGGCSeq_1_5180_50/1 meta data N + ! @AAGGGCSeq_1_5180_50/2 data meta AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGT + JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDED your_output.settings000066400000000000000000000035121350370616400367430ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/incl_adapter/combined_output/interleaved/keep_mate2AdapterRemoval ver. 2.1.7 Trimming of paired-end reads [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 3854997780 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: Yes Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 50 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 [Trimming statistics] Total number of read pairs: 1 Number of unaligned read pairs: 0 Number of well aligned read pairs: 1 Number of discarded mate 1 reads: 1 Number of singleton mate 1 reads: 0 Number of discarded mate 2 reads: 0 Number of singleton mate 2 reads: 1 Number of reads with adapters[1]: 2 Number of retained reads: 1 Number of retained nucleotides: 50 Average length of retained reads: 50 [Length distribution] Length Mate1 Mate2 Singleton Discarded All 0 0 0 0 0 0 1 0 0 0 0 0 2 0 0 0 0 0 3 0 0 0 0 0 4 0 0 0 0 0 5 0 0 0 0 0 6 0 0 0 0 0 7 0 0 0 0 0 8 0 0 0 0 0 9 0 0 0 0 0 10 0 0 0 0 0 11 0 0 0 0 0 12 0 0 0 0 0 13 0 0 0 0 0 14 0 0 0 0 0 15 0 0 0 0 0 16 0 0 0 0 0 17 0 0 0 0 0 18 0 0 0 0 0 19 0 0 0 0 0 20 0 0 0 0 0 21 0 0 0 0 0 22 0 0 0 0 0 23 0 0 0 0 0 24 0 0 0 0 0 25 0 0 0 0 0 26 0 0 0 0 0 27 0 0 0 0 0 28 0 0 0 0 0 29 0 0 0 0 0 30 0 0 0 0 0 31 0 0 0 0 0 32 0 0 0 0 0 33 0 0 0 0 0 34 0 0 0 0 0 35 0 0 0 0 0 36 0 0 0 0 0 37 0 0 0 0 0 38 0 0 0 0 0 39 0 0 0 0 0 40 0 0 0 0 0 41 0 0 0 0 0 42 0 0 0 0 0 43 0 0 0 0 0 44 0 0 0 0 0 45 0 0 0 0 0 46 0 0 0 0 0 47 0 0 0 0 0 48 0 0 0 0 0 49 0 0 0 1 1 50 0 0 1 0 1 adapterremoval-2.3.1/tests/regression/pe/incl_adapter/combined_output/interleaved/keep_neither/000077500000000000000000000000001350370616400332475ustar00rootroot00000000000000info.json000066400000000000000000000002051350370616400350130ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/incl_adapter/combined_output/interleaved/keep_neither{ "arguments": ["--combined-output", "--trimns", "--minlength", "50", "--interleaved-output"], "return_code": 0, "stderr": [ ] } input_1.fastq000066400000000000000000000003551350370616400356120ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/incl_adapter/combined_output/interleaved/keep_neither@AAGGGCSeq_1_5180_50/1 meta data ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCNAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG + IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! input_2.fastq000066400000000000000000000003551350370616400356130ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/incl_adapter/combined_output/interleaved/keep_neither@AAGGGCSeq_1_5180_50/2 data meta AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGNAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCC + JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDEDBDBCBCCBBAA?ADAAA@@@>>>><=><<;<:<;87:78753420/,+)! your_output.paired.truncated000066400000000000000000000001161350370616400407620ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/incl_adapter/combined_output/interleaved/keep_neither@AAGGGCSeq_1_5180_50/1 meta data N + ! @AAGGGCSeq_1_5180_50/2 data meta N + ! your_output.settings000066400000000000000000000034731350370616400373770ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/incl_adapter/combined_output/interleaved/keep_neitherAdapterRemoval ver. 2.1.7 Trimming of paired-end reads [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 3934188119 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: Yes Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 50 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 [Trimming statistics] Total number of read pairs: 1 Number of unaligned read pairs: 0 Number of well aligned read pairs: 1 Number of discarded mate 1 reads: 1 Number of singleton mate 1 reads: 0 Number of discarded mate 2 reads: 1 Number of singleton mate 2 reads: 0 Number of reads with adapters[1]: 2 Number of retained reads: 0 Number of retained nucleotides: 0 Average length of retained reads: 0 [Length distribution] Length Mate1 Mate2 Singleton Discarded All 0 0 0 0 0 0 1 0 0 0 0 0 2 0 0 0 0 0 3 0 0 0 0 0 4 0 0 0 0 0 5 0 0 0 0 0 6 0 0 0 0 0 7 0 0 0 0 0 8 0 0 0 0 0 9 0 0 0 0 0 10 0 0 0 0 0 11 0 0 0 0 0 12 0 0 0 0 0 13 0 0 0 0 0 14 0 0 0 0 0 15 0 0 0 0 0 16 0 0 0 0 0 17 0 0 0 0 0 18 0 0 0 0 0 19 0 0 0 0 0 20 0 0 0 0 0 21 0 0 0 0 0 22 0 0 0 0 0 23 0 0 0 0 0 24 0 0 0 0 0 25 0 0 0 0 0 26 0 0 0 0 0 27 0 0 0 0 0 28 0 0 0 0 0 29 0 0 0 0 0 30 0 0 0 0 0 31 0 0 0 0 0 32 0 0 0 0 0 33 0 0 0 0 0 34 0 0 0 0 0 35 0 0 0 0 0 36 0 0 0 0 0 37 0 0 0 0 0 38 0 0 0 0 0 39 0 0 0 0 0 40 0 0 0 0 0 41 0 0 0 0 0 42 0 0 0 0 0 43 0 0 0 0 0 44 0 0 0 0 0 45 0 0 0 0 0 46 0 0 0 0 0 47 0 0 0 0 0 48 0 0 0 0 0 49 0 0 0 2 2 adapterremoval-2.3.1/tests/regression/pe/incl_adapter/combined_output/keep_both/000077500000000000000000000000001350370616400302435ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/incl_adapter/combined_output/keep_both/info.json000066400000000000000000000001141350370616400320650ustar00rootroot00000000000000{ "arguments": ["--combined-output"], "return_code": 0, "stderr": [ ] } adapterremoval-2.3.1/tests/regression/pe/incl_adapter/combined_output/keep_both/input_1.fastq000066400000000000000000000003551350370616400326650ustar00rootroot00000000000000@AAGGGCSeq_1_5180_50/1 meta data ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG + IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! adapterremoval-2.3.1/tests/regression/pe/incl_adapter/combined_output/keep_both/input_2.fastq000066400000000000000000000003551350370616400326660ustar00rootroot00000000000000@AAGGGCSeq_1_5180_50/2 data meta AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGTAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCC + JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDEDBDBCBCCBBAA?ADAAA@@@>>>><=><<;<:<;87:78753420/,+)! your_output.pair1.truncated000066400000000000000000000002111350370616400355220ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/incl_adapter/combined_output/keep_both@AAGGGCSeq_1_5180_50/1 meta data ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCT + IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECC your_output.pair2.truncated000066400000000000000000000002111350370616400355230ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/incl_adapter/combined_output/keep_both@AAGGGCSeq_1_5180_50/2 data meta AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGT + JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDED adapterremoval-2.3.1/tests/regression/pe/incl_adapter/combined_output/keep_both/your_output.settings000066400000000000000000000035111350370616400344430ustar00rootroot00000000000000AdapterRemoval ver. 2.1.7 Trimming of paired-end reads [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 372265332 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 [Trimming statistics] Total number of read pairs: 1 Number of unaligned read pairs: 0 Number of well aligned read pairs: 1 Number of discarded mate 1 reads: 0 Number of singleton mate 1 reads: 0 Number of discarded mate 2 reads: 0 Number of singleton mate 2 reads: 0 Number of reads with adapters[1]: 2 Number of retained reads: 2 Number of retained nucleotides: 100 Average length of retained reads: 50 [Length distribution] Length Mate1 Mate2 Singleton Discarded All 0 0 0 0 0 0 1 0 0 0 0 0 2 0 0 0 0 0 3 0 0 0 0 0 4 0 0 0 0 0 5 0 0 0 0 0 6 0 0 0 0 0 7 0 0 0 0 0 8 0 0 0 0 0 9 0 0 0 0 0 10 0 0 0 0 0 11 0 0 0 0 0 12 0 0 0 0 0 13 0 0 0 0 0 14 0 0 0 0 0 15 0 0 0 0 0 16 0 0 0 0 0 17 0 0 0 0 0 18 0 0 0 0 0 19 0 0 0 0 0 20 0 0 0 0 0 21 0 0 0 0 0 22 0 0 0 0 0 23 0 0 0 0 0 24 0 0 0 0 0 25 0 0 0 0 0 26 0 0 0 0 0 27 0 0 0 0 0 28 0 0 0 0 0 29 0 0 0 0 0 30 0 0 0 0 0 31 0 0 0 0 0 32 0 0 0 0 0 33 0 0 0 0 0 34 0 0 0 0 0 35 0 0 0 0 0 36 0 0 0 0 0 37 0 0 0 0 0 38 0 0 0 0 0 39 0 0 0 0 0 40 0 0 0 0 0 41 0 0 0 0 0 42 0 0 0 0 0 43 0 0 0 0 0 44 0 0 0 0 0 45 0 0 0 0 0 46 0 0 0 0 0 47 0 0 0 0 0 48 0 0 0 0 0 49 0 0 0 0 0 50 1 1 0 0 2 adapterremoval-2.3.1/tests/regression/pe/incl_adapter/combined_output/keep_mate1/000077500000000000000000000000001350370616400303165ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/incl_adapter/combined_output/keep_mate1/info.json000066400000000000000000000001551350370616400321450ustar00rootroot00000000000000{ "arguments": ["--combined-output", "--trimns", "--minlength", "50"], "return_code": 0, "stderr": [ ] } adapterremoval-2.3.1/tests/regression/pe/incl_adapter/combined_output/keep_mate1/input_1.fastq000066400000000000000000000003551350370616400327400ustar00rootroot00000000000000@AAGGGCSeq_1_5180_50/1 meta data ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG + IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! adapterremoval-2.3.1/tests/regression/pe/incl_adapter/combined_output/keep_mate1/input_2.fastq000066400000000000000000000003551350370616400327410ustar00rootroot00000000000000@AAGGGCSeq_1_5180_50/2 data meta AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGNAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCC + JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDEDBDBCBCCBBAA?ADAAA@@@>>>><=><<;<:<;87:78753420/,+)! your_output.pair1.truncated000066400000000000000000000002111350370616400355750ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/incl_adapter/combined_output/keep_mate1@AAGGGCSeq_1_5180_50/1 meta data ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCT + IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECC your_output.pair2.truncated000066400000000000000000000000471350370616400356050ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/incl_adapter/combined_output/keep_mate1@AAGGGCSeq_1_5180_50/2 data meta N + ! your_output.settings000066400000000000000000000035121350370616400344400ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/incl_adapter/combined_output/keep_mate1AdapterRemoval ver. 2.1.7 Trimming of paired-end reads [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 3738807510 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: Yes Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 50 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 [Trimming statistics] Total number of read pairs: 1 Number of unaligned read pairs: 0 Number of well aligned read pairs: 1 Number of discarded mate 1 reads: 0 Number of singleton mate 1 reads: 1 Number of discarded mate 2 reads: 1 Number of singleton mate 2 reads: 0 Number of reads with adapters[1]: 2 Number of retained reads: 1 Number of retained nucleotides: 50 Average length of retained reads: 50 [Length distribution] Length Mate1 Mate2 Singleton Discarded All 0 0 0 0 0 0 1 0 0 0 0 0 2 0 0 0 0 0 3 0 0 0 0 0 4 0 0 0 0 0 5 0 0 0 0 0 6 0 0 0 0 0 7 0 0 0 0 0 8 0 0 0 0 0 9 0 0 0 0 0 10 0 0 0 0 0 11 0 0 0 0 0 12 0 0 0 0 0 13 0 0 0 0 0 14 0 0 0 0 0 15 0 0 0 0 0 16 0 0 0 0 0 17 0 0 0 0 0 18 0 0 0 0 0 19 0 0 0 0 0 20 0 0 0 0 0 21 0 0 0 0 0 22 0 0 0 0 0 23 0 0 0 0 0 24 0 0 0 0 0 25 0 0 0 0 0 26 0 0 0 0 0 27 0 0 0 0 0 28 0 0 0 0 0 29 0 0 0 0 0 30 0 0 0 0 0 31 0 0 0 0 0 32 0 0 0 0 0 33 0 0 0 0 0 34 0 0 0 0 0 35 0 0 0 0 0 36 0 0 0 0 0 37 0 0 0 0 0 38 0 0 0 0 0 39 0 0 0 0 0 40 0 0 0 0 0 41 0 0 0 0 0 42 0 0 0 0 0 43 0 0 0 0 0 44 0 0 0 0 0 45 0 0 0 0 0 46 0 0 0 0 0 47 0 0 0 0 0 48 0 0 0 0 0 49 0 0 0 1 1 50 0 0 1 0 1 adapterremoval-2.3.1/tests/regression/pe/incl_adapter/combined_output/keep_mate2/000077500000000000000000000000001350370616400303175ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/incl_adapter/combined_output/keep_mate2/info.json000066400000000000000000000001551350370616400321460ustar00rootroot00000000000000{ "arguments": ["--combined-output", "--trimns", "--minlength", "50"], "return_code": 0, "stderr": [ ] } adapterremoval-2.3.1/tests/regression/pe/incl_adapter/combined_output/keep_mate2/input_1.fastq000066400000000000000000000003551350370616400327410ustar00rootroot00000000000000@AAGGGCSeq_1_5180_50/1 meta data ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCNAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG + IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! adapterremoval-2.3.1/tests/regression/pe/incl_adapter/combined_output/keep_mate2/input_2.fastq000066400000000000000000000003551350370616400327420ustar00rootroot00000000000000@AAGGGCSeq_1_5180_50/2 data meta AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGTAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCC + JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDEDBDBCBCCBBAA?ADAAA@@@>>>><=><<;<:<;87:78753420/,+)! your_output.pair1.truncated000066400000000000000000000000471350370616400356050ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/incl_adapter/combined_output/keep_mate2@AAGGGCSeq_1_5180_50/1 meta data N + ! your_output.pair2.truncated000066400000000000000000000002111350370616400355770ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/incl_adapter/combined_output/keep_mate2@AAGGGCSeq_1_5180_50/2 data meta AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGT + JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDED your_output.settings000066400000000000000000000035121350370616400344410ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/incl_adapter/combined_output/keep_mate2AdapterRemoval ver. 2.1.7 Trimming of paired-end reads [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 3854997780 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: Yes Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 50 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 [Trimming statistics] Total number of read pairs: 1 Number of unaligned read pairs: 0 Number of well aligned read pairs: 1 Number of discarded mate 1 reads: 1 Number of singleton mate 1 reads: 0 Number of discarded mate 2 reads: 0 Number of singleton mate 2 reads: 1 Number of reads with adapters[1]: 2 Number of retained reads: 1 Number of retained nucleotides: 50 Average length of retained reads: 50 [Length distribution] Length Mate1 Mate2 Singleton Discarded All 0 0 0 0 0 0 1 0 0 0 0 0 2 0 0 0 0 0 3 0 0 0 0 0 4 0 0 0 0 0 5 0 0 0 0 0 6 0 0 0 0 0 7 0 0 0 0 0 8 0 0 0 0 0 9 0 0 0 0 0 10 0 0 0 0 0 11 0 0 0 0 0 12 0 0 0 0 0 13 0 0 0 0 0 14 0 0 0 0 0 15 0 0 0 0 0 16 0 0 0 0 0 17 0 0 0 0 0 18 0 0 0 0 0 19 0 0 0 0 0 20 0 0 0 0 0 21 0 0 0 0 0 22 0 0 0 0 0 23 0 0 0 0 0 24 0 0 0 0 0 25 0 0 0 0 0 26 0 0 0 0 0 27 0 0 0 0 0 28 0 0 0 0 0 29 0 0 0 0 0 30 0 0 0 0 0 31 0 0 0 0 0 32 0 0 0 0 0 33 0 0 0 0 0 34 0 0 0 0 0 35 0 0 0 0 0 36 0 0 0 0 0 37 0 0 0 0 0 38 0 0 0 0 0 39 0 0 0 0 0 40 0 0 0 0 0 41 0 0 0 0 0 42 0 0 0 0 0 43 0 0 0 0 0 44 0 0 0 0 0 45 0 0 0 0 0 46 0 0 0 0 0 47 0 0 0 0 0 48 0 0 0 0 0 49 0 0 0 1 1 50 0 0 1 0 1 adapterremoval-2.3.1/tests/regression/pe/incl_adapter/combined_output/keep_neither/000077500000000000000000000000001350370616400307455ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/incl_adapter/combined_output/keep_neither/info.json000066400000000000000000000001551350370616400325740ustar00rootroot00000000000000{ "arguments": ["--combined-output", "--trimns", "--minlength", "50"], "return_code": 0, "stderr": [ ] } adapterremoval-2.3.1/tests/regression/pe/incl_adapter/combined_output/keep_neither/input_1.fastq000066400000000000000000000003551350370616400333670ustar00rootroot00000000000000@AAGGGCSeq_1_5180_50/1 meta data ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCNAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG + IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! adapterremoval-2.3.1/tests/regression/pe/incl_adapter/combined_output/keep_neither/input_2.fastq000066400000000000000000000003551350370616400333700ustar00rootroot00000000000000@AAGGGCSeq_1_5180_50/2 data meta AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGNAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCC + JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDEDBDBCBCCBBAA?ADAAA@@@>>>><=><<;<:<;87:78753420/,+)! your_output.pair1.truncated000066400000000000000000000000471350370616400362330ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/incl_adapter/combined_output/keep_neither@AAGGGCSeq_1_5180_50/1 meta data N + ! your_output.pair2.truncated000066400000000000000000000000471350370616400362340ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/incl_adapter/combined_output/keep_neither@AAGGGCSeq_1_5180_50/2 data meta N + ! your_output.settings000066400000000000000000000034731350370616400350750ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/incl_adapter/combined_output/keep_neitherAdapterRemoval ver. 2.1.7 Trimming of paired-end reads [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 3934188119 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: Yes Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 50 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 [Trimming statistics] Total number of read pairs: 1 Number of unaligned read pairs: 0 Number of well aligned read pairs: 1 Number of discarded mate 1 reads: 1 Number of singleton mate 1 reads: 0 Number of discarded mate 2 reads: 1 Number of singleton mate 2 reads: 0 Number of reads with adapters[1]: 2 Number of retained reads: 0 Number of retained nucleotides: 0 Average length of retained reads: 0 [Length distribution] Length Mate1 Mate2 Singleton Discarded All 0 0 0 0 0 0 1 0 0 0 0 0 2 0 0 0 0 0 3 0 0 0 0 0 4 0 0 0 0 0 5 0 0 0 0 0 6 0 0 0 0 0 7 0 0 0 0 0 8 0 0 0 0 0 9 0 0 0 0 0 10 0 0 0 0 0 11 0 0 0 0 0 12 0 0 0 0 0 13 0 0 0 0 0 14 0 0 0 0 0 15 0 0 0 0 0 16 0 0 0 0 0 17 0 0 0 0 0 18 0 0 0 0 0 19 0 0 0 0 0 20 0 0 0 0 0 21 0 0 0 0 0 22 0 0 0 0 0 23 0 0 0 0 0 24 0 0 0 0 0 25 0 0 0 0 0 26 0 0 0 0 0 27 0 0 0 0 0 28 0 0 0 0 0 29 0 0 0 0 0 30 0 0 0 0 0 31 0 0 0 0 0 32 0 0 0 0 0 33 0 0 0 0 0 34 0 0 0 0 0 35 0 0 0 0 0 36 0 0 0 0 0 37 0 0 0 0 0 38 0 0 0 0 0 39 0 0 0 0 0 40 0 0 0 0 0 41 0 0 0 0 0 42 0 0 0 0 0 43 0 0 0 0 0 44 0 0 0 0 0 45 0 0 0 0 0 46 0 0 0 0 0 47 0 0 0 0 0 48 0 0 0 0 0 49 0 0 0 2 2 adapterremoval-2.3.1/tests/regression/pe/incl_adapter/crlf_newlines/000077500000000000000000000000001350370616400257355ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/incl_adapter/crlf_newlines/info.json000066400000000000000000000000711350370616400275610ustar00rootroot00000000000000{ "arguments": [], "return_code": 0, "stderr": [ ] } adapterremoval-2.3.1/tests/regression/pe/incl_adapter/crlf_newlines/input_1.fastq000066400000000000000000000003611350370616400303540ustar00rootroot00000000000000@AAGGGCSeq_1_5180_50/1 meta data ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG + IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! adapterremoval-2.3.1/tests/regression/pe/incl_adapter/crlf_newlines/input_2.fastq000066400000000000000000000003611350370616400303550ustar00rootroot00000000000000@AAGGGCSeq_1_5180_50/2 data meta AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGTAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCC + JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDEDBDBCBCCBBAA?ADAAA@@@>>>><=><<;<:<;87:78753420/,+)! adapterremoval-2.3.1/tests/regression/pe/incl_adapter/crlf_newlines/your_output.discarded000066400000000000000000000000001350370616400322050ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/incl_adapter/crlf_newlines/your_output.pair1.truncated000066400000000000000000000002111350370616400332730ustar00rootroot00000000000000@AAGGGCSeq_1_5180_50/1 meta data ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCT + IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECC adapterremoval-2.3.1/tests/regression/pe/incl_adapter/crlf_newlines/your_output.pair2.truncated000066400000000000000000000002111350370616400332740ustar00rootroot00000000000000@AAGGGCSeq_1_5180_50/2 data meta AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGT + JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDED adapterremoval-2.3.1/tests/regression/pe/incl_adapter/crlf_newlines/your_output.settings000066400000000000000000000035111350370616400321350ustar00rootroot00000000000000AdapterRemoval ver. 2.1.7 Trimming of paired-end reads [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 372265332 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 [Trimming statistics] Total number of read pairs: 1 Number of unaligned read pairs: 0 Number of well aligned read pairs: 1 Number of discarded mate 1 reads: 0 Number of singleton mate 1 reads: 0 Number of discarded mate 2 reads: 0 Number of singleton mate 2 reads: 0 Number of reads with adapters[1]: 2 Number of retained reads: 2 Number of retained nucleotides: 100 Average length of retained reads: 50 [Length distribution] Length Mate1 Mate2 Singleton Discarded All 0 0 0 0 0 0 1 0 0 0 0 0 2 0 0 0 0 0 3 0 0 0 0 0 4 0 0 0 0 0 5 0 0 0 0 0 6 0 0 0 0 0 7 0 0 0 0 0 8 0 0 0 0 0 9 0 0 0 0 0 10 0 0 0 0 0 11 0 0 0 0 0 12 0 0 0 0 0 13 0 0 0 0 0 14 0 0 0 0 0 15 0 0 0 0 0 16 0 0 0 0 0 17 0 0 0 0 0 18 0 0 0 0 0 19 0 0 0 0 0 20 0 0 0 0 0 21 0 0 0 0 0 22 0 0 0 0 0 23 0 0 0 0 0 24 0 0 0 0 0 25 0 0 0 0 0 26 0 0 0 0 0 27 0 0 0 0 0 28 0 0 0 0 0 29 0 0 0 0 0 30 0 0 0 0 0 31 0 0 0 0 0 32 0 0 0 0 0 33 0 0 0 0 0 34 0 0 0 0 0 35 0 0 0 0 0 36 0 0 0 0 0 37 0 0 0 0 0 38 0 0 0 0 0 39 0 0 0 0 0 40 0 0 0 0 0 41 0 0 0 0 0 42 0 0 0 0 0 43 0 0 0 0 0 44 0 0 0 0 0 45 0 0 0 0 0 46 0 0 0 0 0 47 0 0 0 0 0 48 0 0 0 0 0 49 0 0 0 0 0 50 1 1 0 0 2 adapterremoval-2.3.1/tests/regression/pe/incl_adapter/crlf_newlines/your_output.singleton.truncated000066400000000000000000000000001350370616400342550ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/incl_adapter/defaults/000077500000000000000000000000001350370616400247125ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/incl_adapter/defaults/info.json000066400000000000000000000000711350370616400265360ustar00rootroot00000000000000{ "arguments": [], "return_code": 0, "stderr": [ ] } adapterremoval-2.3.1/tests/regression/pe/incl_adapter/defaults/input_1.fastq000066400000000000000000000003551350370616400273340ustar00rootroot00000000000000@AAGGGCSeq_1_5180_50/1 meta data ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG + IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! adapterremoval-2.3.1/tests/regression/pe/incl_adapter/defaults/input_2.fastq000066400000000000000000000003551350370616400273350ustar00rootroot00000000000000@AAGGGCSeq_1_5180_50/2 data meta AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGTAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCC + JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDEDBDBCBCCBBAA?ADAAA@@@>>>><=><<;<:<;87:78753420/,+)! adapterremoval-2.3.1/tests/regression/pe/incl_adapter/defaults/your_output.discarded000066400000000000000000000000001350370616400311620ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/incl_adapter/defaults/your_output.pair1.truncated000066400000000000000000000002111350370616400322500ustar00rootroot00000000000000@AAGGGCSeq_1_5180_50/1 meta data ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCT + IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECC adapterremoval-2.3.1/tests/regression/pe/incl_adapter/defaults/your_output.pair2.truncated000066400000000000000000000002111350370616400322510ustar00rootroot00000000000000@AAGGGCSeq_1_5180_50/2 data meta AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGT + JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDED adapterremoval-2.3.1/tests/regression/pe/incl_adapter/defaults/your_output.settings000066400000000000000000000035111350370616400311120ustar00rootroot00000000000000AdapterRemoval ver. 2.1.7 Trimming of paired-end reads [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 372265332 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 [Trimming statistics] Total number of read pairs: 1 Number of unaligned read pairs: 0 Number of well aligned read pairs: 1 Number of discarded mate 1 reads: 0 Number of singleton mate 1 reads: 0 Number of discarded mate 2 reads: 0 Number of singleton mate 2 reads: 0 Number of reads with adapters[1]: 2 Number of retained reads: 2 Number of retained nucleotides: 100 Average length of retained reads: 50 [Length distribution] Length Mate1 Mate2 Singleton Discarded All 0 0 0 0 0 0 1 0 0 0 0 0 2 0 0 0 0 0 3 0 0 0 0 0 4 0 0 0 0 0 5 0 0 0 0 0 6 0 0 0 0 0 7 0 0 0 0 0 8 0 0 0 0 0 9 0 0 0 0 0 10 0 0 0 0 0 11 0 0 0 0 0 12 0 0 0 0 0 13 0 0 0 0 0 14 0 0 0 0 0 15 0 0 0 0 0 16 0 0 0 0 0 17 0 0 0 0 0 18 0 0 0 0 0 19 0 0 0 0 0 20 0 0 0 0 0 21 0 0 0 0 0 22 0 0 0 0 0 23 0 0 0 0 0 24 0 0 0 0 0 25 0 0 0 0 0 26 0 0 0 0 0 27 0 0 0 0 0 28 0 0 0 0 0 29 0 0 0 0 0 30 0 0 0 0 0 31 0 0 0 0 0 32 0 0 0 0 0 33 0 0 0 0 0 34 0 0 0 0 0 35 0 0 0 0 0 36 0 0 0 0 0 37 0 0 0 0 0 38 0 0 0 0 0 39 0 0 0 0 0 40 0 0 0 0 0 41 0 0 0 0 0 42 0 0 0 0 0 43 0 0 0 0 0 44 0 0 0 0 0 45 0 0 0 0 0 46 0 0 0 0 0 47 0 0 0 0 0 48 0 0 0 0 0 49 0 0 0 0 0 50 1 1 0 0 2 adapterremoval-2.3.1/tests/regression/pe/incl_adapter/defaults/your_output.singleton.truncated000066400000000000000000000000001350370616400332320ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/incl_adapter/maxlength/000077500000000000000000000000001350370616400250725ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/incl_adapter/maxlength/both/000077500000000000000000000000001350370616400260265ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/incl_adapter/maxlength/both/info.json000066400000000000000000000001141350370616400276500ustar00rootroot00000000000000{ "arguments": ["--maxlength", "49"], "return_code": 0, "stderr": [ ] } adapterremoval-2.3.1/tests/regression/pe/incl_adapter/maxlength/both/input_1.fastq000066400000000000000000000003551350370616400304500ustar00rootroot00000000000000@AAGGGCSeq_1_5180_50/1 meta data ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG + IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! adapterremoval-2.3.1/tests/regression/pe/incl_adapter/maxlength/both/input_2.fastq000066400000000000000000000003551350370616400304510ustar00rootroot00000000000000@AAGGGCSeq_1_5180_50/2 data meta AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGTAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCC + JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDEDBDBCBCCBBAA?ADAAA@@@>>>><=><<;<:<;87:78753420/,+)! adapterremoval-2.3.1/tests/regression/pe/incl_adapter/maxlength/both/your_output.discarded000066400000000000000000000004221350370616400323060ustar00rootroot00000000000000@AAGGGCSeq_1_5180_50/1 meta data ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCT + IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECC @AAGGGCSeq_1_5180_50/2 data meta AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGT + JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDED adapterremoval-2.3.1/tests/regression/pe/incl_adapter/maxlength/both/your_output.pair1.truncated000066400000000000000000000000001350370616400333600ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/incl_adapter/maxlength/both/your_output.pair2.truncated000066400000000000000000000000001350370616400333610ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/incl_adapter/maxlength/both/your_output.settings000066400000000000000000000034771350370616400322410ustar00rootroot00000000000000AdapterRemoval ver. 2.1.7 Trimming of paired-end reads [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 1200660835 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 49 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 [Trimming statistics] Total number of read pairs: 1 Number of unaligned read pairs: 0 Number of well aligned read pairs: 1 Number of discarded mate 1 reads: 1 Number of singleton mate 1 reads: 0 Number of discarded mate 2 reads: 1 Number of singleton mate 2 reads: 0 Number of reads with adapters[1]: 2 Number of retained reads: 0 Number of retained nucleotides: 0 Average length of retained reads: 0 [Length distribution] Length Mate1 Mate2 Singleton Discarded All 0 0 0 0 0 0 1 0 0 0 0 0 2 0 0 0 0 0 3 0 0 0 0 0 4 0 0 0 0 0 5 0 0 0 0 0 6 0 0 0 0 0 7 0 0 0 0 0 8 0 0 0 0 0 9 0 0 0 0 0 10 0 0 0 0 0 11 0 0 0 0 0 12 0 0 0 0 0 13 0 0 0 0 0 14 0 0 0 0 0 15 0 0 0 0 0 16 0 0 0 0 0 17 0 0 0 0 0 18 0 0 0 0 0 19 0 0 0 0 0 20 0 0 0 0 0 21 0 0 0 0 0 22 0 0 0 0 0 23 0 0 0 0 0 24 0 0 0 0 0 25 0 0 0 0 0 26 0 0 0 0 0 27 0 0 0 0 0 28 0 0 0 0 0 29 0 0 0 0 0 30 0 0 0 0 0 31 0 0 0 0 0 32 0 0 0 0 0 33 0 0 0 0 0 34 0 0 0 0 0 35 0 0 0 0 0 36 0 0 0 0 0 37 0 0 0 0 0 38 0 0 0 0 0 39 0 0 0 0 0 40 0 0 0 0 0 41 0 0 0 0 0 42 0 0 0 0 0 43 0 0 0 0 0 44 0 0 0 0 0 45 0 0 0 0 0 46 0 0 0 0 0 47 0 0 0 0 0 48 0 0 0 0 0 49 0 0 0 0 0 50 0 0 0 2 2 adapterremoval-2.3.1/tests/regression/pe/incl_adapter/maxlength/both/your_output.singleton.truncated000066400000000000000000000000001350370616400343460ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/incl_adapter/maxlength/mate1/000077500000000000000000000000001350370616400261015ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/incl_adapter/maxlength/mate1/info.json000066400000000000000000000001301350370616400277210ustar00rootroot00000000000000{ "arguments": ["--maxlength", "49", "--trimns"], "return_code": 0, "stderr": [ ] } adapterremoval-2.3.1/tests/regression/pe/incl_adapter/maxlength/mate1/input_1.fastq000066400000000000000000000003551350370616400305230ustar00rootroot00000000000000@AAGGGCSeq_1_5180_50/1 meta data ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG + IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! adapterremoval-2.3.1/tests/regression/pe/incl_adapter/maxlength/mate1/input_2.fastq000066400000000000000000000003551350370616400305240ustar00rootroot00000000000000@AAGGGCSeq_1_5180_50/2 data meta AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGNAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCC + JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDEDBDBCBCCBBAA?ADAAA@@@>>>><=><<;<:<;87:78753420/,+)! adapterremoval-2.3.1/tests/regression/pe/incl_adapter/maxlength/mate1/your_output.discarded000066400000000000000000000002111350370616400323550ustar00rootroot00000000000000@AAGGGCSeq_1_5180_50/1 meta data ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCT + IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECC adapterremoval-2.3.1/tests/regression/pe/incl_adapter/maxlength/mate1/your_output.pair1.truncated000066400000000000000000000000001350370616400334330ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/incl_adapter/maxlength/mate1/your_output.pair2.truncated000066400000000000000000000000001350370616400334340ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/incl_adapter/maxlength/mate1/your_output.settings000066400000000000000000000035021350370616400323010ustar00rootroot00000000000000AdapterRemoval ver. 2.1.7 Trimming of paired-end reads [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 1359054103 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: Yes Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 49 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 [Trimming statistics] Total number of read pairs: 1 Number of unaligned read pairs: 0 Number of well aligned read pairs: 1 Number of discarded mate 1 reads: 1 Number of singleton mate 1 reads: 0 Number of discarded mate 2 reads: 0 Number of singleton mate 2 reads: 1 Number of reads with adapters[1]: 2 Number of retained reads: 1 Number of retained nucleotides: 49 Average length of retained reads: 49 [Length distribution] Length Mate1 Mate2 Singleton Discarded All 0 0 0 0 0 0 1 0 0 0 0 0 2 0 0 0 0 0 3 0 0 0 0 0 4 0 0 0 0 0 5 0 0 0 0 0 6 0 0 0 0 0 7 0 0 0 0 0 8 0 0 0 0 0 9 0 0 0 0 0 10 0 0 0 0 0 11 0 0 0 0 0 12 0 0 0 0 0 13 0 0 0 0 0 14 0 0 0 0 0 15 0 0 0 0 0 16 0 0 0 0 0 17 0 0 0 0 0 18 0 0 0 0 0 19 0 0 0 0 0 20 0 0 0 0 0 21 0 0 0 0 0 22 0 0 0 0 0 23 0 0 0 0 0 24 0 0 0 0 0 25 0 0 0 0 0 26 0 0 0 0 0 27 0 0 0 0 0 28 0 0 0 0 0 29 0 0 0 0 0 30 0 0 0 0 0 31 0 0 0 0 0 32 0 0 0 0 0 33 0 0 0 0 0 34 0 0 0 0 0 35 0 0 0 0 0 36 0 0 0 0 0 37 0 0 0 0 0 38 0 0 0 0 0 39 0 0 0 0 0 40 0 0 0 0 0 41 0 0 0 0 0 42 0 0 0 0 0 43 0 0 0 0 0 44 0 0 0 0 0 45 0 0 0 0 0 46 0 0 0 0 0 47 0 0 0 0 0 48 0 0 0 0 0 49 0 0 1 0 1 50 0 0 0 1 1 your_output.singleton.truncated000066400000000000000000000002071350370616400343530ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/incl_adapter/maxlength/mate1@AAGGGCSeq_1_5180_50/2 data meta AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATG + JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDE adapterremoval-2.3.1/tests/regression/pe/incl_adapter/maxlength/mate2/000077500000000000000000000000001350370616400261025ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/incl_adapter/maxlength/mate2/info.json000066400000000000000000000001301350370616400277220ustar00rootroot00000000000000{ "arguments": ["--maxlength", "49", "--trimns"], "return_code": 0, "stderr": [ ] } adapterremoval-2.3.1/tests/regression/pe/incl_adapter/maxlength/mate2/input_1.fastq000066400000000000000000000003551350370616400305240ustar00rootroot00000000000000@AAGGGCSeq_1_5180_50/1 meta data ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCNAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG + IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! adapterremoval-2.3.1/tests/regression/pe/incl_adapter/maxlength/mate2/input_2.fastq000066400000000000000000000003551350370616400305250ustar00rootroot00000000000000@AAGGGCSeq_1_5180_50/2 data meta AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGTAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCC + JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDEDBDBCBCCBBAA?ADAAA@@@>>>><=><<;<:<;87:78753420/,+)! adapterremoval-2.3.1/tests/regression/pe/incl_adapter/maxlength/mate2/your_output.discarded000066400000000000000000000002111350370616400323560ustar00rootroot00000000000000@AAGGGCSeq_1_5180_50/2 data meta AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGT + JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDED adapterremoval-2.3.1/tests/regression/pe/incl_adapter/maxlength/mate2/your_output.pair1.truncated000066400000000000000000000000001350370616400334340ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/incl_adapter/maxlength/mate2/your_output.pair2.truncated000066400000000000000000000000001350370616400334350ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/incl_adapter/maxlength/mate2/your_output.settings000066400000000000000000000035021350370616400323020ustar00rootroot00000000000000AdapterRemoval ver. 2.1.7 Trimming of paired-end reads [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 1361295368 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: Yes Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 49 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 [Trimming statistics] Total number of read pairs: 1 Number of unaligned read pairs: 0 Number of well aligned read pairs: 1 Number of discarded mate 1 reads: 0 Number of singleton mate 1 reads: 1 Number of discarded mate 2 reads: 1 Number of singleton mate 2 reads: 0 Number of reads with adapters[1]: 2 Number of retained reads: 1 Number of retained nucleotides: 49 Average length of retained reads: 49 [Length distribution] Length Mate1 Mate2 Singleton Discarded All 0 0 0 0 0 0 1 0 0 0 0 0 2 0 0 0 0 0 3 0 0 0 0 0 4 0 0 0 0 0 5 0 0 0 0 0 6 0 0 0 0 0 7 0 0 0 0 0 8 0 0 0 0 0 9 0 0 0 0 0 10 0 0 0 0 0 11 0 0 0 0 0 12 0 0 0 0 0 13 0 0 0 0 0 14 0 0 0 0 0 15 0 0 0 0 0 16 0 0 0 0 0 17 0 0 0 0 0 18 0 0 0 0 0 19 0 0 0 0 0 20 0 0 0 0 0 21 0 0 0 0 0 22 0 0 0 0 0 23 0 0 0 0 0 24 0 0 0 0 0 25 0 0 0 0 0 26 0 0 0 0 0 27 0 0 0 0 0 28 0 0 0 0 0 29 0 0 0 0 0 30 0 0 0 0 0 31 0 0 0 0 0 32 0 0 0 0 0 33 0 0 0 0 0 34 0 0 0 0 0 35 0 0 0 0 0 36 0 0 0 0 0 37 0 0 0 0 0 38 0 0 0 0 0 39 0 0 0 0 0 40 0 0 0 0 0 41 0 0 0 0 0 42 0 0 0 0 0 43 0 0 0 0 0 44 0 0 0 0 0 45 0 0 0 0 0 46 0 0 0 0 0 47 0 0 0 0 0 48 0 0 0 0 0 49 0 0 1 0 1 50 0 0 0 1 1 your_output.singleton.truncated000066400000000000000000000002071350370616400343540ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/incl_adapter/maxlength/mate2@AAGGGCSeq_1_5180_50/1 meta data ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCC + IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDEC adapterremoval-2.3.1/tests/regression/pe/incl_adapter/minlength/000077500000000000000000000000001350370616400250705ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/incl_adapter/minlength/both/000077500000000000000000000000001350370616400260245ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/incl_adapter/minlength/both/info.json000066400000000000000000000001141350370616400276460ustar00rootroot00000000000000{ "arguments": ["--minlength", "50"], "return_code": 0, "stderr": [ ] } adapterremoval-2.3.1/tests/regression/pe/incl_adapter/minlength/both/input_1.fastq000066400000000000000000000003531350370616400304440ustar00rootroot00000000000000@AAGGGCSeq_1_5180_50/1 meta data ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG + IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! adapterremoval-2.3.1/tests/regression/pe/incl_adapter/minlength/both/input_2.fastq000066400000000000000000000003531350370616400304450ustar00rootroot00000000000000@AAGGGCSeq_1_5180_50/2 data meta AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCC + JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDEBDBCBCCBBAA?ADAAA@@@>>>><=><<;<:<;87:78753420/,+)! adapterremoval-2.3.1/tests/regression/pe/incl_adapter/minlength/both/your_output.discarded000066400000000000000000000004161350370616400323070ustar00rootroot00000000000000@AAGGGCSeq_1_5180_50/1 meta data ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCC + IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDEC @AAGGGCSeq_1_5180_50/2 data meta AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATG + JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDE adapterremoval-2.3.1/tests/regression/pe/incl_adapter/minlength/both/your_output.pair1.truncated000066400000000000000000000000001350370616400333560ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/incl_adapter/minlength/both/your_output.pair2.truncated000066400000000000000000000000001350370616400333570ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/incl_adapter/minlength/both/your_output.settings000066400000000000000000000034721350370616400322320ustar00rootroot00000000000000AdapterRemoval ver. 2.1.7 Trimming of paired-end reads [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 1436203328 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 50 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 [Trimming statistics] Total number of read pairs: 1 Number of unaligned read pairs: 0 Number of well aligned read pairs: 1 Number of discarded mate 1 reads: 1 Number of singleton mate 1 reads: 0 Number of discarded mate 2 reads: 1 Number of singleton mate 2 reads: 0 Number of reads with adapters[1]: 2 Number of retained reads: 0 Number of retained nucleotides: 0 Average length of retained reads: 0 [Length distribution] Length Mate1 Mate2 Singleton Discarded All 0 0 0 0 0 0 1 0 0 0 0 0 2 0 0 0 0 0 3 0 0 0 0 0 4 0 0 0 0 0 5 0 0 0 0 0 6 0 0 0 0 0 7 0 0 0 0 0 8 0 0 0 0 0 9 0 0 0 0 0 10 0 0 0 0 0 11 0 0 0 0 0 12 0 0 0 0 0 13 0 0 0 0 0 14 0 0 0 0 0 15 0 0 0 0 0 16 0 0 0 0 0 17 0 0 0 0 0 18 0 0 0 0 0 19 0 0 0 0 0 20 0 0 0 0 0 21 0 0 0 0 0 22 0 0 0 0 0 23 0 0 0 0 0 24 0 0 0 0 0 25 0 0 0 0 0 26 0 0 0 0 0 27 0 0 0 0 0 28 0 0 0 0 0 29 0 0 0 0 0 30 0 0 0 0 0 31 0 0 0 0 0 32 0 0 0 0 0 33 0 0 0 0 0 34 0 0 0 0 0 35 0 0 0 0 0 36 0 0 0 0 0 37 0 0 0 0 0 38 0 0 0 0 0 39 0 0 0 0 0 40 0 0 0 0 0 41 0 0 0 0 0 42 0 0 0 0 0 43 0 0 0 0 0 44 0 0 0 0 0 45 0 0 0 0 0 46 0 0 0 0 0 47 0 0 0 0 0 48 0 0 0 0 0 49 0 0 0 2 2 adapterremoval-2.3.1/tests/regression/pe/incl_adapter/minlength/both/your_output.singleton.truncated000066400000000000000000000000001350370616400343440ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/incl_adapter/minlength/mate1/000077500000000000000000000000001350370616400260775ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/incl_adapter/minlength/mate1/info.json000066400000000000000000000001301350370616400277170ustar00rootroot00000000000000{ "arguments": ["--minlength", "50", "--trimns"], "return_code": 0, "stderr": [ ] } adapterremoval-2.3.1/tests/regression/pe/incl_adapter/minlength/mate1/input_1.fastq000066400000000000000000000003551350370616400305210ustar00rootroot00000000000000@AAGGGCSeq_1_5180_50/1 meta data NCATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG + IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! adapterremoval-2.3.1/tests/regression/pe/incl_adapter/minlength/mate1/input_2.fastq000066400000000000000000000003551350370616400305220ustar00rootroot00000000000000@AAGGGCSeq_1_5180_50/2 data meta AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGTAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCC + JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDEDBDBCBCCBBAA?ADAAA@@@>>>><=><<;<:<;87:78753420/,+)! adapterremoval-2.3.1/tests/regression/pe/incl_adapter/minlength/mate1/your_output.discarded000066400000000000000000000002071350370616400323600ustar00rootroot00000000000000@AAGGGCSeq_1_5180_50/1 meta data CATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCT + JJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECC adapterremoval-2.3.1/tests/regression/pe/incl_adapter/minlength/mate1/your_output.pair1.truncated000066400000000000000000000000001350370616400334310ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/incl_adapter/minlength/mate1/your_output.pair2.truncated000066400000000000000000000000001350370616400334320ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/incl_adapter/minlength/mate1/your_output.settings000066400000000000000000000035121350370616400323000ustar00rootroot00000000000000AdapterRemoval ver. 2.1.7 Trimming of paired-end reads [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 1647601792 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: Yes Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 50 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 [Trimming statistics] Total number of read pairs: 1 Number of unaligned read pairs: 0 Number of well aligned read pairs: 1 Number of discarded mate 1 reads: 1 Number of singleton mate 1 reads: 0 Number of discarded mate 2 reads: 0 Number of singleton mate 2 reads: 1 Number of reads with adapters[1]: 2 Number of retained reads: 1 Number of retained nucleotides: 50 Average length of retained reads: 50 [Length distribution] Length Mate1 Mate2 Singleton Discarded All 0 0 0 0 0 0 1 0 0 0 0 0 2 0 0 0 0 0 3 0 0 0 0 0 4 0 0 0 0 0 5 0 0 0 0 0 6 0 0 0 0 0 7 0 0 0 0 0 8 0 0 0 0 0 9 0 0 0 0 0 10 0 0 0 0 0 11 0 0 0 0 0 12 0 0 0 0 0 13 0 0 0 0 0 14 0 0 0 0 0 15 0 0 0 0 0 16 0 0 0 0 0 17 0 0 0 0 0 18 0 0 0 0 0 19 0 0 0 0 0 20 0 0 0 0 0 21 0 0 0 0 0 22 0 0 0 0 0 23 0 0 0 0 0 24 0 0 0 0 0 25 0 0 0 0 0 26 0 0 0 0 0 27 0 0 0 0 0 28 0 0 0 0 0 29 0 0 0 0 0 30 0 0 0 0 0 31 0 0 0 0 0 32 0 0 0 0 0 33 0 0 0 0 0 34 0 0 0 0 0 35 0 0 0 0 0 36 0 0 0 0 0 37 0 0 0 0 0 38 0 0 0 0 0 39 0 0 0 0 0 40 0 0 0 0 0 41 0 0 0 0 0 42 0 0 0 0 0 43 0 0 0 0 0 44 0 0 0 0 0 45 0 0 0 0 0 46 0 0 0 0 0 47 0 0 0 0 0 48 0 0 0 0 0 49 0 0 0 1 1 50 0 0 1 0 1 your_output.singleton.truncated000066400000000000000000000002111350370616400343440ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/incl_adapter/minlength/mate1@AAGGGCSeq_1_5180_50/2 data meta AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGT + JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDED adapterremoval-2.3.1/tests/regression/pe/incl_adapter/minlength/mate2/000077500000000000000000000000001350370616400261005ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/incl_adapter/minlength/mate2/info.json000066400000000000000000000001301350370616400277200ustar00rootroot00000000000000{ "arguments": ["--minlength", "50", "--trimns"], "return_code": 0, "stderr": [ ] } adapterremoval-2.3.1/tests/regression/pe/incl_adapter/minlength/mate2/input_1.fastq000066400000000000000000000003551350370616400305220ustar00rootroot00000000000000@AAGGGCSeq_1_5180_50/1 meta data ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG + IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! adapterremoval-2.3.1/tests/regression/pe/incl_adapter/minlength/mate2/input_2.fastq000066400000000000000000000003551350370616400305230ustar00rootroot00000000000000@AAGGGCSeq_1_5180_50/2 data meta NGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGTAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCC + JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDEDBDBCBCCBBAA?ADAAA@@@>>>><=><<;<:<;87:78753420/,+)! adapterremoval-2.3.1/tests/regression/pe/incl_adapter/minlength/mate2/your_output.discarded000066400000000000000000000002071350370616400323610ustar00rootroot00000000000000@AAGGGCSeq_1_5180_50/2 data meta GGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGT + IHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDED adapterremoval-2.3.1/tests/regression/pe/incl_adapter/minlength/mate2/your_output.pair1.truncated000066400000000000000000000000001350370616400334320ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/incl_adapter/minlength/mate2/your_output.pair2.truncated000066400000000000000000000000001350370616400334330ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/incl_adapter/minlength/mate2/your_output.settings000066400000000000000000000035121350370616400323010ustar00rootroot00000000000000AdapterRemoval ver. 2.1.7 Trimming of paired-end reads [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 1757553206 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: Yes Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 50 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 [Trimming statistics] Total number of read pairs: 1 Number of unaligned read pairs: 0 Number of well aligned read pairs: 1 Number of discarded mate 1 reads: 0 Number of singleton mate 1 reads: 1 Number of discarded mate 2 reads: 1 Number of singleton mate 2 reads: 0 Number of reads with adapters[1]: 2 Number of retained reads: 1 Number of retained nucleotides: 50 Average length of retained reads: 50 [Length distribution] Length Mate1 Mate2 Singleton Discarded All 0 0 0 0 0 0 1 0 0 0 0 0 2 0 0 0 0 0 3 0 0 0 0 0 4 0 0 0 0 0 5 0 0 0 0 0 6 0 0 0 0 0 7 0 0 0 0 0 8 0 0 0 0 0 9 0 0 0 0 0 10 0 0 0 0 0 11 0 0 0 0 0 12 0 0 0 0 0 13 0 0 0 0 0 14 0 0 0 0 0 15 0 0 0 0 0 16 0 0 0 0 0 17 0 0 0 0 0 18 0 0 0 0 0 19 0 0 0 0 0 20 0 0 0 0 0 21 0 0 0 0 0 22 0 0 0 0 0 23 0 0 0 0 0 24 0 0 0 0 0 25 0 0 0 0 0 26 0 0 0 0 0 27 0 0 0 0 0 28 0 0 0 0 0 29 0 0 0 0 0 30 0 0 0 0 0 31 0 0 0 0 0 32 0 0 0 0 0 33 0 0 0 0 0 34 0 0 0 0 0 35 0 0 0 0 0 36 0 0 0 0 0 37 0 0 0 0 0 38 0 0 0 0 0 39 0 0 0 0 0 40 0 0 0 0 0 41 0 0 0 0 0 42 0 0 0 0 0 43 0 0 0 0 0 44 0 0 0 0 0 45 0 0 0 0 0 46 0 0 0 0 0 47 0 0 0 0 0 48 0 0 0 0 0 49 0 0 0 1 1 50 0 0 1 0 1 your_output.singleton.truncated000066400000000000000000000002111350370616400343450ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/incl_adapter/minlength/mate2@AAGGGCSeq_1_5180_50/1 meta data ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCT + IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECC adapterremoval-2.3.1/tests/regression/pe/incl_adapter/multiple_input/000077500000000000000000000000001350370616400261555ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/incl_adapter/multiple_input/info.json000066400000000000000000000000711350370616400300010ustar00rootroot00000000000000{ "arguments": [], "return_code": 0, "stderr": [ ] } adapterremoval-2.3.1/tests/regression/pe/incl_adapter/multiple_input/input_1a.fastq000066400000000000000000000015501350370616400307360ustar00rootroot00000000000000@read_150_1/1 CTTGGGTACTCAGCCTTAGGGTACCACATAGAGTTATCTTATATATTATAATTGCTCTTTTAACATAATTTTAAAAAATTTATATTAAACTTTCTCTGTT + HHHFFFFBBDGGGGGHHHHHGGFCDHGEE<@;+@C792A.CEEGGFFFFDEFGFHHHH@C2;@F;EDDHFDCCC@.DEEEG=BGEDC5>:=2@GFHHHFF @read_150_2/1 GAGTGGGCTTCATCCCTGGGATGCAAGGCTGGTTCAATATATGCAAATCAATAAATGTAATCCAGCATATAAACAGAACCAAAGAAGATCGGAAGAGCAC + HHHHHHHHHHHHHHHHHHHHHHHGC.@CFGHHHHHHHHFBFFHEHHHHFBGHFFFFFFHEDE@EBHHFHB<<>099BEB@=?*59/''.CCFHFHHHHHH @read_150_3/1 TATGTAATGACATAACTCTTATGGGCAACTTCACAAAAACACAGAAGAAAGCCCTCCTAAAGAATGAAATTCCAAAAAAAATCAGGTTACTGCTCACTGA + HHE=EE@DBBBGHGBFGGDDDDFFFHHHHHGHHHHHHGHHHE7BFHHHHHHG@4FEHHFHHHHFHHHHHHFFFE?EGCDE>CD:9=>+*;=37::ADDHF @read_150_4/1 CTCCTATATAAAGATAGCTCTGTAAAACAGGCCAAAAAGCAGAGTGGGGTGTGGGAAGGCAGGGAAAACTGTCCAGGAATAAAGGCATGAAATGAAACAA + HHHHHHHHHHHHHHHHEG@:EEB4DFHHEHFHHHHEGFFEEFCDHEFF:+1;?GFFCFHHHHHHHHHFHBB>>BEDGCDHHHHF adapterremoval-2.3.1/tests/regression/pe/incl_adapter/multiple_input/input_1b.fastq000066400000000000000000000015501350370616400307370ustar00rootroot00000000000000@read_150_5/1 TACTCACGGACAAAGAATAAATATAGCTCCTCCAGGAGCTTAATAACTCAGTGCTGTCTAAACTCCTTACACCTGATGTTGATGCCATGGTTAGATAGTT + HHFFGGFDBHHEHHHHHHHHHHHHFHHHHFHHFEEDFD8=GHFFHHDHHHCHHFDHBHD:> @read_150_7/1 TAAGTAAGGTAGACAGCTAAGTCTAGTTTGTTCCCAGTGTTGTACCAGTCTCATCAGTGCCGTGTCTGGGTCTCACAGCCTCTGGTGTTCTATGCTGGAT + GFFEEDHHGHHHHHHHHB?GG77-/:>>@?6AC5GIB?BEBHHHHHHHHHHHHFGFHHHHHHEFEGF9?EHHHE@8BB12BEHHH @read_150_8/1 TAAAAACAAAAACCCTGATGAGAGTATTGATGTGTGCATAAACAAAGAAAAACATAATAGGAATAGAATGGTGAATTAAATTTTGTGAATTTTGGAAACC + HGGGGGHHHHHFHHGHHHHHHHEHHHHHHFHHEEHHHHHFE:/CGBHHHHHGFFGHHHHCEHEFECEFHHFEEE>CFFFCE?DEBD @read_150_10/1 TATAGATGAACTCTGATTTAGAATTTGTATAAGCTAAAGCATTATAGTAATAACTTTTAAAGTAGTATTTAAAATATCCTTATCTTACGTATATATGACT + <506@6?GHHHHGFHGFCFHHHHHHHHHHFGFF<3@C43F>AAEEFBFDFFHHHHHHHHED(0DAEBEFC?BFBEHHHHHC@85@GBGGFDCHEHHFCFB adapterremoval-2.3.1/tests/regression/pe/incl_adapter/multiple_input/input_2a.fastq000066400000000000000000000015501350370616400307370ustar00rootroot00000000000000@read_150_1/2 AGAAACCACAGTGACTTAAACAGAGAAAGTTTAATATAAATTTTTTAAAATTATGTTAAAAGAGCAATTATAATATATAAGTTAACTCTATGTGGTACCC + HHHFFHHHHHHGFBGHHEFBDG?B=GHHFGFHFHHHHHHHFBFHHHHHGGEEG=DGGGGCHHHHHHHGEA%5ADHHHH=G&&*>>E6,735@GG @read_150_3/2 GTCATTAACATTCACGAAGATAAATTTCTCCATTTTAAACAGAGACACTCAGTGAGCAGTAACCTGATTTTTTTTGGAATTTCATTCTTCAGGAGGGCTT + HHHHHHHHHHHHHHHHHH?GF5:@AFHHHGHFDDGGFFFHHFGHHHGGHHHHHHHHFGHFGEGC.18984>1BC=GFFAC<>E?..59&&-81:<<5.@ABCDBCE>:>@CDGHHHGEBFE/38@EEFBFGHHHHHHEGH?DHHHH>'9DEC**'*6 adapterremoval-2.3.1/tests/regression/pe/incl_adapter/multiple_input/input_2b.fastq000066400000000000000000000015501350370616400307400ustar00rootroot00000000000000@read_150_5/2 TGGGGCCATCAGGAATTTTGCAGTGGTAATGGGGGACATTTTAGCTGAGACTTGGAAAAATGGTAGAATTTGCTCCAACATGAGGAAATATGAGCATTGA + HHHHGEGHHHHGEG;/FHHHHHHHHE;@==G=DC>DGFHHHHHHHHHHHHHHFD;>A5<(@<4 @read_150_7/2 ACTTGCACCTCTTCATCAGAGGAGCAGATCCAGGAACAGAAGTCCTGCATTTACAGGCTCTTCATATCTTGTGCCGGGTTTGGCTGCCAGGTGGCCAGCT + HHHHG=BDEDFFGGHHHHHHHHHHHHFHHFHHHCGHHHHHEBHHHHHHHHHHHHHHGEEE??6BCFHE624@7=1AFGBDHHHFFE<<.>,1349EEHHHHHHHGFHFHHHHHEHHD=:>-7@BC2BHHHHHHHGBHEFFHHGGHFGFHHEEFHFBEBEFHHFFBCA?B adapterremoval-2.3.1/tests/regression/pe/incl_adapter/multiple_input/input_2c.fastq000066400000000000000000000006651350370616400307470ustar00rootroot00000000000000@read_150_9/2 GCCTTCCCTCTTCACTCCCTCCCTTATCCCAAACCTGCCTAGGTGGGGCTGATACAGACAGCAGGCCTGGCTCTACTTGTTTTGACAAAATATATGCCCT + GGGEBGHHHHHHHHHHHHHHHHHHHHFADHHHFHHHF?DEF@B>C;CDGEHGGHHHE@@DBFGHHHHGB>BBFEGEGHFHF8ADCFDEE4D?>H@:>DD= @read_150_10/2 TAGTCTTCTCTTTCCTGAGAATATTTTTATTGCAAATATGTAGTCATATATACGTAAGATAAGGATATTTTAAATACTACTTTAAAAGTTATTACTATAA + HHHHHHHHHHHHHHHHHHHHHHHHHHHHHFFFGHHHHHHHHHHHHEBDG>CCBB?FHFHHDEFHGDDGHHHHHH@BECHHEHGDHHHHHFHHHGEHHHHH adapterremoval-2.3.1/tests/regression/pe/incl_adapter/multiple_input/your_output.discarded000066400000000000000000000000001350370616400324250ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/incl_adapter/multiple_input/your_output.pair1.truncated000066400000000000000000000041471350370616400335270ustar00rootroot00000000000000@read_150_1/1 CTTGGGTACTCAGCCTTAGGGTACCACATAGAGTTATCTTATATATTATAATTGCTCTTTTAACATAATTTTAAAAAATTTATATTAAACTTTCTCTGTT + HHHFFFFBBDGGGGGHHHHHGGFCDHGEE<@;+@C792A.CEEGGFFFFDEFGFHHHH@C2;@F;EDDHFDCCC@.DEEEG=BGEDC5>:=2@GFHHHFF @read_150_2/1 GAGTGGGCTTCATCCCTGGGATGCAAGGCTGGTTCAATATATGCAAATCAATAAATGTAATCCAGCATATAAACAGAACCAAAGA + HHHHHHHHHHHHHHHHHHHHHHHGC.@CFGHHHHHHHHFBFFHEHHHHFBGHFFFFFFHEDE@EBHHFHB<<>099BEB@=?*59 @read_150_3/1 TATGTAATGACATAACTCTTATGGGCAACTTCACAAAAACACAGAAGAAAGCCCTCCTAAAGAATGAAATTCCAAAAAAAATCAGGTTACTGCTCACTGA + HHE=EE@DBBBGHGBFGGDDDDFFFHHHHHGHHHHHHGHHHE7BFHHHHHHG@4FEHHFHHHHFHHHHHHFFFE?EGCDE>CD:9=>+*;=37::ADDHF @read_150_4/1 CTCCTATATAAAGATAGCTCTGTAAAACAGGCCAAAAAGCAGAGTGGGGTGTGGGAAGGCAGGGAAAACTGTCCAGGAATAAAGGCATGAAATGAAACAA + HHHHHHHHHHHHHHHHEG@:EEB4DFHHEHFHHHHEGFFEEFCDHEFF:+1;?GFFCFHHHHHHHHHFHBB>>BEDGCDHHHHF @read_150_5/1 TACTCACGGACAAAGAATAAATATAGCTCCTCCAGGAGCTTAATAACTCAGTGCTGTCTAAACTCCTTACACCTGATGTTGATGCCATGGTTAGATAGTT + HHFFGGFDBHHEHHHHHHHHHHHHFHHHHFHHFEEDFD8=GHFFHHDHHHCHHFDHBHD:> @read_150_7/1 TAAGTAAGGTAGACAGCTAAGTCTAGTTTGTTCCCAGTGTTGTACCAGTCTCATCAGTGCCGTGTCTGGGTCTCACAGCCTCTGGTGTTCTATGCTGGAT + GFFEEDHHGHHHHHHHHB?GG77-/:>>@?6AC5GIB?BEBHHHHHHHHHHHHFGFHHHHHHEFEGF9?EHHHE@8BB12BEHHH @read_150_8/1 TAAAAACAAAAACCCTGATGAGAGTATTGATGTGTGCATAAACAAAGAAAAACATAATAGGAATAGAATGGTGAATTAAATTTTGTGAATTTTGGAAACC + HGGGGGHHHHHFHHGHHHHHHHEHHHHHHFHHEEHHHHHFE:/CGBHHHHHGFFGHHHHCEHEFECEFHHFEEE>CFFFCE?DEBD @read_150_10/1 TATAGATGAACTCTGATTTAGAATTTGTATAAGCTAAAGCATTATAGTAATAACTTTTAAAGTAGTATTTAAAATATCCTTATCTTACGTATATATGACT + <506@6?GHHHHGFHGFCFHHHHHHHHHHFGFF<3@C43F>AAEEFBFDFFHHHHHHHHED(0DAEBEFC?BFBEHHHHHC@85@GBGGFDCHEHHFCFB adapterremoval-2.3.1/tests/regression/pe/incl_adapter/multiple_input/your_output.pair2.truncated000066400000000000000000000041471350370616400335300ustar00rootroot00000000000000@read_150_1/2 AGAAACCACAGTGACTTAAACAGAGAAAGTTTAATATAAATTTTTTAAAATTATGTTAAAAGAGCAATTATAATATATAAGTTAACTCTATGTGGTACCC + HHHFFHHHHHHGFBGHHEFBDG?B=GHHFGFHFHHHHHHHFBFHHHHHGGEEG=DGGGGCHHHHHHHGEA%5ADHHHH=G&&*>>1BC=GFFAC<>E?..59&&-81:<<5.@ABCDBCE>:>@CDGHHHGEBFE/38@EEFBFGHHHHHHEGH?DHHHH>'9DEC**'*6 @read_150_5/2 TGGGGCCATCAGGAATTTTGCAGTGGTAATGGGGGACATTTTAGCTGAGACTTGGAAAAATGGTAGAATTTGCTCCAACATGAGGAAATATGAGCATTGA + HHHHGEGHHHHGEG;/FHHHHHHHHE;@==G=DC>DGFHHHHHHHHHHHHHHFD;>A5<(@<4 @read_150_7/2 ACTTGCACCTCTTCATCAGAGGAGCAGATCCAGGAACAGAAGTCCTGCATTTACAGGCTCTTCATATCTTGTGCCGGGTTTGGCTGCCAGGTGGCCAGCT + HHHHG=BDEDFFGGHHHHHHHHHHHHFHHFHHHCGHHHHHEBHHHHHHHHHHHHHHGEEE??6BCFHE624@7=1AFGBDHHHFFE<<.>,1349EEHHHHHHHGFHFHHHHHEHHD=:>-7@BC2BHHHHHHHGBHEFFHHGGHFGFHHEEFHFBEBEFHHFFBCA?B @read_150_9/2 GCCTTCCCTCTTCACTCCCTCCCTTATCCCAAACCTGCCTAGGTGGGGCTGATACAGACAGCAGGCCTGGCTCTACTTGTTTTGACAAAATATATGCCCT + GGGEBGHHHHHHHHHHHHHHHHHHHHFADHHHFHHHF?DEF@B>C;CDGEHGGHHHE@@DBFGHHHHGB>BBFEGEGHFHF8ADCFDEE4D?>H@:>DD= @read_150_10/2 TAGTCTTCTCTTTCCTGAGAATATTTTTATTGCAAATATGTAGTCATATATACGTAAGATAAGGATATTTTAAATACTACTTTAAAAGTTATTACTATAA + HHHHHHHHHHHHHHHHHHHHHHHHHHHHHFFFGHHHHHHHHHHHHEBDG>CCBB?FHFHHDEFHGDDGHHHHHH@BECHHEHGDHHHHHFHHHGEHHHHH adapterremoval-2.3.1/tests/regression/pe/incl_adapter/multiple_input/your_output.settings000066400000000000000000000047331350370616400323640ustar00rootroot00000000000000AdapterRemoval ver. 2.2.0 Trimming of paired-end reads [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 4274826581 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 [Trimming statistics] Total number of read pairs: 10 Number of unaligned read pairs: 4 Number of well aligned read pairs: 6 Number of discarded mate 1 reads: 0 Number of singleton mate 1 reads: 0 Number of discarded mate 2 reads: 0 Number of singleton mate 2 reads: 0 Number of reads with adapters[1]: 2 Number of retained reads: 20 Number of retained nucleotides: 1970 Average length of retained reads: 98.5 [Length distribution] Length Mate1 Mate2 Singleton Discarded All 0 0 0 0 0 0 1 0 0 0 0 0 2 0 0 0 0 0 3 0 0 0 0 0 4 0 0 0 0 0 5 0 0 0 0 0 6 0 0 0 0 0 7 0 0 0 0 0 8 0 0 0 0 0 9 0 0 0 0 0 10 0 0 0 0 0 11 0 0 0 0 0 12 0 0 0 0 0 13 0 0 0 0 0 14 0 0 0 0 0 15 0 0 0 0 0 16 0 0 0 0 0 17 0 0 0 0 0 18 0 0 0 0 0 19 0 0 0 0 0 20 0 0 0 0 0 21 0 0 0 0 0 22 0 0 0 0 0 23 0 0 0 0 0 24 0 0 0 0 0 25 0 0 0 0 0 26 0 0 0 0 0 27 0 0 0 0 0 28 0 0 0 0 0 29 0 0 0 0 0 30 0 0 0 0 0 31 0 0 0 0 0 32 0 0 0 0 0 33 0 0 0 0 0 34 0 0 0 0 0 35 0 0 0 0 0 36 0 0 0 0 0 37 0 0 0 0 0 38 0 0 0 0 0 39 0 0 0 0 0 40 0 0 0 0 0 41 0 0 0 0 0 42 0 0 0 0 0 43 0 0 0 0 0 44 0 0 0 0 0 45 0 0 0 0 0 46 0 0 0 0 0 47 0 0 0 0 0 48 0 0 0 0 0 49 0 0 0 0 0 50 0 0 0 0 0 51 0 0 0 0 0 52 0 0 0 0 0 53 0 0 0 0 0 54 0 0 0 0 0 55 0 0 0 0 0 56 0 0 0 0 0 57 0 0 0 0 0 58 0 0 0 0 0 59 0 0 0 0 0 60 0 0 0 0 0 61 0 0 0 0 0 62 0 0 0 0 0 63 0 0 0 0 0 64 0 0 0 0 0 65 0 0 0 0 0 66 0 0 0 0 0 67 0 0 0 0 0 68 0 0 0 0 0 69 0 0 0 0 0 70 0 0 0 0 0 71 0 0 0 0 0 72 0 0 0 0 0 73 0 0 0 0 0 74 0 0 0 0 0 75 0 0 0 0 0 76 0 0 0 0 0 77 0 0 0 0 0 78 0 0 0 0 0 79 0 0 0 0 0 80 0 0 0 0 0 81 0 0 0 0 0 82 0 0 0 0 0 83 0 0 0 0 0 84 0 0 0 0 0 85 1 1 0 0 2 86 0 0 0 0 0 87 0 0 0 0 0 88 0 0 0 0 0 89 0 0 0 0 0 90 0 0 0 0 0 91 0 0 0 0 0 92 0 0 0 0 0 93 0 0 0 0 0 94 0 0 0 0 0 95 0 0 0 0 0 96 0 0 0 0 0 97 0 0 0 0 0 98 0 0 0 0 0 99 0 0 0 0 0 100 9 9 0 0 18 adapterremoval-2.3.1/tests/regression/pe/incl_adapter/multiple_input/your_output.singleton.truncated000066400000000000000000000000001350370616400344750ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/incl_adapter/threads/000077500000000000000000000000001350370616400245355ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/incl_adapter/threads/one/000077500000000000000000000000001350370616400253165ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/incl_adapter/threads/one/info.json000066400000000000000000000001111350370616400271350ustar00rootroot00000000000000{ "arguments": ["--threads", "1"], "return_code": 0, "stderr": [ ] } adapterremoval-2.3.1/tests/regression/pe/incl_adapter/threads/one/input_1.fastq000066400000000000000000000003551350370616400277400ustar00rootroot00000000000000@AAGGGCSeq_1_5180_50/1 meta data ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG + IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! adapterremoval-2.3.1/tests/regression/pe/incl_adapter/threads/one/input_2.fastq000066400000000000000000000003551350370616400277410ustar00rootroot00000000000000@AAGGGCSeq_1_5180_50/2 data meta AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGTAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCC + JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDEDBDBCBCCBBAA?ADAAA@@@>>>><=><<;<:<;87:78753420/,+)! adapterremoval-2.3.1/tests/regression/pe/incl_adapter/threads/one/your_output.discarded000066400000000000000000000000001350370616400315660ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/incl_adapter/threads/one/your_output.pair1.truncated000066400000000000000000000002111350370616400326540ustar00rootroot00000000000000@AAGGGCSeq_1_5180_50/1 meta data ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCT + IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECC adapterremoval-2.3.1/tests/regression/pe/incl_adapter/threads/one/your_output.pair2.truncated000066400000000000000000000002111350370616400326550ustar00rootroot00000000000000@AAGGGCSeq_1_5180_50/2 data meta AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGT + JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDED adapterremoval-2.3.1/tests/regression/pe/incl_adapter/threads/one/your_output.settings000066400000000000000000000035111350370616400315160ustar00rootroot00000000000000AdapterRemoval ver. 2.1.7 Trimming of paired-end reads [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 372265332 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 [Trimming statistics] Total number of read pairs: 1 Number of unaligned read pairs: 0 Number of well aligned read pairs: 1 Number of discarded mate 1 reads: 0 Number of singleton mate 1 reads: 0 Number of discarded mate 2 reads: 0 Number of singleton mate 2 reads: 0 Number of reads with adapters[1]: 2 Number of retained reads: 2 Number of retained nucleotides: 100 Average length of retained reads: 50 [Length distribution] Length Mate1 Mate2 Singleton Discarded All 0 0 0 0 0 0 1 0 0 0 0 0 2 0 0 0 0 0 3 0 0 0 0 0 4 0 0 0 0 0 5 0 0 0 0 0 6 0 0 0 0 0 7 0 0 0 0 0 8 0 0 0 0 0 9 0 0 0 0 0 10 0 0 0 0 0 11 0 0 0 0 0 12 0 0 0 0 0 13 0 0 0 0 0 14 0 0 0 0 0 15 0 0 0 0 0 16 0 0 0 0 0 17 0 0 0 0 0 18 0 0 0 0 0 19 0 0 0 0 0 20 0 0 0 0 0 21 0 0 0 0 0 22 0 0 0 0 0 23 0 0 0 0 0 24 0 0 0 0 0 25 0 0 0 0 0 26 0 0 0 0 0 27 0 0 0 0 0 28 0 0 0 0 0 29 0 0 0 0 0 30 0 0 0 0 0 31 0 0 0 0 0 32 0 0 0 0 0 33 0 0 0 0 0 34 0 0 0 0 0 35 0 0 0 0 0 36 0 0 0 0 0 37 0 0 0 0 0 38 0 0 0 0 0 39 0 0 0 0 0 40 0 0 0 0 0 41 0 0 0 0 0 42 0 0 0 0 0 43 0 0 0 0 0 44 0 0 0 0 0 45 0 0 0 0 0 46 0 0 0 0 0 47 0 0 0 0 0 48 0 0 0 0 0 49 0 0 0 0 0 50 1 1 0 0 2 adapterremoval-2.3.1/tests/regression/pe/incl_adapter/threads/one/your_output.singleton.truncated000066400000000000000000000000001350370616400336360ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/incl_adapter/threads/three/000077500000000000000000000000001350370616400256445ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/incl_adapter/threads/three/info.json000066400000000000000000000001111350370616400274630ustar00rootroot00000000000000{ "arguments": ["--threads", "3"], "return_code": 0, "stderr": [ ] } adapterremoval-2.3.1/tests/regression/pe/incl_adapter/threads/three/input_1.fastq000066400000000000000000000003551350370616400302660ustar00rootroot00000000000000@AAGGGCSeq_1_5180_50/1 meta data ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG + IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! adapterremoval-2.3.1/tests/regression/pe/incl_adapter/threads/three/input_2.fastq000066400000000000000000000003551350370616400302670ustar00rootroot00000000000000@AAGGGCSeq_1_5180_50/2 data meta AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGTAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCC + JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDEDBDBCBCCBBAA?ADAAA@@@>>>><=><<;<:<;87:78753420/,+)! adapterremoval-2.3.1/tests/regression/pe/incl_adapter/threads/three/your_output.discarded000066400000000000000000000000001350370616400321140ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/incl_adapter/threads/three/your_output.pair1.truncated000066400000000000000000000002111350370616400332020ustar00rootroot00000000000000@AAGGGCSeq_1_5180_50/1 meta data ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCT + IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECC adapterremoval-2.3.1/tests/regression/pe/incl_adapter/threads/three/your_output.pair2.truncated000066400000000000000000000002111350370616400332030ustar00rootroot00000000000000@AAGGGCSeq_1_5180_50/2 data meta AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGT + JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDED adapterremoval-2.3.1/tests/regression/pe/incl_adapter/threads/three/your_output.settings000066400000000000000000000035021350370616400320440ustar00rootroot00000000000000AdapterRemoval ver. 2.1.7 Trimming of paired-end reads [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: NA Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 [Trimming statistics] Total number of read pairs: 1 Number of unaligned read pairs: 0 Number of well aligned read pairs: 1 Number of discarded mate 1 reads: 0 Number of singleton mate 1 reads: 0 Number of discarded mate 2 reads: 0 Number of singleton mate 2 reads: 0 Number of reads with adapters[1]: 2 Number of retained reads: 2 Number of retained nucleotides: 100 Average length of retained reads: 50 [Length distribution] Length Mate1 Mate2 Singleton Discarded All 0 0 0 0 0 0 1 0 0 0 0 0 2 0 0 0 0 0 3 0 0 0 0 0 4 0 0 0 0 0 5 0 0 0 0 0 6 0 0 0 0 0 7 0 0 0 0 0 8 0 0 0 0 0 9 0 0 0 0 0 10 0 0 0 0 0 11 0 0 0 0 0 12 0 0 0 0 0 13 0 0 0 0 0 14 0 0 0 0 0 15 0 0 0 0 0 16 0 0 0 0 0 17 0 0 0 0 0 18 0 0 0 0 0 19 0 0 0 0 0 20 0 0 0 0 0 21 0 0 0 0 0 22 0 0 0 0 0 23 0 0 0 0 0 24 0 0 0 0 0 25 0 0 0 0 0 26 0 0 0 0 0 27 0 0 0 0 0 28 0 0 0 0 0 29 0 0 0 0 0 30 0 0 0 0 0 31 0 0 0 0 0 32 0 0 0 0 0 33 0 0 0 0 0 34 0 0 0 0 0 35 0 0 0 0 0 36 0 0 0 0 0 37 0 0 0 0 0 38 0 0 0 0 0 39 0 0 0 0 0 40 0 0 0 0 0 41 0 0 0 0 0 42 0 0 0 0 0 43 0 0 0 0 0 44 0 0 0 0 0 45 0 0 0 0 0 46 0 0 0 0 0 47 0 0 0 0 0 48 0 0 0 0 0 49 0 0 0 0 0 50 1 1 0 0 2 adapterremoval-2.3.1/tests/regression/pe/incl_adapter/threads/three/your_output.singleton.truncated000066400000000000000000000000001350370616400341640ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/incl_adapter/threads/two/000077500000000000000000000000001350370616400253465ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/incl_adapter/threads/two/info.json000066400000000000000000000001111350370616400271650ustar00rootroot00000000000000{ "arguments": ["--threads", "2"], "return_code": 0, "stderr": [ ] } adapterremoval-2.3.1/tests/regression/pe/incl_adapter/threads/two/input_1.fastq000066400000000000000000000003551350370616400277700ustar00rootroot00000000000000@AAGGGCSeq_1_5180_50/1 meta data ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG + IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! adapterremoval-2.3.1/tests/regression/pe/incl_adapter/threads/two/input_2.fastq000066400000000000000000000003551350370616400277710ustar00rootroot00000000000000@AAGGGCSeq_1_5180_50/2 data meta AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGTAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCC + JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDEDBDBCBCCBBAA?ADAAA@@@>>>><=><<;<:<;87:78753420/,+)! adapterremoval-2.3.1/tests/regression/pe/incl_adapter/threads/two/your_output.discarded000066400000000000000000000000001350370616400316160ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/incl_adapter/threads/two/your_output.pair1.truncated000066400000000000000000000002111350370616400327040ustar00rootroot00000000000000@AAGGGCSeq_1_5180_50/1 meta data ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCT + IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECC adapterremoval-2.3.1/tests/regression/pe/incl_adapter/threads/two/your_output.pair2.truncated000066400000000000000000000002111350370616400327050ustar00rootroot00000000000000@AAGGGCSeq_1_5180_50/2 data meta AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGT + JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDED adapterremoval-2.3.1/tests/regression/pe/incl_adapter/threads/two/your_output.settings000066400000000000000000000035021350370616400315460ustar00rootroot00000000000000AdapterRemoval ver. 2.1.7 Trimming of paired-end reads [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: NA Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 [Trimming statistics] Total number of read pairs: 1 Number of unaligned read pairs: 0 Number of well aligned read pairs: 1 Number of discarded mate 1 reads: 0 Number of singleton mate 1 reads: 0 Number of discarded mate 2 reads: 0 Number of singleton mate 2 reads: 0 Number of reads with adapters[1]: 2 Number of retained reads: 2 Number of retained nucleotides: 100 Average length of retained reads: 50 [Length distribution] Length Mate1 Mate2 Singleton Discarded All 0 0 0 0 0 0 1 0 0 0 0 0 2 0 0 0 0 0 3 0 0 0 0 0 4 0 0 0 0 0 5 0 0 0 0 0 6 0 0 0 0 0 7 0 0 0 0 0 8 0 0 0 0 0 9 0 0 0 0 0 10 0 0 0 0 0 11 0 0 0 0 0 12 0 0 0 0 0 13 0 0 0 0 0 14 0 0 0 0 0 15 0 0 0 0 0 16 0 0 0 0 0 17 0 0 0 0 0 18 0 0 0 0 0 19 0 0 0 0 0 20 0 0 0 0 0 21 0 0 0 0 0 22 0 0 0 0 0 23 0 0 0 0 0 24 0 0 0 0 0 25 0 0 0 0 0 26 0 0 0 0 0 27 0 0 0 0 0 28 0 0 0 0 0 29 0 0 0 0 0 30 0 0 0 0 0 31 0 0 0 0 0 32 0 0 0 0 0 33 0 0 0 0 0 34 0 0 0 0 0 35 0 0 0 0 0 36 0 0 0 0 0 37 0 0 0 0 0 38 0 0 0 0 0 39 0 0 0 0 0 40 0 0 0 0 0 41 0 0 0 0 0 42 0 0 0 0 0 43 0 0 0 0 0 44 0 0 0 0 0 45 0 0 0 0 0 46 0 0 0 0 0 47 0 0 0 0 0 48 0 0 0 0 0 49 0 0 0 0 0 50 1 1 0 0 2 adapterremoval-2.3.1/tests/regression/pe/incl_adapter/threads/two/your_output.singleton.truncated000066400000000000000000000000001350370616400336660ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/incl_adapter/trimns/000077500000000000000000000000001350370616400244175ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/incl_adapter/trimns/excl_ns/000077500000000000000000000000001350370616400260525ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/incl_adapter/trimns/excl_ns/info.json000066400000000000000000000001031350370616400276720ustar00rootroot00000000000000{ "arguments": ["--trimns"], "return_code": 0, "stderr": [ ] } adapterremoval-2.3.1/tests/regression/pe/incl_adapter/trimns/excl_ns/input_1.fastq000066400000000000000000000003551350370616400304740ustar00rootroot00000000000000@AAGGGCSeq_1_5180_50/1 meta data ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG + IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! adapterremoval-2.3.1/tests/regression/pe/incl_adapter/trimns/excl_ns/input_2.fastq000066400000000000000000000003551350370616400304750ustar00rootroot00000000000000@AAGGGCSeq_1_5180_50/2 data meta AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGTAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCC + JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDEDBDBCBCCBBAA?ADAAA@@@>>>><=><<;<:<;87:78753420/,+)! adapterremoval-2.3.1/tests/regression/pe/incl_adapter/trimns/excl_ns/your_output.discarded000066400000000000000000000000001350370616400323220ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/incl_adapter/trimns/excl_ns/your_output.pair1.truncated000066400000000000000000000002111350370616400334100ustar00rootroot00000000000000@AAGGGCSeq_1_5180_50/1 meta data ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCT + IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECC adapterremoval-2.3.1/tests/regression/pe/incl_adapter/trimns/excl_ns/your_output.pair2.truncated000066400000000000000000000002111350370616400334110ustar00rootroot00000000000000@AAGGGCSeq_1_5180_50/2 data meta AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGT + JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDED adapterremoval-2.3.1/tests/regression/pe/incl_adapter/trimns/excl_ns/your_output.settings000066400000000000000000000035131350370616400322540ustar00rootroot00000000000000AdapterRemoval ver. 2.1.7 Trimming of paired-end reads [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 2986012581 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: Yes Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 [Trimming statistics] Total number of read pairs: 1 Number of unaligned read pairs: 0 Number of well aligned read pairs: 1 Number of discarded mate 1 reads: 0 Number of singleton mate 1 reads: 0 Number of discarded mate 2 reads: 0 Number of singleton mate 2 reads: 0 Number of reads with adapters[1]: 2 Number of retained reads: 2 Number of retained nucleotides: 100 Average length of retained reads: 50 [Length distribution] Length Mate1 Mate2 Singleton Discarded All 0 0 0 0 0 0 1 0 0 0 0 0 2 0 0 0 0 0 3 0 0 0 0 0 4 0 0 0 0 0 5 0 0 0 0 0 6 0 0 0 0 0 7 0 0 0 0 0 8 0 0 0 0 0 9 0 0 0 0 0 10 0 0 0 0 0 11 0 0 0 0 0 12 0 0 0 0 0 13 0 0 0 0 0 14 0 0 0 0 0 15 0 0 0 0 0 16 0 0 0 0 0 17 0 0 0 0 0 18 0 0 0 0 0 19 0 0 0 0 0 20 0 0 0 0 0 21 0 0 0 0 0 22 0 0 0 0 0 23 0 0 0 0 0 24 0 0 0 0 0 25 0 0 0 0 0 26 0 0 0 0 0 27 0 0 0 0 0 28 0 0 0 0 0 29 0 0 0 0 0 30 0 0 0 0 0 31 0 0 0 0 0 32 0 0 0 0 0 33 0 0 0 0 0 34 0 0 0 0 0 35 0 0 0 0 0 36 0 0 0 0 0 37 0 0 0 0 0 38 0 0 0 0 0 39 0 0 0 0 0 40 0 0 0 0 0 41 0 0 0 0 0 42 0 0 0 0 0 43 0 0 0 0 0 44 0 0 0 0 0 45 0 0 0 0 0 46 0 0 0 0 0 47 0 0 0 0 0 48 0 0 0 0 0 49 0 0 0 0 0 50 1 1 0 0 2 adapterremoval-2.3.1/tests/regression/pe/incl_adapter/trimns/excl_ns/your_output.singleton.truncated000066400000000000000000000000001350370616400343720ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/incl_adapter/trimns/incl_ns/000077500000000000000000000000001350370616400260445ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/incl_adapter/trimns/incl_ns/info.json000066400000000000000000000001031350370616400276640ustar00rootroot00000000000000{ "arguments": ["--trimns"], "return_code": 0, "stderr": [ ] } adapterremoval-2.3.1/tests/regression/pe/incl_adapter/trimns/incl_ns/input_1.fastq000066400000000000000000000003551350370616400304660ustar00rootroot00000000000000@AAGGGCSeq_1_5180_50/1 meta data ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCNAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG + IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! adapterremoval-2.3.1/tests/regression/pe/incl_adapter/trimns/incl_ns/input_2.fastq000066400000000000000000000003551350370616400304670ustar00rootroot00000000000000@AAGGGCSeq_1_5180_50/2 data meta AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGNNNNNNAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCC + JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDEDBDBCBCCBBAA?ADAAA@@@>>>><=><<;<:<;87:78753420/,+)! adapterremoval-2.3.1/tests/regression/pe/incl_adapter/trimns/incl_ns/your_output.discarded000066400000000000000000000000001350370616400323140ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/incl_adapter/trimns/incl_ns/your_output.pair1.truncated000066400000000000000000000002071350370616400334070ustar00rootroot00000000000000@AAGGGCSeq_1_5180_50/1 meta data ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCC + IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDEC adapterremoval-2.3.1/tests/regression/pe/incl_adapter/trimns/incl_ns/your_output.pair2.truncated000066400000000000000000000001751350370616400334140ustar00rootroot00000000000000@AAGGGCSeq_1_5180_50/2 data meta AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAG + JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBE adapterremoval-2.3.1/tests/regression/pe/incl_adapter/trimns/incl_ns/your_output.settings000066400000000000000000000034771350370616400322570ustar00rootroot00000000000000AdapterRemoval ver. 2.1.7 Trimming of paired-end reads [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 3028896355 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: Yes Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 [Trimming statistics] Total number of read pairs: 1 Number of unaligned read pairs: 0 Number of well aligned read pairs: 1 Number of discarded mate 1 reads: 0 Number of singleton mate 1 reads: 0 Number of discarded mate 2 reads: 0 Number of singleton mate 2 reads: 0 Number of reads with adapters[1]: 2 Number of retained reads: 2 Number of retained nucleotides: 93 Average length of retained reads: 46.5 [Length distribution] Length Mate1 Mate2 Singleton Discarded All 0 0 0 0 0 0 1 0 0 0 0 0 2 0 0 0 0 0 3 0 0 0 0 0 4 0 0 0 0 0 5 0 0 0 0 0 6 0 0 0 0 0 7 0 0 0 0 0 8 0 0 0 0 0 9 0 0 0 0 0 10 0 0 0 0 0 11 0 0 0 0 0 12 0 0 0 0 0 13 0 0 0 0 0 14 0 0 0 0 0 15 0 0 0 0 0 16 0 0 0 0 0 17 0 0 0 0 0 18 0 0 0 0 0 19 0 0 0 0 0 20 0 0 0 0 0 21 0 0 0 0 0 22 0 0 0 0 0 23 0 0 0 0 0 24 0 0 0 0 0 25 0 0 0 0 0 26 0 0 0 0 0 27 0 0 0 0 0 28 0 0 0 0 0 29 0 0 0 0 0 30 0 0 0 0 0 31 0 0 0 0 0 32 0 0 0 0 0 33 0 0 0 0 0 34 0 0 0 0 0 35 0 0 0 0 0 36 0 0 0 0 0 37 0 0 0 0 0 38 0 0 0 0 0 39 0 0 0 0 0 40 0 0 0 0 0 41 0 0 0 0 0 42 0 0 0 0 0 43 0 0 0 0 0 44 0 1 0 0 1 45 0 0 0 0 0 46 0 0 0 0 0 47 0 0 0 0 0 48 0 0 0 0 0 49 1 0 0 0 1 adapterremoval-2.3.1/tests/regression/pe/incl_adapter/trimns/incl_ns/your_output.singleton.truncated000066400000000000000000000000001350370616400343640ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/incl_adapter/trimqualities/000077500000000000000000000000001350370616400257775ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/incl_adapter/trimqualities/default/000077500000000000000000000000001350370616400274235ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/incl_adapter/trimqualities/default/info.json000066400000000000000000000001121350370616400312430ustar00rootroot00000000000000{ "arguments": ["--trimqualities"], "return_code": 0, "stderr": [ ] } adapterremoval-2.3.1/tests/regression/pe/incl_adapter/trimqualities/default/input_1.fastq000066400000000000000000000003551350370616400320450ustar00rootroot00000000000000@AAGGGCSeq_1_5180_50/1 meta data ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG + IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! adapterremoval-2.3.1/tests/regression/pe/incl_adapter/trimqualities/default/input_2.fastq000066400000000000000000000003551350370616400320460ustar00rootroot00000000000000@AAGGGCSeq_1_5180_50/2 data meta AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGTAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCC + JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDEDBDBCBCCBBAA?ADAAA@@@>>>><=><<;<:<;87:78753420/,+)! adapterremoval-2.3.1/tests/regression/pe/incl_adapter/trimqualities/default/your_output.discarded000066400000000000000000000000001350370616400336730ustar00rootroot00000000000000your_output.pair1.truncated000066400000000000000000000002111350370616400347020ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/incl_adapter/trimqualities/default@AAGGGCSeq_1_5180_50/1 meta data ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCT + IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECC your_output.pair2.truncated000066400000000000000000000002111350370616400347030ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/incl_adapter/trimqualities/default@AAGGGCSeq_1_5180_50/2 data meta AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGT + JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDED adapterremoval-2.3.1/tests/regression/pe/incl_adapter/trimqualities/default/your_output.settings000066400000000000000000000035131350370616400336250ustar00rootroot00000000000000AdapterRemoval ver. 2.1.7 Trimming of paired-end reads [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 3078066396 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: Yes Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 [Trimming statistics] Total number of read pairs: 1 Number of unaligned read pairs: 0 Number of well aligned read pairs: 1 Number of discarded mate 1 reads: 0 Number of singleton mate 1 reads: 0 Number of discarded mate 2 reads: 0 Number of singleton mate 2 reads: 0 Number of reads with adapters[1]: 2 Number of retained reads: 2 Number of retained nucleotides: 100 Average length of retained reads: 50 [Length distribution] Length Mate1 Mate2 Singleton Discarded All 0 0 0 0 0 0 1 0 0 0 0 0 2 0 0 0 0 0 3 0 0 0 0 0 4 0 0 0 0 0 5 0 0 0 0 0 6 0 0 0 0 0 7 0 0 0 0 0 8 0 0 0 0 0 9 0 0 0 0 0 10 0 0 0 0 0 11 0 0 0 0 0 12 0 0 0 0 0 13 0 0 0 0 0 14 0 0 0 0 0 15 0 0 0 0 0 16 0 0 0 0 0 17 0 0 0 0 0 18 0 0 0 0 0 19 0 0 0 0 0 20 0 0 0 0 0 21 0 0 0 0 0 22 0 0 0 0 0 23 0 0 0 0 0 24 0 0 0 0 0 25 0 0 0 0 0 26 0 0 0 0 0 27 0 0 0 0 0 28 0 0 0 0 0 29 0 0 0 0 0 30 0 0 0 0 0 31 0 0 0 0 0 32 0 0 0 0 0 33 0 0 0 0 0 34 0 0 0 0 0 35 0 0 0 0 0 36 0 0 0 0 0 37 0 0 0 0 0 38 0 0 0 0 0 39 0 0 0 0 0 40 0 0 0 0 0 41 0 0 0 0 0 42 0 0 0 0 0 43 0 0 0 0 0 44 0 0 0 0 0 45 0 0 0 0 0 46 0 0 0 0 0 47 0 0 0 0 0 48 0 0 0 0 0 49 0 0 0 0 0 50 1 1 0 0 2 your_output.singleton.truncated000066400000000000000000000000001350370616400356640ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/incl_adapter/trimqualities/defaultadapterremoval-2.3.1/tests/regression/pe/incl_adapter/trimqualities/minq35/000077500000000000000000000000001350370616400271135ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/incl_adapter/trimqualities/minq35/info.json000066400000000000000000000001401350370616400307340ustar00rootroot00000000000000{ "arguments": ["--trimqualities", "--minquality", "35"], "return_code": 0, "stderr": [ ] } adapterremoval-2.3.1/tests/regression/pe/incl_adapter/trimqualities/minq35/input_1.fastq000066400000000000000000000003551350370616400315350ustar00rootroot00000000000000@AAGGGCSeq_1_5180_50/1 meta data ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG + IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! adapterremoval-2.3.1/tests/regression/pe/incl_adapter/trimqualities/minq35/input_2.fastq000066400000000000000000000003551350370616400315360ustar00rootroot00000000000000@AAGGGCSeq_1_5180_50/2 data meta AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGTAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCC + JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDEDBDBCBCCBBAA?ADAAA@@@>>>><=><<;<:<;87:78753420/,+)! adapterremoval-2.3.1/tests/regression/pe/incl_adapter/trimqualities/minq35/your_output.discarded000066400000000000000000000000001350370616400333630ustar00rootroot00000000000000your_output.pair1.truncated000066400000000000000000000002051350370616400343750ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/incl_adapter/trimqualities/minq35@AAGGGCSeq_1_5180_50/1 meta data ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGC + IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDE your_output.pair2.truncated000066400000000000000000000002071350370616400344000ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/incl_adapter/trimqualities/minq35@AAGGGCSeq_1_5180_50/2 data meta AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATG + JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDE adapterremoval-2.3.1/tests/regression/pe/incl_adapter/trimqualities/minq35/your_output.settings000066400000000000000000000035001350370616400333110ustar00rootroot00000000000000AdapterRemoval ver. 2.1.7 Trimming of paired-end reads [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 3153498613 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 35: Yes Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 [Trimming statistics] Total number of read pairs: 1 Number of unaligned read pairs: 0 Number of well aligned read pairs: 1 Number of discarded mate 1 reads: 0 Number of singleton mate 1 reads: 0 Number of discarded mate 2 reads: 0 Number of singleton mate 2 reads: 0 Number of reads with adapters[1]: 2 Number of retained reads: 2 Number of retained nucleotides: 97 Average length of retained reads: 48.5 [Length distribution] Length Mate1 Mate2 Singleton Discarded All 0 0 0 0 0 0 1 0 0 0 0 0 2 0 0 0 0 0 3 0 0 0 0 0 4 0 0 0 0 0 5 0 0 0 0 0 6 0 0 0 0 0 7 0 0 0 0 0 8 0 0 0 0 0 9 0 0 0 0 0 10 0 0 0 0 0 11 0 0 0 0 0 12 0 0 0 0 0 13 0 0 0 0 0 14 0 0 0 0 0 15 0 0 0 0 0 16 0 0 0 0 0 17 0 0 0 0 0 18 0 0 0 0 0 19 0 0 0 0 0 20 0 0 0 0 0 21 0 0 0 0 0 22 0 0 0 0 0 23 0 0 0 0 0 24 0 0 0 0 0 25 0 0 0 0 0 26 0 0 0 0 0 27 0 0 0 0 0 28 0 0 0 0 0 29 0 0 0 0 0 30 0 0 0 0 0 31 0 0 0 0 0 32 0 0 0 0 0 33 0 0 0 0 0 34 0 0 0 0 0 35 0 0 0 0 0 36 0 0 0 0 0 37 0 0 0 0 0 38 0 0 0 0 0 39 0 0 0 0 0 40 0 0 0 0 0 41 0 0 0 0 0 42 0 0 0 0 0 43 0 0 0 0 0 44 0 0 0 0 0 45 0 0 0 0 0 46 0 0 0 0 0 47 0 0 0 0 0 48 1 0 0 0 1 49 0 1 0 0 1 your_output.singleton.truncated000066400000000000000000000000001350370616400353540ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/incl_adapter/trimqualities/minq35adapterremoval-2.3.1/tests/regression/pe/only_adapter/000077500000000000000000000000001350370616400231375ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/only_adapter/collapse/000077500000000000000000000000001350370616400247415ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/only_adapter/collapse/info.json000066400000000000000000000001051350370616400265630ustar00rootroot00000000000000{ "arguments": ["--collapse"], "return_code": 0, "stderr": [ ] } adapterremoval-2.3.1/tests/regression/pe/only_adapter/collapse/input_1.fastq000066400000000000000000000003551350370616400273630ustar00rootroot00000000000000@CTTTGTSeq_1_14286_0/1 meta data AGATCGGAAGAGCACACGTCTGAACTCCATTCACCTTTGTATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA + JGIJJJIJIJJGJGJIHHHGGIGIHGHGGGHEHEGFDFGEEEEGCFDDCCECDCBBCBBACCAA@BACB?>>>>?;=<;=<<::;:9777664010.-)! adapterremoval-2.3.1/tests/regression/pe/only_adapter/collapse/input_2.fastq000066400000000000000000000003551350370616400273640ustar00rootroot00000000000000@CTTTGTSeq_1_14286_0/2 data meta AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT + JJJJJJHJIHHHHJJHIHJIGHIJHHIGHFHDFFGFFFGEDDFCDEDDEDCCCEDDBBB@CCAABA@@>@?>>?=?>=<;;<:99:7974554410-*'" adapterremoval-2.3.1/tests/regression/pe/only_adapter/collapse/your_output.collapsed000066400000000000000000000000001350370616400312350ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/only_adapter/collapse/your_output.collapsed.truncated000066400000000000000000000000001350370616400332250ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/only_adapter/collapse/your_output.discarded000066400000000000000000000000451350370616400312220ustar00rootroot00000000000000@M_CTTTGTSeq_1_14286_0 meta data + adapterremoval-2.3.1/tests/regression/pe/only_adapter/collapse/your_output.pair1.truncated000066400000000000000000000000001350370616400322730ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/only_adapter/collapse/your_output.pair2.truncated000066400000000000000000000000001350370616400322740ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/only_adapter/collapse/your_output.settings000066400000000000000000000024671350370616400311520ustar00rootroot00000000000000AdapterRemoval ver. 2.1.7 Trimming of paired-end reads [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 416750178 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: Yes Minimum overlap (in case of collapse): 11 [Trimming statistics] Total number of read pairs: 1 Number of unaligned read pairs: 0 Number of well aligned read pairs: 1 Number of discarded mate 1 reads: 1 Number of singleton mate 1 reads: 0 Number of discarded mate 2 reads: 1 Number of singleton mate 2 reads: 0 Number of reads with adapters[1]: 2 Number of full-length collapsed pairs: 0 Number of truncated collapsed pairs: 0 Number of retained reads: 0 Number of retained nucleotides: 0 Average length of retained reads: 0 [Length distribution] Length Mate1 Mate2 Singleton Collapsed CollapsedTruncated Discarded All 0 0 0 0 0 0 1 1 adapterremoval-2.3.1/tests/regression/pe/only_adapter/collapse/your_output.singleton.truncated000066400000000000000000000000001350370616400332610ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/only_adapter/combined_output/000077500000000000000000000000001350370616400263375ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/only_adapter/combined_output/collapse/000077500000000000000000000000001350370616400301415ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/only_adapter/combined_output/collapse/info.json000066400000000000000000000001321350370616400317630ustar00rootroot00000000000000{ "arguments": ["--combined-output", "--collapse"], "return_code": 0, "stderr": [ ] } adapterremoval-2.3.1/tests/regression/pe/only_adapter/combined_output/collapse/input_1.fastq000066400000000000000000000003551350370616400325630ustar00rootroot00000000000000@CTTTGTSeq_1_14286_0/1 meta data AGATCGGAAGAGCACACGTCTGAACTCCATTCACCTTTGTATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA + JGIJJJIJIJJGJGJIHHHGGIGIHGHGGGHEHEGFDFGEEEEGCFDDCCECDCBBCBBACCAA@BACB?>>>>?;=<;=<<::;:9777664010.-)! adapterremoval-2.3.1/tests/regression/pe/only_adapter/combined_output/collapse/input_2.fastq000066400000000000000000000003551350370616400325640ustar00rootroot00000000000000@CTTTGTSeq_1_14286_0/2 data meta AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT + JJJJJJHJIHHHHJJHIHJIGHIJHHIGHFHDFFGFFFGEDDFCDEDDEDCCCEDDBBB@CCAABA@@>@?>>?=?>=<;;<:99:7974554410-*'" your_output.pair1.truncated000066400000000000000000000000511350370616400354220ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/only_adapter/combined_output/collapse@M_CTTTGTSeq_1_14286_0/1 meta data N + ! your_output.pair2.truncated000066400000000000000000000000511350370616400354230ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/only_adapter/combined_output/collapse@M_CTTTGTSeq_1_14286_0/2 data meta N + ! adapterremoval-2.3.1/tests/regression/pe/only_adapter/combined_output/collapse/your_output.settings000066400000000000000000000024671350370616400343520ustar00rootroot00000000000000AdapterRemoval ver. 2.1.7 Trimming of paired-end reads [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 416750178 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: Yes Minimum overlap (in case of collapse): 11 [Trimming statistics] Total number of read pairs: 1 Number of unaligned read pairs: 0 Number of well aligned read pairs: 1 Number of discarded mate 1 reads: 1 Number of singleton mate 1 reads: 0 Number of discarded mate 2 reads: 1 Number of singleton mate 2 reads: 0 Number of reads with adapters[1]: 2 Number of full-length collapsed pairs: 0 Number of truncated collapsed pairs: 0 Number of retained reads: 0 Number of retained nucleotides: 0 Average length of retained reads: 0 [Length distribution] Length Mate1 Mate2 Singleton Collapsed CollapsedTruncated Discarded All 0 0 0 0 0 0 1 1 adapterremoval-2.3.1/tests/regression/pe/only_adapter/combined_output/defaults/000077500000000000000000000000001350370616400301465ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/only_adapter/combined_output/defaults/info.json000066400000000000000000000001141350370616400317700ustar00rootroot00000000000000{ "arguments": ["--combined-output"], "return_code": 0, "stderr": [ ] } adapterremoval-2.3.1/tests/regression/pe/only_adapter/combined_output/defaults/input_1.fastq000066400000000000000000000003551350370616400325700ustar00rootroot00000000000000@CTTTGTSeq_1_14286_0/1 meta data AGATCGGAAGAGCACACGTCTGAACTCCATTCACCTTTGTATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA + JGIJJJIJIJJGJGJIHHHGGIGIHGHGGGHEHEGFDFGEEEEGCFDDCCECDCBBCBBACCAA@BACB?>>>>?;=<;=<<::;:9777664010.-)! adapterremoval-2.3.1/tests/regression/pe/only_adapter/combined_output/defaults/input_2.fastq000066400000000000000000000003551350370616400325710ustar00rootroot00000000000000@CTTTGTSeq_1_14286_0/2 data meta AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT + JJJJJJHJIHHHHJJHIHJIGHIJHHIGHFHDFFGFFFGEDDFCDEDDEDCCCEDDBBB@CCAABA@@>@?>>?=?>=<;;<:99:7974554410-*'" your_output.pair1.truncated000066400000000000000000000000471350370616400354340ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/only_adapter/combined_output/defaults@CTTTGTSeq_1_14286_0/1 meta data N + ! your_output.pair2.truncated000066400000000000000000000000471350370616400354350ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/only_adapter/combined_output/defaults@CTTTGTSeq_1_14286_0/2 data meta N + ! adapterremoval-2.3.1/tests/regression/pe/only_adapter/combined_output/defaults/your_output.settings000066400000000000000000000023051350370616400343460ustar00rootroot00000000000000AdapterRemoval ver. 2.1.7 Trimming of paired-end reads [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 688407609 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 [Trimming statistics] Total number of read pairs: 1 Number of unaligned read pairs: 0 Number of well aligned read pairs: 1 Number of discarded mate 1 reads: 1 Number of singleton mate 1 reads: 0 Number of discarded mate 2 reads: 1 Number of singleton mate 2 reads: 0 Number of reads with adapters[1]: 2 Number of retained reads: 0 Number of retained nucleotides: 0 Average length of retained reads: 0 [Length distribution] Length Mate1 Mate2 Singleton Discarded All 0 0 0 0 2 2 adapterremoval-2.3.1/tests/regression/pe/only_adapter/crlf_newlines/000077500000000000000000000000001350370616400257715ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/only_adapter/crlf_newlines/info.json000066400000000000000000000000711350370616400276150ustar00rootroot00000000000000{ "arguments": [], "return_code": 0, "stderr": [ ] } adapterremoval-2.3.1/tests/regression/pe/only_adapter/crlf_newlines/input_1.fastq000066400000000000000000000003611350370616400304100ustar00rootroot00000000000000@CTTTGTSeq_1_14286_0/1 meta data AGATCGGAAGAGCACACGTCTGAACTCCATTCACCTTTGTATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA + JGIJJJIJIJJGJGJIHHHGGIGIHGHGGGHEHEGFDFGEEEEGCFDDCCECDCBBCBBACCAA@BACB?>>>>?;=<;=<<::;:9777664010.-)! adapterremoval-2.3.1/tests/regression/pe/only_adapter/crlf_newlines/input_2.fastq000066400000000000000000000003611350370616400304110ustar00rootroot00000000000000@CTTTGTSeq_1_14286_0/2 data meta AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT + JJJJJJHJIHHHHJJHIHJIGHIJHHIGHFHDFFGFFFGEDDFCDEDDEDCCCEDDBBB@CCAABA@@>@?>>?=?>=<;;<:99:7974554410-*'" adapterremoval-2.3.1/tests/regression/pe/only_adapter/crlf_newlines/your_output.discarded000066400000000000000000000001121350370616400322450ustar00rootroot00000000000000@CTTTGTSeq_1_14286_0/1 meta data + @CTTTGTSeq_1_14286_0/2 data meta + adapterremoval-2.3.1/tests/regression/pe/only_adapter/crlf_newlines/your_output.pair1.truncated000066400000000000000000000000001350370616400333230ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/only_adapter/crlf_newlines/your_output.pair2.truncated000066400000000000000000000000001350370616400333240ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/only_adapter/crlf_newlines/your_output.settings000066400000000000000000000023051350370616400321710ustar00rootroot00000000000000AdapterRemoval ver. 2.1.7 Trimming of paired-end reads [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 861004460 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 [Trimming statistics] Total number of read pairs: 1 Number of unaligned read pairs: 0 Number of well aligned read pairs: 1 Number of discarded mate 1 reads: 1 Number of singleton mate 1 reads: 0 Number of discarded mate 2 reads: 1 Number of singleton mate 2 reads: 0 Number of reads with adapters[1]: 2 Number of retained reads: 0 Number of retained nucleotides: 0 Average length of retained reads: 0 [Length distribution] Length Mate1 Mate2 Singleton Discarded All 0 0 0 0 2 2 adapterremoval-2.3.1/tests/regression/pe/only_adapter/crlf_newlines/your_output.singleton.truncated000066400000000000000000000000001350370616400343110ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/only_adapter/defaults/000077500000000000000000000000001350370616400247465ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/only_adapter/defaults/info.json000066400000000000000000000000711350370616400265720ustar00rootroot00000000000000{ "arguments": [], "return_code": 0, "stderr": [ ] } adapterremoval-2.3.1/tests/regression/pe/only_adapter/defaults/input_1.fastq000066400000000000000000000003551350370616400273700ustar00rootroot00000000000000@CTTTGTSeq_1_14286_0/1 meta data AGATCGGAAGAGCACACGTCTGAACTCCATTCACCTTTGTATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA + JGIJJJIJIJJGJGJIHHHGGIGIHGHGGGHEHEGFDFGEEEEGCFDDCCECDCBBCBBACCAA@BACB?>>>>?;=<;=<<::;:9777664010.-)! adapterremoval-2.3.1/tests/regression/pe/only_adapter/defaults/input_2.fastq000066400000000000000000000003551350370616400273710ustar00rootroot00000000000000@CTTTGTSeq_1_14286_0/2 data meta AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT + JJJJJJHJIHHHHJJHIHJIGHIJHHIGHFHDFFGFFFGEDDFCDEDDEDCCCEDDBBB@CCAABA@@>@?>>?=?>=<;;<:99:7974554410-*'" adapterremoval-2.3.1/tests/regression/pe/only_adapter/defaults/your_output.discarded000066400000000000000000000001121350370616400312220ustar00rootroot00000000000000@CTTTGTSeq_1_14286_0/1 meta data + @CTTTGTSeq_1_14286_0/2 data meta + adapterremoval-2.3.1/tests/regression/pe/only_adapter/defaults/your_output.pair1.truncated000066400000000000000000000000001350370616400323000ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/only_adapter/defaults/your_output.pair2.truncated000066400000000000000000000000001350370616400323010ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/only_adapter/defaults/your_output.settings000066400000000000000000000023051350370616400311460ustar00rootroot00000000000000AdapterRemoval ver. 2.1.7 Trimming of paired-end reads [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 861004460 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 [Trimming statistics] Total number of read pairs: 1 Number of unaligned read pairs: 0 Number of well aligned read pairs: 1 Number of discarded mate 1 reads: 1 Number of singleton mate 1 reads: 0 Number of discarded mate 2 reads: 1 Number of singleton mate 2 reads: 0 Number of reads with adapters[1]: 2 Number of retained reads: 0 Number of retained nucleotides: 0 Average length of retained reads: 0 [Length distribution] Length Mate1 Mate2 Singleton Discarded All 0 0 0 0 2 2 adapterremoval-2.3.1/tests/regression/pe/only_adapter/defaults/your_output.singleton.truncated000066400000000000000000000000001350370616400332660ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/only_adapter/minlength/000077500000000000000000000000001350370616400251245ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/only_adapter/minlength/info.json000066400000000000000000000001131350370616400267450ustar00rootroot00000000000000{ "arguments": ["--minlength", "0"], "return_code": 0, "stderr": [ ] } adapterremoval-2.3.1/tests/regression/pe/only_adapter/minlength/input_1.fastq000066400000000000000000000003551350370616400275460ustar00rootroot00000000000000@CTTTGTSeq_1_14286_0/1 meta data AGATCGGAAGAGCACACGTCTGAACTCCATTCACCTTTGTATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA + JGIJJJIJIJJGJGJIHHHGGIGIHGHGGGHEHEGFDFGEEEEGCFDDCCECDCBBCBBACCAA@BACB?>>>>?;=<;=<<::;:9777664010.-)! adapterremoval-2.3.1/tests/regression/pe/only_adapter/minlength/input_2.fastq000066400000000000000000000003551350370616400275470ustar00rootroot00000000000000@CTTTGTSeq_1_14286_0/2 data meta AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT + JJJJJJHJIHHHHJJHIHJIGHIJHHIGHFHDFFGFFFGEDDFCDEDDEDCCCEDDBBB@CCAABA@@>@?>>?=?>=<;;<:99:7974554410-*'" adapterremoval-2.3.1/tests/regression/pe/only_adapter/minlength/your_output.discarded000066400000000000000000000000001350370616400313740ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/only_adapter/minlength/your_output.pair1.truncated000066400000000000000000000000451350370616400324670ustar00rootroot00000000000000@CTTTGTSeq_1_14286_0/1 meta data + adapterremoval-2.3.1/tests/regression/pe/only_adapter/minlength/your_output.pair2.truncated000066400000000000000000000000451350370616400324700ustar00rootroot00000000000000@CTTTGTSeq_1_14286_0/2 data meta + adapterremoval-2.3.1/tests/regression/pe/only_adapter/minlength/your_output.settings000066400000000000000000000023041350370616400313230ustar00rootroot00000000000000AdapterRemoval ver. 2.1.7 Trimming of paired-end reads [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 934075502 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 0 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 [Trimming statistics] Total number of read pairs: 1 Number of unaligned read pairs: 0 Number of well aligned read pairs: 1 Number of discarded mate 1 reads: 0 Number of singleton mate 1 reads: 0 Number of discarded mate 2 reads: 0 Number of singleton mate 2 reads: 0 Number of reads with adapters[1]: 2 Number of retained reads: 2 Number of retained nucleotides: 0 Average length of retained reads: 0 [Length distribution] Length Mate1 Mate2 Singleton Discarded All 0 1 1 0 0 2 adapterremoval-2.3.1/tests/regression/pe/only_adapter/minlength/your_output.singleton.truncated000066400000000000000000000000001350370616400334440ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/trimfixed/000077500000000000000000000000001350370616400224515ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/trimfixed/3p/000077500000000000000000000000001350370616400227735ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/trimfixed/3p/info.json000066400000000000000000000001101350370616400246110ustar00rootroot00000000000000{ "arguments": ["--trim3p", "6"], "return_code": 0, "stderr": [ ] } adapterremoval-2.3.1/tests/regression/pe/trimfixed/3p/input_1.fastq000066400000000000000000000003551350370616400254150ustar00rootroot00000000000000@AAGGGCSeq_1_5180_50/1 meta data ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG + IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! adapterremoval-2.3.1/tests/regression/pe/trimfixed/3p/input_2.fastq000066400000000000000000000003551350370616400254160ustar00rootroot00000000000000@AAGGGCSeq_1_5180_50/2 data meta AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGTAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCC + JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDEDBDBCBCCBBAA?ADAAA@@@>>>><=><<;<:<;87:78753420/,+)! adapterremoval-2.3.1/tests/regression/pe/trimfixed/3p/your_output.discarded000066400000000000000000000000001350370616400272430ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/trimfixed/3p/your_output.pair1.truncated000066400000000000000000000001751350370616400303420ustar00rootroot00000000000000@AAGGGCSeq_1_5180_50/1 meta data ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGC + IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFF adapterremoval-2.3.1/tests/regression/pe/trimfixed/3p/your_output.pair2.truncated000066400000000000000000000001751350370616400303430ustar00rootroot00000000000000@AAGGGCSeq_1_5180_50/2 data meta AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAG + JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBE adapterremoval-2.3.1/tests/regression/pe/trimfixed/3p/your_output.settings000066400000000000000000000033721350370616400272000ustar00rootroot00000000000000AdapterRemoval ver. 2.1.7 Trimming of paired-end reads [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 372265332 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 6 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 [Trimming statistics] Total number of read pairs: 1 Number of unaligned read pairs: 0 Number of well aligned read pairs: 1 Number of discarded mate 1 reads: 0 Number of singleton mate 1 reads: 0 Number of discarded mate 2 reads: 0 Number of singleton mate 2 reads: 0 Number of reads with adapters[1]: 2 Number of retained reads: 2 Number of retained nucleotides: 88 Average length of retained reads: 44 [Length distribution] Length Mate1 Mate2 Singleton Discarded All 0 0 0 0 0 0 1 0 0 0 0 0 2 0 0 0 0 0 3 0 0 0 0 0 4 0 0 0 0 0 5 0 0 0 0 0 6 0 0 0 0 0 7 0 0 0 0 0 8 0 0 0 0 0 9 0 0 0 0 0 10 0 0 0 0 0 11 0 0 0 0 0 12 0 0 0 0 0 13 0 0 0 0 0 14 0 0 0 0 0 15 0 0 0 0 0 16 0 0 0 0 0 17 0 0 0 0 0 18 0 0 0 0 0 19 0 0 0 0 0 20 0 0 0 0 0 21 0 0 0 0 0 22 0 0 0 0 0 23 0 0 0 0 0 24 0 0 0 0 0 25 0 0 0 0 0 26 0 0 0 0 0 27 0 0 0 0 0 28 0 0 0 0 0 29 0 0 0 0 0 30 0 0 0 0 0 31 0 0 0 0 0 32 0 0 0 0 0 33 0 0 0 0 0 34 0 0 0 0 0 35 0 0 0 0 0 36 0 0 0 0 0 37 0 0 0 0 0 38 0 0 0 0 0 39 0 0 0 0 0 40 0 0 0 0 0 41 0 0 0 0 0 42 0 0 0 0 0 43 0 0 0 0 0 44 1 1 0 0 2 adapterremoval-2.3.1/tests/regression/pe/trimfixed/3p/your_output.singleton.truncated000066400000000000000000000000001350370616400313130ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/trimfixed/3p_both_set/000077500000000000000000000000001350370616400246625ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/trimfixed/3p_both_set/info.json000066400000000000000000000001151350370616400265050ustar00rootroot00000000000000{ "arguments": ["--trim3p", "3", "1"], "return_code": 0, "stderr": [ ] } adapterremoval-2.3.1/tests/regression/pe/trimfixed/3p_both_set/input_1.fastq000066400000000000000000000003551350370616400273040ustar00rootroot00000000000000@AAGGGCSeq_1_5180_50/1 meta data ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG + IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! adapterremoval-2.3.1/tests/regression/pe/trimfixed/3p_both_set/input_2.fastq000066400000000000000000000003551350370616400273050ustar00rootroot00000000000000@AAGGGCSeq_1_5180_50/2 data meta AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGTAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCC + JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDEDBDBCBCCBBAA?ADAAA@@@>>>><=><<;<:<;87:78753420/,+)! adapterremoval-2.3.1/tests/regression/pe/trimfixed/3p_both_set/your_output.discarded000066400000000000000000000000001350370616400311320ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/trimfixed/3p_both_set/your_output.pair1.truncated000066400000000000000000000002031350370616400322210ustar00rootroot00000000000000@AAGGGCSeq_1_5180_50/1 meta data ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGG + IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFED adapterremoval-2.3.1/tests/regression/pe/trimfixed/3p_both_set/your_output.pair2.truncated000066400000000000000000000002071350370616400322260ustar00rootroot00000000000000@AAGGGCSeq_1_5180_50/2 data meta AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATG + JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDE adapterremoval-2.3.1/tests/regression/pe/trimfixed/3p_both_set/your_output.settings000066400000000000000000000034751350370616400310730ustar00rootroot00000000000000AdapterRemoval ver. 2.1.7 Trimming of paired-end reads [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 372265332 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 3 1 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 [Trimming statistics] Total number of read pairs: 1 Number of unaligned read pairs: 0 Number of well aligned read pairs: 1 Number of discarded mate 1 reads: 0 Number of singleton mate 1 reads: 0 Number of discarded mate 2 reads: 0 Number of singleton mate 2 reads: 0 Number of reads with adapters[1]: 2 Number of retained reads: 2 Number of retained nucleotides: 96 Average length of retained reads: 48 [Length distribution] Length Mate1 Mate2 Singleton Discarded All 0 0 0 0 0 0 1 0 0 0 0 0 2 0 0 0 0 0 3 0 0 0 0 0 4 0 0 0 0 0 5 0 0 0 0 0 6 0 0 0 0 0 7 0 0 0 0 0 8 0 0 0 0 0 9 0 0 0 0 0 10 0 0 0 0 0 11 0 0 0 0 0 12 0 0 0 0 0 13 0 0 0 0 0 14 0 0 0 0 0 15 0 0 0 0 0 16 0 0 0 0 0 17 0 0 0 0 0 18 0 0 0 0 0 19 0 0 0 0 0 20 0 0 0 0 0 21 0 0 0 0 0 22 0 0 0 0 0 23 0 0 0 0 0 24 0 0 0 0 0 25 0 0 0 0 0 26 0 0 0 0 0 27 0 0 0 0 0 28 0 0 0 0 0 29 0 0 0 0 0 30 0 0 0 0 0 31 0 0 0 0 0 32 0 0 0 0 0 33 0 0 0 0 0 34 0 0 0 0 0 35 0 0 0 0 0 36 0 0 0 0 0 37 0 0 0 0 0 38 0 0 0 0 0 39 0 0 0 0 0 40 0 0 0 0 0 41 0 0 0 0 0 42 0 0 0 0 0 43 0 0 0 0 0 44 0 0 0 0 0 45 0 0 0 0 0 46 0 0 0 0 0 47 1 0 0 0 1 48 0 0 0 0 0 49 0 1 0 0 1 adapterremoval-2.3.1/tests/regression/pe/trimfixed/3p_both_set/your_output.singleton.truncated000066400000000000000000000000001350370616400332020ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/trimfixed/5p/000077500000000000000000000000001350370616400227755ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/trimfixed/5p/info.json000066400000000000000000000001101350370616400246130ustar00rootroot00000000000000{ "arguments": ["--trim5p", "8"], "return_code": 0, "stderr": [ ] } adapterremoval-2.3.1/tests/regression/pe/trimfixed/5p/input_1.fastq000066400000000000000000000003551350370616400254170ustar00rootroot00000000000000@AAGGGCSeq_1_5180_50/1 meta data ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG + IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! adapterremoval-2.3.1/tests/regression/pe/trimfixed/5p/input_2.fastq000066400000000000000000000003551350370616400254200ustar00rootroot00000000000000@AAGGGCSeq_1_5180_50/2 data meta AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGTAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCC + JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDEDBDBCBCCBBAA?ADAAA@@@>>>><=><<;<:<;87:78753420/,+)! adapterremoval-2.3.1/tests/regression/pe/trimfixed/5p/your_output.discarded000066400000000000000000000000001350370616400272450ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/trimfixed/5p/your_output.pair1.truncated000066400000000000000000000001711350370616400303400ustar00rootroot00000000000000@AAGGGCSeq_1_5180_50/1 meta data AACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCT + IIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECC adapterremoval-2.3.1/tests/regression/pe/trimfixed/5p/your_output.pair2.truncated000066400000000000000000000001711350370616400303410ustar00rootroot00000000000000@AAGGGCSeq_1_5180_50/2 data meta TAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGT + JJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDED adapterremoval-2.3.1/tests/regression/pe/trimfixed/5p/your_output.settings000066400000000000000000000033401350370616400271750ustar00rootroot00000000000000AdapterRemoval ver. 2.1.7 Trimming of paired-end reads [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 372265332 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 8 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 [Trimming statistics] Total number of read pairs: 1 Number of unaligned read pairs: 0 Number of well aligned read pairs: 1 Number of discarded mate 1 reads: 0 Number of singleton mate 1 reads: 0 Number of discarded mate 2 reads: 0 Number of singleton mate 2 reads: 0 Number of reads with adapters[1]: 2 Number of retained reads: 2 Number of retained nucleotides: 84 Average length of retained reads: 42 [Length distribution] Length Mate1 Mate2 Singleton Discarded All 0 0 0 0 0 0 1 0 0 0 0 0 2 0 0 0 0 0 3 0 0 0 0 0 4 0 0 0 0 0 5 0 0 0 0 0 6 0 0 0 0 0 7 0 0 0 0 0 8 0 0 0 0 0 9 0 0 0 0 0 10 0 0 0 0 0 11 0 0 0 0 0 12 0 0 0 0 0 13 0 0 0 0 0 14 0 0 0 0 0 15 0 0 0 0 0 16 0 0 0 0 0 17 0 0 0 0 0 18 0 0 0 0 0 19 0 0 0 0 0 20 0 0 0 0 0 21 0 0 0 0 0 22 0 0 0 0 0 23 0 0 0 0 0 24 0 0 0 0 0 25 0 0 0 0 0 26 0 0 0 0 0 27 0 0 0 0 0 28 0 0 0 0 0 29 0 0 0 0 0 30 0 0 0 0 0 31 0 0 0 0 0 32 0 0 0 0 0 33 0 0 0 0 0 34 0 0 0 0 0 35 0 0 0 0 0 36 0 0 0 0 0 37 0 0 0 0 0 38 0 0 0 0 0 39 0 0 0 0 0 40 0 0 0 0 0 41 0 0 0 0 0 42 1 1 0 0 2 adapterremoval-2.3.1/tests/regression/pe/trimfixed/5p/your_output.singleton.truncated000066400000000000000000000000001350370616400313150ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/trimfixed/5p_and_3p/000077500000000000000000000000001350370616400242215ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/trimfixed/5p_and_3p/info.json000066400000000000000000000001311350370616400260420ustar00rootroot00000000000000{ "arguments": ["--trim5p", "1", "--trim3p", "4"], "return_code": 0, "stderr": [ ] } adapterremoval-2.3.1/tests/regression/pe/trimfixed/5p_and_3p/input_1.fastq000066400000000000000000000003551350370616400266430ustar00rootroot00000000000000@AAGGGCSeq_1_5180_50/1 meta data ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG + IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! adapterremoval-2.3.1/tests/regression/pe/trimfixed/5p_and_3p/input_2.fastq000066400000000000000000000003551350370616400266440ustar00rootroot00000000000000@AAGGGCSeq_1_5180_50/2 data meta AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGTAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCC + JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDEDBDBCBCCBBAA?ADAAA@@@>>>><=><<;<:<;87:78753420/,+)! adapterremoval-2.3.1/tests/regression/pe/trimfixed/5p_and_3p/your_output.discarded000066400000000000000000000000001350370616400304710ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/trimfixed/5p_and_3p/your_output.pair1.truncated000066400000000000000000000001771350370616400315720ustar00rootroot00000000000000@AAGGGCSeq_1_5180_50/1 meta data CATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAG + JJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFE adapterremoval-2.3.1/tests/regression/pe/trimfixed/5p_and_3p/your_output.pair2.truncated000066400000000000000000000001771350370616400315730ustar00rootroot00000000000000@AAGGGCSeq_1_5180_50/2 data meta GGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTC + IHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDF adapterremoval-2.3.1/tests/regression/pe/trimfixed/5p_and_3p/your_output.settings000066400000000000000000000034071350370616400304250ustar00rootroot00000000000000AdapterRemoval ver. 2.1.7 Trimming of paired-end reads [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 372265332 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 1 Trimming 3p: 4 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 [Trimming statistics] Total number of read pairs: 1 Number of unaligned read pairs: 0 Number of well aligned read pairs: 1 Number of discarded mate 1 reads: 0 Number of singleton mate 1 reads: 0 Number of discarded mate 2 reads: 0 Number of singleton mate 2 reads: 0 Number of reads with adapters[1]: 2 Number of retained reads: 2 Number of retained nucleotides: 90 Average length of retained reads: 45 [Length distribution] Length Mate1 Mate2 Singleton Discarded All 0 0 0 0 0 0 1 0 0 0 0 0 2 0 0 0 0 0 3 0 0 0 0 0 4 0 0 0 0 0 5 0 0 0 0 0 6 0 0 0 0 0 7 0 0 0 0 0 8 0 0 0 0 0 9 0 0 0 0 0 10 0 0 0 0 0 11 0 0 0 0 0 12 0 0 0 0 0 13 0 0 0 0 0 14 0 0 0 0 0 15 0 0 0 0 0 16 0 0 0 0 0 17 0 0 0 0 0 18 0 0 0 0 0 19 0 0 0 0 0 20 0 0 0 0 0 21 0 0 0 0 0 22 0 0 0 0 0 23 0 0 0 0 0 24 0 0 0 0 0 25 0 0 0 0 0 26 0 0 0 0 0 27 0 0 0 0 0 28 0 0 0 0 0 29 0 0 0 0 0 30 0 0 0 0 0 31 0 0 0 0 0 32 0 0 0 0 0 33 0 0 0 0 0 34 0 0 0 0 0 35 0 0 0 0 0 36 0 0 0 0 0 37 0 0 0 0 0 38 0 0 0 0 0 39 0 0 0 0 0 40 0 0 0 0 0 41 0 0 0 0 0 42 0 0 0 0 0 43 0 0 0 0 0 44 0 0 0 0 0 45 1 1 0 0 2 adapterremoval-2.3.1/tests/regression/pe/trimfixed/5p_and_3p/your_output.singleton.truncated000066400000000000000000000000001350370616400325410ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/trimfixed/5p_and_3p_both_set/000077500000000000000000000000001350370616400261105ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/trimfixed/5p_and_3p_both_set/info.json000066400000000000000000000001431350370616400277340ustar00rootroot00000000000000{ "arguments": ["--trim5p", "1", "3", "--trim3p", "4", "2"], "return_code": 0, "stderr": [ ] } adapterremoval-2.3.1/tests/regression/pe/trimfixed/5p_and_3p_both_set/input_1.fastq000066400000000000000000000003551350370616400305320ustar00rootroot00000000000000@AAGGGCSeq_1_5180_50/1 meta data ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG + IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! adapterremoval-2.3.1/tests/regression/pe/trimfixed/5p_and_3p_both_set/input_2.fastq000066400000000000000000000003551350370616400305330ustar00rootroot00000000000000@AAGGGCSeq_1_5180_50/2 data meta AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGTAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCC + JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDEDBDBCBCCBBAA?ADAAA@@@>>>><=><<;<:<;87:78753420/,+)! adapterremoval-2.3.1/tests/regression/pe/trimfixed/5p_and_3p_both_set/your_output.discarded000066400000000000000000000000001350370616400323600ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/trimfixed/5p_and_3p_both_set/your_output.pair1.truncated000066400000000000000000000001771350370616400334610ustar00rootroot00000000000000@AAGGGCSeq_1_5180_50/1 meta data CATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAG + JJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFE adapterremoval-2.3.1/tests/regression/pe/trimfixed/5p_and_3p_both_set/your_output.pair2.truncated000066400000000000000000000001771350370616400334620ustar00rootroot00000000000000@AAGGGCSeq_1_5180_50/2 data meta CCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCAT + JJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFED adapterremoval-2.3.1/tests/regression/pe/trimfixed/5p_and_3p_both_set/your_output.settings000066400000000000000000000034131350370616400323110ustar00rootroot00000000000000AdapterRemoval ver. 2.1.7 Trimming of paired-end reads [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 372265332 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 1 3 Trimming 3p: 4 2 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 [Trimming statistics] Total number of read pairs: 1 Number of unaligned read pairs: 0 Number of well aligned read pairs: 1 Number of discarded mate 1 reads: 0 Number of singleton mate 1 reads: 0 Number of discarded mate 2 reads: 0 Number of singleton mate 2 reads: 0 Number of reads with adapters[1]: 2 Number of retained reads: 2 Number of retained nucleotides: 90 Average length of retained reads: 45 [Length distribution] Length Mate1 Mate2 Singleton Discarded All 0 0 0 0 0 0 1 0 0 0 0 0 2 0 0 0 0 0 3 0 0 0 0 0 4 0 0 0 0 0 5 0 0 0 0 0 6 0 0 0 0 0 7 0 0 0 0 0 8 0 0 0 0 0 9 0 0 0 0 0 10 0 0 0 0 0 11 0 0 0 0 0 12 0 0 0 0 0 13 0 0 0 0 0 14 0 0 0 0 0 15 0 0 0 0 0 16 0 0 0 0 0 17 0 0 0 0 0 18 0 0 0 0 0 19 0 0 0 0 0 20 0 0 0 0 0 21 0 0 0 0 0 22 0 0 0 0 0 23 0 0 0 0 0 24 0 0 0 0 0 25 0 0 0 0 0 26 0 0 0 0 0 27 0 0 0 0 0 28 0 0 0 0 0 29 0 0 0 0 0 30 0 0 0 0 0 31 0 0 0 0 0 32 0 0 0 0 0 33 0 0 0 0 0 34 0 0 0 0 0 35 0 0 0 0 0 36 0 0 0 0 0 37 0 0 0 0 0 38 0 0 0 0 0 39 0 0 0 0 0 40 0 0 0 0 0 41 0 0 0 0 0 42 0 0 0 0 0 43 0 0 0 0 0 44 0 0 0 0 0 45 1 1 0 0 2 your_output.singleton.truncated000066400000000000000000000000001350370616400343510ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/trimfixed/5p_and_3p_both_setadapterremoval-2.3.1/tests/regression/pe/trimfixed/5p_both_set/000077500000000000000000000000001350370616400246645ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/trimfixed/5p_both_set/info.json000066400000000000000000000001151350370616400265070ustar00rootroot00000000000000{ "arguments": ["--trim5p", "5", "7"], "return_code": 0, "stderr": [ ] } adapterremoval-2.3.1/tests/regression/pe/trimfixed/5p_both_set/input_1.fastq000066400000000000000000000003551350370616400273060ustar00rootroot00000000000000@AAGGGCSeq_1_5180_50/1 meta data ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG + IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! adapterremoval-2.3.1/tests/regression/pe/trimfixed/5p_both_set/input_2.fastq000066400000000000000000000003551350370616400273070ustar00rootroot00000000000000@AAGGGCSeq_1_5180_50/2 data meta AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGTAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCC + JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDEDBDBCBCCBBAA?ADAAA@@@>>>><=><<;<:<;87:78753420/,+)! adapterremoval-2.3.1/tests/regression/pe/trimfixed/5p_both_set/your_output.discarded000066400000000000000000000000001350370616400311340ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/trimfixed/5p_both_set/your_output.pair1.truncated000066400000000000000000000001771350370616400322350ustar00rootroot00000000000000@AAGGGCSeq_1_5180_50/1 meta data ACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCT + JIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECC adapterremoval-2.3.1/tests/regression/pe/trimfixed/5p_both_set/your_output.pair2.truncated000066400000000000000000000001731350370616400322320ustar00rootroot00000000000000@AAGGGCSeq_1_5180_50/2 data meta CTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGT + JJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDED adapterremoval-2.3.1/tests/regression/pe/trimfixed/5p_both_set/your_output.settings000066400000000000000000000034111350370616400310630ustar00rootroot00000000000000AdapterRemoval ver. 2.1.7 Trimming of paired-end reads [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 372265332 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 5 7 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 [Trimming statistics] Total number of read pairs: 1 Number of unaligned read pairs: 0 Number of well aligned read pairs: 1 Number of discarded mate 1 reads: 0 Number of singleton mate 1 reads: 0 Number of discarded mate 2 reads: 0 Number of singleton mate 2 reads: 0 Number of reads with adapters[1]: 2 Number of retained reads: 2 Number of retained nucleotides: 88 Average length of retained reads: 44 [Length distribution] Length Mate1 Mate2 Singleton Discarded All 0 0 0 0 0 0 1 0 0 0 0 0 2 0 0 0 0 0 3 0 0 0 0 0 4 0 0 0 0 0 5 0 0 0 0 0 6 0 0 0 0 0 7 0 0 0 0 0 8 0 0 0 0 0 9 0 0 0 0 0 10 0 0 0 0 0 11 0 0 0 0 0 12 0 0 0 0 0 13 0 0 0 0 0 14 0 0 0 0 0 15 0 0 0 0 0 16 0 0 0 0 0 17 0 0 0 0 0 18 0 0 0 0 0 19 0 0 0 0 0 20 0 0 0 0 0 21 0 0 0 0 0 22 0 0 0 0 0 23 0 0 0 0 0 24 0 0 0 0 0 25 0 0 0 0 0 26 0 0 0 0 0 27 0 0 0 0 0 28 0 0 0 0 0 29 0 0 0 0 0 30 0 0 0 0 0 31 0 0 0 0 0 32 0 0 0 0 0 33 0 0 0 0 0 34 0 0 0 0 0 35 0 0 0 0 0 36 0 0 0 0 0 37 0 0 0 0 0 38 0 0 0 0 0 39 0 0 0 0 0 40 0 0 0 0 0 41 0 0 0 0 0 42 0 0 0 0 0 43 0 1 0 0 1 44 0 0 0 0 0 45 1 0 0 0 1 adapterremoval-2.3.1/tests/regression/pe/trimfixed/5p_both_set/your_output.singleton.truncated000066400000000000000000000000001350370616400332040ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/trimfixed/collapse_5p/000077500000000000000000000000001350370616400246575ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/trimfixed/collapse_5p/info.json000066400000000000000000000001261350370616400265040ustar00rootroot00000000000000{ "arguments": ["--collapse", "--trim5p", "6"], "return_code": 0, "stderr": [ ] } adapterremoval-2.3.1/tests/regression/pe/trimfixed/collapse_5p/input_1.fastq000066400000000000000000000003551350370616400273010ustar00rootroot00000000000000@AAGGGCSeq_1_5180_50/1 meta data ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG + IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! adapterremoval-2.3.1/tests/regression/pe/trimfixed/collapse_5p/input_2.fastq000066400000000000000000000003551350370616400273020ustar00rootroot00000000000000@AAGGGCSeq_1_5180_50/2 data meta AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGTAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCC + JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDEDBDBCBCCBBAA?ADAAA@@@>>>><=><<;<:<;87:78753420/,+)! adapterremoval-2.3.1/tests/regression/pe/trimfixed/collapse_5p/your_output.collapsed000066400000000000000000000001611350370616400311630ustar00rootroot00000000000000@M_AAGGGCSeq_1_5180_50 meta data CTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGG + JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ& adapterremoval-2.3.1/tests/regression/pe/trimfixed/collapse_5p/your_output.collapsed.truncated000066400000000000000000000000001350370616400331430ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/trimfixed/collapse_5p/your_output.discarded000066400000000000000000000000001350370616400311270ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/trimfixed/collapse_5p/your_output.pair1.truncated000066400000000000000000000000001350370616400322110ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/trimfixed/collapse_5p/your_output.pair2.truncated000066400000000000000000000000001350370616400322120ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/trimfixed/collapse_5p/your_output.settings000066400000000000000000000036661350370616400310720ustar00rootroot00000000000000AdapterRemoval ver. 2.1.7 Trimming of paired-end reads [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 429139444 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 6 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: Yes Minimum overlap (in case of collapse): 11 [Trimming statistics] Total number of read pairs: 1 Number of unaligned read pairs: 0 Number of well aligned read pairs: 1 Number of discarded mate 1 reads: 0 Number of singleton mate 1 reads: 0 Number of discarded mate 2 reads: 0 Number of singleton mate 2 reads: 0 Number of reads with adapters[1]: 2 Number of full-length collapsed pairs: 1 Number of truncated collapsed pairs: 0 Number of retained reads: 1 Number of retained nucleotides: 38 Average length of retained reads: 38 [Length distribution] Length Mate1 Mate2 Singleton Collapsed CollapsedTruncated Discarded All 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 3 0 0 0 0 0 0 0 4 0 0 0 0 0 0 0 5 0 0 0 0 0 0 0 6 0 0 0 0 0 0 0 7 0 0 0 0 0 0 0 8 0 0 0 0 0 0 0 9 0 0 0 0 0 0 0 10 0 0 0 0 0 0 0 11 0 0 0 0 0 0 0 12 0 0 0 0 0 0 0 13 0 0 0 0 0 0 0 14 0 0 0 0 0 0 0 15 0 0 0 0 0 0 0 16 0 0 0 0 0 0 0 17 0 0 0 0 0 0 0 18 0 0 0 0 0 0 0 19 0 0 0 0 0 0 0 20 0 0 0 0 0 0 0 21 0 0 0 0 0 0 0 22 0 0 0 0 0 0 0 23 0 0 0 0 0 0 0 24 0 0 0 0 0 0 0 25 0 0 0 0 0 0 0 26 0 0 0 0 0 0 0 27 0 0 0 0 0 0 0 28 0 0 0 0 0 0 0 29 0 0 0 0 0 0 0 30 0 0 0 0 0 0 0 31 0 0 0 0 0 0 0 32 0 0 0 0 0 0 0 33 0 0 0 0 0 0 0 34 0 0 0 0 0 0 0 35 0 0 0 0 0 0 0 36 0 0 0 0 0 0 0 37 0 0 0 0 0 0 0 38 0 0 0 1 0 0 1 adapterremoval-2.3.1/tests/regression/pe/trimfixed/collapse_5p/your_output.singleton.truncated000066400000000000000000000000001350370616400331770ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/trimfixed/collapse_5p_and_3p/000077500000000000000000000000001350370616400261035ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/trimfixed/collapse_5p_and_3p/info.json000066400000000000000000000001501350370616400277250ustar00rootroot00000000000000{ "arguments": ["--collapse", "--trim5p", "6", "--trim3p", "20"], "return_code": 0, "stderr": [ ] } adapterremoval-2.3.1/tests/regression/pe/trimfixed/collapse_5p_and_3p/input_1.fastq000066400000000000000000000003551350370616400305250ustar00rootroot00000000000000@AAGGGCSeq_1_5180_50/1 meta data ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG + IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! adapterremoval-2.3.1/tests/regression/pe/trimfixed/collapse_5p_and_3p/input_2.fastq000066400000000000000000000003551350370616400305260ustar00rootroot00000000000000@AAGGGCSeq_1_5180_50/2 data meta AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGTAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCC + JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDEDBDBCBCCBBAA?ADAAA@@@>>>><=><<;<:<;87:78753420/,+)! adapterremoval-2.3.1/tests/regression/pe/trimfixed/collapse_5p_and_3p/your_output.collapsed000066400000000000000000000001611350370616400324070ustar00rootroot00000000000000@M_AAGGGCSeq_1_5180_50 meta data CTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGG + JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ& your_output.collapsed.truncated000066400000000000000000000000001350370616400343100ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/trimfixed/collapse_5p_and_3padapterremoval-2.3.1/tests/regression/pe/trimfixed/collapse_5p_and_3p/your_output.discarded000066400000000000000000000000001350370616400323530ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/trimfixed/collapse_5p_and_3p/your_output.pair1.truncated000066400000000000000000000000001350370616400334350ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/trimfixed/collapse_5p_and_3p/your_output.pair2.truncated000066400000000000000000000000001350370616400334360ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/trimfixed/collapse_5p_and_3p/your_output.settings000066400000000000000000000036671350370616400323170ustar00rootroot00000000000000AdapterRemoval ver. 2.1.7 Trimming of paired-end reads [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 429139444 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 6 Trimming 3p: 20 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: Yes Minimum overlap (in case of collapse): 11 [Trimming statistics] Total number of read pairs: 1 Number of unaligned read pairs: 0 Number of well aligned read pairs: 1 Number of discarded mate 1 reads: 0 Number of singleton mate 1 reads: 0 Number of discarded mate 2 reads: 0 Number of singleton mate 2 reads: 0 Number of reads with adapters[1]: 2 Number of full-length collapsed pairs: 1 Number of truncated collapsed pairs: 0 Number of retained reads: 1 Number of retained nucleotides: 38 Average length of retained reads: 38 [Length distribution] Length Mate1 Mate2 Singleton Collapsed CollapsedTruncated Discarded All 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 3 0 0 0 0 0 0 0 4 0 0 0 0 0 0 0 5 0 0 0 0 0 0 0 6 0 0 0 0 0 0 0 7 0 0 0 0 0 0 0 8 0 0 0 0 0 0 0 9 0 0 0 0 0 0 0 10 0 0 0 0 0 0 0 11 0 0 0 0 0 0 0 12 0 0 0 0 0 0 0 13 0 0 0 0 0 0 0 14 0 0 0 0 0 0 0 15 0 0 0 0 0 0 0 16 0 0 0 0 0 0 0 17 0 0 0 0 0 0 0 18 0 0 0 0 0 0 0 19 0 0 0 0 0 0 0 20 0 0 0 0 0 0 0 21 0 0 0 0 0 0 0 22 0 0 0 0 0 0 0 23 0 0 0 0 0 0 0 24 0 0 0 0 0 0 0 25 0 0 0 0 0 0 0 26 0 0 0 0 0 0 0 27 0 0 0 0 0 0 0 28 0 0 0 0 0 0 0 29 0 0 0 0 0 0 0 30 0 0 0 0 0 0 0 31 0 0 0 0 0 0 0 32 0 0 0 0 0 0 0 33 0 0 0 0 0 0 0 34 0 0 0 0 0 0 0 35 0 0 0 0 0 0 0 36 0 0 0 0 0 0 0 37 0 0 0 0 0 0 0 38 0 0 0 1 0 0 1 your_output.singleton.truncated000066400000000000000000000000001350370616400343440ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/trimfixed/collapse_5p_and_3padapterremoval-2.3.1/tests/regression/pe/trimfixed/collapse_5p_both_set/000077500000000000000000000000001350370616400265465ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/trimfixed/collapse_5p_both_set/info.json000066400000000000000000000001331350370616400303710ustar00rootroot00000000000000{ "arguments": ["--collapse", "--trim5p", "6", "8"], "return_code": 0, "stderr": [ ] } adapterremoval-2.3.1/tests/regression/pe/trimfixed/collapse_5p_both_set/input_1.fastq000066400000000000000000000003551350370616400311700ustar00rootroot00000000000000@AAGGGCSeq_1_5180_50/1 meta data ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG + IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! adapterremoval-2.3.1/tests/regression/pe/trimfixed/collapse_5p_both_set/input_2.fastq000066400000000000000000000003551350370616400311710ustar00rootroot00000000000000@AAGGGCSeq_1_5180_50/2 data meta AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGTAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCC + JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDEDBDBCBCCBBAA?ADAAA@@@>>>><=><<;<:<;87:78753420/,+)! adapterremoval-2.3.1/tests/regression/pe/trimfixed/collapse_5p_both_set/your_output.collapsed000066400000000000000000000001551350370616400330550ustar00rootroot00000000000000@M_AAGGGCSeq_1_5180_50 meta data CTAACACCCTTAATTCCATCCACCCTCCTCTCCCTA + JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ your_output.collapsed.truncated000066400000000000000000000000001350370616400347530ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/trimfixed/collapse_5p_both_setadapterremoval-2.3.1/tests/regression/pe/trimfixed/collapse_5p_both_set/your_output.discarded000066400000000000000000000000001350370616400330160ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/trimfixed/collapse_5p_both_set/your_output.pair1.truncated000066400000000000000000000000001350370616400341000ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/trimfixed/collapse_5p_both_set/your_output.pair2.truncated000066400000000000000000000000001350370616400341010ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/trimfixed/collapse_5p_both_set/your_output.settings000066400000000000000000000036261350370616400327550ustar00rootroot00000000000000AdapterRemoval ver. 2.1.7 Trimming of paired-end reads [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 429139444 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 6 8 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: Yes Minimum overlap (in case of collapse): 11 [Trimming statistics] Total number of read pairs: 1 Number of unaligned read pairs: 0 Number of well aligned read pairs: 1 Number of discarded mate 1 reads: 0 Number of singleton mate 1 reads: 0 Number of discarded mate 2 reads: 0 Number of singleton mate 2 reads: 0 Number of reads with adapters[1]: 2 Number of full-length collapsed pairs: 1 Number of truncated collapsed pairs: 0 Number of retained reads: 1 Number of retained nucleotides: 36 Average length of retained reads: 36 [Length distribution] Length Mate1 Mate2 Singleton Collapsed CollapsedTruncated Discarded All 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 3 0 0 0 0 0 0 0 4 0 0 0 0 0 0 0 5 0 0 0 0 0 0 0 6 0 0 0 0 0 0 0 7 0 0 0 0 0 0 0 8 0 0 0 0 0 0 0 9 0 0 0 0 0 0 0 10 0 0 0 0 0 0 0 11 0 0 0 0 0 0 0 12 0 0 0 0 0 0 0 13 0 0 0 0 0 0 0 14 0 0 0 0 0 0 0 15 0 0 0 0 0 0 0 16 0 0 0 0 0 0 0 17 0 0 0 0 0 0 0 18 0 0 0 0 0 0 0 19 0 0 0 0 0 0 0 20 0 0 0 0 0 0 0 21 0 0 0 0 0 0 0 22 0 0 0 0 0 0 0 23 0 0 0 0 0 0 0 24 0 0 0 0 0 0 0 25 0 0 0 0 0 0 0 26 0 0 0 0 0 0 0 27 0 0 0 0 0 0 0 28 0 0 0 0 0 0 0 29 0 0 0 0 0 0 0 30 0 0 0 0 0 0 0 31 0 0 0 0 0 0 0 32 0 0 0 0 0 0 0 33 0 0 0 0 0 0 0 34 0 0 0 0 0 0 0 35 0 0 0 0 0 0 0 36 0 0 0 1 0 0 1 your_output.singleton.truncated000066400000000000000000000000001350370616400350070ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/pe/trimfixed/collapse_5p_both_setadapterremoval-2.3.1/tests/regression/preserve5p/000077500000000000000000000000001350370616400221525ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/preserve5p/pe/000077500000000000000000000000001350370616400225565ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/preserve5p/pe/collapsed/000077500000000000000000000000001350370616400245245ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/preserve5p/pe/collapsed/info.json000066400000000000000000000001641350370616400263530ustar00rootroot00000000000000{ "arguments": ["--trimns", "--trimqualities", "--preserve5p", "--collapse"], "return_code": 0, "stderr": [ ] } adapterremoval-2.3.1/tests/regression/preserve5p/pe/collapsed/input_1.fastq000066400000000000000000000015571350370616400271530ustar00rootroot00000000000000@read1 should not be trimmed TCTATGAGACGCGATATAACTCGAAACAGTTCTCCAGAGTTCCCTTTCAC + JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ @read2 should be trimmed at 3p TCTATGAGACGCGATATAACTCGAAACAGTTCTCCAGAGTNNNNNNNNNN + JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ @read3 should be trimmed at 3p TCTATGAGACGCGATATAACTCGAAACAGTTCTCCAGAGTTCCCTTTCAC + JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ!!!!!!!!!! @read4 should be trimmed at 5p (if not disabled) NNNNNNNNNNGCGATATAACTCGAAACAGTTCTCCAGAGTTCCCTTTCAC + JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ @read5 should be trimmed at 5p (if not disabled) TCTATGAGACGCGATATAACTCGAAACAGTTCTCCAGAGTTCCCTTTCAC + !!!!!!!!!!JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ @read6 should not be trimmed if collapsed NNNNNGTCATTCTCCCCCTTAACGACACTGCATGGTATAGAGTTTCAGTT + !!!!!JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ adapterremoval-2.3.1/tests/regression/preserve5p/pe/collapsed/input_2.fastq000066400000000000000000000015551350370616400271520ustar00rootroot00000000000000@read1 should not be trimmed TATTGTCCAGAAGGCTGTGGAAGAGAAAGAAGCCTGTGTTTTTGGGCTAC + JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ @read2 should be trimmed at 3p TATTGTCCAGAAGGCTGTGGAAGAGAAAGAAGCCTGTGTTNNNNNNNNNN + JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ @read3 should be trimmed at 3p TATTGTCCAGAAGGCTGTGGAAGAGAAAGAAGCCTGTGTTTTTGGGCTAC + JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ!!!!!!!!!! @read4 should be trimmed at 5p (if not disabled) NNNNNNNNNNAAGGCTGTGGAAGAGAAAGAAGCCTGTGTTTTTGGGCTAC + JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ @read5 should be trimmed at 5p (if not disabled) TATTGTCCAGAAGGCTGTGGAAGAGAAAGAAGCCTGTGTTTTTGGGCTAC + !!!!!!!!!!JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ @read6 should not be trimmed if collapsed NNNNNGCAATGCCAGCGTATAGTGGAACTGAAACTCTATACCATGCAGTG + !!!!!JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJadapterremoval-2.3.1/tests/regression/preserve5p/pe/collapsed/your_output.collapsed000066400000000000000000000003061350370616400310310ustar00rootroot00000000000000@M_read6 should not be trimmed if collapsed NNNNNGTCATTCTCCCCCTTAACGACACTGCATGGTATAGAGTTTCAGTTCCACTATACGCTGGCATTGCNNNNN + !!!!!JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ!!!!! adapterremoval-2.3.1/tests/regression/preserve5p/pe/collapsed/your_output.discarded000066400000000000000000000000001350370616400307740ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/preserve5p/pe/collapsed/your_output.pair1.truncated000066400000000000000000000012351350370616400320710ustar00rootroot00000000000000@read1 should not be trimmed TCTATGAGACGCGATATAACTCGAAACAGTTCTCCAGAGTTCCCTTTCAC + JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ @read2 should be trimmed at 3p TCTATGAGACGCGATATAACTCGAAACAGTTCTCCAGAGT + JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ @read3 should be trimmed at 3p TCTATGAGACGCGATATAACTCGAAACAGTTCTCCAGAGT + JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ @read4 should be trimmed at 5p (if not disabled) NNNNNNNNNNGCGATATAACTCGAAACAGTTCTCCAGAGTTCCCTTTCAC + JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ @read5 should be trimmed at 5p (if not disabled) TCTATGAGACGCGATATAACTCGAAACAGTTCTCCAGAGTTCCCTTTCAC + !!!!!!!!!!JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ adapterremoval-2.3.1/tests/regression/preserve5p/pe/collapsed/your_output.pair2.truncated000066400000000000000000000012351350370616400320720ustar00rootroot00000000000000@read1 should not be trimmed TATTGTCCAGAAGGCTGTGGAAGAGAAAGAAGCCTGTGTTTTTGGGCTAC + JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ @read2 should be trimmed at 3p TATTGTCCAGAAGGCTGTGGAAGAGAAAGAAGCCTGTGTT + JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ @read3 should be trimmed at 3p TATTGTCCAGAAGGCTGTGGAAGAGAAAGAAGCCTGTGTT + JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ @read4 should be trimmed at 5p (if not disabled) NNNNNNNNNNAAGGCTGTGGAAGAGAAAGAAGCCTGTGTTTTTGGGCTAC + JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ @read5 should be trimmed at 5p (if not disabled) TATTGTCCAGAAGGCTGTGGAAGAGAAAGAAGCCTGTGTTTTTGGGCTAC + !!!!!!!!!!JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ adapterremoval-2.3.1/tests/regression/preserve5p/pe/collapsed/your_output.settings000066400000000000000000000050651350370616400307320ustar00rootroot00000000000000AdapterRemoval ver. 2.3.0 Trimming of paired-end reads [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 1718079106 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: Yes Trimming Phred scores <= 2: Yes Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: Yes Minimum overlap (in case of collapse): 11 [Trimming statistics] Total number of read pairs: 6 Number of unaligned read pairs: 5 Number of well aligned read pairs: 1 Number of discarded mate 1 reads: 0 Number of singleton mate 1 reads: 0 Number of discarded mate 2 reads: 0 Number of singleton mate 2 reads: 0 Number of reads with adapters[1]: 0 Number of full-length collapsed pairs: 1 Number of truncated collapsed pairs: 0 Number of retained reads: 11 Number of retained nucleotides: 535 Average length of retained reads: 48.6364 [Length distribution] Length Mate1 Mate2 Singleton Collapsed CollapsedTruncated Discarded All 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 3 0 0 0 0 0 0 0 4 0 0 0 0 0 0 0 5 0 0 0 0 0 0 0 6 0 0 0 0 0 0 0 7 0 0 0 0 0 0 0 8 0 0 0 0 0 0 0 9 0 0 0 0 0 0 0 10 0 0 0 0 0 0 0 11 0 0 0 0 0 0 0 12 0 0 0 0 0 0 0 13 0 0 0 0 0 0 0 14 0 0 0 0 0 0 0 15 0 0 0 0 0 0 0 16 0 0 0 0 0 0 0 17 0 0 0 0 0 0 0 18 0 0 0 0 0 0 0 19 0 0 0 0 0 0 0 20 0 0 0 0 0 0 0 21 0 0 0 0 0 0 0 22 0 0 0 0 0 0 0 23 0 0 0 0 0 0 0 24 0 0 0 0 0 0 0 25 0 0 0 0 0 0 0 26 0 0 0 0 0 0 0 27 0 0 0 0 0 0 0 28 0 0 0 0 0 0 0 29 0 0 0 0 0 0 0 30 0 0 0 0 0 0 0 31 0 0 0 0 0 0 0 32 0 0 0 0 0 0 0 33 0 0 0 0 0 0 0 34 0 0 0 0 0 0 0 35 0 0 0 0 0 0 0 36 0 0 0 0 0 0 0 37 0 0 0 0 0 0 0 38 0 0 0 0 0 0 0 39 0 0 0 0 0 0 0 40 2 2 0 0 0 0 4 41 0 0 0 0 0 0 0 42 0 0 0 0 0 0 0 43 0 0 0 0 0 0 0 44 0 0 0 0 0 0 0 45 0 0 0 0 0 0 0 46 0 0 0 0 0 0 0 47 0 0 0 0 0 0 0 48 0 0 0 0 0 0 0 49 0 0 0 0 0 0 0 50 3 3 0 0 0 0 6 51 0 0 0 0 0 0 0 52 0 0 0 0 0 0 0 53 0 0 0 0 0 0 0 54 0 0 0 0 0 0 0 55 0 0 0 0 0 0 0 56 0 0 0 0 0 0 0 57 0 0 0 0 0 0 0 58 0 0 0 0 0 0 0 59 0 0 0 0 0 0 0 60 0 0 0 0 0 0 0 61 0 0 0 0 0 0 0 62 0 0 0 0 0 0 0 63 0 0 0 0 0 0 0 64 0 0 0 0 0 0 0 65 0 0 0 0 0 0 0 66 0 0 0 0 0 0 0 67 0 0 0 0 0 0 0 68 0 0 0 0 0 0 0 69 0 0 0 0 0 0 0 70 0 0 0 0 0 0 0 71 0 0 0 0 0 0 0 72 0 0 0 0 0 0 0 73 0 0 0 0 0 0 0 74 0 0 0 0 0 0 0 75 0 0 0 1 0 0 1 adapterremoval-2.3.1/tests/regression/preserve5p/pe/collapsed/your_output.singleton.truncated000066400000000000000000000000001350370616400330440ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/preserve5p/pe/disabled/000077500000000000000000000000001350370616400243255ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/preserve5p/pe/disabled/info.json000066400000000000000000000001261350370616400261520ustar00rootroot00000000000000{ "arguments": ["--trimns", "--trimqualities"], "return_code": 0, "stderr": [ ] } adapterremoval-2.3.1/tests/regression/preserve5p/pe/disabled/input_1.fastq000066400000000000000000000015571350370616400267540ustar00rootroot00000000000000@read1 should not be trimmed TCTATGAGACGCGATATAACTCGAAACAGTTCTCCAGAGTTCCCTTTCAC + JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ @read2 should be trimmed at 3p TCTATGAGACGCGATATAACTCGAAACAGTTCTCCAGAGTNNNNNNNNNN + JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ @read3 should be trimmed at 3p TCTATGAGACGCGATATAACTCGAAACAGTTCTCCAGAGTTCCCTTTCAC + JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ!!!!!!!!!! @read4 should be trimmed at 5p (if not disabled) NNNNNNNNNNGCGATATAACTCGAAACAGTTCTCCAGAGTTCCCTTTCAC + JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ @read5 should be trimmed at 5p (if not disabled) TCTATGAGACGCGATATAACTCGAAACAGTTCTCCAGAGTTCCCTTTCAC + !!!!!!!!!!JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ @read6 should not be trimmed if collapsed NNNNNGTCATTCTCCCCCTTAACGACACTGCATGGTATAGAGTTTCAGTT + !!!!!JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ adapterremoval-2.3.1/tests/regression/preserve5p/pe/disabled/input_2.fastq000066400000000000000000000015551350370616400267530ustar00rootroot00000000000000@read1 should not be trimmed TATTGTCCAGAAGGCTGTGGAAGAGAAAGAAGCCTGTGTTTTTGGGCTAC + JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ @read2 should be trimmed at 3p TATTGTCCAGAAGGCTGTGGAAGAGAAAGAAGCCTGTGTTNNNNNNNNNN + JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ @read3 should be trimmed at 3p TATTGTCCAGAAGGCTGTGGAAGAGAAAGAAGCCTGTGTTTTTGGGCTAC + JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ!!!!!!!!!! @read4 should be trimmed at 5p (if not disabled) NNNNNNNNNNAAGGCTGTGGAAGAGAAAGAAGCCTGTGTTTTTGGGCTAC + JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ @read5 should be trimmed at 5p (if not disabled) TATTGTCCAGAAGGCTGTGGAAGAGAAAGAAGCCTGTGTTTTTGGGCTAC + !!!!!!!!!!JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ @read6 should not be trimmed if collapsed NNNNNGCAATGCCAGCGTATAGTGGAACTGAAACTCTATACCATGCAGTG + !!!!!JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJadapterremoval-2.3.1/tests/regression/preserve5p/pe/disabled/your_output.discarded000066400000000000000000000000001350370616400305750ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/preserve5p/pe/disabled/your_output.pair1.truncated000066400000000000000000000013751350370616400316770ustar00rootroot00000000000000@read1 should not be trimmed TCTATGAGACGCGATATAACTCGAAACAGTTCTCCAGAGTTCCCTTTCAC + JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ @read2 should be trimmed at 3p TCTATGAGACGCGATATAACTCGAAACAGTTCTCCAGAGT + JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ @read3 should be trimmed at 3p TCTATGAGACGCGATATAACTCGAAACAGTTCTCCAGAGT + JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ @read4 should be trimmed at 5p (if not disabled) GCGATATAACTCGAAACAGTTCTCCAGAGTTCCCTTTCAC + JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ @read5 should be trimmed at 5p (if not disabled) GCGATATAACTCGAAACAGTTCTCCAGAGTTCCCTTTCAC + JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ @read6 should not be trimmed if collapsed GTCATTCTCCCCCTTAACGACACTGCATGGTATAGAGTTTCAGTT + JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ adapterremoval-2.3.1/tests/regression/preserve5p/pe/disabled/your_output.pair2.truncated000066400000000000000000000013751350370616400317000ustar00rootroot00000000000000@read1 should not be trimmed TATTGTCCAGAAGGCTGTGGAAGAGAAAGAAGCCTGTGTTTTTGGGCTAC + JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ @read2 should be trimmed at 3p TATTGTCCAGAAGGCTGTGGAAGAGAAAGAAGCCTGTGTT + JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ @read3 should be trimmed at 3p TATTGTCCAGAAGGCTGTGGAAGAGAAAGAAGCCTGTGTT + JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ @read4 should be trimmed at 5p (if not disabled) AAGGCTGTGGAAGAGAAAGAAGCCTGTGTTTTTGGGCTAC + JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ @read5 should be trimmed at 5p (if not disabled) AAGGCTGTGGAAGAGAAAGAAGCCTGTGTTTTTGGGCTAC + JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ @read6 should not be trimmed if collapsed GCAATGCCAGCGTATAGTGGAACTGAAACTCTATACCATGCAGTG + JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ adapterremoval-2.3.1/tests/regression/preserve5p/pe/disabled/your_output.settings000066400000000000000000000035171350370616400305330ustar00rootroot00000000000000AdapterRemoval ver. 2.3.0 Trimming of paired-end reads [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 1525257745 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: Yes Trimming Phred scores <= 2: Yes Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 [Trimming statistics] Total number of read pairs: 6 Number of unaligned read pairs: 5 Number of well aligned read pairs: 1 Number of discarded mate 1 reads: 0 Number of singleton mate 1 reads: 0 Number of discarded mate 2 reads: 0 Number of singleton mate 2 reads: 0 Number of reads with adapters[1]: 0 Number of retained reads: 12 Number of retained nucleotides: 510 Average length of retained reads: 42.5 [Length distribution] Length Mate1 Mate2 Singleton Discarded All 0 0 0 0 0 0 1 0 0 0 0 0 2 0 0 0 0 0 3 0 0 0 0 0 4 0 0 0 0 0 5 0 0 0 0 0 6 0 0 0 0 0 7 0 0 0 0 0 8 0 0 0 0 0 9 0 0 0 0 0 10 0 0 0 0 0 11 0 0 0 0 0 12 0 0 0 0 0 13 0 0 0 0 0 14 0 0 0 0 0 15 0 0 0 0 0 16 0 0 0 0 0 17 0 0 0 0 0 18 0 0 0 0 0 19 0 0 0 0 0 20 0 0 0 0 0 21 0 0 0 0 0 22 0 0 0 0 0 23 0 0 0 0 0 24 0 0 0 0 0 25 0 0 0 0 0 26 0 0 0 0 0 27 0 0 0 0 0 28 0 0 0 0 0 29 0 0 0 0 0 30 0 0 0 0 0 31 0 0 0 0 0 32 0 0 0 0 0 33 0 0 0 0 0 34 0 0 0 0 0 35 0 0 0 0 0 36 0 0 0 0 0 37 0 0 0 0 0 38 0 0 0 0 0 39 0 0 0 0 0 40 4 4 0 0 8 41 0 0 0 0 0 42 0 0 0 0 0 43 0 0 0 0 0 44 0 0 0 0 0 45 1 1 0 0 2 46 0 0 0 0 0 47 0 0 0 0 0 48 0 0 0 0 0 49 0 0 0 0 0 50 1 1 0 0 2 adapterremoval-2.3.1/tests/regression/preserve5p/pe/disabled/your_output.singleton.truncated000066400000000000000000000000001350370616400326450ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/preserve5p/pe/enabled/000077500000000000000000000000001350370616400241505ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/preserve5p/pe/enabled/info.json000066400000000000000000000001461350370616400257770ustar00rootroot00000000000000{ "arguments": ["--trimns", "--trimqualities", "--preserve5p"], "return_code": 0, "stderr": [ ] } adapterremoval-2.3.1/tests/regression/preserve5p/pe/enabled/input_1.fastq000066400000000000000000000015571350370616400265770ustar00rootroot00000000000000@read1 should not be trimmed TCTATGAGACGCGATATAACTCGAAACAGTTCTCCAGAGTTCCCTTTCAC + JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ @read2 should be trimmed at 3p TCTATGAGACGCGATATAACTCGAAACAGTTCTCCAGAGTNNNNNNNNNN + JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ @read3 should be trimmed at 3p TCTATGAGACGCGATATAACTCGAAACAGTTCTCCAGAGTTCCCTTTCAC + JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ!!!!!!!!!! @read4 should be trimmed at 5p (if not disabled) NNNNNNNNNNGCGATATAACTCGAAACAGTTCTCCAGAGTTCCCTTTCAC + JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ @read5 should be trimmed at 5p (if not disabled) TCTATGAGACGCGATATAACTCGAAACAGTTCTCCAGAGTTCCCTTTCAC + !!!!!!!!!!JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ @read6 should not be trimmed if collapsed NNNNNGTCATTCTCCCCCTTAACGACACTGCATGGTATAGAGTTTCAGTT + !!!!!JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ adapterremoval-2.3.1/tests/regression/preserve5p/pe/enabled/input_2.fastq000066400000000000000000000015551350370616400265760ustar00rootroot00000000000000@read1 should not be trimmed TATTGTCCAGAAGGCTGTGGAAGAGAAAGAAGCCTGTGTTTTTGGGCTAC + JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ @read2 should be trimmed at 3p TATTGTCCAGAAGGCTGTGGAAGAGAAAGAAGCCTGTGTTNNNNNNNNNN + JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ @read3 should be trimmed at 3p TATTGTCCAGAAGGCTGTGGAAGAGAAAGAAGCCTGTGTTTTTGGGCTAC + JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ!!!!!!!!!! @read4 should be trimmed at 5p (if not disabled) NNNNNNNNNNAAGGCTGTGGAAGAGAAAGAAGCCTGTGTTTTTGGGCTAC + JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ @read5 should be trimmed at 5p (if not disabled) TATTGTCCAGAAGGCTGTGGAAGAGAAAGAAGCCTGTGTTTTTGGGCTAC + !!!!!!!!!!JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ @read6 should not be trimmed if collapsed NNNNNGCAATGCCAGCGTATAGTGGAACTGAAACTCTATACCATGCAGTG + !!!!!JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJadapterremoval-2.3.1/tests/regression/preserve5p/pe/enabled/your_output.discarded000066400000000000000000000000001350370616400304200ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/preserve5p/pe/enabled/your_output.pair1.truncated000066400000000000000000000014571350370616400315230ustar00rootroot00000000000000@read1 should not be trimmed TCTATGAGACGCGATATAACTCGAAACAGTTCTCCAGAGTTCCCTTTCAC + JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ @read2 should be trimmed at 3p TCTATGAGACGCGATATAACTCGAAACAGTTCTCCAGAGT + JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ @read3 should be trimmed at 3p TCTATGAGACGCGATATAACTCGAAACAGTTCTCCAGAGT + JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ @read4 should be trimmed at 5p (if not disabled) NNNNNNNNNNGCGATATAACTCGAAACAGTTCTCCAGAGTTCCCTTTCAC + JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ @read5 should be trimmed at 5p (if not disabled) TCTATGAGACGCGATATAACTCGAAACAGTTCTCCAGAGTTCCCTTTCAC + !!!!!!!!!!JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ @read6 should not be trimmed if collapsed NNNNNGTCATTCTCCCCCTTAACGACACTGCATGGTATAGAGTTTCAGTT + !!!!!JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ adapterremoval-2.3.1/tests/regression/preserve5p/pe/enabled/your_output.pair2.truncated000066400000000000000000000014571350370616400315240ustar00rootroot00000000000000@read1 should not be trimmed TATTGTCCAGAAGGCTGTGGAAGAGAAAGAAGCCTGTGTTTTTGGGCTAC + JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ @read2 should be trimmed at 3p TATTGTCCAGAAGGCTGTGGAAGAGAAAGAAGCCTGTGTT + JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ @read3 should be trimmed at 3p TATTGTCCAGAAGGCTGTGGAAGAGAAAGAAGCCTGTGTT + JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ @read4 should be trimmed at 5p (if not disabled) NNNNNNNNNNAAGGCTGTGGAAGAGAAAGAAGCCTGTGTTTTTGGGCTAC + JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ @read5 should be trimmed at 5p (if not disabled) TATTGTCCAGAAGGCTGTGGAAGAGAAAGAAGCCTGTGTTTTTGGGCTAC + !!!!!!!!!!JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ @read6 should not be trimmed if collapsed NNNNNGCAATGCCAGCGTATAGTGGAACTGAAACTCTATACCATGCAGTG + !!!!!JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ adapterremoval-2.3.1/tests/regression/preserve5p/pe/enabled/your_output.settings000066400000000000000000000035221350370616400303520ustar00rootroot00000000000000AdapterRemoval ver. 2.3.0 Trimming of paired-end reads [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 1592999118 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: Yes Trimming Phred scores <= 2: Yes Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 [Trimming statistics] Total number of read pairs: 6 Number of unaligned read pairs: 5 Number of well aligned read pairs: 1 Number of discarded mate 1 reads: 0 Number of singleton mate 1 reads: 0 Number of discarded mate 2 reads: 0 Number of singleton mate 2 reads: 0 Number of reads with adapters[1]: 0 Number of retained reads: 12 Number of retained nucleotides: 560 Average length of retained reads: 46.6667 [Length distribution] Length Mate1 Mate2 Singleton Discarded All 0 0 0 0 0 0 1 0 0 0 0 0 2 0 0 0 0 0 3 0 0 0 0 0 4 0 0 0 0 0 5 0 0 0 0 0 6 0 0 0 0 0 7 0 0 0 0 0 8 0 0 0 0 0 9 0 0 0 0 0 10 0 0 0 0 0 11 0 0 0 0 0 12 0 0 0 0 0 13 0 0 0 0 0 14 0 0 0 0 0 15 0 0 0 0 0 16 0 0 0 0 0 17 0 0 0 0 0 18 0 0 0 0 0 19 0 0 0 0 0 20 0 0 0 0 0 21 0 0 0 0 0 22 0 0 0 0 0 23 0 0 0 0 0 24 0 0 0 0 0 25 0 0 0 0 0 26 0 0 0 0 0 27 0 0 0 0 0 28 0 0 0 0 0 29 0 0 0 0 0 30 0 0 0 0 0 31 0 0 0 0 0 32 0 0 0 0 0 33 0 0 0 0 0 34 0 0 0 0 0 35 0 0 0 0 0 36 0 0 0 0 0 37 0 0 0 0 0 38 0 0 0 0 0 39 0 0 0 0 0 40 2 2 0 0 4 41 0 0 0 0 0 42 0 0 0 0 0 43 0 0 0 0 0 44 0 0 0 0 0 45 0 0 0 0 0 46 0 0 0 0 0 47 0 0 0 0 0 48 0 0 0 0 0 49 0 0 0 0 0 50 4 4 0 0 8 adapterremoval-2.3.1/tests/regression/preserve5p/pe/enabled/your_output.singleton.truncated000066400000000000000000000000001350370616400324700ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/preserve5p/se/000077500000000000000000000000001350370616400225615ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/preserve5p/se/collapsed/000077500000000000000000000000001350370616400245275ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/preserve5p/se/collapsed/info.json000066400000000000000000000001641350370616400263560ustar00rootroot00000000000000{ "arguments": ["--trimns", "--trimqualities", "--preserve5p", "--collapse"], "return_code": 0, "stderr": [ ] } adapterremoval-2.3.1/tests/regression/preserve5p/se/collapsed/input_1.fastq000066400000000000000000000015571350370616400271560ustar00rootroot00000000000000@read1 should not be trimmed TCTATGAGACGCGATATAACTCGAAACAGTTCTCCAGAGTTCCCTTTCAC + JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ @read2 should be trimmed at 3p TCTATGAGACGCGATATAACTCGAAACAGTTCTCCAGAGTNNNNNNNNNN + JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ @read3 should be trimmed at 3p TCTATGAGACGCGATATAACTCGAAACAGTTCTCCAGAGTTCCCTTTCAC + JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ!!!!!!!!!! @read4 should be trimmed at 5p (if not disabled) NNNNNNNNNNGCGATATAACTCGAAACAGTTCTCCAGAGTTCCCTTTCAC + JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ @read5 should be trimmed at 5p (if not disabled) TCTATGAGACGCGATATAACTCGAAACAGTTCTCCAGAGTTCCCTTTCAC + !!!!!!!!!!JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ @read6 should not be trimmed if collapsed NNNNNGAGACGCGATATAACTCGAAAGATCGGAAGAGCACACGTCTGAAC + JJJJJJJJJJJJJJJJJJJJ!!!!!JJJJJJJJJJJJJJJJJJJJJJJJJ adapterremoval-2.3.1/tests/regression/preserve5p/se/collapsed/your_output.collapsed000066400000000000000000000001421350370616400310320ustar00rootroot00000000000000@M_read6 should not be trimmed if collapsed NNNNNGAGACGCGATATAACTCGAA + JJJJJJJJJJJJJJJJJJJJ!!!!! adapterremoval-2.3.1/tests/regression/preserve5p/se/collapsed/your_output.discarded000066400000000000000000000000001350370616400307770ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/preserve5p/se/collapsed/your_output.settings000066400000000000000000000035571350370616400307410ustar00rootroot00000000000000AdapterRemoval ver. 2.3.0 Trimming of single-end reads [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 911894095 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: Yes Trimming Phred scores <= 2: Yes Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: Yes Minimum overlap (in case of collapse): 11 Minimum adapter overlap: 0 [Trimming statistics] Total number of reads: 6 Number of unaligned reads: 5 Number of well aligned reads: 1 Number of discarded mate 1 reads: 0 Number of singleton mate 1 reads: 5 Number of reads with adapters[1]: 1 Number of full-length collapsed pairs: 1 Number of truncated collapsed pairs: 0 Number of retained reads: 6 Number of retained nucleotides: 255 Average length of retained reads: 42.5 [Length distribution] Length Mate1 Collapsed CollapsedTruncated Discarded All 0 0 0 0 0 0 1 0 0 0 0 0 2 0 0 0 0 0 3 0 0 0 0 0 4 0 0 0 0 0 5 0 0 0 0 0 6 0 0 0 0 0 7 0 0 0 0 0 8 0 0 0 0 0 9 0 0 0 0 0 10 0 0 0 0 0 11 0 0 0 0 0 12 0 0 0 0 0 13 0 0 0 0 0 14 0 0 0 0 0 15 0 0 0 0 0 16 0 0 0 0 0 17 0 0 0 0 0 18 0 0 0 0 0 19 0 0 0 0 0 20 0 0 0 0 0 21 0 0 0 0 0 22 0 0 0 0 0 23 0 0 0 0 0 24 0 0 0 0 0 25 0 1 0 0 1 26 0 0 0 0 0 27 0 0 0 0 0 28 0 0 0 0 0 29 0 0 0 0 0 30 0 0 0 0 0 31 0 0 0 0 0 32 0 0 0 0 0 33 0 0 0 0 0 34 0 0 0 0 0 35 0 0 0 0 0 36 0 0 0 0 0 37 0 0 0 0 0 38 0 0 0 0 0 39 0 0 0 0 0 40 2 0 0 0 2 41 0 0 0 0 0 42 0 0 0 0 0 43 0 0 0 0 0 44 0 0 0 0 0 45 0 0 0 0 0 46 0 0 0 0 0 47 0 0 0 0 0 48 0 0 0 0 0 49 0 0 0 0 0 50 3 0 0 0 3 adapterremoval-2.3.1/tests/regression/preserve5p/se/collapsed/your_output.truncated000066400000000000000000000012351350370616400310610ustar00rootroot00000000000000@read1 should not be trimmed TCTATGAGACGCGATATAACTCGAAACAGTTCTCCAGAGTTCCCTTTCAC + JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ @read2 should be trimmed at 3p TCTATGAGACGCGATATAACTCGAAACAGTTCTCCAGAGT + JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ @read3 should be trimmed at 3p TCTATGAGACGCGATATAACTCGAAACAGTTCTCCAGAGT + JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ @read4 should be trimmed at 5p (if not disabled) NNNNNNNNNNGCGATATAACTCGAAACAGTTCTCCAGAGTTCCCTTTCAC + JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ @read5 should be trimmed at 5p (if not disabled) TCTATGAGACGCGATATAACTCGAAACAGTTCTCCAGAGTTCCCTTTCAC + !!!!!!!!!!JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ adapterremoval-2.3.1/tests/regression/preserve5p/se/disabled/000077500000000000000000000000001350370616400243305ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/preserve5p/se/disabled/info.json000066400000000000000000000001261350370616400261550ustar00rootroot00000000000000{ "arguments": ["--trimns", "--trimqualities"], "return_code": 0, "stderr": [ ] } adapterremoval-2.3.1/tests/regression/preserve5p/se/disabled/input_1.fastq000066400000000000000000000015551350370616400267550ustar00rootroot00000000000000@read1 should not be trimmed TCTATGAGACGCGATATAACTCGAAACAGTTCTCCAGAGTTCCCTTTCAC + JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ @read2 should be trimmed at 3p TCTATGAGACGCGATATAACTCGAAACAGTTCTCCAGAGTNNNNNNNNNN + JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ @read3 should be trimmed at 3p TCTATGAGACGCGATATAACTCGAAACAGTTCTCCAGAGTTCCCTTTCAC + JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ!!!!!!!!!! @read4 should be trimmed at 5p (if not disabled) NNNNNNNNNNGCGATATAACTCGAAACAGTTCTCCAGAGTTCCCTTTCAC + JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ @read5 should be trimmed at 5p (if not disabled) TCTATGAGACGCGATATAACTCGAAACAGTTCTCCAGAGTTCCCTTTCAC + !!!!!!!!!!JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ @read6 should not be trimmed if collapsed NNNNNGAGACGCGATATAACTCGAAAGATCGGAAGAGCACACGTCTGAAC + JJJJJJJJJJJJJJJJJJJJ!!!!!JJJJJJJJJJJJJJJJJJJJJJJJJadapterremoval-2.3.1/tests/regression/preserve5p/se/disabled/your_output.discarded000066400000000000000000000000001350370616400306000ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/preserve5p/se/disabled/your_output.settings000066400000000000000000000030651350370616400305340ustar00rootroot00000000000000AdapterRemoval ver. 2.3.0 Trimming of single-end reads [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 416217354 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: Yes Trimming Phred scores <= 2: Yes Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 Minimum adapter overlap: 0 [Trimming statistics] Total number of reads: 6 Number of unaligned reads: 5 Number of well aligned reads: 1 Number of discarded mate 1 reads: 0 Number of singleton mate 1 reads: 6 Number of reads with adapters[1]: 1 Number of retained reads: 6 Number of retained nucleotides: 225 Average length of retained reads: 37.5 [Length distribution] Length Mate1 Discarded All 0 0 0 0 1 0 0 0 2 0 0 0 3 0 0 0 4 0 0 0 5 0 0 0 6 0 0 0 7 0 0 0 8 0 0 0 9 0 0 0 10 0 0 0 11 0 0 0 12 0 0 0 13 0 0 0 14 0 0 0 15 1 0 1 16 0 0 0 17 0 0 0 18 0 0 0 19 0 0 0 20 0 0 0 21 0 0 0 22 0 0 0 23 0 0 0 24 0 0 0 25 0 0 0 26 0 0 0 27 0 0 0 28 0 0 0 29 0 0 0 30 0 0 0 31 0 0 0 32 0 0 0 33 0 0 0 34 0 0 0 35 0 0 0 36 0 0 0 37 0 0 0 38 0 0 0 39 0 0 0 40 4 0 4 41 0 0 0 42 0 0 0 43 0 0 0 44 0 0 0 45 0 0 0 46 0 0 0 47 0 0 0 48 0 0 0 49 0 0 0 50 1 0 1 adapterremoval-2.3.1/tests/regression/preserve5p/se/disabled/your_output.truncated000066400000000000000000000013011350370616400306540ustar00rootroot00000000000000@read1 should not be trimmed TCTATGAGACGCGATATAACTCGAAACAGTTCTCCAGAGTTCCCTTTCAC + JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ @read2 should be trimmed at 3p TCTATGAGACGCGATATAACTCGAAACAGTTCTCCAGAGT + JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ @read3 should be trimmed at 3p TCTATGAGACGCGATATAACTCGAAACAGTTCTCCAGAGT + JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ @read4 should be trimmed at 5p (if not disabled) GCGATATAACTCGAAACAGTTCTCCAGAGTTCCCTTTCAC + JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ @read5 should be trimmed at 5p (if not disabled) GCGATATAACTCGAAACAGTTCTCCAGAGTTCCCTTTCAC + JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ @read6 should not be trimmed if collapsed GAGACGCGATATAAC + JJJJJJJJJJJJJJJ adapterremoval-2.3.1/tests/regression/preserve5p/se/enabled/000077500000000000000000000000001350370616400241535ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/preserve5p/se/enabled/info.json000066400000000000000000000001461350370616400260020ustar00rootroot00000000000000{ "arguments": ["--trimns", "--trimqualities", "--preserve5p"], "return_code": 0, "stderr": [ ] } adapterremoval-2.3.1/tests/regression/preserve5p/se/enabled/input_1.fastq000066400000000000000000000015571350370616400266020ustar00rootroot00000000000000@read1 should not be trimmed TCTATGAGACGCGATATAACTCGAAACAGTTCTCCAGAGTTCCCTTTCAC + JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ @read2 should be trimmed at 3p TCTATGAGACGCGATATAACTCGAAACAGTTCTCCAGAGTNNNNNNNNNN + JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ @read3 should be trimmed at 3p TCTATGAGACGCGATATAACTCGAAACAGTTCTCCAGAGTTCCCTTTCAC + JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ!!!!!!!!!! @read4 should be trimmed at 5p (if not disabled) NNNNNNNNNNGCGATATAACTCGAAACAGTTCTCCAGAGTTCCCTTTCAC + JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ @read5 should be trimmed at 5p (if not disabled) TCTATGAGACGCGATATAACTCGAAACAGTTCTCCAGAGTTCCCTTTCAC + !!!!!!!!!!JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ @read6 should not be trimmed if collapsed NNNNNGAGACGCGATATAACTCGAAAGATCGGAAGAGCACACGTCTGAAC + JJJJJJJJJJJJJJJJJJJJ!!!!!JJJJJJJJJJJJJJJJJJJJJJJJJ adapterremoval-2.3.1/tests/regression/preserve5p/se/enabled/your_output.discarded000066400000000000000000000000001350370616400304230ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/preserve5p/se/enabled/your_output.settings000066400000000000000000000030701350370616400303530ustar00rootroot00000000000000AdapterRemoval ver. 2.3.0 Trimming of single-end reads [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 519935610 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: Yes Trimming Phred scores <= 2: Yes Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 Minimum adapter overlap: 0 [Trimming statistics] Total number of reads: 6 Number of unaligned reads: 5 Number of well aligned reads: 1 Number of discarded mate 1 reads: 0 Number of singleton mate 1 reads: 6 Number of reads with adapters[1]: 1 Number of retained reads: 6 Number of retained nucleotides: 250 Average length of retained reads: 41.6667 [Length distribution] Length Mate1 Discarded All 0 0 0 0 1 0 0 0 2 0 0 0 3 0 0 0 4 0 0 0 5 0 0 0 6 0 0 0 7 0 0 0 8 0 0 0 9 0 0 0 10 0 0 0 11 0 0 0 12 0 0 0 13 0 0 0 14 0 0 0 15 0 0 0 16 0 0 0 17 0 0 0 18 0 0 0 19 0 0 0 20 1 0 1 21 0 0 0 22 0 0 0 23 0 0 0 24 0 0 0 25 0 0 0 26 0 0 0 27 0 0 0 28 0 0 0 29 0 0 0 30 0 0 0 31 0 0 0 32 0 0 0 33 0 0 0 34 0 0 0 35 0 0 0 36 0 0 0 37 0 0 0 38 0 0 0 39 0 0 0 40 2 0 2 41 0 0 0 42 0 0 0 43 0 0 0 44 0 0 0 45 0 0 0 46 0 0 0 47 0 0 0 48 0 0 0 49 0 0 0 50 3 0 3 adapterremoval-2.3.1/tests/regression/preserve5p/se/enabled/your_output.truncated000066400000000000000000000013631350370616400305070ustar00rootroot00000000000000@read1 should not be trimmed TCTATGAGACGCGATATAACTCGAAACAGTTCTCCAGAGTTCCCTTTCAC + JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ @read2 should be trimmed at 3p TCTATGAGACGCGATATAACTCGAAACAGTTCTCCAGAGT + JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ @read3 should be trimmed at 3p TCTATGAGACGCGATATAACTCGAAACAGTTCTCCAGAGT + JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ @read4 should be trimmed at 5p (if not disabled) NNNNNNNNNNGCGATATAACTCGAAACAGTTCTCCAGAGTTCCCTTTCAC + JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ @read5 should be trimmed at 5p (if not disabled) TCTATGAGACGCGATATAACTCGAAACAGTTCTCCAGAGTTCCCTTTCAC + !!!!!!!!!!JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ @read6 should not be trimmed if collapsed NNNNNGAGACGCGATATAAC + JJJJJJJJJJJJJJJJJJJJ adapterremoval-2.3.1/tests/regression/run000077500000000000000000000460061350370616400206120ustar00rootroot00000000000000#!/usr/bin/env python3 # -*- coding: utf-8 -*- # Copyright (c) 2016 Mikkel Schubert # # Permission is hereby granted, free of charge, to any person obtaining a copy # of this software and associated documentation files (the "Software"), to deal # in the Software without restriction, including without limitation the rights # to use, copy, modify, merge, publish, distribute, sublicense, and/or sell # copies of the Software, and to permit persons to whom the Software is # furnished to do so, subject to the following conditions: # # The above copyright notice and this permission notice shall be included in # all copies or substantial portions of the Software. # # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR # IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, # FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE # AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER # LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, # OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE # SOFTWARE. from __future__ import print_function import argparse import bz2 import difflib import gzip import io import itertools import json import os import re import shutil import subprocess import sys import tempfile ############################################################################# _COLORS_ENABLED = True def _do_print_color(*vargs, **kwargs): """Utility function: Prints using shell colors.""" colorcode = kwargs.pop("colorcode") destination = kwargs.pop("file", sys.stdout) # No colors if output is redirected (e.g. less, file, etc.) if _COLORS_ENABLED and destination.isatty(): vargs = list(vargs) for (index, varg) in enumerate(vargs): varg_lines = [] # Newlines terminate the color-code for e.g. 'less', so ensure that # each line is color-coded, while preserving the list of arguments for line in str(varg).split("\n"): varg_lines.append("\033[00;%im%s\033[00m" % (colorcode, line)) vargs[index] = "\n".join(varg_lines) print(*vargs, file=destination, **kwargs) if '\n' in kwargs.get('end', '\n'): destination.flush() def print_ok(*vargs, **kwargs): """Equivalent to print, but prints using shell colorcodes (green).""" _do_print_color(*vargs, colorcode=32, **kwargs) def print_err(*vargs, **kwargs): """Equivalent to print, but prints using shell colorcodes (red).""" _do_print_color(*vargs, colorcode=31, **kwargs) ############################################################################# UNCOMPRESSED, GZIP, BZIP2 = "raw", "gz", "bz2" def compress(value, compression): if compression == GZIP: fileobj = io.BytesIO() handle = gzip.GzipFile('', 'w', 9, fileobj) handle.write(value) handle.close() return fileobj.getvalue() elif compression == BZIP2: return bz2.compress(value) else: assert False, compression def decompress(filename): with open(filename, "rb") as handle: value = handle.read() if value and filename.endswith(".bz2"): if not value.startswith(b"BZ"): raise TestError("Expected bz2 file at %r, but header is %r" % (filename, value[:2])) value = bz2.decompress(value) elif value and filename.endswith(".gz"): if not value.startswith(b"\x1f\x8b"): raise TestError("Expected gzip file at %r, but header is %r" % (filename, value[:2])) fileobj = io.BytesIO(value) handle = gzip.GzipFile('', 'r', 9, fileobj) value = handle.read() value = value.decode("utf-8") return io.StringIO(value).readlines() ############################################################################# _EXEC = './build/AdapterRemoval' _INFO_FILE = "info.json" _INFO_FIELDS = { 'arguments': list, 'return_code': int, 'stderr': list, 'exhaustive': bool, } def pretty_output(s, padding=0, max_lines=float("inf")): padding = " " * padding lines = s.split("\n") if len(lines) > max_lines: lines = lines[:max_lines] lines.append("...") result = [] for line in lines: result.append("%s> %s" % (padding, line)) return "\n".join(result) def interleave(texts_1, texts_2): files = [] for text_1, text_2 in zip(texts_1, texts_2): lines_1 = text_1.rstrip().split("\n") lines_2 = text_2.rstrip().split("\n") iters = (iter(lines_1).__next__, iter(lines_2).__next__) assert len(lines_1) == len(lines_2) result = [] while True: try: for it in iters: for _ in range(4): result.append(it()) except StopIteration: break files.append("\n".join(result)) return files class TestError(Exception): pass class TestCase(object): def __init__(self, root, path): self.root = root self.path = path self.name = " :: ".join(path) self._files = self._collect_files(root) self._info = self._read_info(os.path.join(root, _INFO_FILE)) def __repr__(self): return "TestCase(%r)" % ({'root': self.root, 'name': self.name, 'info': self._info, 'files': self._files}) def run(self, root, delete_folder): root = os.path.join(root, *self.path) interleaved_tests = [False] if self._is_properly_paired(): interleaved_tests.append(True) parameters = itertools.product( (UNCOMPRESSED, GZIP, BZIP2), (UNCOMPRESSED, GZIP, BZIP2), interleaved_tests, ) for in_compression, out_compression, interleaved in parameters: yield "%s>%s%s" % (in_compression, out_compression, ",intl" if interleaved else "") postfix = "%s_%s%s" % (in_compression, out_compression, "_intl" if interleaved else "") test_folder = os.path.join(root, postfix) self._do_run(root=test_folder, in_compression=in_compression, out_compression=out_compression, interleaved=interleaved) if delete_folder: shutil.rmtree(test_folder) if not self._info['exhaustive']: break def _do_run(self, root, in_compression=UNCOMPRESSED, out_compression=UNCOMPRESSED, interleaved=False): assert in_compression in (UNCOMPRESSED, BZIP2, GZIP) assert out_compression in (UNCOMPRESSED, BZIP2, GZIP) os.makedirs(root) input_1, input_2 = self._setup_input(root, in_compression, interleaved) self._do_call(root, input_1, input_2, out_compression, interleaved) self._check_file_creation(root, input_1, input_2, out_compression) self._check_file_contents(root, out_compression) def _setup_input(self, root, compression, interleaved): input_files = {} for key in ("input_1", "input_2"): input_files[key] = [open(filename).read() for filename in self._files[key]] if interleaved: input_files = {"input_1": interleave(input_files["input_1"], input_files["input_2"]), "input_2": []} final_files = {} for key, values in input_files.items(): filenames = [] for idx, value in enumerate(values): value = value.encode("utf-8") filename = '%s%s.fastq' % (key, chr(ord('a') + idx)) if compression != UNCOMPRESSED: filename += "." + compression value = compress(value, compression) with open(os.path.join(root, filename), "wb") as handle: handle.write(value) filenames.append(filename) final_files[key] = filenames if 'barcodes' in self._files: with open(os.path.join(root, 'barcodes.txt'), 'w') as handle: handle.writelines(self._files['barcodes']) if 'adapters' in self._files: with open(os.path.join(root, 'adapters.txt'), 'w') as handle: handle.writelines(self._files['adapters']) return final_files["input_1"], final_files["input_2"] def _do_call(self, root, input_1, input_2, compression, interleaved): command = self._build_command(root, input_1, input_2, compression, interleaved) with open(os.devnull, "wb") as dev_null: proc = subprocess.Popen(command, stdin=dev_null, stdout=subprocess.PIPE, stderr=subprocess.PIPE, close_fds=True, preexec_fn=os.setsid, cwd=root) stdout, stderr = proc.communicate() stdout = stdout.decode("utf-8") stderr = stderr.decode("utf-8") if stdout: raise TestError("Unexpected output to STDOUT: %r" % (stdout,)) for value in self._info["stderr"]: if re.search(value, stderr) is None: raise TestError("Expected value not found in output:\n" " Searching for:\n%s\n STDERR:\n%s" % (pretty_output(value, 4), pretty_output(stderr, 4))) if proc.returncode != self._info["return_code"]: raise TestError("ERROR: Expected return-code %i, but " "AdapterRemoval returned %i:\n%s" % (self._info["return_code"], proc.returncode, pretty_output(stderr, 2))) def _check_file_creation(self, root, input_1, input_2, compression): expected_files = set(self._files["output"]) for key in ('barcodes', 'adapters'): if key in self._files: expected_files.add(key + '.txt') if compression != UNCOMPRESSED: expected_files_ = set() for value in expected_files: if not (value.endswith("settings") or value.endswith(".txt")): expected_files_.add(value + "." + compression) else: expected_files_.add(value) expected_files = expected_files_ observed_files = frozenset(os.listdir(root)) \ - frozenset(input_1) - frozenset(input_2) if expected_files - observed_files: raise TestError("ERROR: Expected output file(s) not created:\n" " Expected: %r\n Observed: %r" % (sorted(expected_files), sorted(observed_files))) elif observed_files - expected_files: raise TestError("ERROR: Unexpected output file(s) created: %r" % (sorted(observed_files - expected_files))) def _check_file_contents(self, root, compression): for filename, exp_data in sorted(self._files["output"].items()): obs_filename = os.path.join(root, filename) if compression != UNCOMPRESSED: if not filename.endswith("settings"): obs_filename += "." + compression obs_data = decompress(obs_filename) if filename.endswith("settings"): exp_data = self._mangle_settings(exp_data) obs_data = self._mangle_settings(obs_data) self._diff_file_pair_contents(os.path.join(self.root, filename), os.path.join(root, filename), exp_data, obs_data) def _diff_file_pair_contents(self, exp_filename, obs_filename, exp_data, obs_data): if exp_data != obs_data: lines = "".join(difflib.unified_diff(exp_data, obs_data, "expected", "observed")) raise TestError("ERROR: Output file(s) differ:\n" " Expected: %r\n Observed: %r\n Diff:\n%s" % (exp_filename, obs_filename, pretty_output(lines, 4))) def _build_command(self, root, input_1, input_2, compression, interleaved): command = [os.path.abspath(_EXEC)] if interleaved: command.append("--interleaved-input") if 'barcodes' in self._files: command.extend(('--barcode-list', 'barcodes.txt')) if input_1 or input_2: if compression == BZIP2: command.append("--bzip2") elif compression == GZIP: command.append("--gzip") if input_1: command.append('--file1') command.extend(input_1) if input_2: command.append('--file2') command.extend(input_2) command.extend(self._info['arguments']) return [field % {"ROOT": root} for field in command] def _is_properly_paired(self): input_1 = self._files["input_1"] input_2 = self._files["input_2"] return input_1 and len(input_1) == len(input_2) @classmethod def _mangle_settings(cls, handle): result = [] for line in handle: line = re.sub(r"RNG seed: [0-9]+", "RNG seed: Enabled", line) line = re.sub(r"AdapterRemoval ver\. .*", "AdapterRemoval ver. X.Y.Z", line) # Removed keyword to allow automatic interleaved tests line = re.sub(r" interleaved paired-end reads", r" paired-end reads", line) result.append(line) return result @classmethod def _collect_files(cls, root): result = { "input_1": [], "input_2": [], "output": {}, } def read_lines(root, filename): return open(os.path.join(root, filename)).readlines() abs_root = os.path.abspath(root) for filename in sorted(os.listdir(root)): if filename.startswith("input_1"): result["input_1"].append(os.path.join(abs_root, filename)) elif filename.startswith("input_2"): result["input_2"].append(os.path.join(abs_root, filename)) elif filename == 'barcodes.txt': result["barcodes"] = read_lines(root, filename) elif filename == 'adapters.txt': result["adapters"] = read_lines(root, filename) elif filename not in ('info.json', 'README'): result["output"][filename] = read_lines(root, filename) return result @classmethod def _read_info(cls, filename): with open(filename) as handle: text = handle.read() raw_info = json.loads(text) if not isinstance(raw_info, dict): raise TestError('\'info.json\' does not contain dictionary.') elif set(raw_info) - set(_INFO_FIELDS): raise TestError('\'info.json\' does contains unexpected fields; ' 'expected keys %r, but found keys unknown keys %r.' % (sorted(_INFO_FIELDS), sorted(set(raw_info) - set(_INFO_FIELDS)))) info = {"arguments": [], "return_code": 0, "stderr": [], 'exhaustive': True} info.update(raw_info) for key, expected_type in _INFO_FIELDS.items(): if not isinstance(info[key], expected_type): raise TestError('Type of %r in \'info.json\' is %s, not a %s.' % (key, type(info[key]), expected_type)) elif isinstance(info[key], list): for value in info[key]: if not isinstance(value, str): raise TestError('Type of value in %r in \'info.json\' ' 'is %s, not a string.' % (key, type(value))) return info @classmethod def collect(cls, root, path=()): tests = [] for filename in sorted(os.listdir(root)): filepath = os.path.join(root, filename) if os.path.isdir(filepath): tests.extend(cls.collect(filepath, path + (filename,))) elif filename == 'info.json': try: test = TestCase(root, path) except Exception as error: print_err("ERROR: %s reading test %r: %s" % (error.__class__.__name__, ' :: '.join(path), error)) continue tests.append(test) return tests def parse_args(argv): parser = argparse.ArgumentParser() parser.add_argument('work_dir', help="Directory in which to run test-cases.") parser.add_argument('source_dir', help="Directory containing test-cases.") parser.add_argument('--keep-all', help="Keep both completed and failed test folders, " "not just the folders of failed tests.") return parser.parse_args(argv) def main(argv): args = parse_args(argv) if not os.path.exists(_EXEC): print_err("ERROR: Executable does not exist: %r" % (_EXEC,)) return 1 print('Reading test-cases from %r' % (args.source_dir,)) tests = TestCase.collect(args.source_dir) if not os.path.exists(args.work_dir): os.makedirs(args.work_dir) args.work_dir = tempfile.mkdtemp(dir=args.work_dir) print('Writing test-cases results to %r' % (args.work_dir,)) n_failures = 0 print('\nRunning tests:') for idx, test in enumerate(tests, start=1): print(" %i of %i: %s " % (idx, len(tests), test.name), end='') label = 'unknown' try: for label in test.run(args.work_dir, delete_folder=not args.keep_all): print_ok(".", end="") sys.stdout.flush() except TestError as error: n_failures += 1 message = "\n ".join(str(error).split("\n")) print_err(" %s for %s:\n %s" % (error.__class__.__name__, label, message)) else: print_ok(" [OK]") if n_failures: print_err("\n%i of %i tests failed .." % (n_failures, len(tests))) else: print_ok("\nAll %i tests succeeded .." % (len(tests),)) return n_failures if __name__ == '__main__': sys.exit(main(sys.argv[1:])) adapterremoval-2.3.1/tests/regression/se/000077500000000000000000000000001350370616400204615ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/se/excl_adapter/000077500000000000000000000000001350370616400231145ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/se/excl_adapter/collapse/000077500000000000000000000000001350370616400247165ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/se/excl_adapter/collapse/info.json000066400000000000000000000001051350370616400265400ustar00rootroot00000000000000{ "arguments": ["--collapse"], "return_code": 0, "stderr": [ ] } adapterremoval-2.3.1/tests/regression/se/excl_adapter/collapse/input_1.fastq000066400000000000000000000003561350370616400273410ustar00rootroot00000000000000@ATAGCCSeq_1_2959_500/1 meta data TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTG + JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! adapterremoval-2.3.1/tests/regression/se/excl_adapter/collapse/your_output.collapsed000066400000000000000000000000001350370616400312120ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/se/excl_adapter/collapse/your_output.collapsed.truncated000066400000000000000000000000001350370616400332020ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/se/excl_adapter/collapse/your_output.discarded000066400000000000000000000000001350370616400311660ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/se/excl_adapter/collapse/your_output.settings000066400000000000000000000047701350370616400311260ustar00rootroot00000000000000AdapterRemoval ver. 2.1.7 Trimming of single-end reads [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 4051235691 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: Yes Minimum overlap (in case of collapse): 11 Minimum adapter overlap: 0 [Trimming statistics] Total number of reads: 1 Number of unaligned reads: 1 Number of well aligned reads: 0 Number of discarded mate 1 reads: 0 Number of singleton mate 1 reads: 1 Number of reads with adapters[1]: 0 Number of full-length collapsed pairs: 0 Number of truncated collapsed pairs: 0 Number of retained reads: 1 Number of retained nucleotides: 100 Average length of retained reads: 100 [Length distribution] Length Mate1 Collapsed CollapsedTruncated Discarded All 0 0 0 0 0 0 1 0 0 0 0 0 2 0 0 0 0 0 3 0 0 0 0 0 4 0 0 0 0 0 5 0 0 0 0 0 6 0 0 0 0 0 7 0 0 0 0 0 8 0 0 0 0 0 9 0 0 0 0 0 10 0 0 0 0 0 11 0 0 0 0 0 12 0 0 0 0 0 13 0 0 0 0 0 14 0 0 0 0 0 15 0 0 0 0 0 16 0 0 0 0 0 17 0 0 0 0 0 18 0 0 0 0 0 19 0 0 0 0 0 20 0 0 0 0 0 21 0 0 0 0 0 22 0 0 0 0 0 23 0 0 0 0 0 24 0 0 0 0 0 25 0 0 0 0 0 26 0 0 0 0 0 27 0 0 0 0 0 28 0 0 0 0 0 29 0 0 0 0 0 30 0 0 0 0 0 31 0 0 0 0 0 32 0 0 0 0 0 33 0 0 0 0 0 34 0 0 0 0 0 35 0 0 0 0 0 36 0 0 0 0 0 37 0 0 0 0 0 38 0 0 0 0 0 39 0 0 0 0 0 40 0 0 0 0 0 41 0 0 0 0 0 42 0 0 0 0 0 43 0 0 0 0 0 44 0 0 0 0 0 45 0 0 0 0 0 46 0 0 0 0 0 47 0 0 0 0 0 48 0 0 0 0 0 49 0 0 0 0 0 50 0 0 0 0 0 51 0 0 0 0 0 52 0 0 0 0 0 53 0 0 0 0 0 54 0 0 0 0 0 55 0 0 0 0 0 56 0 0 0 0 0 57 0 0 0 0 0 58 0 0 0 0 0 59 0 0 0 0 0 60 0 0 0 0 0 61 0 0 0 0 0 62 0 0 0 0 0 63 0 0 0 0 0 64 0 0 0 0 0 65 0 0 0 0 0 66 0 0 0 0 0 67 0 0 0 0 0 68 0 0 0 0 0 69 0 0 0 0 0 70 0 0 0 0 0 71 0 0 0 0 0 72 0 0 0 0 0 73 0 0 0 0 0 74 0 0 0 0 0 75 0 0 0 0 0 76 0 0 0 0 0 77 0 0 0 0 0 78 0 0 0 0 0 79 0 0 0 0 0 80 0 0 0 0 0 81 0 0 0 0 0 82 0 0 0 0 0 83 0 0 0 0 0 84 0 0 0 0 0 85 0 0 0 0 0 86 0 0 0 0 0 87 0 0 0 0 0 88 0 0 0 0 0 89 0 0 0 0 0 90 0 0 0 0 0 91 0 0 0 0 0 92 0 0 0 0 0 93 0 0 0 0 0 94 0 0 0 0 0 95 0 0 0 0 0 96 0 0 0 0 0 97 0 0 0 0 0 98 0 0 0 0 0 99 0 0 0 0 0 100 1 0 0 0 1 adapterremoval-2.3.1/tests/regression/se/excl_adapter/collapse/your_output.truncated000066400000000000000000000003561350370616400312530ustar00rootroot00000000000000@ATAGCCSeq_1_2959_500/1 meta data TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTG + JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! adapterremoval-2.3.1/tests/regression/se/excl_adapter/combined_output/000077500000000000000000000000001350370616400263145ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/se/excl_adapter/combined_output/collapse/000077500000000000000000000000001350370616400301165ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/se/excl_adapter/combined_output/collapse/info.json000066400000000000000000000001461350370616400317450ustar00rootroot00000000000000{ "arguments": ["--combined-output", "--collapse"], "return_code": 0, "stderr": [ ] } adapterremoval-2.3.1/tests/regression/se/excl_adapter/combined_output/collapse/input_1.fastq000066400000000000000000000003561350370616400325410ustar00rootroot00000000000000@ATAGCCSeq_1_2959_500/1 meta data TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTG + JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! adapterremoval-2.3.1/tests/regression/se/excl_adapter/combined_output/collapse/your_output.settings000066400000000000000000000047701350370616400343260ustar00rootroot00000000000000AdapterRemoval ver. 2.1.7 Trimming of single-end reads [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 4051235691 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: Yes Minimum overlap (in case of collapse): 11 Minimum adapter overlap: 0 [Trimming statistics] Total number of reads: 1 Number of unaligned reads: 1 Number of well aligned reads: 0 Number of discarded mate 1 reads: 0 Number of singleton mate 1 reads: 1 Number of reads with adapters[1]: 0 Number of full-length collapsed pairs: 0 Number of truncated collapsed pairs: 0 Number of retained reads: 1 Number of retained nucleotides: 100 Average length of retained reads: 100 [Length distribution] Length Mate1 Collapsed CollapsedTruncated Discarded All 0 0 0 0 0 0 1 0 0 0 0 0 2 0 0 0 0 0 3 0 0 0 0 0 4 0 0 0 0 0 5 0 0 0 0 0 6 0 0 0 0 0 7 0 0 0 0 0 8 0 0 0 0 0 9 0 0 0 0 0 10 0 0 0 0 0 11 0 0 0 0 0 12 0 0 0 0 0 13 0 0 0 0 0 14 0 0 0 0 0 15 0 0 0 0 0 16 0 0 0 0 0 17 0 0 0 0 0 18 0 0 0 0 0 19 0 0 0 0 0 20 0 0 0 0 0 21 0 0 0 0 0 22 0 0 0 0 0 23 0 0 0 0 0 24 0 0 0 0 0 25 0 0 0 0 0 26 0 0 0 0 0 27 0 0 0 0 0 28 0 0 0 0 0 29 0 0 0 0 0 30 0 0 0 0 0 31 0 0 0 0 0 32 0 0 0 0 0 33 0 0 0 0 0 34 0 0 0 0 0 35 0 0 0 0 0 36 0 0 0 0 0 37 0 0 0 0 0 38 0 0 0 0 0 39 0 0 0 0 0 40 0 0 0 0 0 41 0 0 0 0 0 42 0 0 0 0 0 43 0 0 0 0 0 44 0 0 0 0 0 45 0 0 0 0 0 46 0 0 0 0 0 47 0 0 0 0 0 48 0 0 0 0 0 49 0 0 0 0 0 50 0 0 0 0 0 51 0 0 0 0 0 52 0 0 0 0 0 53 0 0 0 0 0 54 0 0 0 0 0 55 0 0 0 0 0 56 0 0 0 0 0 57 0 0 0 0 0 58 0 0 0 0 0 59 0 0 0 0 0 60 0 0 0 0 0 61 0 0 0 0 0 62 0 0 0 0 0 63 0 0 0 0 0 64 0 0 0 0 0 65 0 0 0 0 0 66 0 0 0 0 0 67 0 0 0 0 0 68 0 0 0 0 0 69 0 0 0 0 0 70 0 0 0 0 0 71 0 0 0 0 0 72 0 0 0 0 0 73 0 0 0 0 0 74 0 0 0 0 0 75 0 0 0 0 0 76 0 0 0 0 0 77 0 0 0 0 0 78 0 0 0 0 0 79 0 0 0 0 0 80 0 0 0 0 0 81 0 0 0 0 0 82 0 0 0 0 0 83 0 0 0 0 0 84 0 0 0 0 0 85 0 0 0 0 0 86 0 0 0 0 0 87 0 0 0 0 0 88 0 0 0 0 0 89 0 0 0 0 0 90 0 0 0 0 0 91 0 0 0 0 0 92 0 0 0 0 0 93 0 0 0 0 0 94 0 0 0 0 0 95 0 0 0 0 0 96 0 0 0 0 0 97 0 0 0 0 0 98 0 0 0 0 0 99 0 0 0 0 0 100 1 0 0 0 1 adapterremoval-2.3.1/tests/regression/se/excl_adapter/combined_output/collapse/your_output.truncated000066400000000000000000000003561350370616400344530ustar00rootroot00000000000000@ATAGCCSeq_1_2959_500/1 meta data TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTG + JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! adapterremoval-2.3.1/tests/regression/se/excl_adapter/combined_output/discarded/000077500000000000000000000000001350370616400302365ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/se/excl_adapter/combined_output/discarded/info.json000066400000000000000000000001421350370616400320610ustar00rootroot00000000000000{ "arguments": ["--combined-output", "--minlength", "999"], "return_code": 0, "stderr": [ ] } adapterremoval-2.3.1/tests/regression/se/excl_adapter/combined_output/discarded/input_1.fastq000066400000000000000000000003561350370616400326610ustar00rootroot00000000000000@ATAGCCSeq_1_2959_500/1 meta data TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTG + JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! adapterremoval-2.3.1/tests/regression/se/excl_adapter/combined_output/discarded/your_output.settings000066400000000000000000000037631350370616400344470ustar00rootroot00000000000000AdapterRemoval ver. 2.1.7 Trimming of single-end reads [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 3702281079 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 999 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 Minimum adapter overlap: 0 [Trimming statistics] Total number of reads: 1 Number of unaligned reads: 1 Number of well aligned reads: 0 Number of discarded mate 1 reads: 1 Number of singleton mate 1 reads: 0 Number of reads with adapters[1]: 0 Number of retained reads: 0 Number of retained nucleotides: 0 Average length of retained reads: 0 [Length distribution] Length Mate1 Discarded All 0 0 0 0 1 0 0 0 2 0 0 0 3 0 0 0 4 0 0 0 5 0 0 0 6 0 0 0 7 0 0 0 8 0 0 0 9 0 0 0 10 0 0 0 11 0 0 0 12 0 0 0 13 0 0 0 14 0 0 0 15 0 0 0 16 0 0 0 17 0 0 0 18 0 0 0 19 0 0 0 20 0 0 0 21 0 0 0 22 0 0 0 23 0 0 0 24 0 0 0 25 0 0 0 26 0 0 0 27 0 0 0 28 0 0 0 29 0 0 0 30 0 0 0 31 0 0 0 32 0 0 0 33 0 0 0 34 0 0 0 35 0 0 0 36 0 0 0 37 0 0 0 38 0 0 0 39 0 0 0 40 0 0 0 41 0 0 0 42 0 0 0 43 0 0 0 44 0 0 0 45 0 0 0 46 0 0 0 47 0 0 0 48 0 0 0 49 0 0 0 50 0 0 0 51 0 0 0 52 0 0 0 53 0 0 0 54 0 0 0 55 0 0 0 56 0 0 0 57 0 0 0 58 0 0 0 59 0 0 0 60 0 0 0 61 0 0 0 62 0 0 0 63 0 0 0 64 0 0 0 65 0 0 0 66 0 0 0 67 0 0 0 68 0 0 0 69 0 0 0 70 0 0 0 71 0 0 0 72 0 0 0 73 0 0 0 74 0 0 0 75 0 0 0 76 0 0 0 77 0 0 0 78 0 0 0 79 0 0 0 80 0 0 0 81 0 0 0 82 0 0 0 83 0 0 0 84 0 0 0 85 0 0 0 86 0 0 0 87 0 0 0 88 0 0 0 89 0 0 0 90 0 0 0 91 0 0 0 92 0 0 0 93 0 0 0 94 0 0 0 95 0 0 0 96 0 0 0 97 0 0 0 98 0 0 0 99 0 0 0 100 0 1 1 your_output.truncated000066400000000000000000000000501350370616400345030ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/se/excl_adapter/combined_output/discarded@ATAGCCSeq_1_2959_500/1 meta data N + ! adapterremoval-2.3.1/tests/regression/se/excl_adapter/combined_output/retained/000077500000000000000000000000001350370616400301075ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/se/excl_adapter/combined_output/retained/info.json000066400000000000000000000001171350370616400317340ustar00rootroot00000000000000{ "arguments": ["--combined-output"], "return_code": 0, "stderr": [ ] } adapterremoval-2.3.1/tests/regression/se/excl_adapter/combined_output/retained/input_1.fastq000066400000000000000000000003561350370616400325320ustar00rootroot00000000000000@ATAGCCSeq_1_2959_500/1 meta data TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTG + JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! adapterremoval-2.3.1/tests/regression/se/excl_adapter/combined_output/retained/your_output.settings000066400000000000000000000037661350370616400343230ustar00rootroot00000000000000AdapterRemoval ver. 2.1.7 Trimming of single-end reads [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 3702281079 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 Minimum adapter overlap: 0 [Trimming statistics] Total number of reads: 1 Number of unaligned reads: 1 Number of well aligned reads: 0 Number of discarded mate 1 reads: 0 Number of singleton mate 1 reads: 1 Number of reads with adapters[1]: 0 Number of retained reads: 1 Number of retained nucleotides: 100 Average length of retained reads: 100 [Length distribution] Length Mate1 Discarded All 0 0 0 0 1 0 0 0 2 0 0 0 3 0 0 0 4 0 0 0 5 0 0 0 6 0 0 0 7 0 0 0 8 0 0 0 9 0 0 0 10 0 0 0 11 0 0 0 12 0 0 0 13 0 0 0 14 0 0 0 15 0 0 0 16 0 0 0 17 0 0 0 18 0 0 0 19 0 0 0 20 0 0 0 21 0 0 0 22 0 0 0 23 0 0 0 24 0 0 0 25 0 0 0 26 0 0 0 27 0 0 0 28 0 0 0 29 0 0 0 30 0 0 0 31 0 0 0 32 0 0 0 33 0 0 0 34 0 0 0 35 0 0 0 36 0 0 0 37 0 0 0 38 0 0 0 39 0 0 0 40 0 0 0 41 0 0 0 42 0 0 0 43 0 0 0 44 0 0 0 45 0 0 0 46 0 0 0 47 0 0 0 48 0 0 0 49 0 0 0 50 0 0 0 51 0 0 0 52 0 0 0 53 0 0 0 54 0 0 0 55 0 0 0 56 0 0 0 57 0 0 0 58 0 0 0 59 0 0 0 60 0 0 0 61 0 0 0 62 0 0 0 63 0 0 0 64 0 0 0 65 0 0 0 66 0 0 0 67 0 0 0 68 0 0 0 69 0 0 0 70 0 0 0 71 0 0 0 72 0 0 0 73 0 0 0 74 0 0 0 75 0 0 0 76 0 0 0 77 0 0 0 78 0 0 0 79 0 0 0 80 0 0 0 81 0 0 0 82 0 0 0 83 0 0 0 84 0 0 0 85 0 0 0 86 0 0 0 87 0 0 0 88 0 0 0 89 0 0 0 90 0 0 0 91 0 0 0 92 0 0 0 93 0 0 0 94 0 0 0 95 0 0 0 96 0 0 0 97 0 0 0 98 0 0 0 99 0 0 0 100 1 0 1 adapterremoval-2.3.1/tests/regression/se/excl_adapter/combined_output/retained/your_output.truncated000066400000000000000000000003561350370616400344440ustar00rootroot00000000000000@ATAGCCSeq_1_2959_500/1 meta data TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTG + JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! adapterremoval-2.3.1/tests/regression/se/excl_adapter/crlf_newlines/000077500000000000000000000000001350370616400257465ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/se/excl_adapter/crlf_newlines/info.json000066400000000000000000000000711350370616400275720ustar00rootroot00000000000000{ "arguments": [], "return_code": 0, "stderr": [ ] } adapterremoval-2.3.1/tests/regression/se/excl_adapter/crlf_newlines/input_1.fastq000066400000000000000000000003621350370616400303660ustar00rootroot00000000000000@ATAGCCSeq_1_2959_500/1 meta data TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTG + JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! adapterremoval-2.3.1/tests/regression/se/excl_adapter/crlf_newlines/your_output.discarded000066400000000000000000000000001350370616400322160ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/se/excl_adapter/crlf_newlines/your_output.settings000066400000000000000000000037661350370616400321620ustar00rootroot00000000000000AdapterRemoval ver. 2.1.7 Trimming of single-end reads [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 3702281079 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 Minimum adapter overlap: 0 [Trimming statistics] Total number of reads: 1 Number of unaligned reads: 1 Number of well aligned reads: 0 Number of discarded mate 1 reads: 0 Number of singleton mate 1 reads: 1 Number of reads with adapters[1]: 0 Number of retained reads: 1 Number of retained nucleotides: 100 Average length of retained reads: 100 [Length distribution] Length Mate1 Discarded All 0 0 0 0 1 0 0 0 2 0 0 0 3 0 0 0 4 0 0 0 5 0 0 0 6 0 0 0 7 0 0 0 8 0 0 0 9 0 0 0 10 0 0 0 11 0 0 0 12 0 0 0 13 0 0 0 14 0 0 0 15 0 0 0 16 0 0 0 17 0 0 0 18 0 0 0 19 0 0 0 20 0 0 0 21 0 0 0 22 0 0 0 23 0 0 0 24 0 0 0 25 0 0 0 26 0 0 0 27 0 0 0 28 0 0 0 29 0 0 0 30 0 0 0 31 0 0 0 32 0 0 0 33 0 0 0 34 0 0 0 35 0 0 0 36 0 0 0 37 0 0 0 38 0 0 0 39 0 0 0 40 0 0 0 41 0 0 0 42 0 0 0 43 0 0 0 44 0 0 0 45 0 0 0 46 0 0 0 47 0 0 0 48 0 0 0 49 0 0 0 50 0 0 0 51 0 0 0 52 0 0 0 53 0 0 0 54 0 0 0 55 0 0 0 56 0 0 0 57 0 0 0 58 0 0 0 59 0 0 0 60 0 0 0 61 0 0 0 62 0 0 0 63 0 0 0 64 0 0 0 65 0 0 0 66 0 0 0 67 0 0 0 68 0 0 0 69 0 0 0 70 0 0 0 71 0 0 0 72 0 0 0 73 0 0 0 74 0 0 0 75 0 0 0 76 0 0 0 77 0 0 0 78 0 0 0 79 0 0 0 80 0 0 0 81 0 0 0 82 0 0 0 83 0 0 0 84 0 0 0 85 0 0 0 86 0 0 0 87 0 0 0 88 0 0 0 89 0 0 0 90 0 0 0 91 0 0 0 92 0 0 0 93 0 0 0 94 0 0 0 95 0 0 0 96 0 0 0 97 0 0 0 98 0 0 0 99 0 0 0 100 1 0 1 adapterremoval-2.3.1/tests/regression/se/excl_adapter/crlf_newlines/your_output.truncated000066400000000000000000000003561350370616400323030ustar00rootroot00000000000000@ATAGCCSeq_1_2959_500/1 meta data TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTG + JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! adapterremoval-2.3.1/tests/regression/se/excl_adapter/defaults/000077500000000000000000000000001350370616400247235ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/se/excl_adapter/defaults/info.json000066400000000000000000000000711350370616400265470ustar00rootroot00000000000000{ "arguments": [], "return_code": 0, "stderr": [ ] } adapterremoval-2.3.1/tests/regression/se/excl_adapter/defaults/input_1.fastq000066400000000000000000000003561350370616400273460ustar00rootroot00000000000000@ATAGCCSeq_1_2959_500/1 meta data TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTG + JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! adapterremoval-2.3.1/tests/regression/se/excl_adapter/defaults/your_output.discarded000066400000000000000000000000001350370616400311730ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/se/excl_adapter/defaults/your_output.settings000066400000000000000000000037661350370616400311370ustar00rootroot00000000000000AdapterRemoval ver. 2.1.7 Trimming of single-end reads [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 3702281079 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 Minimum adapter overlap: 0 [Trimming statistics] Total number of reads: 1 Number of unaligned reads: 1 Number of well aligned reads: 0 Number of discarded mate 1 reads: 0 Number of singleton mate 1 reads: 1 Number of reads with adapters[1]: 0 Number of retained reads: 1 Number of retained nucleotides: 100 Average length of retained reads: 100 [Length distribution] Length Mate1 Discarded All 0 0 0 0 1 0 0 0 2 0 0 0 3 0 0 0 4 0 0 0 5 0 0 0 6 0 0 0 7 0 0 0 8 0 0 0 9 0 0 0 10 0 0 0 11 0 0 0 12 0 0 0 13 0 0 0 14 0 0 0 15 0 0 0 16 0 0 0 17 0 0 0 18 0 0 0 19 0 0 0 20 0 0 0 21 0 0 0 22 0 0 0 23 0 0 0 24 0 0 0 25 0 0 0 26 0 0 0 27 0 0 0 28 0 0 0 29 0 0 0 30 0 0 0 31 0 0 0 32 0 0 0 33 0 0 0 34 0 0 0 35 0 0 0 36 0 0 0 37 0 0 0 38 0 0 0 39 0 0 0 40 0 0 0 41 0 0 0 42 0 0 0 43 0 0 0 44 0 0 0 45 0 0 0 46 0 0 0 47 0 0 0 48 0 0 0 49 0 0 0 50 0 0 0 51 0 0 0 52 0 0 0 53 0 0 0 54 0 0 0 55 0 0 0 56 0 0 0 57 0 0 0 58 0 0 0 59 0 0 0 60 0 0 0 61 0 0 0 62 0 0 0 63 0 0 0 64 0 0 0 65 0 0 0 66 0 0 0 67 0 0 0 68 0 0 0 69 0 0 0 70 0 0 0 71 0 0 0 72 0 0 0 73 0 0 0 74 0 0 0 75 0 0 0 76 0 0 0 77 0 0 0 78 0 0 0 79 0 0 0 80 0 0 0 81 0 0 0 82 0 0 0 83 0 0 0 84 0 0 0 85 0 0 0 86 0 0 0 87 0 0 0 88 0 0 0 89 0 0 0 90 0 0 0 91 0 0 0 92 0 0 0 93 0 0 0 94 0 0 0 95 0 0 0 96 0 0 0 97 0 0 0 98 0 0 0 99 0 0 0 100 1 0 1 adapterremoval-2.3.1/tests/regression/se/excl_adapter/defaults/your_output.truncated000066400000000000000000000003561350370616400312600ustar00rootroot00000000000000@ATAGCCSeq_1_2959_500/1 meta data TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTG + JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! adapterremoval-2.3.1/tests/regression/se/excl_adapter/maxlength/000077500000000000000000000000001350370616400251035ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/se/excl_adapter/maxlength/info.json000066400000000000000000000001141350370616400267250ustar00rootroot00000000000000{ "arguments": ["--maxlength", "13"], "return_code": 0, "stderr": [ ] } adapterremoval-2.3.1/tests/regression/se/excl_adapter/maxlength/input_1.fastq000066400000000000000000000003561350370616400275260ustar00rootroot00000000000000@ATAGCCSeq_1_2959_500/1 meta data TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTG + JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! adapterremoval-2.3.1/tests/regression/se/excl_adapter/maxlength/your_output.discarded000066400000000000000000000003561350370616400313710ustar00rootroot00000000000000@ATAGCCSeq_1_2959_500/1 meta data TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTG + JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! adapterremoval-2.3.1/tests/regression/se/excl_adapter/maxlength/your_output.settings000066400000000000000000000037521350370616400313120ustar00rootroot00000000000000AdapterRemoval ver. 2.1.7 Trimming of single-end reads [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 1833120783 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 13 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 Minimum adapter overlap: 0 [Trimming statistics] Total number of reads: 1 Number of unaligned reads: 1 Number of well aligned reads: 0 Number of discarded mate 1 reads: 1 Number of singleton mate 1 reads: 0 Number of reads with adapters[1]: 0 Number of retained reads: 0 Number of retained nucleotides: 0 Average length of retained reads: 0 [Length distribution] Length Mate1 Discarded All 0 0 0 0 1 0 0 0 2 0 0 0 3 0 0 0 4 0 0 0 5 0 0 0 6 0 0 0 7 0 0 0 8 0 0 0 9 0 0 0 10 0 0 0 11 0 0 0 12 0 0 0 13 0 0 0 14 0 0 0 15 0 0 0 16 0 0 0 17 0 0 0 18 0 0 0 19 0 0 0 20 0 0 0 21 0 0 0 22 0 0 0 23 0 0 0 24 0 0 0 25 0 0 0 26 0 0 0 27 0 0 0 28 0 0 0 29 0 0 0 30 0 0 0 31 0 0 0 32 0 0 0 33 0 0 0 34 0 0 0 35 0 0 0 36 0 0 0 37 0 0 0 38 0 0 0 39 0 0 0 40 0 0 0 41 0 0 0 42 0 0 0 43 0 0 0 44 0 0 0 45 0 0 0 46 0 0 0 47 0 0 0 48 0 0 0 49 0 0 0 50 0 0 0 51 0 0 0 52 0 0 0 53 0 0 0 54 0 0 0 55 0 0 0 56 0 0 0 57 0 0 0 58 0 0 0 59 0 0 0 60 0 0 0 61 0 0 0 62 0 0 0 63 0 0 0 64 0 0 0 65 0 0 0 66 0 0 0 67 0 0 0 68 0 0 0 69 0 0 0 70 0 0 0 71 0 0 0 72 0 0 0 73 0 0 0 74 0 0 0 75 0 0 0 76 0 0 0 77 0 0 0 78 0 0 0 79 0 0 0 80 0 0 0 81 0 0 0 82 0 0 0 83 0 0 0 84 0 0 0 85 0 0 0 86 0 0 0 87 0 0 0 88 0 0 0 89 0 0 0 90 0 0 0 91 0 0 0 92 0 0 0 93 0 0 0 94 0 0 0 95 0 0 0 96 0 0 0 97 0 0 0 98 0 0 0 99 0 0 0 100 0 1 1 adapterremoval-2.3.1/tests/regression/se/excl_adapter/maxlength/your_output.truncated000066400000000000000000000000001350370616400314220ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/se/excl_adapter/minlength/000077500000000000000000000000001350370616400251015ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/se/excl_adapter/minlength/info.json000066400000000000000000000001151350370616400267240ustar00rootroot00000000000000{ "arguments": ["--minlength", "999"], "return_code": 0, "stderr": [ ] } adapterremoval-2.3.1/tests/regression/se/excl_adapter/minlength/input_1.fastq000066400000000000000000000003561350370616400275240ustar00rootroot00000000000000@ATAGCCSeq_1_2959_500/1 meta data TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTG + JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! adapterremoval-2.3.1/tests/regression/se/excl_adapter/minlength/your_output.discarded000066400000000000000000000003561350370616400313670ustar00rootroot00000000000000@ATAGCCSeq_1_2959_500/1 meta data TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTG + JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! adapterremoval-2.3.1/tests/regression/se/excl_adapter/minlength/your_output.settings000066400000000000000000000037631350370616400313120ustar00rootroot00000000000000AdapterRemoval ver. 2.1.7 Trimming of single-end reads [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 1752967089 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 999 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 Minimum adapter overlap: 0 [Trimming statistics] Total number of reads: 1 Number of unaligned reads: 1 Number of well aligned reads: 0 Number of discarded mate 1 reads: 1 Number of singleton mate 1 reads: 0 Number of reads with adapters[1]: 0 Number of retained reads: 0 Number of retained nucleotides: 0 Average length of retained reads: 0 [Length distribution] Length Mate1 Discarded All 0 0 0 0 1 0 0 0 2 0 0 0 3 0 0 0 4 0 0 0 5 0 0 0 6 0 0 0 7 0 0 0 8 0 0 0 9 0 0 0 10 0 0 0 11 0 0 0 12 0 0 0 13 0 0 0 14 0 0 0 15 0 0 0 16 0 0 0 17 0 0 0 18 0 0 0 19 0 0 0 20 0 0 0 21 0 0 0 22 0 0 0 23 0 0 0 24 0 0 0 25 0 0 0 26 0 0 0 27 0 0 0 28 0 0 0 29 0 0 0 30 0 0 0 31 0 0 0 32 0 0 0 33 0 0 0 34 0 0 0 35 0 0 0 36 0 0 0 37 0 0 0 38 0 0 0 39 0 0 0 40 0 0 0 41 0 0 0 42 0 0 0 43 0 0 0 44 0 0 0 45 0 0 0 46 0 0 0 47 0 0 0 48 0 0 0 49 0 0 0 50 0 0 0 51 0 0 0 52 0 0 0 53 0 0 0 54 0 0 0 55 0 0 0 56 0 0 0 57 0 0 0 58 0 0 0 59 0 0 0 60 0 0 0 61 0 0 0 62 0 0 0 63 0 0 0 64 0 0 0 65 0 0 0 66 0 0 0 67 0 0 0 68 0 0 0 69 0 0 0 70 0 0 0 71 0 0 0 72 0 0 0 73 0 0 0 74 0 0 0 75 0 0 0 76 0 0 0 77 0 0 0 78 0 0 0 79 0 0 0 80 0 0 0 81 0 0 0 82 0 0 0 83 0 0 0 84 0 0 0 85 0 0 0 86 0 0 0 87 0 0 0 88 0 0 0 89 0 0 0 90 0 0 0 91 0 0 0 92 0 0 0 93 0 0 0 94 0 0 0 95 0 0 0 96 0 0 0 97 0 0 0 98 0 0 0 99 0 0 0 100 0 1 1 adapterremoval-2.3.1/tests/regression/se/excl_adapter/minlength/your_output.truncated000066400000000000000000000000001350370616400314200ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/se/excl_adapter/trimns/000077500000000000000000000000001350370616400244305ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/se/excl_adapter/trimns/excl_ns/000077500000000000000000000000001350370616400260635ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/se/excl_adapter/trimns/excl_ns/info.json000066400000000000000000000001031350370616400277030ustar00rootroot00000000000000{ "arguments": ["--trimns"], "return_code": 0, "stderr": [ ] } adapterremoval-2.3.1/tests/regression/se/excl_adapter/trimns/excl_ns/input_1.fastq000066400000000000000000000003561350370616400305060ustar00rootroot00000000000000@ATAGCCSeq_1_2959_500/1 meta data TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTG + JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! adapterremoval-2.3.1/tests/regression/se/excl_adapter/trimns/excl_ns/your_output.discarded000066400000000000000000000000001350370616400323330ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/se/excl_adapter/trimns/excl_ns/your_output.settings000066400000000000000000000037661350370616400322770ustar00rootroot00000000000000AdapterRemoval ver. 2.1.7 Trimming of single-end reads [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 217798732 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: Yes Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 Minimum adapter overlap: 0 [Trimming statistics] Total number of reads: 1 Number of unaligned reads: 1 Number of well aligned reads: 0 Number of discarded mate 1 reads: 0 Number of singleton mate 1 reads: 1 Number of reads with adapters[1]: 0 Number of retained reads: 1 Number of retained nucleotides: 100 Average length of retained reads: 100 [Length distribution] Length Mate1 Discarded All 0 0 0 0 1 0 0 0 2 0 0 0 3 0 0 0 4 0 0 0 5 0 0 0 6 0 0 0 7 0 0 0 8 0 0 0 9 0 0 0 10 0 0 0 11 0 0 0 12 0 0 0 13 0 0 0 14 0 0 0 15 0 0 0 16 0 0 0 17 0 0 0 18 0 0 0 19 0 0 0 20 0 0 0 21 0 0 0 22 0 0 0 23 0 0 0 24 0 0 0 25 0 0 0 26 0 0 0 27 0 0 0 28 0 0 0 29 0 0 0 30 0 0 0 31 0 0 0 32 0 0 0 33 0 0 0 34 0 0 0 35 0 0 0 36 0 0 0 37 0 0 0 38 0 0 0 39 0 0 0 40 0 0 0 41 0 0 0 42 0 0 0 43 0 0 0 44 0 0 0 45 0 0 0 46 0 0 0 47 0 0 0 48 0 0 0 49 0 0 0 50 0 0 0 51 0 0 0 52 0 0 0 53 0 0 0 54 0 0 0 55 0 0 0 56 0 0 0 57 0 0 0 58 0 0 0 59 0 0 0 60 0 0 0 61 0 0 0 62 0 0 0 63 0 0 0 64 0 0 0 65 0 0 0 66 0 0 0 67 0 0 0 68 0 0 0 69 0 0 0 70 0 0 0 71 0 0 0 72 0 0 0 73 0 0 0 74 0 0 0 75 0 0 0 76 0 0 0 77 0 0 0 78 0 0 0 79 0 0 0 80 0 0 0 81 0 0 0 82 0 0 0 83 0 0 0 84 0 0 0 85 0 0 0 86 0 0 0 87 0 0 0 88 0 0 0 89 0 0 0 90 0 0 0 91 0 0 0 92 0 0 0 93 0 0 0 94 0 0 0 95 0 0 0 96 0 0 0 97 0 0 0 98 0 0 0 99 0 0 0 100 1 0 1 adapterremoval-2.3.1/tests/regression/se/excl_adapter/trimns/excl_ns/your_output.truncated000066400000000000000000000003561350370616400324200ustar00rootroot00000000000000@ATAGCCSeq_1_2959_500/1 meta data TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTG + JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! adapterremoval-2.3.1/tests/regression/se/excl_adapter/trimns/incl_ns/000077500000000000000000000000001350370616400260555ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/se/excl_adapter/trimns/incl_ns/info.json000066400000000000000000000001031350370616400276750ustar00rootroot00000000000000{ "arguments": ["--trimns"], "return_code": 0, "stderr": [ ] } adapterremoval-2.3.1/tests/regression/se/excl_adapter/trimns/incl_ns/input_1.fastq000066400000000000000000000003561350370616400305000ustar00rootroot00000000000000@ATAGCCSeq_1_2959_500/1 meta data TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGNTCAACGATTAAANNNNNN + JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! adapterremoval-2.3.1/tests/regression/se/excl_adapter/trimns/incl_ns/your_output.discarded000066400000000000000000000000001350370616400323250ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/se/excl_adapter/trimns/incl_ns/your_output.settings000066400000000000000000000036741350370616400322670ustar00rootroot00000000000000AdapterRemoval ver. 2.1.7 Trimming of single-end reads [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 87921694 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: Yes Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 Minimum adapter overlap: 0 [Trimming statistics] Total number of reads: 1 Number of unaligned reads: 1 Number of well aligned reads: 0 Number of discarded mate 1 reads: 0 Number of singleton mate 1 reads: 1 Number of reads with adapters[1]: 0 Number of retained reads: 1 Number of retained nucleotides: 94 Average length of retained reads: 94 [Length distribution] Length Mate1 Discarded All 0 0 0 0 1 0 0 0 2 0 0 0 3 0 0 0 4 0 0 0 5 0 0 0 6 0 0 0 7 0 0 0 8 0 0 0 9 0 0 0 10 0 0 0 11 0 0 0 12 0 0 0 13 0 0 0 14 0 0 0 15 0 0 0 16 0 0 0 17 0 0 0 18 0 0 0 19 0 0 0 20 0 0 0 21 0 0 0 22 0 0 0 23 0 0 0 24 0 0 0 25 0 0 0 26 0 0 0 27 0 0 0 28 0 0 0 29 0 0 0 30 0 0 0 31 0 0 0 32 0 0 0 33 0 0 0 34 0 0 0 35 0 0 0 36 0 0 0 37 0 0 0 38 0 0 0 39 0 0 0 40 0 0 0 41 0 0 0 42 0 0 0 43 0 0 0 44 0 0 0 45 0 0 0 46 0 0 0 47 0 0 0 48 0 0 0 49 0 0 0 50 0 0 0 51 0 0 0 52 0 0 0 53 0 0 0 54 0 0 0 55 0 0 0 56 0 0 0 57 0 0 0 58 0 0 0 59 0 0 0 60 0 0 0 61 0 0 0 62 0 0 0 63 0 0 0 64 0 0 0 65 0 0 0 66 0 0 0 67 0 0 0 68 0 0 0 69 0 0 0 70 0 0 0 71 0 0 0 72 0 0 0 73 0 0 0 74 0 0 0 75 0 0 0 76 0 0 0 77 0 0 0 78 0 0 0 79 0 0 0 80 0 0 0 81 0 0 0 82 0 0 0 83 0 0 0 84 0 0 0 85 0 0 0 86 0 0 0 87 0 0 0 88 0 0 0 89 0 0 0 90 0 0 0 91 0 0 0 92 0 0 0 93 0 0 0 94 1 0 1 adapterremoval-2.3.1/tests/regression/se/excl_adapter/trimns/incl_ns/your_output.truncated000066400000000000000000000003421350370616400324050ustar00rootroot00000000000000@ATAGCCSeq_1_2959_500/1 meta data TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGNTCAACGATTAAA + JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:977775532 adapterremoval-2.3.1/tests/regression/se/excl_adapter/trimqualities/000077500000000000000000000000001350370616400260105ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/se/excl_adapter/trimqualities/default/000077500000000000000000000000001350370616400274345ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/se/excl_adapter/trimqualities/default/info.json000066400000000000000000000001121350370616400312540ustar00rootroot00000000000000{ "arguments": ["--trimqualities"], "return_code": 0, "stderr": [ ] } adapterremoval-2.3.1/tests/regression/se/excl_adapter/trimqualities/default/input_1.fastq000066400000000000000000000003561350370616400320570ustar00rootroot00000000000000@ATAGCCSeq_1_2959_500/1 meta data TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTG + JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! adapterremoval-2.3.1/tests/regression/se/excl_adapter/trimqualities/default/your_output.discarded000066400000000000000000000000001350370616400337040ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/se/excl_adapter/trimqualities/default/your_output.settings000066400000000000000000000037531350370616400336440ustar00rootroot00000000000000AdapterRemoval ver. 2.1.7 Trimming of single-end reads [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 1434085985 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: Yes Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 Minimum adapter overlap: 0 [Trimming statistics] Total number of reads: 1 Number of unaligned reads: 1 Number of well aligned reads: 0 Number of discarded mate 1 reads: 0 Number of singleton mate 1 reads: 1 Number of reads with adapters[1]: 0 Number of retained reads: 1 Number of retained nucleotides: 99 Average length of retained reads: 99 [Length distribution] Length Mate1 Discarded All 0 0 0 0 1 0 0 0 2 0 0 0 3 0 0 0 4 0 0 0 5 0 0 0 6 0 0 0 7 0 0 0 8 0 0 0 9 0 0 0 10 0 0 0 11 0 0 0 12 0 0 0 13 0 0 0 14 0 0 0 15 0 0 0 16 0 0 0 17 0 0 0 18 0 0 0 19 0 0 0 20 0 0 0 21 0 0 0 22 0 0 0 23 0 0 0 24 0 0 0 25 0 0 0 26 0 0 0 27 0 0 0 28 0 0 0 29 0 0 0 30 0 0 0 31 0 0 0 32 0 0 0 33 0 0 0 34 0 0 0 35 0 0 0 36 0 0 0 37 0 0 0 38 0 0 0 39 0 0 0 40 0 0 0 41 0 0 0 42 0 0 0 43 0 0 0 44 0 0 0 45 0 0 0 46 0 0 0 47 0 0 0 48 0 0 0 49 0 0 0 50 0 0 0 51 0 0 0 52 0 0 0 53 0 0 0 54 0 0 0 55 0 0 0 56 0 0 0 57 0 0 0 58 0 0 0 59 0 0 0 60 0 0 0 61 0 0 0 62 0 0 0 63 0 0 0 64 0 0 0 65 0 0 0 66 0 0 0 67 0 0 0 68 0 0 0 69 0 0 0 70 0 0 0 71 0 0 0 72 0 0 0 73 0 0 0 74 0 0 0 75 0 0 0 76 0 0 0 77 0 0 0 78 0 0 0 79 0 0 0 80 0 0 0 81 0 0 0 82 0 0 0 83 0 0 0 84 0 0 0 85 0 0 0 86 0 0 0 87 0 0 0 88 0 0 0 89 0 0 0 90 0 0 0 91 0 0 0 92 0 0 0 93 0 0 0 94 0 0 0 95 0 0 0 96 0 0 0 97 0 0 0 98 0 0 0 99 1 0 1 adapterremoval-2.3.1/tests/regression/se/excl_adapter/trimqualities/default/your_output.truncated000066400000000000000000000003541350370616400337670ustar00rootroot00000000000000@ATAGCCSeq_1_2959_500/1 meta data TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCT + JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)' adapterremoval-2.3.1/tests/regression/se/excl_adapter/trimqualities/minq31/000077500000000000000000000000001350370616400271205ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/se/excl_adapter/trimqualities/minq31/info.json000066400000000000000000000001401350370616400307410ustar00rootroot00000000000000{ "arguments": ["--trimqualities", "--minquality", "31"], "return_code": 0, "stderr": [ ] } adapterremoval-2.3.1/tests/regression/se/excl_adapter/trimqualities/minq31/input_1.fastq000066400000000000000000000003561350370616400315430ustar00rootroot00000000000000@ATAGCCSeq_1_2959_500/1 meta data TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTG + JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! adapterremoval-2.3.1/tests/regression/se/excl_adapter/trimqualities/minq31/your_output.discarded000066400000000000000000000000001350370616400333700ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/se/excl_adapter/trimqualities/minq31/your_output.settings000066400000000000000000000033141350370616400333210ustar00rootroot00000000000000AdapterRemoval ver. 2.1.7 Trimming of single-end reads [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 1585058107 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 31: Yes Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 Minimum adapter overlap: 0 [Trimming statistics] Total number of reads: 1 Number of unaligned reads: 1 Number of well aligned reads: 0 Number of discarded mate 1 reads: 0 Number of singleton mate 1 reads: 1 Number of reads with adapters[1]: 0 Number of retained reads: 1 Number of retained nucleotides: 67 Average length of retained reads: 67 [Length distribution] Length Mate1 Discarded All 0 0 0 0 1 0 0 0 2 0 0 0 3 0 0 0 4 0 0 0 5 0 0 0 6 0 0 0 7 0 0 0 8 0 0 0 9 0 0 0 10 0 0 0 11 0 0 0 12 0 0 0 13 0 0 0 14 0 0 0 15 0 0 0 16 0 0 0 17 0 0 0 18 0 0 0 19 0 0 0 20 0 0 0 21 0 0 0 22 0 0 0 23 0 0 0 24 0 0 0 25 0 0 0 26 0 0 0 27 0 0 0 28 0 0 0 29 0 0 0 30 0 0 0 31 0 0 0 32 0 0 0 33 0 0 0 34 0 0 0 35 0 0 0 36 0 0 0 37 0 0 0 38 0 0 0 39 0 0 0 40 0 0 0 41 0 0 0 42 0 0 0 43 0 0 0 44 0 0 0 45 0 0 0 46 0 0 0 47 0 0 0 48 0 0 0 49 0 0 0 50 0 0 0 51 0 0 0 52 0 0 0 53 0 0 0 54 0 0 0 55 0 0 0 56 0 0 0 57 0 0 0 58 0 0 0 59 0 0 0 60 0 0 0 61 0 0 0 62 0 0 0 63 0 0 0 64 0 0 0 65 0 0 0 66 0 0 0 67 1 0 1 adapterremoval-2.3.1/tests/regression/se/excl_adapter/trimqualities/minq31/your_output.truncated000066400000000000000000000002541350370616400334520ustar00rootroot00000000000000@ATAGCCSeq_1_2959_500/1 meta data TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTAT + JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A adapterremoval-2.3.1/tests/regression/se/incl_adapter/000077500000000000000000000000001350370616400231065ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/se/incl_adapter/collapse/000077500000000000000000000000001350370616400247105ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/se/incl_adapter/collapse/info.json000066400000000000000000000001051350370616400265320ustar00rootroot00000000000000{ "arguments": ["--collapse"], "return_code": 0, "stderr": [ ] } adapterremoval-2.3.1/tests/regression/se/incl_adapter/collapse/input_1.fastq000066400000000000000000000003551350370616400273320ustar00rootroot00000000000000@AAGGGCSeq_1_5180_50/1 meta data ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG + IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! adapterremoval-2.3.1/tests/regression/se/incl_adapter/collapse/your_output.collapsed000066400000000000000000000002131350370616400312120ustar00rootroot00000000000000@M_AAGGGCSeq_1_5180_50/1 meta data ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCT + IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECC adapterremoval-2.3.1/tests/regression/se/incl_adapter/collapse/your_output.collapsed.truncated000066400000000000000000000000001350370616400331740ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/se/incl_adapter/collapse/your_output.discarded000066400000000000000000000000001350370616400311600ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/se/incl_adapter/collapse/your_output.settings000066400000000000000000000035521350370616400311150ustar00rootroot00000000000000AdapterRemoval ver. 2.1.7 Trimming of single-end reads [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 566778642 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: Yes Minimum overlap (in case of collapse): 11 Minimum adapter overlap: 0 [Trimming statistics] Total number of reads: 1 Number of unaligned reads: 0 Number of well aligned reads: 1 Number of discarded mate 1 reads: 0 Number of singleton mate 1 reads: 0 Number of reads with adapters[1]: 1 Number of full-length collapsed pairs: 1 Number of truncated collapsed pairs: 0 Number of retained reads: 1 Number of retained nucleotides: 50 Average length of retained reads: 50 [Length distribution] Length Mate1 Collapsed CollapsedTruncated Discarded All 0 0 0 0 0 0 1 0 0 0 0 0 2 0 0 0 0 0 3 0 0 0 0 0 4 0 0 0 0 0 5 0 0 0 0 0 6 0 0 0 0 0 7 0 0 0 0 0 8 0 0 0 0 0 9 0 0 0 0 0 10 0 0 0 0 0 11 0 0 0 0 0 12 0 0 0 0 0 13 0 0 0 0 0 14 0 0 0 0 0 15 0 0 0 0 0 16 0 0 0 0 0 17 0 0 0 0 0 18 0 0 0 0 0 19 0 0 0 0 0 20 0 0 0 0 0 21 0 0 0 0 0 22 0 0 0 0 0 23 0 0 0 0 0 24 0 0 0 0 0 25 0 0 0 0 0 26 0 0 0 0 0 27 0 0 0 0 0 28 0 0 0 0 0 29 0 0 0 0 0 30 0 0 0 0 0 31 0 0 0 0 0 32 0 0 0 0 0 33 0 0 0 0 0 34 0 0 0 0 0 35 0 0 0 0 0 36 0 0 0 0 0 37 0 0 0 0 0 38 0 0 0 0 0 39 0 0 0 0 0 40 0 0 0 0 0 41 0 0 0 0 0 42 0 0 0 0 0 43 0 0 0 0 0 44 0 0 0 0 0 45 0 0 0 0 0 46 0 0 0 0 0 47 0 0 0 0 0 48 0 0 0 0 0 49 0 0 0 0 0 50 0 1 0 0 1 adapterremoval-2.3.1/tests/regression/se/incl_adapter/collapse/your_output.truncated000066400000000000000000000000001350370616400312270ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/se/incl_adapter/collapse_truncated/000077500000000000000000000000001350370616400267615ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/se/incl_adapter/collapse_truncated/info.json000066400000000000000000000001211350370616400306010ustar00rootroot00000000000000{ "arguments": ["--collapse", "--trimns"], "return_code": 0, "stderr": [ ] } adapterremoval-2.3.1/tests/regression/se/incl_adapter/collapse_truncated/input_1.fastq000066400000000000000000000003551350370616400314030ustar00rootroot00000000000000@AAGGGCSeq_1_5180_50/1 meta data ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCNAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG + IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! adapterremoval-2.3.1/tests/regression/se/incl_adapter/collapse_truncated/your_output.collapsed000066400000000000000000000000001350370616400332550ustar00rootroot00000000000000your_output.collapsed.truncated000066400000000000000000000002121350370616400351730ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/se/incl_adapter/collapse_truncated@MT_AAGGGCSeq_1_5180_50/1 meta data ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCC + IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDEC adapterremoval-2.3.1/tests/regression/se/incl_adapter/collapse_truncated/your_output.discarded000066400000000000000000000000001350370616400332310ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/se/incl_adapter/collapse_truncated/your_output.settings000066400000000000000000000035361350370616400331700ustar00rootroot00000000000000AdapterRemoval ver. 2.1.7 Trimming of single-end reads [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 566778642 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: Yes Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: Yes Minimum overlap (in case of collapse): 11 Minimum adapter overlap: 0 [Trimming statistics] Total number of reads: 1 Number of unaligned reads: 0 Number of well aligned reads: 1 Number of discarded mate 1 reads: 0 Number of singleton mate 1 reads: 0 Number of reads with adapters[1]: 1 Number of full-length collapsed pairs: 0 Number of truncated collapsed pairs: 1 Number of retained reads: 1 Number of retained nucleotides: 49 Average length of retained reads: 49 [Length distribution] Length Mate1 Collapsed CollapsedTruncated Discarded All 0 0 0 0 0 0 1 0 0 0 0 0 2 0 0 0 0 0 3 0 0 0 0 0 4 0 0 0 0 0 5 0 0 0 0 0 6 0 0 0 0 0 7 0 0 0 0 0 8 0 0 0 0 0 9 0 0 0 0 0 10 0 0 0 0 0 11 0 0 0 0 0 12 0 0 0 0 0 13 0 0 0 0 0 14 0 0 0 0 0 15 0 0 0 0 0 16 0 0 0 0 0 17 0 0 0 0 0 18 0 0 0 0 0 19 0 0 0 0 0 20 0 0 0 0 0 21 0 0 0 0 0 22 0 0 0 0 0 23 0 0 0 0 0 24 0 0 0 0 0 25 0 0 0 0 0 26 0 0 0 0 0 27 0 0 0 0 0 28 0 0 0 0 0 29 0 0 0 0 0 30 0 0 0 0 0 31 0 0 0 0 0 32 0 0 0 0 0 33 0 0 0 0 0 34 0 0 0 0 0 35 0 0 0 0 0 36 0 0 0 0 0 37 0 0 0 0 0 38 0 0 0 0 0 39 0 0 0 0 0 40 0 0 0 0 0 41 0 0 0 0 0 42 0 0 0 0 0 43 0 0 0 0 0 44 0 0 0 0 0 45 0 0 0 0 0 46 0 0 0 0 0 47 0 0 0 0 0 48 0 0 0 0 0 49 0 0 1 0 1 adapterremoval-2.3.1/tests/regression/se/incl_adapter/collapse_truncated/your_output.truncated000066400000000000000000000000001350370616400333000ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/se/incl_adapter/combined_output/000077500000000000000000000000001350370616400263065ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/se/incl_adapter/combined_output/collapse/000077500000000000000000000000001350370616400301105ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/se/incl_adapter/combined_output/collapse/info.json000066400000000000000000000001461350370616400317370ustar00rootroot00000000000000{ "arguments": ["--combined-output", "--collapse"], "return_code": 0, "stderr": [ ] } adapterremoval-2.3.1/tests/regression/se/incl_adapter/combined_output/collapse/input_1.fastq000066400000000000000000000003551350370616400325320ustar00rootroot00000000000000@AAGGGCSeq_1_5180_50/1 meta data ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG + IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! adapterremoval-2.3.1/tests/regression/se/incl_adapter/combined_output/collapse/your_output.settings000066400000000000000000000035531350370616400343160ustar00rootroot00000000000000AdapterRemoval ver. 2.1.7 Trimming of single-end reads [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 1432823771 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: Yes Minimum overlap (in case of collapse): 11 Minimum adapter overlap: 0 [Trimming statistics] Total number of reads: 1 Number of unaligned reads: 0 Number of well aligned reads: 1 Number of discarded mate 1 reads: 0 Number of singleton mate 1 reads: 0 Number of reads with adapters[1]: 1 Number of full-length collapsed pairs: 1 Number of truncated collapsed pairs: 0 Number of retained reads: 1 Number of retained nucleotides: 50 Average length of retained reads: 50 [Length distribution] Length Mate1 Collapsed CollapsedTruncated Discarded All 0 0 0 0 0 0 1 0 0 0 0 0 2 0 0 0 0 0 3 0 0 0 0 0 4 0 0 0 0 0 5 0 0 0 0 0 6 0 0 0 0 0 7 0 0 0 0 0 8 0 0 0 0 0 9 0 0 0 0 0 10 0 0 0 0 0 11 0 0 0 0 0 12 0 0 0 0 0 13 0 0 0 0 0 14 0 0 0 0 0 15 0 0 0 0 0 16 0 0 0 0 0 17 0 0 0 0 0 18 0 0 0 0 0 19 0 0 0 0 0 20 0 0 0 0 0 21 0 0 0 0 0 22 0 0 0 0 0 23 0 0 0 0 0 24 0 0 0 0 0 25 0 0 0 0 0 26 0 0 0 0 0 27 0 0 0 0 0 28 0 0 0 0 0 29 0 0 0 0 0 30 0 0 0 0 0 31 0 0 0 0 0 32 0 0 0 0 0 33 0 0 0 0 0 34 0 0 0 0 0 35 0 0 0 0 0 36 0 0 0 0 0 37 0 0 0 0 0 38 0 0 0 0 0 39 0 0 0 0 0 40 0 0 0 0 0 41 0 0 0 0 0 42 0 0 0 0 0 43 0 0 0 0 0 44 0 0 0 0 0 45 0 0 0 0 0 46 0 0 0 0 0 47 0 0 0 0 0 48 0 0 0 0 0 49 0 0 0 0 0 50 0 1 0 0 1 adapterremoval-2.3.1/tests/regression/se/incl_adapter/combined_output/collapse/your_output.truncated000066400000000000000000000002131350370616400344350ustar00rootroot00000000000000@M_AAGGGCSeq_1_5180_50/1 meta data ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCT + IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECC adapterremoval-2.3.1/tests/regression/se/incl_adapter/combined_output/collapse_truncated/000077500000000000000000000000001350370616400321615ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/se/incl_adapter/combined_output/collapse_truncated/info.json000066400000000000000000000001621350370616400340060ustar00rootroot00000000000000{ "arguments": ["--combined-output", "--collapse", "--trimns"], "return_code": 0, "stderr": [ ] } input_1.fastq000066400000000000000000000003551350370616400345240ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/se/incl_adapter/combined_output/collapse_truncated@AAGGGCSeq_1_5180_50/1 meta data ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCNAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG + IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! your_output.settings000066400000000000000000000035371350370616400363120ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/se/incl_adapter/combined_output/collapse_truncatedAdapterRemoval ver. 2.1.7 Trimming of single-end reads [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 1432823771 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: Yes Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: Yes Minimum overlap (in case of collapse): 11 Minimum adapter overlap: 0 [Trimming statistics] Total number of reads: 1 Number of unaligned reads: 0 Number of well aligned reads: 1 Number of discarded mate 1 reads: 0 Number of singleton mate 1 reads: 0 Number of reads with adapters[1]: 1 Number of full-length collapsed pairs: 0 Number of truncated collapsed pairs: 1 Number of retained reads: 1 Number of retained nucleotides: 49 Average length of retained reads: 49 [Length distribution] Length Mate1 Collapsed CollapsedTruncated Discarded All 0 0 0 0 0 0 1 0 0 0 0 0 2 0 0 0 0 0 3 0 0 0 0 0 4 0 0 0 0 0 5 0 0 0 0 0 6 0 0 0 0 0 7 0 0 0 0 0 8 0 0 0 0 0 9 0 0 0 0 0 10 0 0 0 0 0 11 0 0 0 0 0 12 0 0 0 0 0 13 0 0 0 0 0 14 0 0 0 0 0 15 0 0 0 0 0 16 0 0 0 0 0 17 0 0 0 0 0 18 0 0 0 0 0 19 0 0 0 0 0 20 0 0 0 0 0 21 0 0 0 0 0 22 0 0 0 0 0 23 0 0 0 0 0 24 0 0 0 0 0 25 0 0 0 0 0 26 0 0 0 0 0 27 0 0 0 0 0 28 0 0 0 0 0 29 0 0 0 0 0 30 0 0 0 0 0 31 0 0 0 0 0 32 0 0 0 0 0 33 0 0 0 0 0 34 0 0 0 0 0 35 0 0 0 0 0 36 0 0 0 0 0 37 0 0 0 0 0 38 0 0 0 0 0 39 0 0 0 0 0 40 0 0 0 0 0 41 0 0 0 0 0 42 0 0 0 0 0 43 0 0 0 0 0 44 0 0 0 0 0 45 0 0 0 0 0 46 0 0 0 0 0 47 0 0 0 0 0 48 0 0 0 0 0 49 0 0 1 0 1 your_output.truncated000066400000000000000000000002121350370616400364260ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/se/incl_adapter/combined_output/collapse_truncated@MT_AAGGGCSeq_1_5180_50/1 meta data ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCC + IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDEC adapterremoval-2.3.1/tests/regression/se/incl_adapter/combined_output/discarded/000077500000000000000000000000001350370616400302305ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/se/incl_adapter/combined_output/discarded/info.json000066400000000000000000000001421350370616400320530ustar00rootroot00000000000000{ "arguments": ["--combined-output", "--minlength", "999"], "return_code": 0, "stderr": [ ] } adapterremoval-2.3.1/tests/regression/se/incl_adapter/combined_output/discarded/input_1.fastq000066400000000000000000000003431350370616400326470ustar00rootroot00000000000000@AAGGGCSeq_1_5180_50/1 ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG + IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! adapterremoval-2.3.1/tests/regression/se/incl_adapter/combined_output/discarded/your_output.settings000066400000000000000000000030601350370616400344270ustar00rootroot00000000000000AdapterRemoval ver. 2.1.7 Trimming of single-end reads [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 1529034138 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 999 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 Minimum adapter overlap: 0 [Trimming statistics] Total number of reads: 1 Number of unaligned reads: 0 Number of well aligned reads: 1 Number of discarded mate 1 reads: 1 Number of singleton mate 1 reads: 0 Number of reads with adapters[1]: 1 Number of retained reads: 0 Number of retained nucleotides: 0 Average length of retained reads: 0 [Length distribution] Length Mate1 Discarded All 0 0 0 0 1 0 0 0 2 0 0 0 3 0 0 0 4 0 0 0 5 0 0 0 6 0 0 0 7 0 0 0 8 0 0 0 9 0 0 0 10 0 0 0 11 0 0 0 12 0 0 0 13 0 0 0 14 0 0 0 15 0 0 0 16 0 0 0 17 0 0 0 18 0 0 0 19 0 0 0 20 0 0 0 21 0 0 0 22 0 0 0 23 0 0 0 24 0 0 0 25 0 0 0 26 0 0 0 27 0 0 0 28 0 0 0 29 0 0 0 30 0 0 0 31 0 0 0 32 0 0 0 33 0 0 0 34 0 0 0 35 0 0 0 36 0 0 0 37 0 0 0 38 0 0 0 39 0 0 0 40 0 0 0 41 0 0 0 42 0 0 0 43 0 0 0 44 0 0 0 45 0 0 0 46 0 0 0 47 0 0 0 48 0 0 0 49 0 0 0 50 0 1 1 your_output.truncated000066400000000000000000000000351350370616400345000ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/se/incl_adapter/combined_output/discarded@AAGGGCSeq_1_5180_50/1 N + ! adapterremoval-2.3.1/tests/regression/se/incl_adapter/combined_output/retained/000077500000000000000000000000001350370616400301015ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/se/incl_adapter/combined_output/retained/info.json000066400000000000000000000001171350370616400317260ustar00rootroot00000000000000{ "arguments": ["--combined-output"], "return_code": 0, "stderr": [ ] } adapterremoval-2.3.1/tests/regression/se/incl_adapter/combined_output/retained/input_1.fastq000066400000000000000000000003551350370616400325230ustar00rootroot00000000000000@AAGGGCSeq_1_5180_50/1 meta data ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG + IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! adapterremoval-2.3.1/tests/regression/se/incl_adapter/combined_output/retained/your_output.settings000066400000000000000000000030611350370616400343010ustar00rootroot00000000000000AdapterRemoval ver. 2.1.7 Trimming of single-end reads [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 1756794576 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 Minimum adapter overlap: 0 [Trimming statistics] Total number of reads: 1 Number of unaligned reads: 0 Number of well aligned reads: 1 Number of discarded mate 1 reads: 0 Number of singleton mate 1 reads: 1 Number of reads with adapters[1]: 1 Number of retained reads: 1 Number of retained nucleotides: 50 Average length of retained reads: 50 [Length distribution] Length Mate1 Discarded All 0 0 0 0 1 0 0 0 2 0 0 0 3 0 0 0 4 0 0 0 5 0 0 0 6 0 0 0 7 0 0 0 8 0 0 0 9 0 0 0 10 0 0 0 11 0 0 0 12 0 0 0 13 0 0 0 14 0 0 0 15 0 0 0 16 0 0 0 17 0 0 0 18 0 0 0 19 0 0 0 20 0 0 0 21 0 0 0 22 0 0 0 23 0 0 0 24 0 0 0 25 0 0 0 26 0 0 0 27 0 0 0 28 0 0 0 29 0 0 0 30 0 0 0 31 0 0 0 32 0 0 0 33 0 0 0 34 0 0 0 35 0 0 0 36 0 0 0 37 0 0 0 38 0 0 0 39 0 0 0 40 0 0 0 41 0 0 0 42 0 0 0 43 0 0 0 44 0 0 0 45 0 0 0 46 0 0 0 47 0 0 0 48 0 0 0 49 0 0 0 50 1 0 1 adapterremoval-2.3.1/tests/regression/se/incl_adapter/combined_output/retained/your_output.truncated000066400000000000000000000002111350370616400344240ustar00rootroot00000000000000@AAGGGCSeq_1_5180_50/1 meta data ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCT + IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECC adapterremoval-2.3.1/tests/regression/se/incl_adapter/crlf_newlines/000077500000000000000000000000001350370616400257405ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/se/incl_adapter/crlf_newlines/info.json000066400000000000000000000000711350370616400275640ustar00rootroot00000000000000{ "arguments": [], "return_code": 0, "stderr": [ ] } adapterremoval-2.3.1/tests/regression/se/incl_adapter/crlf_newlines/input_1.fastq000066400000000000000000000003471350370616400303630ustar00rootroot00000000000000@AAGGGCSeq_1_5180_50/1 ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG + IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! adapterremoval-2.3.1/tests/regression/se/incl_adapter/crlf_newlines/your_output.discarded000066400000000000000000000000001350370616400322100ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/se/incl_adapter/crlf_newlines/your_output.settings000066400000000000000000000030601350370616400321370ustar00rootroot00000000000000AdapterRemoval ver. 2.1.7 Trimming of single-end reads [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 667770639 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 Minimum adapter overlap: 0 [Trimming statistics] Total number of reads: 1 Number of unaligned reads: 0 Number of well aligned reads: 1 Number of discarded mate 1 reads: 0 Number of singleton mate 1 reads: 1 Number of reads with adapters[1]: 1 Number of retained reads: 1 Number of retained nucleotides: 50 Average length of retained reads: 50 [Length distribution] Length Mate1 Discarded All 0 0 0 0 1 0 0 0 2 0 0 0 3 0 0 0 4 0 0 0 5 0 0 0 6 0 0 0 7 0 0 0 8 0 0 0 9 0 0 0 10 0 0 0 11 0 0 0 12 0 0 0 13 0 0 0 14 0 0 0 15 0 0 0 16 0 0 0 17 0 0 0 18 0 0 0 19 0 0 0 20 0 0 0 21 0 0 0 22 0 0 0 23 0 0 0 24 0 0 0 25 0 0 0 26 0 0 0 27 0 0 0 28 0 0 0 29 0 0 0 30 0 0 0 31 0 0 0 32 0 0 0 33 0 0 0 34 0 0 0 35 0 0 0 36 0 0 0 37 0 0 0 38 0 0 0 39 0 0 0 40 0 0 0 41 0 0 0 42 0 0 0 43 0 0 0 44 0 0 0 45 0 0 0 46 0 0 0 47 0 0 0 48 0 0 0 49 0 0 0 50 1 0 1 adapterremoval-2.3.1/tests/regression/se/incl_adapter/crlf_newlines/your_output.truncated000066400000000000000000000001771350370616400322760ustar00rootroot00000000000000@AAGGGCSeq_1_5180_50/1 ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCT + IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECC adapterremoval-2.3.1/tests/regression/se/incl_adapter/defaults/000077500000000000000000000000001350370616400247155ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/se/incl_adapter/defaults/info.json000066400000000000000000000000711350370616400265410ustar00rootroot00000000000000{ "arguments": [], "return_code": 0, "stderr": [ ] } adapterremoval-2.3.1/tests/regression/se/incl_adapter/defaults/input_1.fastq000066400000000000000000000003431350370616400273340ustar00rootroot00000000000000@AAGGGCSeq_1_5180_50/1 ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG + IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! adapterremoval-2.3.1/tests/regression/se/incl_adapter/defaults/your_output.discarded000066400000000000000000000000001350370616400311650ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/se/incl_adapter/defaults/your_output.settings000066400000000000000000000030601350370616400311140ustar00rootroot00000000000000AdapterRemoval ver. 2.1.7 Trimming of single-end reads [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 667770639 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 Minimum adapter overlap: 0 [Trimming statistics] Total number of reads: 1 Number of unaligned reads: 0 Number of well aligned reads: 1 Number of discarded mate 1 reads: 0 Number of singleton mate 1 reads: 1 Number of reads with adapters[1]: 1 Number of retained reads: 1 Number of retained nucleotides: 50 Average length of retained reads: 50 [Length distribution] Length Mate1 Discarded All 0 0 0 0 1 0 0 0 2 0 0 0 3 0 0 0 4 0 0 0 5 0 0 0 6 0 0 0 7 0 0 0 8 0 0 0 9 0 0 0 10 0 0 0 11 0 0 0 12 0 0 0 13 0 0 0 14 0 0 0 15 0 0 0 16 0 0 0 17 0 0 0 18 0 0 0 19 0 0 0 20 0 0 0 21 0 0 0 22 0 0 0 23 0 0 0 24 0 0 0 25 0 0 0 26 0 0 0 27 0 0 0 28 0 0 0 29 0 0 0 30 0 0 0 31 0 0 0 32 0 0 0 33 0 0 0 34 0 0 0 35 0 0 0 36 0 0 0 37 0 0 0 38 0 0 0 39 0 0 0 40 0 0 0 41 0 0 0 42 0 0 0 43 0 0 0 44 0 0 0 45 0 0 0 46 0 0 0 47 0 0 0 48 0 0 0 49 0 0 0 50 1 0 1 adapterremoval-2.3.1/tests/regression/se/incl_adapter/defaults/your_output.truncated000066400000000000000000000001771350370616400312530ustar00rootroot00000000000000@AAGGGCSeq_1_5180_50/1 ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCT + IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECC adapterremoval-2.3.1/tests/regression/se/incl_adapter/maxlength/000077500000000000000000000000001350370616400250755ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/se/incl_adapter/maxlength/info.json000066400000000000000000000001141350370616400267170ustar00rootroot00000000000000{ "arguments": ["--maxlength", "13"], "return_code": 0, "stderr": [ ] } adapterremoval-2.3.1/tests/regression/se/incl_adapter/maxlength/input_1.fastq000066400000000000000000000003551350370616400275170ustar00rootroot00000000000000@AAGGGCSeq_1_5180_50/1 meta data ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG + IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! adapterremoval-2.3.1/tests/regression/se/incl_adapter/maxlength/your_output.discarded000066400000000000000000000002111350370616400313510ustar00rootroot00000000000000@AAGGGCSeq_1_5180_50/1 meta data ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCT + IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECC adapterremoval-2.3.1/tests/regression/se/incl_adapter/maxlength/your_output.settings000066400000000000000000000030471350370616400313010ustar00rootroot00000000000000AdapterRemoval ver. 2.1.7 Trimming of single-end reads [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 2394757988 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 13 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 Minimum adapter overlap: 0 [Trimming statistics] Total number of reads: 1 Number of unaligned reads: 0 Number of well aligned reads: 1 Number of discarded mate 1 reads: 1 Number of singleton mate 1 reads: 0 Number of reads with adapters[1]: 1 Number of retained reads: 0 Number of retained nucleotides: 0 Average length of retained reads: 0 [Length distribution] Length Mate1 Discarded All 0 0 0 0 1 0 0 0 2 0 0 0 3 0 0 0 4 0 0 0 5 0 0 0 6 0 0 0 7 0 0 0 8 0 0 0 9 0 0 0 10 0 0 0 11 0 0 0 12 0 0 0 13 0 0 0 14 0 0 0 15 0 0 0 16 0 0 0 17 0 0 0 18 0 0 0 19 0 0 0 20 0 0 0 21 0 0 0 22 0 0 0 23 0 0 0 24 0 0 0 25 0 0 0 26 0 0 0 27 0 0 0 28 0 0 0 29 0 0 0 30 0 0 0 31 0 0 0 32 0 0 0 33 0 0 0 34 0 0 0 35 0 0 0 36 0 0 0 37 0 0 0 38 0 0 0 39 0 0 0 40 0 0 0 41 0 0 0 42 0 0 0 43 0 0 0 44 0 0 0 45 0 0 0 46 0 0 0 47 0 0 0 48 0 0 0 49 0 0 0 50 0 1 1 adapterremoval-2.3.1/tests/regression/se/incl_adapter/maxlength/your_output.truncated000066400000000000000000000000001350370616400314140ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/se/incl_adapter/minlength/000077500000000000000000000000001350370616400250735ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/se/incl_adapter/minlength/info.json000066400000000000000000000001151350370616400267160ustar00rootroot00000000000000{ "arguments": ["--minlength", "999"], "return_code": 0, "stderr": [ ] } adapterremoval-2.3.1/tests/regression/se/incl_adapter/minlength/input_1.fastq000066400000000000000000000003551350370616400275150ustar00rootroot00000000000000@AAGGGCSeq_1_5180_50/1 meta data ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG + IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! adapterremoval-2.3.1/tests/regression/se/incl_adapter/minlength/your_output.discarded000066400000000000000000000002111350370616400313470ustar00rootroot00000000000000@AAGGGCSeq_1_5180_50/1 meta data ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCT + IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECC adapterremoval-2.3.1/tests/regression/se/incl_adapter/minlength/your_output.settings000066400000000000000000000030601350370616400312720ustar00rootroot00000000000000AdapterRemoval ver. 2.1.7 Trimming of single-end reads [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 2314668317 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 999 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 Minimum adapter overlap: 0 [Trimming statistics] Total number of reads: 1 Number of unaligned reads: 0 Number of well aligned reads: 1 Number of discarded mate 1 reads: 1 Number of singleton mate 1 reads: 0 Number of reads with adapters[1]: 1 Number of retained reads: 0 Number of retained nucleotides: 0 Average length of retained reads: 0 [Length distribution] Length Mate1 Discarded All 0 0 0 0 1 0 0 0 2 0 0 0 3 0 0 0 4 0 0 0 5 0 0 0 6 0 0 0 7 0 0 0 8 0 0 0 9 0 0 0 10 0 0 0 11 0 0 0 12 0 0 0 13 0 0 0 14 0 0 0 15 0 0 0 16 0 0 0 17 0 0 0 18 0 0 0 19 0 0 0 20 0 0 0 21 0 0 0 22 0 0 0 23 0 0 0 24 0 0 0 25 0 0 0 26 0 0 0 27 0 0 0 28 0 0 0 29 0 0 0 30 0 0 0 31 0 0 0 32 0 0 0 33 0 0 0 34 0 0 0 35 0 0 0 36 0 0 0 37 0 0 0 38 0 0 0 39 0 0 0 40 0 0 0 41 0 0 0 42 0 0 0 43 0 0 0 44 0 0 0 45 0 0 0 46 0 0 0 47 0 0 0 48 0 0 0 49 0 0 0 50 0 1 1 adapterremoval-2.3.1/tests/regression/se/incl_adapter/minlength/your_output.truncated000066400000000000000000000000001350370616400314120ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/se/incl_adapter/multiple_input/000077500000000000000000000000001350370616400261605ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/se/incl_adapter/multiple_input/info.json000066400000000000000000000000711350370616400300040ustar00rootroot00000000000000{ "arguments": [], "return_code": 0, "stderr": [ ] } adapterremoval-2.3.1/tests/regression/se/incl_adapter/multiple_input/input_1a.fastq000066400000000000000000000015501350370616400307410ustar00rootroot00000000000000@read_150_1/1 CTTGGGTACTCAGCCTTAGGGTACCACATAGAGTTATCTTATATATTATAATTGCTCTTTTAACATAATTTTAAAAAATTTATATTAAACTTTCTCTGTT + HHHFFFFBBDGGGGGHHHHHGGFCDHGEE<@;+@C792A.CEEGGFFFFDEFGFHHHH@C2;@F;EDDHFDCCC@.DEEEG=BGEDC5>:=2@GFHHHFF @read_150_2/1 GAGTGGGCTTCATCCCTGGGATGCAAGGCTGGTTCAATATATGCAAATCAATAAATGTAATCCAGCATATAAACAGAACCAAAGAAGATCGGAAGAGCAC + HHHHHHHHHHHHHHHHHHHHHHHGC.@CFGHHHHHHHHFBFFHEHHHHFBGHFFFFFFHEDE@EBHHFHB<<>099BEB@=?*59/''.CCFHFHHHHHH @read_150_3/1 TATGTAATGACATAACTCTTATGGGCAACTTCACAAAAACACAGAAGAAAGCCCTCCTAAAGAATGAAATTCCAAAAAAAATCAGGTTACTGCTCACTGA + HHE=EE@DBBBGHGBFGGDDDDFFFHHHHHGHHHHHHGHHHE7BFHHHHHHG@4FEHHFHHHHFHHHHHHFFFE?EGCDE>CD:9=>+*;=37::ADDHF @read_150_4/1 CTCCTATATAAAGATAGCTCTGTAAAACAGGCCAAAAAGCAGAGTGGGGTGTGGGAAGGCAGGGAAAACTGTCCAGGAATAAAGGCATGAAATGAAACAA + HHHHHHHHHHHHHHHHEG@:EEB4DFHHEHFHHHHEGFFEEFCDHEFF:+1;?GFFCFHHHHHHHHHFHBB>>BEDGCDHHHHF adapterremoval-2.3.1/tests/regression/se/incl_adapter/multiple_input/input_1b.fastq000066400000000000000000000015501350370616400307420ustar00rootroot00000000000000@read_150_5/1 TACTCACGGACAAAGAATAAATATAGCTCCTCCAGGAGCTTAATAACTCAGTGCTGTCTAAACTCCTTACACCTGATGTTGATGCCATGGTTAGATAGTT + HHFFGGFDBHHEHHHHHHHHHHHHFHHHHFHHFEEDFD8=GHFFHHDHHHCHHFDHBHD:> @read_150_7/1 TAAGTAAGGTAGACAGCTAAGTCTAGTTTGTTCCCAGTGTTGTACCAGTCTCATCAGTGCCGTGTCTGGGTCTCACAGCCTCTGGTGTTCTATGCTGGAT + GFFEEDHHGHHHHHHHHB?GG77-/:>>@?6AC5GIB?BEBHHHHHHHHHHHHFGFHHHHHHEFEGF9?EHHHE@8BB12BEHHH @read_150_8/1 TAAAAACAAAAACCCTGATGAGAGTATTGATGTGTGCATAAACAAAGAAAAACATAATAGGAATAGAATGGTGAATTAAATTTTGTGAATTTTGGAAACC + HGGGGGHHHHHFHHGHHHHHHHEHHHHHHFHHEEHHHHHFE:/CGBHHHHHGFFGHHHHCEHEFECEFHHFEEE>CFFFCE?DEBD @read_150_10/1 TATAGATGAACTCTGATTTAGAATTTGTATAAGCTAAAGCATTATAGTAATAACTTTTAAAGTAGTATTTAAAATATCCTTATCTTACGTATATATGACT + <506@6?GHHHHGFHGFCFHHHHHHHHHHFGFF<3@C43F>AAEEFBFDFFHHHHHHHHED(0DAEBEFC?BFBEHHHHHC@85@GBGGFDCHEHHFCFB adapterremoval-2.3.1/tests/regression/se/incl_adapter/multiple_input/your_output.discarded000066400000000000000000000000001350370616400324300ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/se/incl_adapter/multiple_input/your_output.settings000066400000000000000000000037701350370616400323670ustar00rootroot00000000000000AdapterRemoval ver. 2.2.0 Trimming of single-end reads [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 35713051 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 Minimum adapter overlap: 0 [Trimming statistics] Total number of reads: 10 Number of unaligned reads: 8 Number of well aligned reads: 2 Number of discarded mate 1 reads: 0 Number of singleton mate 1 reads: 10 Number of reads with adapters[1]: 2 Number of retained reads: 10 Number of retained nucleotides: 984 Average length of retained reads: 98.4 [Length distribution] Length Mate1 Discarded All 0 0 0 0 1 0 0 0 2 0 0 0 3 0 0 0 4 0 0 0 5 0 0 0 6 0 0 0 7 0 0 0 8 0 0 0 9 0 0 0 10 0 0 0 11 0 0 0 12 0 0 0 13 0 0 0 14 0 0 0 15 0 0 0 16 0 0 0 17 0 0 0 18 0 0 0 19 0 0 0 20 0 0 0 21 0 0 0 22 0 0 0 23 0 0 0 24 0 0 0 25 0 0 0 26 0 0 0 27 0 0 0 28 0 0 0 29 0 0 0 30 0 0 0 31 0 0 0 32 0 0 0 33 0 0 0 34 0 0 0 35 0 0 0 36 0 0 0 37 0 0 0 38 0 0 0 39 0 0 0 40 0 0 0 41 0 0 0 42 0 0 0 43 0 0 0 44 0 0 0 45 0 0 0 46 0 0 0 47 0 0 0 48 0 0 0 49 0 0 0 50 0 0 0 51 0 0 0 52 0 0 0 53 0 0 0 54 0 0 0 55 0 0 0 56 0 0 0 57 0 0 0 58 0 0 0 59 0 0 0 60 0 0 0 61 0 0 0 62 0 0 0 63 0 0 0 64 0 0 0 65 0 0 0 66 0 0 0 67 0 0 0 68 0 0 0 69 0 0 0 70 0 0 0 71 0 0 0 72 0 0 0 73 0 0 0 74 0 0 0 75 0 0 0 76 0 0 0 77 0 0 0 78 0 0 0 79 0 0 0 80 0 0 0 81 0 0 0 82 0 0 0 83 0 0 0 84 0 0 0 85 1 0 1 86 0 0 0 87 0 0 0 88 0 0 0 89 0 0 0 90 0 0 0 91 0 0 0 92 0 0 0 93 0 0 0 94 0 0 0 95 0 0 0 96 0 0 0 97 0 0 0 98 0 0 0 99 1 0 1 100 8 0 8 adapterremoval-2.3.1/tests/regression/se/incl_adapter/multiple_input/your_output.truncated000066400000000000000000000041451350370616400325150ustar00rootroot00000000000000@read_150_1/1 CTTGGGTACTCAGCCTTAGGGTACCACATAGAGTTATCTTATATATTATAATTGCTCTTTTAACATAATTTTAAAAAATTTATATTAAACTTTCTCTGTT + HHHFFFFBBDGGGGGHHHHHGGFCDHGEE<@;+@C792A.CEEGGFFFFDEFGFHHHH@C2;@F;EDDHFDCCC@.DEEEG=BGEDC5>:=2@GFHHHFF @read_150_2/1 GAGTGGGCTTCATCCCTGGGATGCAAGGCTGGTTCAATATATGCAAATCAATAAATGTAATCCAGCATATAAACAGAACCAAAGA + HHHHHHHHHHHHHHHHHHHHHHHGC.@CFGHHHHHHHHFBFFHEHHHHFBGHFFFFFFHEDE@EBHHFHB<<>099BEB@=?*59 @read_150_3/1 TATGTAATGACATAACTCTTATGGGCAACTTCACAAAAACACAGAAGAAAGCCCTCCTAAAGAATGAAATTCCAAAAAAAATCAGGTTACTGCTCACTGA + HHE=EE@DBBBGHGBFGGDDDDFFFHHHHHGHHHHHHGHHHE7BFHHHHHHG@4FEHHFHHHHFHHHHHHFFFE?EGCDE>CD:9=>+*;=37::ADDHF @read_150_4/1 CTCCTATATAAAGATAGCTCTGTAAAACAGGCCAAAAAGCAGAGTGGGGTGTGGGAAGGCAGGGAAAACTGTCCAGGAATAAAGGCATGAAATGAAACA + HHHHHHHHHHHHHHHHEG@:EEB4DFHHEHFHHHHEGFFEEFCDHEFF:+1;?GFFCFHHHHHHHHHFHBB>>BEDGCDHHHH @read_150_5/1 TACTCACGGACAAAGAATAAATATAGCTCCTCCAGGAGCTTAATAACTCAGTGCTGTCTAAACTCCTTACACCTGATGTTGATGCCATGGTTAGATAGTT + HHFFGGFDBHHEHHHHHHHHHHHHFHHHHFHHFEEDFD8=GHFFHHDHHHCHHFDHBHD:> @read_150_7/1 TAAGTAAGGTAGACAGCTAAGTCTAGTTTGTTCCCAGTGTTGTACCAGTCTCATCAGTGCCGTGTCTGGGTCTCACAGCCTCTGGTGTTCTATGCTGGAT + GFFEEDHHGHHHHHHHHB?GG77-/:>>@?6AC5GIB?BEBHHHHHHHHHHHHFGFHHHHHHEFEGF9?EHHHE@8BB12BEHHH @read_150_8/1 TAAAAACAAAAACCCTGATGAGAGTATTGATGTGTGCATAAACAAAGAAAAACATAATAGGAATAGAATGGTGAATTAAATTTTGTGAATTTTGGAAACC + HGGGGGHHHHHFHHGHHHHHHHEHHHHHHFHHEEHHHHHFE:/CGBHHHHHGFFGHHHHCEHEFECEFHHFEEE>CFFFCE?DEBD @read_150_10/1 TATAGATGAACTCTGATTTAGAATTTGTATAAGCTAAAGCATTATAGTAATAACTTTTAAAGTAGTATTTAAAATATCCTTATCTTACGTATATATGACT + <506@6?GHHHHGFHGFCFHHHHHHHHHHFGFF<3@C43F>AAEEFBFDFFHHHHHHHHED(0DAEBEFC?BFBEHHHHHC@85@GBGGFDCHEHHFCFB adapterremoval-2.3.1/tests/regression/se/incl_adapter/threads/000077500000000000000000000000001350370616400245405ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/se/incl_adapter/threads/one/000077500000000000000000000000001350370616400253215ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/se/incl_adapter/threads/one/info.json000066400000000000000000000001111350370616400271400ustar00rootroot00000000000000{ "arguments": ["--threads", "1"], "return_code": 0, "stderr": [ ] } adapterremoval-2.3.1/tests/regression/se/incl_adapter/threads/one/input_1.fastq000066400000000000000000000003431350370616400277400ustar00rootroot00000000000000@AAGGGCSeq_1_5180_50/1 ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG + IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! adapterremoval-2.3.1/tests/regression/se/incl_adapter/threads/one/your_output.discarded000066400000000000000000000000001350370616400315710ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/se/incl_adapter/threads/one/your_output.settings000066400000000000000000000030601350370616400315200ustar00rootroot00000000000000AdapterRemoval ver. 2.1.7 Trimming of single-end reads [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 667770639 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 Minimum adapter overlap: 0 [Trimming statistics] Total number of reads: 1 Number of unaligned reads: 0 Number of well aligned reads: 1 Number of discarded mate 1 reads: 0 Number of singleton mate 1 reads: 1 Number of reads with adapters[1]: 1 Number of retained reads: 1 Number of retained nucleotides: 50 Average length of retained reads: 50 [Length distribution] Length Mate1 Discarded All 0 0 0 0 1 0 0 0 2 0 0 0 3 0 0 0 4 0 0 0 5 0 0 0 6 0 0 0 7 0 0 0 8 0 0 0 9 0 0 0 10 0 0 0 11 0 0 0 12 0 0 0 13 0 0 0 14 0 0 0 15 0 0 0 16 0 0 0 17 0 0 0 18 0 0 0 19 0 0 0 20 0 0 0 21 0 0 0 22 0 0 0 23 0 0 0 24 0 0 0 25 0 0 0 26 0 0 0 27 0 0 0 28 0 0 0 29 0 0 0 30 0 0 0 31 0 0 0 32 0 0 0 33 0 0 0 34 0 0 0 35 0 0 0 36 0 0 0 37 0 0 0 38 0 0 0 39 0 0 0 40 0 0 0 41 0 0 0 42 0 0 0 43 0 0 0 44 0 0 0 45 0 0 0 46 0 0 0 47 0 0 0 48 0 0 0 49 0 0 0 50 1 0 1 adapterremoval-2.3.1/tests/regression/se/incl_adapter/threads/one/your_output.truncated000066400000000000000000000001771350370616400316570ustar00rootroot00000000000000@AAGGGCSeq_1_5180_50/1 ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCT + IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECC adapterremoval-2.3.1/tests/regression/se/incl_adapter/threads/three/000077500000000000000000000000001350370616400256475ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/se/incl_adapter/threads/three/info.json000066400000000000000000000001111350370616400274660ustar00rootroot00000000000000{ "arguments": ["--threads", "3"], "return_code": 0, "stderr": [ ] } adapterremoval-2.3.1/tests/regression/se/incl_adapter/threads/three/input_1.fastq000066400000000000000000000003431350370616400302660ustar00rootroot00000000000000@AAGGGCSeq_1_5180_50/1 ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG + IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! adapterremoval-2.3.1/tests/regression/se/incl_adapter/threads/three/your_output.discarded000066400000000000000000000000001350370616400321170ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/se/incl_adapter/threads/three/your_output.settings000066400000000000000000000030511350370616400320460ustar00rootroot00000000000000AdapterRemoval ver. 2.1.7 Trimming of single-end reads [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: NA Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 Minimum adapter overlap: 0 [Trimming statistics] Total number of reads: 1 Number of unaligned reads: 0 Number of well aligned reads: 1 Number of discarded mate 1 reads: 0 Number of singleton mate 1 reads: 1 Number of reads with adapters[1]: 1 Number of retained reads: 1 Number of retained nucleotides: 50 Average length of retained reads: 50 [Length distribution] Length Mate1 Discarded All 0 0 0 0 1 0 0 0 2 0 0 0 3 0 0 0 4 0 0 0 5 0 0 0 6 0 0 0 7 0 0 0 8 0 0 0 9 0 0 0 10 0 0 0 11 0 0 0 12 0 0 0 13 0 0 0 14 0 0 0 15 0 0 0 16 0 0 0 17 0 0 0 18 0 0 0 19 0 0 0 20 0 0 0 21 0 0 0 22 0 0 0 23 0 0 0 24 0 0 0 25 0 0 0 26 0 0 0 27 0 0 0 28 0 0 0 29 0 0 0 30 0 0 0 31 0 0 0 32 0 0 0 33 0 0 0 34 0 0 0 35 0 0 0 36 0 0 0 37 0 0 0 38 0 0 0 39 0 0 0 40 0 0 0 41 0 0 0 42 0 0 0 43 0 0 0 44 0 0 0 45 0 0 0 46 0 0 0 47 0 0 0 48 0 0 0 49 0 0 0 50 1 0 1 adapterremoval-2.3.1/tests/regression/se/incl_adapter/threads/three/your_output.truncated000066400000000000000000000001771350370616400322050ustar00rootroot00000000000000@AAGGGCSeq_1_5180_50/1 ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCT + IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECC adapterremoval-2.3.1/tests/regression/se/incl_adapter/threads/two/000077500000000000000000000000001350370616400253515ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/se/incl_adapter/threads/two/info.json000066400000000000000000000001111350370616400271700ustar00rootroot00000000000000{ "arguments": ["--threads", "2"], "return_code": 0, "stderr": [ ] } adapterremoval-2.3.1/tests/regression/se/incl_adapter/threads/two/input_1.fastq000066400000000000000000000003431350370616400277700ustar00rootroot00000000000000@AAGGGCSeq_1_5180_50/1 ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG + IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! adapterremoval-2.3.1/tests/regression/se/incl_adapter/threads/two/your_output.discarded000066400000000000000000000000001350370616400316210ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/se/incl_adapter/threads/two/your_output.settings000066400000000000000000000030511350370616400315500ustar00rootroot00000000000000AdapterRemoval ver. 2.1.7 Trimming of single-end reads [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: NA Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 Minimum adapter overlap: 0 [Trimming statistics] Total number of reads: 1 Number of unaligned reads: 0 Number of well aligned reads: 1 Number of discarded mate 1 reads: 0 Number of singleton mate 1 reads: 1 Number of reads with adapters[1]: 1 Number of retained reads: 1 Number of retained nucleotides: 50 Average length of retained reads: 50 [Length distribution] Length Mate1 Discarded All 0 0 0 0 1 0 0 0 2 0 0 0 3 0 0 0 4 0 0 0 5 0 0 0 6 0 0 0 7 0 0 0 8 0 0 0 9 0 0 0 10 0 0 0 11 0 0 0 12 0 0 0 13 0 0 0 14 0 0 0 15 0 0 0 16 0 0 0 17 0 0 0 18 0 0 0 19 0 0 0 20 0 0 0 21 0 0 0 22 0 0 0 23 0 0 0 24 0 0 0 25 0 0 0 26 0 0 0 27 0 0 0 28 0 0 0 29 0 0 0 30 0 0 0 31 0 0 0 32 0 0 0 33 0 0 0 34 0 0 0 35 0 0 0 36 0 0 0 37 0 0 0 38 0 0 0 39 0 0 0 40 0 0 0 41 0 0 0 42 0 0 0 43 0 0 0 44 0 0 0 45 0 0 0 46 0 0 0 47 0 0 0 48 0 0 0 49 0 0 0 50 1 0 1 adapterremoval-2.3.1/tests/regression/se/incl_adapter/threads/two/your_output.truncated000066400000000000000000000001771350370616400317070ustar00rootroot00000000000000@AAGGGCSeq_1_5180_50/1 ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCT + IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECC adapterremoval-2.3.1/tests/regression/se/incl_adapter/trimns/000077500000000000000000000000001350370616400244225ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/se/incl_adapter/trimns/excl_ns/000077500000000000000000000000001350370616400260555ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/se/incl_adapter/trimns/excl_ns/info.json000066400000000000000000000001031350370616400276750ustar00rootroot00000000000000{ "arguments": ["--trimns"], "return_code": 0, "stderr": [ ] } adapterremoval-2.3.1/tests/regression/se/incl_adapter/trimns/excl_ns/input_1.fastq000066400000000000000000000003551350370616400304770ustar00rootroot00000000000000@AAGGGCSeq_1_5180_50/1 meta data ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG + IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! adapterremoval-2.3.1/tests/regression/se/incl_adapter/trimns/excl_ns/your_output.discarded000066400000000000000000000000001350370616400323250ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/se/incl_adapter/trimns/excl_ns/your_output.settings000066400000000000000000000030621350370616400322560ustar00rootroot00000000000000AdapterRemoval ver. 2.1.7 Trimming of single-end reads [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 2489899758 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: Yes Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 Minimum adapter overlap: 0 [Trimming statistics] Total number of reads: 1 Number of unaligned reads: 0 Number of well aligned reads: 1 Number of discarded mate 1 reads: 0 Number of singleton mate 1 reads: 1 Number of reads with adapters[1]: 1 Number of retained reads: 1 Number of retained nucleotides: 50 Average length of retained reads: 50 [Length distribution] Length Mate1 Discarded All 0 0 0 0 1 0 0 0 2 0 0 0 3 0 0 0 4 0 0 0 5 0 0 0 6 0 0 0 7 0 0 0 8 0 0 0 9 0 0 0 10 0 0 0 11 0 0 0 12 0 0 0 13 0 0 0 14 0 0 0 15 0 0 0 16 0 0 0 17 0 0 0 18 0 0 0 19 0 0 0 20 0 0 0 21 0 0 0 22 0 0 0 23 0 0 0 24 0 0 0 25 0 0 0 26 0 0 0 27 0 0 0 28 0 0 0 29 0 0 0 30 0 0 0 31 0 0 0 32 0 0 0 33 0 0 0 34 0 0 0 35 0 0 0 36 0 0 0 37 0 0 0 38 0 0 0 39 0 0 0 40 0 0 0 41 0 0 0 42 0 0 0 43 0 0 0 44 0 0 0 45 0 0 0 46 0 0 0 47 0 0 0 48 0 0 0 49 0 0 0 50 1 0 1 adapterremoval-2.3.1/tests/regression/se/incl_adapter/trimns/excl_ns/your_output.truncated000066400000000000000000000002111350370616400324000ustar00rootroot00000000000000@AAGGGCSeq_1_5180_50/1 meta data ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCT + IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECC adapterremoval-2.3.1/tests/regression/se/incl_adapter/trimns/incl_ns/000077500000000000000000000000001350370616400260475ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/se/incl_adapter/trimns/incl_ns/info.json000066400000000000000000000001031350370616400276670ustar00rootroot00000000000000{ "arguments": ["--trimns"], "return_code": 0, "stderr": [ ] } adapterremoval-2.3.1/tests/regression/se/incl_adapter/trimns/incl_ns/input_1.fastq000066400000000000000000000003551350370616400304710ustar00rootroot00000000000000@AAGGGCSeq_1_5180_50/1 meta data ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCNNNNNNNNATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG + IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! adapterremoval-2.3.1/tests/regression/se/incl_adapter/trimns/incl_ns/your_output.discarded000066400000000000000000000000001350370616400323170ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/se/incl_adapter/trimns/incl_ns/your_output.settings000066400000000000000000000027741350370616400322610ustar00rootroot00000000000000AdapterRemoval ver. 2.1.7 Trimming of single-end reads [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 2566824554 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: Yes Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 Minimum adapter overlap: 0 [Trimming statistics] Total number of reads: 1 Number of unaligned reads: 0 Number of well aligned reads: 1 Number of discarded mate 1 reads: 0 Number of singleton mate 1 reads: 1 Number of reads with adapters[1]: 1 Number of retained reads: 1 Number of retained nucleotides: 44 Average length of retained reads: 44 [Length distribution] Length Mate1 Discarded All 0 0 0 0 1 0 0 0 2 0 0 0 3 0 0 0 4 0 0 0 5 0 0 0 6 0 0 0 7 0 0 0 8 0 0 0 9 0 0 0 10 0 0 0 11 0 0 0 12 0 0 0 13 0 0 0 14 0 0 0 15 0 0 0 16 0 0 0 17 0 0 0 18 0 0 0 19 0 0 0 20 0 0 0 21 0 0 0 22 0 0 0 23 0 0 0 24 0 0 0 25 0 0 0 26 0 0 0 27 0 0 0 28 0 0 0 29 0 0 0 30 0 0 0 31 0 0 0 32 0 0 0 33 0 0 0 34 0 0 0 35 0 0 0 36 0 0 0 37 0 0 0 38 0 0 0 39 0 0 0 40 0 0 0 41 0 0 0 42 0 0 0 43 0 0 0 44 1 0 1 adapterremoval-2.3.1/tests/regression/se/incl_adapter/trimns/incl_ns/your_output.truncated000066400000000000000000000001751350370616400324030ustar00rootroot00000000000000@AAGGGCSeq_1_5180_50/1 meta data ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGC + IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFF adapterremoval-2.3.1/tests/regression/se/incl_adapter/trimqualities/000077500000000000000000000000001350370616400260025ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/se/incl_adapter/trimqualities/default/000077500000000000000000000000001350370616400274265ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/se/incl_adapter/trimqualities/default/info.json000066400000000000000000000001121350370616400312460ustar00rootroot00000000000000{ "arguments": ["--trimqualities"], "return_code": 0, "stderr": [ ] } adapterremoval-2.3.1/tests/regression/se/incl_adapter/trimqualities/default/input_1.fastq000066400000000000000000000003551350370616400320500ustar00rootroot00000000000000@AAGGGCSeq_1_5180_50/1 meta data ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG + IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! adapterremoval-2.3.1/tests/regression/se/incl_adapter/trimqualities/default/your_output.discarded000066400000000000000000000000001350370616400336760ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/se/incl_adapter/trimqualities/default/your_output.settings000066400000000000000000000030621350370616400336270ustar00rootroot00000000000000AdapterRemoval ver. 2.1.7 Trimming of single-end reads [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 2679028121 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: Yes Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 Minimum adapter overlap: 0 [Trimming statistics] Total number of reads: 1 Number of unaligned reads: 0 Number of well aligned reads: 1 Number of discarded mate 1 reads: 0 Number of singleton mate 1 reads: 1 Number of reads with adapters[1]: 1 Number of retained reads: 1 Number of retained nucleotides: 50 Average length of retained reads: 50 [Length distribution] Length Mate1 Discarded All 0 0 0 0 1 0 0 0 2 0 0 0 3 0 0 0 4 0 0 0 5 0 0 0 6 0 0 0 7 0 0 0 8 0 0 0 9 0 0 0 10 0 0 0 11 0 0 0 12 0 0 0 13 0 0 0 14 0 0 0 15 0 0 0 16 0 0 0 17 0 0 0 18 0 0 0 19 0 0 0 20 0 0 0 21 0 0 0 22 0 0 0 23 0 0 0 24 0 0 0 25 0 0 0 26 0 0 0 27 0 0 0 28 0 0 0 29 0 0 0 30 0 0 0 31 0 0 0 32 0 0 0 33 0 0 0 34 0 0 0 35 0 0 0 36 0 0 0 37 0 0 0 38 0 0 0 39 0 0 0 40 0 0 0 41 0 0 0 42 0 0 0 43 0 0 0 44 0 0 0 45 0 0 0 46 0 0 0 47 0 0 0 48 0 0 0 49 0 0 0 50 1 0 1 adapterremoval-2.3.1/tests/regression/se/incl_adapter/trimqualities/default/your_output.truncated000066400000000000000000000002111350370616400337510ustar00rootroot00000000000000@AAGGGCSeq_1_5180_50/1 meta data ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCT + IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECC adapterremoval-2.3.1/tests/regression/se/incl_adapter/trimqualities/minq36/000077500000000000000000000000001350370616400271175ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/se/incl_adapter/trimqualities/minq36/info.json000066400000000000000000000001401350370616400307400ustar00rootroot00000000000000{ "arguments": ["--trimqualities", "--minquality", "36"], "return_code": 0, "stderr": [ ] } adapterremoval-2.3.1/tests/regression/se/incl_adapter/trimqualities/minq36/input_1.fastq000066400000000000000000000003551350370616400315410ustar00rootroot00000000000000@AAGGGCSeq_1_5180_50/1 meta data ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG + IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! adapterremoval-2.3.1/tests/regression/se/incl_adapter/trimqualities/minq36/your_output.discarded000066400000000000000000000000001350370616400333670ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/se/incl_adapter/trimqualities/minq36/your_output.settings000066400000000000000000000030061350370616400333160ustar00rootroot00000000000000AdapterRemoval ver. 2.1.7 Trimming of single-end reads [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 2816594278 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 36: Yes Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 Minimum adapter overlap: 0 [Trimming statistics] Total number of reads: 1 Number of unaligned reads: 0 Number of well aligned reads: 1 Number of discarded mate 1 reads: 0 Number of singleton mate 1 reads: 1 Number of reads with adapters[1]: 1 Number of retained reads: 1 Number of retained nucleotides: 45 Average length of retained reads: 45 [Length distribution] Length Mate1 Discarded All 0 0 0 0 1 0 0 0 2 0 0 0 3 0 0 0 4 0 0 0 5 0 0 0 6 0 0 0 7 0 0 0 8 0 0 0 9 0 0 0 10 0 0 0 11 0 0 0 12 0 0 0 13 0 0 0 14 0 0 0 15 0 0 0 16 0 0 0 17 0 0 0 18 0 0 0 19 0 0 0 20 0 0 0 21 0 0 0 22 0 0 0 23 0 0 0 24 0 0 0 25 0 0 0 26 0 0 0 27 0 0 0 28 0 0 0 29 0 0 0 30 0 0 0 31 0 0 0 32 0 0 0 33 0 0 0 34 0 0 0 35 0 0 0 36 0 0 0 37 0 0 0 38 0 0 0 39 0 0 0 40 0 0 0 41 0 0 0 42 0 0 0 43 0 0 0 44 0 0 0 45 1 0 1 adapterremoval-2.3.1/tests/regression/se/incl_adapter/trimqualities/minq36/your_output.truncated000066400000000000000000000001771350370616400334550ustar00rootroot00000000000000@AAGGGCSeq_1_5180_50/1 meta data ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCA + IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFF adapterremoval-2.3.1/tests/regression/se/only_adapter/000077500000000000000000000000001350370616400231425ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/se/only_adapter/collapse/000077500000000000000000000000001350370616400247445ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/se/only_adapter/collapse/info.json000066400000000000000000000001051350370616400265660ustar00rootroot00000000000000{ "arguments": ["--collapse"], "return_code": 0, "stderr": [ ] } adapterremoval-2.3.1/tests/regression/se/only_adapter/collapse/input_1.fastq000066400000000000000000000003551350370616400273660ustar00rootroot00000000000000@CTTTGTSeq_1_14286_0/1 meta data AGATCGGAAGAGCACACGTCTGAACTCCATTCACCTTTGTATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA + JGIJJJIJIJJGJGJIHHHGGIGIHGHGGGHEHEGFDFGEEEEGCFDDCCECDCBBCBBACCAA@BACB?>>>>?;=<;=<<::;:9777664010.-)! adapterremoval-2.3.1/tests/regression/se/only_adapter/collapse/your_output.collapsed000066400000000000000000000000001350370616400312400ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/se/only_adapter/collapse/your_output.collapsed.truncated000066400000000000000000000000001350370616400332300ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/se/only_adapter/collapse/your_output.discarded000066400000000000000000000000471350370616400312270ustar00rootroot00000000000000@M_CTTTGTSeq_1_14286_0/1 meta data + adapterremoval-2.3.1/tests/regression/se/only_adapter/collapse/your_output.settings000066400000000000000000000023501350370616400311440ustar00rootroot00000000000000AdapterRemoval ver. 2.1.7 Trimming of single-end reads [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 4215296776 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: Yes Minimum overlap (in case of collapse): 11 Minimum adapter overlap: 0 [Trimming statistics] Total number of reads: 1 Number of unaligned reads: 0 Number of well aligned reads: 1 Number of discarded mate 1 reads: 1 Number of singleton mate 1 reads: 0 Number of reads with adapters[1]: 1 Number of full-length collapsed pairs: 0 Number of truncated collapsed pairs: 0 Number of retained reads: 0 Number of retained nucleotides: 0 Average length of retained reads: 0 [Length distribution] Length Mate1 Collapsed CollapsedTruncated Discarded All 0 0 0 0 1 1 adapterremoval-2.3.1/tests/regression/se/only_adapter/collapse/your_output.truncated000066400000000000000000000000001350370616400312630ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/se/only_adapter/combined_output/000077500000000000000000000000001350370616400263425ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/se/only_adapter/combined_output/discarded/000077500000000000000000000000001350370616400302645ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/se/only_adapter/combined_output/discarded/info.json000066400000000000000000000001141350370616400321060ustar00rootroot00000000000000{ "arguments": ["--combined-output"], "return_code": 0, "stderr": [ ] } adapterremoval-2.3.1/tests/regression/se/only_adapter/combined_output/discarded/input_1.fastq000066400000000000000000000003551350370616400327060ustar00rootroot00000000000000@CTTTGTSeq_1_14286_0/1 meta data AGATCGGAAGAGCACACGTCTGAACTCCATTCACCTTTGTATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA + JGIJJJIJIJJGJGJIHHHGGIGIHGHGGGHEHEGFDFGEEEEGCFDDCCECDCBBCBBACCAA@BACB?>>>>?;=<;=<<::;:9777664010.-)! adapterremoval-2.3.1/tests/regression/se/only_adapter/combined_output/discarded/your_output.settings000066400000000000000000000021651350370616400344700ustar00rootroot00000000000000AdapterRemoval ver. 2.1.7 Trimming of single-end reads [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 913821732 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 Minimum adapter overlap: 0 [Trimming statistics] Total number of reads: 1 Number of unaligned reads: 0 Number of well aligned reads: 1 Number of discarded mate 1 reads: 1 Number of singleton mate 1 reads: 0 Number of reads with adapters[1]: 1 Number of retained reads: 0 Number of retained nucleotides: 0 Average length of retained reads: 0 [Length distribution] Length Mate1 Discarded All 0 0 1 1 your_output.truncated000066400000000000000000000000471350370616400345370ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/se/only_adapter/combined_output/discarded@CTTTGTSeq_1_14286_0/1 meta data N + ! adapterremoval-2.3.1/tests/regression/se/only_adapter/combined_output/retained/000077500000000000000000000000001350370616400301355ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/se/only_adapter/combined_output/retained/info.json000066400000000000000000000001431350370616400317610ustar00rootroot00000000000000{ "arguments": ["--combined-output", "--minlength", "0"], "return_code": 0, "stderr": [ ] } adapterremoval-2.3.1/tests/regression/se/only_adapter/combined_output/retained/input_1.fastq000066400000000000000000000003551350370616400325570ustar00rootroot00000000000000@CTTTGTSeq_1_14286_0/1 meta data AGATCGGAAGAGCACACGTCTGAACTCCATTCACCTTTGTATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA + JGIJJJIJIJJGJGJIHHHGGIGIHGHGGGHEHEGFDFGEEEEGCFDDCCECDCBBCBBACCAA@BACB?>>>>?;=<;=<<::;:9777664010.-)! adapterremoval-2.3.1/tests/regression/se/only_adapter/combined_output/retained/your_output.settings000066400000000000000000000021641350370616400343400ustar00rootroot00000000000000AdapterRemoval ver. 2.1.7 Trimming of single-end reads [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 984265443 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 0 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 Minimum adapter overlap: 0 [Trimming statistics] Total number of reads: 1 Number of unaligned reads: 0 Number of well aligned reads: 1 Number of discarded mate 1 reads: 0 Number of singleton mate 1 reads: 1 Number of reads with adapters[1]: 1 Number of retained reads: 1 Number of retained nucleotides: 0 Average length of retained reads: 0 [Length distribution] Length Mate1 Discarded All 0 1 0 1 adapterremoval-2.3.1/tests/regression/se/only_adapter/combined_output/retained/your_output.truncated000066400000000000000000000000451350370616400344650ustar00rootroot00000000000000@CTTTGTSeq_1_14286_0/1 meta data + adapterremoval-2.3.1/tests/regression/se/only_adapter/crlf_newlines/000077500000000000000000000000001350370616400257745ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/se/only_adapter/crlf_newlines/info.json000066400000000000000000000000711350370616400276200ustar00rootroot00000000000000{ "arguments": [], "return_code": 0, "stderr": [ ] } adapterremoval-2.3.1/tests/regression/se/only_adapter/crlf_newlines/input_1.fastq000066400000000000000000000003611350370616400304130ustar00rootroot00000000000000@CTTTGTSeq_1_14286_0/1 meta data AGATCGGAAGAGCACACGTCTGAACTCCATTCACCTTTGTATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA + JGIJJJIJIJJGJGJIHHHGGIGIHGHGGGHEHEGFDFGEEEEGCFDDCCECDCBBCBBACCAA@BACB?>>>>?;=<;=<<::;:9777664010.-)! adapterremoval-2.3.1/tests/regression/se/only_adapter/crlf_newlines/your_output.discarded000066400000000000000000000000451350370616400322550ustar00rootroot00000000000000@CTTTGTSeq_1_14286_0/1 meta data + adapterremoval-2.3.1/tests/regression/se/only_adapter/crlf_newlines/your_output.settings000066400000000000000000000021661350370616400322010ustar00rootroot00000000000000AdapterRemoval ver. 2.1.7 Trimming of single-end reads [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 4288002672 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 Minimum adapter overlap: 0 [Trimming statistics] Total number of reads: 1 Number of unaligned reads: 0 Number of well aligned reads: 1 Number of discarded mate 1 reads: 1 Number of singleton mate 1 reads: 0 Number of reads with adapters[1]: 1 Number of retained reads: 0 Number of retained nucleotides: 0 Average length of retained reads: 0 [Length distribution] Length Mate1 Discarded All 0 0 1 1 adapterremoval-2.3.1/tests/regression/se/only_adapter/crlf_newlines/your_output.truncated000066400000000000000000000000001350370616400323130ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/se/only_adapter/defaults/000077500000000000000000000000001350370616400247515ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/se/only_adapter/defaults/info.json000066400000000000000000000000711350370616400265750ustar00rootroot00000000000000{ "arguments": [], "return_code": 0, "stderr": [ ] } adapterremoval-2.3.1/tests/regression/se/only_adapter/defaults/input_1.fastq000066400000000000000000000003551350370616400273730ustar00rootroot00000000000000@CTTTGTSeq_1_14286_0/1 meta data AGATCGGAAGAGCACACGTCTGAACTCCATTCACCTTTGTATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA + JGIJJJIJIJJGJGJIHHHGGIGIHGHGGGHEHEGFDFGEEEEGCFDDCCECDCBBCBBACCAA@BACB?>>>>?;=<;=<<::;:9777664010.-)! adapterremoval-2.3.1/tests/regression/se/only_adapter/defaults/your_output.discarded000066400000000000000000000000451350370616400312320ustar00rootroot00000000000000@CTTTGTSeq_1_14286_0/1 meta data + adapterremoval-2.3.1/tests/regression/se/only_adapter/defaults/your_output.settings000066400000000000000000000021661350370616400311560ustar00rootroot00000000000000AdapterRemoval ver. 2.1.7 Trimming of single-end reads [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 4288002672 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 Minimum adapter overlap: 0 [Trimming statistics] Total number of reads: 1 Number of unaligned reads: 0 Number of well aligned reads: 1 Number of discarded mate 1 reads: 1 Number of singleton mate 1 reads: 0 Number of reads with adapters[1]: 1 Number of retained reads: 0 Number of retained nucleotides: 0 Average length of retained reads: 0 [Length distribution] Length Mate1 Discarded All 0 0 1 1 adapterremoval-2.3.1/tests/regression/se/only_adapter/defaults/your_output.truncated000066400000000000000000000000001350370616400312700ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/se/only_adapter/minlength/000077500000000000000000000000001350370616400251275ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/se/only_adapter/minlength/info.json000066400000000000000000000001131350370616400267500ustar00rootroot00000000000000{ "arguments": ["--minlength", "0"], "return_code": 0, "stderr": [ ] } adapterremoval-2.3.1/tests/regression/se/only_adapter/minlength/input_1.fastq000066400000000000000000000003551350370616400275510ustar00rootroot00000000000000@CTTTGTSeq_1_14286_0/1 meta data AGATCGGAAGAGCACACGTCTGAACTCCATTCACCTTTGTATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA + JGIJJJIJIJJGJGJIHHHGGIGIHGHGGGHEHEGFDFGEEEEGCFDDCCECDCBBCBBACCAA@BACB?>>>>?;=<;=<<::;:9777664010.-)! adapterremoval-2.3.1/tests/regression/se/only_adapter/minlength/your_output.discarded000066400000000000000000000000001350370616400313770ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/se/only_adapter/minlength/your_output.settings000066400000000000000000000021641350370616400313320ustar00rootroot00000000000000AdapterRemoval ver. 2.1.7 Trimming of single-end reads [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 120751608 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 0 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 Minimum adapter overlap: 0 [Trimming statistics] Total number of reads: 1 Number of unaligned reads: 0 Number of well aligned reads: 1 Number of discarded mate 1 reads: 0 Number of singleton mate 1 reads: 1 Number of reads with adapters[1]: 1 Number of retained reads: 1 Number of retained nucleotides: 0 Average length of retained reads: 0 [Length distribution] Length Mate1 Discarded All 0 1 0 1 adapterremoval-2.3.1/tests/regression/se/only_adapter/minlength/your_output.truncated000066400000000000000000000000451350370616400314570ustar00rootroot00000000000000@CTTTGTSeq_1_14286_0/1 meta data + adapterremoval-2.3.1/tests/regression/se/trimfixed/000077500000000000000000000000001350370616400224545ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/se/trimfixed/3p/000077500000000000000000000000001350370616400227765ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/se/trimfixed/3p/info.json000066400000000000000000000001101350370616400246140ustar00rootroot00000000000000{ "arguments": ["--trim3p", "5"], "return_code": 0, "stderr": [ ] } adapterremoval-2.3.1/tests/regression/se/trimfixed/3p/input_1.fastq000066400000000000000000000003431350370616400254150ustar00rootroot00000000000000@AAGGGCSeq_1_5180_50/1 ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG + IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! adapterremoval-2.3.1/tests/regression/se/trimfixed/3p/your_output.discarded000066400000000000000000000000001350370616400272460ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/se/trimfixed/3p/your_output.settings000066400000000000000000000030031350370616400271720ustar00rootroot00000000000000AdapterRemoval ver. 2.1.7 Trimming of single-end reads [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 667770639 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 5 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 Minimum adapter overlap: 0 [Trimming statistics] Total number of reads: 1 Number of unaligned reads: 0 Number of well aligned reads: 1 Number of discarded mate 1 reads: 0 Number of singleton mate 1 reads: 1 Number of reads with adapters[1]: 1 Number of retained reads: 1 Number of retained nucleotides: 45 Average length of retained reads: 45 [Length distribution] Length Mate1 Discarded All 0 0 0 0 1 0 0 0 2 0 0 0 3 0 0 0 4 0 0 0 5 0 0 0 6 0 0 0 7 0 0 0 8 0 0 0 9 0 0 0 10 0 0 0 11 0 0 0 12 0 0 0 13 0 0 0 14 0 0 0 15 0 0 0 16 0 0 0 17 0 0 0 18 0 0 0 19 0 0 0 20 0 0 0 21 0 0 0 22 0 0 0 23 0 0 0 24 0 0 0 25 0 0 0 26 0 0 0 27 0 0 0 28 0 0 0 29 0 0 0 30 0 0 0 31 0 0 0 32 0 0 0 33 0 0 0 34 0 0 0 35 0 0 0 36 0 0 0 37 0 0 0 38 0 0 0 39 0 0 0 40 0 0 0 41 0 0 0 42 0 0 0 43 0 0 0 44 0 0 0 45 1 0 1 adapterremoval-2.3.1/tests/regression/se/trimfixed/3p/your_output.truncated000066400000000000000000000001651350370616400273310ustar00rootroot00000000000000@AAGGGCSeq_1_5180_50/1 ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCA + IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFF adapterremoval-2.3.1/tests/regression/se/trimfixed/3p_both_set/000077500000000000000000000000001350370616400246655ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/se/trimfixed/3p_both_set/info.json000066400000000000000000000001161350370616400265110ustar00rootroot00000000000000{ "arguments": ["--trim3p", "5", "20"], "return_code": 0, "stderr": [ ] } adapterremoval-2.3.1/tests/regression/se/trimfixed/3p_both_set/input_1.fastq000066400000000000000000000003431350370616400273040ustar00rootroot00000000000000@AAGGGCSeq_1_5180_50/1 ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG + IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! adapterremoval-2.3.1/tests/regression/se/trimfixed/3p_both_set/your_output.discarded000066400000000000000000000000001350370616400311350ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/se/trimfixed/3p_both_set/your_output.settings000066400000000000000000000030061350370616400310640ustar00rootroot00000000000000AdapterRemoval ver. 2.1.7 Trimming of single-end reads [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 667770639 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 5 20 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 Minimum adapter overlap: 0 [Trimming statistics] Total number of reads: 1 Number of unaligned reads: 0 Number of well aligned reads: 1 Number of discarded mate 1 reads: 0 Number of singleton mate 1 reads: 1 Number of reads with adapters[1]: 1 Number of retained reads: 1 Number of retained nucleotides: 45 Average length of retained reads: 45 [Length distribution] Length Mate1 Discarded All 0 0 0 0 1 0 0 0 2 0 0 0 3 0 0 0 4 0 0 0 5 0 0 0 6 0 0 0 7 0 0 0 8 0 0 0 9 0 0 0 10 0 0 0 11 0 0 0 12 0 0 0 13 0 0 0 14 0 0 0 15 0 0 0 16 0 0 0 17 0 0 0 18 0 0 0 19 0 0 0 20 0 0 0 21 0 0 0 22 0 0 0 23 0 0 0 24 0 0 0 25 0 0 0 26 0 0 0 27 0 0 0 28 0 0 0 29 0 0 0 30 0 0 0 31 0 0 0 32 0 0 0 33 0 0 0 34 0 0 0 35 0 0 0 36 0 0 0 37 0 0 0 38 0 0 0 39 0 0 0 40 0 0 0 41 0 0 0 42 0 0 0 43 0 0 0 44 0 0 0 45 1 0 1 adapterremoval-2.3.1/tests/regression/se/trimfixed/3p_both_set/your_output.truncated000066400000000000000000000001651350370616400312200ustar00rootroot00000000000000@AAGGGCSeq_1_5180_50/1 ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCA + IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFF adapterremoval-2.3.1/tests/regression/se/trimfixed/5p/000077500000000000000000000000001350370616400230005ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/se/trimfixed/5p/info.json000066400000000000000000000001101350370616400246160ustar00rootroot00000000000000{ "arguments": ["--trim5p", "5"], "return_code": 0, "stderr": [ ] } adapterremoval-2.3.1/tests/regression/se/trimfixed/5p/input_1.fastq000066400000000000000000000003431350370616400254170ustar00rootroot00000000000000@AAGGGCSeq_1_5180_50/1 ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG + IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! adapterremoval-2.3.1/tests/regression/se/trimfixed/5p/your_output.discarded000066400000000000000000000000001350370616400272500ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/se/trimfixed/5p/your_output.settings000066400000000000000000000030031350370616400271740ustar00rootroot00000000000000AdapterRemoval ver. 2.1.7 Trimming of single-end reads [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 667770639 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 5 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 Minimum adapter overlap: 0 [Trimming statistics] Total number of reads: 1 Number of unaligned reads: 0 Number of well aligned reads: 1 Number of discarded mate 1 reads: 0 Number of singleton mate 1 reads: 1 Number of reads with adapters[1]: 1 Number of retained reads: 1 Number of retained nucleotides: 45 Average length of retained reads: 45 [Length distribution] Length Mate1 Discarded All 0 0 0 0 1 0 0 0 2 0 0 0 3 0 0 0 4 0 0 0 5 0 0 0 6 0 0 0 7 0 0 0 8 0 0 0 9 0 0 0 10 0 0 0 11 0 0 0 12 0 0 0 13 0 0 0 14 0 0 0 15 0 0 0 16 0 0 0 17 0 0 0 18 0 0 0 19 0 0 0 20 0 0 0 21 0 0 0 22 0 0 0 23 0 0 0 24 0 0 0 25 0 0 0 26 0 0 0 27 0 0 0 28 0 0 0 29 0 0 0 30 0 0 0 31 0 0 0 32 0 0 0 33 0 0 0 34 0 0 0 35 0 0 0 36 0 0 0 37 0 0 0 38 0 0 0 39 0 0 0 40 0 0 0 41 0 0 0 42 0 0 0 43 0 0 0 44 0 0 0 45 1 0 1 adapterremoval-2.3.1/tests/regression/se/trimfixed/5p/your_output.truncated000066400000000000000000000001651350370616400273330ustar00rootroot00000000000000@AAGGGCSeq_1_5180_50/1 ACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCT + JIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECC adapterremoval-2.3.1/tests/regression/se/trimfixed/5p_and_3p/000077500000000000000000000000001350370616400242245ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/se/trimfixed/5p_and_3p/info.json000066400000000000000000000001311350370616400260450ustar00rootroot00000000000000{ "arguments": ["--trim5p", "4", "--trim3p", "5"], "return_code": 0, "stderr": [ ] } adapterremoval-2.3.1/tests/regression/se/trimfixed/5p_and_3p/input_1.fastq000066400000000000000000000003431350370616400266430ustar00rootroot00000000000000@AAGGGCSeq_1_5180_50/1 ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG + IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! adapterremoval-2.3.1/tests/regression/se/trimfixed/5p_and_3p/your_output.discarded000066400000000000000000000000001350370616400304740ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/se/trimfixed/5p_and_3p/your_output.settings000066400000000000000000000027371350370616400304350ustar00rootroot00000000000000AdapterRemoval ver. 2.1.7 Trimming of single-end reads [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 667770639 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 4 Trimming 3p: 5 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 Minimum adapter overlap: 0 [Trimming statistics] Total number of reads: 1 Number of unaligned reads: 0 Number of well aligned reads: 1 Number of discarded mate 1 reads: 0 Number of singleton mate 1 reads: 1 Number of reads with adapters[1]: 1 Number of retained reads: 1 Number of retained nucleotides: 41 Average length of retained reads: 41 [Length distribution] Length Mate1 Discarded All 0 0 0 0 1 0 0 0 2 0 0 0 3 0 0 0 4 0 0 0 5 0 0 0 6 0 0 0 7 0 0 0 8 0 0 0 9 0 0 0 10 0 0 0 11 0 0 0 12 0 0 0 13 0 0 0 14 0 0 0 15 0 0 0 16 0 0 0 17 0 0 0 18 0 0 0 19 0 0 0 20 0 0 0 21 0 0 0 22 0 0 0 23 0 0 0 24 0 0 0 25 0 0 0 26 0 0 0 27 0 0 0 28 0 0 0 29 0 0 0 30 0 0 0 31 0 0 0 32 0 0 0 33 0 0 0 34 0 0 0 35 0 0 0 36 0 0 0 37 0 0 0 38 0 0 0 39 0 0 0 40 0 0 0 41 1 0 1 adapterremoval-2.3.1/tests/regression/se/trimfixed/5p_and_3p/your_output.truncated000066400000000000000000000001551350370616400305560ustar00rootroot00000000000000@AAGGGCSeq_1_5180_50/1 GACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCA + JJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFF adapterremoval-2.3.1/tests/regression/se/trimfixed/5p_and_3p_both_set/000077500000000000000000000000001350370616400261135ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/se/trimfixed/5p_and_3p_both_set/info.json000066400000000000000000000001431350370616400277370ustar00rootroot00000000000000{ "arguments": ["--trim5p", "4", "3", "--trim3p", "5", "7"], "return_code": 0, "stderr": [ ] } adapterremoval-2.3.1/tests/regression/se/trimfixed/5p_and_3p_both_set/input_1.fastq000066400000000000000000000003431350370616400305320ustar00rootroot00000000000000@AAGGGCSeq_1_5180_50/1 ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG + IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! adapterremoval-2.3.1/tests/regression/se/trimfixed/5p_and_3p_both_set/your_output.discarded000066400000000000000000000000001350370616400323630ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/se/trimfixed/5p_and_3p_both_set/your_output.settings000066400000000000000000000027431350370616400323210ustar00rootroot00000000000000AdapterRemoval ver. 2.1.7 Trimming of single-end reads [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 667770639 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 4 3 Trimming 3p: 5 7 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 Minimum adapter overlap: 0 [Trimming statistics] Total number of reads: 1 Number of unaligned reads: 0 Number of well aligned reads: 1 Number of discarded mate 1 reads: 0 Number of singleton mate 1 reads: 1 Number of reads with adapters[1]: 1 Number of retained reads: 1 Number of retained nucleotides: 41 Average length of retained reads: 41 [Length distribution] Length Mate1 Discarded All 0 0 0 0 1 0 0 0 2 0 0 0 3 0 0 0 4 0 0 0 5 0 0 0 6 0 0 0 7 0 0 0 8 0 0 0 9 0 0 0 10 0 0 0 11 0 0 0 12 0 0 0 13 0 0 0 14 0 0 0 15 0 0 0 16 0 0 0 17 0 0 0 18 0 0 0 19 0 0 0 20 0 0 0 21 0 0 0 22 0 0 0 23 0 0 0 24 0 0 0 25 0 0 0 26 0 0 0 27 0 0 0 28 0 0 0 29 0 0 0 30 0 0 0 31 0 0 0 32 0 0 0 33 0 0 0 34 0 0 0 35 0 0 0 36 0 0 0 37 0 0 0 38 0 0 0 39 0 0 0 40 0 0 0 41 1 0 1 adapterremoval-2.3.1/tests/regression/se/trimfixed/5p_and_3p_both_set/your_output.truncated000066400000000000000000000001551350370616400324450ustar00rootroot00000000000000@AAGGGCSeq_1_5180_50/1 GACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCA + JJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFF adapterremoval-2.3.1/tests/regression/se/trimfixed/5p_both_set/000077500000000000000000000000001350370616400246675ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/se/trimfixed/5p_both_set/info.json000066400000000000000000000001161350370616400265130ustar00rootroot00000000000000{ "arguments": ["--trim5p", "5", "20"], "return_code": 0, "stderr": [ ] } adapterremoval-2.3.1/tests/regression/se/trimfixed/5p_both_set/input_1.fastq000066400000000000000000000003431350370616400273060ustar00rootroot00000000000000@AAGGGCSeq_1_5180_50/1 ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG + IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! adapterremoval-2.3.1/tests/regression/se/trimfixed/5p_both_set/your_output.discarded000066400000000000000000000000001350370616400311370ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/se/trimfixed/5p_both_set/your_output.settings000066400000000000000000000030061350370616400310660ustar00rootroot00000000000000AdapterRemoval ver. 2.1.7 Trimming of single-end reads [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 667770639 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 5 20 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 Minimum adapter overlap: 0 [Trimming statistics] Total number of reads: 1 Number of unaligned reads: 0 Number of well aligned reads: 1 Number of discarded mate 1 reads: 0 Number of singleton mate 1 reads: 1 Number of reads with adapters[1]: 1 Number of retained reads: 1 Number of retained nucleotides: 45 Average length of retained reads: 45 [Length distribution] Length Mate1 Discarded All 0 0 0 0 1 0 0 0 2 0 0 0 3 0 0 0 4 0 0 0 5 0 0 0 6 0 0 0 7 0 0 0 8 0 0 0 9 0 0 0 10 0 0 0 11 0 0 0 12 0 0 0 13 0 0 0 14 0 0 0 15 0 0 0 16 0 0 0 17 0 0 0 18 0 0 0 19 0 0 0 20 0 0 0 21 0 0 0 22 0 0 0 23 0 0 0 24 0 0 0 25 0 0 0 26 0 0 0 27 0 0 0 28 0 0 0 29 0 0 0 30 0 0 0 31 0 0 0 32 0 0 0 33 0 0 0 34 0 0 0 35 0 0 0 36 0 0 0 37 0 0 0 38 0 0 0 39 0 0 0 40 0 0 0 41 0 0 0 42 0 0 0 43 0 0 0 44 0 0 0 45 1 0 1 adapterremoval-2.3.1/tests/regression/se/trimfixed/5p_both_set/your_output.truncated000066400000000000000000000001651350370616400312220ustar00rootroot00000000000000@AAGGGCSeq_1_5180_50/1 ACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCT + JIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECC adapterremoval-2.3.1/tests/regression/se/trimfixed/collapse_5p/000077500000000000000000000000001350370616400246625ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/se/trimfixed/collapse_5p/info.json000066400000000000000000000001261350370616400265070ustar00rootroot00000000000000{ "arguments": ["--collapse", "--trim5p", "7"], "return_code": 0, "stderr": [ ] } adapterremoval-2.3.1/tests/regression/se/trimfixed/collapse_5p/input_1.fastq000066400000000000000000000003551350370616400273040ustar00rootroot00000000000000@AAGGGCSeq_1_5180_50/1 meta data ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG + IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! adapterremoval-2.3.1/tests/regression/se/trimfixed/collapse_5p/your_output.collapsed000066400000000000000000000001751350370616400311730ustar00rootroot00000000000000@M_AAGGGCSeq_1_5180_50/1 meta data TAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCT + JIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECC adapterremoval-2.3.1/tests/regression/se/trimfixed/collapse_5p/your_output.collapsed.truncated000066400000000000000000000000001350370616400331460ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/se/trimfixed/collapse_5p/your_output.discarded000066400000000000000000000000001350370616400311320ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/se/trimfixed/collapse_5p/your_output.settings000066400000000000000000000034171350370616400310670ustar00rootroot00000000000000AdapterRemoval ver. 2.1.7 Trimming of single-end reads [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 566778642 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 7 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: Yes Minimum overlap (in case of collapse): 11 Minimum adapter overlap: 0 [Trimming statistics] Total number of reads: 1 Number of unaligned reads: 0 Number of well aligned reads: 1 Number of discarded mate 1 reads: 0 Number of singleton mate 1 reads: 0 Number of reads with adapters[1]: 1 Number of full-length collapsed pairs: 1 Number of truncated collapsed pairs: 0 Number of retained reads: 1 Number of retained nucleotides: 43 Average length of retained reads: 43 [Length distribution] Length Mate1 Collapsed CollapsedTruncated Discarded All 0 0 0 0 0 0 1 0 0 0 0 0 2 0 0 0 0 0 3 0 0 0 0 0 4 0 0 0 0 0 5 0 0 0 0 0 6 0 0 0 0 0 7 0 0 0 0 0 8 0 0 0 0 0 9 0 0 0 0 0 10 0 0 0 0 0 11 0 0 0 0 0 12 0 0 0 0 0 13 0 0 0 0 0 14 0 0 0 0 0 15 0 0 0 0 0 16 0 0 0 0 0 17 0 0 0 0 0 18 0 0 0 0 0 19 0 0 0 0 0 20 0 0 0 0 0 21 0 0 0 0 0 22 0 0 0 0 0 23 0 0 0 0 0 24 0 0 0 0 0 25 0 0 0 0 0 26 0 0 0 0 0 27 0 0 0 0 0 28 0 0 0 0 0 29 0 0 0 0 0 30 0 0 0 0 0 31 0 0 0 0 0 32 0 0 0 0 0 33 0 0 0 0 0 34 0 0 0 0 0 35 0 0 0 0 0 36 0 0 0 0 0 37 0 0 0 0 0 38 0 0 0 0 0 39 0 0 0 0 0 40 0 0 0 0 0 41 0 0 0 0 0 42 0 0 0 0 0 43 0 1 0 0 1 adapterremoval-2.3.1/tests/regression/se/trimfixed/collapse_5p/your_output.truncated000066400000000000000000000000001350370616400312010ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/se/trimfixed/collapse_5p_and_3p/000077500000000000000000000000001350370616400261065ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/se/trimfixed/collapse_5p_and_3p/info.json000066400000000000000000000001471350370616400277360ustar00rootroot00000000000000{ "arguments": ["--collapse", "--trim5p", "4", "--trim3p", "5"], "return_code": 0, "stderr": [ ] } adapterremoval-2.3.1/tests/regression/se/trimfixed/collapse_5p_and_3p/input_1.fastq000066400000000000000000000003551350370616400305300ustar00rootroot00000000000000@AAGGGCSeq_1_5180_50/1 meta data ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG + IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! adapterremoval-2.3.1/tests/regression/se/trimfixed/collapse_5p_and_3p/your_output.collapsed000066400000000000000000000001711350370616400324130ustar00rootroot00000000000000@M_AAGGGCSeq_1_5180_50/1 meta data GACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCA + JJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFF your_output.collapsed.truncated000066400000000000000000000000001350370616400343130ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/se/trimfixed/collapse_5p_and_3padapterremoval-2.3.1/tests/regression/se/trimfixed/collapse_5p_and_3p/your_output.discarded000066400000000000000000000000001350370616400323560ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/se/trimfixed/collapse_5p_and_3p/your_output.settings000066400000000000000000000033651350370616400323150ustar00rootroot00000000000000AdapterRemoval ver. 2.1.7 Trimming of single-end reads [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 566778642 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 4 Trimming 3p: 5 Trimming Ns: No Trimming Phred scores <= 2: No Trimming using sliding windows: No Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: Yes Minimum overlap (in case of collapse): 11 Minimum adapter overlap: 0 [Trimming statistics] Total number of reads: 1 Number of unaligned reads: 0 Number of well aligned reads: 1 Number of discarded mate 1 reads: 0 Number of singleton mate 1 reads: 0 Number of reads with adapters[1]: 1 Number of full-length collapsed pairs: 1 Number of truncated collapsed pairs: 0 Number of retained reads: 1 Number of retained nucleotides: 41 Average length of retained reads: 41 [Length distribution] Length Mate1 Collapsed CollapsedTruncated Discarded All 0 0 0 0 0 0 1 0 0 0 0 0 2 0 0 0 0 0 3 0 0 0 0 0 4 0 0 0 0 0 5 0 0 0 0 0 6 0 0 0 0 0 7 0 0 0 0 0 8 0 0 0 0 0 9 0 0 0 0 0 10 0 0 0 0 0 11 0 0 0 0 0 12 0 0 0 0 0 13 0 0 0 0 0 14 0 0 0 0 0 15 0 0 0 0 0 16 0 0 0 0 0 17 0 0 0 0 0 18 0 0 0 0 0 19 0 0 0 0 0 20 0 0 0 0 0 21 0 0 0 0 0 22 0 0 0 0 0 23 0 0 0 0 0 24 0 0 0 0 0 25 0 0 0 0 0 26 0 0 0 0 0 27 0 0 0 0 0 28 0 0 0 0 0 29 0 0 0 0 0 30 0 0 0 0 0 31 0 0 0 0 0 32 0 0 0 0 0 33 0 0 0 0 0 34 0 0 0 0 0 35 0 0 0 0 0 36 0 0 0 0 0 37 0 0 0 0 0 38 0 0 0 0 0 39 0 0 0 0 0 40 0 0 0 0 0 41 0 1 0 0 1 adapterremoval-2.3.1/tests/regression/se/trimfixed/collapse_5p_and_3p/your_output.truncated000066400000000000000000000000001350370616400324250ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/trimwindows/000077500000000000000000000000001350370616400224405ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/trimwindows/pe/000077500000000000000000000000001350370616400230445ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/trimwindows/pe/excl_n/000077500000000000000000000000001350370616400243145ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/trimwindows/pe/excl_n/info.json000066400000000000000000000001431350370616400261400ustar00rootroot00000000000000{ "arguments": ["--trimwindows", "4", "--minquality", "20"], "return_code": 0, "stderr": [ ] } adapterremoval-2.3.1/tests/regression/trimwindows/pe/excl_n/input_1.fastq000066400000000000000000000001641350370616400267340ustar00rootroot00000000000000@ATAGCCSeq_1_2959_500/1 meta data TCCANNTCAACAATAGGGTTTACGACCTCGATGNTGGAT + 7555IIIIIJJGJHGJJJGHJJJFGIIIGFC?:75565+ adapterremoval-2.3.1/tests/regression/trimwindows/pe/excl_n/input_2.fastq000066400000000000000000000001161350370616400267320ustar00rootroot00000000000000@ATAGCCSeq_1_2959_500/2 data meta GTCAGCGAAGGGTTGTAGTA + IGHHFEIIIGFC5675565+ adapterremoval-2.3.1/tests/regression/trimwindows/pe/excl_n/your_output.discarded000066400000000000000000000000761350370616400306010ustar00rootroot00000000000000@ATAGCCSeq_1_2959_500/2 data meta GTCAGCGAAGGG + IGHHFEIIIGFC adapterremoval-2.3.1/tests/regression/trimwindows/pe/excl_n/your_output.pair1.truncated000066400000000000000000000000001350370616400316460ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/trimwindows/pe/excl_n/your_output.pair2.truncated000066400000000000000000000000001350370616400316470ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/trimwindows/pe/excl_n/your_output.settings000066400000000000000000000031051350370616400305130ustar00rootroot00000000000000AdapterRemoval ver. 2.1.7 Trimming of paired-end reads [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 981230521 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 20: Yes Trimming using sliding windows: 4 Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 [Trimming statistics] Total number of read pairs: 1 Number of unaligned read pairs: 0 Number of well aligned read pairs: 1 Number of discarded mate 1 reads: 0 Number of singleton mate 1 reads: 1 Number of discarded mate 2 reads: 1 Number of singleton mate 2 reads: 0 Number of reads with adapters[1]: 0 Number of retained reads: 1 Number of retained nucleotides: 30 Average length of retained reads: 30 [Length distribution] Length Mate1 Mate2 Singleton Discarded All 0 0 0 0 0 0 1 0 0 0 0 0 2 0 0 0 0 0 3 0 0 0 0 0 4 0 0 0 0 0 5 0 0 0 0 0 6 0 0 0 0 0 7 0 0 0 0 0 8 0 0 0 0 0 9 0 0 0 0 0 10 0 0 0 0 0 11 0 0 0 0 0 12 0 0 0 1 1 13 0 0 0 0 0 14 0 0 0 0 0 15 0 0 0 0 0 16 0 0 0 0 0 17 0 0 0 0 0 18 0 0 0 0 0 19 0 0 0 0 0 20 0 0 0 0 0 21 0 0 0 0 0 22 0 0 0 0 0 23 0 0 0 0 0 24 0 0 0 0 0 25 0 0 0 0 0 26 0 0 0 0 0 27 0 0 0 0 0 28 0 0 0 0 0 29 0 0 0 0 0 30 0 0 1 0 1 adapterremoval-2.3.1/tests/regression/trimwindows/pe/excl_n/your_output.singleton.truncated000066400000000000000000000001421350370616400326430ustar00rootroot00000000000000@ATAGCCSeq_1_2959_500/1 meta data NNTCAACAATAGGGTTTACGACCTCGATGN + IIIIIJJGJHGJJJGHJJJFGIIIGFC?:7 adapterremoval-2.3.1/tests/regression/trimwindows/pe/incl_n/000077500000000000000000000000001350370616400243065ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/trimwindows/pe/incl_n/info.json000066400000000000000000000001571350370616400261370ustar00rootroot00000000000000{ "arguments": ["--trimwindows", "4", "--minquality", "20", "--trimns"], "return_code": 0, "stderr": [ ] } adapterremoval-2.3.1/tests/regression/trimwindows/pe/incl_n/input_1.fastq000066400000000000000000000001641350370616400267260ustar00rootroot00000000000000@ATAGCCSeq_1_2959_500/1 meta data TCCANNTCAACAATAGGGTTTACGACCTCGATGNTGGAT + 7555IIIIIJJGJHGJJJGHJJJFGIIIGFC?:75565+ adapterremoval-2.3.1/tests/regression/trimwindows/pe/incl_n/input_2.fastq000066400000000000000000000001161350370616400267240ustar00rootroot00000000000000@ATAGCCSeq_1_2959_500/2 data meta GTCAGCGAAGGGTTGTAGTA + IGHHFEIIIGFC5675565+ adapterremoval-2.3.1/tests/regression/trimwindows/pe/incl_n/your_output.discarded000066400000000000000000000000761350370616400305730ustar00rootroot00000000000000@ATAGCCSeq_1_2959_500/2 data meta GTCAGCGAAGGG + IGHHFEIIIGFC adapterremoval-2.3.1/tests/regression/trimwindows/pe/incl_n/your_output.pair1.truncated000066400000000000000000000000001350370616400316400ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/trimwindows/pe/incl_n/your_output.pair2.truncated000066400000000000000000000000001350370616400316410ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/trimwindows/pe/incl_n/your_output.settings000066400000000000000000000030371350370616400305110ustar00rootroot00000000000000AdapterRemoval ver. 2.1.7 Trimming of paired-end reads [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 981230521 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: Yes Trimming Phred scores <= 20: Yes Trimming using sliding windows: 4 Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 [Trimming statistics] Total number of read pairs: 1 Number of unaligned read pairs: 0 Number of well aligned read pairs: 1 Number of discarded mate 1 reads: 0 Number of singleton mate 1 reads: 1 Number of discarded mate 2 reads: 1 Number of singleton mate 2 reads: 0 Number of reads with adapters[1]: 0 Number of retained reads: 1 Number of retained nucleotides: 27 Average length of retained reads: 27 [Length distribution] Length Mate1 Mate2 Singleton Discarded All 0 0 0 0 0 0 1 0 0 0 0 0 2 0 0 0 0 0 3 0 0 0 0 0 4 0 0 0 0 0 5 0 0 0 0 0 6 0 0 0 0 0 7 0 0 0 0 0 8 0 0 0 0 0 9 0 0 0 0 0 10 0 0 0 0 0 11 0 0 0 0 0 12 0 0 0 1 1 13 0 0 0 0 0 14 0 0 0 0 0 15 0 0 0 0 0 16 0 0 0 0 0 17 0 0 0 0 0 18 0 0 0 0 0 19 0 0 0 0 0 20 0 0 0 0 0 21 0 0 0 0 0 22 0 0 0 0 0 23 0 0 0 0 0 24 0 0 0 0 0 25 0 0 0 0 0 26 0 0 0 0 0 27 0 0 1 0 1 adapterremoval-2.3.1/tests/regression/trimwindows/pe/incl_n/your_output.singleton.truncated000066400000000000000000000001341350370616400326360ustar00rootroot00000000000000@ATAGCCSeq_1_2959_500/1 meta data TCAACAATAGGGTTTACGACCTCGATG + IIIJJGJHGJJJGHJJJFGIIIGFC?: adapterremoval-2.3.1/tests/regression/trimwindows/se/000077500000000000000000000000001350370616400230475ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/trimwindows/se/excl_n/000077500000000000000000000000001350370616400243175ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/trimwindows/se/excl_n/info.json000066400000000000000000000001431350370616400261430ustar00rootroot00000000000000{ "arguments": ["--trimwindows", "4", "--minquality", "20"], "return_code": 0, "stderr": [ ] } adapterremoval-2.3.1/tests/regression/trimwindows/se/excl_n/input_1.fastq000066400000000000000000000001641350370616400267370ustar00rootroot00000000000000@ATAGCCSeq_1_2959_500/1 meta data TCCANNTCAACAATAGGGTTTACGACCTCGATGNTGGAT + 7555IIIIIJJGJHGJJJGHJJJFGIIIGFC?:75565+ adapterremoval-2.3.1/tests/regression/trimwindows/se/excl_n/your_output.discarded000066400000000000000000000000001350370616400305670ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/trimwindows/se/excl_n/your_output.settings000066400000000000000000000025761350370616400305310ustar00rootroot00000000000000AdapterRemoval ver. 2.1.7 Trimming of single-end reads [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 3702281079 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: No Trimming Phred scores <= 20: Yes Trimming using sliding windows: 4 Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 Minimum adapter overlap: 0 [Trimming statistics] Total number of reads: 1 Number of unaligned reads: 1 Number of well aligned reads: 0 Number of discarded mate 1 reads: 0 Number of singleton mate 1 reads: 1 Number of reads with adapters[1]: 0 Number of retained reads: 1 Number of retained nucleotides: 30 Average length of retained reads: 30 [Length distribution] Length Mate1 Discarded All 0 0 0 0 1 0 0 0 2 0 0 0 3 0 0 0 4 0 0 0 5 0 0 0 6 0 0 0 7 0 0 0 8 0 0 0 9 0 0 0 10 0 0 0 11 0 0 0 12 0 0 0 13 0 0 0 14 0 0 0 15 0 0 0 16 0 0 0 17 0 0 0 18 0 0 0 19 0 0 0 20 0 0 0 21 0 0 0 22 0 0 0 23 0 0 0 24 0 0 0 25 0 0 0 26 0 0 0 27 0 0 0 28 0 0 0 29 0 0 0 30 1 0 1 adapterremoval-2.3.1/tests/regression/trimwindows/se/excl_n/your_output.truncated000066400000000000000000000001421350370616400306450ustar00rootroot00000000000000@ATAGCCSeq_1_2959_500/1 meta data NNTCAACAATAGGGTTTACGACCTCGATGN + IIIIIJJGJHGJJJGHJJJFGIIIGFC?:7 adapterremoval-2.3.1/tests/regression/trimwindows/se/incl_n/000077500000000000000000000000001350370616400243115ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/trimwindows/se/incl_n/info.json000066400000000000000000000001571350370616400261420ustar00rootroot00000000000000{ "arguments": ["--trimwindows", "4", "--minquality", "20", "--trimns"], "return_code": 0, "stderr": [ ] } adapterremoval-2.3.1/tests/regression/trimwindows/se/incl_n/input_1.fastq000066400000000000000000000001641350370616400267310ustar00rootroot00000000000000@ATAGCCSeq_1_2959_500/1 meta data TCCANNTCAACAATAGGGTTTACGACCTCGATGNTGGAT + 7555IIIIIJJGJHGJJJGHJJJFGIIIGFC?:75565+ adapterremoval-2.3.1/tests/regression/trimwindows/se/incl_n/your_output.discarded000066400000000000000000000000001350370616400305610ustar00rootroot00000000000000adapterremoval-2.3.1/tests/regression/trimwindows/se/incl_n/your_output.settings000066400000000000000000000025441350370616400305160ustar00rootroot00000000000000AdapterRemoval ver. 2.1.7 Trimming of single-end reads [Adapter sequences] Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT [Adapter trimming] RNG seed: 3702281079 Alignment shift value: 2 Global mismatch threshold: 0.333333 Quality format (input): Phred+33 Quality score max (input): 41 Quality format (output): Phred+33 Quality score max (output): 41 Mate-number separator (input): '/' Trimming 5p: 0 Trimming 3p: 0 Trimming Ns: Yes Trimming Phred scores <= 20: Yes Trimming using sliding windows: 4 Minimum genomic length: 15 Maximum genomic length: 4294967295 Collapse overlapping reads: No Minimum overlap (in case of collapse): 11 Minimum adapter overlap: 0 [Trimming statistics] Total number of reads: 1 Number of unaligned reads: 1 Number of well aligned reads: 0 Number of discarded mate 1 reads: 0 Number of singleton mate 1 reads: 1 Number of reads with adapters[1]: 0 Number of retained reads: 1 Number of retained nucleotides: 27 Average length of retained reads: 27 [Length distribution] Length Mate1 Discarded All 0 0 0 0 1 0 0 0 2 0 0 0 3 0 0 0 4 0 0 0 5 0 0 0 6 0 0 0 7 0 0 0 8 0 0 0 9 0 0 0 10 0 0 0 11 0 0 0 12 0 0 0 13 0 0 0 14 0 0 0 15 0 0 0 16 0 0 0 17 0 0 0 18 0 0 0 19 0 0 0 20 0 0 0 21 0 0 0 22 0 0 0 23 0 0 0 24 0 0 0 25 0 0 0 26 0 0 0 27 1 0 1 adapterremoval-2.3.1/tests/regression/trimwindows/se/incl_n/your_output.truncated000066400000000000000000000001341350370616400306400ustar00rootroot00000000000000@ATAGCCSeq_1_2959_500/1 meta data TCAACAATAGGGTTTACGACCTCGATG + IIIJJGJHGJJJGHJJJFGIIIGFC?: adapterremoval-2.3.1/tests/unit/000077500000000000000000000000001350370616400166515ustar00rootroot00000000000000adapterremoval-2.3.1/tests/unit/alignment_test.cpp000066400000000000000000001374751350370616400224130ustar00rootroot00000000000000/*************************************************************************\ * AdapterRemoval - cleaning next-generation sequencing reads * * * * Copyright (C) 2011 by Stinus Lindgreen - stinus@binf.ku.dk * * Copyright (C) 2014 by Mikkel Schubert - mikkelsch@gmail.com * * * * If you use the program, please cite the paper: * * S. Lindgreen (2012): AdapterRemoval: Easy Cleaning of Next Generation * * Sequencing Reads, BMC Research Notes, 5:337 * * http://www.biomedcentral.com/1756-0500/5/337/ * * * * This program is free software: you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation, either version 3 of the License, or * * (at your option) any later version. * * * * This program is distributed in the hope that it will be useful, * * but WITHOUT ANY WARRANTY; without even the implied warranty of * * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * * GNU General Public License for more details. * * * * You should have received a copy of the GNU General Public License * * along with this program. If not, see . * \*************************************************************************/ #include #include #include #include "testing.hpp" #include "alignment.hpp" #include "fastq.hpp" #define TEST_ALIGNMENT_SETTER(TYPE, NAME) \ ALN& NAME(TYPE value) \ { \ info.adapter_id = 0; \ info.NAME = value; \ return *this; \ } namespace ar { bool operator==(const alignment_info& first, const alignment_info& second) { return (first.offset == second.offset) && (first.score == second.score) && (first.length == second.length) && (first.n_mismatches == second.n_mismatches) && (first.n_ambiguous == second.n_ambiguous) && (first.adapter_id == second.adapter_id); } struct ALN { ALN() : info() {} TEST_ALIGNMENT_SETTER(int, score); TEST_ALIGNMENT_SETTER(int, offset); TEST_ALIGNMENT_SETTER(size_t, length); TEST_ALIGNMENT_SETTER(size_t, n_mismatches); TEST_ALIGNMENT_SETTER(size_t, n_ambiguous); TEST_ALIGNMENT_SETTER(int, adapter_id); operator alignment_info() { return info; } alignment_info info; }; bool operator==(const alignment_info& first, const ALN& second) { return first == second.info; } std::ostream& operator<<(std::ostream& stream, const alignment_info& aln) { std::vector labels = { "score", "offset", "length", "n_mismatches", "n_ambiguous", "adapter_id" }; std::vector values = { static_cast(aln.score), static_cast(aln.offset), static_cast(aln.length), static_cast(aln.n_mismatches), static_cast(aln.n_ambiguous), static_cast(aln.adapter_id), }; stream << "alignment_info("; bool any_streamed = false; for (size_t i = 0; i < labels.size(); ++i) { if (values.at(i)) { if (any_streamed) { stream << "\n "; } stream << labels.at(i) << " = " << values.at(i); any_streamed = true; } } return stream << ")"; } void REQUIRE_TRUNCATED_PE_IS_UNCHANGED(const alignment_info& alignment, const fastq& record1, const fastq& record2) { fastq tmp_record1 = record1; fastq tmp_record2 = record2; REQUIRE(truncate_paired_ended_sequences(alignment, tmp_record1, tmp_record2) == 0); REQUIRE(tmp_record1 == record1); REQUIRE(tmp_record2 == record2); } fastq_pair_vec create_adapter_vec(const fastq& pcr1, const fastq& pcr2 = fastq()) { fastq_pair_vec adapters; adapters.push_back(fastq_pair(pcr1, pcr2)); return adapters; } std::random_device g_seed; std::mt19937 g_rng_instance(g_seed()); std::mt19937* g_rng(&g_rng_instance); /////////////////////////////////////////////////////////////////////////////// // Cases for SE alignments (a = read 1, b = adapter, o = overlap): // 1. No overlap = aaaaaa bbbbbb // 2. Partial overlap = aaaaaooobbbbbb // 3. Complete overlap = ooooooooo // 4. a contains b = aaaaoooooo // 5. b contains a = ooooobbbbb // 6. a extends past b = aaaaoooooaaaa // 7. b extends past a = bbbbooooobbbb // 8. both extends past other = bbbbooooaaaa /////////////////////////////////////////////////////////////////////////////// // Case 1: No overlap between sequences: // AAAAAAAAAAA // BBBBBBBBBBBBBBB // Expected result = suboptimal alignment or no overlap TEST_CASE("SE: Unalignable sequence yields default alignment", "[alignment::single_end]") { const fastq record("Rec", "AAAA", "!!!!"); const fastq_pair_vec adapters = create_adapter_vec(fastq("Rec", "TTTT", "!!!!")); REQUIRE(align_single_ended_sequence(record, adapters, 0) == ALN()); } TEST_CASE("SE: Random sequences yields suboptimal alignment", "[alignment::single_end]") { const fastq record("Rec", "ACGTAGTA", "!!!!!!!!"); const fastq_pair_vec adapters = create_adapter_vec(fastq("Rec", "TGAGACGGT", "!!!!!!!!!")); REQUIRE(align_single_ended_sequence(record, adapters, 0) == ALN().offset(6) .length(2) .n_mismatches(1)); } /////////////////////////////////////////////////////////////////////////////// // Case 2: Partial overlap between sequences: // AAAAAAAAAAA // BBBBBBBBBBBBBBB // Expected result = optimal alignment between ends TEST_CASE("SE: Partial alignment between ends", "[alignment::single_end]") { const fastq record("Rec", "ACGTAGTAA", "123457890"); const fastq_pair_vec adapters = create_adapter_vec(fastq("Rec", "AGTAAGGT", "!!!!!!!!")); const alignment_info expected = ALN().score(5).offset(4).length(5); const alignment_info result = align_single_ended_sequence(record, adapters, 0); REQUIRE(result == expected); fastq tmp_record = record; truncate_single_ended_sequence(result, tmp_record); REQUIRE(tmp_record == fastq("Rec", "ACGT", "1234")); } TEST_CASE("SE: Partial alignment with mismatches between ends", "[alignment::single_end]") { const fastq record("Rec", "ACGTAGTAA", "123457890"); const fastq_pair_vec adapters = create_adapter_vec(fastq("Rec", "AGGAAGGT", "!!!!!!!!")); const alignment_info expected = ALN().score(3).offset(4).length(5).n_mismatches(1); const alignment_info result = align_single_ended_sequence(record, adapters, 0); REQUIRE(result == expected); fastq tmp_record = record; truncate_single_ended_sequence(result, tmp_record); REQUIRE(tmp_record == fastq("Rec", "ACGT", "1234")); } TEST_CASE("SE: Partial alignment with ambiguous between ends", "[alignment::single_end]") { const fastq record("Rec", "ACGTAGTAA", "123457890"); const fastq_pair_vec adapters = create_adapter_vec(fastq("Rec", "AGNAAGGT", "!!!!!!!!")); const alignment_info expected = ALN().score(4).offset(4).length(5).n_ambiguous(1); const alignment_info result = align_single_ended_sequence(record, adapters, 0); REQUIRE(result == expected); fastq tmp_record = record; truncate_single_ended_sequence(result, tmp_record); REQUIRE(tmp_record == fastq("Rec", "ACGT", "1234")); } /////////////////////////////////////////////////////////////////////////////// // Case 3: Complete overlap between sequences: // AAAAAAAAAAA // BBBBBBBBBBB // Expected result = Optimal alignment involving all bases TEST_CASE("SE: Completely overlapping sequences", "[alignment::single_end]") { const fastq record("Rec", "ACGTAGTA", "!!!!!!!!"); const fastq_pair_vec adapters = create_adapter_vec(record); const alignment_info expected = ALN().score(8).length(8); const alignment_info result = align_single_ended_sequence(record, adapters, 0); REQUIRE(result == expected); fastq tmp_record = record; truncate_single_ended_sequence(result, tmp_record); REQUIRE(tmp_record == fastq("Rec", "", "")); } TEST_CASE("SE: Completely overlapping sequences with mismatches", "[alignment::single_end]") { const fastq record("Rec", "ACGTAGTA", "!!!!!!!!"); const fastq_pair_vec adapters = create_adapter_vec(fastq("Rec", "GCGTAGTA", "!!!!!!!!")); const alignment_info expected = ALN().score(6).length(8).n_mismatches(1); const alignment_info result = align_single_ended_sequence(record, adapters, 0); REQUIRE(result == expected); fastq tmp_record = record; truncate_single_ended_sequence(result, tmp_record); REQUIRE(tmp_record == fastq("Rec", "", "")); } TEST_CASE("SE: Completely overlapping sequences with mismatches and ambiguous", "[alignment::single_end]") { const fastq record("Rec", "ACGTAGTA", "!!!!!!!!"); const fastq_pair_vec adapter = create_adapter_vec(fastq("Rec", "GCGTAGTN", "!!!!!!!!")); const alignment_info expected = ALN().score(5).length(8).n_mismatches(1).n_ambiguous(1); const alignment_info result = align_single_ended_sequence(record, adapter, 0); REQUIRE(result == expected); fastq tmp_record = record; truncate_single_ended_sequence(result, tmp_record); REQUIRE(tmp_record == fastq("Rec", "", "")); } /////////////////////////////////////////////////////////////////////////////// // Cases 4 and 5: Sequence A completely contains sequence B (and vice versa) // AAAAAAAAAAA AAAA // BBBBB BBBBBBBBBB // Expected result = Optimal alignment involving all bases of the shortest read TEST_CASE("Complete adapter inside sequence", "[alignment::single_end]") { const fastq record("Rec", "ACGTAGTA", "ABCDEFGH"); const fastq_pair_vec adapters = create_adapter_vec(fastq("Adp", "TAGTA", "!!!!!")); const alignment_info expected = ALN().score(5).offset(3).length(5); const alignment_info result = align_single_ended_sequence(record, adapters, 0); REQUIRE(result == expected); fastq tmp_record = record; truncate_single_ended_sequence(result, tmp_record); REQUIRE(tmp_record == fastq("Rec", "ACG", "ABC")); } TEST_CASE("Complete adapter inside sequence with mismatch", "[alignment::single_end]") { const fastq record("Rec", "ACGTAGTA", "ABCDEFGH"); const fastq_pair_vec adapters = create_adapter_vec(fastq("Adp", "TATTA", "!!!!!")); const alignment_info expected = ALN().score(3).offset(3).length(5).n_mismatches(1); const alignment_info result = align_single_ended_sequence(record, adapters, 0); REQUIRE(result == expected); fastq tmp_record = record; truncate_single_ended_sequence(result, tmp_record); REQUIRE(tmp_record == fastq("Rec", "ACG", "ABC")); } TEST_CASE("Complete adapter inside sequence with ambiguous", "[alignment::single_end]") { const fastq record("Rec", "ACGTAGTA", "ABCDEFGH"); const fastq_pair_vec adapters = create_adapter_vec(fastq("Adp", "TAGNA", "!!!!!")); const alignment_info expected = ALN().score(4).offset(3).length(5).n_ambiguous(1); const alignment_info result = align_single_ended_sequence(record, adapters, 0); REQUIRE(result == expected); fastq tmp_record = record; truncate_single_ended_sequence(result, tmp_record); REQUIRE(tmp_record == fastq("Rec", "ACG", "ABC")); } TEST_CASE("Complete sequence inside adapter", "[alignment::single_end]") { const fastq record("Rec", "ACGT", "!!!!"); const fastq_pair_vec adapters = create_adapter_vec(fastq("Adp", "ACGTAGTA", "!!!!!!!!")); const alignment_info expected = ALN().score(4).length(4); const alignment_info result = align_single_ended_sequence(record, adapters, 0); REQUIRE(result == expected); fastq tmp_record = record; truncate_single_ended_sequence(result, tmp_record); REQUIRE(tmp_record == fastq("Rec", "", "")); } TEST_CASE("Complete sequence inside adapter with mismatches", "[alignment::single_end]") { const fastq record("Rec", "ACGT", "!!!!"); const fastq_pair_vec adapters = create_adapter_vec(fastq("Adp", "GCGTAGTA", "!!!!!!!!")); const alignment_info expected = ALN().score(2).length(4).n_mismatches(1); const alignment_info result = align_single_ended_sequence(record, adapters, 0); REQUIRE(result == expected); fastq tmp_record = record; truncate_single_ended_sequence(result, tmp_record); REQUIRE(tmp_record == fastq("Rec", "", "")); } TEST_CASE("Complete sequence inside adapter with ambiguous", "[alignment::single_end]") { const fastq record("Rec", "ACGT", "!!!!"); const fastq_pair_vec adapters = create_adapter_vec(fastq("Adp", "ACGNAGTA", "!!!!!!!!")); const alignment_info expected = ALN().score(3).length(4).n_ambiguous(1); const alignment_info result = align_single_ended_sequence(record, adapters, 0); REQUIRE(result == expected); fastq tmp_record = record; truncate_single_ended_sequence(result, tmp_record); REQUIRE(tmp_record == fastq("Rec", "", "")); } /////////////////////////////////////////////////////////////////////////////// // Cases 6 and 7: Sequence A extends past sequence B (and vice versa) // AAAAAAAAAAAAAA AAAA // BBBBB BBBBBBBBBBBBB TEST_CASE("Sequence extends past adapter", "[alignment::single_end]") { const fastq record("Rec", "ACGTAGTATA", "0123456789"); const fastq_pair_vec adapters = create_adapter_vec(fastq("Adp", "AGTA", "!!!!")); const alignment_info expected = ALN().score(4).offset(4).length(4); const alignment_info result = align_single_ended_sequence(record, adapters, 0); REQUIRE(result == expected); fastq tmp_record = record; truncate_single_ended_sequence(result, tmp_record); REQUIRE(tmp_record == fastq("Rec", "ACGT", "0123")); } TEST_CASE("Sequence extends past adapter, no shift", "[alignment::single_end]") { const fastq record("Rec", "CGTA", "#!%%"); const fastq_pair_vec adapters = create_adapter_vec(fastq("Adp", "ACGTAGTATA", "!!!!!!!!!!")); const alignment_info expected = ALN().score(1).offset(3).length(1); const alignment_info result = align_single_ended_sequence(record, adapters, 0); REQUIRE(result == expected); fastq tmp_record = record; truncate_single_ended_sequence(result, tmp_record); REQUIRE(tmp_record == fastq("Rec", "CGT", "#!%")); } TEST_CASE("Sequence extends past adapter, shift 1", "[alignment::single_end]") { const fastq record("Rec", "CGTA", "#!%%"); const fastq_pair_vec adapters = create_adapter_vec(fastq("Adp", "ACGTAGTATA", "!!!!!!!!!!")); const alignment_info expected = ALN().score(4).offset(-1).length(4); const alignment_info result = align_single_ended_sequence(record, adapters, 1); REQUIRE(result == expected); fastq tmp_record = record; truncate_single_ended_sequence(result, tmp_record); REQUIRE(tmp_record == fastq("Rec", "", "")); } /////////////////////////////////////////////////////////////////////////////// // Cases 8: Both sequences extends past the other // AAAAAAAAAAAAAAAAAA // BBBBBBBBBBBBBBBBBB // Expected result = Optimal alignment involving all overlapping bases TEST_CASE("Sequence and adapter extends past each other", "[alignment::single_end]") { const fastq record("Rec", "ACGTAGTATATAGT", "!!!!!!!!!!!!!!"); const fastq_pair_vec adapters = create_adapter_vec(fastq("Adp", "CCGAACGTAGTATA", "!!!!!!!!!!!!!!")); const alignment_info expected = ALN().score(10).offset(-4).length(10); const alignment_info result = align_single_ended_sequence(record, adapters, 4); REQUIRE(result == expected); fastq tmp_record = record; truncate_single_ended_sequence(result, tmp_record); REQUIRE(tmp_record == fastq("Rec", "", "")); } /////////////////////////////////////////////////////////////////////////////// // Empty sequence or adapter TEST_CASE("Empty sequence alignment", "[alignment::single_end]") { const fastq record; const fastq_pair_vec adapters = create_adapter_vec(fastq("Adp", "CCGAACGTAGTATA", "!!!!!!!!!!!!!!")); const alignment_info expected; const alignment_info result = align_single_ended_sequence(record, adapters, 0); REQUIRE(result == expected); } TEST_CASE("Empty adapter alignment", "[alignment::single_end]") { const fastq record("Rec", "ACGTAGTATATAGT", "!!!!!!!!!!!!!!"); const fastq_pair_vec adapters = create_adapter_vec(fastq()); const alignment_info expected; const alignment_info result = align_single_ended_sequence(record, adapters, 0); REQUIRE(result == expected); } /////////////////////////////////////////////////////////////////////////////// // Misc TEST_CASE("Lower than possible shift is allowed", "[alignment::single_end]") { const fastq record("Rec", "AAAA", "!!!!"); const fastq_pair_vec adapters = create_adapter_vec(fastq("Adp", "TTTT", "!!!!")); const alignment_info expected; const alignment_info result = align_single_ended_sequence(record, adapters, -10); REQUIRE(result == expected); } TEST_CASE("Only adapter 1 is used", "[alignment::single_end]") { const fastq_pair_vec adapters = create_adapter_vec(fastq("barcode", "AAA", "JJJ"), fastq("barcode", "TTTAAA", "JJJJJJ")); const fastq record("Rec", "CCCCTTTAAA", "0987654321"); const alignment_info expected = ALN().score(3).offset(7).length(3); const alignment_info result = align_single_ended_sequence(record, adapters, 0); REQUIRE(result == expected); } TEST_CASE("Best matching adapter is returned: First", "[alignment::single_end]") { fastq_pair_vec adapters; adapters.push_back(fastq_pair(fastq("adapter", "TGCTGC", "JJJJJJ"), fastq())); adapters.push_back(fastq_pair(fastq("adapter", "TGCTGA", "JJJJJJ"), fastq())); const fastq record("Read", "TAGTCGCTATGCTGC", "!!!!!!!!!103459"); const alignment_info expected = ALN().score(6).offset(9).length(6); const alignment_info result = align_single_ended_sequence(record, adapters, 0); REQUIRE(result == expected); } TEST_CASE("Best matching adapter returned: Second", "[alignment::single_end]") { fastq_pair_vec adapters; adapters.push_back(fastq_pair(fastq("adapter", "TGCTGA", "JJJJJJ"), fastq())); adapters.push_back(fastq_pair(fastq("adapter", "TGCTGC", "JJJJJJ"), fastq())); const fastq record("Read", "TAGTCGCTATGCTGC", "!!!!!!!!!103459"); const alignment_info expected = ALN().score(6).offset(9).length(6).adapter_id(1); const alignment_info result = align_single_ended_sequence(record, adapters, 0); REQUIRE(result == expected); } TEST_CASE("Best matching adapter returned: Neither", "[alignment::single_end]") { fastq_pair_vec barcodes; barcodes.push_back(fastq_pair(fastq("barcode", "AAAAAA", "JJJJJJ"), fastq())); barcodes.push_back(fastq_pair(fastq("barcode", "CCCCCC", "JJJJJJ"), fastq())); const fastq record = fastq("Read", "AACTGTACGTAGTT", "!!!!!!10345923"); const alignment_info result = align_single_ended_sequence(record, barcodes, 0); REQUIRE(result == ALN()); } /////////////////////////////////////////////////////////////////////////////// // Case 1 PE: No overlap between sequences: // AAAAAAAAAAA // BBBBBBBBBBBBBBB // Expected result = suboptimal alignment or no overlap TEST_CASE("Unalignable sequence pair", "[alignment::paired_end]") { const fastq record1("Rec", "AAAA", "!!!!"); const fastq record2("Rec", "TTTT", "!!!!"); const fastq_pair_vec adapters = create_adapter_vec(fastq("PCR1", "CGCTGA", "!!!!!!"), fastq("PCR2", "TGTAC", "!!!!!")); const alignment_info expected; const alignment_info result = align_paired_ended_sequences(record1, record2, adapters, 0); REQUIRE(result == expected); REQUIRE_TRUNCATED_PE_IS_UNCHANGED(result, record1, record2); } TEST_CASE("No overlap in sequence pair", "[alignment::paired_end]") { const fastq record1("Rec", "ACGTAGTA", "!!!!!!!!"); const fastq record2("Rec", "TGAGACGGT", "!!!!!!!!!"); const fastq_pair_vec adapters = create_adapter_vec(fastq("PCR1", "CGCTGA", "!!!!!!"), fastq("PCR2", "TGTAC", "!!!!!")); const alignment_info expected = ALN().offset(6).length(2).n_mismatches(1); const alignment_info result = align_paired_ended_sequences(record1, record2, adapters, 0); REQUIRE(result == expected); REQUIRE_TRUNCATED_PE_IS_UNCHANGED(result, record1, record2); } /////////////////////////////////////////////////////////////////////////////// // Case 2 PE: Partial overlap between sequences: // AAAAAAAAAAA // BBBBBBBBBBBBBBB // Expected result = optimal alignment between ends TEST_CASE("Partial overlap in sequence pair", "[alignment::paired_end]") { const fastq record1("Rec", "ACGTAGTAA", "!!!!!!!!!"); const fastq record2("Rec", "AGTAAGGT", "!!!!!!!!"); const fastq_pair_vec adapters = create_adapter_vec(fastq("PCR1", "CGCTGA", "!!!!!!"), fastq("PCR2", "TGTAC", "!!!!!")); const alignment_info expected = ALN().score(5).offset(4).length(5); const alignment_info result = align_paired_ended_sequences(record1, record2, adapters, 0); REQUIRE(result == expected); REQUIRE_TRUNCATED_PE_IS_UNCHANGED(result, record1, record2); } /////////////////////////////////////////////////////////////////////////////// // Case 3 PE: Complete overlap between sequences: // AAAAAAAAAAA // BBBBBBBBBBB // Expected result = Optimal alignment involving all bases TEST_CASE("Completely overlapping sequence pair", "[alignment::paired_end]") { const fastq record1("Rec", "ACGTAGTA", "!!!!!!!!"); const fastq record2 = record1; const fastq_pair_vec adapters = create_adapter_vec(fastq("PCR1", "CGCTGA", "!!!!!!"), fastq("PCR2", "TGTAC", "!!!!!")); const alignment_info expected = ALN().score(8).length(8); const alignment_info result = align_paired_ended_sequences(record1, record2, adapters, 0); REQUIRE(result == expected); REQUIRE_TRUNCATED_PE_IS_UNCHANGED(result, record1, record2); } /////////////////////////////////////////////////////////////////////////////// // Cases 4 and 5 PE: Sequence A completely contains sequence B (and vice versa) // AAAAAAAAAAA AAAA // BBBBB BBBBBBBBBB // Expected result = Optimal alignment involving all bases of the shortest read TEST_CASE("Sequence A contains sequence B", "[alignment::paired_end]") { const fastq record1("Rec1", "ACGTAGTA", "!!!!!!!!"); const fastq record2("Rec2", "TAGTA", "!!!!!"); const fastq_pair_vec adapters = create_adapter_vec(fastq("PCR1", "CGCTGA", "!!!!!!"), fastq("PCR2", "TGTAC", "!!!!!")); const alignment_info expected = ALN().score(5).offset(3).length(5); const alignment_info result = align_paired_ended_sequences(record1, record2, adapters, 0); REQUIRE(result == expected); REQUIRE_TRUNCATED_PE_IS_UNCHANGED(result, record1, record2); } TEST_CASE("Sequence B contains sequence A", "[alignment::paired_end]") { const fastq record1("Rec1", "ACGT", "!!!!"); const fastq record2("Rec2", "ACGTAGTA", "!!!!!!!!"); const fastq_pair_vec adapters = create_adapter_vec(fastq("PCR1", "CGCTGA", "!!!!!!"), fastq("PCR2", "TGTAC", "!!!!!")); const alignment_info expected = ALN().score(4).length(4); const alignment_info result = align_paired_ended_sequences(record1, record2, adapters, 0); REQUIRE(result == expected); REQUIRE_TRUNCATED_PE_IS_UNCHANGED(result, record1, record2); } /////////////////////////////////////////////////////////////////////////////// // Cases 6 and 7 PE: Sequence A extends past sequence B (and vice versa) // AAAAAAAAAAAAAA AAAA // BBBBB BBBBBBBBBBBBB TEST_CASE("Sequence A extends past sequence B", "[alignment::paired_end]") { const fastq record1("Rec1", "ACGTAGTACG", "!!!!!!!!!!"); const fastq record2("Rec2", "AGTA", "!!!!"); const fastq_pair_vec adapters = create_adapter_vec(fastq("PCR1", "CGCTGA", "!!!!!!"), fastq("PCR2", "TGTAC", "!!!!!")); const alignment_info expected = ALN().score(6).offset(4).length(6); const alignment_info result = align_paired_ended_sequences(record1, record2, adapters, 0); REQUIRE(result == expected); fastq tmp_record1 = record1; fastq tmp_record2 = record2; REQUIRE(truncate_paired_ended_sequences(result, tmp_record1, tmp_record2) == 1); REQUIRE(tmp_record1 == fastq("Rec1", "ACGTAGTA", "!!!!!!!!")); REQUIRE(tmp_record2 == fastq("Rec2", "AGTA", "!!!!")); } TEST_CASE("Sequence B extends past sequence A", "[alignment::paired_end]") { const fastq record1("Rec1", "CGTA", "!!!!"); const fastq record2("Rec2", "ACCGTAGTAT", "!!!!!!!!!!"); const fastq_pair_vec adapters = create_adapter_vec(fastq("PCR1", "CGCTGA", "!!!!!!"), fastq("PCR2", "TGTAC", "!!!!!")); const alignment_info expected = ALN().score(6).offset(-2).length(6); const alignment_info result = align_paired_ended_sequences(record1, record2, adapters, 0); REQUIRE(result == expected); fastq tmp_record1 = record1; fastq tmp_record2 = record2; REQUIRE(truncate_paired_ended_sequences(result, tmp_record1, tmp_record2) == 1); REQUIRE(tmp_record1 == fastq("Rec1", "CGTA", "!!!!")); REQUIRE(tmp_record2 == fastq("Rec2", "CGTAGTAT", "!!!!!!!!")); } /////////////////////////////////////////////////////////////////////////////// // Cases 8 PE: Both sequences extends past the other // AAAAAAAAAAAAAAAAAA // BBBBBBBBBBBBBBBBBB // Expected result = Optimal alignment involving all overlapping bases TEST_CASE("Sequences extends past each other", "[alignment::paired_end]") { const fastq record1("Rec1", "ACGTAGTATACGCT", "!!!!!!!!!!!!!!"); const fastq record2("Rec2", "GTACACGTAGTATA", "!!!!!!!!!!!!!!"); const fastq_pair_vec adapters = create_adapter_vec(fastq("PCR1", "CGCTGA", "!!!!!!"), fastq("PCR2", "TGTAC", "!!!!!")); const alignment_info expected = ALN().score(18).offset(-4).length(18); const alignment_info result = align_paired_ended_sequences(record1, record2, adapters, 0); REQUIRE(result == expected); fastq tmp_record1 = record1; fastq tmp_record2 = record2; REQUIRE(truncate_paired_ended_sequences(result, tmp_record1, tmp_record2) == 2); REQUIRE(tmp_record1 == fastq("Rec1", "ACGTAGTATA", "!!!!!!!!!!")); REQUIRE(tmp_record2 == fastq("Rec2", "ACGTAGTATA", "!!!!!!!!!!")); } TEST_CASE("Adapter only sequences", "[alignment::paired_end]") { const fastq record1("Rec1", "CCCGAC", "!!!!!!"); const fastq record2("Rec2", "ATGCCTT", "!!!!!!!"); const fastq_pair_vec adapters = create_adapter_vec(fastq("PCR1", "CCCGACCCGT", "!!!!!!!!!!"), fastq("PCR2", "AAGATGCCTT", "!!!!!!!!!!")); const alignment_info expected = ALN().score(13).offset(-7).length(13); const alignment_info result = align_paired_ended_sequences(record1, record2, adapters, 0); REQUIRE(result == expected); } TEST_CASE("Adapter only sequences, with missing base", "[alignment::paired_end]") { // Test the case where both reads are adapters, but are missing a single base // Normally, alignments that do not invovle read1 vs read2 are skipped, but // missing bases may cause some alignments to be missed. const fastq record1("Rec1", "CCGACC", "!!!!!!"); const fastq record2("Rec2", "ATGCCT", "!!!!!!"); const fastq_pair_vec adapters = create_adapter_vec(fastq("PCR1", "CCCGACCCGT", "!!!!!!!!!!"), fastq("PCR2", "AAGATGCCTT", "!!!!!!!!!!")); // Sub-optimal alignment: // aagatgccttCCGACC // ATGCCTcccgacccgt const alignment_info expected_1 = ALN().score(1).offset(-3).length(9).n_mismatches(4); const alignment_info result_1 = align_paired_ended_sequences(record1, record2, adapters, 0); REQUIRE(result_1 == expected_1); // Optimal alignment, only possible with shift // aagatgccttCCGACC // ATGCCTcccgacccgt const alignment_info expected_2 = ALN().score(11).offset(-7).length(13).n_mismatches(1); const alignment_info result_2 = align_paired_ended_sequences(record1, record2, adapters, 1); REQUIRE(result_2 == expected_2); } /////////////////////////////////////////////////////////////////////////////// // TEST_CASE("Invalid alignment", "[alignment::paired_end]") { fastq record1("Rec", "", ""); fastq record2("Rec", "", ""); const alignment_info alignment = ALN().offset(1); REQUIRE_THROWS_AS(truncate_paired_ended_sequences(alignment, record1, record2), std::invalid_argument); } /////////////////////////////////////////////////////////////////////////////// // Collapsing of reads TEST_CASE("Collapse partial overlap", "[alignment::collapse]") { fastq record1("Rec1", "ATATTATA", "01234567"); fastq record2("Rec2", "NNNNACGT", "ABCDEFGH"); const alignment_info alignment = ALN().offset(4); REQUIRE(truncate_paired_ended_sequences(alignment, record1, record2) == 0); const fastq collapsed_expected = fastq("Rec1", "ATATTATAACGT", "01234567EFGH"); const fastq collapsed_result = collapse_paired_ended_sequences(alignment, record1, record2, g_rng); REQUIRE(collapsed_result == collapsed_expected); } TEST_CASE("Collapse complete overlap", "[alignment::collapse]") { fastq record1("Rec1", "ATATTATAA", "JJJJJJJJJ"); fastq record2("Rec2", "AATATTATA", "JJJJJJJJJ"); const alignment_info alignment = ALN().offset(-1); REQUIRE(truncate_paired_ended_sequences(alignment, record1, record2) == 2); const fastq collapsed_expected = fastq("Rec1", "ATATTATA", "wwwwwwww", FASTQ_ENCODING_SAM); const fastq collapsed_result = collapse_paired_ended_sequences(alignment, record1, record2, g_rng); REQUIRE(collapsed_result == collapsed_expected); } TEST_CASE("Collapse complete overlap for mate 1", "[alignment::collapse]") { fastq record1("Rec1", "ATATTATAG", "JJJJJJJJJ"); fastq record2("Rec2", "ATATTATA", "JJJJJJJJ"); const alignment_info alignment = ALN(); REQUIRE(truncate_paired_ended_sequences(alignment, record1, record2) == 1); const fastq collapsed_expected = fastq("Rec1", "ATATTATA", "wwwwwwww", FASTQ_ENCODING_SAM); const fastq collapsed_result = collapse_paired_ended_sequences(alignment, record1, record2, g_rng); REQUIRE(collapsed_result == collapsed_expected); } TEST_CASE("Collapse complete overlap for mate 2", "[alignment::collapse]") { fastq record1("Rec1", "ATATTATA", "JJJJJJJJ"); fastq record2("Rec2", "AATATTATA", "JJJJJJJJJ"); const alignment_info alignment = ALN().offset(-1); REQUIRE(truncate_paired_ended_sequences(alignment, record1, record2) == 1); const fastq collapsed_expected = fastq("Rec1", "ATATTATA", "wwwwwwww", FASTQ_ENCODING_SAM); const fastq collapsed_result = collapse_paired_ended_sequences(alignment, record1, record2, g_rng); REQUIRE(collapsed_result == collapsed_expected); } TEST_CASE("Unequal sequence lengths, mate 1 shorter", "[alignment::collapse]") { fastq record1("Rec1", "ATA", "012"); fastq record2("Rec2", "NNNNACGT", "ABCDEFGH"); const alignment_info alignment = ALN().offset(3); REQUIRE(truncate_paired_ended_sequences(alignment, record1, record2) == 0); const fastq collapsed_expected = fastq("Rec1", "ATANNNNACGT", "012ABCDEFGH"); const fastq collapsed_result = collapse_paired_ended_sequences(alignment, record1, record2, g_rng); REQUIRE(collapsed_result == collapsed_expected); } TEST_CASE("Unequal sequence lengths, mate 1 shorter, mate 2 extends past", "[alignment::collapse]") { fastq record1("Rec1", "ATA", "012"); fastq record2("Rec2", "AANNNNACGT", "90ABCDEFGH"); const alignment_info alignment = ALN().offset(-2); REQUIRE(truncate_paired_ended_sequences(alignment, record1, record2) == 1); const fastq collapsed_expected = fastq("Rec1", "ATANACGT", "012DEFGH"); const fastq collapsed_result = collapse_paired_ended_sequences(alignment, record1, record2, g_rng); REQUIRE(collapsed_result == collapsed_expected); } TEST_CASE("Unequal sequence lengths, mate 2 shorter", "[alignment::collapse]") { fastq record1("Rec1", "ATATTATA", "01234567"); fastq record2("Rec2", "ACG", "EFG"); const alignment_info alignment = ALN().offset(8); REQUIRE(truncate_paired_ended_sequences(alignment, record1, record2) == 0); const fastq collapsed_expected = fastq("Rec1", "ATATTATAACG", "01234567EFG"); const fastq collapsed_result = collapse_paired_ended_sequences(alignment, record1, record2, g_rng); REQUIRE(collapsed_result == collapsed_expected); } TEST_CASE("Ambiguous sites are filled from mate", "[alignment::collapse]") { fastq record1("Rec1", "NNNNNNTATA", "0123456789"); fastq record2("Rec2", "ACGTNNNNNN", "ABCDEFGHIJ"); const alignment_info alignment; REQUIRE(truncate_paired_ended_sequences(alignment, record1, record2) == 0); const fastq collapsed_expected = fastq("Rec1", "ACGTNNTATA", "ABCD!!6789"); const fastq collapsed_result = collapse_paired_ended_sequences(alignment, record1, record2, g_rng); REQUIRE(collapsed_result == collapsed_expected); } TEST_CASE("Identical nucleotides gets higher qualities", "[alignment::collapse]") { fastq record1("Rec1", "GCATGATATA", "012345!0:A"); fastq record2("Rec2", "TATATACAAC", "(3&?EFGHIJ"); const alignment_info alignment = ALN().offset(6); REQUIRE(truncate_paired_ended_sequences(alignment, record1, record2) == 0); const fastq collapsed_expected = fastq("Rec1", "GCATGATATATACAAC", "012345(FBcEFGHIJ", FASTQ_ENCODING_SAM); const fastq collapsed_result = collapse_paired_ended_sequences(alignment, record1, record2, g_rng); REQUIRE(collapsed_result == collapsed_expected); } TEST_CASE("Identical nucleotides gets higher qualities, no more than 41", "[alignment::collapse]") { fastq record1("Rec1", "GCATGATATA", "0123456789"); fastq record2("Rec2", "TATATACAAC", "ABCDEFGHIJ"); const alignment_info alignment = ALN().offset(6); REQUIRE(truncate_paired_ended_sequences(alignment, record1, record2) == 0); const fastq collapsed_expected = fastq("Rec1", "GCATGATATATACAAC", "012345Z\\^`EFGHIJ", FASTQ_ENCODING_SAM); const fastq collapsed_result = collapse_paired_ended_sequences(alignment, record1, record2, g_rng); REQUIRE(collapsed_result == collapsed_expected); } TEST_CASE("Higher quality nucleotide is selected", "[alignment::collapse]") { fastq record1("Rec1", "GCATGAGCAT", "012345!0:A"); fastq record2("Rec2", "TATATACAAC", "(3&?EFGHIJ"); const alignment_info alignment = ALN().offset(6); REQUIRE(truncate_paired_ended_sequences(alignment, record1, record2) == 0); const fastq collapsed_expected = fastq("Rec1", "GCATGATAATTACAAC", "012345(%5%EFGHIJ"); const fastq collapsed_result = collapse_paired_ended_sequences(alignment, record1, record2, g_rng); REQUIRE(collapsed_result == collapsed_expected); } TEST_CASE("Randomly select between different nucleotides with same quality #1", "[alignment::collapse]") { const fastq record1("Rec1", "G", "1"); const fastq record2("Rec2", "T", "1"); const alignment_info alignment; std::seed_seq seed{1}; std::mt19937 rng(seed); const fastq collapsed_expected = fastq("Rec1", "G", "#"); const fastq collapsed_result = collapse_paired_ended_sequences(alignment, record1, record2, &rng); REQUIRE(collapsed_result == collapsed_expected); } TEST_CASE("Randomly select between different nucleotides with same quality #2", "[alignment::collapse]") { const fastq record1("Rec1", "G", "1"); const fastq record2("Rec2", "T", "1"); const alignment_info alignment; std::seed_seq seed{2}; std::mt19937 rng(seed); const fastq collapsed_expected = fastq("Rec1", "T", "#"); const fastq collapsed_result = collapse_paired_ended_sequences(alignment, record1, record2, &rng); REQUIRE(collapsed_result == collapsed_expected); } TEST_CASE("Set conflicts to N/! if no RNG is provided", "[alignment::collapse]") { const fastq record1("Rec1", "G", "1"); const fastq record2("Rec2", "T", "1"); const alignment_info alignment; std::seed_seq seed{2}; std::mt19937 rng(seed); const fastq collapsed_expected = fastq("Rec1", "N", "!"); const fastq collapsed_result = collapse_paired_ended_sequences(alignment, record1, record2, nullptr); REQUIRE(collapsed_result == collapsed_expected); } TEST_CASE("Offsets past the end throws", "[alignment::collapse]") { const fastq record1("Rec1", "G", "1"); const fastq record2("Rec2", "T", "1"); const alignment_info alignment = ALN().offset(2); REQUIRE_THROWS_AS(collapse_paired_ended_sequences(alignment, record1, record2, g_rng), std::invalid_argument); } TEST_CASE("Mate numbering is removed", "[alignment::collapse]") { const fastq record1("Read/1", "ATATTATA", "01234567"); const fastq record2("Read/2", "NNNNACGT", "ABCDEFGH"); const alignment_info alignment = ALN().offset(4); const fastq collapsed_expected = fastq("Read", "ATATTATAACGT", "01234567EFGH"); const fastq collapsed_result = collapse_paired_ended_sequences(alignment, record1, record2, g_rng); REQUIRE(collapsed_result == collapsed_expected); } TEST_CASE("Mate numbering removed, meta from 1 kept", "[alignment::collapse]") { const fastq record1("Read/1 Meta1", "ATATTATA", "01234567"); const fastq record2("Read/2 Meta2", "NNNNACGT", "ABCDEFGH"); const alignment_info alignment = ALN().offset(4); const fastq collapsed_expected = fastq("Read Meta1", "ATATTATAACGT", "01234567EFGH"); const fastq collapsed_result = collapse_paired_ended_sequences(alignment, record1, record2, g_rng); REQUIRE(collapsed_result == collapsed_expected); } TEST_CASE("Mate numbering removed, non-standard separator", "[alignment::collapse]") { const fastq record1("Read:1", "ATATTATA", "01234567"); const fastq record2("Read:2", "NNNNACGT", "ABCDEFGH"); const alignment_info alignment = ALN().offset(4); const fastq collapsed_expected = fastq("Read", "ATATTATAACGT", "01234567EFGH"); const fastq collapsed_result = collapse_paired_ended_sequences(alignment, record1, record2, g_rng, ':'); REQUIRE(collapsed_result == collapsed_expected); } TEST_CASE("Mate numbering removed, non-standard separator, not set", "[alignment::collapse]") { const fastq record1("Read:1", "ATATTATA", "01234567"); const fastq record2("Read:2", "NNNNACGT", "ABCDEFGH"); const alignment_info alignment = ALN().offset(4); const fastq collapsed_expected = fastq("Read:1", "ATATTATAACGT", "01234567EFGH"); const fastq collapsed_result = collapse_paired_ended_sequences(alignment, record1, record2, g_rng); REQUIRE(collapsed_result == collapsed_expected); } /////////////////////////////////////////////////////////////////////////////// // Adapter extraction TEST_CASE("Extracting empty sequences yields empty sequences #1", "[alignment::extract_adapter_sequences]") { const fastq expected_1 = fastq("read1", "", ""); const fastq expected_2 = fastq("read2", "", ""); fastq read1 = expected_1; fastq read2 = expected_2; extract_adapter_sequences(ALN(), read1, read2); REQUIRE(read1 == expected_1); REQUIRE(read2 == expected_2); } TEST_CASE("Extracting empty sequences yields empty sequences #2", "[alignment::extract_adapter_sequences]") { const fastq expected_1 = fastq("read1", "", ""); const fastq expected_2 = fastq("read2", "GGGGCC", "!!!!!!"); fastq read1 = expected_1; fastq read2 = fastq("read2", "GGGGCC", "!!!!!!"); extract_adapter_sequences(ALN(), read1, read2); REQUIRE(read1 == fastq("read1", "", "")); REQUIRE(read2 == fastq("read2", "", "")); } TEST_CASE("Extracting empty sequences yields empty sequences #3", "[alignment::extract_adapter_sequences]") { const fastq expected_1 = fastq("read1", "AATTTT", "!!!!!!"); const fastq expected_2 = fastq("read2", "", ""); fastq read1 = fastq("read1", "", ""); fastq read2 = expected_2; extract_adapter_sequences(ALN(), read1, read2); REQUIRE(read1 == fastq("read1", "", "")); REQUIRE(read2 == fastq("read2", "", "")); } TEST_CASE("Extracting empty sequences yields empty sequences #4", "[alignment::extract_adapter_sequences]") { const fastq expected_1 = fastq("read1", "", ""); const fastq expected_2 = fastq("read2", "", ""); fastq read1 = expected_1; fastq read2 = expected_2; extract_adapter_sequences(ALN(), read1, read2); REQUIRE(read1 == fastq("read1", "", "")); REQUIRE(read2 == fastq("read2", "", "")); } TEST_CASE("Extracting with no alignment yields empty sequences", "[alignment::extract_adapter_sequences]") { const fastq expected_1 = fastq("read1", "AATTTT", "!!!!!!"); const fastq expected_2 = fastq("read2", "GGGGCC", "!!!!!!"); fastq read1 = expected_1; fastq read2 = expected_2; extract_adapter_sequences(ALN(), read1, read2); REQUIRE(read1 == fastq("read1", "", "")); REQUIRE(read2 == fastq("read2", "", "")); } TEST_CASE("Extracting with partial overlap yields empty sequences", "[alignment::extract_adapter_sequences]") { const fastq expected_1 = fastq("read1", "AATTTT", "!!!!!!"); const fastq expected_2 = fastq("read2", "GGGGCC", "!!!!!!"); fastq read1 = expected_1; fastq read2 = expected_2; extract_adapter_sequences(ALN().offset(2), read1, read2); REQUIRE(read1 == fastq("read1", "", "")); REQUIRE(read2 == fastq("read2", "", "")); } TEST_CASE("Extracting with complete overlap yields empty sequences", "[alignment::extract_adapter_sequences]") { const fastq expected_1 = fastq("read1", "AATTTT", "!!!!!!"); const fastq expected_2 = fastq("read2", "GGGGCC", "!!!!!!"); fastq read1 = expected_1; fastq read2 = expected_2; extract_adapter_sequences(ALN(), read1, read2); REQUIRE(read1 == fastq("read1", "", "")); REQUIRE(read2 == fastq("read2", "", "")); } TEST_CASE("Extracting sequence 2 inside sequence 1 yields empty sequences", "[alignment::extract_adapter_sequences]") { const fastq expected_1 = fastq("read1", "AATTTT", "!!!!!!"); const fastq expected_2 = fastq("read2", "GGCC", "!!!!"); fastq read1 = expected_1; fastq read2 = expected_2; extract_adapter_sequences(ALN().offset(2), read1, read2); REQUIRE(read1 == fastq("read1", "", "")); REQUIRE(read2 == fastq("read2", "", "")); } TEST_CASE("Extracting sequence 1 inside sequence 2 yields empty sequences", "[alignment::extract_adapter_sequences]") { const fastq expected_1 = fastq("read1", "AATT", "!!!!"); const fastq expected_2 = fastq("read2", "GGGGCC", "!!!!!!"); fastq read1 = expected_1; fastq read2 = expected_2; extract_adapter_sequences(ALN(), read1, read2); REQUIRE(read1 == fastq("read1", "", "")); REQUIRE(read2 == fastq("read2", "", "")); } TEST_CASE("Extracting sequence 1 extending past sequence 2", "[alignment::extract_adapter_sequences]") { const fastq expected_1 = fastq("read1", "AATTTTCC", "12345678"); const fastq expected_2 = fastq("read2", "GGGGGG", "!!!!!!"); fastq read1 = expected_1; fastq read2 = expected_2; extract_adapter_sequences(ALN(), read1, read2); REQUIRE(read1 == fastq("read1", "CC", "78")); REQUIRE(read2 == fastq("read2", "", "")); } TEST_CASE("Extracting sequence 2 extending past sequence 1", "[alignment::extract_adapter_sequences]") { const fastq expected_1 = fastq("read1", "TTTTTT", "!!!!!!"); const fastq expected_2 = fastq("read2", "AAGGGGGG", "12345678"); fastq read1 = expected_1; fastq read2 = expected_2; extract_adapter_sequences(ALN().offset(-2), read1, read2); REQUIRE(read1 == fastq("read1", "", "")); REQUIRE(read2 == fastq("read2", "AA", "12")); } TEST_CASE("Extracting both sequences extending past each other", "[alignment::extract_adapter_sequences]") { const fastq expected_1 = fastq("read1", "TTTTTTCCC", "ABCDEFGHI"); const fastq expected_2 = fastq("read2", "AAGGGGGG", "12345678"); fastq read1 = expected_1; fastq read2 = expected_2; extract_adapter_sequences(ALN().offset(-2), read1, read2); REQUIRE(read1 == fastq("read1", "CCC", "GHI")); REQUIRE(read2 == fastq("read2", "AA", "12")); } /////////////////////////////////////////////////////////////////////////////// // Brute-force checking of alignment calculations // Simply check all combinations involving 3 bases varying, for a range of // sequence lengths to help catch corner cases with the optimizations // The function is not exposed, so a declaration is required bool compare_subsequences(const alignment_info& best, alignment_info& current, const char* seq_1_ptr, const char* seq_2_ptr); /** Naive reimplementation of alignment calculation. **/ void update_alignment(alignment_info& aln, const std::string& a, const std::string& b, size_t nbases) { // Don't count all these checks in test statistics if (a.length() != b.length()) { REQUIRE(a.length() == b.length()); } for (size_t i = 0; i < nbases; ++i) { const char nt1 = a.at(i); const char nt2 = b.at(i); if (nt1 == 'N' || nt2 == 'N') { aln.n_ambiguous++; } else if (nt1 == nt2) { aln.score++; } else { aln.n_mismatches++; aln.score--; } } } /** Returns all 3 nt combinations of the bases ACGTN. **/ std::vector get_combinations() { std::vector result; const std::string nts = "ACGTN"; for (size_t i = 0; i < nts.length(); ++i) { for (size_t j = 0; j < nts.length(); ++j) { for (size_t k = 0; k < nts.length(); ++k) { std::string combination(3, 'A'); combination.at(0) = nts.at(i); combination.at(1) = nts.at(j); combination.at(2) = nts.at(k); result.push_back(combination); } } } return result; } TEST_CASE("Brute-force validation", "[alignment::compare_subsequences]") { const alignment_info best; const std::vector combinations = get_combinations(); for (size_t seqlen = 10; seqlen <= 20; ++seqlen) { for (size_t pos = 0; pos < seqlen; ++pos) { const size_t nbases = std::min(3, seqlen - pos); for (size_t i = 0; i < combinations.size(); ++i) { for (size_t j = 0; j < combinations.size(); ++j) { alignment_info expected; expected.length = seqlen; expected.score = seqlen - nbases; update_alignment(expected, combinations.at(i), combinations.at(j), nbases); std::string mate1 = std::string(seqlen, 'A'); mate1.replace(pos, nbases, combinations.at(i).substr(0, nbases)); std::string mate2 = std::string(seqlen, 'A'); mate2.replace(pos, nbases, combinations.at(j).substr(0, nbases)); alignment_info current; current.length = seqlen; compare_subsequences(best, current, mate1.c_str(), mate2.c_str()); // Don't count all these checks in test statistics if (!(current == expected)) { REQUIRE(current == expected); } } } } } } } // namespace ar adapterremoval-2.3.1/tests/unit/argparse_test.cpp000066400000000000000000000340651350370616400222300ustar00rootroot00000000000000/*************************************************************************\ * AdapterRemoval - cleaning next-generation sequencing reads * * * * Copyright (C) 2011 by Stinus Lindgreen - stinus@binf.ku.dk * * Copyright (C) 2014 by Mikkel Schubert - mikkelsch@gmail.com * * * * If you use the program, please cite the paper: * * S. Lindgreen (2012): AdapterRemoval: Easy Cleaning of Next Generation * * Sequencing Reads, BMC Research Notes, 5:337 * * http://www.biomedcentral.com/1756-0500/5/337/ * * * * This program is free software: you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation, either version 3 of the License, or * * (at your option) any later version. * * * * This program is distributed in the hope that it will be useful, * * but WITHOUT ANY WARRANTY; without even the implied warranty of * * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * * GNU General Public License for more details. * * * * You should have received a copy of the GNU General Public License * * along with this program. If not, see . * \*************************************************************************/ #include #include #include #include "testing.hpp" #include "argparse.hpp" #include "debug.hpp" namespace ar { typedef std::unique_ptr consumer_autoptr; /////////////////////////////////////////////////////////////////////////////// // flag -- boolean TEST_CASE("Flag defaults", "[argparse::flag]") { consumer_autoptr ptr(new argparse::flag()); CHECK(!ptr->is_set()); REQUIRE(ptr->metavar() == " "); REQUIRE(ptr->help() == ""); REQUIRE(ptr->to_str() == "off"); } TEST_CASE("Flag help", "[argparse::flag]") { consumer_autoptr ptr(new argparse::flag(nullptr, "help! help!")); REQUIRE(ptr->help() == "help! help!"); } TEST_CASE("Flag consumes no arguments", "[argparse::flag]") { string_vec arguments; arguments.push_back("--foo"); consumer_autoptr ptr(new argparse::flag()); CHECK(!ptr->is_set()); REQUIRE(ptr->consume(arguments.begin(), arguments.end()) == 0); CHECK(ptr->is_set()); } TEST_CASE("Flag may be called on end of arguments", "[argparse::flag]") { const string_vec arguments; consumer_autoptr ptr(new argparse::flag()); CHECK(!ptr->is_set()); REQUIRE(ptr->consume(arguments.begin(), arguments.end()) == 0); CHECK(ptr->is_set()); } TEST_CASE("Flag uses sink with true", "[argparse::flag]") { bool sink = true; consumer_autoptr ptr(new argparse::flag(&sink)); REQUIRE(ptr->to_str() == "on"); const string_vec arguments; REQUIRE(ptr->consume(arguments.begin(), arguments.end()) == 0); CHECK(ptr->is_set()); CHECK(sink); REQUIRE(ptr->to_str() == "on"); } TEST_CASE("Flag uses sink with false", "[argparse::flag]") { bool sink = false; consumer_autoptr ptr(new argparse::flag(&sink)); REQUIRE(ptr->to_str() == "off"); const string_vec arguments; REQUIRE(ptr->consume(arguments.begin(), arguments.end()) == 0); CHECK(ptr->is_set()); CHECK(sink); REQUIRE(ptr->to_str() == "on"); } /////////////////////////////////////////////////////////////////////////////// // any -- string TEST_CASE("Any defaults", "[argparse::any]") { consumer_autoptr ptr(new argparse::any()); CHECK(!ptr->is_set()); REQUIRE(ptr->metavar() == ""); REQUIRE(ptr->help() == ""); REQUIRE(ptr->to_str() == ""); } TEST_CASE("Any value set", "[argparse::any]") { std::string sink = "kitchensink"; consumer_autoptr ptr(new argparse::any(&sink, "a metavar", "help!")); CHECK(!ptr->is_set()); REQUIRE(ptr->metavar() == "a metavar"); REQUIRE(ptr->help() == "help!"); REQUIRE(ptr->to_str() == "kitchensink"); } TEST_CASE("Any consumes one argument", "[argparse::any]") { string_vec arguments; arguments.push_back("foo"); arguments.push_back("bar"); consumer_autoptr ptr(new argparse::any()); CHECK(!ptr->is_set()); REQUIRE(ptr->consume(arguments.begin(), arguments.end()) == 1); CHECK(ptr->is_set()); REQUIRE(ptr->to_str() == "foo"); } TEST_CASE("Any cannot consume empty list of arguments", "[argparse::any]") { const string_vec arguments; consumer_autoptr ptr(new argparse::any()); CHECK(!ptr->is_set()); REQUIRE(ptr->consume(arguments.begin(), arguments.end()) == static_cast(-1)); CHECK(!ptr->is_set()); REQUIRE(ptr->to_str() == ""); } TEST_CASE("Any with empty sink", "[argparse::any]") { std::string sink; consumer_autoptr ptr(new argparse::any(&sink)); REQUIRE(ptr->to_str() == ""); string_vec arguments; arguments.push_back("foo"); REQUIRE(ptr->consume(arguments.begin(), arguments.end()) == 1); CHECK(ptr->is_set()); REQUIRE(sink == "foo"); REQUIRE(ptr->to_str() == "foo"); } TEST_CASE("Any with preset sink", "[argparse::any]") { std::string sink = "kitchensink"; consumer_autoptr ptr(new argparse::any(&sink)); REQUIRE(ptr->to_str() == "kitchensink"); string_vec arguments; arguments.push_back("foo"); REQUIRE(ptr->consume(arguments.begin(), arguments.end()) == 1); CHECK(ptr->is_set()); REQUIRE(sink == "foo"); REQUIRE(ptr->to_str() == "foo"); } /////////////////////////////////////////////////////////////////////////////// // many -- strings TEST_CASE("Many defaults", "[argparse::many]") { string_vec sink; consumer_autoptr ptr(new argparse::many(&sink)); CHECK(!ptr->is_set()); REQUIRE(ptr->metavar() == ""); REQUIRE(ptr->help() == ""); REQUIRE(ptr->to_str() == ""); } TEST_CASE("Many with defaults", "[argparse::many]") { string_vec sink; sink.push_back("kitchensink"); consumer_autoptr ptr(new argparse::many(&sink, "a metavar", "help!")); CHECK(!ptr->is_set()); REQUIRE(ptr->metavar() == "a metavar"); REQUIRE(ptr->help() == "help!"); REQUIRE(ptr->to_str() == "kitchensink"); } TEST_CASE("Many consumes one argument", "[argparse::many]") { string_vec arguments; arguments.push_back("foo"); string_vec sink; consumer_autoptr ptr(new argparse::many(&sink)); CHECK(!ptr->is_set()); REQUIRE(ptr->consume(arguments.begin(), arguments.end()) == 1); CHECK(ptr->is_set()); REQUIRE(ptr->to_str() == "foo"); } TEST_CASE("Many consumes two arguments", "[argparse::many]") { string_vec arguments; arguments.push_back("foo"); arguments.push_back("bar"); string_vec sink; consumer_autoptr ptr(new argparse::many(&sink)); CHECK(!ptr->is_set()); REQUIRE(ptr->consume(arguments.begin(), arguments.end()) == 2); CHECK(ptr->is_set()); REQUIRE(ptr->to_str() == "foo;bar"); } TEST_CASE("Many consumes until next option", "[argparse::many]") { string_vec arguments; arguments.push_back("foo"); arguments.push_back("--zoo"); arguments.push_back("bar"); string_vec sink; consumer_autoptr ptr(new argparse::many(&sink)); CHECK(!ptr->is_set()); REQUIRE(ptr->consume(arguments.begin(), arguments.end()) == 1); CHECK(ptr->is_set()); REQUIRE(ptr->to_str() == "foo"); } TEST_CASE("Many does not consume empty list of arguments", "[argparse::many]") { string_vec sink; const string_vec arguments; consumer_autoptr ptr(new argparse::many(&sink)); CHECK(!ptr->is_set()); REQUIRE(ptr->consume(arguments.begin(), arguments.end()) == 0); CHECK(ptr->is_set()); REQUIRE(ptr->to_str() == ""); } TEST_CASE("Many with empty sink", "[argparse::many]") { string_vec sink; string_vec expected; expected.push_back("foo"); consumer_autoptr ptr(new argparse::many(&sink)); REQUIRE(ptr->to_str() == ""); string_vec arguments; arguments.push_back("foo"); REQUIRE(ptr->consume(arguments.begin(), arguments.end()) == 1); CHECK(ptr->is_set()); REQUIRE(sink == expected); REQUIRE(ptr->to_str() == "foo"); } TEST_CASE("many with preset sink", "[argparse::many]") { string_vec sink; sink.push_back("kitchensink"); string_vec expected; expected.push_back("foo"); consumer_autoptr ptr(new argparse::many(&sink)); REQUIRE(ptr->to_str() == "kitchensink"); string_vec arguments; arguments.push_back("foo"); REQUIRE(ptr->consume(arguments.begin(), arguments.end()) == 1); CHECK(ptr->is_set()); REQUIRE(sink == expected); REQUIRE(ptr->to_str() == "foo"); } /////////////////////////////////////////////////////////////////////////////// // knob -- unsigned TEST_CASE("Knob defaults", "[argparse::knob]") { unsigned sink = 0; consumer_autoptr ptr(new argparse::knob(&sink)); CHECK(!ptr->is_set()); REQUIRE(ptr->metavar() == ""); REQUIRE(ptr->help() == ""); REQUIRE(ptr->to_str() == "0"); } TEST_CASE("Knob requires a sink", "[argparse::knob]") { REQUIRE_THROWS_AS(argparse::knob(nullptr), assert_failed); } TEST_CASE("Knot values are set", "[argparse::knob]") { unsigned sink = 7913; consumer_autoptr ptr(new argparse::knob(&sink, "a metavar", "help!")); CHECK(!ptr->is_set()); REQUIRE(ptr->metavar() == "a metavar"); REQUIRE(ptr->help() == "help!"); REQUIRE(ptr->to_str() == "7913"); } TEST_CASE("Knob consumes one argument", "[argparse::knob]") { unsigned sink = 0; string_vec arguments; arguments.push_back("47"); arguments.push_back("bar"); consumer_autoptr ptr(new argparse::knob(&sink)); CHECK(!ptr->is_set()); REQUIRE(ptr->consume(arguments.begin(), arguments.end()) == 1); CHECK(ptr->is_set()); REQUIRE(sink == 47); REQUIRE(ptr->to_str() == "47"); } TEST_CASE("Knob does not consume empty list of arguments", "[argparse::knob]") { unsigned sink = 13; const string_vec arguments; consumer_autoptr ptr(new argparse::knob(&sink)); CHECK(!ptr->is_set()); REQUIRE(ptr->consume(arguments.begin(), arguments.end()) == static_cast(-1)); CHECK(!ptr->is_set()); REQUIRE(sink == 13); REQUIRE(ptr->to_str() == "13"); } TEST_CASE("Knob rejects negative values", "[argparse::knob]") { unsigned sink = 13; string_vec arguments; consumer_autoptr ptr(new argparse::knob(&sink)); arguments.push_back("-47"); CHECK(!ptr->is_set()); REQUIRE(ptr->consume(arguments.begin(), arguments.end()) == static_cast(-1)); CHECK(!ptr->is_set()); REQUIRE(sink == 13); REQUIRE(ptr->to_str() == "13"); } TEST_CASE("Knob accepts zero", "[argparse::knob]") { unsigned sink = 13; string_vec arguments; consumer_autoptr ptr(new argparse::knob(&sink)); arguments.push_back("0"); CHECK(!ptr->is_set()); REQUIRE(ptr->consume(arguments.begin(), arguments.end()) == 1); CHECK(ptr->is_set()); REQUIRE(sink == 0); REQUIRE(ptr->to_str() == "0"); } TEST_CASE("Knob accepts unsigned upper bound", "[argparse::knob]") { unsigned sink = 13; string_vec arguments; consumer_autoptr ptr(new argparse::knob(&sink)); arguments.push_back("4294967295"); CHECK(!ptr->is_set()); REQUIRE(ptr->consume(arguments.begin(), arguments.end()) == 1); CHECK(ptr->is_set()); REQUIRE(sink == 4294967295); REQUIRE(ptr->to_str() == "4294967295"); } TEST_CASE("Knob rejects past unsigned upper bound", "[argparse::knob]") { unsigned sink = 13; string_vec arguments; consumer_autoptr ptr(new argparse::knob(&sink)); arguments.push_back("4294967296"); CHECK(!ptr->is_set()); REQUIRE(ptr->consume(arguments.begin(), arguments.end()) == -1); CHECK(!ptr->is_set()); } TEST_CASE("Knob rejects trailing garbage", "[argparse::knob]") { unsigned sink = 13; string_vec arguments; consumer_autoptr ptr(new argparse::knob(&sink)); arguments.push_back("7913w"); CHECK(!ptr->is_set()); REQUIRE(ptr->consume(arguments.begin(), arguments.end()) == -1); CHECK(!ptr->is_set()); } /////////////////////////////////////////////////////////////////////////////// // floaty_knob -- double TEST_CASE("Floaty knob defaults", "[argparse::floaty_knob]") { double sink = 0; consumer_autoptr ptr(new argparse::floaty_knob(&sink)); CHECK(!ptr->is_set()); REQUIRE(ptr->metavar() == ""); REQUIRE(ptr->help() == ""); REQUIRE(ptr->to_str() == "0"); } TEST_CASE("Floaty knob treats NaN as unset", "[argparse::floaty_knob]") { double sink = std::numeric_limits::quiet_NaN(); consumer_autoptr ptr(new argparse::floaty_knob(&sink)); CHECK(!ptr->is_set()); REQUIRE(ptr->metavar() == ""); REQUIRE(ptr->help() == ""); REQUIRE(ptr->to_str() == ""); } TEST_CASE("Floaty knob requires sink", "[argparse::floaty_knob]") { REQUIRE_THROWS_AS(argparse::floaty_knob(nullptr), assert_failed); } TEST_CASE("Floaty knob with values", "[argparse::floaty_knob]") { double sink = 3.142; consumer_autoptr ptr(new argparse::floaty_knob(&sink, "a metavar", "help!")); CHECK(!ptr->is_set()); REQUIRE(ptr->metavar() == "a metavar"); REQUIRE(ptr->help() == "help!"); REQUIRE(ptr->to_str() == "3.142"); } TEST_CASE("Floaty knob consumes one argument", "[argparse::floaty_knob]") { double sink = 47.0; string_vec arguments; arguments.push_back("-19.84"); arguments.push_back("bar"); consumer_autoptr ptr(new argparse::floaty_knob(&sink)); CHECK(!ptr->is_set()); REQUIRE(ptr->consume(arguments.begin(), arguments.end()) == 1); CHECK(ptr->is_set()); REQUIRE(sink == -19.84); REQUIRE(ptr->to_str() == "-19.84"); } TEST_CASE("Floaty knob does not consume empty list of arguments", "[argparse::floaty_knob]") { double sink = 13; const string_vec arguments; consumer_autoptr ptr(new argparse::floaty_knob(&sink)); CHECK(!ptr->is_set()); REQUIRE(ptr->consume(arguments.begin(), arguments.end()) == static_cast(-1)); CHECK(!ptr->is_set()); REQUIRE(sink == 13); REQUIRE(ptr->to_str() == "13"); } TEST_CASE("Floaty knob rejects trailing garbage", "[argparse::floaty_knob]") { double sink = 47.0; string_vec arguments; arguments.push_back("-19.84wat"); consumer_autoptr ptr(new argparse::floaty_knob(&sink)); CHECK(!ptr->is_set()); REQUIRE(ptr->consume(arguments.begin(), arguments.end()) == -1); CHECK(!ptr->is_set()); } /////////////////////////////////////////////////////////////////////////////// // parser } // namespace ar adapterremoval-2.3.1/tests/unit/barcodes_test.cpp000066400000000000000000000645151350370616400222110ustar00rootroot00000000000000/*************************************************************************\ * AdapterRemoval - cleaning next-generation sequencing reads * * * * Copyright (C) 2011 by Stinus Lindgreen - stinus@binf.ku.dk * * Copyright (C) 2014 by Mikkel Schubert - mikkelsch@gmail.com * * * * If you use the program, please cite the paper: * * S. Lindgreen (2012): AdapterRemoval: Easy Cleaning of Next Generation * * Sequencing Reads, BMC Research Notes, 5:337 * * http://www.biomedcentral.com/1756-0500/5/337/ * * * * This program is free software: you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation, either version 3 of the License, or * * (at your option) any later version. * * * * This program is distributed in the hope that it will be useful, * * but WITHOUT ANY WARRANTY; without even the implied warranty of * * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * * GNU General Public License for more details. * * * * You should have received a copy of the GNU General Public License * * along with this program. If not, see . * \*************************************************************************/ #include #include #include #include "barcode_table.hpp" #include "debug.hpp" #include "fastq.hpp" #include "testing.hpp" namespace ar { TEST_CASE("what()", "[barcodes::errors]") { barcode_error err("test error"); REQUIRE(std::string(err.what()) == "test error"); } TEST_CASE("copy constructor", "[barcodes::errors]") { barcode_error err("test error"); barcode_error copy(err); REQUIRE(std::string(copy.what()) == "test error"); } TEST_CASE("Empty barcode-table is OK", "[barcodes::constuctor]") { const fastq_pair_vec barcodes; barcode_table table(barcodes, 0, 0, 0); } TEST_CASE("Overlapping SE barcodes fail", "[barcodes::constuctor]") { fastq_pair_vec barcodes; barcodes.push_back(fastq_pair(fastq("1", "ACGT"), fastq())); barcodes.push_back(fastq_pair(fastq("2", "ACGT"), fastq())); REQUIRE_THROWS_AS(barcode_table(barcodes, 0, 0, 0), barcode_error); } TEST_CASE("Overlapping PE barcodes fail", "[barcodes::constuctor]") { fastq_pair_vec barcodes; barcodes.push_back(fastq_pair(fastq("1", "ACGT"), fastq("3", "CGTG"))); barcodes.push_back(fastq_pair(fastq("2", "ACGT"), fastq("4", "CGTG"))); REQUIRE_THROWS_AS(barcode_table(barcodes, 0, 0, 0), barcode_error); } TEST_CASE("Partially overlapping PE barcodes are OK", "[barcodes::constuctor]") { fastq_pair_vec barcodes; barcodes.push_back(fastq_pair(fastq("1", "ACGT"), fastq("3", "CGTG"))); barcodes.push_back(fastq_pair(fastq("2", "CGTG"), fastq("4", "ACGT"))); barcode_table table(barcodes, 0, 0, 0); } TEST_CASE("Variable length SE barcodes fail #1", "[barcodes::construction]") { fastq_pair_vec barcodes; barcodes.push_back(fastq_pair(fastq("1", "ACGT"), fastq())); barcodes.push_back(fastq_pair(fastq("2", "TGCTA"), fastq())); REQUIRE_THROWS_AS(barcode_table(barcodes, 0, 0, 0), barcode_error); } TEST_CASE("Variable length SE barcodes fail #2", "[barcodes::construction]") { fastq_pair_vec barcodes; barcodes.push_back(fastq_pair(fastq("1", "ACGT"), fastq())); barcodes.push_back(fastq_pair(fastq("2", "TGCTA"), fastq())); REQUIRE_THROWS_AS(barcode_table(barcodes, 0, 0, 0), barcode_error); } TEST_CASE("Variable length PE barcodes fail #1", "[barcodes::construction]") { fastq_pair_vec barcodes; barcodes.push_back(fastq_pair(fastq("1", "ACGTT"), fastq("3", "CGTG"))); barcodes.push_back(fastq_pair(fastq("2", "CGTG"), fastq("4", "ACGT"))); REQUIRE_THROWS_AS(barcode_table(barcodes, 0, 0, 0), barcode_error); } TEST_CASE("Variable length PE barcodes fail #2", "[barcodes::construction]") { fastq_pair_vec barcodes; barcodes.push_back(fastq_pair(fastq("1", "ACGT"), fastq("3", "CGTGT"))); barcodes.push_back(fastq_pair(fastq("2", "CGTG"), fastq("4", "ACGT"))); REQUIRE_THROWS_AS(barcode_table(barcodes, 0, 0, 0), barcode_error); } TEST_CASE("Variable length PE barcodes fail #3", "[barcodes::construction]") { fastq_pair_vec barcodes; barcodes.push_back(fastq_pair(fastq("1", "ACGT"), fastq("3", "CGTG"))); barcodes.push_back(fastq_pair(fastq("2", "CGTGA"), fastq("4", "ACGT"))); REQUIRE_THROWS_AS(barcode_table(barcodes, 0, 0, 0), barcode_error); } TEST_CASE("Variable length PE barcodes fail #4", "[barcodes::construction]") { fastq_pair_vec barcodes; barcodes.push_back(fastq_pair(fastq("1", "ACGT"), fastq("3", "CGTG"))); barcodes.push_back(fastq_pair(fastq("2", "CGTGA"), fastq("4", "ACGTA"))); REQUIRE_THROWS_AS(barcode_table(barcodes, 0, 0, 0), barcode_error); } /////////////////////////////////////////////////////////////////////////////// // Exact matches for SE reads, when using a table containing SE barcodes TEST_CASE("Exact match among different SE barcodes for SE reads", "[barcodes::exact]") { fastq_pair_vec barcodes; barcodes.push_back(fastq_pair(fastq("1", "ACCCA"), fastq())); barcodes.push_back(fastq_pair(fastq("2", "CACAC"), fastq())); barcodes.push_back(fastq_pair(fastq("3", "AATTC"), fastq())); const barcode_table table(barcodes, 0, 0, 0); REQUIRE(table.identify(fastq("A", "ACCCA"), fastq()) == 0); REQUIRE(table.identify(fastq("B", "CACAC"), fastq()) == 1); REQUIRE(table.identify(fastq("C", "AATTC"), fastq()) == 2); } TEST_CASE("Exact match among similar SE barcodes for SE reads - differs at 5p", "[barcodes::exact::se]") { fastq_pair_vec barcodes; barcodes.push_back(fastq_pair(fastq("1", "ACCCA"), fastq())); barcodes.push_back(fastq_pair(fastq("2", "TCCCA"), fastq())); barcodes.push_back(fastq_pair(fastq("3", "AGCCA"), fastq())); const barcode_table table(barcodes, 0, 0, 0); REQUIRE(table.identify(fastq("B", "TCCCA")) == 1); REQUIRE(table.identify(fastq("A", "ACCCA")) == 0); REQUIRE(table.identify(fastq("C", "AGCCA")) == 2); } TEST_CASE("Exact match among similar SE barcodes for SE reads - differs at 3p", "[barcodes::exact::se]") { fastq_pair_vec barcodes; barcodes.push_back(fastq_pair(fastq("1", "ACCCA"), fastq())); barcodes.push_back(fastq_pair(fastq("2", "ACCCT"), fastq())); barcodes.push_back(fastq_pair(fastq("3", "ACCTA"), fastq())); const barcode_table table(barcodes, 0, 0, 0); REQUIRE(table.identify(fastq("C", "ACCTA")) == 2); REQUIRE(table.identify(fastq("A", "ACCCA")) == 0); REQUIRE(table.identify(fastq("B", "ACCCT")) == 1); } TEST_CASE("Shorter and longer reads for SE barcodes and SE reads", "[barcodes::exact::se]") { fastq_pair_vec barcodes; barcodes.push_back(fastq_pair(fastq("1", "ACCCA"), fastq())); const barcode_table table(barcodes, 0, 0, 0); REQUIRE(table.identify(fastq("A", "ACCC")) == -1); REQUIRE(table.identify(fastq("A", "ACCCA")) == 0); REQUIRE(table.identify(fastq("A", "ACCCAG")) == 0); } /////////////////////////////////////////////////////////////////////////////// // Exact matches for SE reads, when using a table containing PE barcodes TEST_CASE("Exact match among different PE barcodes for SE reads", "[barcodes::exact::se]") { fastq_pair_vec barcodes; barcodes.push_back(fastq_pair(fastq("1", "ACCCA"), fastq("4", "GTTTC"))); barcodes.push_back(fastq_pair(fastq("2", "CACAC"), fastq("5", "GATGC"))); barcodes.push_back(fastq_pair(fastq("3", "AATTC"), fastq("6", "TGCGG"))); const barcode_table table(barcodes, 0, 0, 0); REQUIRE(table.identify(fastq("A", "ACCCA")) == 0); REQUIRE(table.identify(fastq("C", "AATTC")) == 2); REQUIRE(table.identify(fastq("B", "CACAC")) == 1); } TEST_CASE("Exact match among similar PE barcodes for SE reads - differs at 5p", "[barcodes::exact::se]") { fastq_pair_vec barcodes; barcodes.push_back(fastq_pair(fastq("1", "ACCCA"), fastq("4", "GTTTC"))); barcodes.push_back(fastq_pair(fastq("2", "TCCCA"), fastq("5", "GTTTC"))); barcodes.push_back(fastq_pair(fastq("3", "AGCCA"), fastq("6", "ATTTC"))); const barcode_table table(barcodes, 0, 0, 0); REQUIRE(table.identify(fastq("A", "ACCCA")) == 0); REQUIRE(table.identify(fastq("B", "TCCCA")) == 1); REQUIRE(table.identify(fastq("C", "AGCCA")) == 2); } TEST_CASE("Exact match among similar PE barcodes for SE reads - differs at 3p", "[barcodes::exact::se]") { fastq_pair_vec barcodes; barcodes.push_back(fastq_pair(fastq("1", "ACCCA"), fastq("4", "GTTTC"))); barcodes.push_back(fastq_pair(fastq("2", "ACCCT"), fastq("5", "GTTTC"))); barcodes.push_back(fastq_pair(fastq("3", "AGCCA"), fastq("6", "GTTTA"))); const barcode_table table(barcodes, 0, 0, 0); REQUIRE(table.identify(fastq("C", "AGCCA")) == 2); REQUIRE(table.identify(fastq("A", "ACCCA")) == 0); REQUIRE(table.identify(fastq("B", "ACCCT")) == 1); } TEST_CASE("Shorter and longer reads for PE barcodes and SE reads", "[barcodes::exact::se]") { fastq_pair_vec barcodes; barcodes.push_back(fastq_pair(fastq("1", "ACCCA"), fastq("2", "TGATA"))); const barcode_table table(barcodes, 0, 0, 0); REQUIRE(table.identify(fastq("A", "ACCC")) == -1); REQUIRE(table.identify(fastq("A", "ACCCA")) == 0); REQUIRE(table.identify(fastq("A", "ACCCAG")) == 0); } TEST_CASE("Exact match among different PE barcodes for SE reads with ambigous results", "[barcodes::exact::se]") { fastq_pair_vec barcodes; barcodes.push_back(fastq_pair(fastq("1", "ACCCA"), fastq("4", "GTTTC"))); barcodes.push_back(fastq_pair(fastq("2", "AATTC"), fastq("5", "GATGC"))); barcodes.push_back(fastq_pair(fastq("3", "AATTC"), fastq("6", "TGCGG"))); const barcode_table table(barcodes, 0, 0, 0); REQUIRE(table.identify(fastq("A", "ACCCA")) == 0); REQUIRE(table.identify(fastq("C", "AATTC")) == -2); } /////////////////////////////////////////////////////////////////////////////// // Exact matches for PE reads, when using a table containing SE barcodes TEST_CASE("Exact match among different SE barcodes for PE reads", "[barcodes::exact::pe]") { fastq_pair_vec barcodes; barcodes.push_back(fastq_pair(fastq("1", "ACCCA"), fastq())); barcodes.push_back(fastq_pair(fastq("2", "CACAC"), fastq())); barcodes.push_back(fastq_pair(fastq("3", "AATTC"), fastq())); const barcode_table table(barcodes, 0, 0, 0); REQUIRE(table.identify(fastq("A", "ACCCA"), fastq("D", "GTTTC")) == 0); REQUIRE(table.identify(fastq("B", "CACAC"), fastq("E", "GATGC")) == 1); REQUIRE(table.identify(fastq("C", "AATTC"), fastq("F", "TGCGG")) == 2); } TEST_CASE("Exact match among similar SE barcodes for PE reads - differs at 5p", "[barcodes::exact::pe]") { fastq_pair_vec barcodes; barcodes.push_back(fastq_pair(fastq("1", "ACCCA"), fastq())); barcodes.push_back(fastq_pair(fastq("2", "TCCCA"), fastq())); barcodes.push_back(fastq_pair(fastq("3", "ATCCA"), fastq())); const barcode_table table(barcodes, 0, 0, 0); REQUIRE(table.identify(fastq("A", "ACCCA"), fastq("D", "GTTTC")) == 0); REQUIRE(table.identify(fastq("B", "TCCCA"), fastq("E", "GTTTC")) == 1); REQUIRE(table.identify(fastq("C", "ATCCA"), fastq("F", "ATTTC")) == 2); } TEST_CASE("Exact match among similar SE barcodes for PE reads - differs at 3p", "[barcodes::exact::pe]") { fastq_pair_vec barcodes; barcodes.push_back(fastq_pair(fastq("1", "ACCCA"), fastq())); barcodes.push_back(fastq_pair(fastq("2", "ACCCT"), fastq())); barcodes.push_back(fastq_pair(fastq("3", "ACCGA"), fastq())); const barcode_table table(barcodes, 0, 0, 0); REQUIRE(table.identify(fastq("A", "ACCCA"), fastq("D", "GTTTC")) == 0); REQUIRE(table.identify(fastq("B", "ACCCT"), fastq("E", "GTTTC")) == 1); REQUIRE(table.identify(fastq("C", "ACCGA"), fastq("F", "GTTTA")) == 2); } TEST_CASE("Shorter and longer reads for SE barcodes and PE reads", "[barcodes::exact::se]") { fastq_pair_vec barcodes; barcodes.push_back(fastq_pair(fastq("1", "ACCCA"), fastq())); const barcode_table table(barcodes, 0, 0, 0); REQUIRE(table.identify(fastq("A", "ACCC"), fastq("B", "TGATGA")) == -1); REQUIRE(table.identify(fastq("A", "ACCCA"), fastq("B", "TGATGA")) == 0); REQUIRE(table.identify(fastq("A", "ACCCAG"), fastq("B", "TGATGA")) == 0); } /////////////////////////////////////////////////////////////////////////////// // Exact matches for PE reads, when using a table containing PE barcodes TEST_CASE("Exact match among different PE barcodes for PE reads", "[barcodes::exact::pe]") { fastq_pair_vec barcodes; barcodes.push_back(fastq_pair(fastq("1", "ACCCA"), fastq("4", "GTTTC"))); barcodes.push_back(fastq_pair(fastq("2", "CACAC"), fastq("5", "GATGC"))); barcodes.push_back(fastq_pair(fastq("3", "AATTC"), fastq("6", "TGCGG"))); const barcode_table table(barcodes, 0, 0, 0); REQUIRE(table.identify(fastq("A", "ACCCA"), fastq("D", "GTTTC")) == 0); REQUIRE(table.identify(fastq("B", "CACAC"), fastq("E", "GATGC")) == 1); REQUIRE(table.identify(fastq("C", "AATTC"), fastq("F", "TGCGG")) == 2); } TEST_CASE("Exact match among similar PE barcodes for PE reads - differs at 5p", "[barcodes::exact::pe]") { fastq_pair_vec barcodes; barcodes.push_back(fastq_pair(fastq("1", "ACCCA"), fastq("4", "GTTTC"))); barcodes.push_back(fastq_pair(fastq("2", "TCCCA"), fastq("5", "GTTTC"))); barcodes.push_back(fastq_pair(fastq("3", "ACCCA"), fastq("6", "ATTTC"))); const barcode_table table(barcodes, 0, 0, 0); REQUIRE(table.identify(fastq("A", "ACCCA"), fastq("D", "GTTTC")) == 0); REQUIRE(table.identify(fastq("B", "TCCCA"), fastq("E", "GTTTC")) == 1); REQUIRE(table.identify(fastq("C", "ACCCA"), fastq("F", "ATTTC")) == 2); } TEST_CASE("Exact match among similar PE barcodes for PE reads - differs at 3p", "[barcodes::exact::pe]") { fastq_pair_vec barcodes; barcodes.push_back(fastq_pair(fastq("1", "ACCCA"), fastq("4", "GTTTC"))); barcodes.push_back(fastq_pair(fastq("2", "ACCCT"), fastq("5", "GTTTC"))); barcodes.push_back(fastq_pair(fastq("3", "ACCCA"), fastq("6", "GTTTA"))); const barcode_table table(barcodes, 0, 0, 0); REQUIRE(table.identify(fastq("A", "ACCCA"), fastq("D", "GTTTC")) == 0); REQUIRE(table.identify(fastq("B", "ACCCT"), fastq("E", "GTTTC")) == 1); REQUIRE(table.identify(fastq("C", "ACCCA"), fastq("F", "GTTTA")) == 2); } TEST_CASE("Shorter and longer reads for PE barcodes and PE reads", "[barcodes::exact::pe]") { fastq_pair_vec barcodes; barcodes.push_back(fastq_pair(fastq("1", "ACCCA"), fastq("2", "TGATGA"))); const barcode_table table(barcodes, 0, 0, 0); REQUIRE(table.identify(fastq("A", "ACCC"), fastq("B", "TGATG")) == -1); REQUIRE(table.identify(fastq("A", "ACCC"), fastq("B", "TGATGA")) == -1); REQUIRE(table.identify(fastq("A", "ACCC"), fastq("B", "TGATGAT")) == -1); REQUIRE(table.identify(fastq("A", "ACCCA"), fastq("B", "TGATG")) == -1); REQUIRE(table.identify(fastq("A", "ACCCA"), fastq("B", "TGATGA")) == 0); REQUIRE(table.identify(fastq("A", "ACCCA"), fastq("B", "TGATGAG")) == 0); REQUIRE(table.identify(fastq("A", "ACCCAT"), fastq("B", "TGATG")) == -1); REQUIRE(table.identify(fastq("A", "ACCCAT"), fastq("B", "TGATGA")) == 0); REQUIRE(table.identify(fastq("A", "ACCCAT"), fastq("B", "TGATGAG")) == 0); } /////////////////////////////////////////////////////////////////////////////// // Exact matches for SE reads, when reads have mismatches TEST_CASE("Exact matching reads with mismatches for SE barcodes", "[barcodes::exact::se]") { fastq_pair_vec barcodes; barcodes.push_back(fastq_pair(fastq("1", "ACCCA"), fastq())); const barcode_table table(barcodes, 0, 0, 0); REQUIRE(table.identify(fastq("A", "ACCCA")) == 0); REQUIRE(table.identify(fastq("A", "TCCCA")) == -1); REQUIRE(table.identify(fastq("A", "AGCCA")) == -1); REQUIRE(table.identify(fastq("A", "ACACA")) == -1); REQUIRE(table.identify(fastq("A", "ACCTA")) == -1); REQUIRE(table.identify(fastq("A", "ACCTT")) == -1); REQUIRE(table.identify(fastq("A", "NCCCA")) == -1); REQUIRE(table.identify(fastq("A", "ACCCA"), fastq("B", "GTTTC")) == 0); REQUIRE(table.identify(fastq("A", "TCCCA"), fastq("B", "GTTTC")) == -1); REQUIRE(table.identify(fastq("A", "AGCCA"), fastq("B", "GTTTC")) == -1); REQUIRE(table.identify(fastq("A", "ACACA"), fastq("B", "GTTTC")) == -1); REQUIRE(table.identify(fastq("A", "ACCTA"), fastq("B", "GTTTC")) == -1); REQUIRE(table.identify(fastq("A", "ACCTT"), fastq("B", "GTTTC")) == -1); REQUIRE(table.identify(fastq("A", "ANCCA"), fastq("B", "GTTTC")) == -1); } TEST_CASE("Exact matching reads with mismatches for PE barcodes", "[barcodes::exact::pe]") { fastq_pair_vec barcodes; barcodes.push_back(fastq_pair(fastq("1", "ACCCA"), fastq("B", "GTTTC"))); const barcode_table table(barcodes, 0, 0, 0); REQUIRE(table.identify(fastq("A", "ACCCA")) == 0); REQUIRE(table.identify(fastq("A", "TCCCA")) == -1); REQUIRE(table.identify(fastq("A", "AGCCA")) == -1); REQUIRE(table.identify(fastq("A", "ACACA")) == -1); REQUIRE(table.identify(fastq("A", "ACCTA")) == -1); REQUIRE(table.identify(fastq("A", "ACCTT")) == -1); REQUIRE(table.identify(fastq("A", "NCCCA")) == -1); REQUIRE(table.identify(fastq("A", "ACCCA"), fastq("B", "GTTTC")) == 0); REQUIRE(table.identify(fastq("A", "ACTCA"), fastq("B", "GTTTC")) == -1); REQUIRE(table.identify(fastq("A", "ACCCA"), fastq("B", "GTTTA")) == -1); REQUIRE(table.identify(fastq("A", "GCCCA"), fastq("B", "GATTC")) == -1); REQUIRE(table.identify(fastq("A", "ANCCA"), fastq("B", "GTTTC")) == -1); REQUIRE(table.identify(fastq("A", "ACCCA"), fastq("B", "GTTTN")) == -1); } /////////////////////////////////////////////////////////////////////////////// // Inexact matching with global limits TEST_CASE("Global limits override local limits for SE barcodes", "[barcodes::inexact::se]") { fastq_pair_vec barcodes; barcodes.push_back(fastq_pair(fastq("1", "ACCCA"), fastq())); const barcode_table table(barcodes, 0, 1, 1); REQUIRE(table.identify(fastq("A", "ACCCA")) == 0); REQUIRE(table.identify(fastq("A", "TCCCA")) == -1); REQUIRE(table.identify(fastq("A", "NCCCA")) == -1); REQUIRE(table.identify(fastq("A", "ACCCA"), fastq("B", "GTTTC")) == 0); REQUIRE(table.identify(fastq("A", "ACACA"), fastq("B", "GTTTC")) == -1); } TEST_CASE("Global limits override local limits for PE barcodes", "[barcodes::inexact::se]") { fastq_pair_vec barcodes; barcodes.push_back(fastq_pair(fastq("1", "ACCCA"), fastq("2", "GTTTC"))); const barcode_table table(barcodes, 0, 1, 1); REQUIRE(table.identify(fastq("A", "ACCCA")) == 0); REQUIRE(table.identify(fastq("A", "TCCCA")) == -1); REQUIRE(table.identify(fastq("A", "ACCNA")) == -1); REQUIRE(table.identify(fastq("A", "ACCCA"), fastq("B", "GTTTC")) == 0); REQUIRE(table.identify(fastq("A", "ACACA"), fastq("B", "GTTTC")) == -1); REQUIRE(table.identify(fastq("A", "ACCCA"), fastq("B", "GTTAG")) == -1); REQUIRE(table.identify(fastq("A", "ANCCA"), fastq("B", "GTTTC")) == -1); REQUIRE(table.identify(fastq("A", "ACCCA"), fastq("B", "NTTTC")) == -1); } TEST_CASE("Mismatches in R1 only with SE table", "[barcodes::inexact::se]") { fastq_pair_vec barcodes; barcodes.push_back(fastq_pair(fastq("1", "ACCCA"), fastq())); const barcode_table table(barcodes, 1, 1, 0); REQUIRE(table.identify(fastq("A", "ACCCA")) == 0); REQUIRE(table.identify(fastq("A", "TCCCA")) == 0); REQUIRE(table.identify(fastq("A", "TCCCT")) == -1); REQUIRE(table.identify(fastq("A", "ACCCN")) == 0); REQUIRE(table.identify(fastq("A", "ANCCN")) == -1); REQUIRE(table.identify(fastq("A", "ACCCA"), fastq("B", "GTTTC")) == 0); REQUIRE(table.identify(fastq("A", "ACTCA"), fastq("B", "GTTTC")) == 0); REQUIRE(table.identify(fastq("A", "GCTCA"), fastq("B", "GTTTC")) == -1); REQUIRE(table.identify(fastq("A", "ACCCT"), fastq("B", "GTTTG")) == 0); REQUIRE(table.identify(fastq("A", "ACCNA"), fastq("B", "GTTTC")) == 0); REQUIRE(table.identify(fastq("A", "NCCNA"), fastq("B", "GTTTC")) == -1); } TEST_CASE("Mismatches in R1 only with PE table", "[barcodes::inexact::se]") { fastq_pair_vec barcodes; barcodes.push_back(fastq_pair(fastq("1", "ACCCA"), fastq("2", "GTTTC"))); const barcode_table table(barcodes, 1, 1, 0); REQUIRE(table.identify(fastq("A", "ACCCA")) == 0); REQUIRE(table.identify(fastq("A", "TCCCA")) == 0); REQUIRE(table.identify(fastq("A", "TCCCT")) == -1); REQUIRE(table.identify(fastq("A", "ACCCN")) == 0); REQUIRE(table.identify(fastq("A", "ANCCN")) == -1); REQUIRE(table.identify(fastq("A", "ACCCA"), fastq("B", "GTTTC")) == 0); REQUIRE(table.identify(fastq("A", "ACTCA"), fastq("B", "GTTTC")) == 0); REQUIRE(table.identify(fastq("A", "GCTCA"), fastq("B", "GTTTC")) == -1); REQUIRE(table.identify(fastq("A", "ACCCA"), fastq("B", "GTTTG")) == -1); REQUIRE(table.identify(fastq("A", "ACCCN"), fastq("B", "GTTTC")) == 0); REQUIRE(table.identify(fastq("A", "ACCCA"), fastq("B", "NTTTC")) == -1); } TEST_CASE("Mismatches in R2 only with SE table", "[barcodes::inexact::pe]") { fastq_pair_vec barcodes; barcodes.push_back(fastq_pair(fastq("1", "ACCCA"), fastq())); const barcode_table table(barcodes, 1, 0, 1); REQUIRE(table.identify(fastq("A", "ACCCT"), fastq("B", "GTTTC")) == -1); REQUIRE(table.identify(fastq("A", "ACCCA"), fastq("B", "ATTTC")) == 0); REQUIRE(table.identify(fastq("A", "ACCCA"), fastq("B", "GTTTT")) == 0); REQUIRE(table.identify(fastq("A", "ACCCA"), fastq("B", "ATTTG")) == 0); REQUIRE(table.identify(fastq("A", "ACCCA"), fastq("B", "ANTTG")) == 0); } TEST_CASE("Mismatches in R2 only with PE table", "[barcodes::inexact::pe]") { fastq_pair_vec barcodes; barcodes.push_back(fastq_pair(fastq("1", "ACCCA"), fastq("2", "GTTTC"))); const barcode_table table(barcodes, 1, 0, 1); REQUIRE(table.identify(fastq("A", "ACCCT"), fastq("B", "GTTTC")) == -1); REQUIRE(table.identify(fastq("A", "ACCCA"), fastq("B", "ATTTC")) == 0); REQUIRE(table.identify(fastq("A", "ACCCA"), fastq("B", "GTTTT")) == 0); REQUIRE(table.identify(fastq("A", "ACCCA"), fastq("B", "ATTTG")) == -1); REQUIRE(table.identify(fastq("A", "ACCCA"), fastq("B", "GTTTN")) == 0); REQUIRE(table.identify(fastq("A", "ACCCN"), fastq("B", "GTTTT")) == -1); REQUIRE(table.identify(fastq("A", "ACTCA"), fastq("B", "GTNTT")) == -1); } TEST_CASE("Mismatches in R1/R2 with PE table", "[barcodes::inexact::pe]") { fastq_pair_vec barcodes; barcodes.push_back(fastq_pair(fastq("1", "ACCCA"), fastq("2", "GTTTC"))); const barcode_table table(barcodes, 1, 1, 1); REQUIRE(table.identify(fastq("A", "ACCCA"), fastq("B", "GTTTC")) == 0); REQUIRE(table.identify(fastq("A", "ACCCT"), fastq("B", "GTTTC")) == 0); REQUIRE(table.identify(fastq("A", "ACCCA"), fastq("B", "GTTAC")) == 0); REQUIRE(table.identify(fastq("A", "ACCCT"), fastq("B", "GTTAC")) == -1); REQUIRE(table.identify(fastq("A", "TCCAA"), fastq("B", "GTTTC")) == -1); REQUIRE(table.identify(fastq("A", "ACCCA"), fastq("B", "GGTGC")) == -1); REQUIRE(table.identify(fastq("A", "ANCCA"), fastq("B", "GTTTC")) == 0); REQUIRE(table.identify(fastq("A", "ACCCA"), fastq("B", "GTTNC")) == 0); REQUIRE(table.identify(fastq("A", "ACTCA"), fastq("B", "GTNTC")) == -1); } TEST_CASE("Multiple mismatches in R1/R2 with PE table", "[barcodes::inexact::pe]") { fastq_pair_vec barcodes; barcodes.push_back(fastq_pair(fastq("1", "ACCCA"), fastq("2", "GTTTC"))); const barcode_table table(barcodes, 2, 2, 2); REQUIRE(table.identify(fastq("A", "ACCCA"), fastq("B", "GTTTC")) == 0); REQUIRE(table.identify(fastq("A", "ACCCT"), fastq("B", "GTTTC")) == 0); REQUIRE(table.identify(fastq("A", "ACCCA"), fastq("B", "GTTAC")) == 0); REQUIRE(table.identify(fastq("A", "ACCCT"), fastq("B", "GTTAC")) == 0); REQUIRE(table.identify(fastq("A", "TCCAA"), fastq("B", "GTTTC")) == 0); REQUIRE(table.identify(fastq("A", "ACCCA"), fastq("B", "GGTGC")) == 0); REQUIRE(table.identify(fastq("A", "TCCCT"), fastq("B", "CTTTC")) == -1); REQUIRE(table.identify(fastq("A", "TCCNA"), fastq("B", "GTTTC")) == 0); REQUIRE(table.identify(fastq("A", "ACCCT"), fastq("B", "NTTTC")) == 0); REQUIRE(table.identify(fastq("A", "NCCCN"), fastq("B", "GTTTA")) == -1); } TEST_CASE("Ambigious matches in R1 for SE table", "[barcodes::inexact::se]") { fastq_pair_vec barcodes; barcodes.push_back(fastq_pair(fastq("1", "ACCCA"), fastq())); barcodes.push_back(fastq_pair(fastq("2", "TCCCA"), fastq())); barcodes.push_back(fastq_pair(fastq("3", "ACCCG"), fastq())); const barcode_table table(barcodes, 1, 1, 1); REQUIRE(table.identify(fastq("A", "TCCCA")) == 1); REQUIRE(table.identify(fastq("A", "CCCCA")) == -2); REQUIRE(table.identify(fastq("A", "ACCCC")) == -2); REQUIRE(table.identify(fastq("A", "ACCCN")) == -2); } TEST_CASE("Ambigious matches in SE R1 for PE table", "[barcodes::inexact::se]") { fastq_pair_vec barcodes; barcodes.push_back(fastq_pair(fastq("1", "ACCCA"), fastq("4", "TGCGT"))); barcodes.push_back(fastq_pair(fastq("2", "TCCCA"), fastq("5", "AAGTT"))); barcodes.push_back(fastq_pair(fastq("3", "ACCCG"), fastq("6", "CGGCA"))); const barcode_table table(barcodes, 1, 1, 1); REQUIRE(table.identify(fastq("A", "TCCCA")) == 1); REQUIRE(table.identify(fastq("A", "CCCCA")) == -2); REQUIRE(table.identify(fastq("A", "ACCCC")) == -2); REQUIRE(table.identify(fastq("A", "ACCCN")) == -2); } TEST_CASE("Mismatch resulting in apparent match", "[barcodes::inexact::se]") { fastq_pair_vec barcodes; barcodes.push_back(fastq_pair(fastq("1", "ACCCA"), fastq("4", "TGCGT"))); barcodes.push_back(fastq_pair(fastq("2", "TCCTT"), fastq("5", "AAGTT"))); const barcode_table table(barcodes, 1, 1, 1); REQUIRE(table.identify(fastq("A", "ACCCA")) == 0); REQUIRE(table.identify(fastq("A", "TCCTT")) == 1); REQUIRE(table.identify(fastq("A", "TCCCA")) == 0); REQUIRE(table.identify(fastq("A", "ACCTT")) == 1); } } // namespace aradapterremoval-2.3.1/tests/unit/catch.hpp000077500000000000000000017374661350370616400204770ustar00rootroot00000000000000/* * Catch v2.6.0 * Generated: 2019-01-31 22:25:55.560884 * ---------------------------------------------------------- * This file has been merged from multiple headers. Please don't edit it directly * Copyright (c) 2019 Two Blue Cubes Ltd. All rights reserved. * * Distributed under the Boost Software License, Version 1.0. (See accompanying * file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt) */ #ifndef TWOBLUECUBES_SINGLE_INCLUDE_CATCH_HPP_INCLUDED #define TWOBLUECUBES_SINGLE_INCLUDE_CATCH_HPP_INCLUDED // start catch.hpp #define CATCH_VERSION_MAJOR 2 #define CATCH_VERSION_MINOR 6 #define CATCH_VERSION_PATCH 0 #ifdef __clang__ # pragma clang system_header #elif defined __GNUC__ # pragma GCC system_header #endif // start catch_suppress_warnings.h #ifdef __clang__ # ifdef __ICC // icpc defines the __clang__ macro # pragma warning(push) # pragma warning(disable: 161 1682) # else // __ICC # pragma clang diagnostic push # pragma clang diagnostic ignored "-Wpadded" # pragma clang diagnostic ignored "-Wswitch-enum" # pragma clang diagnostic ignored "-Wcovered-switch-default" # endif #elif defined __GNUC__ // Because REQUIREs trigger GCC's -Wparentheses, and because still // supported version of g++ have only buggy support for _Pragmas, // Wparentheses have to be suppressed globally. # pragma GCC diagnostic ignored "-Wparentheses" // See #674 for details # pragma GCC diagnostic push # pragma GCC diagnostic ignored "-Wunused-variable" # pragma GCC diagnostic ignored "-Wpadded" #endif // end catch_suppress_warnings.h #if defined(CATCH_CONFIG_MAIN) || defined(CATCH_CONFIG_RUNNER) # define CATCH_IMPL # define CATCH_CONFIG_ALL_PARTS #endif // In the impl file, we want to have access to all parts of the headers // Can also be used to sanely support PCHs #if defined(CATCH_CONFIG_ALL_PARTS) # define CATCH_CONFIG_EXTERNAL_INTERFACES # if defined(CATCH_CONFIG_DISABLE_MATCHERS) # undef CATCH_CONFIG_DISABLE_MATCHERS # endif # if !defined(CATCH_CONFIG_ENABLE_CHRONO_STRINGMAKER) # define CATCH_CONFIG_ENABLE_CHRONO_STRINGMAKER # endif #endif #if !defined(CATCH_CONFIG_IMPL_ONLY) // start catch_platform.h #ifdef __APPLE__ # include # if TARGET_OS_OSX == 1 # define CATCH_PLATFORM_MAC # elif TARGET_OS_IPHONE == 1 # define CATCH_PLATFORM_IPHONE # endif #elif defined(linux) || defined(__linux) || defined(__linux__) # define CATCH_PLATFORM_LINUX #elif defined(WIN32) || defined(__WIN32__) || defined(_WIN32) || defined(_MSC_VER) || defined(__MINGW32__) # define CATCH_PLATFORM_WINDOWS #endif // end catch_platform.h #ifdef CATCH_IMPL # ifndef CLARA_CONFIG_MAIN # define CLARA_CONFIG_MAIN_NOT_DEFINED # define CLARA_CONFIG_MAIN # endif #endif // start catch_user_interfaces.h namespace Catch { unsigned int rngSeed(); } // end catch_user_interfaces.h // start catch_tag_alias_autoregistrar.h // start catch_common.h // start catch_compiler_capabilities.h // Detect a number of compiler features - by compiler // The following features are defined: // // CATCH_CONFIG_COUNTER : is the __COUNTER__ macro supported? // CATCH_CONFIG_WINDOWS_SEH : is Windows SEH supported? // CATCH_CONFIG_POSIX_SIGNALS : are POSIX signals supported? // CATCH_CONFIG_DISABLE_EXCEPTIONS : Are exceptions enabled? // **************** // Note to maintainers: if new toggles are added please document them // in configuration.md, too // **************** // In general each macro has a _NO_ form // (e.g. CATCH_CONFIG_NO_POSIX_SIGNALS) which disables the feature. // Many features, at point of detection, define an _INTERNAL_ macro, so they // can be combined, en-mass, with the _NO_ forms later. #ifdef __cplusplus # if (__cplusplus >= 201402L) || (defined(_MSVC_LANG) && _MSVC_LANG >= 201402L) # define CATCH_CPP14_OR_GREATER # endif # if (__cplusplus >= 201703L) || (defined(_MSVC_LANG) && _MSVC_LANG >= 201703L) # define CATCH_CPP17_OR_GREATER # endif #endif #if defined(CATCH_CPP17_OR_GREATER) # define CATCH_INTERNAL_CONFIG_CPP17_UNCAUGHT_EXCEPTIONS #endif #ifdef __clang__ # define CATCH_INTERNAL_SUPPRESS_GLOBALS_WARNINGS \ _Pragma( "clang diagnostic push" ) \ _Pragma( "clang diagnostic ignored \"-Wexit-time-destructors\"" ) \ _Pragma( "clang diagnostic ignored \"-Wglobal-constructors\"") # define CATCH_INTERNAL_UNSUPPRESS_GLOBALS_WARNINGS \ _Pragma( "clang diagnostic pop" ) # define CATCH_INTERNAL_SUPPRESS_PARENTHESES_WARNINGS \ _Pragma( "clang diagnostic push" ) \ _Pragma( "clang diagnostic ignored \"-Wparentheses\"" ) # define CATCH_INTERNAL_UNSUPPRESS_PARENTHESES_WARNINGS \ _Pragma( "clang diagnostic pop" ) # define CATCH_INTERNAL_SUPPRESS_UNUSED_WARNINGS \ _Pragma( "clang diagnostic push" ) \ _Pragma( "clang diagnostic ignored \"-Wunused-variable\"" ) # define CATCH_INTERNAL_UNSUPPRESS_UNUSED_WARNINGS \ _Pragma( "clang diagnostic pop" ) #endif // __clang__ //////////////////////////////////////////////////////////////////////////////// // Assume that non-Windows platforms support posix signals by default #if !defined(CATCH_PLATFORM_WINDOWS) #define CATCH_INTERNAL_CONFIG_POSIX_SIGNALS #endif //////////////////////////////////////////////////////////////////////////////// // We know some environments not to support full POSIX signals #if defined(__CYGWIN__) || defined(__QNX__) || defined(__EMSCRIPTEN__) || defined(__DJGPP__) #define CATCH_INTERNAL_CONFIG_NO_POSIX_SIGNALS #endif #ifdef __OS400__ # define CATCH_INTERNAL_CONFIG_NO_POSIX_SIGNALS # define CATCH_CONFIG_COLOUR_NONE #endif //////////////////////////////////////////////////////////////////////////////// // Android somehow still does not support std::to_string #if defined(__ANDROID__) # define CATCH_INTERNAL_CONFIG_NO_CPP11_TO_STRING #endif //////////////////////////////////////////////////////////////////////////////// // Not all Windows environments support SEH properly #if defined(__MINGW32__) # define CATCH_INTERNAL_CONFIG_NO_WINDOWS_SEH #endif //////////////////////////////////////////////////////////////////////////////// // PS4 #if defined(__ORBIS__) # define CATCH_INTERNAL_CONFIG_NO_NEW_CAPTURE #endif //////////////////////////////////////////////////////////////////////////////// // Cygwin #ifdef __CYGWIN__ // Required for some versions of Cygwin to declare gettimeofday // see: http://stackoverflow.com/questions/36901803/gettimeofday-not-declared-in-this-scope-cygwin # define _BSD_SOURCE // some versions of cygwin (most) do not support std::to_string. Use the libstd check. // https://gcc.gnu.org/onlinedocs/gcc-4.8.2/libstdc++/api/a01053_source.html line 2812-2813 # if !((__cplusplus >= 201103L) && defined(_GLIBCXX_USE_C99) \ && !defined(_GLIBCXX_HAVE_BROKEN_VSWPRINTF)) # define CATCH_INTERNAL_CONFIG_NO_CPP11_TO_STRING # endif #endif // __CYGWIN__ //////////////////////////////////////////////////////////////////////////////// // Visual C++ #ifdef _MSC_VER # if _MSC_VER >= 1900 // Visual Studio 2015 or newer # define CATCH_INTERNAL_CONFIG_CPP17_UNCAUGHT_EXCEPTIONS # endif // Universal Windows platform does not support SEH // Or console colours (or console at all...) # if defined(WINAPI_FAMILY) && (WINAPI_FAMILY == WINAPI_FAMILY_APP) # define CATCH_CONFIG_COLOUR_NONE # else # define CATCH_INTERNAL_CONFIG_WINDOWS_SEH # endif // MSVC traditional preprocessor needs some workaround for __VA_ARGS__ // _MSVC_TRADITIONAL == 0 means new conformant preprocessor // _MSVC_TRADITIONAL == 1 means old traditional non-conformant preprocessor # if !defined(_MSVC_TRADITIONAL) || (defined(_MSVC_TRADITIONAL) && _MSVC_TRADITIONAL) # define CATCH_INTERNAL_CONFIG_TRADITIONAL_MSVC_PREPROCESSOR # endif #endif // _MSC_VER //////////////////////////////////////////////////////////////////////////////// // Check if we are compiled with -fno-exceptions or equivalent #if defined(__EXCEPTIONS) || defined(__cpp_exceptions) || defined(_CPPUNWIND) # define CATCH_INTERNAL_CONFIG_EXCEPTIONS_ENABLED #endif //////////////////////////////////////////////////////////////////////////////// // DJGPP #ifdef __DJGPP__ # define CATCH_INTERNAL_CONFIG_NO_WCHAR #endif // __DJGPP__ //////////////////////////////////////////////////////////////////////////////// // Embarcadero C++Build #if defined(__BORLANDC__) #define CATCH_INTERNAL_CONFIG_POLYFILL_ISNAN #endif //////////////////////////////////////////////////////////////////////////////// // Use of __COUNTER__ is suppressed during code analysis in // CLion/AppCode 2017.2.x and former, because __COUNTER__ is not properly // handled by it. // Otherwise all supported compilers support COUNTER macro, // but user still might want to turn it off #if ( !defined(__JETBRAINS_IDE__) || __JETBRAINS_IDE__ >= 20170300L ) #define CATCH_INTERNAL_CONFIG_COUNTER #endif //////////////////////////////////////////////////////////////////////////////// // Check if string_view is available and usable // The check is split apart to work around v140 (VS2015) preprocessor issue... #if defined(__has_include) #if __has_include() && defined(CATCH_CPP17_OR_GREATER) # define CATCH_INTERNAL_CONFIG_CPP17_STRING_VIEW #endif #endif //////////////////////////////////////////////////////////////////////////////// // Check if optional is available and usable #if defined(__has_include) # if __has_include() && defined(CATCH_CPP17_OR_GREATER) # define CATCH_INTERNAL_CONFIG_CPP17_OPTIONAL # endif // __has_include() && defined(CATCH_CPP17_OR_GREATER) #endif // __has_include //////////////////////////////////////////////////////////////////////////////// // Check if variant is available and usable #if defined(__has_include) # if __has_include() && defined(CATCH_CPP17_OR_GREATER) # if defined(__clang__) && (__clang_major__ < 8) // work around clang bug with libstdc++ https://bugs.llvm.org/show_bug.cgi?id=31852 // fix should be in clang 8, workaround in libstdc++ 8.2 # include # if defined(__GLIBCXX__) && defined(_GLIBCXX_RELEASE) && (_GLIBCXX_RELEASE < 9) # define CATCH_CONFIG_NO_CPP17_VARIANT # else # define CATCH_INTERNAL_CONFIG_CPP17_VARIANT # endif // defined(__GLIBCXX__) && defined(_GLIBCXX_RELEASE) && (_GLIBCXX_RELEASE < 9) # else # define CATCH_INTERNAL_CONFIG_CPP17_VARIANT # endif // defined(__clang__) && (__clang_major__ < 8) # endif // __has_include() && defined(CATCH_CPP17_OR_GREATER) #endif // __has_include #if defined(CATCH_INTERNAL_CONFIG_COUNTER) && !defined(CATCH_CONFIG_NO_COUNTER) && !defined(CATCH_CONFIG_COUNTER) # define CATCH_CONFIG_COUNTER #endif #if defined(CATCH_INTERNAL_CONFIG_WINDOWS_SEH) && !defined(CATCH_CONFIG_NO_WINDOWS_SEH) && !defined(CATCH_CONFIG_WINDOWS_SEH) && !defined(CATCH_INTERNAL_CONFIG_NO_WINDOWS_SEH) # define CATCH_CONFIG_WINDOWS_SEH #endif // This is set by default, because we assume that unix compilers are posix-signal-compatible by default. #if defined(CATCH_INTERNAL_CONFIG_POSIX_SIGNALS) && !defined(CATCH_INTERNAL_CONFIG_NO_POSIX_SIGNALS) && !defined(CATCH_CONFIG_NO_POSIX_SIGNALS) && !defined(CATCH_CONFIG_POSIX_SIGNALS) # define CATCH_CONFIG_POSIX_SIGNALS #endif // This is set by default, because we assume that compilers with no wchar_t support are just rare exceptions. #if !defined(CATCH_INTERNAL_CONFIG_NO_WCHAR) && !defined(CATCH_CONFIG_NO_WCHAR) && !defined(CATCH_CONFIG_WCHAR) # define CATCH_CONFIG_WCHAR #endif #if !defined(CATCH_INTERNAL_CONFIG_NO_CPP11_TO_STRING) && !defined(CATCH_CONFIG_NO_CPP11_TO_STRING) && !defined(CATCH_CONFIG_CPP11_TO_STRING) # define CATCH_CONFIG_CPP11_TO_STRING #endif #if defined(CATCH_INTERNAL_CONFIG_CPP17_OPTIONAL) && !defined(CATCH_CONFIG_NO_CPP17_OPTIONAL) && !defined(CATCH_CONFIG_CPP17_OPTIONAL) # define CATCH_CONFIG_CPP17_OPTIONAL #endif #if defined(CATCH_INTERNAL_CONFIG_CPP17_UNCAUGHT_EXCEPTIONS) && !defined(CATCH_CONFIG_NO_CPP17_UNCAUGHT_EXCEPTIONS) && !defined(CATCH_CONFIG_CPP17_UNCAUGHT_EXCEPTIONS) # define CATCH_CONFIG_CPP17_UNCAUGHT_EXCEPTIONS #endif #if defined(CATCH_INTERNAL_CONFIG_CPP17_STRING_VIEW) && !defined(CATCH_CONFIG_NO_CPP17_STRING_VIEW) && !defined(CATCH_CONFIG_CPP17_STRING_VIEW) # define CATCH_CONFIG_CPP17_STRING_VIEW #endif #if defined(CATCH_INTERNAL_CONFIG_CPP17_VARIANT) && !defined(CATCH_CONFIG_NO_CPP17_VARIANT) && !defined(CATCH_CONFIG_CPP17_VARIANT) # define CATCH_CONFIG_CPP17_VARIANT #endif #if defined(CATCH_CONFIG_EXPERIMENTAL_REDIRECT) # define CATCH_INTERNAL_CONFIG_NEW_CAPTURE #endif #if defined(CATCH_INTERNAL_CONFIG_NEW_CAPTURE) && !defined(CATCH_INTERNAL_CONFIG_NO_NEW_CAPTURE) && !defined(CATCH_CONFIG_NO_NEW_CAPTURE) && !defined(CATCH_CONFIG_NEW_CAPTURE) # define CATCH_CONFIG_NEW_CAPTURE #endif #if !defined(CATCH_INTERNAL_CONFIG_EXCEPTIONS_ENABLED) && !defined(CATCH_CONFIG_DISABLE_EXCEPTIONS) # define CATCH_CONFIG_DISABLE_EXCEPTIONS #endif #if defined(CATCH_INTERNAL_CONFIG_POLYFILL_ISNAN) && !defined(CATCH_CONFIG_NO_POLYFILL_ISNAN) && !defined(CATCH_CONFIG_POLYFILL_ISNAN) # define CATCH_CONFIG_POLYFILL_ISNAN #endif #if !defined(CATCH_INTERNAL_SUPPRESS_PARENTHESES_WARNINGS) # define CATCH_INTERNAL_SUPPRESS_PARENTHESES_WARNINGS # define CATCH_INTERNAL_UNSUPPRESS_PARENTHESES_WARNINGS #endif #if !defined(CATCH_INTERNAL_SUPPRESS_GLOBALS_WARNINGS) # define CATCH_INTERNAL_SUPPRESS_GLOBALS_WARNINGS # define CATCH_INTERNAL_UNSUPPRESS_GLOBALS_WARNINGS #endif #if !defined(CATCH_INTERNAL_SUPPRESS_UNUSED_WARNINGS) # define CATCH_INTERNAL_SUPPRESS_UNUSED_WARNINGS # define CATCH_INTERNAL_UNSUPPRESS_UNUSED_WARNINGS #endif #if defined(CATCH_CONFIG_DISABLE_EXCEPTIONS) #define CATCH_TRY if ((true)) #define CATCH_CATCH_ALL if ((false)) #define CATCH_CATCH_ANON(type) if ((false)) #else #define CATCH_TRY try #define CATCH_CATCH_ALL catch (...) #define CATCH_CATCH_ANON(type) catch (type) #endif #if defined(CATCH_INTERNAL_CONFIG_TRADITIONAL_MSVC_PREPROCESSOR) && !defined(CATCH_CONFIG_NO_TRADITIONAL_MSVC_PREPROCESSOR) && !defined(CATCH_CONFIG_TRADITIONAL_MSVC_PREPROCESSOR) #define CATCH_CONFIG_TRADITIONAL_MSVC_PREPROCESSOR #endif // end catch_compiler_capabilities.h #define INTERNAL_CATCH_UNIQUE_NAME_LINE2( name, line ) name##line #define INTERNAL_CATCH_UNIQUE_NAME_LINE( name, line ) INTERNAL_CATCH_UNIQUE_NAME_LINE2( name, line ) #ifdef CATCH_CONFIG_COUNTER # define INTERNAL_CATCH_UNIQUE_NAME( name ) INTERNAL_CATCH_UNIQUE_NAME_LINE( name, __COUNTER__ ) #else # define INTERNAL_CATCH_UNIQUE_NAME( name ) INTERNAL_CATCH_UNIQUE_NAME_LINE( name, __LINE__ ) #endif #include #include #include // We need a dummy global operator<< so we can bring it into Catch namespace later struct Catch_global_namespace_dummy {}; std::ostream& operator<<(std::ostream&, Catch_global_namespace_dummy); namespace Catch { struct CaseSensitive { enum Choice { Yes, No }; }; class NonCopyable { NonCopyable( NonCopyable const& ) = delete; NonCopyable( NonCopyable && ) = delete; NonCopyable& operator = ( NonCopyable const& ) = delete; NonCopyable& operator = ( NonCopyable && ) = delete; protected: NonCopyable(); virtual ~NonCopyable(); }; struct SourceLineInfo { SourceLineInfo() = delete; SourceLineInfo( char const* _file, std::size_t _line ) noexcept : file( _file ), line( _line ) {} SourceLineInfo( SourceLineInfo const& other ) = default; SourceLineInfo& operator = ( SourceLineInfo const& ) = default; SourceLineInfo( SourceLineInfo&& ) noexcept = default; SourceLineInfo& operator = ( SourceLineInfo&& ) noexcept = default; bool empty() const noexcept; bool operator == ( SourceLineInfo const& other ) const noexcept; bool operator < ( SourceLineInfo const& other ) const noexcept; char const* file; std::size_t line; }; std::ostream& operator << ( std::ostream& os, SourceLineInfo const& info ); // Bring in operator<< from global namespace into Catch namespace // This is necessary because the overload of operator<< above makes // lookup stop at namespace Catch using ::operator<<; // Use this in variadic streaming macros to allow // >> +StreamEndStop // as well as // >> stuff +StreamEndStop struct StreamEndStop { std::string operator+() const; }; template T const& operator + ( T const& value, StreamEndStop ) { return value; } } #define CATCH_INTERNAL_LINEINFO \ ::Catch::SourceLineInfo( __FILE__, static_cast( __LINE__ ) ) // end catch_common.h namespace Catch { struct RegistrarForTagAliases { RegistrarForTagAliases( char const* alias, char const* tag, SourceLineInfo const& lineInfo ); }; } // end namespace Catch #define CATCH_REGISTER_TAG_ALIAS( alias, spec ) \ CATCH_INTERNAL_SUPPRESS_GLOBALS_WARNINGS \ namespace{ Catch::RegistrarForTagAliases INTERNAL_CATCH_UNIQUE_NAME( AutoRegisterTagAlias )( alias, spec, CATCH_INTERNAL_LINEINFO ); } \ CATCH_INTERNAL_UNSUPPRESS_GLOBALS_WARNINGS // end catch_tag_alias_autoregistrar.h // start catch_test_registry.h // start catch_interfaces_testcase.h #include namespace Catch { class TestSpec; struct ITestInvoker { virtual void invoke () const = 0; virtual ~ITestInvoker(); }; class TestCase; struct IConfig; struct ITestCaseRegistry { virtual ~ITestCaseRegistry(); virtual std::vector const& getAllTests() const = 0; virtual std::vector const& getAllTestsSorted( IConfig const& config ) const = 0; }; bool matchTest( TestCase const& testCase, TestSpec const& testSpec, IConfig const& config ); std::vector filterTests( std::vector const& testCases, TestSpec const& testSpec, IConfig const& config ); std::vector const& getAllTestCasesSorted( IConfig const& config ); } // end catch_interfaces_testcase.h // start catch_stringref.h #include #include #include namespace Catch { /// A non-owning string class (similar to the forthcoming std::string_view) /// Note that, because a StringRef may be a substring of another string, /// it may not be null terminated. c_str() must return a null terminated /// string, however, and so the StringRef will internally take ownership /// (taking a copy), if necessary. In theory this ownership is not externally /// visible - but it does mean (substring) StringRefs should not be shared between /// threads. class StringRef { public: using size_type = std::size_t; private: friend struct StringRefTestAccess; char const* m_start; size_type m_size; char* m_data = nullptr; void takeOwnership(); static constexpr char const* const s_empty = ""; public: // construction/ assignment StringRef() noexcept : StringRef( s_empty, 0 ) {} StringRef( StringRef const& other ) noexcept : m_start( other.m_start ), m_size( other.m_size ) {} StringRef( StringRef&& other ) noexcept : m_start( other.m_start ), m_size( other.m_size ), m_data( other.m_data ) { other.m_data = nullptr; } StringRef( char const* rawChars ) noexcept; StringRef( char const* rawChars, size_type size ) noexcept : m_start( rawChars ), m_size( size ) {} StringRef( std::string const& stdString ) noexcept : m_start( stdString.c_str() ), m_size( stdString.size() ) {} ~StringRef() noexcept { delete[] m_data; } auto operator = ( StringRef const &other ) noexcept -> StringRef& { delete[] m_data; m_data = nullptr; m_start = other.m_start; m_size = other.m_size; return *this; } operator std::string() const; void swap( StringRef& other ) noexcept; public: // operators auto operator == ( StringRef const& other ) const noexcept -> bool; auto operator != ( StringRef const& other ) const noexcept -> bool; auto operator[] ( size_type index ) const noexcept -> char; public: // named queries auto empty() const noexcept -> bool { return m_size == 0; } auto size() const noexcept -> size_type { return m_size; } auto numberOfCharacters() const noexcept -> size_type; auto c_str() const -> char const*; public: // substrings and searches auto substr( size_type start, size_type size ) const noexcept -> StringRef; // Returns the current start pointer. // Note that the pointer can change when if the StringRef is a substring auto currentData() const noexcept -> char const*; private: // ownership queries - may not be consistent between calls auto isOwned() const noexcept -> bool; auto isSubstring() const noexcept -> bool; }; auto operator + ( StringRef const& lhs, StringRef const& rhs ) -> std::string; auto operator + ( StringRef const& lhs, char const* rhs ) -> std::string; auto operator + ( char const* lhs, StringRef const& rhs ) -> std::string; auto operator += ( std::string& lhs, StringRef const& sr ) -> std::string&; auto operator << ( std::ostream& os, StringRef const& sr ) -> std::ostream&; inline auto operator "" _sr( char const* rawChars, std::size_t size ) noexcept -> StringRef { return StringRef( rawChars, size ); } } // namespace Catch inline auto operator "" _catch_sr( char const* rawChars, std::size_t size ) noexcept -> Catch::StringRef { return Catch::StringRef( rawChars, size ); } // end catch_stringref.h // start catch_type_traits.hpp #include namespace Catch{ #ifdef CATCH_CPP17_OR_GREATER template inline constexpr auto is_unique = std::true_type{}; template inline constexpr auto is_unique = std::bool_constant< (!std::is_same_v && ...) && is_unique >{}; #else template struct is_unique : std::true_type{}; template struct is_unique : std::integral_constant ::value && is_unique::value && is_unique::value >{}; #endif } // end catch_type_traits.hpp // start catch_preprocessor.hpp #define CATCH_RECURSION_LEVEL0(...) __VA_ARGS__ #define CATCH_RECURSION_LEVEL1(...) CATCH_RECURSION_LEVEL0(CATCH_RECURSION_LEVEL0(CATCH_RECURSION_LEVEL0(__VA_ARGS__))) #define CATCH_RECURSION_LEVEL2(...) CATCH_RECURSION_LEVEL1(CATCH_RECURSION_LEVEL1(CATCH_RECURSION_LEVEL1(__VA_ARGS__))) #define CATCH_RECURSION_LEVEL3(...) CATCH_RECURSION_LEVEL2(CATCH_RECURSION_LEVEL2(CATCH_RECURSION_LEVEL2(__VA_ARGS__))) #define CATCH_RECURSION_LEVEL4(...) CATCH_RECURSION_LEVEL3(CATCH_RECURSION_LEVEL3(CATCH_RECURSION_LEVEL3(__VA_ARGS__))) #define CATCH_RECURSION_LEVEL5(...) CATCH_RECURSION_LEVEL4(CATCH_RECURSION_LEVEL4(CATCH_RECURSION_LEVEL4(__VA_ARGS__))) #ifdef CATCH_CONFIG_TRADITIONAL_MSVC_PREPROCESSOR #define INTERNAL_CATCH_EXPAND_VARGS(...) __VA_ARGS__ // MSVC needs more evaluations #define CATCH_RECURSION_LEVEL6(...) CATCH_RECURSION_LEVEL5(CATCH_RECURSION_LEVEL5(CATCH_RECURSION_LEVEL5(__VA_ARGS__))) #define CATCH_RECURSE(...) CATCH_RECURSION_LEVEL6(CATCH_RECURSION_LEVEL6(__VA_ARGS__)) #else #define CATCH_RECURSE(...) CATCH_RECURSION_LEVEL5(__VA_ARGS__) #endif #define CATCH_REC_END(...) #define CATCH_REC_OUT #define CATCH_EMPTY() #define CATCH_DEFER(id) id CATCH_EMPTY() #define CATCH_REC_GET_END2() 0, CATCH_REC_END #define CATCH_REC_GET_END1(...) CATCH_REC_GET_END2 #define CATCH_REC_GET_END(...) CATCH_REC_GET_END1 #define CATCH_REC_NEXT0(test, next, ...) next CATCH_REC_OUT #define CATCH_REC_NEXT1(test, next) CATCH_DEFER ( CATCH_REC_NEXT0 ) ( test, next, 0) #define CATCH_REC_NEXT(test, next) CATCH_REC_NEXT1(CATCH_REC_GET_END test, next) #define CATCH_REC_LIST0(f, x, peek, ...) , f(x) CATCH_DEFER ( CATCH_REC_NEXT(peek, CATCH_REC_LIST1) ) ( f, peek, __VA_ARGS__ ) #define CATCH_REC_LIST1(f, x, peek, ...) , f(x) CATCH_DEFER ( CATCH_REC_NEXT(peek, CATCH_REC_LIST0) ) ( f, peek, __VA_ARGS__ ) #define CATCH_REC_LIST2(f, x, peek, ...) f(x) CATCH_DEFER ( CATCH_REC_NEXT(peek, CATCH_REC_LIST1) ) ( f, peek, __VA_ARGS__ ) #define CATCH_REC_LIST0_UD(f, userdata, x, peek, ...) , f(userdata, x) CATCH_DEFER ( CATCH_REC_NEXT(peek, CATCH_REC_LIST1_UD) ) ( f, userdata, peek, __VA_ARGS__ ) #define CATCH_REC_LIST1_UD(f, userdata, x, peek, ...) , f(userdata, x) CATCH_DEFER ( CATCH_REC_NEXT(peek, CATCH_REC_LIST0_UD) ) ( f, userdata, peek, __VA_ARGS__ ) #define CATCH_REC_LIST2_UD(f, userdata, x, peek, ...) f(userdata, x) CATCH_DEFER ( CATCH_REC_NEXT(peek, CATCH_REC_LIST1_UD) ) ( f, userdata, peek, __VA_ARGS__ ) // Applies the function macro `f` to each of the remaining parameters, inserts commas between the results, // and passes userdata as the first parameter to each invocation, // e.g. CATCH_REC_LIST_UD(f, x, a, b, c) evaluates to f(x, a), f(x, b), f(x, c) #define CATCH_REC_LIST_UD(f, userdata, ...) CATCH_RECURSE(CATCH_REC_LIST2_UD(f, userdata, __VA_ARGS__, ()()(), ()()(), ()()(), 0)) #define CATCH_REC_LIST(f, ...) CATCH_RECURSE(CATCH_REC_LIST2(f, __VA_ARGS__, ()()(), ()()(), ()()(), 0)) #define INTERNAL_CATCH_EXPAND1(param) INTERNAL_CATCH_EXPAND2(param) #define INTERNAL_CATCH_EXPAND2(...) INTERNAL_CATCH_NO## __VA_ARGS__ #define INTERNAL_CATCH_DEF(...) INTERNAL_CATCH_DEF __VA_ARGS__ #define INTERNAL_CATCH_NOINTERNAL_CATCH_DEF #define INTERNAL_CATCH_REMOVE_PARENS(...) INTERNAL_CATCH_EXPAND1(INTERNAL_CATCH_DEF __VA_ARGS__) #define INTERNAL_CATCH_TEMPLATE_UNIQUE_NAME2(Name, ...) INTERNAL_CATCH_TEMPLATE_UNIQUE_NAME3(Name, __VA_ARGS__) #ifndef CATCH_CONFIG_TRADITIONAL_MSVC_PREPROCESSOR #define INTERNAL_CATCH_TEMPLATE_UNIQUE_NAME3(Name,...) Name " - " #__VA_ARGS__ #define INTERNAL_CATCH_TEMPLATE_UNIQUE_NAME(Name,...) INTERNAL_CATCH_TEMPLATE_UNIQUE_NAME2(Name, INTERNAL_CATCH_REMOVE_PARENS(__VA_ARGS__)) #else // MSVC is adding extra space and needs more calls to properly remove () #define INTERNAL_CATCH_TEMPLATE_UNIQUE_NAME3(Name,...) Name " -" #__VA_ARGS__ #define INTERNAL_CATCH_TEMPLATE_UNIQUE_NAME1(Name, ...) INTERNAL_CATCH_TEMPLATE_UNIQUE_NAME2(Name, __VA_ARGS__) #define INTERNAL_CATCH_TEMPLATE_UNIQUE_NAME(Name, ...) INTERNAL_CATCH_TEMPLATE_UNIQUE_NAME1(Name, INTERNAL_CATCH_EXPAND_VARGS(INTERNAL_CATCH_REMOVE_PARENS(__VA_ARGS__))) #endif #define INTERNAL_CATCH_MAKE_TYPE_LIST(types) TypeList #define INTERNAL_CATCH_MAKE_TYPE_LISTS_FROM_TYPES(types)\ CATCH_REC_LIST(INTERNAL_CATCH_MAKE_TYPE_LIST,INTERNAL_CATCH_REMOVE_PARENS(types)) // end catch_preprocessor.hpp // start catch_meta.hpp #include template< typename... > struct TypeList{}; template< typename... > struct append; template< template class L1 , typename...E1 , template class L2 , typename...E2 > struct append< L1, L2 > { using type = L1; }; template< template class L1 , typename...E1 , template class L2 , typename...E2 , typename...Rest > struct append< L1, L2, Rest...> { using type = typename append< L1, Rest... >::type; }; template< template class , typename... > struct rewrap; template< template class Container , template class List , typename...elems > struct rewrap> { using type = TypeList< Container< elems... > >; }; template< template class Container , template class List , class...Elems , typename...Elements> struct rewrap, Elements...> { using type = typename append>, typename rewrap::type>::type; }; template< template class...Containers > struct combine { template< typename...Types > struct with_types { template< template class Final > struct into { using type = typename append, typename rewrap::type...>::type; }; }; }; template struct always_false : std::false_type {}; // end catch_meta.hpp namespace Catch { template class TestInvokerAsMethod : public ITestInvoker { void (C::*m_testAsMethod)(); public: TestInvokerAsMethod( void (C::*testAsMethod)() ) noexcept : m_testAsMethod( testAsMethod ) {} void invoke() const override { C obj; (obj.*m_testAsMethod)(); } }; auto makeTestInvoker( void(*testAsFunction)() ) noexcept -> ITestInvoker*; template auto makeTestInvoker( void (C::*testAsMethod)() ) noexcept -> ITestInvoker* { return new(std::nothrow) TestInvokerAsMethod( testAsMethod ); } struct NameAndTags { NameAndTags( StringRef const& name_ = StringRef(), StringRef const& tags_ = StringRef() ) noexcept; StringRef name; StringRef tags; }; struct AutoReg : NonCopyable { AutoReg( ITestInvoker* invoker, SourceLineInfo const& lineInfo, StringRef const& classOrMethod, NameAndTags const& nameAndTags ) noexcept; ~AutoReg(); }; } // end namespace Catch #if defined(CATCH_CONFIG_DISABLE) #define INTERNAL_CATCH_TESTCASE_NO_REGISTRATION( TestName, ... ) \ static void TestName() #define INTERNAL_CATCH_TESTCASE_METHOD_NO_REGISTRATION( TestName, ClassName, ... ) \ namespace{ \ struct TestName : INTERNAL_CATCH_REMOVE_PARENS(ClassName) { \ void test(); \ }; \ } \ void TestName::test() #define INTERNAL_CATCH_TEMPLATE_TEST_CASE_NO_REGISTRATION( TestName, ... ) \ template \ static void TestName() #define INTERNAL_CATCH_TEMPLATE_TEST_CASE_METHOD_NO_REGISTRATION( TestName, ClassName, ... ) \ namespace{ \ template \ struct TestName : INTERNAL_CATCH_REMOVE_PARENS(ClassName ) { \ void test(); \ }; \ } \ template \ void TestName::test() #endif /////////////////////////////////////////////////////////////////////////////// #define INTERNAL_CATCH_TESTCASE2( TestName, ... ) \ static void TestName(); \ CATCH_INTERNAL_SUPPRESS_GLOBALS_WARNINGS \ namespace{ Catch::AutoReg INTERNAL_CATCH_UNIQUE_NAME( autoRegistrar )( Catch::makeTestInvoker( &TestName ), CATCH_INTERNAL_LINEINFO, Catch::StringRef(), Catch::NameAndTags{ __VA_ARGS__ } ); } /* NOLINT */ \ CATCH_INTERNAL_UNSUPPRESS_GLOBALS_WARNINGS \ static void TestName() #define INTERNAL_CATCH_TESTCASE( ... ) \ INTERNAL_CATCH_TESTCASE2( INTERNAL_CATCH_UNIQUE_NAME( ____C_A_T_C_H____T_E_S_T____ ), __VA_ARGS__ ) /////////////////////////////////////////////////////////////////////////////// #define INTERNAL_CATCH_METHOD_AS_TEST_CASE( QualifiedMethod, ... ) \ CATCH_INTERNAL_SUPPRESS_GLOBALS_WARNINGS \ namespace{ Catch::AutoReg INTERNAL_CATCH_UNIQUE_NAME( autoRegistrar )( Catch::makeTestInvoker( &QualifiedMethod ), CATCH_INTERNAL_LINEINFO, "&" #QualifiedMethod, Catch::NameAndTags{ __VA_ARGS__ } ); } /* NOLINT */ \ CATCH_INTERNAL_UNSUPPRESS_GLOBALS_WARNINGS /////////////////////////////////////////////////////////////////////////////// #define INTERNAL_CATCH_TEST_CASE_METHOD2( TestName, ClassName, ... )\ CATCH_INTERNAL_SUPPRESS_GLOBALS_WARNINGS \ namespace{ \ struct TestName : INTERNAL_CATCH_REMOVE_PARENS(ClassName) { \ void test(); \ }; \ Catch::AutoReg INTERNAL_CATCH_UNIQUE_NAME( autoRegistrar ) ( Catch::makeTestInvoker( &TestName::test ), CATCH_INTERNAL_LINEINFO, #ClassName, Catch::NameAndTags{ __VA_ARGS__ } ); /* NOLINT */ \ } \ CATCH_INTERNAL_UNSUPPRESS_GLOBALS_WARNINGS \ void TestName::test() #define INTERNAL_CATCH_TEST_CASE_METHOD( ClassName, ... ) \ INTERNAL_CATCH_TEST_CASE_METHOD2( INTERNAL_CATCH_UNIQUE_NAME( ____C_A_T_C_H____T_E_S_T____ ), ClassName, __VA_ARGS__ ) /////////////////////////////////////////////////////////////////////////////// #define INTERNAL_CATCH_REGISTER_TESTCASE( Function, ... ) \ CATCH_INTERNAL_SUPPRESS_GLOBALS_WARNINGS \ Catch::AutoReg INTERNAL_CATCH_UNIQUE_NAME( autoRegistrar )( Catch::makeTestInvoker( Function ), CATCH_INTERNAL_LINEINFO, Catch::StringRef(), Catch::NameAndTags{ __VA_ARGS__ } ); /* NOLINT */ \ CATCH_INTERNAL_UNSUPPRESS_GLOBALS_WARNINGS /////////////////////////////////////////////////////////////////////////////// #define INTERNAL_CATCH_TEMPLATE_TEST_CASE_2(TestName, TestFunc, Name, Tags, ... )\ CATCH_INTERNAL_SUPPRESS_GLOBALS_WARNINGS \ template \ static void TestFunc();\ namespace {\ template \ struct TestName{\ template \ TestName(Ts...names){\ CATCH_INTERNAL_CHECK_UNIQUE_TYPES(CATCH_REC_LIST(INTERNAL_CATCH_REMOVE_PARENS, __VA_ARGS__)) \ using expander = int[];\ (void)expander{(Catch::AutoReg( Catch::makeTestInvoker( &TestFunc ), CATCH_INTERNAL_LINEINFO, Catch::StringRef(), Catch::NameAndTags{ names, Tags } ), 0)... };/* NOLINT */ \ }\ };\ INTERNAL_CATCH_TEMPLATE_REGISTRY_INITIATE(TestName, Name, __VA_ARGS__) \ }\ CATCH_INTERNAL_UNSUPPRESS_GLOBALS_WARNINGS \ template \ static void TestFunc() #if defined(CATCH_CPP17_OR_GREATER) #define CATCH_INTERNAL_CHECK_UNIQUE_TYPES(...) static_assert(Catch::is_unique<__VA_ARGS__>,"Duplicate type detected in declaration of template test case"); #else #define CATCH_INTERNAL_CHECK_UNIQUE_TYPES(...) static_assert(Catch::is_unique<__VA_ARGS__>::value,"Duplicate type detected in declaration of template test case"); #endif #ifndef CATCH_CONFIG_TRADITIONAL_MSVC_PREPROCESSOR #define INTERNAL_CATCH_TEMPLATE_TEST_CASE(Name, Tags, ...) \ INTERNAL_CATCH_TEMPLATE_TEST_CASE_2( INTERNAL_CATCH_UNIQUE_NAME( ____C_A_T_C_H____T_E_M_P_L_A_T_E____T_E_S_T____ ), INTERNAL_CATCH_UNIQUE_NAME( ____C_A_T_C_H____T_E_M_P_L_A_T_E____T_E_S_T____F_U_N_C____ ), Name, Tags, __VA_ARGS__ ) #else #define INTERNAL_CATCH_TEMPLATE_TEST_CASE(Name, Tags, ...) \ INTERNAL_CATCH_EXPAND_VARGS( INTERNAL_CATCH_TEMPLATE_TEST_CASE_2( INTERNAL_CATCH_UNIQUE_NAME( ____C_A_T_C_H____T_E_M_P_L_A_T_E____T_E_S_T____ ), INTERNAL_CATCH_UNIQUE_NAME( ____C_A_T_C_H____T_E_M_P_L_A_T_E____T_E_S_T____F_U_N_C____ ), Name, Tags, __VA_ARGS__ ) ) #endif #define INTERNAL_CATCH_TEMPLATE_REGISTRY_INITIATE(TestName, Name, ...)\ static int INTERNAL_CATCH_UNIQUE_NAME( globalRegistrar ) = [](){\ TestName(CATCH_REC_LIST_UD(INTERNAL_CATCH_TEMPLATE_UNIQUE_NAME,Name, __VA_ARGS__));\ return 0;\ }(); #define INTERNAL_CATCH_TEMPLATE_PRODUCT_TEST_CASE2(TestName, TestFuncName, Name, Tags, TmplTypes, TypesList) \ CATCH_INTERNAL_SUPPRESS_GLOBALS_WARNINGS \ template static void TestFuncName(); \ namespace { \ template \ struct TestName { \ TestName() { \ CATCH_INTERNAL_CHECK_UNIQUE_TYPES(Types...) \ int index = 0; \ using expander = int[]; \ (void)expander{(Catch::AutoReg( Catch::makeTestInvoker( &TestFuncName ), CATCH_INTERNAL_LINEINFO, Catch::StringRef(), Catch::NameAndTags{ Name " - " + Catch::StringMaker::convert(index++), Tags } ), 0)... };/* NOLINT */ \ } \ }; \ static int INTERNAL_CATCH_UNIQUE_NAME( globalRegistrar ) = [](){ \ using TestInit = combine \ ::with_types::into::type; \ TestInit(); \ return 0; \ }(); \ } \ CATCH_INTERNAL_UNSUPPRESS_GLOBALS_WARNINGS \ template \ static void TestFuncName() #ifndef CATCH_CONFIG_TRADITIONAL_MSVC_PREPROCESSOR #define INTERNAL_CATCH_TEMPLATE_PRODUCT_TEST_CASE(Name, Tags, ...)\ INTERNAL_CATCH_TEMPLATE_PRODUCT_TEST_CASE2(INTERNAL_CATCH_UNIQUE_NAME( ____C_A_T_C_H____T_E_M_P_L_A_T_E____T_E_S_T____ ), INTERNAL_CATCH_UNIQUE_NAME( ____C_A_T_C_H____T_E_M_P_L_A_T_E____T_E_S_T____F_U_N_C____ ),Name,Tags,__VA_ARGS__) #else #define INTERNAL_CATCH_TEMPLATE_PRODUCT_TEST_CASE(Name, Tags, ...)\ INTERNAL_CATCH_EXPAND_VARGS( INTERNAL_CATCH_TEMPLATE_PRODUCT_TEST_CASE2( INTERNAL_CATCH_UNIQUE_NAME( ____C_A_T_C_H____T_E_M_P_L_A_T_E____T_E_S_T____ ), INTERNAL_CATCH_UNIQUE_NAME( ____C_A_T_C_H____T_E_M_P_L_A_T_E____T_E_S_T____F_U_N_C____ ), Name, Tags, __VA_ARGS__ ) ) #endif #define INTERNAL_CATCH_TEMPLATE_TEST_CASE_METHOD_2( TestNameClass, TestName, ClassName, Name, Tags, ... ) \ CATCH_INTERNAL_SUPPRESS_GLOBALS_WARNINGS \ namespace{ \ template \ struct TestName : INTERNAL_CATCH_REMOVE_PARENS(ClassName ) { \ void test();\ };\ template \ struct TestNameClass{\ template \ TestNameClass(Ts...names){\ CATCH_INTERNAL_CHECK_UNIQUE_TYPES(CATCH_REC_LIST(INTERNAL_CATCH_REMOVE_PARENS, __VA_ARGS__)) \ using expander = int[];\ (void)expander{(Catch::AutoReg( Catch::makeTestInvoker( &TestName::test ), CATCH_INTERNAL_LINEINFO, #ClassName, Catch::NameAndTags{ names, Tags } ), 0)... };/* NOLINT */ \ }\ };\ INTERNAL_CATCH_TEMPLATE_REGISTRY_INITIATE(TestNameClass, Name, __VA_ARGS__)\ }\ CATCH_INTERNAL_UNSUPPRESS_GLOBALS_WARNINGS\ template \ void TestName::test() #ifndef CATCH_CONFIG_TRADITIONAL_MSVC_PREPROCESSOR #define INTERNAL_CATCH_TEMPLATE_TEST_CASE_METHOD( ClassName, Name, Tags,... ) \ INTERNAL_CATCH_TEMPLATE_TEST_CASE_METHOD_2( INTERNAL_CATCH_UNIQUE_NAME( ____C_A_T_C_H____T_E_M_P_L_A_T_E____T_E_S_T____C_L_A_S_S____ ), INTERNAL_CATCH_UNIQUE_NAME( ____C_A_T_C_H____T_E_M_P_L_A_T_E____T_E_S_T____ ) , ClassName, Name, Tags, __VA_ARGS__ ) #else #define INTERNAL_CATCH_TEMPLATE_TEST_CASE_METHOD( ClassName, Name, Tags,... ) \ INTERNAL_CATCH_EXPAND_VARGS( INTERNAL_CATCH_TEMPLATE_TEST_CASE_METHOD_2( INTERNAL_CATCH_UNIQUE_NAME( ____C_A_T_C_H____T_E_M_P_L_A_T_E____T_E_S_T____C_L_A_S_S____ ), INTERNAL_CATCH_UNIQUE_NAME( ____C_A_T_C_H____T_E_M_P_L_A_T_E____T_E_S_T____ ) , ClassName, Name, Tags, __VA_ARGS__ ) ) #endif #define INTERNAL_CATCH_TEMPLATE_PRODUCT_TEST_CASE_METHOD_2(TestNameClass, TestName, ClassName, Name, Tags, TmplTypes, TypesList)\ CATCH_INTERNAL_SUPPRESS_GLOBALS_WARNINGS \ template \ struct TestName : INTERNAL_CATCH_REMOVE_PARENS(ClassName ) { \ void test();\ };\ namespace {\ template\ struct TestNameClass{\ TestNameClass(){\ CATCH_INTERNAL_CHECK_UNIQUE_TYPES(Types...)\ int index = 0;\ using expander = int[];\ (void)expander{(Catch::AutoReg( Catch::makeTestInvoker( &TestName::test ), CATCH_INTERNAL_LINEINFO, #ClassName, Catch::NameAndTags{ Name " - " + Catch::StringMaker::convert(index++), Tags } ), 0)... };/* NOLINT */ \ }\ };\ static int INTERNAL_CATCH_UNIQUE_NAME( globalRegistrar ) = [](){\ using TestInit = combine\ ::with_types::into::type;\ TestInit();\ return 0;\ }(); \ }\ CATCH_INTERNAL_UNSUPPRESS_GLOBALS_WARNINGS \ template \ void TestName::test() #ifndef CATCH_CONFIG_TRADITIONAL_MSVC_PREPROCESSOR #define INTERNAL_CATCH_TEMPLATE_PRODUCT_TEST_CASE_METHOD( ClassName, Name, Tags, ... )\ INTERNAL_CATCH_TEMPLATE_PRODUCT_TEST_CASE_METHOD_2( INTERNAL_CATCH_UNIQUE_NAME( ____C_A_T_C_H____T_E_M_P_L_A_T_E____T_E_S_T____ ), INTERNAL_CATCH_UNIQUE_NAME( ____C_A_T_C_H____T_E_M_P_L_A_T_E____T_E_S_T____F_U_N_C____ ), ClassName, Name, Tags, __VA_ARGS__ ) #else #define INTERNAL_CATCH_TEMPLATE_PRODUCT_TEST_CASE_METHOD( ClassName, Name, Tags, ... )\ INTERNAL_CATCH_EXPAND_VARGS( INTERNAL_CATCH_TEMPLATE_PRODUCT_TEST_CASE_METHOD_2( INTERNAL_CATCH_UNIQUE_NAME( ____C_A_T_C_H____T_E_M_P_L_A_T_E____T_E_S_T____ ), INTERNAL_CATCH_UNIQUE_NAME( ____C_A_T_C_H____T_E_M_P_L_A_T_E____T_E_S_T____F_U_N_C____ ), ClassName, Name, Tags, __VA_ARGS__ ) ) #endif // end catch_test_registry.h // start catch_capture.hpp // start catch_assertionhandler.h // start catch_assertioninfo.h // start catch_result_type.h namespace Catch { // ResultWas::OfType enum struct ResultWas { enum OfType { Unknown = -1, Ok = 0, Info = 1, Warning = 2, FailureBit = 0x10, ExpressionFailed = FailureBit | 1, ExplicitFailure = FailureBit | 2, Exception = 0x100 | FailureBit, ThrewException = Exception | 1, DidntThrowException = Exception | 2, FatalErrorCondition = 0x200 | FailureBit }; }; bool isOk( ResultWas::OfType resultType ); bool isJustInfo( int flags ); // ResultDisposition::Flags enum struct ResultDisposition { enum Flags { Normal = 0x01, ContinueOnFailure = 0x02, // Failures fail test, but execution continues FalseTest = 0x04, // Prefix expression with ! SuppressFail = 0x08 // Failures are reported but do not fail the test }; }; ResultDisposition::Flags operator | ( ResultDisposition::Flags lhs, ResultDisposition::Flags rhs ); bool shouldContinueOnFailure( int flags ); inline bool isFalseTest( int flags ) { return ( flags & ResultDisposition::FalseTest ) != 0; } bool shouldSuppressFailure( int flags ); } // end namespace Catch // end catch_result_type.h namespace Catch { struct AssertionInfo { StringRef macroName; SourceLineInfo lineInfo; StringRef capturedExpression; ResultDisposition::Flags resultDisposition; // We want to delete this constructor but a compiler bug in 4.8 means // the struct is then treated as non-aggregate //AssertionInfo() = delete; }; } // end namespace Catch // end catch_assertioninfo.h // start catch_decomposer.h // start catch_tostring.h #include #include #include #include // start catch_stream.h #include #include #include namespace Catch { std::ostream& cout(); std::ostream& cerr(); std::ostream& clog(); class StringRef; struct IStream { virtual ~IStream(); virtual std::ostream& stream() const = 0; }; auto makeStream( StringRef const &filename ) -> IStream const*; class ReusableStringStream { std::size_t m_index; std::ostream* m_oss; public: ReusableStringStream(); ~ReusableStringStream(); auto str() const -> std::string; template auto operator << ( T const& value ) -> ReusableStringStream& { *m_oss << value; return *this; } auto get() -> std::ostream& { return *m_oss; } }; } // end catch_stream.h #ifdef CATCH_CONFIG_CPP17_STRING_VIEW #include #endif #ifdef __OBJC__ // start catch_objc_arc.hpp #import #ifdef __has_feature #define CATCH_ARC_ENABLED __has_feature(objc_arc) #else #define CATCH_ARC_ENABLED 0 #endif void arcSafeRelease( NSObject* obj ); id performOptionalSelector( id obj, SEL sel ); #if !CATCH_ARC_ENABLED inline void arcSafeRelease( NSObject* obj ) { [obj release]; } inline id performOptionalSelector( id obj, SEL sel ) { if( [obj respondsToSelector: sel] ) return [obj performSelector: sel]; return nil; } #define CATCH_UNSAFE_UNRETAINED #define CATCH_ARC_STRONG #else inline void arcSafeRelease( NSObject* ){} inline id performOptionalSelector( id obj, SEL sel ) { #ifdef __clang__ #pragma clang diagnostic push #pragma clang diagnostic ignored "-Warc-performSelector-leaks" #endif if( [obj respondsToSelector: sel] ) return [obj performSelector: sel]; #ifdef __clang__ #pragma clang diagnostic pop #endif return nil; } #define CATCH_UNSAFE_UNRETAINED __unsafe_unretained #define CATCH_ARC_STRONG __strong #endif // end catch_objc_arc.hpp #endif #ifdef _MSC_VER #pragma warning(push) #pragma warning(disable:4180) // We attempt to stream a function (address) by const&, which MSVC complains about but is harmless #endif namespace Catch { namespace Detail { extern const std::string unprintableString; std::string rawMemoryToString( const void *object, std::size_t size ); template std::string rawMemoryToString( const T& object ) { return rawMemoryToString( &object, sizeof(object) ); } template class IsStreamInsertable { template static auto test(int) -> decltype(std::declval() << std::declval(), std::true_type()); template static auto test(...)->std::false_type; public: static const bool value = decltype(test(0))::value; }; template std::string convertUnknownEnumToString( E e ); template typename std::enable_if< !std::is_enum::value && !std::is_base_of::value, std::string>::type convertUnstreamable( T const& ) { return Detail::unprintableString; } template typename std::enable_if< !std::is_enum::value && std::is_base_of::value, std::string>::type convertUnstreamable(T const& ex) { return ex.what(); } template typename std::enable_if< std::is_enum::value , std::string>::type convertUnstreamable( T const& value ) { return convertUnknownEnumToString( value ); } #if defined(_MANAGED) //! Convert a CLR string to a utf8 std::string template std::string clrReferenceToString( T^ ref ) { if (ref == nullptr) return std::string("null"); auto bytes = System::Text::Encoding::UTF8->GetBytes(ref->ToString()); cli::pin_ptr p = &bytes[0]; return std::string(reinterpret_cast(p), bytes->Length); } #endif } // namespace Detail // If we decide for C++14, change these to enable_if_ts template struct StringMaker { template static typename std::enable_if<::Catch::Detail::IsStreamInsertable::value, std::string>::type convert(const Fake& value) { ReusableStringStream rss; // NB: call using the function-like syntax to avoid ambiguity with // user-defined templated operator<< under clang. rss.operator<<(value); return rss.str(); } template static typename std::enable_if::value, std::string>::type convert( const Fake& value ) { #if !defined(CATCH_CONFIG_FALLBACK_STRINGIFIER) return Detail::convertUnstreamable(value); #else return CATCH_CONFIG_FALLBACK_STRINGIFIER(value); #endif } }; namespace Detail { // This function dispatches all stringification requests inside of Catch. // Should be preferably called fully qualified, like ::Catch::Detail::stringify template std::string stringify(const T& e) { return ::Catch::StringMaker::type>::type>::convert(e); } template std::string convertUnknownEnumToString( E e ) { return ::Catch::Detail::stringify(static_cast::type>(e)); } #if defined(_MANAGED) template std::string stringify( T^ e ) { return ::Catch::StringMaker::convert(e); } #endif } // namespace Detail // Some predefined specializations template<> struct StringMaker { static std::string convert(const std::string& str); }; #ifdef CATCH_CONFIG_CPP17_STRING_VIEW template<> struct StringMaker { static std::string convert(std::string_view str); }; #endif template<> struct StringMaker { static std::string convert(char const * str); }; template<> struct StringMaker { static std::string convert(char * str); }; #ifdef CATCH_CONFIG_WCHAR template<> struct StringMaker { static std::string convert(const std::wstring& wstr); }; # ifdef CATCH_CONFIG_CPP17_STRING_VIEW template<> struct StringMaker { static std::string convert(std::wstring_view str); }; # endif template<> struct StringMaker { static std::string convert(wchar_t const * str); }; template<> struct StringMaker { static std::string convert(wchar_t * str); }; #endif // TBD: Should we use `strnlen` to ensure that we don't go out of the buffer, // while keeping string semantics? template struct StringMaker { static std::string convert(char const* str) { return ::Catch::Detail::stringify(std::string{ str }); } }; template struct StringMaker { static std::string convert(signed char const* str) { return ::Catch::Detail::stringify(std::string{ reinterpret_cast(str) }); } }; template struct StringMaker { static std::string convert(unsigned char const* str) { return ::Catch::Detail::stringify(std::string{ reinterpret_cast(str) }); } }; template<> struct StringMaker { static std::string convert(int value); }; template<> struct StringMaker { static std::string convert(long value); }; template<> struct StringMaker { static std::string convert(long long value); }; template<> struct StringMaker { static std::string convert(unsigned int value); }; template<> struct StringMaker { static std::string convert(unsigned long value); }; template<> struct StringMaker { static std::string convert(unsigned long long value); }; template<> struct StringMaker { static std::string convert(bool b); }; template<> struct StringMaker { static std::string convert(char c); }; template<> struct StringMaker { static std::string convert(signed char c); }; template<> struct StringMaker { static std::string convert(unsigned char c); }; template<> struct StringMaker { static std::string convert(std::nullptr_t); }; template<> struct StringMaker { static std::string convert(float value); }; template<> struct StringMaker { static std::string convert(double value); }; template struct StringMaker { template static std::string convert(U* p) { if (p) { return ::Catch::Detail::rawMemoryToString(p); } else { return "nullptr"; } } }; template struct StringMaker { static std::string convert(R C::* p) { if (p) { return ::Catch::Detail::rawMemoryToString(p); } else { return "nullptr"; } } }; #if defined(_MANAGED) template struct StringMaker { static std::string convert( T^ ref ) { return ::Catch::Detail::clrReferenceToString(ref); } }; #endif namespace Detail { template std::string rangeToString(InputIterator first, InputIterator last) { ReusableStringStream rss; rss << "{ "; if (first != last) { rss << ::Catch::Detail::stringify(*first); for (++first; first != last; ++first) rss << ", " << ::Catch::Detail::stringify(*first); } rss << " }"; return rss.str(); } } #ifdef __OBJC__ template<> struct StringMaker { static std::string convert(NSString * nsstring) { if (!nsstring) return "nil"; return std::string("@") + [nsstring UTF8String]; } }; template<> struct StringMaker { static std::string convert(NSObject* nsObject) { return ::Catch::Detail::stringify([nsObject description]); } }; namespace Detail { inline std::string stringify( NSString* nsstring ) { return StringMaker::convert( nsstring ); } } // namespace Detail #endif // __OBJC__ } // namespace Catch ////////////////////////////////////////////////////// // Separate std-lib types stringification, so it can be selectively enabled // This means that we do not bring in #if defined(CATCH_CONFIG_ENABLE_ALL_STRINGMAKERS) # define CATCH_CONFIG_ENABLE_PAIR_STRINGMAKER # define CATCH_CONFIG_ENABLE_TUPLE_STRINGMAKER # define CATCH_CONFIG_ENABLE_VARIANT_STRINGMAKER # define CATCH_CONFIG_ENABLE_CHRONO_STRINGMAKER # define CATCH_CONFIG_ENABLE_OPTIONAL_STRINGMAKER #endif // Separate std::pair specialization #if defined(CATCH_CONFIG_ENABLE_PAIR_STRINGMAKER) #include namespace Catch { template struct StringMaker > { static std::string convert(const std::pair& pair) { ReusableStringStream rss; rss << "{ " << ::Catch::Detail::stringify(pair.first) << ", " << ::Catch::Detail::stringify(pair.second) << " }"; return rss.str(); } }; } #endif // CATCH_CONFIG_ENABLE_PAIR_STRINGMAKER #if defined(CATCH_CONFIG_ENABLE_OPTIONAL_STRINGMAKER) && defined(CATCH_CONFIG_CPP17_OPTIONAL) #include namespace Catch { template struct StringMaker > { static std::string convert(const std::optional& optional) { ReusableStringStream rss; if (optional.has_value()) { rss << ::Catch::Detail::stringify(*optional); } else { rss << "{ }"; } return rss.str(); } }; } #endif // CATCH_CONFIG_ENABLE_OPTIONAL_STRINGMAKER // Separate std::tuple specialization #if defined(CATCH_CONFIG_ENABLE_TUPLE_STRINGMAKER) #include namespace Catch { namespace Detail { template< typename Tuple, std::size_t N = 0, bool = (N < std::tuple_size::value) > struct TupleElementPrinter { static void print(const Tuple& tuple, std::ostream& os) { os << (N ? ", " : " ") << ::Catch::Detail::stringify(std::get(tuple)); TupleElementPrinter::print(tuple, os); } }; template< typename Tuple, std::size_t N > struct TupleElementPrinter { static void print(const Tuple&, std::ostream&) {} }; } template struct StringMaker> { static std::string convert(const std::tuple& tuple) { ReusableStringStream rss; rss << '{'; Detail::TupleElementPrinter>::print(tuple, rss.get()); rss << " }"; return rss.str(); } }; } #endif // CATCH_CONFIG_ENABLE_TUPLE_STRINGMAKER #if defined(CATCH_CONFIG_ENABLE_VARIANT_STRINGMAKER) && defined(CATCH_CONFIG_CPP17_VARIANT) #include namespace Catch { template<> struct StringMaker { static std::string convert(const std::monostate&) { return "{ }"; } }; template struct StringMaker> { static std::string convert(const std::variant& variant) { if (variant.valueless_by_exception()) { return "{valueless variant}"; } else { return std::visit( [](const auto& value) { return ::Catch::Detail::stringify(value); }, variant ); } } }; } #endif // CATCH_CONFIG_ENABLE_VARIANT_STRINGMAKER namespace Catch { struct not_this_one {}; // Tag type for detecting which begin/ end are being selected // Import begin/ end from std here so they are considered alongside the fallback (...) overloads in this namespace using std::begin; using std::end; not_this_one begin( ... ); not_this_one end( ... ); template struct is_range { static const bool value = !std::is_same())), not_this_one>::value && !std::is_same())), not_this_one>::value; }; #if defined(_MANAGED) // Managed types are never ranges template struct is_range { static const bool value = false; }; #endif template std::string rangeToString( Range const& range ) { return ::Catch::Detail::rangeToString( begin( range ), end( range ) ); } // Handle vector specially template std::string rangeToString( std::vector const& v ) { ReusableStringStream rss; rss << "{ "; bool first = true; for( bool b : v ) { if( first ) first = false; else rss << ", "; rss << ::Catch::Detail::stringify( b ); } rss << " }"; return rss.str(); } template struct StringMaker::value && !::Catch::Detail::IsStreamInsertable::value>::type> { static std::string convert( R const& range ) { return rangeToString( range ); } }; template struct StringMaker { static std::string convert(T const(&arr)[SZ]) { return rangeToString(arr); } }; } // namespace Catch // Separate std::chrono::duration specialization #if defined(CATCH_CONFIG_ENABLE_CHRONO_STRINGMAKER) #include #include #include namespace Catch { template struct ratio_string { static std::string symbol(); }; template std::string ratio_string::symbol() { Catch::ReusableStringStream rss; rss << '[' << Ratio::num << '/' << Ratio::den << ']'; return rss.str(); } template <> struct ratio_string { static std::string symbol(); }; template <> struct ratio_string { static std::string symbol(); }; template <> struct ratio_string { static std::string symbol(); }; template <> struct ratio_string { static std::string symbol(); }; template <> struct ratio_string { static std::string symbol(); }; template <> struct ratio_string { static std::string symbol(); }; //////////// // std::chrono::duration specializations template struct StringMaker> { static std::string convert(std::chrono::duration const& duration) { ReusableStringStream rss; rss << duration.count() << ' ' << ratio_string::symbol() << 's'; return rss.str(); } }; template struct StringMaker>> { static std::string convert(std::chrono::duration> const& duration) { ReusableStringStream rss; rss << duration.count() << " s"; return rss.str(); } }; template struct StringMaker>> { static std::string convert(std::chrono::duration> const& duration) { ReusableStringStream rss; rss << duration.count() << " m"; return rss.str(); } }; template struct StringMaker>> { static std::string convert(std::chrono::duration> const& duration) { ReusableStringStream rss; rss << duration.count() << " h"; return rss.str(); } }; //////////// // std::chrono::time_point specialization // Generic time_point cannot be specialized, only std::chrono::time_point template struct StringMaker> { static std::string convert(std::chrono::time_point const& time_point) { return ::Catch::Detail::stringify(time_point.time_since_epoch()) + " since epoch"; } }; // std::chrono::time_point specialization template struct StringMaker> { static std::string convert(std::chrono::time_point const& time_point) { auto converted = std::chrono::system_clock::to_time_t(time_point); #ifdef _MSC_VER std::tm timeInfo = {}; gmtime_s(&timeInfo, &converted); #else std::tm* timeInfo = std::gmtime(&converted); #endif auto const timeStampSize = sizeof("2017-01-16T17:06:45Z"); char timeStamp[timeStampSize]; const char * const fmt = "%Y-%m-%dT%H:%M:%SZ"; #ifdef _MSC_VER std::strftime(timeStamp, timeStampSize, fmt, &timeInfo); #else std::strftime(timeStamp, timeStampSize, fmt, timeInfo); #endif return std::string(timeStamp); } }; } #endif // CATCH_CONFIG_ENABLE_CHRONO_STRINGMAKER #ifdef _MSC_VER #pragma warning(pop) #endif // end catch_tostring.h #include #ifdef _MSC_VER #pragma warning(push) #pragma warning(disable:4389) // '==' : signed/unsigned mismatch #pragma warning(disable:4018) // more "signed/unsigned mismatch" #pragma warning(disable:4312) // Converting int to T* using reinterpret_cast (issue on x64 platform) #pragma warning(disable:4180) // qualifier applied to function type has no meaning #pragma warning(disable:4800) // Forcing result to true or false #endif namespace Catch { struct ITransientExpression { auto isBinaryExpression() const -> bool { return m_isBinaryExpression; } auto getResult() const -> bool { return m_result; } virtual void streamReconstructedExpression( std::ostream &os ) const = 0; ITransientExpression( bool isBinaryExpression, bool result ) : m_isBinaryExpression( isBinaryExpression ), m_result( result ) {} // We don't actually need a virtual destructor, but many static analysers // complain if it's not here :-( virtual ~ITransientExpression(); bool m_isBinaryExpression; bool m_result; }; void formatReconstructedExpression( std::ostream &os, std::string const& lhs, StringRef op, std::string const& rhs ); template class BinaryExpr : public ITransientExpression { LhsT m_lhs; StringRef m_op; RhsT m_rhs; void streamReconstructedExpression( std::ostream &os ) const override { formatReconstructedExpression ( os, Catch::Detail::stringify( m_lhs ), m_op, Catch::Detail::stringify( m_rhs ) ); } public: BinaryExpr( bool comparisonResult, LhsT lhs, StringRef op, RhsT rhs ) : ITransientExpression{ true, comparisonResult }, m_lhs( lhs ), m_op( op ), m_rhs( rhs ) {} template auto operator && ( T ) const -> BinaryExpr const { static_assert(always_false::value, "chained comparisons are not supported inside assertions, " "wrap the expression inside parentheses, or decompose it"); } template auto operator || ( T ) const -> BinaryExpr const { static_assert(always_false::value, "chained comparisons are not supported inside assertions, " "wrap the expression inside parentheses, or decompose it"); } template auto operator == ( T ) const -> BinaryExpr const { static_assert(always_false::value, "chained comparisons are not supported inside assertions, " "wrap the expression inside parentheses, or decompose it"); } template auto operator != ( T ) const -> BinaryExpr const { static_assert(always_false::value, "chained comparisons are not supported inside assertions, " "wrap the expression inside parentheses, or decompose it"); } template auto operator > ( T ) const -> BinaryExpr const { static_assert(always_false::value, "chained comparisons are not supported inside assertions, " "wrap the expression inside parentheses, or decompose it"); } template auto operator < ( T ) const -> BinaryExpr const { static_assert(always_false::value, "chained comparisons are not supported inside assertions, " "wrap the expression inside parentheses, or decompose it"); } template auto operator >= ( T ) const -> BinaryExpr const { static_assert(always_false::value, "chained comparisons are not supported inside assertions, " "wrap the expression inside parentheses, or decompose it"); } template auto operator <= ( T ) const -> BinaryExpr const { static_assert(always_false::value, "chained comparisons are not supported inside assertions, " "wrap the expression inside parentheses, or decompose it"); } }; template class UnaryExpr : public ITransientExpression { LhsT m_lhs; void streamReconstructedExpression( std::ostream &os ) const override { os << Catch::Detail::stringify( m_lhs ); } public: explicit UnaryExpr( LhsT lhs ) : ITransientExpression{ false, static_cast(lhs) }, m_lhs( lhs ) {} }; // Specialised comparison functions to handle equality comparisons between ints and pointers (NULL deduces as an int) template auto compareEqual( LhsT const& lhs, RhsT const& rhs ) -> bool { return static_cast(lhs == rhs); } template auto compareEqual( T* const& lhs, int rhs ) -> bool { return lhs == reinterpret_cast( rhs ); } template auto compareEqual( T* const& lhs, long rhs ) -> bool { return lhs == reinterpret_cast( rhs ); } template auto compareEqual( int lhs, T* const& rhs ) -> bool { return reinterpret_cast( lhs ) == rhs; } template auto compareEqual( long lhs, T* const& rhs ) -> bool { return reinterpret_cast( lhs ) == rhs; } template auto compareNotEqual( LhsT const& lhs, RhsT&& rhs ) -> bool { return static_cast(lhs != rhs); } template auto compareNotEqual( T* const& lhs, int rhs ) -> bool { return lhs != reinterpret_cast( rhs ); } template auto compareNotEqual( T* const& lhs, long rhs ) -> bool { return lhs != reinterpret_cast( rhs ); } template auto compareNotEqual( int lhs, T* const& rhs ) -> bool { return reinterpret_cast( lhs ) != rhs; } template auto compareNotEqual( long lhs, T* const& rhs ) -> bool { return reinterpret_cast( lhs ) != rhs; } template class ExprLhs { LhsT m_lhs; public: explicit ExprLhs( LhsT lhs ) : m_lhs( lhs ) {} template auto operator == ( RhsT const& rhs ) -> BinaryExpr const { return { compareEqual( m_lhs, rhs ), m_lhs, "==", rhs }; } auto operator == ( bool rhs ) -> BinaryExpr const { return { m_lhs == rhs, m_lhs, "==", rhs }; } template auto operator != ( RhsT const& rhs ) -> BinaryExpr const { return { compareNotEqual( m_lhs, rhs ), m_lhs, "!=", rhs }; } auto operator != ( bool rhs ) -> BinaryExpr const { return { m_lhs != rhs, m_lhs, "!=", rhs }; } template auto operator > ( RhsT const& rhs ) -> BinaryExpr const { return { static_cast(m_lhs > rhs), m_lhs, ">", rhs }; } template auto operator < ( RhsT const& rhs ) -> BinaryExpr const { return { static_cast(m_lhs < rhs), m_lhs, "<", rhs }; } template auto operator >= ( RhsT const& rhs ) -> BinaryExpr const { return { static_cast(m_lhs >= rhs), m_lhs, ">=", rhs }; } template auto operator <= ( RhsT const& rhs ) -> BinaryExpr const { return { static_cast(m_lhs <= rhs), m_lhs, "<=", rhs }; } template auto operator && ( RhsT const& ) -> BinaryExpr const { static_assert(always_false::value, "operator&& is not supported inside assertions, " "wrap the expression inside parentheses, or decompose it"); } template auto operator || ( RhsT const& ) -> BinaryExpr const { static_assert(always_false::value, "operator|| is not supported inside assertions, " "wrap the expression inside parentheses, or decompose it"); } auto makeUnaryExpr() const -> UnaryExpr { return UnaryExpr{ m_lhs }; } }; void handleExpression( ITransientExpression const& expr ); template void handleExpression( ExprLhs const& expr ) { handleExpression( expr.makeUnaryExpr() ); } struct Decomposer { template auto operator <= ( T const& lhs ) -> ExprLhs { return ExprLhs{ lhs }; } auto operator <=( bool value ) -> ExprLhs { return ExprLhs{ value }; } }; } // end namespace Catch #ifdef _MSC_VER #pragma warning(pop) #endif // end catch_decomposer.h // start catch_interfaces_capture.h #include namespace Catch { class AssertionResult; struct AssertionInfo; struct SectionInfo; struct SectionEndInfo; struct MessageInfo; struct Counts; struct BenchmarkInfo; struct BenchmarkStats; struct AssertionReaction; struct SourceLineInfo; struct ITransientExpression; struct IGeneratorTracker; struct IResultCapture { virtual ~IResultCapture(); virtual bool sectionStarted( SectionInfo const& sectionInfo, Counts& assertions ) = 0; virtual void sectionEnded( SectionEndInfo const& endInfo ) = 0; virtual void sectionEndedEarly( SectionEndInfo const& endInfo ) = 0; virtual auto acquireGeneratorTracker( SourceLineInfo const& lineInfo ) -> IGeneratorTracker& = 0; virtual void benchmarkStarting( BenchmarkInfo const& info ) = 0; virtual void benchmarkEnded( BenchmarkStats const& stats ) = 0; virtual void pushScopedMessage( MessageInfo const& message ) = 0; virtual void popScopedMessage( MessageInfo const& message ) = 0; virtual void handleFatalErrorCondition( StringRef message ) = 0; virtual void handleExpr ( AssertionInfo const& info, ITransientExpression const& expr, AssertionReaction& reaction ) = 0; virtual void handleMessage ( AssertionInfo const& info, ResultWas::OfType resultType, StringRef const& message, AssertionReaction& reaction ) = 0; virtual void handleUnexpectedExceptionNotThrown ( AssertionInfo const& info, AssertionReaction& reaction ) = 0; virtual void handleUnexpectedInflightException ( AssertionInfo const& info, std::string const& message, AssertionReaction& reaction ) = 0; virtual void handleIncomplete ( AssertionInfo const& info ) = 0; virtual void handleNonExpr ( AssertionInfo const &info, ResultWas::OfType resultType, AssertionReaction &reaction ) = 0; virtual bool lastAssertionPassed() = 0; virtual void assertionPassed() = 0; // Deprecated, do not use: virtual std::string getCurrentTestName() const = 0; virtual const AssertionResult* getLastResult() const = 0; virtual void exceptionEarlyReported() = 0; }; IResultCapture& getResultCapture(); } // end catch_interfaces_capture.h namespace Catch { struct TestFailureException{}; struct AssertionResultData; struct IResultCapture; class RunContext; class LazyExpression { friend class AssertionHandler; friend struct AssertionStats; friend class RunContext; ITransientExpression const* m_transientExpression = nullptr; bool m_isNegated; public: LazyExpression( bool isNegated ); LazyExpression( LazyExpression const& other ); LazyExpression& operator = ( LazyExpression const& ) = delete; explicit operator bool() const; friend auto operator << ( std::ostream& os, LazyExpression const& lazyExpr ) -> std::ostream&; }; struct AssertionReaction { bool shouldDebugBreak = false; bool shouldThrow = false; }; class AssertionHandler { AssertionInfo m_assertionInfo; AssertionReaction m_reaction; bool m_completed = false; IResultCapture& m_resultCapture; public: AssertionHandler ( StringRef const& macroName, SourceLineInfo const& lineInfo, StringRef capturedExpression, ResultDisposition::Flags resultDisposition ); ~AssertionHandler() { if ( !m_completed ) { m_resultCapture.handleIncomplete( m_assertionInfo ); } } template void handleExpr( ExprLhs const& expr ) { handleExpr( expr.makeUnaryExpr() ); } void handleExpr( ITransientExpression const& expr ); void handleMessage(ResultWas::OfType resultType, StringRef const& message); void handleExceptionThrownAsExpected(); void handleUnexpectedExceptionNotThrown(); void handleExceptionNotThrownAsExpected(); void handleThrowingCallSkipped(); void handleUnexpectedInflightException(); void complete(); void setCompleted(); // query auto allowThrows() const -> bool; }; void handleExceptionMatchExpr( AssertionHandler& handler, std::string const& str, StringRef const& matcherString ); } // namespace Catch // end catch_assertionhandler.h // start catch_message.h #include #include namespace Catch { struct MessageInfo { MessageInfo( StringRef const& _macroName, SourceLineInfo const& _lineInfo, ResultWas::OfType _type ); StringRef macroName; std::string message; SourceLineInfo lineInfo; ResultWas::OfType type; unsigned int sequence; bool operator == ( MessageInfo const& other ) const; bool operator < ( MessageInfo const& other ) const; private: static unsigned int globalCount; }; struct MessageStream { template MessageStream& operator << ( T const& value ) { m_stream << value; return *this; } ReusableStringStream m_stream; }; struct MessageBuilder : MessageStream { MessageBuilder( StringRef const& macroName, SourceLineInfo const& lineInfo, ResultWas::OfType type ); template MessageBuilder& operator << ( T const& value ) { m_stream << value; return *this; } MessageInfo m_info; }; class ScopedMessage { public: explicit ScopedMessage( MessageBuilder const& builder ); ~ScopedMessage(); MessageInfo m_info; }; class Capturer { std::vector m_messages; IResultCapture& m_resultCapture = getResultCapture(); size_t m_captured = 0; public: Capturer( StringRef macroName, SourceLineInfo const& lineInfo, ResultWas::OfType resultType, StringRef names ); ~Capturer(); void captureValue( size_t index, std::string const& value ); template void captureValues( size_t index, T const& value ) { captureValue( index, Catch::Detail::stringify( value ) ); } template void captureValues( size_t index, T const& value, Ts const&... values ) { captureValue( index, Catch::Detail::stringify(value) ); captureValues( index+1, values... ); } }; } // end namespace Catch // end catch_message.h #if !defined(CATCH_CONFIG_DISABLE) #if !defined(CATCH_CONFIG_DISABLE_STRINGIFICATION) #define CATCH_INTERNAL_STRINGIFY(...) #__VA_ARGS__ #else #define CATCH_INTERNAL_STRINGIFY(...) "Disabled by CATCH_CONFIG_DISABLE_STRINGIFICATION" #endif #if defined(CATCH_CONFIG_FAST_COMPILE) || defined(CATCH_CONFIG_DISABLE_EXCEPTIONS) /////////////////////////////////////////////////////////////////////////////// // Another way to speed-up compilation is to omit local try-catch for REQUIRE* // macros. #define INTERNAL_CATCH_TRY #define INTERNAL_CATCH_CATCH( capturer ) #else // CATCH_CONFIG_FAST_COMPILE #define INTERNAL_CATCH_TRY try #define INTERNAL_CATCH_CATCH( handler ) catch(...) { handler.handleUnexpectedInflightException(); } #endif #define INTERNAL_CATCH_REACT( handler ) handler.complete(); /////////////////////////////////////////////////////////////////////////////// #define INTERNAL_CATCH_TEST( macroName, resultDisposition, ... ) \ do { \ Catch::AssertionHandler catchAssertionHandler( macroName##_catch_sr, CATCH_INTERNAL_LINEINFO, CATCH_INTERNAL_STRINGIFY(__VA_ARGS__), resultDisposition ); \ INTERNAL_CATCH_TRY { \ CATCH_INTERNAL_SUPPRESS_PARENTHESES_WARNINGS \ catchAssertionHandler.handleExpr( Catch::Decomposer() <= __VA_ARGS__ ); \ CATCH_INTERNAL_UNSUPPRESS_PARENTHESES_WARNINGS \ } INTERNAL_CATCH_CATCH( catchAssertionHandler ) \ INTERNAL_CATCH_REACT( catchAssertionHandler ) \ } while( (void)0, false && static_cast( !!(__VA_ARGS__) ) ) // the expression here is never evaluated at runtime but it forces the compiler to give it a look // The double negation silences MSVC's C4800 warning, the static_cast forces short-circuit evaluation if the type has overloaded &&. /////////////////////////////////////////////////////////////////////////////// #define INTERNAL_CATCH_IF( macroName, resultDisposition, ... ) \ INTERNAL_CATCH_TEST( macroName, resultDisposition, __VA_ARGS__ ); \ if( Catch::getResultCapture().lastAssertionPassed() ) /////////////////////////////////////////////////////////////////////////////// #define INTERNAL_CATCH_ELSE( macroName, resultDisposition, ... ) \ INTERNAL_CATCH_TEST( macroName, resultDisposition, __VA_ARGS__ ); \ if( !Catch::getResultCapture().lastAssertionPassed() ) /////////////////////////////////////////////////////////////////////////////// #define INTERNAL_CATCH_NO_THROW( macroName, resultDisposition, ... ) \ do { \ Catch::AssertionHandler catchAssertionHandler( macroName##_catch_sr, CATCH_INTERNAL_LINEINFO, CATCH_INTERNAL_STRINGIFY(__VA_ARGS__), resultDisposition ); \ try { \ static_cast(__VA_ARGS__); \ catchAssertionHandler.handleExceptionNotThrownAsExpected(); \ } \ catch( ... ) { \ catchAssertionHandler.handleUnexpectedInflightException(); \ } \ INTERNAL_CATCH_REACT( catchAssertionHandler ) \ } while( false ) /////////////////////////////////////////////////////////////////////////////// #define INTERNAL_CATCH_THROWS( macroName, resultDisposition, ... ) \ do { \ Catch::AssertionHandler catchAssertionHandler( macroName##_catch_sr, CATCH_INTERNAL_LINEINFO, CATCH_INTERNAL_STRINGIFY(__VA_ARGS__), resultDisposition); \ if( catchAssertionHandler.allowThrows() ) \ try { \ static_cast(__VA_ARGS__); \ catchAssertionHandler.handleUnexpectedExceptionNotThrown(); \ } \ catch( ... ) { \ catchAssertionHandler.handleExceptionThrownAsExpected(); \ } \ else \ catchAssertionHandler.handleThrowingCallSkipped(); \ INTERNAL_CATCH_REACT( catchAssertionHandler ) \ } while( false ) /////////////////////////////////////////////////////////////////////////////// #define INTERNAL_CATCH_THROWS_AS( macroName, exceptionType, resultDisposition, expr ) \ do { \ Catch::AssertionHandler catchAssertionHandler( macroName##_catch_sr, CATCH_INTERNAL_LINEINFO, CATCH_INTERNAL_STRINGIFY(expr) ", " CATCH_INTERNAL_STRINGIFY(exceptionType), resultDisposition ); \ if( catchAssertionHandler.allowThrows() ) \ try { \ static_cast(expr); \ catchAssertionHandler.handleUnexpectedExceptionNotThrown(); \ } \ catch( exceptionType const& ) { \ catchAssertionHandler.handleExceptionThrownAsExpected(); \ } \ catch( ... ) { \ catchAssertionHandler.handleUnexpectedInflightException(); \ } \ else \ catchAssertionHandler.handleThrowingCallSkipped(); \ INTERNAL_CATCH_REACT( catchAssertionHandler ) \ } while( false ) /////////////////////////////////////////////////////////////////////////////// #define INTERNAL_CATCH_MSG( macroName, messageType, resultDisposition, ... ) \ do { \ Catch::AssertionHandler catchAssertionHandler( macroName##_catch_sr, CATCH_INTERNAL_LINEINFO, Catch::StringRef(), resultDisposition ); \ catchAssertionHandler.handleMessage( messageType, ( Catch::MessageStream() << __VA_ARGS__ + ::Catch::StreamEndStop() ).m_stream.str() ); \ INTERNAL_CATCH_REACT( catchAssertionHandler ) \ } while( false ) /////////////////////////////////////////////////////////////////////////////// #define INTERNAL_CATCH_CAPTURE( varName, macroName, ... ) \ auto varName = Catch::Capturer( macroName, CATCH_INTERNAL_LINEINFO, Catch::ResultWas::Info, #__VA_ARGS__ ); \ varName.captureValues( 0, __VA_ARGS__ ) /////////////////////////////////////////////////////////////////////////////// #define INTERNAL_CATCH_INFO( macroName, log ) \ Catch::ScopedMessage INTERNAL_CATCH_UNIQUE_NAME( scopedMessage )( Catch::MessageBuilder( macroName##_catch_sr, CATCH_INTERNAL_LINEINFO, Catch::ResultWas::Info ) << log ); /////////////////////////////////////////////////////////////////////////////// // Although this is matcher-based, it can be used with just a string #define INTERNAL_CATCH_THROWS_STR_MATCHES( macroName, resultDisposition, matcher, ... ) \ do { \ Catch::AssertionHandler catchAssertionHandler( macroName##_catch_sr, CATCH_INTERNAL_LINEINFO, CATCH_INTERNAL_STRINGIFY(__VA_ARGS__) ", " CATCH_INTERNAL_STRINGIFY(matcher), resultDisposition ); \ if( catchAssertionHandler.allowThrows() ) \ try { \ static_cast(__VA_ARGS__); \ catchAssertionHandler.handleUnexpectedExceptionNotThrown(); \ } \ catch( ... ) { \ Catch::handleExceptionMatchExpr( catchAssertionHandler, matcher, #matcher##_catch_sr ); \ } \ else \ catchAssertionHandler.handleThrowingCallSkipped(); \ INTERNAL_CATCH_REACT( catchAssertionHandler ) \ } while( false ) #endif // CATCH_CONFIG_DISABLE // end catch_capture.hpp // start catch_section.h // start catch_section_info.h // start catch_totals.h #include namespace Catch { struct Counts { Counts operator - ( Counts const& other ) const; Counts& operator += ( Counts const& other ); std::size_t total() const; bool allPassed() const; bool allOk() const; std::size_t passed = 0; std::size_t failed = 0; std::size_t failedButOk = 0; }; struct Totals { Totals operator - ( Totals const& other ) const; Totals& operator += ( Totals const& other ); Totals delta( Totals const& prevTotals ) const; int error = 0; Counts assertions; Counts testCases; }; } // end catch_totals.h #include namespace Catch { struct SectionInfo { SectionInfo ( SourceLineInfo const& _lineInfo, std::string const& _name ); // Deprecated SectionInfo ( SourceLineInfo const& _lineInfo, std::string const& _name, std::string const& ) : SectionInfo( _lineInfo, _name ) {} std::string name; std::string description; // !Deprecated: this will always be empty SourceLineInfo lineInfo; }; struct SectionEndInfo { SectionInfo sectionInfo; Counts prevAssertions; double durationInSeconds; }; } // end namespace Catch // end catch_section_info.h // start catch_timer.h #include namespace Catch { auto getCurrentNanosecondsSinceEpoch() -> uint64_t; auto getEstimatedClockResolution() -> uint64_t; class Timer { uint64_t m_nanoseconds = 0; public: void start(); auto getElapsedNanoseconds() const -> uint64_t; auto getElapsedMicroseconds() const -> uint64_t; auto getElapsedMilliseconds() const -> unsigned int; auto getElapsedSeconds() const -> double; }; } // namespace Catch // end catch_timer.h #include namespace Catch { class Section : NonCopyable { public: Section( SectionInfo const& info ); ~Section(); // This indicates whether the section should be executed or not explicit operator bool() const; private: SectionInfo m_info; std::string m_name; Counts m_assertions; bool m_sectionIncluded; Timer m_timer; }; } // end namespace Catch #define INTERNAL_CATCH_SECTION( ... ) \ CATCH_INTERNAL_SUPPRESS_UNUSED_WARNINGS \ if( Catch::Section const& INTERNAL_CATCH_UNIQUE_NAME( catch_internal_Section ) = Catch::SectionInfo( CATCH_INTERNAL_LINEINFO, __VA_ARGS__ ) ) \ CATCH_INTERNAL_UNSUPPRESS_UNUSED_WARNINGS #define INTERNAL_CATCH_DYNAMIC_SECTION( ... ) \ CATCH_INTERNAL_SUPPRESS_UNUSED_WARNINGS \ if( Catch::Section const& INTERNAL_CATCH_UNIQUE_NAME( catch_internal_Section ) = Catch::SectionInfo( CATCH_INTERNAL_LINEINFO, (Catch::ReusableStringStream() << __VA_ARGS__).str() ) ) \ CATCH_INTERNAL_UNSUPPRESS_UNUSED_WARNINGS // end catch_section.h // start catch_benchmark.h #include #include namespace Catch { class BenchmarkLooper { std::string m_name; std::size_t m_count = 0; std::size_t m_iterationsToRun = 1; uint64_t m_resolution; Timer m_timer; static auto getResolution() -> uint64_t; public: // Keep most of this inline as it's on the code path that is being timed BenchmarkLooper( StringRef name ) : m_name( name ), m_resolution( getResolution() ) { reportStart(); m_timer.start(); } explicit operator bool() { if( m_count < m_iterationsToRun ) return true; return needsMoreIterations(); } void increment() { ++m_count; } void reportStart(); auto needsMoreIterations() -> bool; }; } // end namespace Catch #define BENCHMARK( name ) \ for( Catch::BenchmarkLooper looper( name ); looper; looper.increment() ) // end catch_benchmark.h // start catch_interfaces_exception.h // start catch_interfaces_registry_hub.h #include #include namespace Catch { class TestCase; struct ITestCaseRegistry; struct IExceptionTranslatorRegistry; struct IExceptionTranslator; struct IReporterRegistry; struct IReporterFactory; struct ITagAliasRegistry; class StartupExceptionRegistry; using IReporterFactoryPtr = std::shared_ptr; struct IRegistryHub { virtual ~IRegistryHub(); virtual IReporterRegistry const& getReporterRegistry() const = 0; virtual ITestCaseRegistry const& getTestCaseRegistry() const = 0; virtual ITagAliasRegistry const& getTagAliasRegistry() const = 0; virtual IExceptionTranslatorRegistry const& getExceptionTranslatorRegistry() const = 0; virtual StartupExceptionRegistry const& getStartupExceptionRegistry() const = 0; }; struct IMutableRegistryHub { virtual ~IMutableRegistryHub(); virtual void registerReporter( std::string const& name, IReporterFactoryPtr const& factory ) = 0; virtual void registerListener( IReporterFactoryPtr const& factory ) = 0; virtual void registerTest( TestCase const& testInfo ) = 0; virtual void registerTranslator( const IExceptionTranslator* translator ) = 0; virtual void registerTagAlias( std::string const& alias, std::string const& tag, SourceLineInfo const& lineInfo ) = 0; virtual void registerStartupException() noexcept = 0; }; IRegistryHub const& getRegistryHub(); IMutableRegistryHub& getMutableRegistryHub(); void cleanUp(); std::string translateActiveException(); } // end catch_interfaces_registry_hub.h #if defined(CATCH_CONFIG_DISABLE) #define INTERNAL_CATCH_TRANSLATE_EXCEPTION_NO_REG( translatorName, signature) \ static std::string translatorName( signature ) #endif #include #include #include namespace Catch { using exceptionTranslateFunction = std::string(*)(); struct IExceptionTranslator; using ExceptionTranslators = std::vector>; struct IExceptionTranslator { virtual ~IExceptionTranslator(); virtual std::string translate( ExceptionTranslators::const_iterator it, ExceptionTranslators::const_iterator itEnd ) const = 0; }; struct IExceptionTranslatorRegistry { virtual ~IExceptionTranslatorRegistry(); virtual std::string translateActiveException() const = 0; }; class ExceptionTranslatorRegistrar { template class ExceptionTranslator : public IExceptionTranslator { public: ExceptionTranslator( std::string(*translateFunction)( T& ) ) : m_translateFunction( translateFunction ) {} std::string translate( ExceptionTranslators::const_iterator it, ExceptionTranslators::const_iterator itEnd ) const override { try { if( it == itEnd ) std::rethrow_exception(std::current_exception()); else return (*it)->translate( it+1, itEnd ); } catch( T& ex ) { return m_translateFunction( ex ); } } protected: std::string(*m_translateFunction)( T& ); }; public: template ExceptionTranslatorRegistrar( std::string(*translateFunction)( T& ) ) { getMutableRegistryHub().registerTranslator ( new ExceptionTranslator( translateFunction ) ); } }; } /////////////////////////////////////////////////////////////////////////////// #define INTERNAL_CATCH_TRANSLATE_EXCEPTION2( translatorName, signature ) \ static std::string translatorName( signature ); \ CATCH_INTERNAL_SUPPRESS_GLOBALS_WARNINGS \ namespace{ Catch::ExceptionTranslatorRegistrar INTERNAL_CATCH_UNIQUE_NAME( catch_internal_ExceptionRegistrar )( &translatorName ); } \ CATCH_INTERNAL_UNSUPPRESS_GLOBALS_WARNINGS \ static std::string translatorName( signature ) #define INTERNAL_CATCH_TRANSLATE_EXCEPTION( signature ) INTERNAL_CATCH_TRANSLATE_EXCEPTION2( INTERNAL_CATCH_UNIQUE_NAME( catch_internal_ExceptionTranslator ), signature ) // end catch_interfaces_exception.h // start catch_approx.h #include namespace Catch { namespace Detail { class Approx { private: bool equalityComparisonImpl(double other) const; // Validates the new margin (margin >= 0) // out-of-line to avoid including stdexcept in the header void setMargin(double margin); // Validates the new epsilon (0 < epsilon < 1) // out-of-line to avoid including stdexcept in the header void setEpsilon(double epsilon); public: explicit Approx ( double value ); static Approx custom(); Approx operator-() const; template ::value>::type> Approx operator()( T const& value ) { Approx approx( static_cast(value) ); approx.m_epsilon = m_epsilon; approx.m_margin = m_margin; approx.m_scale = m_scale; return approx; } template ::value>::type> explicit Approx( T const& value ): Approx(static_cast(value)) {} template ::value>::type> friend bool operator == ( const T& lhs, Approx const& rhs ) { auto lhs_v = static_cast(lhs); return rhs.equalityComparisonImpl(lhs_v); } template ::value>::type> friend bool operator == ( Approx const& lhs, const T& rhs ) { return operator==( rhs, lhs ); } template ::value>::type> friend bool operator != ( T const& lhs, Approx const& rhs ) { return !operator==( lhs, rhs ); } template ::value>::type> friend bool operator != ( Approx const& lhs, T const& rhs ) { return !operator==( rhs, lhs ); } template ::value>::type> friend bool operator <= ( T const& lhs, Approx const& rhs ) { return static_cast(lhs) < rhs.m_value || lhs == rhs; } template ::value>::type> friend bool operator <= ( Approx const& lhs, T const& rhs ) { return lhs.m_value < static_cast(rhs) || lhs == rhs; } template ::value>::type> friend bool operator >= ( T const& lhs, Approx const& rhs ) { return static_cast(lhs) > rhs.m_value || lhs == rhs; } template ::value>::type> friend bool operator >= ( Approx const& lhs, T const& rhs ) { return lhs.m_value > static_cast(rhs) || lhs == rhs; } template ::value>::type> Approx& epsilon( T const& newEpsilon ) { double epsilonAsDouble = static_cast(newEpsilon); setEpsilon(epsilonAsDouble); return *this; } template ::value>::type> Approx& margin( T const& newMargin ) { double marginAsDouble = static_cast(newMargin); setMargin(marginAsDouble); return *this; } template ::value>::type> Approx& scale( T const& newScale ) { m_scale = static_cast(newScale); return *this; } std::string toString() const; private: double m_epsilon; double m_margin; double m_scale; double m_value; }; } // end namespace Detail namespace literals { Detail::Approx operator "" _a(long double val); Detail::Approx operator "" _a(unsigned long long val); } // end namespace literals template<> struct StringMaker { static std::string convert(Catch::Detail::Approx const& value); }; } // end namespace Catch // end catch_approx.h // start catch_string_manip.h #include #include namespace Catch { bool startsWith( std::string const& s, std::string const& prefix ); bool startsWith( std::string const& s, char prefix ); bool endsWith( std::string const& s, std::string const& suffix ); bool endsWith( std::string const& s, char suffix ); bool contains( std::string const& s, std::string const& infix ); void toLowerInPlace( std::string& s ); std::string toLower( std::string const& s ); std::string trim( std::string const& str ); bool replaceInPlace( std::string& str, std::string const& replaceThis, std::string const& withThis ); struct pluralise { pluralise( std::size_t count, std::string const& label ); friend std::ostream& operator << ( std::ostream& os, pluralise const& pluraliser ); std::size_t m_count; std::string m_label; }; } // end catch_string_manip.h #ifndef CATCH_CONFIG_DISABLE_MATCHERS // start catch_capture_matchers.h // start catch_matchers.h #include #include namespace Catch { namespace Matchers { namespace Impl { template struct MatchAllOf; template struct MatchAnyOf; template struct MatchNotOf; class MatcherUntypedBase { public: MatcherUntypedBase() = default; MatcherUntypedBase ( MatcherUntypedBase const& ) = default; MatcherUntypedBase& operator = ( MatcherUntypedBase const& ) = delete; std::string toString() const; protected: virtual ~MatcherUntypedBase(); virtual std::string describe() const = 0; mutable std::string m_cachedToString; }; #ifdef __clang__ # pragma clang diagnostic push # pragma clang diagnostic ignored "-Wnon-virtual-dtor" #endif template struct MatcherMethod { virtual bool match( ObjectT const& arg ) const = 0; }; #ifdef __clang__ # pragma clang diagnostic pop #endif template struct MatcherBase : MatcherUntypedBase, MatcherMethod { MatchAllOf operator && ( MatcherBase const& other ) const; MatchAnyOf operator || ( MatcherBase const& other ) const; MatchNotOf operator ! () const; }; template struct MatchAllOf : MatcherBase { bool match( ArgT const& arg ) const override { for( auto matcher : m_matchers ) { if (!matcher->match(arg)) return false; } return true; } std::string describe() const override { std::string description; description.reserve( 4 + m_matchers.size()*32 ); description += "( "; bool first = true; for( auto matcher : m_matchers ) { if( first ) first = false; else description += " and "; description += matcher->toString(); } description += " )"; return description; } MatchAllOf& operator && ( MatcherBase const& other ) { m_matchers.push_back( &other ); return *this; } std::vector const*> m_matchers; }; template struct MatchAnyOf : MatcherBase { bool match( ArgT const& arg ) const override { for( auto matcher : m_matchers ) { if (matcher->match(arg)) return true; } return false; } std::string describe() const override { std::string description; description.reserve( 4 + m_matchers.size()*32 ); description += "( "; bool first = true; for( auto matcher : m_matchers ) { if( first ) first = false; else description += " or "; description += matcher->toString(); } description += " )"; return description; } MatchAnyOf& operator || ( MatcherBase const& other ) { m_matchers.push_back( &other ); return *this; } std::vector const*> m_matchers; }; template struct MatchNotOf : MatcherBase { MatchNotOf( MatcherBase const& underlyingMatcher ) : m_underlyingMatcher( underlyingMatcher ) {} bool match( ArgT const& arg ) const override { return !m_underlyingMatcher.match( arg ); } std::string describe() const override { return "not " + m_underlyingMatcher.toString(); } MatcherBase const& m_underlyingMatcher; }; template MatchAllOf MatcherBase::operator && ( MatcherBase const& other ) const { return MatchAllOf() && *this && other; } template MatchAnyOf MatcherBase::operator || ( MatcherBase const& other ) const { return MatchAnyOf() || *this || other; } template MatchNotOf MatcherBase::operator ! () const { return MatchNotOf( *this ); } } // namespace Impl } // namespace Matchers using namespace Matchers; using Matchers::Impl::MatcherBase; } // namespace Catch // end catch_matchers.h // start catch_matchers_floating.h #include #include namespace Catch { namespace Matchers { namespace Floating { enum class FloatingPointKind : uint8_t; struct WithinAbsMatcher : MatcherBase { WithinAbsMatcher(double target, double margin); bool match(double const& matchee) const override; std::string describe() const override; private: double m_target; double m_margin; }; struct WithinUlpsMatcher : MatcherBase { WithinUlpsMatcher(double target, int ulps, FloatingPointKind baseType); bool match(double const& matchee) const override; std::string describe() const override; private: double m_target; int m_ulps; FloatingPointKind m_type; }; } // namespace Floating // The following functions create the actual matcher objects. // This allows the types to be inferred Floating::WithinUlpsMatcher WithinULP(double target, int maxUlpDiff); Floating::WithinUlpsMatcher WithinULP(float target, int maxUlpDiff); Floating::WithinAbsMatcher WithinAbs(double target, double margin); } // namespace Matchers } // namespace Catch // end catch_matchers_floating.h // start catch_matchers_generic.hpp #include #include namespace Catch { namespace Matchers { namespace Generic { namespace Detail { std::string finalizeDescription(const std::string& desc); } template class PredicateMatcher : public MatcherBase { std::function m_predicate; std::string m_description; public: PredicateMatcher(std::function const& elem, std::string const& descr) :m_predicate(std::move(elem)), m_description(Detail::finalizeDescription(descr)) {} bool match( T const& item ) const override { return m_predicate(item); } std::string describe() const override { return m_description; } }; } // namespace Generic // The following functions create the actual matcher objects. // The user has to explicitly specify type to the function, because // infering std::function is hard (but possible) and // requires a lot of TMP. template Generic::PredicateMatcher Predicate(std::function const& predicate, std::string const& description = "") { return Generic::PredicateMatcher(predicate, description); } } // namespace Matchers } // namespace Catch // end catch_matchers_generic.hpp // start catch_matchers_string.h #include namespace Catch { namespace Matchers { namespace StdString { struct CasedString { CasedString( std::string const& str, CaseSensitive::Choice caseSensitivity ); std::string adjustString( std::string const& str ) const; std::string caseSensitivitySuffix() const; CaseSensitive::Choice m_caseSensitivity; std::string m_str; }; struct StringMatcherBase : MatcherBase { StringMatcherBase( std::string const& operation, CasedString const& comparator ); std::string describe() const override; CasedString m_comparator; std::string m_operation; }; struct EqualsMatcher : StringMatcherBase { EqualsMatcher( CasedString const& comparator ); bool match( std::string const& source ) const override; }; struct ContainsMatcher : StringMatcherBase { ContainsMatcher( CasedString const& comparator ); bool match( std::string const& source ) const override; }; struct StartsWithMatcher : StringMatcherBase { StartsWithMatcher( CasedString const& comparator ); bool match( std::string const& source ) const override; }; struct EndsWithMatcher : StringMatcherBase { EndsWithMatcher( CasedString const& comparator ); bool match( std::string const& source ) const override; }; struct RegexMatcher : MatcherBase { RegexMatcher( std::string regex, CaseSensitive::Choice caseSensitivity ); bool match( std::string const& matchee ) const override; std::string describe() const override; private: std::string m_regex; CaseSensitive::Choice m_caseSensitivity; }; } // namespace StdString // The following functions create the actual matcher objects. // This allows the types to be inferred StdString::EqualsMatcher Equals( std::string const& str, CaseSensitive::Choice caseSensitivity = CaseSensitive::Yes ); StdString::ContainsMatcher Contains( std::string const& str, CaseSensitive::Choice caseSensitivity = CaseSensitive::Yes ); StdString::EndsWithMatcher EndsWith( std::string const& str, CaseSensitive::Choice caseSensitivity = CaseSensitive::Yes ); StdString::StartsWithMatcher StartsWith( std::string const& str, CaseSensitive::Choice caseSensitivity = CaseSensitive::Yes ); StdString::RegexMatcher Matches( std::string const& regex, CaseSensitive::Choice caseSensitivity = CaseSensitive::Yes ); } // namespace Matchers } // namespace Catch // end catch_matchers_string.h // start catch_matchers_vector.h #include namespace Catch { namespace Matchers { namespace Vector { namespace Detail { template size_t count(InputIterator first, InputIterator last, T const& item) { size_t cnt = 0; for (; first != last; ++first) { if (*first == item) { ++cnt; } } return cnt; } template bool contains(InputIterator first, InputIterator last, T const& item) { for (; first != last; ++first) { if (*first == item) { return true; } } return false; } } template struct ContainsElementMatcher : MatcherBase> { ContainsElementMatcher(T const &comparator) : m_comparator( comparator) {} bool match(std::vector const &v) const override { for (auto const& el : v) { if (el == m_comparator) { return true; } } return false; } std::string describe() const override { return "Contains: " + ::Catch::Detail::stringify( m_comparator ); } T const& m_comparator; }; template struct ContainsMatcher : MatcherBase> { ContainsMatcher(std::vector const &comparator) : m_comparator( comparator ) {} bool match(std::vector const &v) const override { // !TBD: see note in EqualsMatcher if (m_comparator.size() > v.size()) return false; for (auto const& comparator : m_comparator) { auto present = false; for (const auto& el : v) { if (el == comparator) { present = true; break; } } if (!present) { return false; } } return true; } std::string describe() const override { return "Contains: " + ::Catch::Detail::stringify( m_comparator ); } std::vector const& m_comparator; }; template struct EqualsMatcher : MatcherBase> { EqualsMatcher(std::vector const &comparator) : m_comparator( comparator ) {} bool match(std::vector const &v) const override { // !TBD: This currently works if all elements can be compared using != // - a more general approach would be via a compare template that defaults // to using !=. but could be specialised for, e.g. std::vector etc // - then just call that directly if (m_comparator.size() != v.size()) return false; for (std::size_t i = 0; i < v.size(); ++i) if (m_comparator[i] != v[i]) return false; return true; } std::string describe() const override { return "Equals: " + ::Catch::Detail::stringify( m_comparator ); } std::vector const& m_comparator; }; template struct UnorderedEqualsMatcher : MatcherBase> { UnorderedEqualsMatcher(std::vector const& target) : m_target(target) {} bool match(std::vector const& vec) const override { // Note: This is a reimplementation of std::is_permutation, // because I don't want to include inside the common path if (m_target.size() != vec.size()) { return false; } auto lfirst = m_target.begin(), llast = m_target.end(); auto rfirst = vec.begin(), rlast = vec.end(); // Cut common prefix to optimize checking of permuted parts while (lfirst != llast && *lfirst == *rfirst) { ++lfirst; ++rfirst; } if (lfirst == llast) { return true; } for (auto mid = lfirst; mid != llast; ++mid) { // Skip already counted items if (Detail::contains(lfirst, mid, *mid)) { continue; } size_t num_vec = Detail::count(rfirst, rlast, *mid); if (num_vec == 0 || Detail::count(lfirst, llast, *mid) != num_vec) { return false; } } return true; } std::string describe() const override { return "UnorderedEquals: " + ::Catch::Detail::stringify(m_target); } private: std::vector const& m_target; }; } // namespace Vector // The following functions create the actual matcher objects. // This allows the types to be inferred template Vector::ContainsMatcher Contains( std::vector const& comparator ) { return Vector::ContainsMatcher( comparator ); } template Vector::ContainsElementMatcher VectorContains( T const& comparator ) { return Vector::ContainsElementMatcher( comparator ); } template Vector::EqualsMatcher Equals( std::vector const& comparator ) { return Vector::EqualsMatcher( comparator ); } template Vector::UnorderedEqualsMatcher UnorderedEquals(std::vector const& target) { return Vector::UnorderedEqualsMatcher(target); } } // namespace Matchers } // namespace Catch // end catch_matchers_vector.h namespace Catch { template class MatchExpr : public ITransientExpression { ArgT const& m_arg; MatcherT m_matcher; StringRef m_matcherString; public: MatchExpr( ArgT const& arg, MatcherT const& matcher, StringRef const& matcherString ) : ITransientExpression{ true, matcher.match( arg ) }, m_arg( arg ), m_matcher( matcher ), m_matcherString( matcherString ) {} void streamReconstructedExpression( std::ostream &os ) const override { auto matcherAsString = m_matcher.toString(); os << Catch::Detail::stringify( m_arg ) << ' '; if( matcherAsString == Detail::unprintableString ) os << m_matcherString; else os << matcherAsString; } }; using StringMatcher = Matchers::Impl::MatcherBase; void handleExceptionMatchExpr( AssertionHandler& handler, StringMatcher const& matcher, StringRef const& matcherString ); template auto makeMatchExpr( ArgT const& arg, MatcherT const& matcher, StringRef const& matcherString ) -> MatchExpr { return MatchExpr( arg, matcher, matcherString ); } } // namespace Catch /////////////////////////////////////////////////////////////////////////////// #define INTERNAL_CHECK_THAT( macroName, matcher, resultDisposition, arg ) \ do { \ Catch::AssertionHandler catchAssertionHandler( macroName##_catch_sr, CATCH_INTERNAL_LINEINFO, CATCH_INTERNAL_STRINGIFY(arg) ", " CATCH_INTERNAL_STRINGIFY(matcher), resultDisposition ); \ INTERNAL_CATCH_TRY { \ catchAssertionHandler.handleExpr( Catch::makeMatchExpr( arg, matcher, #matcher##_catch_sr ) ); \ } INTERNAL_CATCH_CATCH( catchAssertionHandler ) \ INTERNAL_CATCH_REACT( catchAssertionHandler ) \ } while( false ) /////////////////////////////////////////////////////////////////////////////// #define INTERNAL_CATCH_THROWS_MATCHES( macroName, exceptionType, resultDisposition, matcher, ... ) \ do { \ Catch::AssertionHandler catchAssertionHandler( macroName##_catch_sr, CATCH_INTERNAL_LINEINFO, CATCH_INTERNAL_STRINGIFY(__VA_ARGS__) ", " CATCH_INTERNAL_STRINGIFY(exceptionType) ", " CATCH_INTERNAL_STRINGIFY(matcher), resultDisposition ); \ if( catchAssertionHandler.allowThrows() ) \ try { \ static_cast(__VA_ARGS__ ); \ catchAssertionHandler.handleUnexpectedExceptionNotThrown(); \ } \ catch( exceptionType const& ex ) { \ catchAssertionHandler.handleExpr( Catch::makeMatchExpr( ex, matcher, #matcher##_catch_sr ) ); \ } \ catch( ... ) { \ catchAssertionHandler.handleUnexpectedInflightException(); \ } \ else \ catchAssertionHandler.handleThrowingCallSkipped(); \ INTERNAL_CATCH_REACT( catchAssertionHandler ) \ } while( false ) // end catch_capture_matchers.h #endif // start catch_generators.hpp // start catch_interfaces_generatortracker.h #include namespace Catch { namespace Generators { class GeneratorUntypedBase { public: GeneratorUntypedBase() = default; virtual ~GeneratorUntypedBase(); // Attempts to move the generator to the next element // // Returns true iff the move succeeded (and a valid element // can be retrieved). virtual bool next() = 0; }; using GeneratorBasePtr = std::unique_ptr; } // namespace Generators struct IGeneratorTracker { virtual ~IGeneratorTracker(); virtual auto hasGenerator() const -> bool = 0; virtual auto getGenerator() const -> Generators::GeneratorBasePtr const& = 0; virtual void setGenerator( Generators::GeneratorBasePtr&& generator ) = 0; }; } // namespace Catch // end catch_interfaces_generatortracker.h // start catch_enforce.h #include namespace Catch { #if !defined(CATCH_CONFIG_DISABLE_EXCEPTIONS) template [[noreturn]] void throw_exception(Ex const& e) { throw e; } #else // ^^ Exceptions are enabled // Exceptions are disabled vv [[noreturn]] void throw_exception(std::exception const& e); #endif } // namespace Catch; #define CATCH_PREPARE_EXCEPTION( type, msg ) \ type( ( Catch::ReusableStringStream() << msg ).str() ) #define CATCH_INTERNAL_ERROR( msg ) \ Catch::throw_exception(CATCH_PREPARE_EXCEPTION( std::logic_error, CATCH_INTERNAL_LINEINFO << ": Internal Catch error: " << msg)) #define CATCH_ERROR( msg ) \ Catch::throw_exception(CATCH_PREPARE_EXCEPTION( std::domain_error, msg )) #define CATCH_RUNTIME_ERROR( msg ) \ Catch::throw_exception(CATCH_PREPARE_EXCEPTION( std::runtime_error, msg )) #define CATCH_ENFORCE( condition, msg ) \ do{ if( !(condition) ) CATCH_ERROR( msg ); } while(false) // end catch_enforce.h #include #include #include #include #include namespace Catch { class GeneratorException : public std::exception { const char* const m_msg = ""; public: GeneratorException(const char* msg): m_msg(msg) {} const char* what() const noexcept override final; }; namespace Generators { // !TBD move this into its own location? namespace pf{ template std::unique_ptr make_unique( Args&&... args ) { return std::unique_ptr(new T(std::forward(args)...)); } } template struct IGenerator : GeneratorUntypedBase { virtual ~IGenerator() = default; // Returns the current element of the generator // // \Precondition The generator is either freshly constructed, // or the last call to `next()` returned true virtual T const& get() const = 0; using type = T; }; template class SingleValueGenerator final : public IGenerator { T m_value; public: SingleValueGenerator(T const& value) : m_value( value ) {} SingleValueGenerator(T&& value) : m_value(std::move(value)) {} T const& get() const override { return m_value; } bool next() override { return false; } }; template class FixedValuesGenerator final : public IGenerator { std::vector m_values; size_t m_idx = 0; public: FixedValuesGenerator( std::initializer_list values ) : m_values( values ) {} T const& get() const override { return m_values[m_idx]; } bool next() override { ++m_idx; return m_idx < m_values.size(); } }; template class GeneratorWrapper final { std::unique_ptr> m_generator; public: GeneratorWrapper(std::unique_ptr> generator): m_generator(std::move(generator)) {} T const& get() const { return m_generator->get(); } bool next() { return m_generator->next(); } }; template GeneratorWrapper value(T&& value) { return GeneratorWrapper(pf::make_unique>(std::forward(value))); } template GeneratorWrapper values(std::initializer_list values) { return GeneratorWrapper(pf::make_unique>(values)); } template class Generators : public IGenerator { std::vector> m_generators; size_t m_current = 0; void populate(GeneratorWrapper&& generator) { m_generators.emplace_back(std::move(generator)); } void populate(T&& val) { m_generators.emplace_back(value(std::move(val))); } template void populate(U&& val) { populate(T(std::move(val))); } template void populate(U&& valueOrGenerator, Gs... moreGenerators) { populate(std::forward(valueOrGenerator)); populate(std::forward(moreGenerators)...); } public: template Generators(Gs... moreGenerators) { m_generators.reserve(sizeof...(Gs)); populate(std::forward(moreGenerators)...); } T const& get() const override { return m_generators[m_current].get(); } bool next() override { if (m_current >= m_generators.size()) { return false; } const bool current_status = m_generators[m_current].next(); if (!current_status) { ++m_current; } return m_current < m_generators.size(); } }; template GeneratorWrapper> table( std::initializer_list::type...>> tuples ) { return values>( tuples ); } // Tag type to signal that a generator sequence should convert arguments to a specific type template struct as {}; template auto makeGenerators( GeneratorWrapper&& generator, Gs... moreGenerators ) -> Generators { return Generators(std::move(generator), std::forward(moreGenerators)...); } template auto makeGenerators( GeneratorWrapper&& generator ) -> Generators { return Generators(std::move(generator)); } template auto makeGenerators( T&& val, Gs... moreGenerators ) -> Generators { return makeGenerators( value( std::forward( val ) ), std::forward( moreGenerators )... ); } template auto makeGenerators( as, U&& val, Gs... moreGenerators ) -> Generators { return makeGenerators( value( T( std::forward( val ) ) ), std::forward( moreGenerators )... ); } template class TakeGenerator : public IGenerator { GeneratorWrapper m_generator; size_t m_returned = 0; size_t m_target; public: TakeGenerator(size_t target, GeneratorWrapper&& generator): m_generator(std::move(generator)), m_target(target) { assert(target != 0 && "Empty generators are not allowed"); } T const& get() const override { return m_generator.get(); } bool next() override { ++m_returned; if (m_returned >= m_target) { return false; } const auto success = m_generator.next(); // If the underlying generator does not contain enough values // then we cut short as well if (!success) { m_returned = m_target; } return success; } }; template GeneratorWrapper take(size_t target, GeneratorWrapper&& generator) { return GeneratorWrapper(pf::make_unique>(target, std::move(generator))); } template class FilterGenerator : public IGenerator { GeneratorWrapper m_generator; Predicate m_predicate; public: template FilterGenerator(P&& pred, GeneratorWrapper&& generator): m_generator(std::move(generator)), m_predicate(std::forward

(pred)) { if (!m_predicate(m_generator.get())) { // It might happen that there are no values that pass the // filter. In that case we throw an exception. auto has_initial_value = next(); if (!has_initial_value) { Catch::throw_exception(GeneratorException("No valid value found in filtered generator")); } } } T const& get() const override { return m_generator.get(); } bool next() override { bool success = m_generator.next(); if (!success) { return false; } while (!m_predicate(m_generator.get()) && (success = m_generator.next()) == true); return success; } }; template GeneratorWrapper filter(Predicate&& pred, GeneratorWrapper&& generator) { return GeneratorWrapper(std::unique_ptr>(pf::make_unique>(std::forward(pred), std::move(generator)))); } template class RepeatGenerator : public IGenerator { GeneratorWrapper m_generator; mutable std::vector m_returned; size_t m_target_repeats; size_t m_current_repeat = 0; size_t m_repeat_index = 0; public: RepeatGenerator(size_t repeats, GeneratorWrapper&& generator): m_generator(std::move(generator)), m_target_repeats(repeats) { assert(m_target_repeats > 0 && "Repeat generator must repeat at least once"); } T const& get() const override { if (m_current_repeat == 0) { m_returned.push_back(m_generator.get()); return m_returned.back(); } return m_returned[m_repeat_index]; } bool next() override { // There are 2 basic cases: // 1) We are still reading the generator // 2) We are reading our own cache // In the first case, we need to poke the underlying generator. // If it happily moves, we are left in that state, otherwise it is time to start reading from our cache if (m_current_repeat == 0) { const auto success = m_generator.next(); if (!success) { ++m_current_repeat; } return m_current_repeat < m_target_repeats; } // In the second case, we need to move indices forward and check that we haven't run up against the end ++m_repeat_index; if (m_repeat_index == m_returned.size()) { m_repeat_index = 0; ++m_current_repeat; } return m_current_repeat < m_target_repeats; } }; template GeneratorWrapper repeat(size_t repeats, GeneratorWrapper&& generator) { return GeneratorWrapper(pf::make_unique>(repeats, std::move(generator))); } template class MapGenerator : public IGenerator { // TBD: provide static assert for mapping function, for friendly error message GeneratorWrapper m_generator; Func m_function; // To avoid returning dangling reference, we have to save the values T m_cache; public: template MapGenerator(F2&& function, GeneratorWrapper&& generator) : m_generator(std::move(generator)), m_function(std::forward(function)), m_cache(m_function(m_generator.get())) {} T const& get() const override { return m_cache; } bool next() override { const auto success = m_generator.next(); if (success) { m_cache = m_function(m_generator.get()); } return success; } }; template GeneratorWrapper map(Func&& function, GeneratorWrapper&& generator) { return GeneratorWrapper( pf::make_unique>(std::forward(function), std::move(generator)) ); } template GeneratorWrapper map(Func&& function, GeneratorWrapper&& generator) { return GeneratorWrapper( pf::make_unique>(std::forward(function), std::move(generator)) ); } auto acquireGeneratorTracker( SourceLineInfo const& lineInfo ) -> IGeneratorTracker&; template // Note: The type after -> is weird, because VS2015 cannot parse // the expression used in the typedef inside, when it is in // return type. Yeah, ¯\_(ツ)_/¯ auto generate( SourceLineInfo const& lineInfo, L const& generatorExpression ) -> decltype(std::declval().get()) { using UnderlyingType = typename decltype(generatorExpression())::type; IGeneratorTracker& tracker = acquireGeneratorTracker( lineInfo ); if (!tracker.hasGenerator()) { tracker.setGenerator(pf::make_unique>(generatorExpression())); } auto const& generator = static_cast const&>( *tracker.getGenerator() ); return generator.get(); } } // namespace Generators } // namespace Catch #define GENERATE( ... ) \ Catch::Generators::generate( CATCH_INTERNAL_LINEINFO, []{ using namespace Catch::Generators; return makeGenerators( __VA_ARGS__ ); } ) // end catch_generators.hpp // These files are included here so the single_include script doesn't put them // in the conditionally compiled sections // start catch_test_case_info.h #include #include #include #ifdef __clang__ #pragma clang diagnostic push #pragma clang diagnostic ignored "-Wpadded" #endif namespace Catch { struct ITestInvoker; struct TestCaseInfo { enum SpecialProperties{ None = 0, IsHidden = 1 << 1, ShouldFail = 1 << 2, MayFail = 1 << 3, Throws = 1 << 4, NonPortable = 1 << 5, Benchmark = 1 << 6 }; TestCaseInfo( std::string const& _name, std::string const& _className, std::string const& _description, std::vector const& _tags, SourceLineInfo const& _lineInfo ); friend void setTags( TestCaseInfo& testCaseInfo, std::vector tags ); bool isHidden() const; bool throws() const; bool okToFail() const; bool expectedToFail() const; std::string tagsAsString() const; std::string name; std::string className; std::string description; std::vector tags; std::vector lcaseTags; SourceLineInfo lineInfo; SpecialProperties properties; }; class TestCase : public TestCaseInfo { public: TestCase( ITestInvoker* testCase, TestCaseInfo&& info ); TestCase withName( std::string const& _newName ) const; void invoke() const; TestCaseInfo const& getTestCaseInfo() const; bool operator == ( TestCase const& other ) const; bool operator < ( TestCase const& other ) const; private: std::shared_ptr test; }; TestCase makeTestCase( ITestInvoker* testCase, std::string const& className, NameAndTags const& nameAndTags, SourceLineInfo const& lineInfo ); } #ifdef __clang__ #pragma clang diagnostic pop #endif // end catch_test_case_info.h // start catch_interfaces_runner.h namespace Catch { struct IRunner { virtual ~IRunner(); virtual bool aborting() const = 0; }; } // end catch_interfaces_runner.h #ifdef __OBJC__ // start catch_objc.hpp #import #include // NB. Any general catch headers included here must be included // in catch.hpp first to make sure they are included by the single // header for non obj-usage /////////////////////////////////////////////////////////////////////////////// // This protocol is really only here for (self) documenting purposes, since // all its methods are optional. @protocol OcFixture @optional -(void) setUp; -(void) tearDown; @end namespace Catch { class OcMethod : public ITestInvoker { public: OcMethod( Class cls, SEL sel ) : m_cls( cls ), m_sel( sel ) {} virtual void invoke() const { id obj = [[m_cls alloc] init]; performOptionalSelector( obj, @selector(setUp) ); performOptionalSelector( obj, m_sel ); performOptionalSelector( obj, @selector(tearDown) ); arcSafeRelease( obj ); } private: virtual ~OcMethod() {} Class m_cls; SEL m_sel; }; namespace Detail{ inline std::string getAnnotation( Class cls, std::string const& annotationName, std::string const& testCaseName ) { NSString* selStr = [[NSString alloc] initWithFormat:@"Catch_%s_%s", annotationName.c_str(), testCaseName.c_str()]; SEL sel = NSSelectorFromString( selStr ); arcSafeRelease( selStr ); id value = performOptionalSelector( cls, sel ); if( value ) return [(NSString*)value UTF8String]; return ""; } } inline std::size_t registerTestMethods() { std::size_t noTestMethods = 0; int noClasses = objc_getClassList( nullptr, 0 ); Class* classes = (CATCH_UNSAFE_UNRETAINED Class *)malloc( sizeof(Class) * noClasses); objc_getClassList( classes, noClasses ); for( int c = 0; c < noClasses; c++ ) { Class cls = classes[c]; { u_int count; Method* methods = class_copyMethodList( cls, &count ); for( u_int m = 0; m < count ; m++ ) { SEL selector = method_getName(methods[m]); std::string methodName = sel_getName(selector); if( startsWith( methodName, "Catch_TestCase_" ) ) { std::string testCaseName = methodName.substr( 15 ); std::string name = Detail::getAnnotation( cls, "Name", testCaseName ); std::string desc = Detail::getAnnotation( cls, "Description", testCaseName ); const char* className = class_getName( cls ); getMutableRegistryHub().registerTest( makeTestCase( new OcMethod( cls, selector ), className, NameAndTags( name.c_str(), desc.c_str() ), SourceLineInfo("",0) ) ); noTestMethods++; } } free(methods); } } return noTestMethods; } #if !defined(CATCH_CONFIG_DISABLE_MATCHERS) namespace Matchers { namespace Impl { namespace NSStringMatchers { struct StringHolder : MatcherBase{ StringHolder( NSString* substr ) : m_substr( [substr copy] ){} StringHolder( StringHolder const& other ) : m_substr( [other.m_substr copy] ){} StringHolder() { arcSafeRelease( m_substr ); } bool match( NSString* arg ) const override { return false; } NSString* CATCH_ARC_STRONG m_substr; }; struct Equals : StringHolder { Equals( NSString* substr ) : StringHolder( substr ){} bool match( NSString* str ) const override { return (str != nil || m_substr == nil ) && [str isEqualToString:m_substr]; } std::string describe() const override { return "equals string: " + Catch::Detail::stringify( m_substr ); } }; struct Contains : StringHolder { Contains( NSString* substr ) : StringHolder( substr ){} bool match( NSString* str ) const { return (str != nil || m_substr == nil ) && [str rangeOfString:m_substr].location != NSNotFound; } std::string describe() const override { return "contains string: " + Catch::Detail::stringify( m_substr ); } }; struct StartsWith : StringHolder { StartsWith( NSString* substr ) : StringHolder( substr ){} bool match( NSString* str ) const override { return (str != nil || m_substr == nil ) && [str rangeOfString:m_substr].location == 0; } std::string describe() const override { return "starts with: " + Catch::Detail::stringify( m_substr ); } }; struct EndsWith : StringHolder { EndsWith( NSString* substr ) : StringHolder( substr ){} bool match( NSString* str ) const override { return (str != nil || m_substr == nil ) && [str rangeOfString:m_substr].location == [str length] - [m_substr length]; } std::string describe() const override { return "ends with: " + Catch::Detail::stringify( m_substr ); } }; } // namespace NSStringMatchers } // namespace Impl inline Impl::NSStringMatchers::Equals Equals( NSString* substr ){ return Impl::NSStringMatchers::Equals( substr ); } inline Impl::NSStringMatchers::Contains Contains( NSString* substr ){ return Impl::NSStringMatchers::Contains( substr ); } inline Impl::NSStringMatchers::StartsWith StartsWith( NSString* substr ){ return Impl::NSStringMatchers::StartsWith( substr ); } inline Impl::NSStringMatchers::EndsWith EndsWith( NSString* substr ){ return Impl::NSStringMatchers::EndsWith( substr ); } } // namespace Matchers using namespace Matchers; #endif // CATCH_CONFIG_DISABLE_MATCHERS } // namespace Catch /////////////////////////////////////////////////////////////////////////////// #define OC_MAKE_UNIQUE_NAME( root, uniqueSuffix ) root##uniqueSuffix #define OC_TEST_CASE2( name, desc, uniqueSuffix ) \ +(NSString*) OC_MAKE_UNIQUE_NAME( Catch_Name_test_, uniqueSuffix ) \ { \ return @ name; \ } \ +(NSString*) OC_MAKE_UNIQUE_NAME( Catch_Description_test_, uniqueSuffix ) \ { \ return @ desc; \ } \ -(void) OC_MAKE_UNIQUE_NAME( Catch_TestCase_test_, uniqueSuffix ) #define OC_TEST_CASE( name, desc ) OC_TEST_CASE2( name, desc, __LINE__ ) // end catch_objc.hpp #endif #ifdef CATCH_CONFIG_EXTERNAL_INTERFACES // start catch_external_interfaces.h // start catch_reporter_bases.hpp // start catch_interfaces_reporter.h // start catch_config.hpp // start catch_test_spec_parser.h #ifdef __clang__ #pragma clang diagnostic push #pragma clang diagnostic ignored "-Wpadded" #endif // start catch_test_spec.h #ifdef __clang__ #pragma clang diagnostic push #pragma clang diagnostic ignored "-Wpadded" #endif // start catch_wildcard_pattern.h namespace Catch { class WildcardPattern { enum WildcardPosition { NoWildcard = 0, WildcardAtStart = 1, WildcardAtEnd = 2, WildcardAtBothEnds = WildcardAtStart | WildcardAtEnd }; public: WildcardPattern( std::string const& pattern, CaseSensitive::Choice caseSensitivity ); virtual ~WildcardPattern() = default; virtual bool matches( std::string const& str ) const; private: std::string adjustCase( std::string const& str ) const; CaseSensitive::Choice m_caseSensitivity; WildcardPosition m_wildcard = NoWildcard; std::string m_pattern; }; } // end catch_wildcard_pattern.h #include #include #include namespace Catch { class TestSpec { struct Pattern { virtual ~Pattern(); virtual bool matches( TestCaseInfo const& testCase ) const = 0; }; using PatternPtr = std::shared_ptr; class NamePattern : public Pattern { public: NamePattern( std::string const& name ); virtual ~NamePattern(); virtual bool matches( TestCaseInfo const& testCase ) const override; private: WildcardPattern m_wildcardPattern; }; class TagPattern : public Pattern { public: TagPattern( std::string const& tag ); virtual ~TagPattern(); virtual bool matches( TestCaseInfo const& testCase ) const override; private: std::string m_tag; }; class ExcludedPattern : public Pattern { public: ExcludedPattern( PatternPtr const& underlyingPattern ); virtual ~ExcludedPattern(); virtual bool matches( TestCaseInfo const& testCase ) const override; private: PatternPtr m_underlyingPattern; }; struct Filter { std::vector m_patterns; bool matches( TestCaseInfo const& testCase ) const; }; public: bool hasFilters() const; bool matches( TestCaseInfo const& testCase ) const; private: std::vector m_filters; friend class TestSpecParser; }; } #ifdef __clang__ #pragma clang diagnostic pop #endif // end catch_test_spec.h // start catch_interfaces_tag_alias_registry.h #include namespace Catch { struct TagAlias; struct ITagAliasRegistry { virtual ~ITagAliasRegistry(); // Nullptr if not present virtual TagAlias const* find( std::string const& alias ) const = 0; virtual std::string expandAliases( std::string const& unexpandedTestSpec ) const = 0; static ITagAliasRegistry const& get(); }; } // end namespace Catch // end catch_interfaces_tag_alias_registry.h namespace Catch { class TestSpecParser { enum Mode{ None, Name, QuotedName, Tag, EscapedName }; Mode m_mode = None; bool m_exclusion = false; std::size_t m_start = std::string::npos, m_pos = 0; std::string m_arg; std::vector m_escapeChars; TestSpec::Filter m_currentFilter; TestSpec m_testSpec; ITagAliasRegistry const* m_tagAliases = nullptr; public: TestSpecParser( ITagAliasRegistry const& tagAliases ); TestSpecParser& parse( std::string const& arg ); TestSpec testSpec(); private: void visitChar( char c ); void startNewMode( Mode mode, std::size_t start ); void escape(); std::string subString() const; template void addPattern() { std::string token = subString(); for( std::size_t i = 0; i < m_escapeChars.size(); ++i ) token = token.substr( 0, m_escapeChars[i]-m_start-i ) + token.substr( m_escapeChars[i]-m_start-i+1 ); m_escapeChars.clear(); if( startsWith( token, "exclude:" ) ) { m_exclusion = true; token = token.substr( 8 ); } if( !token.empty() ) { TestSpec::PatternPtr pattern = std::make_shared( token ); if( m_exclusion ) pattern = std::make_shared( pattern ); m_currentFilter.m_patterns.push_back( pattern ); } m_exclusion = false; m_mode = None; } void addFilter(); }; TestSpec parseTestSpec( std::string const& arg ); } // namespace Catch #ifdef __clang__ #pragma clang diagnostic pop #endif // end catch_test_spec_parser.h // start catch_interfaces_config.h #include #include #include #include namespace Catch { enum class Verbosity { Quiet = 0, Normal, High }; struct WarnAbout { enum What { Nothing = 0x00, NoAssertions = 0x01, NoTests = 0x02 }; }; struct ShowDurations { enum OrNot { DefaultForReporter, Always, Never }; }; struct RunTests { enum InWhatOrder { InDeclarationOrder, InLexicographicalOrder, InRandomOrder }; }; struct UseColour { enum YesOrNo { Auto, Yes, No }; }; struct WaitForKeypress { enum When { Never, BeforeStart = 1, BeforeExit = 2, BeforeStartAndExit = BeforeStart | BeforeExit }; }; class TestSpec; struct IConfig : NonCopyable { virtual ~IConfig(); virtual bool allowThrows() const = 0; virtual std::ostream& stream() const = 0; virtual std::string name() const = 0; virtual bool includeSuccessfulResults() const = 0; virtual bool shouldDebugBreak() const = 0; virtual bool warnAboutMissingAssertions() const = 0; virtual bool warnAboutNoTests() const = 0; virtual int abortAfter() const = 0; virtual bool showInvisibles() const = 0; virtual ShowDurations::OrNot showDurations() const = 0; virtual TestSpec const& testSpec() const = 0; virtual bool hasTestFilters() const = 0; virtual RunTests::InWhatOrder runOrder() const = 0; virtual unsigned int rngSeed() const = 0; virtual int benchmarkResolutionMultiple() const = 0; virtual UseColour::YesOrNo useColour() const = 0; virtual std::vector const& getSectionsToRun() const = 0; virtual Verbosity verbosity() const = 0; }; using IConfigPtr = std::shared_ptr; } // end catch_interfaces_config.h // Libstdc++ doesn't like incomplete classes for unique_ptr #include #include #include #ifndef CATCH_CONFIG_CONSOLE_WIDTH #define CATCH_CONFIG_CONSOLE_WIDTH 80 #endif namespace Catch { struct IStream; struct ConfigData { bool listTests = false; bool listTags = false; bool listReporters = false; bool listTestNamesOnly = false; bool showSuccessfulTests = false; bool shouldDebugBreak = false; bool noThrow = false; bool showHelp = false; bool showInvisibles = false; bool filenamesAsTags = false; bool libIdentify = false; int abortAfter = -1; unsigned int rngSeed = 0; int benchmarkResolutionMultiple = 100; Verbosity verbosity = Verbosity::Normal; WarnAbout::What warnings = WarnAbout::Nothing; ShowDurations::OrNot showDurations = ShowDurations::DefaultForReporter; RunTests::InWhatOrder runOrder = RunTests::InDeclarationOrder; UseColour::YesOrNo useColour = UseColour::Auto; WaitForKeypress::When waitForKeypress = WaitForKeypress::Never; std::string outputFilename; std::string name; std::string processName; #ifndef CATCH_CONFIG_DEFAULT_REPORTER #define CATCH_CONFIG_DEFAULT_REPORTER "console" #endif std::string reporterName = CATCH_CONFIG_DEFAULT_REPORTER; #undef CATCH_CONFIG_DEFAULT_REPORTER std::vector testsOrTags; std::vector sectionsToRun; }; class Config : public IConfig { public: Config() = default; Config( ConfigData const& data ); virtual ~Config() = default; std::string const& getFilename() const; bool listTests() const; bool listTestNamesOnly() const; bool listTags() const; bool listReporters() const; std::string getProcessName() const; std::string const& getReporterName() const; std::vector const& getTestsOrTags() const; std::vector const& getSectionsToRun() const override; virtual TestSpec const& testSpec() const override; bool hasTestFilters() const override; bool showHelp() const; // IConfig interface bool allowThrows() const override; std::ostream& stream() const override; std::string name() const override; bool includeSuccessfulResults() const override; bool warnAboutMissingAssertions() const override; bool warnAboutNoTests() const override; ShowDurations::OrNot showDurations() const override; RunTests::InWhatOrder runOrder() const override; unsigned int rngSeed() const override; int benchmarkResolutionMultiple() const override; UseColour::YesOrNo useColour() const override; bool shouldDebugBreak() const override; int abortAfter() const override; bool showInvisibles() const override; Verbosity verbosity() const override; private: IStream const* openStream(); ConfigData m_data; std::unique_ptr m_stream; TestSpec m_testSpec; bool m_hasTestFilters = false; }; } // end namespace Catch // end catch_config.hpp // start catch_assertionresult.h #include namespace Catch { struct AssertionResultData { AssertionResultData() = delete; AssertionResultData( ResultWas::OfType _resultType, LazyExpression const& _lazyExpression ); std::string message; mutable std::string reconstructedExpression; LazyExpression lazyExpression; ResultWas::OfType resultType; std::string reconstructExpression() const; }; class AssertionResult { public: AssertionResult() = delete; AssertionResult( AssertionInfo const& info, AssertionResultData const& data ); bool isOk() const; bool succeeded() const; ResultWas::OfType getResultType() const; bool hasExpression() const; bool hasMessage() const; std::string getExpression() const; std::string getExpressionInMacro() const; bool hasExpandedExpression() const; std::string getExpandedExpression() const; std::string getMessage() const; SourceLineInfo getSourceInfo() const; StringRef getTestMacroName() const; //protected: AssertionInfo m_info; AssertionResultData m_resultData; }; } // end namespace Catch // end catch_assertionresult.h // start catch_option.hpp namespace Catch { // An optional type template class Option { public: Option() : nullableValue( nullptr ) {} Option( T const& _value ) : nullableValue( new( storage ) T( _value ) ) {} Option( Option const& _other ) : nullableValue( _other ? new( storage ) T( *_other ) : nullptr ) {} ~Option() { reset(); } Option& operator= ( Option const& _other ) { if( &_other != this ) { reset(); if( _other ) nullableValue = new( storage ) T( *_other ); } return *this; } Option& operator = ( T const& _value ) { reset(); nullableValue = new( storage ) T( _value ); return *this; } void reset() { if( nullableValue ) nullableValue->~T(); nullableValue = nullptr; } T& operator*() { return *nullableValue; } T const& operator*() const { return *nullableValue; } T* operator->() { return nullableValue; } const T* operator->() const { return nullableValue; } T valueOr( T const& defaultValue ) const { return nullableValue ? *nullableValue : defaultValue; } bool some() const { return nullableValue != nullptr; } bool none() const { return nullableValue == nullptr; } bool operator !() const { return nullableValue == nullptr; } explicit operator bool() const { return some(); } private: T *nullableValue; alignas(alignof(T)) char storage[sizeof(T)]; }; } // end namespace Catch // end catch_option.hpp #include #include #include #include #include namespace Catch { struct ReporterConfig { explicit ReporterConfig( IConfigPtr const& _fullConfig ); ReporterConfig( IConfigPtr const& _fullConfig, std::ostream& _stream ); std::ostream& stream() const; IConfigPtr fullConfig() const; private: std::ostream* m_stream; IConfigPtr m_fullConfig; }; struct ReporterPreferences { bool shouldRedirectStdOut = false; bool shouldReportAllAssertions = false; }; template struct LazyStat : Option { LazyStat& operator=( T const& _value ) { Option::operator=( _value ); used = false; return *this; } void reset() { Option::reset(); used = false; } bool used = false; }; struct TestRunInfo { TestRunInfo( std::string const& _name ); std::string name; }; struct GroupInfo { GroupInfo( std::string const& _name, std::size_t _groupIndex, std::size_t _groupsCount ); std::string name; std::size_t groupIndex; std::size_t groupsCounts; }; struct AssertionStats { AssertionStats( AssertionResult const& _assertionResult, std::vector const& _infoMessages, Totals const& _totals ); AssertionStats( AssertionStats const& ) = default; AssertionStats( AssertionStats && ) = default; AssertionStats& operator = ( AssertionStats const& ) = default; AssertionStats& operator = ( AssertionStats && ) = default; virtual ~AssertionStats(); AssertionResult assertionResult; std::vector infoMessages; Totals totals; }; struct SectionStats { SectionStats( SectionInfo const& _sectionInfo, Counts const& _assertions, double _durationInSeconds, bool _missingAssertions ); SectionStats( SectionStats const& ) = default; SectionStats( SectionStats && ) = default; SectionStats& operator = ( SectionStats const& ) = default; SectionStats& operator = ( SectionStats && ) = default; virtual ~SectionStats(); SectionInfo sectionInfo; Counts assertions; double durationInSeconds; bool missingAssertions; }; struct TestCaseStats { TestCaseStats( TestCaseInfo const& _testInfo, Totals const& _totals, std::string const& _stdOut, std::string const& _stdErr, bool _aborting ); TestCaseStats( TestCaseStats const& ) = default; TestCaseStats( TestCaseStats && ) = default; TestCaseStats& operator = ( TestCaseStats const& ) = default; TestCaseStats& operator = ( TestCaseStats && ) = default; virtual ~TestCaseStats(); TestCaseInfo testInfo; Totals totals; std::string stdOut; std::string stdErr; bool aborting; }; struct TestGroupStats { TestGroupStats( GroupInfo const& _groupInfo, Totals const& _totals, bool _aborting ); TestGroupStats( GroupInfo const& _groupInfo ); TestGroupStats( TestGroupStats const& ) = default; TestGroupStats( TestGroupStats && ) = default; TestGroupStats& operator = ( TestGroupStats const& ) = default; TestGroupStats& operator = ( TestGroupStats && ) = default; virtual ~TestGroupStats(); GroupInfo groupInfo; Totals totals; bool aborting; }; struct TestRunStats { TestRunStats( TestRunInfo const& _runInfo, Totals const& _totals, bool _aborting ); TestRunStats( TestRunStats const& ) = default; TestRunStats( TestRunStats && ) = default; TestRunStats& operator = ( TestRunStats const& ) = default; TestRunStats& operator = ( TestRunStats && ) = default; virtual ~TestRunStats(); TestRunInfo runInfo; Totals totals; bool aborting; }; struct BenchmarkInfo { std::string name; }; struct BenchmarkStats { BenchmarkInfo info; std::size_t iterations; uint64_t elapsedTimeInNanoseconds; }; struct IStreamingReporter { virtual ~IStreamingReporter() = default; // Implementing class must also provide the following static methods: // static std::string getDescription(); // static std::set getSupportedVerbosities() virtual ReporterPreferences getPreferences() const = 0; virtual void noMatchingTestCases( std::string const& spec ) = 0; virtual void testRunStarting( TestRunInfo const& testRunInfo ) = 0; virtual void testGroupStarting( GroupInfo const& groupInfo ) = 0; virtual void testCaseStarting( TestCaseInfo const& testInfo ) = 0; virtual void sectionStarting( SectionInfo const& sectionInfo ) = 0; // *** experimental *** virtual void benchmarkStarting( BenchmarkInfo const& ) {} virtual void assertionStarting( AssertionInfo const& assertionInfo ) = 0; // The return value indicates if the messages buffer should be cleared: virtual bool assertionEnded( AssertionStats const& assertionStats ) = 0; // *** experimental *** virtual void benchmarkEnded( BenchmarkStats const& ) {} virtual void sectionEnded( SectionStats const& sectionStats ) = 0; virtual void testCaseEnded( TestCaseStats const& testCaseStats ) = 0; virtual void testGroupEnded( TestGroupStats const& testGroupStats ) = 0; virtual void testRunEnded( TestRunStats const& testRunStats ) = 0; virtual void skipTest( TestCaseInfo const& testInfo ) = 0; // Default empty implementation provided virtual void fatalErrorEncountered( StringRef name ); virtual bool isMulti() const; }; using IStreamingReporterPtr = std::unique_ptr; struct IReporterFactory { virtual ~IReporterFactory(); virtual IStreamingReporterPtr create( ReporterConfig const& config ) const = 0; virtual std::string getDescription() const = 0; }; using IReporterFactoryPtr = std::shared_ptr; struct IReporterRegistry { using FactoryMap = std::map; using Listeners = std::vector; virtual ~IReporterRegistry(); virtual IStreamingReporterPtr create( std::string const& name, IConfigPtr const& config ) const = 0; virtual FactoryMap const& getFactories() const = 0; virtual Listeners const& getListeners() const = 0; }; } // end namespace Catch // end catch_interfaces_reporter.h #include #include #include #include #include #include #include namespace Catch { void prepareExpandedExpression(AssertionResult& result); // Returns double formatted as %.3f (format expected on output) std::string getFormattedDuration( double duration ); template struct StreamingReporterBase : IStreamingReporter { StreamingReporterBase( ReporterConfig const& _config ) : m_config( _config.fullConfig() ), stream( _config.stream() ) { m_reporterPrefs.shouldRedirectStdOut = false; if( !DerivedT::getSupportedVerbosities().count( m_config->verbosity() ) ) CATCH_ERROR( "Verbosity level not supported by this reporter" ); } ReporterPreferences getPreferences() const override { return m_reporterPrefs; } static std::set getSupportedVerbosities() { return { Verbosity::Normal }; } ~StreamingReporterBase() override = default; void noMatchingTestCases(std::string const&) override {} void testRunStarting(TestRunInfo const& _testRunInfo) override { currentTestRunInfo = _testRunInfo; } void testGroupStarting(GroupInfo const& _groupInfo) override { currentGroupInfo = _groupInfo; } void testCaseStarting(TestCaseInfo const& _testInfo) override { currentTestCaseInfo = _testInfo; } void sectionStarting(SectionInfo const& _sectionInfo) override { m_sectionStack.push_back(_sectionInfo); } void sectionEnded(SectionStats const& /* _sectionStats */) override { m_sectionStack.pop_back(); } void testCaseEnded(TestCaseStats const& /* _testCaseStats */) override { currentTestCaseInfo.reset(); } void testGroupEnded(TestGroupStats const& /* _testGroupStats */) override { currentGroupInfo.reset(); } void testRunEnded(TestRunStats const& /* _testRunStats */) override { currentTestCaseInfo.reset(); currentGroupInfo.reset(); currentTestRunInfo.reset(); } void skipTest(TestCaseInfo const&) override { // Don't do anything with this by default. // It can optionally be overridden in the derived class. } IConfigPtr m_config; std::ostream& stream; LazyStat currentTestRunInfo; LazyStat currentGroupInfo; LazyStat currentTestCaseInfo; std::vector m_sectionStack; ReporterPreferences m_reporterPrefs; }; template struct CumulativeReporterBase : IStreamingReporter { template struct Node { explicit Node( T const& _value ) : value( _value ) {} virtual ~Node() {} using ChildNodes = std::vector>; T value; ChildNodes children; }; struct SectionNode { explicit SectionNode(SectionStats const& _stats) : stats(_stats) {} virtual ~SectionNode() = default; bool operator == (SectionNode const& other) const { return stats.sectionInfo.lineInfo == other.stats.sectionInfo.lineInfo; } bool operator == (std::shared_ptr const& other) const { return operator==(*other); } SectionStats stats; using ChildSections = std::vector>; using Assertions = std::vector; ChildSections childSections; Assertions assertions; std::string stdOut; std::string stdErr; }; struct BySectionInfo { BySectionInfo( SectionInfo const& other ) : m_other( other ) {} BySectionInfo( BySectionInfo const& other ) : m_other( other.m_other ) {} bool operator() (std::shared_ptr const& node) const { return ((node->stats.sectionInfo.name == m_other.name) && (node->stats.sectionInfo.lineInfo == m_other.lineInfo)); } void operator=(BySectionInfo const&) = delete; private: SectionInfo const& m_other; }; using TestCaseNode = Node; using TestGroupNode = Node; using TestRunNode = Node; CumulativeReporterBase( ReporterConfig const& _config ) : m_config( _config.fullConfig() ), stream( _config.stream() ) { m_reporterPrefs.shouldRedirectStdOut = false; if( !DerivedT::getSupportedVerbosities().count( m_config->verbosity() ) ) CATCH_ERROR( "Verbosity level not supported by this reporter" ); } ~CumulativeReporterBase() override = default; ReporterPreferences getPreferences() const override { return m_reporterPrefs; } static std::set getSupportedVerbosities() { return { Verbosity::Normal }; } void testRunStarting( TestRunInfo const& ) override {} void testGroupStarting( GroupInfo const& ) override {} void testCaseStarting( TestCaseInfo const& ) override {} void sectionStarting( SectionInfo const& sectionInfo ) override { SectionStats incompleteStats( sectionInfo, Counts(), 0, false ); std::shared_ptr node; if( m_sectionStack.empty() ) { if( !m_rootSection ) m_rootSection = std::make_shared( incompleteStats ); node = m_rootSection; } else { SectionNode& parentNode = *m_sectionStack.back(); auto it = std::find_if( parentNode.childSections.begin(), parentNode.childSections.end(), BySectionInfo( sectionInfo ) ); if( it == parentNode.childSections.end() ) { node = std::make_shared( incompleteStats ); parentNode.childSections.push_back( node ); } else node = *it; } m_sectionStack.push_back( node ); m_deepestSection = std::move(node); } void assertionStarting(AssertionInfo const&) override {} bool assertionEnded(AssertionStats const& assertionStats) override { assert(!m_sectionStack.empty()); // AssertionResult holds a pointer to a temporary DecomposedExpression, // which getExpandedExpression() calls to build the expression string. // Our section stack copy of the assertionResult will likely outlive the // temporary, so it must be expanded or discarded now to avoid calling // a destroyed object later. prepareExpandedExpression(const_cast( assertionStats.assertionResult ) ); SectionNode& sectionNode = *m_sectionStack.back(); sectionNode.assertions.push_back(assertionStats); return true; } void sectionEnded(SectionStats const& sectionStats) override { assert(!m_sectionStack.empty()); SectionNode& node = *m_sectionStack.back(); node.stats = sectionStats; m_sectionStack.pop_back(); } void testCaseEnded(TestCaseStats const& testCaseStats) override { auto node = std::make_shared(testCaseStats); assert(m_sectionStack.size() == 0); node->children.push_back(m_rootSection); m_testCases.push_back(node); m_rootSection.reset(); assert(m_deepestSection); m_deepestSection->stdOut = testCaseStats.stdOut; m_deepestSection->stdErr = testCaseStats.stdErr; } void testGroupEnded(TestGroupStats const& testGroupStats) override { auto node = std::make_shared(testGroupStats); node->children.swap(m_testCases); m_testGroups.push_back(node); } void testRunEnded(TestRunStats const& testRunStats) override { auto node = std::make_shared(testRunStats); node->children.swap(m_testGroups); m_testRuns.push_back(node); testRunEndedCumulative(); } virtual void testRunEndedCumulative() = 0; void skipTest(TestCaseInfo const&) override {} IConfigPtr m_config; std::ostream& stream; std::vector m_assertions; std::vector>> m_sections; std::vector> m_testCases; std::vector> m_testGroups; std::vector> m_testRuns; std::shared_ptr m_rootSection; std::shared_ptr m_deepestSection; std::vector> m_sectionStack; ReporterPreferences m_reporterPrefs; }; template char const* getLineOfChars() { static char line[CATCH_CONFIG_CONSOLE_WIDTH] = {0}; if( !*line ) { std::memset( line, C, CATCH_CONFIG_CONSOLE_WIDTH-1 ); line[CATCH_CONFIG_CONSOLE_WIDTH-1] = 0; } return line; } struct TestEventListenerBase : StreamingReporterBase { TestEventListenerBase( ReporterConfig const& _config ); static std::set getSupportedVerbosities(); void assertionStarting(AssertionInfo const&) override; bool assertionEnded(AssertionStats const&) override; }; } // end namespace Catch // end catch_reporter_bases.hpp // start catch_console_colour.h namespace Catch { struct Colour { enum Code { None = 0, White, Red, Green, Blue, Cyan, Yellow, Grey, Bright = 0x10, BrightRed = Bright | Red, BrightGreen = Bright | Green, LightGrey = Bright | Grey, BrightWhite = Bright | White, BrightYellow = Bright | Yellow, // By intention FileName = LightGrey, Warning = BrightYellow, ResultError = BrightRed, ResultSuccess = BrightGreen, ResultExpectedFailure = Warning, Error = BrightRed, Success = Green, OriginalExpression = Cyan, ReconstructedExpression = BrightYellow, SecondaryText = LightGrey, Headers = White }; // Use constructed object for RAII guard Colour( Code _colourCode ); Colour( Colour&& other ) noexcept; Colour& operator=( Colour&& other ) noexcept; ~Colour(); // Use static method for one-shot changes static void use( Code _colourCode ); private: bool m_moved = false; }; std::ostream& operator << ( std::ostream& os, Colour const& ); } // end namespace Catch // end catch_console_colour.h // start catch_reporter_registrars.hpp namespace Catch { template class ReporterRegistrar { class ReporterFactory : public IReporterFactory { virtual IStreamingReporterPtr create( ReporterConfig const& config ) const override { return std::unique_ptr( new T( config ) ); } virtual std::string getDescription() const override { return T::getDescription(); } }; public: explicit ReporterRegistrar( std::string const& name ) { getMutableRegistryHub().registerReporter( name, std::make_shared() ); } }; template class ListenerRegistrar { class ListenerFactory : public IReporterFactory { virtual IStreamingReporterPtr create( ReporterConfig const& config ) const override { return std::unique_ptr( new T( config ) ); } virtual std::string getDescription() const override { return std::string(); } }; public: ListenerRegistrar() { getMutableRegistryHub().registerListener( std::make_shared() ); } }; } #if !defined(CATCH_CONFIG_DISABLE) #define CATCH_REGISTER_REPORTER( name, reporterType ) \ CATCH_INTERNAL_SUPPRESS_GLOBALS_WARNINGS \ namespace{ Catch::ReporterRegistrar catch_internal_RegistrarFor##reporterType( name ); } \ CATCH_INTERNAL_UNSUPPRESS_GLOBALS_WARNINGS #define CATCH_REGISTER_LISTENER( listenerType ) \ CATCH_INTERNAL_SUPPRESS_GLOBALS_WARNINGS \ namespace{ Catch::ListenerRegistrar catch_internal_RegistrarFor##listenerType; } \ CATCH_INTERNAL_SUPPRESS_GLOBALS_WARNINGS #else // CATCH_CONFIG_DISABLE #define CATCH_REGISTER_REPORTER(name, reporterType) #define CATCH_REGISTER_LISTENER(listenerType) #endif // CATCH_CONFIG_DISABLE // end catch_reporter_registrars.hpp // Allow users to base their work off existing reporters // start catch_reporter_compact.h namespace Catch { struct CompactReporter : StreamingReporterBase { using StreamingReporterBase::StreamingReporterBase; ~CompactReporter() override; static std::string getDescription(); ReporterPreferences getPreferences() const override; void noMatchingTestCases(std::string const& spec) override; void assertionStarting(AssertionInfo const&) override; bool assertionEnded(AssertionStats const& _assertionStats) override; void sectionEnded(SectionStats const& _sectionStats) override; void testRunEnded(TestRunStats const& _testRunStats) override; }; } // end namespace Catch // end catch_reporter_compact.h // start catch_reporter_console.h #if defined(_MSC_VER) #pragma warning(push) #pragma warning(disable:4061) // Not all labels are EXPLICITLY handled in switch // Note that 4062 (not all labels are handled // and default is missing) is enabled #endif namespace Catch { // Fwd decls struct SummaryColumn; class TablePrinter; struct ConsoleReporter : StreamingReporterBase { std::unique_ptr m_tablePrinter; ConsoleReporter(ReporterConfig const& config); ~ConsoleReporter() override; static std::string getDescription(); void noMatchingTestCases(std::string const& spec) override; void assertionStarting(AssertionInfo const&) override; bool assertionEnded(AssertionStats const& _assertionStats) override; void sectionStarting(SectionInfo const& _sectionInfo) override; void sectionEnded(SectionStats const& _sectionStats) override; void benchmarkStarting(BenchmarkInfo const& info) override; void benchmarkEnded(BenchmarkStats const& stats) override; void testCaseEnded(TestCaseStats const& _testCaseStats) override; void testGroupEnded(TestGroupStats const& _testGroupStats) override; void testRunEnded(TestRunStats const& _testRunStats) override; private: void lazyPrint(); void lazyPrintWithoutClosingBenchmarkTable(); void lazyPrintRunInfo(); void lazyPrintGroupInfo(); void printTestCaseAndSectionHeader(); void printClosedHeader(std::string const& _name); void printOpenHeader(std::string const& _name); // if string has a : in first line will set indent to follow it on // subsequent lines void printHeaderString(std::string const& _string, std::size_t indent = 0); void printTotals(Totals const& totals); void printSummaryRow(std::string const& label, std::vector const& cols, std::size_t row); void printTotalsDivider(Totals const& totals); void printSummaryDivider(); private: bool m_headerPrinted = false; }; } // end namespace Catch #if defined(_MSC_VER) #pragma warning(pop) #endif // end catch_reporter_console.h // start catch_reporter_junit.h // start catch_xmlwriter.h #include namespace Catch { class XmlEncode { public: enum ForWhat { ForTextNodes, ForAttributes }; XmlEncode( std::string const& str, ForWhat forWhat = ForTextNodes ); void encodeTo( std::ostream& os ) const; friend std::ostream& operator << ( std::ostream& os, XmlEncode const& xmlEncode ); private: std::string m_str; ForWhat m_forWhat; }; class XmlWriter { public: class ScopedElement { public: ScopedElement( XmlWriter* writer ); ScopedElement( ScopedElement&& other ) noexcept; ScopedElement& operator=( ScopedElement&& other ) noexcept; ~ScopedElement(); ScopedElement& writeText( std::string const& text, bool indent = true ); template ScopedElement& writeAttribute( std::string const& name, T const& attribute ) { m_writer->writeAttribute( name, attribute ); return *this; } private: mutable XmlWriter* m_writer = nullptr; }; XmlWriter( std::ostream& os = Catch::cout() ); ~XmlWriter(); XmlWriter( XmlWriter const& ) = delete; XmlWriter& operator=( XmlWriter const& ) = delete; XmlWriter& startElement( std::string const& name ); ScopedElement scopedElement( std::string const& name ); XmlWriter& endElement(); XmlWriter& writeAttribute( std::string const& name, std::string const& attribute ); XmlWriter& writeAttribute( std::string const& name, bool attribute ); template XmlWriter& writeAttribute( std::string const& name, T const& attribute ) { ReusableStringStream rss; rss << attribute; return writeAttribute( name, rss.str() ); } XmlWriter& writeText( std::string const& text, bool indent = true ); XmlWriter& writeComment( std::string const& text ); void writeStylesheetRef( std::string const& url ); XmlWriter& writeBlankLine(); void ensureTagClosed(); private: void writeDeclaration(); void newlineIfNecessary(); bool m_tagIsOpen = false; bool m_needsNewline = false; std::vector m_tags; std::string m_indent; std::ostream& m_os; }; } // end catch_xmlwriter.h namespace Catch { class JunitReporter : public CumulativeReporterBase { public: JunitReporter(ReporterConfig const& _config); ~JunitReporter() override; static std::string getDescription(); void noMatchingTestCases(std::string const& /*spec*/) override; void testRunStarting(TestRunInfo const& runInfo) override; void testGroupStarting(GroupInfo const& groupInfo) override; void testCaseStarting(TestCaseInfo const& testCaseInfo) override; bool assertionEnded(AssertionStats const& assertionStats) override; void testCaseEnded(TestCaseStats const& testCaseStats) override; void testGroupEnded(TestGroupStats const& testGroupStats) override; void testRunEndedCumulative() override; void writeGroup(TestGroupNode const& groupNode, double suiteTime); void writeTestCase(TestCaseNode const& testCaseNode); void writeSection(std::string const& className, std::string const& rootName, SectionNode const& sectionNode); void writeAssertions(SectionNode const& sectionNode); void writeAssertion(AssertionStats const& stats); XmlWriter xml; Timer suiteTimer; std::string stdOutForSuite; std::string stdErrForSuite; unsigned int unexpectedExceptions = 0; bool m_okToFail = false; }; } // end namespace Catch // end catch_reporter_junit.h // start catch_reporter_xml.h namespace Catch { class XmlReporter : public StreamingReporterBase { public: XmlReporter(ReporterConfig const& _config); ~XmlReporter() override; static std::string getDescription(); virtual std::string getStylesheetRef() const; void writeSourceInfo(SourceLineInfo const& sourceInfo); public: // StreamingReporterBase void noMatchingTestCases(std::string const& s) override; void testRunStarting(TestRunInfo const& testInfo) override; void testGroupStarting(GroupInfo const& groupInfo) override; void testCaseStarting(TestCaseInfo const& testInfo) override; void sectionStarting(SectionInfo const& sectionInfo) override; void assertionStarting(AssertionInfo const&) override; bool assertionEnded(AssertionStats const& assertionStats) override; void sectionEnded(SectionStats const& sectionStats) override; void testCaseEnded(TestCaseStats const& testCaseStats) override; void testGroupEnded(TestGroupStats const& testGroupStats) override; void testRunEnded(TestRunStats const& testRunStats) override; private: Timer m_testCaseTimer; XmlWriter m_xml; int m_sectionDepth = 0; }; } // end namespace Catch // end catch_reporter_xml.h // end catch_external_interfaces.h #endif #endif // ! CATCH_CONFIG_IMPL_ONLY #ifdef CATCH_IMPL // start catch_impl.hpp #ifdef __clang__ #pragma clang diagnostic push #pragma clang diagnostic ignored "-Wweak-vtables" #endif // Keep these here for external reporters // start catch_test_case_tracker.h #include #include #include namespace Catch { namespace TestCaseTracking { struct NameAndLocation { std::string name; SourceLineInfo location; NameAndLocation( std::string const& _name, SourceLineInfo const& _location ); }; struct ITracker; using ITrackerPtr = std::shared_ptr; struct ITracker { virtual ~ITracker(); // static queries virtual NameAndLocation const& nameAndLocation() const = 0; // dynamic queries virtual bool isComplete() const = 0; // Successfully completed or failed virtual bool isSuccessfullyCompleted() const = 0; virtual bool isOpen() const = 0; // Started but not complete virtual bool hasChildren() const = 0; virtual ITracker& parent() = 0; // actions virtual void close() = 0; // Successfully complete virtual void fail() = 0; virtual void markAsNeedingAnotherRun() = 0; virtual void addChild( ITrackerPtr const& child ) = 0; virtual ITrackerPtr findChild( NameAndLocation const& nameAndLocation ) = 0; virtual void openChild() = 0; // Debug/ checking virtual bool isSectionTracker() const = 0; virtual bool isGeneratorTracker() const = 0; }; class TrackerContext { enum RunState { NotStarted, Executing, CompletedCycle }; ITrackerPtr m_rootTracker; ITracker* m_currentTracker = nullptr; RunState m_runState = NotStarted; public: static TrackerContext& instance(); ITracker& startRun(); void endRun(); void startCycle(); void completeCycle(); bool completedCycle() const; ITracker& currentTracker(); void setCurrentTracker( ITracker* tracker ); }; class TrackerBase : public ITracker { protected: enum CycleState { NotStarted, Executing, ExecutingChildren, NeedsAnotherRun, CompletedSuccessfully, Failed }; using Children = std::vector; NameAndLocation m_nameAndLocation; TrackerContext& m_ctx; ITracker* m_parent; Children m_children; CycleState m_runState = NotStarted; public: TrackerBase( NameAndLocation const& nameAndLocation, TrackerContext& ctx, ITracker* parent ); NameAndLocation const& nameAndLocation() const override; bool isComplete() const override; bool isSuccessfullyCompleted() const override; bool isOpen() const override; bool hasChildren() const override; void addChild( ITrackerPtr const& child ) override; ITrackerPtr findChild( NameAndLocation const& nameAndLocation ) override; ITracker& parent() override; void openChild() override; bool isSectionTracker() const override; bool isGeneratorTracker() const override; void open(); void close() override; void fail() override; void markAsNeedingAnotherRun() override; private: void moveToParent(); void moveToThis(); }; class SectionTracker : public TrackerBase { std::vector m_filters; public: SectionTracker( NameAndLocation const& nameAndLocation, TrackerContext& ctx, ITracker* parent ); bool isSectionTracker() const override; bool isComplete() const override; static SectionTracker& acquire( TrackerContext& ctx, NameAndLocation const& nameAndLocation ); void tryOpen(); void addInitialFilters( std::vector const& filters ); void addNextFilters( std::vector const& filters ); }; } // namespace TestCaseTracking using TestCaseTracking::ITracker; using TestCaseTracking::TrackerContext; using TestCaseTracking::SectionTracker; } // namespace Catch // end catch_test_case_tracker.h // start catch_leak_detector.h namespace Catch { struct LeakDetector { LeakDetector(); ~LeakDetector(); }; } // end catch_leak_detector.h // Cpp files will be included in the single-header file here // start catch_approx.cpp #include #include namespace { // Performs equivalent check of std::fabs(lhs - rhs) <= margin // But without the subtraction to allow for INFINITY in comparison bool marginComparison(double lhs, double rhs, double margin) { return (lhs + margin >= rhs) && (rhs + margin >= lhs); } } namespace Catch { namespace Detail { Approx::Approx ( double value ) : m_epsilon( std::numeric_limits::epsilon()*100 ), m_margin( 0.0 ), m_scale( 0.0 ), m_value( value ) {} Approx Approx::custom() { return Approx( 0 ); } Approx Approx::operator-() const { auto temp(*this); temp.m_value = -temp.m_value; return temp; } std::string Approx::toString() const { ReusableStringStream rss; rss << "Approx( " << ::Catch::Detail::stringify( m_value ) << " )"; return rss.str(); } bool Approx::equalityComparisonImpl(const double other) const { // First try with fixed margin, then compute margin based on epsilon, scale and Approx's value // Thanks to Richard Harris for his help refining the scaled margin value return marginComparison(m_value, other, m_margin) || marginComparison(m_value, other, m_epsilon * (m_scale + std::fabs(m_value))); } void Approx::setMargin(double margin) { CATCH_ENFORCE(margin >= 0, "Invalid Approx::margin: " << margin << '.' << " Approx::Margin has to be non-negative."); m_margin = margin; } void Approx::setEpsilon(double epsilon) { CATCH_ENFORCE(epsilon >= 0 && epsilon <= 1.0, "Invalid Approx::epsilon: " << epsilon << '.' << " Approx::epsilon has to be in [0, 1]"); m_epsilon = epsilon; } } // end namespace Detail namespace literals { Detail::Approx operator "" _a(long double val) { return Detail::Approx(val); } Detail::Approx operator "" _a(unsigned long long val) { return Detail::Approx(val); } } // end namespace literals std::string StringMaker::convert(Catch::Detail::Approx const& value) { return value.toString(); } } // end namespace Catch // end catch_approx.cpp // start catch_assertionhandler.cpp // start catch_context.h #include namespace Catch { struct IResultCapture; struct IRunner; struct IConfig; struct IMutableContext; using IConfigPtr = std::shared_ptr; struct IContext { virtual ~IContext(); virtual IResultCapture* getResultCapture() = 0; virtual IRunner* getRunner() = 0; virtual IConfigPtr const& getConfig() const = 0; }; struct IMutableContext : IContext { virtual ~IMutableContext(); virtual void setResultCapture( IResultCapture* resultCapture ) = 0; virtual void setRunner( IRunner* runner ) = 0; virtual void setConfig( IConfigPtr const& config ) = 0; private: static IMutableContext *currentContext; friend IMutableContext& getCurrentMutableContext(); friend void cleanUpContext(); static void createContext(); }; inline IMutableContext& getCurrentMutableContext() { if( !IMutableContext::currentContext ) IMutableContext::createContext(); return *IMutableContext::currentContext; } inline IContext& getCurrentContext() { return getCurrentMutableContext(); } void cleanUpContext(); } // end catch_context.h // start catch_debugger.h namespace Catch { bool isDebuggerActive(); } #ifdef CATCH_PLATFORM_MAC #define CATCH_TRAP() __asm__("int $3\n" : : ) /* NOLINT */ #elif defined(CATCH_PLATFORM_LINUX) // If we can use inline assembler, do it because this allows us to break // directly at the location of the failing check instead of breaking inside // raise() called from it, i.e. one stack frame below. #if defined(__GNUC__) && (defined(__i386) || defined(__x86_64)) #define CATCH_TRAP() asm volatile ("int $3") /* NOLINT */ #else // Fall back to the generic way. #include #define CATCH_TRAP() raise(SIGTRAP) #endif #elif defined(_MSC_VER) #define CATCH_TRAP() __debugbreak() #elif defined(__MINGW32__) extern "C" __declspec(dllimport) void __stdcall DebugBreak(); #define CATCH_TRAP() DebugBreak() #endif #ifdef CATCH_TRAP #define CATCH_BREAK_INTO_DEBUGGER() []{ if( Catch::isDebuggerActive() ) { CATCH_TRAP(); } }() #else #define CATCH_BREAK_INTO_DEBUGGER() []{}() #endif // end catch_debugger.h // start catch_run_context.h // start catch_fatal_condition.h // start catch_windows_h_proxy.h #if defined(CATCH_PLATFORM_WINDOWS) #if !defined(NOMINMAX) && !defined(CATCH_CONFIG_NO_NOMINMAX) # define CATCH_DEFINED_NOMINMAX # define NOMINMAX #endif #if !defined(WIN32_LEAN_AND_MEAN) && !defined(CATCH_CONFIG_NO_WIN32_LEAN_AND_MEAN) # define CATCH_DEFINED_WIN32_LEAN_AND_MEAN # define WIN32_LEAN_AND_MEAN #endif #ifdef __AFXDLL #include #else #include #endif #ifdef CATCH_DEFINED_NOMINMAX # undef NOMINMAX #endif #ifdef CATCH_DEFINED_WIN32_LEAN_AND_MEAN # undef WIN32_LEAN_AND_MEAN #endif #endif // defined(CATCH_PLATFORM_WINDOWS) // end catch_windows_h_proxy.h #if defined( CATCH_CONFIG_WINDOWS_SEH ) namespace Catch { struct FatalConditionHandler { static LONG CALLBACK handleVectoredException(PEXCEPTION_POINTERS ExceptionInfo); FatalConditionHandler(); static void reset(); ~FatalConditionHandler(); private: static bool isSet; static ULONG guaranteeSize; static PVOID exceptionHandlerHandle; }; } // namespace Catch #elif defined ( CATCH_CONFIG_POSIX_SIGNALS ) #include namespace Catch { struct FatalConditionHandler { static bool isSet; static struct sigaction oldSigActions[]; static stack_t oldSigStack; static char altStackMem[]; static void handleSignal( int sig ); FatalConditionHandler(); ~FatalConditionHandler(); static void reset(); }; } // namespace Catch #else namespace Catch { struct FatalConditionHandler { void reset(); }; } #endif // end catch_fatal_condition.h #include namespace Catch { struct IMutableContext; /////////////////////////////////////////////////////////////////////////// class RunContext : public IResultCapture, public IRunner { public: RunContext( RunContext const& ) = delete; RunContext& operator =( RunContext const& ) = delete; explicit RunContext( IConfigPtr const& _config, IStreamingReporterPtr&& reporter ); ~RunContext() override; void testGroupStarting( std::string const& testSpec, std::size_t groupIndex, std::size_t groupsCount ); void testGroupEnded( std::string const& testSpec, Totals const& totals, std::size_t groupIndex, std::size_t groupsCount ); Totals runTest(TestCase const& testCase); IConfigPtr config() const; IStreamingReporter& reporter() const; public: // IResultCapture // Assertion handlers void handleExpr ( AssertionInfo const& info, ITransientExpression const& expr, AssertionReaction& reaction ) override; void handleMessage ( AssertionInfo const& info, ResultWas::OfType resultType, StringRef const& message, AssertionReaction& reaction ) override; void handleUnexpectedExceptionNotThrown ( AssertionInfo const& info, AssertionReaction& reaction ) override; void handleUnexpectedInflightException ( AssertionInfo const& info, std::string const& message, AssertionReaction& reaction ) override; void handleIncomplete ( AssertionInfo const& info ) override; void handleNonExpr ( AssertionInfo const &info, ResultWas::OfType resultType, AssertionReaction &reaction ) override; bool sectionStarted( SectionInfo const& sectionInfo, Counts& assertions ) override; void sectionEnded( SectionEndInfo const& endInfo ) override; void sectionEndedEarly( SectionEndInfo const& endInfo ) override; auto acquireGeneratorTracker( SourceLineInfo const& lineInfo ) -> IGeneratorTracker& override; void benchmarkStarting( BenchmarkInfo const& info ) override; void benchmarkEnded( BenchmarkStats const& stats ) override; void pushScopedMessage( MessageInfo const& message ) override; void popScopedMessage( MessageInfo const& message ) override; std::string getCurrentTestName() const override; const AssertionResult* getLastResult() const override; void exceptionEarlyReported() override; void handleFatalErrorCondition( StringRef message ) override; bool lastAssertionPassed() override; void assertionPassed() override; public: // !TBD We need to do this another way! bool aborting() const final; private: void runCurrentTest( std::string& redirectedCout, std::string& redirectedCerr ); void invokeActiveTestCase(); void resetAssertionInfo(); bool testForMissingAssertions( Counts& assertions ); void assertionEnded( AssertionResult const& result ); void reportExpr ( AssertionInfo const &info, ResultWas::OfType resultType, ITransientExpression const *expr, bool negated ); void populateReaction( AssertionReaction& reaction ); private: void handleUnfinishedSections(); TestRunInfo m_runInfo; IMutableContext& m_context; TestCase const* m_activeTestCase = nullptr; ITracker* m_testCaseTracker = nullptr; Option m_lastResult; IConfigPtr m_config; Totals m_totals; IStreamingReporterPtr m_reporter; std::vector m_messages; AssertionInfo m_lastAssertionInfo; std::vector m_unfinishedSections; std::vector m_activeSections; TrackerContext m_trackerContext; bool m_lastAssertionPassed = false; bool m_shouldReportUnexpected = true; bool m_includeSuccessfulResults; }; } // end namespace Catch // end catch_run_context.h namespace Catch { namespace { auto operator <<( std::ostream& os, ITransientExpression const& expr ) -> std::ostream& { expr.streamReconstructedExpression( os ); return os; } } LazyExpression::LazyExpression( bool isNegated ) : m_isNegated( isNegated ) {} LazyExpression::LazyExpression( LazyExpression const& other ) : m_isNegated( other.m_isNegated ) {} LazyExpression::operator bool() const { return m_transientExpression != nullptr; } auto operator << ( std::ostream& os, LazyExpression const& lazyExpr ) -> std::ostream& { if( lazyExpr.m_isNegated ) os << "!"; if( lazyExpr ) { if( lazyExpr.m_isNegated && lazyExpr.m_transientExpression->isBinaryExpression() ) os << "(" << *lazyExpr.m_transientExpression << ")"; else os << *lazyExpr.m_transientExpression; } else { os << "{** error - unchecked empty expression requested **}"; } return os; } AssertionHandler::AssertionHandler ( StringRef const& macroName, SourceLineInfo const& lineInfo, StringRef capturedExpression, ResultDisposition::Flags resultDisposition ) : m_assertionInfo{ macroName, lineInfo, capturedExpression, resultDisposition }, m_resultCapture( getResultCapture() ) {} void AssertionHandler::handleExpr( ITransientExpression const& expr ) { m_resultCapture.handleExpr( m_assertionInfo, expr, m_reaction ); } void AssertionHandler::handleMessage(ResultWas::OfType resultType, StringRef const& message) { m_resultCapture.handleMessage( m_assertionInfo, resultType, message, m_reaction ); } auto AssertionHandler::allowThrows() const -> bool { return getCurrentContext().getConfig()->allowThrows(); } void AssertionHandler::complete() { setCompleted(); if( m_reaction.shouldDebugBreak ) { // If you find your debugger stopping you here then go one level up on the // call-stack for the code that caused it (typically a failed assertion) // (To go back to the test and change execution, jump over the throw, next) CATCH_BREAK_INTO_DEBUGGER(); } if (m_reaction.shouldThrow) { #if !defined(CATCH_CONFIG_DISABLE_EXCEPTIONS) throw Catch::TestFailureException(); #else CATCH_ERROR( "Test failure requires aborting test!" ); #endif } } void AssertionHandler::setCompleted() { m_completed = true; } void AssertionHandler::handleUnexpectedInflightException() { m_resultCapture.handleUnexpectedInflightException( m_assertionInfo, Catch::translateActiveException(), m_reaction ); } void AssertionHandler::handleExceptionThrownAsExpected() { m_resultCapture.handleNonExpr(m_assertionInfo, ResultWas::Ok, m_reaction); } void AssertionHandler::handleExceptionNotThrownAsExpected() { m_resultCapture.handleNonExpr(m_assertionInfo, ResultWas::Ok, m_reaction); } void AssertionHandler::handleUnexpectedExceptionNotThrown() { m_resultCapture.handleUnexpectedExceptionNotThrown( m_assertionInfo, m_reaction ); } void AssertionHandler::handleThrowingCallSkipped() { m_resultCapture.handleNonExpr(m_assertionInfo, ResultWas::Ok, m_reaction); } // This is the overload that takes a string and infers the Equals matcher from it // The more general overload, that takes any string matcher, is in catch_capture_matchers.cpp void handleExceptionMatchExpr( AssertionHandler& handler, std::string const& str, StringRef const& matcherString ) { handleExceptionMatchExpr( handler, Matchers::Equals( str ), matcherString ); } } // namespace Catch // end catch_assertionhandler.cpp // start catch_assertionresult.cpp namespace Catch { AssertionResultData::AssertionResultData(ResultWas::OfType _resultType, LazyExpression const & _lazyExpression): lazyExpression(_lazyExpression), resultType(_resultType) {} std::string AssertionResultData::reconstructExpression() const { if( reconstructedExpression.empty() ) { if( lazyExpression ) { ReusableStringStream rss; rss << lazyExpression; reconstructedExpression = rss.str(); } } return reconstructedExpression; } AssertionResult::AssertionResult( AssertionInfo const& info, AssertionResultData const& data ) : m_info( info ), m_resultData( data ) {} // Result was a success bool AssertionResult::succeeded() const { return Catch::isOk( m_resultData.resultType ); } // Result was a success, or failure is suppressed bool AssertionResult::isOk() const { return Catch::isOk( m_resultData.resultType ) || shouldSuppressFailure( m_info.resultDisposition ); } ResultWas::OfType AssertionResult::getResultType() const { return m_resultData.resultType; } bool AssertionResult::hasExpression() const { return m_info.capturedExpression[0] != 0; } bool AssertionResult::hasMessage() const { return !m_resultData.message.empty(); } std::string AssertionResult::getExpression() const { if( isFalseTest( m_info.resultDisposition ) ) return "!(" + m_info.capturedExpression + ")"; else return m_info.capturedExpression; } std::string AssertionResult::getExpressionInMacro() const { std::string expr; if( m_info.macroName[0] == 0 ) expr = m_info.capturedExpression; else { expr.reserve( m_info.macroName.size() + m_info.capturedExpression.size() + 4 ); expr += m_info.macroName; expr += "( "; expr += m_info.capturedExpression; expr += " )"; } return expr; } bool AssertionResult::hasExpandedExpression() const { return hasExpression() && getExpandedExpression() != getExpression(); } std::string AssertionResult::getExpandedExpression() const { std::string expr = m_resultData.reconstructExpression(); return expr.empty() ? getExpression() : expr; } std::string AssertionResult::getMessage() const { return m_resultData.message; } SourceLineInfo AssertionResult::getSourceInfo() const { return m_info.lineInfo; } StringRef AssertionResult::getTestMacroName() const { return m_info.macroName; } } // end namespace Catch // end catch_assertionresult.cpp // start catch_benchmark.cpp namespace Catch { auto BenchmarkLooper::getResolution() -> uint64_t { return getEstimatedClockResolution() * getCurrentContext().getConfig()->benchmarkResolutionMultiple(); } void BenchmarkLooper::reportStart() { getResultCapture().benchmarkStarting( { m_name } ); } auto BenchmarkLooper::needsMoreIterations() -> bool { auto elapsed = m_timer.getElapsedNanoseconds(); // Exponentially increasing iterations until we're confident in our timer resolution if( elapsed < m_resolution ) { m_iterationsToRun *= 10; return true; } getResultCapture().benchmarkEnded( { { m_name }, m_count, elapsed } ); return false; } } // end namespace Catch // end catch_benchmark.cpp // start catch_capture_matchers.cpp namespace Catch { using StringMatcher = Matchers::Impl::MatcherBase; // This is the general overload that takes a any string matcher // There is another overload, in catch_assertionhandler.h/.cpp, that only takes a string and infers // the Equals matcher (so the header does not mention matchers) void handleExceptionMatchExpr( AssertionHandler& handler, StringMatcher const& matcher, StringRef const& matcherString ) { std::string exceptionMessage = Catch::translateActiveException(); MatchExpr expr( exceptionMessage, matcher, matcherString ); handler.handleExpr( expr ); } } // namespace Catch // end catch_capture_matchers.cpp // start catch_commandline.cpp // start catch_commandline.h // start catch_clara.h // Use Catch's value for console width (store Clara's off to the side, if present) #ifdef CLARA_CONFIG_CONSOLE_WIDTH #define CATCH_TEMP_CLARA_CONFIG_CONSOLE_WIDTH CATCH_CLARA_TEXTFLOW_CONFIG_CONSOLE_WIDTH #undef CATCH_CLARA_TEXTFLOW_CONFIG_CONSOLE_WIDTH #endif #define CATCH_CLARA_TEXTFLOW_CONFIG_CONSOLE_WIDTH CATCH_CONFIG_CONSOLE_WIDTH-1 #ifdef __clang__ #pragma clang diagnostic push #pragma clang diagnostic ignored "-Wweak-vtables" #pragma clang diagnostic ignored "-Wexit-time-destructors" #pragma clang diagnostic ignored "-Wshadow" #endif // start clara.hpp // Copyright 2017 Two Blue Cubes Ltd. All rights reserved. // // Distributed under the Boost Software License, Version 1.0. (See accompanying // file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt) // // See https://github.com/philsquared/Clara for more details // Clara v1.1.5 #ifndef CATCH_CLARA_CONFIG_CONSOLE_WIDTH #define CATCH_CLARA_CONFIG_CONSOLE_WIDTH 80 #endif #ifndef CATCH_CLARA_TEXTFLOW_CONFIG_CONSOLE_WIDTH #define CATCH_CLARA_TEXTFLOW_CONFIG_CONSOLE_WIDTH CATCH_CLARA_CONFIG_CONSOLE_WIDTH #endif #ifndef CLARA_CONFIG_OPTIONAL_TYPE #ifdef __has_include #if __has_include() && __cplusplus >= 201703L #include #define CLARA_CONFIG_OPTIONAL_TYPE std::optional #endif #endif #endif // ----------- #included from clara_textflow.hpp ----------- // TextFlowCpp // // A single-header library for wrapping and laying out basic text, by Phil Nash // // Distributed under the Boost Software License, Version 1.0. (See accompanying // file LICENSE.txt or copy at http://www.boost.org/LICENSE_1_0.txt) // // This project is hosted at https://github.com/philsquared/textflowcpp #include #include #include #include #ifndef CATCH_CLARA_TEXTFLOW_CONFIG_CONSOLE_WIDTH #define CATCH_CLARA_TEXTFLOW_CONFIG_CONSOLE_WIDTH 80 #endif namespace Catch { namespace clara { namespace TextFlow { inline auto isWhitespace(char c) -> bool { static std::string chars = " \t\n\r"; return chars.find(c) != std::string::npos; } inline auto isBreakableBefore(char c) -> bool { static std::string chars = "[({<|"; return chars.find(c) != std::string::npos; } inline auto isBreakableAfter(char c) -> bool { static std::string chars = "])}>.,:;*+-=&/\\"; return chars.find(c) != std::string::npos; } class Columns; class Column { std::vector m_strings; size_t m_width = CATCH_CLARA_TEXTFLOW_CONFIG_CONSOLE_WIDTH; size_t m_indent = 0; size_t m_initialIndent = std::string::npos; public: class iterator { friend Column; Column const& m_column; size_t m_stringIndex = 0; size_t m_pos = 0; size_t m_len = 0; size_t m_end = 0; bool m_suffix = false; iterator(Column const& column, size_t stringIndex) : m_column(column), m_stringIndex(stringIndex) {} auto line() const -> std::string const& { return m_column.m_strings[m_stringIndex]; } auto isBoundary(size_t at) const -> bool { assert(at > 0); assert(at <= line().size()); return at == line().size() || (isWhitespace(line()[at]) && !isWhitespace(line()[at - 1])) || isBreakableBefore(line()[at]) || isBreakableAfter(line()[at - 1]); } void calcLength() { assert(m_stringIndex < m_column.m_strings.size()); m_suffix = false; auto width = m_column.m_width - indent(); m_end = m_pos; while (m_end < line().size() && line()[m_end] != '\n') ++m_end; if (m_end < m_pos + width) { m_len = m_end - m_pos; } else { size_t len = width; while (len > 0 && !isBoundary(m_pos + len)) --len; while (len > 0 && isWhitespace(line()[m_pos + len - 1])) --len; if (len > 0) { m_len = len; } else { m_suffix = true; m_len = width - 1; } } } auto indent() const -> size_t { auto initial = m_pos == 0 && m_stringIndex == 0 ? m_column.m_initialIndent : std::string::npos; return initial == std::string::npos ? m_column.m_indent : initial; } auto addIndentAndSuffix(std::string const &plain) const -> std::string { return std::string(indent(), ' ') + (m_suffix ? plain + "-" : plain); } public: using difference_type = std::ptrdiff_t; using value_type = std::string; using pointer = value_type * ; using reference = value_type & ; using iterator_category = std::forward_iterator_tag; explicit iterator(Column const& column) : m_column(column) { assert(m_column.m_width > m_column.m_indent); assert(m_column.m_initialIndent == std::string::npos || m_column.m_width > m_column.m_initialIndent); calcLength(); if (m_len == 0) m_stringIndex++; // Empty string } auto operator *() const -> std::string { assert(m_stringIndex < m_column.m_strings.size()); assert(m_pos <= m_end); return addIndentAndSuffix(line().substr(m_pos, m_len)); } auto operator ++() -> iterator& { m_pos += m_len; if (m_pos < line().size() && line()[m_pos] == '\n') m_pos += 1; else while (m_pos < line().size() && isWhitespace(line()[m_pos])) ++m_pos; if (m_pos == line().size()) { m_pos = 0; ++m_stringIndex; } if (m_stringIndex < m_column.m_strings.size()) calcLength(); return *this; } auto operator ++(int) -> iterator { iterator prev(*this); operator++(); return prev; } auto operator ==(iterator const& other) const -> bool { return m_pos == other.m_pos && m_stringIndex == other.m_stringIndex && &m_column == &other.m_column; } auto operator !=(iterator const& other) const -> bool { return !operator==(other); } }; using const_iterator = iterator; explicit Column(std::string const& text) { m_strings.push_back(text); } auto width(size_t newWidth) -> Column& { assert(newWidth > 0); m_width = newWidth; return *this; } auto indent(size_t newIndent) -> Column& { m_indent = newIndent; return *this; } auto initialIndent(size_t newIndent) -> Column& { m_initialIndent = newIndent; return *this; } auto width() const -> size_t { return m_width; } auto begin() const -> iterator { return iterator(*this); } auto end() const -> iterator { return { *this, m_strings.size() }; } inline friend std::ostream& operator << (std::ostream& os, Column const& col) { bool first = true; for (auto line : col) { if (first) first = false; else os << "\n"; os << line; } return os; } auto operator + (Column const& other)->Columns; auto toString() const -> std::string { std::ostringstream oss; oss << *this; return oss.str(); } }; class Spacer : public Column { public: explicit Spacer(size_t spaceWidth) : Column("") { width(spaceWidth); } }; class Columns { std::vector m_columns; public: class iterator { friend Columns; struct EndTag {}; std::vector const& m_columns; std::vector m_iterators; size_t m_activeIterators; iterator(Columns const& columns, EndTag) : m_columns(columns.m_columns), m_activeIterators(0) { m_iterators.reserve(m_columns.size()); for (auto const& col : m_columns) m_iterators.push_back(col.end()); } public: using difference_type = std::ptrdiff_t; using value_type = std::string; using pointer = value_type * ; using reference = value_type & ; using iterator_category = std::forward_iterator_tag; explicit iterator(Columns const& columns) : m_columns(columns.m_columns), m_activeIterators(m_columns.size()) { m_iterators.reserve(m_columns.size()); for (auto const& col : m_columns) m_iterators.push_back(col.begin()); } auto operator ==(iterator const& other) const -> bool { return m_iterators == other.m_iterators; } auto operator !=(iterator const& other) const -> bool { return m_iterators != other.m_iterators; } auto operator *() const -> std::string { std::string row, padding; for (size_t i = 0; i < m_columns.size(); ++i) { auto width = m_columns[i].width(); if (m_iterators[i] != m_columns[i].end()) { std::string col = *m_iterators[i]; row += padding + col; if (col.size() < width) padding = std::string(width - col.size(), ' '); else padding = ""; } else { padding += std::string(width, ' '); } } return row; } auto operator ++() -> iterator& { for (size_t i = 0; i < m_columns.size(); ++i) { if (m_iterators[i] != m_columns[i].end()) ++m_iterators[i]; } return *this; } auto operator ++(int) -> iterator { iterator prev(*this); operator++(); return prev; } }; using const_iterator = iterator; auto begin() const -> iterator { return iterator(*this); } auto end() const -> iterator { return { *this, iterator::EndTag() }; } auto operator += (Column const& col) -> Columns& { m_columns.push_back(col); return *this; } auto operator + (Column const& col) -> Columns { Columns combined = *this; combined += col; return combined; } inline friend std::ostream& operator << (std::ostream& os, Columns const& cols) { bool first = true; for (auto line : cols) { if (first) first = false; else os << "\n"; os << line; } return os; } auto toString() const -> std::string { std::ostringstream oss; oss << *this; return oss.str(); } }; inline auto Column::operator + (Column const& other) -> Columns { Columns cols; cols += *this; cols += other; return cols; } } } } // ----------- end of #include from clara_textflow.hpp ----------- // ........... back in clara.hpp #include #include #include #include #if !defined(CATCH_PLATFORM_WINDOWS) && ( defined(WIN32) || defined(__WIN32__) || defined(_WIN32) || defined(_MSC_VER) ) #define CATCH_PLATFORM_WINDOWS #endif namespace Catch { namespace clara { namespace detail { // Traits for extracting arg and return type of lambdas (for single argument lambdas) template struct UnaryLambdaTraits : UnaryLambdaTraits {}; template struct UnaryLambdaTraits { static const bool isValid = false; }; template struct UnaryLambdaTraits { static const bool isValid = true; using ArgType = typename std::remove_const::type>::type; using ReturnType = ReturnT; }; class TokenStream; // Transport for raw args (copied from main args, or supplied via init list for testing) class Args { friend TokenStream; std::string m_exeName; std::vector m_args; public: Args( int argc, char const* const* argv ) : m_exeName(argv[0]), m_args(argv + 1, argv + argc) {} Args( std::initializer_list args ) : m_exeName( *args.begin() ), m_args( args.begin()+1, args.end() ) {} auto exeName() const -> std::string { return m_exeName; } }; // Wraps a token coming from a token stream. These may not directly correspond to strings as a single string // may encode an option + its argument if the : or = form is used enum class TokenType { Option, Argument }; struct Token { TokenType type; std::string token; }; inline auto isOptPrefix( char c ) -> bool { return c == '-' #ifdef CATCH_PLATFORM_WINDOWS || c == '/' #endif ; } // Abstracts iterators into args as a stream of tokens, with option arguments uniformly handled class TokenStream { using Iterator = std::vector::const_iterator; Iterator it; Iterator itEnd; std::vector m_tokenBuffer; void loadBuffer() { m_tokenBuffer.resize( 0 ); // Skip any empty strings while( it != itEnd && it->empty() ) ++it; if( it != itEnd ) { auto const &next = *it; if( isOptPrefix( next[0] ) ) { auto delimiterPos = next.find_first_of( " :=" ); if( delimiterPos != std::string::npos ) { m_tokenBuffer.push_back( { TokenType::Option, next.substr( 0, delimiterPos ) } ); m_tokenBuffer.push_back( { TokenType::Argument, next.substr( delimiterPos + 1 ) } ); } else { if( next[1] != '-' && next.size() > 2 ) { std::string opt = "- "; for( size_t i = 1; i < next.size(); ++i ) { opt[1] = next[i]; m_tokenBuffer.push_back( { TokenType::Option, opt } ); } } else { m_tokenBuffer.push_back( { TokenType::Option, next } ); } } } else { m_tokenBuffer.push_back( { TokenType::Argument, next } ); } } } public: explicit TokenStream( Args const &args ) : TokenStream( args.m_args.begin(), args.m_args.end() ) {} TokenStream( Iterator it, Iterator itEnd ) : it( it ), itEnd( itEnd ) { loadBuffer(); } explicit operator bool() const { return !m_tokenBuffer.empty() || it != itEnd; } auto count() const -> size_t { return m_tokenBuffer.size() + (itEnd - it); } auto operator*() const -> Token { assert( !m_tokenBuffer.empty() ); return m_tokenBuffer.front(); } auto operator->() const -> Token const * { assert( !m_tokenBuffer.empty() ); return &m_tokenBuffer.front(); } auto operator++() -> TokenStream & { if( m_tokenBuffer.size() >= 2 ) { m_tokenBuffer.erase( m_tokenBuffer.begin() ); } else { if( it != itEnd ) ++it; loadBuffer(); } return *this; } }; class ResultBase { public: enum Type { Ok, LogicError, RuntimeError }; protected: ResultBase( Type type ) : m_type( type ) {} virtual ~ResultBase() = default; virtual void enforceOk() const = 0; Type m_type; }; template class ResultValueBase : public ResultBase { public: auto value() const -> T const & { enforceOk(); return m_value; } protected: ResultValueBase( Type type ) : ResultBase( type ) {} ResultValueBase( ResultValueBase const &other ) : ResultBase( other ) { if( m_type == ResultBase::Ok ) new( &m_value ) T( other.m_value ); } ResultValueBase( Type, T const &value ) : ResultBase( Ok ) { new( &m_value ) T( value ); } auto operator=( ResultValueBase const &other ) -> ResultValueBase & { if( m_type == ResultBase::Ok ) m_value.~T(); ResultBase::operator=(other); if( m_type == ResultBase::Ok ) new( &m_value ) T( other.m_value ); return *this; } ~ResultValueBase() override { if( m_type == Ok ) m_value.~T(); } union { T m_value; }; }; template<> class ResultValueBase : public ResultBase { protected: using ResultBase::ResultBase; }; template class BasicResult : public ResultValueBase { public: template explicit BasicResult( BasicResult const &other ) : ResultValueBase( other.type() ), m_errorMessage( other.errorMessage() ) { assert( type() != ResultBase::Ok ); } template static auto ok( U const &value ) -> BasicResult { return { ResultBase::Ok, value }; } static auto ok() -> BasicResult { return { ResultBase::Ok }; } static auto logicError( std::string const &message ) -> BasicResult { return { ResultBase::LogicError, message }; } static auto runtimeError( std::string const &message ) -> BasicResult { return { ResultBase::RuntimeError, message }; } explicit operator bool() const { return m_type == ResultBase::Ok; } auto type() const -> ResultBase::Type { return m_type; } auto errorMessage() const -> std::string { return m_errorMessage; } protected: void enforceOk() const override { // Errors shouldn't reach this point, but if they do // the actual error message will be in m_errorMessage assert( m_type != ResultBase::LogicError ); assert( m_type != ResultBase::RuntimeError ); if( m_type != ResultBase::Ok ) std::abort(); } std::string m_errorMessage; // Only populated if resultType is an error BasicResult( ResultBase::Type type, std::string const &message ) : ResultValueBase(type), m_errorMessage(message) { assert( m_type != ResultBase::Ok ); } using ResultValueBase::ResultValueBase; using ResultBase::m_type; }; enum class ParseResultType { Matched, NoMatch, ShortCircuitAll, ShortCircuitSame }; class ParseState { public: ParseState( ParseResultType type, TokenStream const &remainingTokens ) : m_type(type), m_remainingTokens( remainingTokens ) {} auto type() const -> ParseResultType { return m_type; } auto remainingTokens() const -> TokenStream { return m_remainingTokens; } private: ParseResultType m_type; TokenStream m_remainingTokens; }; using Result = BasicResult; using ParserResult = BasicResult; using InternalParseResult = BasicResult; struct HelpColumns { std::string left; std::string right; }; template inline auto convertInto( std::string const &source, T& target ) -> ParserResult { std::stringstream ss; ss << source; ss >> target; if( ss.fail() ) return ParserResult::runtimeError( "Unable to convert '" + source + "' to destination type" ); else return ParserResult::ok( ParseResultType::Matched ); } inline auto convertInto( std::string const &source, std::string& target ) -> ParserResult { target = source; return ParserResult::ok( ParseResultType::Matched ); } inline auto convertInto( std::string const &source, bool &target ) -> ParserResult { std::string srcLC = source; std::transform( srcLC.begin(), srcLC.end(), srcLC.begin(), []( char c ) { return static_cast( ::tolower(c) ); } ); if (srcLC == "y" || srcLC == "1" || srcLC == "true" || srcLC == "yes" || srcLC == "on") target = true; else if (srcLC == "n" || srcLC == "0" || srcLC == "false" || srcLC == "no" || srcLC == "off") target = false; else return ParserResult::runtimeError( "Expected a boolean value but did not recognise: '" + source + "'" ); return ParserResult::ok( ParseResultType::Matched ); } #ifdef CLARA_CONFIG_OPTIONAL_TYPE template inline auto convertInto( std::string const &source, CLARA_CONFIG_OPTIONAL_TYPE& target ) -> ParserResult { T temp; auto result = convertInto( source, temp ); if( result ) target = std::move(temp); return result; } #endif // CLARA_CONFIG_OPTIONAL_TYPE struct NonCopyable { NonCopyable() = default; NonCopyable( NonCopyable const & ) = delete; NonCopyable( NonCopyable && ) = delete; NonCopyable &operator=( NonCopyable const & ) = delete; NonCopyable &operator=( NonCopyable && ) = delete; }; struct BoundRef : NonCopyable { virtual ~BoundRef() = default; virtual auto isContainer() const -> bool { return false; } virtual auto isFlag() const -> bool { return false; } }; struct BoundValueRefBase : BoundRef { virtual auto setValue( std::string const &arg ) -> ParserResult = 0; }; struct BoundFlagRefBase : BoundRef { virtual auto setFlag( bool flag ) -> ParserResult = 0; virtual auto isFlag() const -> bool { return true; } }; template struct BoundValueRef : BoundValueRefBase { T &m_ref; explicit BoundValueRef( T &ref ) : m_ref( ref ) {} auto setValue( std::string const &arg ) -> ParserResult override { return convertInto( arg, m_ref ); } }; template struct BoundValueRef> : BoundValueRefBase { std::vector &m_ref; explicit BoundValueRef( std::vector &ref ) : m_ref( ref ) {} auto isContainer() const -> bool override { return true; } auto setValue( std::string const &arg ) -> ParserResult override { T temp; auto result = convertInto( arg, temp ); if( result ) m_ref.push_back( temp ); return result; } }; struct BoundFlagRef : BoundFlagRefBase { bool &m_ref; explicit BoundFlagRef( bool &ref ) : m_ref( ref ) {} auto setFlag( bool flag ) -> ParserResult override { m_ref = flag; return ParserResult::ok( ParseResultType::Matched ); } }; template struct LambdaInvoker { static_assert( std::is_same::value, "Lambda must return void or clara::ParserResult" ); template static auto invoke( L const &lambda, ArgType const &arg ) -> ParserResult { return lambda( arg ); } }; template<> struct LambdaInvoker { template static auto invoke( L const &lambda, ArgType const &arg ) -> ParserResult { lambda( arg ); return ParserResult::ok( ParseResultType::Matched ); } }; template inline auto invokeLambda( L const &lambda, std::string const &arg ) -> ParserResult { ArgType temp{}; auto result = convertInto( arg, temp ); return !result ? result : LambdaInvoker::ReturnType>::invoke( lambda, temp ); } template struct BoundLambda : BoundValueRefBase { L m_lambda; static_assert( UnaryLambdaTraits::isValid, "Supplied lambda must take exactly one argument" ); explicit BoundLambda( L const &lambda ) : m_lambda( lambda ) {} auto setValue( std::string const &arg ) -> ParserResult override { return invokeLambda::ArgType>( m_lambda, arg ); } }; template struct BoundFlagLambda : BoundFlagRefBase { L m_lambda; static_assert( UnaryLambdaTraits::isValid, "Supplied lambda must take exactly one argument" ); static_assert( std::is_same::ArgType, bool>::value, "flags must be boolean" ); explicit BoundFlagLambda( L const &lambda ) : m_lambda( lambda ) {} auto setFlag( bool flag ) -> ParserResult override { return LambdaInvoker::ReturnType>::invoke( m_lambda, flag ); } }; enum class Optionality { Optional, Required }; struct Parser; class ParserBase { public: virtual ~ParserBase() = default; virtual auto validate() const -> Result { return Result::ok(); } virtual auto parse( std::string const& exeName, TokenStream const &tokens) const -> InternalParseResult = 0; virtual auto cardinality() const -> size_t { return 1; } auto parse( Args const &args ) const -> InternalParseResult { return parse( args.exeName(), TokenStream( args ) ); } }; template class ComposableParserImpl : public ParserBase { public: template auto operator|( T const &other ) const -> Parser; template auto operator+( T const &other ) const -> Parser; }; // Common code and state for Args and Opts template class ParserRefImpl : public ComposableParserImpl { protected: Optionality m_optionality = Optionality::Optional; std::shared_ptr m_ref; std::string m_hint; std::string m_description; explicit ParserRefImpl( std::shared_ptr const &ref ) : m_ref( ref ) {} public: template ParserRefImpl( T &ref, std::string const &hint ) : m_ref( std::make_shared>( ref ) ), m_hint( hint ) {} template ParserRefImpl( LambdaT const &ref, std::string const &hint ) : m_ref( std::make_shared>( ref ) ), m_hint(hint) {} auto operator()( std::string const &description ) -> DerivedT & { m_description = description; return static_cast( *this ); } auto optional() -> DerivedT & { m_optionality = Optionality::Optional; return static_cast( *this ); }; auto required() -> DerivedT & { m_optionality = Optionality::Required; return static_cast( *this ); }; auto isOptional() const -> bool { return m_optionality == Optionality::Optional; } auto cardinality() const -> size_t override { if( m_ref->isContainer() ) return 0; else return 1; } auto hint() const -> std::string { return m_hint; } }; class ExeName : public ComposableParserImpl { std::shared_ptr m_name; std::shared_ptr m_ref; template static auto makeRef(LambdaT const &lambda) -> std::shared_ptr { return std::make_shared>( lambda) ; } public: ExeName() : m_name( std::make_shared( "" ) ) {} explicit ExeName( std::string &ref ) : ExeName() { m_ref = std::make_shared>( ref ); } template explicit ExeName( LambdaT const& lambda ) : ExeName() { m_ref = std::make_shared>( lambda ); } // The exe name is not parsed out of the normal tokens, but is handled specially auto parse( std::string const&, TokenStream const &tokens ) const -> InternalParseResult override { return InternalParseResult::ok( ParseState( ParseResultType::NoMatch, tokens ) ); } auto name() const -> std::string { return *m_name; } auto set( std::string const& newName ) -> ParserResult { auto lastSlash = newName.find_last_of( "\\/" ); auto filename = ( lastSlash == std::string::npos ) ? newName : newName.substr( lastSlash+1 ); *m_name = filename; if( m_ref ) return m_ref->setValue( filename ); else return ParserResult::ok( ParseResultType::Matched ); } }; class Arg : public ParserRefImpl { public: using ParserRefImpl::ParserRefImpl; auto parse( std::string const &, TokenStream const &tokens ) const -> InternalParseResult override { auto validationResult = validate(); if( !validationResult ) return InternalParseResult( validationResult ); auto remainingTokens = tokens; auto const &token = *remainingTokens; if( token.type != TokenType::Argument ) return InternalParseResult::ok( ParseState( ParseResultType::NoMatch, remainingTokens ) ); assert( !m_ref->isFlag() ); auto valueRef = static_cast( m_ref.get() ); auto result = valueRef->setValue( remainingTokens->token ); if( !result ) return InternalParseResult( result ); else return InternalParseResult::ok( ParseState( ParseResultType::Matched, ++remainingTokens ) ); } }; inline auto normaliseOpt( std::string const &optName ) -> std::string { #ifdef CATCH_PLATFORM_WINDOWS if( optName[0] == '/' ) return "-" + optName.substr( 1 ); else #endif return optName; } class Opt : public ParserRefImpl { protected: std::vector m_optNames; public: template explicit Opt( LambdaT const &ref ) : ParserRefImpl( std::make_shared>( ref ) ) {} explicit Opt( bool &ref ) : ParserRefImpl( std::make_shared( ref ) ) {} template Opt( LambdaT const &ref, std::string const &hint ) : ParserRefImpl( ref, hint ) {} template Opt( T &ref, std::string const &hint ) : ParserRefImpl( ref, hint ) {} auto operator[]( std::string const &optName ) -> Opt & { m_optNames.push_back( optName ); return *this; } auto getHelpColumns() const -> std::vector { std::ostringstream oss; bool first = true; for( auto const &opt : m_optNames ) { if (first) first = false; else oss << ", "; oss << opt; } if( !m_hint.empty() ) oss << " <" << m_hint << ">"; return { { oss.str(), m_description } }; } auto isMatch( std::string const &optToken ) const -> bool { auto normalisedToken = normaliseOpt( optToken ); for( auto const &name : m_optNames ) { if( normaliseOpt( name ) == normalisedToken ) return true; } return false; } using ParserBase::parse; auto parse( std::string const&, TokenStream const &tokens ) const -> InternalParseResult override { auto validationResult = validate(); if( !validationResult ) return InternalParseResult( validationResult ); auto remainingTokens = tokens; if( remainingTokens && remainingTokens->type == TokenType::Option ) { auto const &token = *remainingTokens; if( isMatch(token.token ) ) { if( m_ref->isFlag() ) { auto flagRef = static_cast( m_ref.get() ); auto result = flagRef->setFlag( true ); if( !result ) return InternalParseResult( result ); if( result.value() == ParseResultType::ShortCircuitAll ) return InternalParseResult::ok( ParseState( result.value(), remainingTokens ) ); } else { auto valueRef = static_cast( m_ref.get() ); ++remainingTokens; if( !remainingTokens ) return InternalParseResult::runtimeError( "Expected argument following " + token.token ); auto const &argToken = *remainingTokens; if( argToken.type != TokenType::Argument ) return InternalParseResult::runtimeError( "Expected argument following " + token.token ); auto result = valueRef->setValue( argToken.token ); if( !result ) return InternalParseResult( result ); if( result.value() == ParseResultType::ShortCircuitAll ) return InternalParseResult::ok( ParseState( result.value(), remainingTokens ) ); } return InternalParseResult::ok( ParseState( ParseResultType::Matched, ++remainingTokens ) ); } } return InternalParseResult::ok( ParseState( ParseResultType::NoMatch, remainingTokens ) ); } auto validate() const -> Result override { if( m_optNames.empty() ) return Result::logicError( "No options supplied to Opt" ); for( auto const &name : m_optNames ) { if( name.empty() ) return Result::logicError( "Option name cannot be empty" ); #ifdef CATCH_PLATFORM_WINDOWS if( name[0] != '-' && name[0] != '/' ) return Result::logicError( "Option name must begin with '-' or '/'" ); #else if( name[0] != '-' ) return Result::logicError( "Option name must begin with '-'" ); #endif } return ParserRefImpl::validate(); } }; struct Help : Opt { Help( bool &showHelpFlag ) : Opt([&]( bool flag ) { showHelpFlag = flag; return ParserResult::ok( ParseResultType::ShortCircuitAll ); }) { static_cast( *this ) ("display usage information") ["-?"]["-h"]["--help"] .optional(); } }; struct Parser : ParserBase { mutable ExeName m_exeName; std::vector m_options; std::vector m_args; auto operator|=( ExeName const &exeName ) -> Parser & { m_exeName = exeName; return *this; } auto operator|=( Arg const &arg ) -> Parser & { m_args.push_back(arg); return *this; } auto operator|=( Opt const &opt ) -> Parser & { m_options.push_back(opt); return *this; } auto operator|=( Parser const &other ) -> Parser & { m_options.insert(m_options.end(), other.m_options.begin(), other.m_options.end()); m_args.insert(m_args.end(), other.m_args.begin(), other.m_args.end()); return *this; } template auto operator|( T const &other ) const -> Parser { return Parser( *this ) |= other; } // Forward deprecated interface with '+' instead of '|' template auto operator+=( T const &other ) -> Parser & { return operator|=( other ); } template auto operator+( T const &other ) const -> Parser { return operator|( other ); } auto getHelpColumns() const -> std::vector { std::vector cols; for (auto const &o : m_options) { auto childCols = o.getHelpColumns(); cols.insert( cols.end(), childCols.begin(), childCols.end() ); } return cols; } void writeToStream( std::ostream &os ) const { if (!m_exeName.name().empty()) { os << "usage:\n" << " " << m_exeName.name() << " "; bool required = true, first = true; for( auto const &arg : m_args ) { if (first) first = false; else os << " "; if( arg.isOptional() && required ) { os << "["; required = false; } os << "<" << arg.hint() << ">"; if( arg.cardinality() == 0 ) os << " ... "; } if( !required ) os << "]"; if( !m_options.empty() ) os << " options"; os << "\n\nwhere options are:" << std::endl; } auto rows = getHelpColumns(); size_t consoleWidth = CATCH_CLARA_CONFIG_CONSOLE_WIDTH; size_t optWidth = 0; for( auto const &cols : rows ) optWidth = (std::max)(optWidth, cols.left.size() + 2); optWidth = (std::min)(optWidth, consoleWidth/2); for( auto const &cols : rows ) { auto row = TextFlow::Column( cols.left ).width( optWidth ).indent( 2 ) + TextFlow::Spacer(4) + TextFlow::Column( cols.right ).width( consoleWidth - 7 - optWidth ); os << row << std::endl; } } friend auto operator<<( std::ostream &os, Parser const &parser ) -> std::ostream& { parser.writeToStream( os ); return os; } auto validate() const -> Result override { for( auto const &opt : m_options ) { auto result = opt.validate(); if( !result ) return result; } for( auto const &arg : m_args ) { auto result = arg.validate(); if( !result ) return result; } return Result::ok(); } using ParserBase::parse; auto parse( std::string const& exeName, TokenStream const &tokens ) const -> InternalParseResult override { struct ParserInfo { ParserBase const* parser = nullptr; size_t count = 0; }; const size_t totalParsers = m_options.size() + m_args.size(); assert( totalParsers < 512 ); // ParserInfo parseInfos[totalParsers]; // <-- this is what we really want to do ParserInfo parseInfos[512]; { size_t i = 0; for (auto const &opt : m_options) parseInfos[i++].parser = &opt; for (auto const &arg : m_args) parseInfos[i++].parser = &arg; } m_exeName.set( exeName ); auto result = InternalParseResult::ok( ParseState( ParseResultType::NoMatch, tokens ) ); while( result.value().remainingTokens() ) { bool tokenParsed = false; for( size_t i = 0; i < totalParsers; ++i ) { auto& parseInfo = parseInfos[i]; if( parseInfo.parser->cardinality() == 0 || parseInfo.count < parseInfo.parser->cardinality() ) { result = parseInfo.parser->parse(exeName, result.value().remainingTokens()); if (!result) return result; if (result.value().type() != ParseResultType::NoMatch) { tokenParsed = true; ++parseInfo.count; break; } } } if( result.value().type() == ParseResultType::ShortCircuitAll ) return result; if( !tokenParsed ) return InternalParseResult::runtimeError( "Unrecognised token: " + result.value().remainingTokens()->token ); } // !TBD Check missing required options return result; } }; template template auto ComposableParserImpl::operator|( T const &other ) const -> Parser { return Parser() | static_cast( *this ) | other; } } // namespace detail // A Combined parser using detail::Parser; // A parser for options using detail::Opt; // A parser for arguments using detail::Arg; // Wrapper for argc, argv from main() using detail::Args; // Specifies the name of the executable using detail::ExeName; // Convenience wrapper for option parser that specifies the help option using detail::Help; // enum of result types from a parse using detail::ParseResultType; // Result type for parser operation using detail::ParserResult; }} // namespace Catch::clara // end clara.hpp #ifdef __clang__ #pragma clang diagnostic pop #endif // Restore Clara's value for console width, if present #ifdef CATCH_TEMP_CLARA_CONFIG_CONSOLE_WIDTH #define CATCH_CLARA_TEXTFLOW_CONFIG_CONSOLE_WIDTH CATCH_TEMP_CLARA_CONFIG_CONSOLE_WIDTH #undef CATCH_TEMP_CLARA_CONFIG_CONSOLE_WIDTH #endif // end catch_clara.h namespace Catch { clara::Parser makeCommandLineParser( ConfigData& config ); } // end namespace Catch // end catch_commandline.h #include #include namespace Catch { clara::Parser makeCommandLineParser( ConfigData& config ) { using namespace clara; auto const setWarning = [&]( std::string const& warning ) { auto warningSet = [&]() { if( warning == "NoAssertions" ) return WarnAbout::NoAssertions; if ( warning == "NoTests" ) return WarnAbout::NoTests; return WarnAbout::Nothing; }(); if (warningSet == WarnAbout::Nothing) return ParserResult::runtimeError( "Unrecognised warning: '" + warning + "'" ); config.warnings = static_cast( config.warnings | warningSet ); return ParserResult::ok( ParseResultType::Matched ); }; auto const loadTestNamesFromFile = [&]( std::string const& filename ) { std::ifstream f( filename.c_str() ); if( !f.is_open() ) return ParserResult::runtimeError( "Unable to load input file: '" + filename + "'" ); std::string line; while( std::getline( f, line ) ) { line = trim(line); if( !line.empty() && !startsWith( line, '#' ) ) { if( !startsWith( line, '"' ) ) line = '"' + line + '"'; config.testsOrTags.push_back( line + ',' ); } } return ParserResult::ok( ParseResultType::Matched ); }; auto const setTestOrder = [&]( std::string const& order ) { if( startsWith( "declared", order ) ) config.runOrder = RunTests::InDeclarationOrder; else if( startsWith( "lexical", order ) ) config.runOrder = RunTests::InLexicographicalOrder; else if( startsWith( "random", order ) ) config.runOrder = RunTests::InRandomOrder; else return clara::ParserResult::runtimeError( "Unrecognised ordering: '" + order + "'" ); return ParserResult::ok( ParseResultType::Matched ); }; auto const setRngSeed = [&]( std::string const& seed ) { if( seed != "time" ) return clara::detail::convertInto( seed, config.rngSeed ); config.rngSeed = static_cast( std::time(nullptr) ); return ParserResult::ok( ParseResultType::Matched ); }; auto const setColourUsage = [&]( std::string const& useColour ) { auto mode = toLower( useColour ); if( mode == "yes" ) config.useColour = UseColour::Yes; else if( mode == "no" ) config.useColour = UseColour::No; else if( mode == "auto" ) config.useColour = UseColour::Auto; else return ParserResult::runtimeError( "colour mode must be one of: auto, yes or no. '" + useColour + "' not recognised" ); return ParserResult::ok( ParseResultType::Matched ); }; auto const setWaitForKeypress = [&]( std::string const& keypress ) { auto keypressLc = toLower( keypress ); if( keypressLc == "start" ) config.waitForKeypress = WaitForKeypress::BeforeStart; else if( keypressLc == "exit" ) config.waitForKeypress = WaitForKeypress::BeforeExit; else if( keypressLc == "both" ) config.waitForKeypress = WaitForKeypress::BeforeStartAndExit; else return ParserResult::runtimeError( "keypress argument must be one of: start, exit or both. '" + keypress + "' not recognised" ); return ParserResult::ok( ParseResultType::Matched ); }; auto const setVerbosity = [&]( std::string const& verbosity ) { auto lcVerbosity = toLower( verbosity ); if( lcVerbosity == "quiet" ) config.verbosity = Verbosity::Quiet; else if( lcVerbosity == "normal" ) config.verbosity = Verbosity::Normal; else if( lcVerbosity == "high" ) config.verbosity = Verbosity::High; else return ParserResult::runtimeError( "Unrecognised verbosity, '" + verbosity + "'" ); return ParserResult::ok( ParseResultType::Matched ); }; auto const setReporter = [&]( std::string const& reporter ) { IReporterRegistry::FactoryMap const& factories = getRegistryHub().getReporterRegistry().getFactories(); auto lcReporter = toLower( reporter ); auto result = factories.find( lcReporter ); if( factories.end() != result ) config.reporterName = lcReporter; else return ParserResult::runtimeError( "Unrecognized reporter, '" + reporter + "'. Check available with --list-reporters" ); return ParserResult::ok( ParseResultType::Matched ); }; auto cli = ExeName( config.processName ) | Help( config.showHelp ) | Opt( config.listTests ) ["-l"]["--list-tests"] ( "list all/matching test cases" ) | Opt( config.listTags ) ["-t"]["--list-tags"] ( "list all/matching tags" ) | Opt( config.showSuccessfulTests ) ["-s"]["--success"] ( "include successful tests in output" ) | Opt( config.shouldDebugBreak ) ["-b"]["--break"] ( "break into debugger on failure" ) | Opt( config.noThrow ) ["-e"]["--nothrow"] ( "skip exception tests" ) | Opt( config.showInvisibles ) ["-i"]["--invisibles"] ( "show invisibles (tabs, newlines)" ) | Opt( config.outputFilename, "filename" ) ["-o"]["--out"] ( "output filename" ) | Opt( setReporter, "name" ) ["-r"]["--reporter"] ( "reporter to use (defaults to console)" ) | Opt( config.name, "name" ) ["-n"]["--name"] ( "suite name" ) | Opt( [&]( bool ){ config.abortAfter = 1; } ) ["-a"]["--abort"] ( "abort at first failure" ) | Opt( [&]( int x ){ config.abortAfter = x; }, "no. failures" ) ["-x"]["--abortx"] ( "abort after x failures" ) | Opt( setWarning, "warning name" ) ["-w"]["--warn"] ( "enable warnings" ) | Opt( [&]( bool flag ) { config.showDurations = flag ? ShowDurations::Always : ShowDurations::Never; }, "yes|no" ) ["-d"]["--durations"] ( "show test durations" ) | Opt( loadTestNamesFromFile, "filename" ) ["-f"]["--input-file"] ( "load test names to run from a file" ) | Opt( config.filenamesAsTags ) ["-#"]["--filenames-as-tags"] ( "adds a tag for the filename" ) | Opt( config.sectionsToRun, "section name" ) ["-c"]["--section"] ( "specify section to run" ) | Opt( setVerbosity, "quiet|normal|high" ) ["-v"]["--verbosity"] ( "set output verbosity" ) | Opt( config.listTestNamesOnly ) ["--list-test-names-only"] ( "list all/matching test cases names only" ) | Opt( config.listReporters ) ["--list-reporters"] ( "list all reporters" ) | Opt( setTestOrder, "decl|lex|rand" ) ["--order"] ( "test case order (defaults to decl)" ) | Opt( setRngSeed, "'time'|number" ) ["--rng-seed"] ( "set a specific seed for random numbers" ) | Opt( setColourUsage, "yes|no" ) ["--use-colour"] ( "should output be colourised" ) | Opt( config.libIdentify ) ["--libidentify"] ( "report name and version according to libidentify standard" ) | Opt( setWaitForKeypress, "start|exit|both" ) ["--wait-for-keypress"] ( "waits for a keypress before exiting" ) | Opt( config.benchmarkResolutionMultiple, "multiplier" ) ["--benchmark-resolution-multiple"] ( "multiple of clock resolution to run benchmarks" ) | Arg( config.testsOrTags, "test name|pattern|tags" ) ( "which test or tests to use" ); return cli; } } // end namespace Catch // end catch_commandline.cpp // start catch_common.cpp #include #include namespace Catch { bool SourceLineInfo::empty() const noexcept { return file[0] == '\0'; } bool SourceLineInfo::operator == ( SourceLineInfo const& other ) const noexcept { return line == other.line && (file == other.file || std::strcmp(file, other.file) == 0); } bool SourceLineInfo::operator < ( SourceLineInfo const& other ) const noexcept { // We can assume that the same file will usually have the same pointer. // Thus, if the pointers are the same, there is no point in calling the strcmp return line < other.line || ( line == other.line && file != other.file && (std::strcmp(file, other.file) < 0)); } std::ostream& operator << ( std::ostream& os, SourceLineInfo const& info ) { #ifndef __GNUG__ os << info.file << '(' << info.line << ')'; #else os << info.file << ':' << info.line; #endif return os; } std::string StreamEndStop::operator+() const { return std::string(); } NonCopyable::NonCopyable() = default; NonCopyable::~NonCopyable() = default; } // end catch_common.cpp // start catch_config.cpp namespace Catch { Config::Config( ConfigData const& data ) : m_data( data ), m_stream( openStream() ) { TestSpecParser parser(ITagAliasRegistry::get()); if (data.testsOrTags.empty()) { parser.parse("~[.]"); // All not hidden tests } else { m_hasTestFilters = true; for( auto const& testOrTags : data.testsOrTags ) parser.parse( testOrTags ); } m_testSpec = parser.testSpec(); } std::string const& Config::getFilename() const { return m_data.outputFilename ; } bool Config::listTests() const { return m_data.listTests; } bool Config::listTestNamesOnly() const { return m_data.listTestNamesOnly; } bool Config::listTags() const { return m_data.listTags; } bool Config::listReporters() const { return m_data.listReporters; } std::string Config::getProcessName() const { return m_data.processName; } std::string const& Config::getReporterName() const { return m_data.reporterName; } std::vector const& Config::getTestsOrTags() const { return m_data.testsOrTags; } std::vector const& Config::getSectionsToRun() const { return m_data.sectionsToRun; } TestSpec const& Config::testSpec() const { return m_testSpec; } bool Config::hasTestFilters() const { return m_hasTestFilters; } bool Config::showHelp() const { return m_data.showHelp; } // IConfig interface bool Config::allowThrows() const { return !m_data.noThrow; } std::ostream& Config::stream() const { return m_stream->stream(); } std::string Config::name() const { return m_data.name.empty() ? m_data.processName : m_data.name; } bool Config::includeSuccessfulResults() const { return m_data.showSuccessfulTests; } bool Config::warnAboutMissingAssertions() const { return !!(m_data.warnings & WarnAbout::NoAssertions); } bool Config::warnAboutNoTests() const { return !!(m_data.warnings & WarnAbout::NoTests); } ShowDurations::OrNot Config::showDurations() const { return m_data.showDurations; } RunTests::InWhatOrder Config::runOrder() const { return m_data.runOrder; } unsigned int Config::rngSeed() const { return m_data.rngSeed; } int Config::benchmarkResolutionMultiple() const { return m_data.benchmarkResolutionMultiple; } UseColour::YesOrNo Config::useColour() const { return m_data.useColour; } bool Config::shouldDebugBreak() const { return m_data.shouldDebugBreak; } int Config::abortAfter() const { return m_data.abortAfter; } bool Config::showInvisibles() const { return m_data.showInvisibles; } Verbosity Config::verbosity() const { return m_data.verbosity; } IStream const* Config::openStream() { return Catch::makeStream(m_data.outputFilename); } } // end namespace Catch // end catch_config.cpp // start catch_console_colour.cpp #if defined(__clang__) # pragma clang diagnostic push # pragma clang diagnostic ignored "-Wexit-time-destructors" #endif // start catch_errno_guard.h namespace Catch { class ErrnoGuard { public: ErrnoGuard(); ~ErrnoGuard(); private: int m_oldErrno; }; } // end catch_errno_guard.h #include namespace Catch { namespace { struct IColourImpl { virtual ~IColourImpl() = default; virtual void use( Colour::Code _colourCode ) = 0; }; struct NoColourImpl : IColourImpl { void use( Colour::Code ) {} static IColourImpl* instance() { static NoColourImpl s_instance; return &s_instance; } }; } // anon namespace } // namespace Catch #if !defined( CATCH_CONFIG_COLOUR_NONE ) && !defined( CATCH_CONFIG_COLOUR_WINDOWS ) && !defined( CATCH_CONFIG_COLOUR_ANSI ) # ifdef CATCH_PLATFORM_WINDOWS # define CATCH_CONFIG_COLOUR_WINDOWS # else # define CATCH_CONFIG_COLOUR_ANSI # endif #endif #if defined ( CATCH_CONFIG_COLOUR_WINDOWS ) ///////////////////////////////////////// namespace Catch { namespace { class Win32ColourImpl : public IColourImpl { public: Win32ColourImpl() : stdoutHandle( GetStdHandle(STD_OUTPUT_HANDLE) ) { CONSOLE_SCREEN_BUFFER_INFO csbiInfo; GetConsoleScreenBufferInfo( stdoutHandle, &csbiInfo ); originalForegroundAttributes = csbiInfo.wAttributes & ~( BACKGROUND_GREEN | BACKGROUND_RED | BACKGROUND_BLUE | BACKGROUND_INTENSITY ); originalBackgroundAttributes = csbiInfo.wAttributes & ~( FOREGROUND_GREEN | FOREGROUND_RED | FOREGROUND_BLUE | FOREGROUND_INTENSITY ); } virtual void use( Colour::Code _colourCode ) override { switch( _colourCode ) { case Colour::None: return setTextAttribute( originalForegroundAttributes ); case Colour::White: return setTextAttribute( FOREGROUND_GREEN | FOREGROUND_RED | FOREGROUND_BLUE ); case Colour::Red: return setTextAttribute( FOREGROUND_RED ); case Colour::Green: return setTextAttribute( FOREGROUND_GREEN ); case Colour::Blue: return setTextAttribute( FOREGROUND_BLUE ); case Colour::Cyan: return setTextAttribute( FOREGROUND_BLUE | FOREGROUND_GREEN ); case Colour::Yellow: return setTextAttribute( FOREGROUND_RED | FOREGROUND_GREEN ); case Colour::Grey: return setTextAttribute( 0 ); case Colour::LightGrey: return setTextAttribute( FOREGROUND_INTENSITY ); case Colour::BrightRed: return setTextAttribute( FOREGROUND_INTENSITY | FOREGROUND_RED ); case Colour::BrightGreen: return setTextAttribute( FOREGROUND_INTENSITY | FOREGROUND_GREEN ); case Colour::BrightWhite: return setTextAttribute( FOREGROUND_INTENSITY | FOREGROUND_GREEN | FOREGROUND_RED | FOREGROUND_BLUE ); case Colour::BrightYellow: return setTextAttribute( FOREGROUND_INTENSITY | FOREGROUND_RED | FOREGROUND_GREEN ); case Colour::Bright: CATCH_INTERNAL_ERROR( "not a colour" ); default: CATCH_ERROR( "Unknown colour requested" ); } } private: void setTextAttribute( WORD _textAttribute ) { SetConsoleTextAttribute( stdoutHandle, _textAttribute | originalBackgroundAttributes ); } HANDLE stdoutHandle; WORD originalForegroundAttributes; WORD originalBackgroundAttributes; }; IColourImpl* platformColourInstance() { static Win32ColourImpl s_instance; IConfigPtr config = getCurrentContext().getConfig(); UseColour::YesOrNo colourMode = config ? config->useColour() : UseColour::Auto; if( colourMode == UseColour::Auto ) colourMode = UseColour::Yes; return colourMode == UseColour::Yes ? &s_instance : NoColourImpl::instance(); } } // end anon namespace } // end namespace Catch #elif defined( CATCH_CONFIG_COLOUR_ANSI ) ////////////////////////////////////// #include namespace Catch { namespace { // use POSIX/ ANSI console terminal codes // Thanks to Adam Strzelecki for original contribution // (http://github.com/nanoant) // https://github.com/philsquared/Catch/pull/131 class PosixColourImpl : public IColourImpl { public: virtual void use( Colour::Code _colourCode ) override { switch( _colourCode ) { case Colour::None: case Colour::White: return setColour( "[0m" ); case Colour::Red: return setColour( "[0;31m" ); case Colour::Green: return setColour( "[0;32m" ); case Colour::Blue: return setColour( "[0;34m" ); case Colour::Cyan: return setColour( "[0;36m" ); case Colour::Yellow: return setColour( "[0;33m" ); case Colour::Grey: return setColour( "[1;30m" ); case Colour::LightGrey: return setColour( "[0;37m" ); case Colour::BrightRed: return setColour( "[1;31m" ); case Colour::BrightGreen: return setColour( "[1;32m" ); case Colour::BrightWhite: return setColour( "[1;37m" ); case Colour::BrightYellow: return setColour( "[1;33m" ); case Colour::Bright: CATCH_INTERNAL_ERROR( "not a colour" ); default: CATCH_INTERNAL_ERROR( "Unknown colour requested" ); } } static IColourImpl* instance() { static PosixColourImpl s_instance; return &s_instance; } private: void setColour( const char* _escapeCode ) { getCurrentContext().getConfig()->stream() << '\033' << _escapeCode; } }; bool useColourOnPlatform() { return #ifdef CATCH_PLATFORM_MAC !isDebuggerActive() && #endif #if !(defined(__DJGPP__) && defined(__STRICT_ANSI__)) isatty(STDOUT_FILENO) #else false #endif ; } IColourImpl* platformColourInstance() { ErrnoGuard guard; IConfigPtr config = getCurrentContext().getConfig(); UseColour::YesOrNo colourMode = config ? config->useColour() : UseColour::Auto; if( colourMode == UseColour::Auto ) colourMode = useColourOnPlatform() ? UseColour::Yes : UseColour::No; return colourMode == UseColour::Yes ? PosixColourImpl::instance() : NoColourImpl::instance(); } } // end anon namespace } // end namespace Catch #else // not Windows or ANSI /////////////////////////////////////////////// namespace Catch { static IColourImpl* platformColourInstance() { return NoColourImpl::instance(); } } // end namespace Catch #endif // Windows/ ANSI/ None namespace Catch { Colour::Colour( Code _colourCode ) { use( _colourCode ); } Colour::Colour( Colour&& rhs ) noexcept { m_moved = rhs.m_moved; rhs.m_moved = true; } Colour& Colour::operator=( Colour&& rhs ) noexcept { m_moved = rhs.m_moved; rhs.m_moved = true; return *this; } Colour::~Colour(){ if( !m_moved ) use( None ); } void Colour::use( Code _colourCode ) { static IColourImpl* impl = platformColourInstance(); impl->use( _colourCode ); } std::ostream& operator << ( std::ostream& os, Colour const& ) { return os; } } // end namespace Catch #if defined(__clang__) # pragma clang diagnostic pop #endif // end catch_console_colour.cpp // start catch_context.cpp namespace Catch { class Context : public IMutableContext, NonCopyable { public: // IContext virtual IResultCapture* getResultCapture() override { return m_resultCapture; } virtual IRunner* getRunner() override { return m_runner; } virtual IConfigPtr const& getConfig() const override { return m_config; } virtual ~Context() override; public: // IMutableContext virtual void setResultCapture( IResultCapture* resultCapture ) override { m_resultCapture = resultCapture; } virtual void setRunner( IRunner* runner ) override { m_runner = runner; } virtual void setConfig( IConfigPtr const& config ) override { m_config = config; } friend IMutableContext& getCurrentMutableContext(); private: IConfigPtr m_config; IRunner* m_runner = nullptr; IResultCapture* m_resultCapture = nullptr; }; IMutableContext *IMutableContext::currentContext = nullptr; void IMutableContext::createContext() { currentContext = new Context(); } void cleanUpContext() { delete IMutableContext::currentContext; IMutableContext::currentContext = nullptr; } IContext::~IContext() = default; IMutableContext::~IMutableContext() = default; Context::~Context() = default; } // end catch_context.cpp // start catch_debug_console.cpp // start catch_debug_console.h #include namespace Catch { void writeToDebugConsole( std::string const& text ); } // end catch_debug_console.h #ifdef CATCH_PLATFORM_WINDOWS namespace Catch { void writeToDebugConsole( std::string const& text ) { ::OutputDebugStringA( text.c_str() ); } } #else namespace Catch { void writeToDebugConsole( std::string const& text ) { // !TBD: Need a version for Mac/ XCode and other IDEs Catch::cout() << text; } } #endif // Platform // end catch_debug_console.cpp // start catch_debugger.cpp #ifdef CATCH_PLATFORM_MAC # include # include # include # include # include # include # include namespace Catch { // The following function is taken directly from the following technical note: // http://developer.apple.com/library/mac/#qa/qa2004/qa1361.html // Returns true if the current process is being debugged (either // running under the debugger or has a debugger attached post facto). bool isDebuggerActive(){ int mib[4]; struct kinfo_proc info; std::size_t size; // Initialize the flags so that, if sysctl fails for some bizarre // reason, we get a predictable result. info.kp_proc.p_flag = 0; // Initialize mib, which tells sysctl the info we want, in this case // we're looking for information about a specific process ID. mib[0] = CTL_KERN; mib[1] = KERN_PROC; mib[2] = KERN_PROC_PID; mib[3] = getpid(); // Call sysctl. size = sizeof(info); if( sysctl(mib, sizeof(mib) / sizeof(*mib), &info, &size, nullptr, 0) != 0 ) { Catch::cerr() << "\n** Call to sysctl failed - unable to determine if debugger is active **\n" << std::endl; return false; } // We're being debugged if the P_TRACED flag is set. return ( (info.kp_proc.p_flag & P_TRACED) != 0 ); } } // namespace Catch #elif defined(CATCH_PLATFORM_LINUX) #include #include namespace Catch{ // The standard POSIX way of detecting a debugger is to attempt to // ptrace() the process, but this needs to be done from a child and not // this process itself to still allow attaching to this process later // if wanted, so is rather heavy. Under Linux we have the PID of the // "debugger" (which doesn't need to be gdb, of course, it could also // be strace, for example) in /proc/$PID/status, so just get it from // there instead. bool isDebuggerActive(){ // Libstdc++ has a bug, where std::ifstream sets errno to 0 // This way our users can properly assert over errno values ErrnoGuard guard; std::ifstream in("/proc/self/status"); for( std::string line; std::getline(in, line); ) { static const int PREFIX_LEN = 11; if( line.compare(0, PREFIX_LEN, "TracerPid:\t") == 0 ) { // We're traced if the PID is not 0 and no other PID starts // with 0 digit, so it's enough to check for just a single // character. return line.length() > PREFIX_LEN && line[PREFIX_LEN] != '0'; } } return false; } } // namespace Catch #elif defined(_MSC_VER) extern "C" __declspec(dllimport) int __stdcall IsDebuggerPresent(); namespace Catch { bool isDebuggerActive() { return IsDebuggerPresent() != 0; } } #elif defined(__MINGW32__) extern "C" __declspec(dllimport) int __stdcall IsDebuggerPresent(); namespace Catch { bool isDebuggerActive() { return IsDebuggerPresent() != 0; } } #else namespace Catch { bool isDebuggerActive() { return false; } } #endif // Platform // end catch_debugger.cpp // start catch_decomposer.cpp namespace Catch { ITransientExpression::~ITransientExpression() = default; void formatReconstructedExpression( std::ostream &os, std::string const& lhs, StringRef op, std::string const& rhs ) { if( lhs.size() + rhs.size() < 40 && lhs.find('\n') == std::string::npos && rhs.find('\n') == std::string::npos ) os << lhs << " " << op << " " << rhs; else os << lhs << "\n" << op << "\n" << rhs; } } // end catch_decomposer.cpp // start catch_enforce.cpp namespace Catch { #if defined(CATCH_CONFIG_DISABLE_EXCEPTIONS) && !defined(CATCH_CONFIG_DISABLE_EXCEPTIONS_CUSTOM_HANDLER) [[noreturn]] void throw_exception(std::exception const& e) { Catch::cerr() << "Catch will terminate because it needed to throw an exception.\n" << "The message was: " << e.what() << '\n'; std::terminate(); } #endif } // namespace Catch; // end catch_enforce.cpp // start catch_errno_guard.cpp #include namespace Catch { ErrnoGuard::ErrnoGuard():m_oldErrno(errno){} ErrnoGuard::~ErrnoGuard() { errno = m_oldErrno; } } // end catch_errno_guard.cpp // start catch_exception_translator_registry.cpp // start catch_exception_translator_registry.h #include #include #include namespace Catch { class ExceptionTranslatorRegistry : public IExceptionTranslatorRegistry { public: ~ExceptionTranslatorRegistry(); virtual void registerTranslator( const IExceptionTranslator* translator ); virtual std::string translateActiveException() const override; std::string tryTranslators() const; private: std::vector> m_translators; }; } // end catch_exception_translator_registry.h #ifdef __OBJC__ #import "Foundation/Foundation.h" #endif namespace Catch { ExceptionTranslatorRegistry::~ExceptionTranslatorRegistry() { } void ExceptionTranslatorRegistry::registerTranslator( const IExceptionTranslator* translator ) { m_translators.push_back( std::unique_ptr( translator ) ); } #if !defined(CATCH_CONFIG_DISABLE_EXCEPTIONS) std::string ExceptionTranslatorRegistry::translateActiveException() const { try { #ifdef __OBJC__ // In Objective-C try objective-c exceptions first @try { return tryTranslators(); } @catch (NSException *exception) { return Catch::Detail::stringify( [exception description] ); } #else // Compiling a mixed mode project with MSVC means that CLR // exceptions will be caught in (...) as well. However, these // do not fill-in std::current_exception and thus lead to crash // when attempting rethrow. // /EHa switch also causes structured exceptions to be caught // here, but they fill-in current_exception properly, so // at worst the output should be a little weird, instead of // causing a crash. if (std::current_exception() == nullptr) { return "Non C++ exception. Possibly a CLR exception."; } return tryTranslators(); #endif } catch( TestFailureException& ) { std::rethrow_exception(std::current_exception()); } catch( std::exception& ex ) { return ex.what(); } catch( std::string& msg ) { return msg; } catch( const char* msg ) { return msg; } catch(...) { return "Unknown exception"; } } std::string ExceptionTranslatorRegistry::tryTranslators() const { if (m_translators.empty()) { std::rethrow_exception(std::current_exception()); } else { return m_translators[0]->translate(m_translators.begin() + 1, m_translators.end()); } } #else // ^^ Exceptions are enabled // Exceptions are disabled vv std::string ExceptionTranslatorRegistry::translateActiveException() const { CATCH_INTERNAL_ERROR("Attempted to translate active exception under CATCH_CONFIG_DISABLE_EXCEPTIONS!"); } std::string ExceptionTranslatorRegistry::tryTranslators() const { CATCH_INTERNAL_ERROR("Attempted to use exception translators under CATCH_CONFIG_DISABLE_EXCEPTIONS!"); } #endif } // end catch_exception_translator_registry.cpp // start catch_fatal_condition.cpp #if defined(__GNUC__) # pragma GCC diagnostic push # pragma GCC diagnostic ignored "-Wmissing-field-initializers" #endif #if defined( CATCH_CONFIG_WINDOWS_SEH ) || defined( CATCH_CONFIG_POSIX_SIGNALS ) namespace { // Report the error condition void reportFatal( char const * const message ) { Catch::getCurrentContext().getResultCapture()->handleFatalErrorCondition( message ); } } #endif // signals/SEH handling #if defined( CATCH_CONFIG_WINDOWS_SEH ) namespace Catch { struct SignalDefs { DWORD id; const char* name; }; // There is no 1-1 mapping between signals and windows exceptions. // Windows can easily distinguish between SO and SigSegV, // but SigInt, SigTerm, etc are handled differently. static SignalDefs signalDefs[] = { { EXCEPTION_ILLEGAL_INSTRUCTION, "SIGILL - Illegal instruction signal" }, { EXCEPTION_STACK_OVERFLOW, "SIGSEGV - Stack overflow" }, { EXCEPTION_ACCESS_VIOLATION, "SIGSEGV - Segmentation violation signal" }, { EXCEPTION_INT_DIVIDE_BY_ZERO, "Divide by zero error" }, }; LONG CALLBACK FatalConditionHandler::handleVectoredException(PEXCEPTION_POINTERS ExceptionInfo) { for (auto const& def : signalDefs) { if (ExceptionInfo->ExceptionRecord->ExceptionCode == def.id) { reportFatal(def.name); } } // If its not an exception we care about, pass it along. // This stops us from eating debugger breaks etc. return EXCEPTION_CONTINUE_SEARCH; } FatalConditionHandler::FatalConditionHandler() { isSet = true; // 32k seems enough for Catch to handle stack overflow, // but the value was found experimentally, so there is no strong guarantee guaranteeSize = 32 * 1024; exceptionHandlerHandle = nullptr; // Register as first handler in current chain exceptionHandlerHandle = AddVectoredExceptionHandler(1, handleVectoredException); // Pass in guarantee size to be filled SetThreadStackGuarantee(&guaranteeSize); } void FatalConditionHandler::reset() { if (isSet) { RemoveVectoredExceptionHandler(exceptionHandlerHandle); SetThreadStackGuarantee(&guaranteeSize); exceptionHandlerHandle = nullptr; isSet = false; } } FatalConditionHandler::~FatalConditionHandler() { reset(); } bool FatalConditionHandler::isSet = false; ULONG FatalConditionHandler::guaranteeSize = 0; PVOID FatalConditionHandler::exceptionHandlerHandle = nullptr; } // namespace Catch #elif defined( CATCH_CONFIG_POSIX_SIGNALS ) namespace Catch { struct SignalDefs { int id; const char* name; }; // 32kb for the alternate stack seems to be sufficient. However, this value // is experimentally determined, so that's not guaranteed. constexpr static std::size_t sigStackSize = 32768 >= MINSIGSTKSZ ? 32768 : MINSIGSTKSZ; static SignalDefs signalDefs[] = { { SIGINT, "SIGINT - Terminal interrupt signal" }, { SIGILL, "SIGILL - Illegal instruction signal" }, { SIGFPE, "SIGFPE - Floating point error signal" }, { SIGSEGV, "SIGSEGV - Segmentation violation signal" }, { SIGTERM, "SIGTERM - Termination request signal" }, { SIGABRT, "SIGABRT - Abort (abnormal termination) signal" } }; void FatalConditionHandler::handleSignal( int sig ) { char const * name = ""; for (auto const& def : signalDefs) { if (sig == def.id) { name = def.name; break; } } reset(); reportFatal(name); raise( sig ); } FatalConditionHandler::FatalConditionHandler() { isSet = true; stack_t sigStack; sigStack.ss_sp = altStackMem; sigStack.ss_size = sigStackSize; sigStack.ss_flags = 0; sigaltstack(&sigStack, &oldSigStack); struct sigaction sa = { }; sa.sa_handler = handleSignal; sa.sa_flags = SA_ONSTACK; for (std::size_t i = 0; i < sizeof(signalDefs)/sizeof(SignalDefs); ++i) { sigaction(signalDefs[i].id, &sa, &oldSigActions[i]); } } FatalConditionHandler::~FatalConditionHandler() { reset(); } void FatalConditionHandler::reset() { if( isSet ) { // Set signals back to previous values -- hopefully nobody overwrote them in the meantime for( std::size_t i = 0; i < sizeof(signalDefs)/sizeof(SignalDefs); ++i ) { sigaction(signalDefs[i].id, &oldSigActions[i], nullptr); } // Return the old stack sigaltstack(&oldSigStack, nullptr); isSet = false; } } bool FatalConditionHandler::isSet = false; struct sigaction FatalConditionHandler::oldSigActions[sizeof(signalDefs)/sizeof(SignalDefs)] = {}; stack_t FatalConditionHandler::oldSigStack = {}; char FatalConditionHandler::altStackMem[sigStackSize] = {}; } // namespace Catch #else namespace Catch { void FatalConditionHandler::reset() {} } #endif // signals/SEH handling #if defined(__GNUC__) # pragma GCC diagnostic pop #endif // end catch_fatal_condition.cpp // start catch_generators.cpp // start catch_random_number_generator.h #include #include namespace Catch { struct IConfig; std::mt19937& rng(); void seedRng( IConfig const& config ); unsigned int rngSeed(); } // end catch_random_number_generator.h #include #include namespace Catch { IGeneratorTracker::~IGeneratorTracker() {} const char* GeneratorException::what() const noexcept { return m_msg; } namespace Generators { GeneratorUntypedBase::~GeneratorUntypedBase() {} auto acquireGeneratorTracker( SourceLineInfo const& lineInfo ) -> IGeneratorTracker& { return getResultCapture().acquireGeneratorTracker( lineInfo ); } } // namespace Generators } // namespace Catch // end catch_generators.cpp // start catch_interfaces_capture.cpp namespace Catch { IResultCapture::~IResultCapture() = default; } // end catch_interfaces_capture.cpp // start catch_interfaces_config.cpp namespace Catch { IConfig::~IConfig() = default; } // end catch_interfaces_config.cpp // start catch_interfaces_exception.cpp namespace Catch { IExceptionTranslator::~IExceptionTranslator() = default; IExceptionTranslatorRegistry::~IExceptionTranslatorRegistry() = default; } // end catch_interfaces_exception.cpp // start catch_interfaces_registry_hub.cpp namespace Catch { IRegistryHub::~IRegistryHub() = default; IMutableRegistryHub::~IMutableRegistryHub() = default; } // end catch_interfaces_registry_hub.cpp // start catch_interfaces_reporter.cpp // start catch_reporter_listening.h namespace Catch { class ListeningReporter : public IStreamingReporter { using Reporters = std::vector; Reporters m_listeners; IStreamingReporterPtr m_reporter = nullptr; ReporterPreferences m_preferences; public: ListeningReporter(); void addListener( IStreamingReporterPtr&& listener ); void addReporter( IStreamingReporterPtr&& reporter ); public: // IStreamingReporter ReporterPreferences getPreferences() const override; void noMatchingTestCases( std::string const& spec ) override; static std::set getSupportedVerbosities(); void benchmarkStarting( BenchmarkInfo const& benchmarkInfo ) override; void benchmarkEnded( BenchmarkStats const& benchmarkStats ) override; void testRunStarting( TestRunInfo const& testRunInfo ) override; void testGroupStarting( GroupInfo const& groupInfo ) override; void testCaseStarting( TestCaseInfo const& testInfo ) override; void sectionStarting( SectionInfo const& sectionInfo ) override; void assertionStarting( AssertionInfo const& assertionInfo ) override; // The return value indicates if the messages buffer should be cleared: bool assertionEnded( AssertionStats const& assertionStats ) override; void sectionEnded( SectionStats const& sectionStats ) override; void testCaseEnded( TestCaseStats const& testCaseStats ) override; void testGroupEnded( TestGroupStats const& testGroupStats ) override; void testRunEnded( TestRunStats const& testRunStats ) override; void skipTest( TestCaseInfo const& testInfo ) override; bool isMulti() const override; }; } // end namespace Catch // end catch_reporter_listening.h namespace Catch { ReporterConfig::ReporterConfig( IConfigPtr const& _fullConfig ) : m_stream( &_fullConfig->stream() ), m_fullConfig( _fullConfig ) {} ReporterConfig::ReporterConfig( IConfigPtr const& _fullConfig, std::ostream& _stream ) : m_stream( &_stream ), m_fullConfig( _fullConfig ) {} std::ostream& ReporterConfig::stream() const { return *m_stream; } IConfigPtr ReporterConfig::fullConfig() const { return m_fullConfig; } TestRunInfo::TestRunInfo( std::string const& _name ) : name( _name ) {} GroupInfo::GroupInfo( std::string const& _name, std::size_t _groupIndex, std::size_t _groupsCount ) : name( _name ), groupIndex( _groupIndex ), groupsCounts( _groupsCount ) {} AssertionStats::AssertionStats( AssertionResult const& _assertionResult, std::vector const& _infoMessages, Totals const& _totals ) : assertionResult( _assertionResult ), infoMessages( _infoMessages ), totals( _totals ) { assertionResult.m_resultData.lazyExpression.m_transientExpression = _assertionResult.m_resultData.lazyExpression.m_transientExpression; if( assertionResult.hasMessage() ) { // Copy message into messages list. // !TBD This should have been done earlier, somewhere MessageBuilder builder( assertionResult.getTestMacroName(), assertionResult.getSourceInfo(), assertionResult.getResultType() ); builder << assertionResult.getMessage(); builder.m_info.message = builder.m_stream.str(); infoMessages.push_back( builder.m_info ); } } AssertionStats::~AssertionStats() = default; SectionStats::SectionStats( SectionInfo const& _sectionInfo, Counts const& _assertions, double _durationInSeconds, bool _missingAssertions ) : sectionInfo( _sectionInfo ), assertions( _assertions ), durationInSeconds( _durationInSeconds ), missingAssertions( _missingAssertions ) {} SectionStats::~SectionStats() = default; TestCaseStats::TestCaseStats( TestCaseInfo const& _testInfo, Totals const& _totals, std::string const& _stdOut, std::string const& _stdErr, bool _aborting ) : testInfo( _testInfo ), totals( _totals ), stdOut( _stdOut ), stdErr( _stdErr ), aborting( _aborting ) {} TestCaseStats::~TestCaseStats() = default; TestGroupStats::TestGroupStats( GroupInfo const& _groupInfo, Totals const& _totals, bool _aborting ) : groupInfo( _groupInfo ), totals( _totals ), aborting( _aborting ) {} TestGroupStats::TestGroupStats( GroupInfo const& _groupInfo ) : groupInfo( _groupInfo ), aborting( false ) {} TestGroupStats::~TestGroupStats() = default; TestRunStats::TestRunStats( TestRunInfo const& _runInfo, Totals const& _totals, bool _aborting ) : runInfo( _runInfo ), totals( _totals ), aborting( _aborting ) {} TestRunStats::~TestRunStats() = default; void IStreamingReporter::fatalErrorEncountered( StringRef ) {} bool IStreamingReporter::isMulti() const { return false; } IReporterFactory::~IReporterFactory() = default; IReporterRegistry::~IReporterRegistry() = default; } // end namespace Catch // end catch_interfaces_reporter.cpp // start catch_interfaces_runner.cpp namespace Catch { IRunner::~IRunner() = default; } // end catch_interfaces_runner.cpp // start catch_interfaces_testcase.cpp namespace Catch { ITestInvoker::~ITestInvoker() = default; ITestCaseRegistry::~ITestCaseRegistry() = default; } // end catch_interfaces_testcase.cpp // start catch_leak_detector.cpp #ifdef CATCH_CONFIG_WINDOWS_CRTDBG #include namespace Catch { LeakDetector::LeakDetector() { int flag = _CrtSetDbgFlag(_CRTDBG_REPORT_FLAG); flag |= _CRTDBG_LEAK_CHECK_DF; flag |= _CRTDBG_ALLOC_MEM_DF; _CrtSetDbgFlag(flag); _CrtSetReportMode(_CRT_WARN, _CRTDBG_MODE_FILE | _CRTDBG_MODE_DEBUG); _CrtSetReportFile(_CRT_WARN, _CRTDBG_FILE_STDERR); // Change this to leaking allocation's number to break there _CrtSetBreakAlloc(-1); } } #else Catch::LeakDetector::LeakDetector() {} #endif Catch::LeakDetector::~LeakDetector() { Catch::cleanUp(); } // end catch_leak_detector.cpp // start catch_list.cpp // start catch_list.h #include namespace Catch { std::size_t listTests( Config const& config ); std::size_t listTestsNamesOnly( Config const& config ); struct TagInfo { void add( std::string const& spelling ); std::string all() const; std::set spellings; std::size_t count = 0; }; std::size_t listTags( Config const& config ); std::size_t listReporters(); Option list( Config const& config ); } // end namespace Catch // end catch_list.h // start catch_text.h namespace Catch { using namespace clara::TextFlow; } // end catch_text.h #include #include #include namespace Catch { std::size_t listTests( Config const& config ) { TestSpec testSpec = config.testSpec(); if( config.hasTestFilters() ) Catch::cout() << "Matching test cases:\n"; else { Catch::cout() << "All available test cases:\n"; } auto matchedTestCases = filterTests( getAllTestCasesSorted( config ), testSpec, config ); for( auto const& testCaseInfo : matchedTestCases ) { Colour::Code colour = testCaseInfo.isHidden() ? Colour::SecondaryText : Colour::None; Colour colourGuard( colour ); Catch::cout() << Column( testCaseInfo.name ).initialIndent( 2 ).indent( 4 ) << "\n"; if( config.verbosity() >= Verbosity::High ) { Catch::cout() << Column( Catch::Detail::stringify( testCaseInfo.lineInfo ) ).indent(4) << std::endl; std::string description = testCaseInfo.description; if( description.empty() ) description = "(NO DESCRIPTION)"; Catch::cout() << Column( description ).indent(4) << std::endl; } if( !testCaseInfo.tags.empty() ) Catch::cout() << Column( testCaseInfo.tagsAsString() ).indent( 6 ) << "\n"; } if( !config.hasTestFilters() ) Catch::cout() << pluralise( matchedTestCases.size(), "test case" ) << '\n' << std::endl; else Catch::cout() << pluralise( matchedTestCases.size(), "matching test case" ) << '\n' << std::endl; return matchedTestCases.size(); } std::size_t listTestsNamesOnly( Config const& config ) { TestSpec testSpec = config.testSpec(); std::size_t matchedTests = 0; std::vector matchedTestCases = filterTests( getAllTestCasesSorted( config ), testSpec, config ); for( auto const& testCaseInfo : matchedTestCases ) { matchedTests++; if( startsWith( testCaseInfo.name, '#' ) ) Catch::cout() << '"' << testCaseInfo.name << '"'; else Catch::cout() << testCaseInfo.name; if ( config.verbosity() >= Verbosity::High ) Catch::cout() << "\t@" << testCaseInfo.lineInfo; Catch::cout() << std::endl; } return matchedTests; } void TagInfo::add( std::string const& spelling ) { ++count; spellings.insert( spelling ); } std::string TagInfo::all() const { std::string out; for( auto const& spelling : spellings ) out += "[" + spelling + "]"; return out; } std::size_t listTags( Config const& config ) { TestSpec testSpec = config.testSpec(); if( config.hasTestFilters() ) Catch::cout() << "Tags for matching test cases:\n"; else { Catch::cout() << "All available tags:\n"; } std::map tagCounts; std::vector matchedTestCases = filterTests( getAllTestCasesSorted( config ), testSpec, config ); for( auto const& testCase : matchedTestCases ) { for( auto const& tagName : testCase.getTestCaseInfo().tags ) { std::string lcaseTagName = toLower( tagName ); auto countIt = tagCounts.find( lcaseTagName ); if( countIt == tagCounts.end() ) countIt = tagCounts.insert( std::make_pair( lcaseTagName, TagInfo() ) ).first; countIt->second.add( tagName ); } } for( auto const& tagCount : tagCounts ) { ReusableStringStream rss; rss << " " << std::setw(2) << tagCount.second.count << " "; auto str = rss.str(); auto wrapper = Column( tagCount.second.all() ) .initialIndent( 0 ) .indent( str.size() ) .width( CATCH_CONFIG_CONSOLE_WIDTH-10 ); Catch::cout() << str << wrapper << '\n'; } Catch::cout() << pluralise( tagCounts.size(), "tag" ) << '\n' << std::endl; return tagCounts.size(); } std::size_t listReporters() { Catch::cout() << "Available reporters:\n"; IReporterRegistry::FactoryMap const& factories = getRegistryHub().getReporterRegistry().getFactories(); std::size_t maxNameLen = 0; for( auto const& factoryKvp : factories ) maxNameLen = (std::max)( maxNameLen, factoryKvp.first.size() ); for( auto const& factoryKvp : factories ) { Catch::cout() << Column( factoryKvp.first + ":" ) .indent(2) .width( 5+maxNameLen ) + Column( factoryKvp.second->getDescription() ) .initialIndent(0) .indent(2) .width( CATCH_CONFIG_CONSOLE_WIDTH - maxNameLen-8 ) << "\n"; } Catch::cout() << std::endl; return factories.size(); } Option list( Config const& config ) { Option listedCount; if( config.listTests() ) listedCount = listedCount.valueOr(0) + listTests( config ); if( config.listTestNamesOnly() ) listedCount = listedCount.valueOr(0) + listTestsNamesOnly( config ); if( config.listTags() ) listedCount = listedCount.valueOr(0) + listTags( config ); if( config.listReporters() ) listedCount = listedCount.valueOr(0) + listReporters(); return listedCount; } } // end namespace Catch // end catch_list.cpp // start catch_matchers.cpp namespace Catch { namespace Matchers { namespace Impl { std::string MatcherUntypedBase::toString() const { if( m_cachedToString.empty() ) m_cachedToString = describe(); return m_cachedToString; } MatcherUntypedBase::~MatcherUntypedBase() = default; } // namespace Impl } // namespace Matchers using namespace Matchers; using Matchers::Impl::MatcherBase; } // namespace Catch // end catch_matchers.cpp // start catch_matchers_floating.cpp // start catch_polyfills.hpp namespace Catch { bool isnan(float f); bool isnan(double d); } // end catch_polyfills.hpp // start catch_to_string.hpp #include namespace Catch { template std::string to_string(T const& t) { #if defined(CATCH_CONFIG_CPP11_TO_STRING) return std::to_string(t); #else ReusableStringStream rss; rss << t; return rss.str(); #endif } } // end namespace Catch // end catch_to_string.hpp #include #include #include namespace Catch { namespace Matchers { namespace Floating { enum class FloatingPointKind : uint8_t { Float, Double }; } } } namespace { template struct Converter; template <> struct Converter { static_assert(sizeof(float) == sizeof(int32_t), "Important ULP matcher assumption violated"); Converter(float f) { std::memcpy(&i, &f, sizeof(f)); } int32_t i; }; template <> struct Converter { static_assert(sizeof(double) == sizeof(int64_t), "Important ULP matcher assumption violated"); Converter(double d) { std::memcpy(&i, &d, sizeof(d)); } int64_t i; }; template auto convert(T t) -> Converter { return Converter(t); } template bool almostEqualUlps(FP lhs, FP rhs, int maxUlpDiff) { // Comparison with NaN should always be false. // This way we can rule it out before getting into the ugly details if (Catch::isnan(lhs) || Catch::isnan(rhs)) { return false; } auto lc = convert(lhs); auto rc = convert(rhs); if ((lc.i < 0) != (rc.i < 0)) { // Potentially we can have +0 and -0 return lhs == rhs; } auto ulpDiff = std::abs(lc.i - rc.i); return ulpDiff <= maxUlpDiff; } } namespace Catch { namespace Matchers { namespace Floating { WithinAbsMatcher::WithinAbsMatcher(double target, double margin) :m_target{ target }, m_margin{ margin } { CATCH_ENFORCE(margin >= 0, "Invalid margin: " << margin << '.' << " Margin has to be non-negative."); } // Performs equivalent check of std::fabs(lhs - rhs) <= margin // But without the subtraction to allow for INFINITY in comparison bool WithinAbsMatcher::match(double const& matchee) const { return (matchee + m_margin >= m_target) && (m_target + m_margin >= matchee); } std::string WithinAbsMatcher::describe() const { return "is within " + ::Catch::Detail::stringify(m_margin) + " of " + ::Catch::Detail::stringify(m_target); } WithinUlpsMatcher::WithinUlpsMatcher(double target, int ulps, FloatingPointKind baseType) :m_target{ target }, m_ulps{ ulps }, m_type{ baseType } { CATCH_ENFORCE(ulps >= 0, "Invalid ULP setting: " << ulps << '.' << " ULPs have to be non-negative."); } #if defined(__clang__) #pragma clang diagnostic push // Clang <3.5 reports on the default branch in the switch below #pragma clang diagnostic ignored "-Wunreachable-code" #endif bool WithinUlpsMatcher::match(double const& matchee) const { switch (m_type) { case FloatingPointKind::Float: return almostEqualUlps(static_cast(matchee), static_cast(m_target), m_ulps); case FloatingPointKind::Double: return almostEqualUlps(matchee, m_target, m_ulps); default: CATCH_INTERNAL_ERROR( "Unknown FloatingPointKind value" ); } } #if defined(__clang__) #pragma clang diagnostic pop #endif std::string WithinUlpsMatcher::describe() const { return "is within " + Catch::to_string(m_ulps) + " ULPs of " + ::Catch::Detail::stringify(m_target) + ((m_type == FloatingPointKind::Float)? "f" : ""); } }// namespace Floating Floating::WithinUlpsMatcher WithinULP(double target, int maxUlpDiff) { return Floating::WithinUlpsMatcher(target, maxUlpDiff, Floating::FloatingPointKind::Double); } Floating::WithinUlpsMatcher WithinULP(float target, int maxUlpDiff) { return Floating::WithinUlpsMatcher(target, maxUlpDiff, Floating::FloatingPointKind::Float); } Floating::WithinAbsMatcher WithinAbs(double target, double margin) { return Floating::WithinAbsMatcher(target, margin); } } // namespace Matchers } // namespace Catch // end catch_matchers_floating.cpp // start catch_matchers_generic.cpp std::string Catch::Matchers::Generic::Detail::finalizeDescription(const std::string& desc) { if (desc.empty()) { return "matches undescribed predicate"; } else { return "matches predicate: \"" + desc + '"'; } } // end catch_matchers_generic.cpp // start catch_matchers_string.cpp #include namespace Catch { namespace Matchers { namespace StdString { CasedString::CasedString( std::string const& str, CaseSensitive::Choice caseSensitivity ) : m_caseSensitivity( caseSensitivity ), m_str( adjustString( str ) ) {} std::string CasedString::adjustString( std::string const& str ) const { return m_caseSensitivity == CaseSensitive::No ? toLower( str ) : str; } std::string CasedString::caseSensitivitySuffix() const { return m_caseSensitivity == CaseSensitive::No ? " (case insensitive)" : std::string(); } StringMatcherBase::StringMatcherBase( std::string const& operation, CasedString const& comparator ) : m_comparator( comparator ), m_operation( operation ) { } std::string StringMatcherBase::describe() const { std::string description; description.reserve(5 + m_operation.size() + m_comparator.m_str.size() + m_comparator.caseSensitivitySuffix().size()); description += m_operation; description += ": \""; description += m_comparator.m_str; description += "\""; description += m_comparator.caseSensitivitySuffix(); return description; } EqualsMatcher::EqualsMatcher( CasedString const& comparator ) : StringMatcherBase( "equals", comparator ) {} bool EqualsMatcher::match( std::string const& source ) const { return m_comparator.adjustString( source ) == m_comparator.m_str; } ContainsMatcher::ContainsMatcher( CasedString const& comparator ) : StringMatcherBase( "contains", comparator ) {} bool ContainsMatcher::match( std::string const& source ) const { return contains( m_comparator.adjustString( source ), m_comparator.m_str ); } StartsWithMatcher::StartsWithMatcher( CasedString const& comparator ) : StringMatcherBase( "starts with", comparator ) {} bool StartsWithMatcher::match( std::string const& source ) const { return startsWith( m_comparator.adjustString( source ), m_comparator.m_str ); } EndsWithMatcher::EndsWithMatcher( CasedString const& comparator ) : StringMatcherBase( "ends with", comparator ) {} bool EndsWithMatcher::match( std::string const& source ) const { return endsWith( m_comparator.adjustString( source ), m_comparator.m_str ); } RegexMatcher::RegexMatcher(std::string regex, CaseSensitive::Choice caseSensitivity): m_regex(std::move(regex)), m_caseSensitivity(caseSensitivity) {} bool RegexMatcher::match(std::string const& matchee) const { auto flags = std::regex::ECMAScript; // ECMAScript is the default syntax option anyway if (m_caseSensitivity == CaseSensitive::Choice::No) { flags |= std::regex::icase; } auto reg = std::regex(m_regex, flags); return std::regex_match(matchee, reg); } std::string RegexMatcher::describe() const { return "matches " + ::Catch::Detail::stringify(m_regex) + ((m_caseSensitivity == CaseSensitive::Choice::Yes)? " case sensitively" : " case insensitively"); } } // namespace StdString StdString::EqualsMatcher Equals( std::string const& str, CaseSensitive::Choice caseSensitivity ) { return StdString::EqualsMatcher( StdString::CasedString( str, caseSensitivity) ); } StdString::ContainsMatcher Contains( std::string const& str, CaseSensitive::Choice caseSensitivity ) { return StdString::ContainsMatcher( StdString::CasedString( str, caseSensitivity) ); } StdString::EndsWithMatcher EndsWith( std::string const& str, CaseSensitive::Choice caseSensitivity ) { return StdString::EndsWithMatcher( StdString::CasedString( str, caseSensitivity) ); } StdString::StartsWithMatcher StartsWith( std::string const& str, CaseSensitive::Choice caseSensitivity ) { return StdString::StartsWithMatcher( StdString::CasedString( str, caseSensitivity) ); } StdString::RegexMatcher Matches(std::string const& regex, CaseSensitive::Choice caseSensitivity) { return StdString::RegexMatcher(regex, caseSensitivity); } } // namespace Matchers } // namespace Catch // end catch_matchers_string.cpp // start catch_message.cpp // start catch_uncaught_exceptions.h namespace Catch { bool uncaught_exceptions(); } // end namespace Catch // end catch_uncaught_exceptions.h #include #include namespace Catch { MessageInfo::MessageInfo( StringRef const& _macroName, SourceLineInfo const& _lineInfo, ResultWas::OfType _type ) : macroName( _macroName ), lineInfo( _lineInfo ), type( _type ), sequence( ++globalCount ) {} bool MessageInfo::operator==( MessageInfo const& other ) const { return sequence == other.sequence; } bool MessageInfo::operator<( MessageInfo const& other ) const { return sequence < other.sequence; } // This may need protecting if threading support is added unsigned int MessageInfo::globalCount = 0; //////////////////////////////////////////////////////////////////////////// Catch::MessageBuilder::MessageBuilder( StringRef const& macroName, SourceLineInfo const& lineInfo, ResultWas::OfType type ) :m_info(macroName, lineInfo, type) {} //////////////////////////////////////////////////////////////////////////// ScopedMessage::ScopedMessage( MessageBuilder const& builder ) : m_info( builder.m_info ) { m_info.message = builder.m_stream.str(); getResultCapture().pushScopedMessage( m_info ); } ScopedMessage::~ScopedMessage() { if ( !uncaught_exceptions() ){ getResultCapture().popScopedMessage(m_info); } } Capturer::Capturer( StringRef macroName, SourceLineInfo const& lineInfo, ResultWas::OfType resultType, StringRef names ) { auto trimmed = [&] (size_t start, size_t end) { while (names[start] == ',' || isspace(names[start])) { ++start; } while (names[end] == ',' || isspace(names[end])) { --end; } return names.substr(start, end - start + 1); }; size_t start = 0; std::stack openings; for (size_t pos = 0; pos < names.size(); ++pos) { char c = names[pos]; switch (c) { case '[': case '{': case '(': // It is basically impossible to disambiguate between // comparison and start of template args in this context // case '<': openings.push(c); break; case ']': case '}': case ')': // case '>': openings.pop(); break; case ',': if (start != pos && openings.size() == 0) { m_messages.emplace_back(macroName, lineInfo, resultType); m_messages.back().message = trimmed(start, pos); m_messages.back().message += " := "; start = pos; } } } assert(openings.size() == 0 && "Mismatched openings"); m_messages.emplace_back(macroName, lineInfo, resultType); m_messages.back().message = trimmed(start, names.size() - 1); m_messages.back().message += " := "; } Capturer::~Capturer() { if ( !uncaught_exceptions() ){ assert( m_captured == m_messages.size() ); for( size_t i = 0; i < m_captured; ++i ) m_resultCapture.popScopedMessage( m_messages[i] ); } } void Capturer::captureValue( size_t index, std::string const& value ) { assert( index < m_messages.size() ); m_messages[index].message += value; m_resultCapture.pushScopedMessage( m_messages[index] ); m_captured++; } } // end namespace Catch // end catch_message.cpp // start catch_output_redirect.cpp // start catch_output_redirect.h #ifndef TWOBLUECUBES_CATCH_OUTPUT_REDIRECT_H #define TWOBLUECUBES_CATCH_OUTPUT_REDIRECT_H #include #include #include namespace Catch { class RedirectedStream { std::ostream& m_originalStream; std::ostream& m_redirectionStream; std::streambuf* m_prevBuf; public: RedirectedStream( std::ostream& originalStream, std::ostream& redirectionStream ); ~RedirectedStream(); }; class RedirectedStdOut { ReusableStringStream m_rss; RedirectedStream m_cout; public: RedirectedStdOut(); auto str() const -> std::string; }; // StdErr has two constituent streams in C++, std::cerr and std::clog // This means that we need to redirect 2 streams into 1 to keep proper // order of writes class RedirectedStdErr { ReusableStringStream m_rss; RedirectedStream m_cerr; RedirectedStream m_clog; public: RedirectedStdErr(); auto str() const -> std::string; }; #if defined(CATCH_CONFIG_NEW_CAPTURE) // Windows's implementation of std::tmpfile is terrible (it tries // to create a file inside system folder, thus requiring elevated // privileges for the binary), so we have to use tmpnam(_s) and // create the file ourselves there. class TempFile { public: TempFile(TempFile const&) = delete; TempFile& operator=(TempFile const&) = delete; TempFile(TempFile&&) = delete; TempFile& operator=(TempFile&&) = delete; TempFile(); ~TempFile(); std::FILE* getFile(); std::string getContents(); private: std::FILE* m_file = nullptr; #if defined(_MSC_VER) char m_buffer[L_tmpnam] = { 0 }; #endif }; class OutputRedirect { public: OutputRedirect(OutputRedirect const&) = delete; OutputRedirect& operator=(OutputRedirect const&) = delete; OutputRedirect(OutputRedirect&&) = delete; OutputRedirect& operator=(OutputRedirect&&) = delete; OutputRedirect(std::string& stdout_dest, std::string& stderr_dest); ~OutputRedirect(); private: int m_originalStdout = -1; int m_originalStderr = -1; TempFile m_stdoutFile; TempFile m_stderrFile; std::string& m_stdoutDest; std::string& m_stderrDest; }; #endif } // end namespace Catch #endif // TWOBLUECUBES_CATCH_OUTPUT_REDIRECT_H // end catch_output_redirect.h #include #include #include #include #include #if defined(CATCH_CONFIG_NEW_CAPTURE) #if defined(_MSC_VER) #include //_dup and _dup2 #define dup _dup #define dup2 _dup2 #define fileno _fileno #else #include // dup and dup2 #endif #endif namespace Catch { RedirectedStream::RedirectedStream( std::ostream& originalStream, std::ostream& redirectionStream ) : m_originalStream( originalStream ), m_redirectionStream( redirectionStream ), m_prevBuf( m_originalStream.rdbuf() ) { m_originalStream.rdbuf( m_redirectionStream.rdbuf() ); } RedirectedStream::~RedirectedStream() { m_originalStream.rdbuf( m_prevBuf ); } RedirectedStdOut::RedirectedStdOut() : m_cout( Catch::cout(), m_rss.get() ) {} auto RedirectedStdOut::str() const -> std::string { return m_rss.str(); } RedirectedStdErr::RedirectedStdErr() : m_cerr( Catch::cerr(), m_rss.get() ), m_clog( Catch::clog(), m_rss.get() ) {} auto RedirectedStdErr::str() const -> std::string { return m_rss.str(); } #if defined(CATCH_CONFIG_NEW_CAPTURE) #if defined(_MSC_VER) TempFile::TempFile() { if (tmpnam_s(m_buffer)) { CATCH_RUNTIME_ERROR("Could not get a temp filename"); } if (fopen_s(&m_file, m_buffer, "w")) { char buffer[100]; if (strerror_s(buffer, errno)) { CATCH_RUNTIME_ERROR("Could not translate errno to a string"); } CATCH_RUNTIME_ERROR("Coul dnot open the temp file: '" << m_buffer << "' because: " << buffer); } } #else TempFile::TempFile() { m_file = std::tmpfile(); if (!m_file) { CATCH_RUNTIME_ERROR("Could not create a temp file."); } } #endif TempFile::~TempFile() { // TBD: What to do about errors here? std::fclose(m_file); // We manually create the file on Windows only, on Linux // it will be autodeleted #if defined(_MSC_VER) std::remove(m_buffer); #endif } FILE* TempFile::getFile() { return m_file; } std::string TempFile::getContents() { std::stringstream sstr; char buffer[100] = {}; std::rewind(m_file); while (std::fgets(buffer, sizeof(buffer), m_file)) { sstr << buffer; } return sstr.str(); } OutputRedirect::OutputRedirect(std::string& stdout_dest, std::string& stderr_dest) : m_originalStdout(dup(1)), m_originalStderr(dup(2)), m_stdoutDest(stdout_dest), m_stderrDest(stderr_dest) { dup2(fileno(m_stdoutFile.getFile()), 1); dup2(fileno(m_stderrFile.getFile()), 2); } OutputRedirect::~OutputRedirect() { Catch::cout() << std::flush; fflush(stdout); // Since we support overriding these streams, we flush cerr // even though std::cerr is unbuffered Catch::cerr() << std::flush; Catch::clog() << std::flush; fflush(stderr); dup2(m_originalStdout, 1); dup2(m_originalStderr, 2); m_stdoutDest += m_stdoutFile.getContents(); m_stderrDest += m_stderrFile.getContents(); } #endif // CATCH_CONFIG_NEW_CAPTURE } // namespace Catch #if defined(CATCH_CONFIG_NEW_CAPTURE) #if defined(_MSC_VER) #undef dup #undef dup2 #undef fileno #endif #endif // end catch_output_redirect.cpp // start catch_polyfills.cpp #include namespace Catch { #if !defined(CATCH_CONFIG_POLYFILL_ISNAN) bool isnan(float f) { return std::isnan(f); } bool isnan(double d) { return std::isnan(d); } #else // For now we only use this for embarcadero bool isnan(float f) { return std::_isnan(f); } bool isnan(double d) { return std::_isnan(d); } #endif } // end namespace Catch // end catch_polyfills.cpp // start catch_random_number_generator.cpp namespace Catch { std::mt19937& rng() { static std::mt19937 s_rng; return s_rng; } void seedRng( IConfig const& config ) { if( config.rngSeed() != 0 ) { std::srand( config.rngSeed() ); rng().seed( config.rngSeed() ); } } unsigned int rngSeed() { return getCurrentContext().getConfig()->rngSeed(); } } // end catch_random_number_generator.cpp // start catch_registry_hub.cpp // start catch_test_case_registry_impl.h #include #include #include #include namespace Catch { class TestCase; struct IConfig; std::vector sortTests( IConfig const& config, std::vector const& unsortedTestCases ); bool matchTest( TestCase const& testCase, TestSpec const& testSpec, IConfig const& config ); void enforceNoDuplicateTestCases( std::vector const& functions ); std::vector filterTests( std::vector const& testCases, TestSpec const& testSpec, IConfig const& config ); std::vector const& getAllTestCasesSorted( IConfig const& config ); class TestRegistry : public ITestCaseRegistry { public: virtual ~TestRegistry() = default; virtual void registerTest( TestCase const& testCase ); std::vector const& getAllTests() const override; std::vector const& getAllTestsSorted( IConfig const& config ) const override; private: std::vector m_functions; mutable RunTests::InWhatOrder m_currentSortOrder = RunTests::InDeclarationOrder; mutable std::vector m_sortedFunctions; std::size_t m_unnamedCount = 0; std::ios_base::Init m_ostreamInit; // Forces cout/ cerr to be initialised }; /////////////////////////////////////////////////////////////////////////// class TestInvokerAsFunction : public ITestInvoker { void(*m_testAsFunction)(); public: TestInvokerAsFunction( void(*testAsFunction)() ) noexcept; void invoke() const override; }; std::string extractClassName( StringRef const& classOrQualifiedMethodName ); /////////////////////////////////////////////////////////////////////////// } // end namespace Catch // end catch_test_case_registry_impl.h // start catch_reporter_registry.h #include namespace Catch { class ReporterRegistry : public IReporterRegistry { public: ~ReporterRegistry() override; IStreamingReporterPtr create( std::string const& name, IConfigPtr const& config ) const override; void registerReporter( std::string const& name, IReporterFactoryPtr const& factory ); void registerListener( IReporterFactoryPtr const& factory ); FactoryMap const& getFactories() const override; Listeners const& getListeners() const override; private: FactoryMap m_factories; Listeners m_listeners; }; } // end catch_reporter_registry.h // start catch_tag_alias_registry.h // start catch_tag_alias.h #include namespace Catch { struct TagAlias { TagAlias(std::string const& _tag, SourceLineInfo _lineInfo); std::string tag; SourceLineInfo lineInfo; }; } // end namespace Catch // end catch_tag_alias.h #include namespace Catch { class TagAliasRegistry : public ITagAliasRegistry { public: ~TagAliasRegistry() override; TagAlias const* find( std::string const& alias ) const override; std::string expandAliases( std::string const& unexpandedTestSpec ) const override; void add( std::string const& alias, std::string const& tag, SourceLineInfo const& lineInfo ); private: std::map m_registry; }; } // end namespace Catch // end catch_tag_alias_registry.h // start catch_startup_exception_registry.h #include #include namespace Catch { class StartupExceptionRegistry { public: void add(std::exception_ptr const& exception) noexcept; std::vector const& getExceptions() const noexcept; private: std::vector m_exceptions; }; } // end namespace Catch // end catch_startup_exception_registry.h // start catch_singletons.hpp namespace Catch { struct ISingleton { virtual ~ISingleton(); }; void addSingleton( ISingleton* singleton ); void cleanupSingletons(); template class Singleton : SingletonImplT, public ISingleton { static auto getInternal() -> Singleton* { static Singleton* s_instance = nullptr; if( !s_instance ) { s_instance = new Singleton; addSingleton( s_instance ); } return s_instance; } public: static auto get() -> InterfaceT const& { return *getInternal(); } static auto getMutable() -> MutableInterfaceT& { return *getInternal(); } }; } // namespace Catch // end catch_singletons.hpp namespace Catch { namespace { class RegistryHub : public IRegistryHub, public IMutableRegistryHub, private NonCopyable { public: // IRegistryHub RegistryHub() = default; IReporterRegistry const& getReporterRegistry() const override { return m_reporterRegistry; } ITestCaseRegistry const& getTestCaseRegistry() const override { return m_testCaseRegistry; } IExceptionTranslatorRegistry const& getExceptionTranslatorRegistry() const override { return m_exceptionTranslatorRegistry; } ITagAliasRegistry const& getTagAliasRegistry() const override { return m_tagAliasRegistry; } StartupExceptionRegistry const& getStartupExceptionRegistry() const override { return m_exceptionRegistry; } public: // IMutableRegistryHub void registerReporter( std::string const& name, IReporterFactoryPtr const& factory ) override { m_reporterRegistry.registerReporter( name, factory ); } void registerListener( IReporterFactoryPtr const& factory ) override { m_reporterRegistry.registerListener( factory ); } void registerTest( TestCase const& testInfo ) override { m_testCaseRegistry.registerTest( testInfo ); } void registerTranslator( const IExceptionTranslator* translator ) override { m_exceptionTranslatorRegistry.registerTranslator( translator ); } void registerTagAlias( std::string const& alias, std::string const& tag, SourceLineInfo const& lineInfo ) override { m_tagAliasRegistry.add( alias, tag, lineInfo ); } void registerStartupException() noexcept override { m_exceptionRegistry.add(std::current_exception()); } private: TestRegistry m_testCaseRegistry; ReporterRegistry m_reporterRegistry; ExceptionTranslatorRegistry m_exceptionTranslatorRegistry; TagAliasRegistry m_tagAliasRegistry; StartupExceptionRegistry m_exceptionRegistry; }; } using RegistryHubSingleton = Singleton; IRegistryHub const& getRegistryHub() { return RegistryHubSingleton::get(); } IMutableRegistryHub& getMutableRegistryHub() { return RegistryHubSingleton::getMutable(); } void cleanUp() { cleanupSingletons(); cleanUpContext(); } std::string translateActiveException() { return getRegistryHub().getExceptionTranslatorRegistry().translateActiveException(); } } // end namespace Catch // end catch_registry_hub.cpp // start catch_reporter_registry.cpp namespace Catch { ReporterRegistry::~ReporterRegistry() = default; IStreamingReporterPtr ReporterRegistry::create( std::string const& name, IConfigPtr const& config ) const { auto it = m_factories.find( name ); if( it == m_factories.end() ) return nullptr; return it->second->create( ReporterConfig( config ) ); } void ReporterRegistry::registerReporter( std::string const& name, IReporterFactoryPtr const& factory ) { m_factories.emplace(name, factory); } void ReporterRegistry::registerListener( IReporterFactoryPtr const& factory ) { m_listeners.push_back( factory ); } IReporterRegistry::FactoryMap const& ReporterRegistry::getFactories() const { return m_factories; } IReporterRegistry::Listeners const& ReporterRegistry::getListeners() const { return m_listeners; } } // end catch_reporter_registry.cpp // start catch_result_type.cpp namespace Catch { bool isOk( ResultWas::OfType resultType ) { return ( resultType & ResultWas::FailureBit ) == 0; } bool isJustInfo( int flags ) { return flags == ResultWas::Info; } ResultDisposition::Flags operator | ( ResultDisposition::Flags lhs, ResultDisposition::Flags rhs ) { return static_cast( static_cast( lhs ) | static_cast( rhs ) ); } bool shouldContinueOnFailure( int flags ) { return ( flags & ResultDisposition::ContinueOnFailure ) != 0; } bool shouldSuppressFailure( int flags ) { return ( flags & ResultDisposition::SuppressFail ) != 0; } } // end namespace Catch // end catch_result_type.cpp // start catch_run_context.cpp #include #include #include namespace Catch { namespace Generators { struct GeneratorTracker : TestCaseTracking::TrackerBase, IGeneratorTracker { GeneratorBasePtr m_generator; GeneratorTracker( TestCaseTracking::NameAndLocation const& nameAndLocation, TrackerContext& ctx, ITracker* parent ) : TrackerBase( nameAndLocation, ctx, parent ) {} ~GeneratorTracker(); static GeneratorTracker& acquire( TrackerContext& ctx, TestCaseTracking::NameAndLocation const& nameAndLocation ) { std::shared_ptr tracker; ITracker& currentTracker = ctx.currentTracker(); if( TestCaseTracking::ITrackerPtr childTracker = currentTracker.findChild( nameAndLocation ) ) { assert( childTracker ); assert( childTracker->isGeneratorTracker() ); tracker = std::static_pointer_cast( childTracker ); } else { tracker = std::make_shared( nameAndLocation, ctx, ¤tTracker ); currentTracker.addChild( tracker ); } if( !ctx.completedCycle() && !tracker->isComplete() ) { tracker->open(); } return *tracker; } // TrackerBase interface bool isGeneratorTracker() const override { return true; } auto hasGenerator() const -> bool override { return !!m_generator; } void close() override { TrackerBase::close(); // Generator interface only finds out if it has another item on atual move if (m_runState == CompletedSuccessfully && m_generator->next()) { m_children.clear(); m_runState = Executing; } } // IGeneratorTracker interface auto getGenerator() const -> GeneratorBasePtr const& override { return m_generator; } void setGenerator( GeneratorBasePtr&& generator ) override { m_generator = std::move( generator ); } }; GeneratorTracker::~GeneratorTracker() {} } RunContext::RunContext(IConfigPtr const& _config, IStreamingReporterPtr&& reporter) : m_runInfo(_config->name()), m_context(getCurrentMutableContext()), m_config(_config), m_reporter(std::move(reporter)), m_lastAssertionInfo{ StringRef(), SourceLineInfo("",0), StringRef(), ResultDisposition::Normal }, m_includeSuccessfulResults( m_config->includeSuccessfulResults() || m_reporter->getPreferences().shouldReportAllAssertions ) { m_context.setRunner(this); m_context.setConfig(m_config); m_context.setResultCapture(this); m_reporter->testRunStarting(m_runInfo); } RunContext::~RunContext() { m_reporter->testRunEnded(TestRunStats(m_runInfo, m_totals, aborting())); } void RunContext::testGroupStarting(std::string const& testSpec, std::size_t groupIndex, std::size_t groupsCount) { m_reporter->testGroupStarting(GroupInfo(testSpec, groupIndex, groupsCount)); } void RunContext::testGroupEnded(std::string const& testSpec, Totals const& totals, std::size_t groupIndex, std::size_t groupsCount) { m_reporter->testGroupEnded(TestGroupStats(GroupInfo(testSpec, groupIndex, groupsCount), totals, aborting())); } Totals RunContext::runTest(TestCase const& testCase) { Totals prevTotals = m_totals; std::string redirectedCout; std::string redirectedCerr; auto const& testInfo = testCase.getTestCaseInfo(); m_reporter->testCaseStarting(testInfo); m_activeTestCase = &testCase; ITracker& rootTracker = m_trackerContext.startRun(); assert(rootTracker.isSectionTracker()); static_cast(rootTracker).addInitialFilters(m_config->getSectionsToRun()); do { m_trackerContext.startCycle(); m_testCaseTracker = &SectionTracker::acquire(m_trackerContext, TestCaseTracking::NameAndLocation(testInfo.name, testInfo.lineInfo)); runCurrentTest(redirectedCout, redirectedCerr); } while (!m_testCaseTracker->isSuccessfullyCompleted() && !aborting()); Totals deltaTotals = m_totals.delta(prevTotals); if (testInfo.expectedToFail() && deltaTotals.testCases.passed > 0) { deltaTotals.assertions.failed++; deltaTotals.testCases.passed--; deltaTotals.testCases.failed++; } m_totals.testCases += deltaTotals.testCases; m_reporter->testCaseEnded(TestCaseStats(testInfo, deltaTotals, redirectedCout, redirectedCerr, aborting())); m_activeTestCase = nullptr; m_testCaseTracker = nullptr; return deltaTotals; } IConfigPtr RunContext::config() const { return m_config; } IStreamingReporter& RunContext::reporter() const { return *m_reporter; } void RunContext::assertionEnded(AssertionResult const & result) { if (result.getResultType() == ResultWas::Ok) { m_totals.assertions.passed++; m_lastAssertionPassed = true; } else if (!result.isOk()) { m_lastAssertionPassed = false; if( m_activeTestCase->getTestCaseInfo().okToFail() ) m_totals.assertions.failedButOk++; else m_totals.assertions.failed++; } else { m_lastAssertionPassed = true; } // We have no use for the return value (whether messages should be cleared), because messages were made scoped // and should be let to clear themselves out. static_cast(m_reporter->assertionEnded(AssertionStats(result, m_messages, m_totals))); // Reset working state resetAssertionInfo(); m_lastResult = result; } void RunContext::resetAssertionInfo() { m_lastAssertionInfo.macroName = StringRef(); m_lastAssertionInfo.capturedExpression = "{Unknown expression after the reported line}"_sr; } bool RunContext::sectionStarted(SectionInfo const & sectionInfo, Counts & assertions) { ITracker& sectionTracker = SectionTracker::acquire(m_trackerContext, TestCaseTracking::NameAndLocation(sectionInfo.name, sectionInfo.lineInfo)); if (!sectionTracker.isOpen()) return false; m_activeSections.push_back(§ionTracker); m_lastAssertionInfo.lineInfo = sectionInfo.lineInfo; m_reporter->sectionStarting(sectionInfo); assertions = m_totals.assertions; return true; } auto RunContext::acquireGeneratorTracker( SourceLineInfo const& lineInfo ) -> IGeneratorTracker& { using namespace Generators; GeneratorTracker& tracker = GeneratorTracker::acquire( m_trackerContext, TestCaseTracking::NameAndLocation( "generator", lineInfo ) ); assert( tracker.isOpen() ); m_lastAssertionInfo.lineInfo = lineInfo; return tracker; } bool RunContext::testForMissingAssertions(Counts& assertions) { if (assertions.total() != 0) return false; if (!m_config->warnAboutMissingAssertions()) return false; if (m_trackerContext.currentTracker().hasChildren()) return false; m_totals.assertions.failed++; assertions.failed++; return true; } void RunContext::sectionEnded(SectionEndInfo const & endInfo) { Counts assertions = m_totals.assertions - endInfo.prevAssertions; bool missingAssertions = testForMissingAssertions(assertions); if (!m_activeSections.empty()) { m_activeSections.back()->close(); m_activeSections.pop_back(); } m_reporter->sectionEnded(SectionStats(endInfo.sectionInfo, assertions, endInfo.durationInSeconds, missingAssertions)); m_messages.clear(); } void RunContext::sectionEndedEarly(SectionEndInfo const & endInfo) { if (m_unfinishedSections.empty()) m_activeSections.back()->fail(); else m_activeSections.back()->close(); m_activeSections.pop_back(); m_unfinishedSections.push_back(endInfo); } void RunContext::benchmarkStarting( BenchmarkInfo const& info ) { m_reporter->benchmarkStarting( info ); } void RunContext::benchmarkEnded( BenchmarkStats const& stats ) { m_reporter->benchmarkEnded( stats ); } void RunContext::pushScopedMessage(MessageInfo const & message) { m_messages.push_back(message); } void RunContext::popScopedMessage(MessageInfo const & message) { m_messages.erase(std::remove(m_messages.begin(), m_messages.end(), message), m_messages.end()); } std::string RunContext::getCurrentTestName() const { return m_activeTestCase ? m_activeTestCase->getTestCaseInfo().name : std::string(); } const AssertionResult * RunContext::getLastResult() const { return &(*m_lastResult); } void RunContext::exceptionEarlyReported() { m_shouldReportUnexpected = false; } void RunContext::handleFatalErrorCondition( StringRef message ) { // First notify reporter that bad things happened m_reporter->fatalErrorEncountered(message); // Don't rebuild the result -- the stringification itself can cause more fatal errors // Instead, fake a result data. AssertionResultData tempResult( ResultWas::FatalErrorCondition, { false } ); tempResult.message = message; AssertionResult result(m_lastAssertionInfo, tempResult); assertionEnded(result); handleUnfinishedSections(); // Recreate section for test case (as we will lose the one that was in scope) auto const& testCaseInfo = m_activeTestCase->getTestCaseInfo(); SectionInfo testCaseSection(testCaseInfo.lineInfo, testCaseInfo.name); Counts assertions; assertions.failed = 1; SectionStats testCaseSectionStats(testCaseSection, assertions, 0, false); m_reporter->sectionEnded(testCaseSectionStats); auto const& testInfo = m_activeTestCase->getTestCaseInfo(); Totals deltaTotals; deltaTotals.testCases.failed = 1; deltaTotals.assertions.failed = 1; m_reporter->testCaseEnded(TestCaseStats(testInfo, deltaTotals, std::string(), std::string(), false)); m_totals.testCases.failed++; testGroupEnded(std::string(), m_totals, 1, 1); m_reporter->testRunEnded(TestRunStats(m_runInfo, m_totals, false)); } bool RunContext::lastAssertionPassed() { return m_lastAssertionPassed; } void RunContext::assertionPassed() { m_lastAssertionPassed = true; ++m_totals.assertions.passed; resetAssertionInfo(); } bool RunContext::aborting() const { return m_totals.assertions.failed >= static_cast(m_config->abortAfter()); } void RunContext::runCurrentTest(std::string & redirectedCout, std::string & redirectedCerr) { auto const& testCaseInfo = m_activeTestCase->getTestCaseInfo(); SectionInfo testCaseSection(testCaseInfo.lineInfo, testCaseInfo.name); m_reporter->sectionStarting(testCaseSection); Counts prevAssertions = m_totals.assertions; double duration = 0; m_shouldReportUnexpected = true; m_lastAssertionInfo = { "TEST_CASE"_sr, testCaseInfo.lineInfo, StringRef(), ResultDisposition::Normal }; seedRng(*m_config); Timer timer; CATCH_TRY { if (m_reporter->getPreferences().shouldRedirectStdOut) { #if !defined(CATCH_CONFIG_EXPERIMENTAL_REDIRECT) RedirectedStdOut redirectedStdOut; RedirectedStdErr redirectedStdErr; timer.start(); invokeActiveTestCase(); redirectedCout += redirectedStdOut.str(); redirectedCerr += redirectedStdErr.str(); #else OutputRedirect r(redirectedCout, redirectedCerr); timer.start(); invokeActiveTestCase(); #endif } else { timer.start(); invokeActiveTestCase(); } duration = timer.getElapsedSeconds(); } CATCH_CATCH_ANON (TestFailureException&) { // This just means the test was aborted due to failure } CATCH_CATCH_ALL { // Under CATCH_CONFIG_FAST_COMPILE, unexpected exceptions under REQUIRE assertions // are reported without translation at the point of origin. if( m_shouldReportUnexpected ) { AssertionReaction dummyReaction; handleUnexpectedInflightException( m_lastAssertionInfo, translateActiveException(), dummyReaction ); } } Counts assertions = m_totals.assertions - prevAssertions; bool missingAssertions = testForMissingAssertions(assertions); m_testCaseTracker->close(); handleUnfinishedSections(); m_messages.clear(); SectionStats testCaseSectionStats(testCaseSection, assertions, duration, missingAssertions); m_reporter->sectionEnded(testCaseSectionStats); } void RunContext::invokeActiveTestCase() { FatalConditionHandler fatalConditionHandler; // Handle signals m_activeTestCase->invoke(); fatalConditionHandler.reset(); } void RunContext::handleUnfinishedSections() { // If sections ended prematurely due to an exception we stored their // infos here so we can tear them down outside the unwind process. for (auto it = m_unfinishedSections.rbegin(), itEnd = m_unfinishedSections.rend(); it != itEnd; ++it) sectionEnded(*it); m_unfinishedSections.clear(); } void RunContext::handleExpr( AssertionInfo const& info, ITransientExpression const& expr, AssertionReaction& reaction ) { m_reporter->assertionStarting( info ); bool negated = isFalseTest( info.resultDisposition ); bool result = expr.getResult() != negated; if( result ) { if (!m_includeSuccessfulResults) { assertionPassed(); } else { reportExpr(info, ResultWas::Ok, &expr, negated); } } else { reportExpr(info, ResultWas::ExpressionFailed, &expr, negated ); populateReaction( reaction ); } } void RunContext::reportExpr( AssertionInfo const &info, ResultWas::OfType resultType, ITransientExpression const *expr, bool negated ) { m_lastAssertionInfo = info; AssertionResultData data( resultType, LazyExpression( negated ) ); AssertionResult assertionResult{ info, data }; assertionResult.m_resultData.lazyExpression.m_transientExpression = expr; assertionEnded( assertionResult ); } void RunContext::handleMessage( AssertionInfo const& info, ResultWas::OfType resultType, StringRef const& message, AssertionReaction& reaction ) { m_reporter->assertionStarting( info ); m_lastAssertionInfo = info; AssertionResultData data( resultType, LazyExpression( false ) ); data.message = message; AssertionResult assertionResult{ m_lastAssertionInfo, data }; assertionEnded( assertionResult ); if( !assertionResult.isOk() ) populateReaction( reaction ); } void RunContext::handleUnexpectedExceptionNotThrown( AssertionInfo const& info, AssertionReaction& reaction ) { handleNonExpr(info, Catch::ResultWas::DidntThrowException, reaction); } void RunContext::handleUnexpectedInflightException( AssertionInfo const& info, std::string const& message, AssertionReaction& reaction ) { m_lastAssertionInfo = info; AssertionResultData data( ResultWas::ThrewException, LazyExpression( false ) ); data.message = message; AssertionResult assertionResult{ info, data }; assertionEnded( assertionResult ); populateReaction( reaction ); } void RunContext::populateReaction( AssertionReaction& reaction ) { reaction.shouldDebugBreak = m_config->shouldDebugBreak(); reaction.shouldThrow = aborting() || (m_lastAssertionInfo.resultDisposition & ResultDisposition::Normal); } void RunContext::handleIncomplete( AssertionInfo const& info ) { m_lastAssertionInfo = info; AssertionResultData data( ResultWas::ThrewException, LazyExpression( false ) ); data.message = "Exception translation was disabled by CATCH_CONFIG_FAST_COMPILE"; AssertionResult assertionResult{ info, data }; assertionEnded( assertionResult ); } void RunContext::handleNonExpr( AssertionInfo const &info, ResultWas::OfType resultType, AssertionReaction &reaction ) { m_lastAssertionInfo = info; AssertionResultData data( resultType, LazyExpression( false ) ); AssertionResult assertionResult{ info, data }; assertionEnded( assertionResult ); if( !assertionResult.isOk() ) populateReaction( reaction ); } IResultCapture& getResultCapture() { if (auto* capture = getCurrentContext().getResultCapture()) return *capture; else CATCH_INTERNAL_ERROR("No result capture instance"); } } // end catch_run_context.cpp // start catch_section.cpp namespace Catch { Section::Section( SectionInfo const& info ) : m_info( info ), m_sectionIncluded( getResultCapture().sectionStarted( m_info, m_assertions ) ) { m_timer.start(); } Section::~Section() { if( m_sectionIncluded ) { SectionEndInfo endInfo{ m_info, m_assertions, m_timer.getElapsedSeconds() }; if( uncaught_exceptions() ) getResultCapture().sectionEndedEarly( endInfo ); else getResultCapture().sectionEnded( endInfo ); } } // This indicates whether the section should be executed or not Section::operator bool() const { return m_sectionIncluded; } } // end namespace Catch // end catch_section.cpp // start catch_section_info.cpp namespace Catch { SectionInfo::SectionInfo ( SourceLineInfo const& _lineInfo, std::string const& _name ) : name( _name ), lineInfo( _lineInfo ) {} } // end namespace Catch // end catch_section_info.cpp // start catch_session.cpp // start catch_session.h #include namespace Catch { class Session : NonCopyable { public: Session(); ~Session() override; void showHelp() const; void libIdentify(); int applyCommandLine( int argc, char const * const * argv ); #if defined(CATCH_CONFIG_WCHAR) && defined(WIN32) && defined(UNICODE) int applyCommandLine( int argc, wchar_t const * const * argv ); #endif void useConfigData( ConfigData const& configData ); template int run(int argc, CharT const * const argv[]) { if (m_startupExceptions) return 1; int returnCode = applyCommandLine(argc, argv); if (returnCode == 0) returnCode = run(); return returnCode; } int run(); clara::Parser const& cli() const; void cli( clara::Parser const& newParser ); ConfigData& configData(); Config& config(); private: int runInternal(); clara::Parser m_cli; ConfigData m_configData; std::shared_ptr m_config; bool m_startupExceptions = false; }; } // end namespace Catch // end catch_session.h // start catch_version.h #include namespace Catch { // Versioning information struct Version { Version( Version const& ) = delete; Version& operator=( Version const& ) = delete; Version( unsigned int _majorVersion, unsigned int _minorVersion, unsigned int _patchNumber, char const * const _branchName, unsigned int _buildNumber ); unsigned int const majorVersion; unsigned int const minorVersion; unsigned int const patchNumber; // buildNumber is only used if branchName is not null char const * const branchName; unsigned int const buildNumber; friend std::ostream& operator << ( std::ostream& os, Version const& version ); }; Version const& libraryVersion(); } // end catch_version.h #include #include namespace Catch { namespace { const int MaxExitCode = 255; IStreamingReporterPtr createReporter(std::string const& reporterName, IConfigPtr const& config) { auto reporter = Catch::getRegistryHub().getReporterRegistry().create(reporterName, config); CATCH_ENFORCE(reporter, "No reporter registered with name: '" << reporterName << "'"); return reporter; } IStreamingReporterPtr makeReporter(std::shared_ptr const& config) { if (Catch::getRegistryHub().getReporterRegistry().getListeners().empty()) { return createReporter(config->getReporterName(), config); } // On older platforms, returning std::unique_ptr // when the return type is std::unique_ptr // doesn't compile without a std::move call. However, this causes // a warning on newer platforms. Thus, we have to work around // it a bit and downcast the pointer manually. auto ret = std::unique_ptr(new ListeningReporter); auto& multi = static_cast(*ret); auto const& listeners = Catch::getRegistryHub().getReporterRegistry().getListeners(); for (auto const& listener : listeners) { multi.addListener(listener->create(Catch::ReporterConfig(config))); } multi.addReporter(createReporter(config->getReporterName(), config)); return ret; } Catch::Totals runTests(std::shared_ptr const& config) { auto reporter = makeReporter(config); RunContext context(config, std::move(reporter)); Totals totals; context.testGroupStarting(config->name(), 1, 1); TestSpec testSpec = config->testSpec(); auto const& allTestCases = getAllTestCasesSorted(*config); for (auto const& testCase : allTestCases) { if (!context.aborting() && matchTest(testCase, testSpec, *config)) totals += context.runTest(testCase); else context.reporter().skipTest(testCase); } if (config->warnAboutNoTests() && totals.testCases.total() == 0) { ReusableStringStream testConfig; bool first = true; for (const auto& input : config->getTestsOrTags()) { if (!first) { testConfig << ' '; } first = false; testConfig << input; } context.reporter().noMatchingTestCases(testConfig.str()); totals.error = -1; } context.testGroupEnded(config->name(), totals, 1, 1); return totals; } void applyFilenamesAsTags(Catch::IConfig const& config) { auto& tests = const_cast&>(getAllTestCasesSorted(config)); for (auto& testCase : tests) { auto tags = testCase.tags; std::string filename = testCase.lineInfo.file; auto lastSlash = filename.find_last_of("\\/"); if (lastSlash != std::string::npos) { filename.erase(0, lastSlash); filename[0] = '#'; } auto lastDot = filename.find_last_of('.'); if (lastDot != std::string::npos) { filename.erase(lastDot); } tags.push_back(std::move(filename)); setTags(testCase, tags); } } } // anon namespace Session::Session() { static bool alreadyInstantiated = false; if( alreadyInstantiated ) { CATCH_TRY { CATCH_INTERNAL_ERROR( "Only one instance of Catch::Session can ever be used" ); } CATCH_CATCH_ALL { getMutableRegistryHub().registerStartupException(); } } // There cannot be exceptions at startup in no-exception mode. #if !defined(CATCH_CONFIG_DISABLE_EXCEPTIONS) const auto& exceptions = getRegistryHub().getStartupExceptionRegistry().getExceptions(); if ( !exceptions.empty() ) { m_startupExceptions = true; Colour colourGuard( Colour::Red ); Catch::cerr() << "Errors occurred during startup!" << '\n'; // iterate over all exceptions and notify user for ( const auto& ex_ptr : exceptions ) { try { std::rethrow_exception(ex_ptr); } catch ( std::exception const& ex ) { Catch::cerr() << Column( ex.what() ).indent(2) << '\n'; } } } #endif alreadyInstantiated = true; m_cli = makeCommandLineParser( m_configData ); } Session::~Session() { Catch::cleanUp(); } void Session::showHelp() const { Catch::cout() << "\nCatch v" << libraryVersion() << "\n" << m_cli << std::endl << "For more detailed usage please see the project docs\n" << std::endl; } void Session::libIdentify() { Catch::cout() << std::left << std::setw(16) << "description: " << "A Catch test executable\n" << std::left << std::setw(16) << "category: " << "testframework\n" << std::left << std::setw(16) << "framework: " << "Catch Test\n" << std::left << std::setw(16) << "version: " << libraryVersion() << std::endl; } int Session::applyCommandLine( int argc, char const * const * argv ) { if( m_startupExceptions ) return 1; auto result = m_cli.parse( clara::Args( argc, argv ) ); if( !result ) { Catch::cerr() << Colour( Colour::Red ) << "\nError(s) in input:\n" << Column( result.errorMessage() ).indent( 2 ) << "\n\n"; Catch::cerr() << "Run with -? for usage\n" << std::endl; return MaxExitCode; } if( m_configData.showHelp ) showHelp(); if( m_configData.libIdentify ) libIdentify(); m_config.reset(); return 0; } #if defined(CATCH_CONFIG_WCHAR) && defined(WIN32) && defined(UNICODE) int Session::applyCommandLine( int argc, wchar_t const * const * argv ) { char **utf8Argv = new char *[ argc ]; for ( int i = 0; i < argc; ++i ) { int bufSize = WideCharToMultiByte( CP_UTF8, 0, argv[i], -1, NULL, 0, NULL, NULL ); utf8Argv[ i ] = new char[ bufSize ]; WideCharToMultiByte( CP_UTF8, 0, argv[i], -1, utf8Argv[i], bufSize, NULL, NULL ); } int returnCode = applyCommandLine( argc, utf8Argv ); for ( int i = 0; i < argc; ++i ) delete [] utf8Argv[ i ]; delete [] utf8Argv; return returnCode; } #endif void Session::useConfigData( ConfigData const& configData ) { m_configData = configData; m_config.reset(); } int Session::run() { if( ( m_configData.waitForKeypress & WaitForKeypress::BeforeStart ) != 0 ) { Catch::cout() << "...waiting for enter/ return before starting" << std::endl; static_cast(std::getchar()); } int exitCode = runInternal(); if( ( m_configData.waitForKeypress & WaitForKeypress::BeforeExit ) != 0 ) { Catch::cout() << "...waiting for enter/ return before exiting, with code: " << exitCode << std::endl; static_cast(std::getchar()); } return exitCode; } clara::Parser const& Session::cli() const { return m_cli; } void Session::cli( clara::Parser const& newParser ) { m_cli = newParser; } ConfigData& Session::configData() { return m_configData; } Config& Session::config() { if( !m_config ) m_config = std::make_shared( m_configData ); return *m_config; } int Session::runInternal() { if( m_startupExceptions ) return 1; if (m_configData.showHelp || m_configData.libIdentify) { return 0; } CATCH_TRY { config(); // Force config to be constructed seedRng( *m_config ); if( m_configData.filenamesAsTags ) applyFilenamesAsTags( *m_config ); // Handle list request if( Option listed = list( config() ) ) return static_cast( *listed ); auto totals = runTests( m_config ); // Note that on unices only the lower 8 bits are usually used, clamping // the return value to 255 prevents false negative when some multiple // of 256 tests has failed return (std::min) (MaxExitCode, (std::max) (totals.error, static_cast(totals.assertions.failed))); } #if !defined(CATCH_CONFIG_DISABLE_EXCEPTIONS) catch( std::exception& ex ) { Catch::cerr() << ex.what() << std::endl; return MaxExitCode; } #endif } } // end namespace Catch // end catch_session.cpp // start catch_singletons.cpp #include namespace Catch { namespace { static auto getSingletons() -> std::vector*& { static std::vector* g_singletons = nullptr; if( !g_singletons ) g_singletons = new std::vector(); return g_singletons; } } ISingleton::~ISingleton() {} void addSingleton(ISingleton* singleton ) { getSingletons()->push_back( singleton ); } void cleanupSingletons() { auto& singletons = getSingletons(); for( auto singleton : *singletons ) delete singleton; delete singletons; singletons = nullptr; } } // namespace Catch // end catch_singletons.cpp // start catch_startup_exception_registry.cpp namespace Catch { void StartupExceptionRegistry::add( std::exception_ptr const& exception ) noexcept { CATCH_TRY { m_exceptions.push_back(exception); } CATCH_CATCH_ALL { // If we run out of memory during start-up there's really not a lot more we can do about it std::terminate(); } } std::vector const& StartupExceptionRegistry::getExceptions() const noexcept { return m_exceptions; } } // end namespace Catch // end catch_startup_exception_registry.cpp // start catch_stream.cpp #include #include #include #include #include #include namespace Catch { Catch::IStream::~IStream() = default; namespace detail { namespace { template class StreamBufImpl : public std::streambuf { char data[bufferSize]; WriterF m_writer; public: StreamBufImpl() { setp( data, data + sizeof(data) ); } ~StreamBufImpl() noexcept { StreamBufImpl::sync(); } private: int overflow( int c ) override { sync(); if( c != EOF ) { if( pbase() == epptr() ) m_writer( std::string( 1, static_cast( c ) ) ); else sputc( static_cast( c ) ); } return 0; } int sync() override { if( pbase() != pptr() ) { m_writer( std::string( pbase(), static_cast( pptr() - pbase() ) ) ); setp( pbase(), epptr() ); } return 0; } }; /////////////////////////////////////////////////////////////////////////// struct OutputDebugWriter { void operator()( std::string const&str ) { writeToDebugConsole( str ); } }; /////////////////////////////////////////////////////////////////////////// class FileStream : public IStream { mutable std::ofstream m_ofs; public: FileStream( StringRef filename ) { m_ofs.open( filename.c_str() ); CATCH_ENFORCE( !m_ofs.fail(), "Unable to open file: '" << filename << "'" ); } ~FileStream() override = default; public: // IStream std::ostream& stream() const override { return m_ofs; } }; /////////////////////////////////////////////////////////////////////////// class CoutStream : public IStream { mutable std::ostream m_os; public: // Store the streambuf from cout up-front because // cout may get redirected when running tests CoutStream() : m_os( Catch::cout().rdbuf() ) {} ~CoutStream() override = default; public: // IStream std::ostream& stream() const override { return m_os; } }; /////////////////////////////////////////////////////////////////////////// class DebugOutStream : public IStream { std::unique_ptr> m_streamBuf; mutable std::ostream m_os; public: DebugOutStream() : m_streamBuf( new StreamBufImpl() ), m_os( m_streamBuf.get() ) {} ~DebugOutStream() override = default; public: // IStream std::ostream& stream() const override { return m_os; } }; }} // namespace anon::detail /////////////////////////////////////////////////////////////////////////// auto makeStream( StringRef const &filename ) -> IStream const* { if( filename.empty() ) return new detail::CoutStream(); else if( filename[0] == '%' ) { if( filename == "%debug" ) return new detail::DebugOutStream(); else CATCH_ERROR( "Unrecognised stream: '" << filename << "'" ); } else return new detail::FileStream( filename ); } // This class encapsulates the idea of a pool of ostringstreams that can be reused. struct StringStreams { std::vector> m_streams; std::vector m_unused; std::ostringstream m_referenceStream; // Used for copy state/ flags from auto add() -> std::size_t { if( m_unused.empty() ) { m_streams.push_back( std::unique_ptr( new std::ostringstream ) ); return m_streams.size()-1; } else { auto index = m_unused.back(); m_unused.pop_back(); return index; } } void release( std::size_t index ) { m_streams[index]->copyfmt( m_referenceStream ); // Restore initial flags and other state m_unused.push_back(index); } }; ReusableStringStream::ReusableStringStream() : m_index( Singleton::getMutable().add() ), m_oss( Singleton::getMutable().m_streams[m_index].get() ) {} ReusableStringStream::~ReusableStringStream() { static_cast( m_oss )->str(""); m_oss->clear(); Singleton::getMutable().release( m_index ); } auto ReusableStringStream::str() const -> std::string { return static_cast( m_oss )->str(); } /////////////////////////////////////////////////////////////////////////// #ifndef CATCH_CONFIG_NOSTDOUT // If you #define this you must implement these functions std::ostream& cout() { return std::cout; } std::ostream& cerr() { return std::cerr; } std::ostream& clog() { return std::clog; } #endif } // end catch_stream.cpp // start catch_string_manip.cpp #include #include #include #include namespace Catch { namespace { char toLowerCh(char c) { return static_cast( std::tolower( c ) ); } } bool startsWith( std::string const& s, std::string const& prefix ) { return s.size() >= prefix.size() && std::equal(prefix.begin(), prefix.end(), s.begin()); } bool startsWith( std::string const& s, char prefix ) { return !s.empty() && s[0] == prefix; } bool endsWith( std::string const& s, std::string const& suffix ) { return s.size() >= suffix.size() && std::equal(suffix.rbegin(), suffix.rend(), s.rbegin()); } bool endsWith( std::string const& s, char suffix ) { return !s.empty() && s[s.size()-1] == suffix; } bool contains( std::string const& s, std::string const& infix ) { return s.find( infix ) != std::string::npos; } void toLowerInPlace( std::string& s ) { std::transform( s.begin(), s.end(), s.begin(), toLowerCh ); } std::string toLower( std::string const& s ) { std::string lc = s; toLowerInPlace( lc ); return lc; } std::string trim( std::string const& str ) { static char const* whitespaceChars = "\n\r\t "; std::string::size_type start = str.find_first_not_of( whitespaceChars ); std::string::size_type end = str.find_last_not_of( whitespaceChars ); return start != std::string::npos ? str.substr( start, 1+end-start ) : std::string(); } bool replaceInPlace( std::string& str, std::string const& replaceThis, std::string const& withThis ) { bool replaced = false; std::size_t i = str.find( replaceThis ); while( i != std::string::npos ) { replaced = true; str = str.substr( 0, i ) + withThis + str.substr( i+replaceThis.size() ); if( i < str.size()-withThis.size() ) i = str.find( replaceThis, i+withThis.size() ); else i = std::string::npos; } return replaced; } pluralise::pluralise( std::size_t count, std::string const& label ) : m_count( count ), m_label( label ) {} std::ostream& operator << ( std::ostream& os, pluralise const& pluraliser ) { os << pluraliser.m_count << ' ' << pluraliser.m_label; if( pluraliser.m_count != 1 ) os << 's'; return os; } } // end catch_string_manip.cpp // start catch_stringref.cpp #if defined(__clang__) # pragma clang diagnostic push # pragma clang diagnostic ignored "-Wexit-time-destructors" #endif #include #include #include namespace { const uint32_t byte_2_lead = 0xC0; const uint32_t byte_3_lead = 0xE0; const uint32_t byte_4_lead = 0xF0; } namespace Catch { StringRef::StringRef( char const* rawChars ) noexcept : StringRef( rawChars, static_cast(std::strlen(rawChars) ) ) {} StringRef::operator std::string() const { return std::string( m_start, m_size ); } void StringRef::swap( StringRef& other ) noexcept { std::swap( m_start, other.m_start ); std::swap( m_size, other.m_size ); std::swap( m_data, other.m_data ); } auto StringRef::c_str() const -> char const* { if( isSubstring() ) const_cast( this )->takeOwnership(); return m_start; } auto StringRef::currentData() const noexcept -> char const* { return m_start; } auto StringRef::isOwned() const noexcept -> bool { return m_data != nullptr; } auto StringRef::isSubstring() const noexcept -> bool { return m_start[m_size] != '\0'; } void StringRef::takeOwnership() { if( !isOwned() ) { m_data = new char[m_size+1]; memcpy( m_data, m_start, m_size ); m_data[m_size] = '\0'; m_start = m_data; } } auto StringRef::substr( size_type start, size_type size ) const noexcept -> StringRef { if( start < m_size ) return StringRef( m_start+start, size ); else return StringRef(); } auto StringRef::operator == ( StringRef const& other ) const noexcept -> bool { return size() == other.size() && (std::strncmp( m_start, other.m_start, size() ) == 0); } auto StringRef::operator != ( StringRef const& other ) const noexcept -> bool { return !operator==( other ); } auto StringRef::operator[](size_type index) const noexcept -> char { return m_start[index]; } auto StringRef::numberOfCharacters() const noexcept -> size_type { size_type noChars = m_size; // Make adjustments for uft encodings for( size_type i=0; i < m_size; ++i ) { char c = m_start[i]; if( ( c & byte_2_lead ) == byte_2_lead ) { noChars--; if (( c & byte_3_lead ) == byte_3_lead ) noChars--; if( ( c & byte_4_lead ) == byte_4_lead ) noChars--; } } return noChars; } auto operator + ( StringRef const& lhs, StringRef const& rhs ) -> std::string { std::string str; str.reserve( lhs.size() + rhs.size() ); str += lhs; str += rhs; return str; } auto operator + ( StringRef const& lhs, const char* rhs ) -> std::string { return std::string( lhs ) + std::string( rhs ); } auto operator + ( char const* lhs, StringRef const& rhs ) -> std::string { return std::string( lhs ) + std::string( rhs ); } auto operator << ( std::ostream& os, StringRef const& str ) -> std::ostream& { return os.write(str.currentData(), str.size()); } auto operator+=( std::string& lhs, StringRef const& rhs ) -> std::string& { lhs.append(rhs.currentData(), rhs.size()); return lhs; } } // namespace Catch #if defined(__clang__) # pragma clang diagnostic pop #endif // end catch_stringref.cpp // start catch_tag_alias.cpp namespace Catch { TagAlias::TagAlias(std::string const & _tag, SourceLineInfo _lineInfo): tag(_tag), lineInfo(_lineInfo) {} } // end catch_tag_alias.cpp // start catch_tag_alias_autoregistrar.cpp namespace Catch { RegistrarForTagAliases::RegistrarForTagAliases(char const* alias, char const* tag, SourceLineInfo const& lineInfo) { CATCH_TRY { getMutableRegistryHub().registerTagAlias(alias, tag, lineInfo); } CATCH_CATCH_ALL { // Do not throw when constructing global objects, instead register the exception to be processed later getMutableRegistryHub().registerStartupException(); } } } // end catch_tag_alias_autoregistrar.cpp // start catch_tag_alias_registry.cpp #include namespace Catch { TagAliasRegistry::~TagAliasRegistry() {} TagAlias const* TagAliasRegistry::find( std::string const& alias ) const { auto it = m_registry.find( alias ); if( it != m_registry.end() ) return &(it->second); else return nullptr; } std::string TagAliasRegistry::expandAliases( std::string const& unexpandedTestSpec ) const { std::string expandedTestSpec = unexpandedTestSpec; for( auto const& registryKvp : m_registry ) { std::size_t pos = expandedTestSpec.find( registryKvp.first ); if( pos != std::string::npos ) { expandedTestSpec = expandedTestSpec.substr( 0, pos ) + registryKvp.second.tag + expandedTestSpec.substr( pos + registryKvp.first.size() ); } } return expandedTestSpec; } void TagAliasRegistry::add( std::string const& alias, std::string const& tag, SourceLineInfo const& lineInfo ) { CATCH_ENFORCE( startsWith(alias, "[@") && endsWith(alias, ']'), "error: tag alias, '" << alias << "' is not of the form [@alias name].\n" << lineInfo ); CATCH_ENFORCE( m_registry.insert(std::make_pair(alias, TagAlias(tag, lineInfo))).second, "error: tag alias, '" << alias << "' already registered.\n" << "\tFirst seen at: " << find(alias)->lineInfo << "\n" << "\tRedefined at: " << lineInfo ); } ITagAliasRegistry::~ITagAliasRegistry() {} ITagAliasRegistry const& ITagAliasRegistry::get() { return getRegistryHub().getTagAliasRegistry(); } } // end namespace Catch // end catch_tag_alias_registry.cpp // start catch_test_case_info.cpp #include #include #include #include namespace Catch { namespace { TestCaseInfo::SpecialProperties parseSpecialTag( std::string const& tag ) { if( startsWith( tag, '.' ) || tag == "!hide" ) return TestCaseInfo::IsHidden; else if( tag == "!throws" ) return TestCaseInfo::Throws; else if( tag == "!shouldfail" ) return TestCaseInfo::ShouldFail; else if( tag == "!mayfail" ) return TestCaseInfo::MayFail; else if( tag == "!nonportable" ) return TestCaseInfo::NonPortable; else if( tag == "!benchmark" ) return static_cast( TestCaseInfo::Benchmark | TestCaseInfo::IsHidden ); else return TestCaseInfo::None; } bool isReservedTag( std::string const& tag ) { return parseSpecialTag( tag ) == TestCaseInfo::None && tag.size() > 0 && !std::isalnum( static_cast(tag[0]) ); } void enforceNotReservedTag( std::string const& tag, SourceLineInfo const& _lineInfo ) { CATCH_ENFORCE( !isReservedTag(tag), "Tag name: [" << tag << "] is not allowed.\n" << "Tag names starting with non alpha-numeric characters are reserved\n" << _lineInfo ); } } TestCase makeTestCase( ITestInvoker* _testCase, std::string const& _className, NameAndTags const& nameAndTags, SourceLineInfo const& _lineInfo ) { bool isHidden = false; // Parse out tags std::vector tags; std::string desc, tag; bool inTag = false; std::string _descOrTags = nameAndTags.tags; for (char c : _descOrTags) { if( !inTag ) { if( c == '[' ) inTag = true; else desc += c; } else { if( c == ']' ) { TestCaseInfo::SpecialProperties prop = parseSpecialTag( tag ); if( ( prop & TestCaseInfo::IsHidden ) != 0 ) isHidden = true; else if( prop == TestCaseInfo::None ) enforceNotReservedTag( tag, _lineInfo ); tags.push_back( tag ); tag.clear(); inTag = false; } else tag += c; } } if( isHidden ) { tags.push_back( "." ); } TestCaseInfo info( nameAndTags.name, _className, desc, tags, _lineInfo ); return TestCase( _testCase, std::move(info) ); } void setTags( TestCaseInfo& testCaseInfo, std::vector tags ) { std::sort(begin(tags), end(tags)); tags.erase(std::unique(begin(tags), end(tags)), end(tags)); testCaseInfo.lcaseTags.clear(); for( auto const& tag : tags ) { std::string lcaseTag = toLower( tag ); testCaseInfo.properties = static_cast( testCaseInfo.properties | parseSpecialTag( lcaseTag ) ); testCaseInfo.lcaseTags.push_back( lcaseTag ); } testCaseInfo.tags = std::move(tags); } TestCaseInfo::TestCaseInfo( std::string const& _name, std::string const& _className, std::string const& _description, std::vector const& _tags, SourceLineInfo const& _lineInfo ) : name( _name ), className( _className ), description( _description ), lineInfo( _lineInfo ), properties( None ) { setTags( *this, _tags ); } bool TestCaseInfo::isHidden() const { return ( properties & IsHidden ) != 0; } bool TestCaseInfo::throws() const { return ( properties & Throws ) != 0; } bool TestCaseInfo::okToFail() const { return ( properties & (ShouldFail | MayFail ) ) != 0; } bool TestCaseInfo::expectedToFail() const { return ( properties & (ShouldFail ) ) != 0; } std::string TestCaseInfo::tagsAsString() const { std::string ret; // '[' and ']' per tag std::size_t full_size = 2 * tags.size(); for (const auto& tag : tags) { full_size += tag.size(); } ret.reserve(full_size); for (const auto& tag : tags) { ret.push_back('['); ret.append(tag); ret.push_back(']'); } return ret; } TestCase::TestCase( ITestInvoker* testCase, TestCaseInfo&& info ) : TestCaseInfo( std::move(info) ), test( testCase ) {} TestCase TestCase::withName( std::string const& _newName ) const { TestCase other( *this ); other.name = _newName; return other; } void TestCase::invoke() const { test->invoke(); } bool TestCase::operator == ( TestCase const& other ) const { return test.get() == other.test.get() && name == other.name && className == other.className; } bool TestCase::operator < ( TestCase const& other ) const { return name < other.name; } TestCaseInfo const& TestCase::getTestCaseInfo() const { return *this; } } // end namespace Catch // end catch_test_case_info.cpp // start catch_test_case_registry_impl.cpp #include namespace Catch { std::vector sortTests( IConfig const& config, std::vector const& unsortedTestCases ) { std::vector sorted = unsortedTestCases; switch( config.runOrder() ) { case RunTests::InLexicographicalOrder: std::sort( sorted.begin(), sorted.end() ); break; case RunTests::InRandomOrder: seedRng( config ); std::shuffle( sorted.begin(), sorted.end(), rng() ); break; case RunTests::InDeclarationOrder: // already in declaration order break; } return sorted; } bool matchTest( TestCase const& testCase, TestSpec const& testSpec, IConfig const& config ) { return testSpec.matches( testCase ) && ( config.allowThrows() || !testCase.throws() ); } void enforceNoDuplicateTestCases( std::vector const& functions ) { std::set seenFunctions; for( auto const& function : functions ) { auto prev = seenFunctions.insert( function ); CATCH_ENFORCE( prev.second, "error: TEST_CASE( \"" << function.name << "\" ) already defined.\n" << "\tFirst seen at " << prev.first->getTestCaseInfo().lineInfo << "\n" << "\tRedefined at " << function.getTestCaseInfo().lineInfo ); } } std::vector filterTests( std::vector const& testCases, TestSpec const& testSpec, IConfig const& config ) { std::vector filtered; filtered.reserve( testCases.size() ); for( auto const& testCase : testCases ) if( matchTest( testCase, testSpec, config ) ) filtered.push_back( testCase ); return filtered; } std::vector const& getAllTestCasesSorted( IConfig const& config ) { return getRegistryHub().getTestCaseRegistry().getAllTestsSorted( config ); } void TestRegistry::registerTest( TestCase const& testCase ) { std::string name = testCase.getTestCaseInfo().name; if( name.empty() ) { ReusableStringStream rss; rss << "Anonymous test case " << ++m_unnamedCount; return registerTest( testCase.withName( rss.str() ) ); } m_functions.push_back( testCase ); } std::vector const& TestRegistry::getAllTests() const { return m_functions; } std::vector const& TestRegistry::getAllTestsSorted( IConfig const& config ) const { if( m_sortedFunctions.empty() ) enforceNoDuplicateTestCases( m_functions ); if( m_currentSortOrder != config.runOrder() || m_sortedFunctions.empty() ) { m_sortedFunctions = sortTests( config, m_functions ); m_currentSortOrder = config.runOrder(); } return m_sortedFunctions; } /////////////////////////////////////////////////////////////////////////// TestInvokerAsFunction::TestInvokerAsFunction( void(*testAsFunction)() ) noexcept : m_testAsFunction( testAsFunction ) {} void TestInvokerAsFunction::invoke() const { m_testAsFunction(); } std::string extractClassName( StringRef const& classOrQualifiedMethodName ) { std::string className = classOrQualifiedMethodName; if( startsWith( className, '&' ) ) { std::size_t lastColons = className.rfind( "::" ); std::size_t penultimateColons = className.rfind( "::", lastColons-1 ); if( penultimateColons == std::string::npos ) penultimateColons = 1; className = className.substr( penultimateColons, lastColons-penultimateColons ); } return className; } } // end namespace Catch // end catch_test_case_registry_impl.cpp // start catch_test_case_tracker.cpp #include #include #include #include #include #if defined(__clang__) # pragma clang diagnostic push # pragma clang diagnostic ignored "-Wexit-time-destructors" #endif namespace Catch { namespace TestCaseTracking { NameAndLocation::NameAndLocation( std::string const& _name, SourceLineInfo const& _location ) : name( _name ), location( _location ) {} ITracker::~ITracker() = default; TrackerContext& TrackerContext::instance() { static TrackerContext s_instance; return s_instance; } ITracker& TrackerContext::startRun() { m_rootTracker = std::make_shared( NameAndLocation( "{root}", CATCH_INTERNAL_LINEINFO ), *this, nullptr ); m_currentTracker = nullptr; m_runState = Executing; return *m_rootTracker; } void TrackerContext::endRun() { m_rootTracker.reset(); m_currentTracker = nullptr; m_runState = NotStarted; } void TrackerContext::startCycle() { m_currentTracker = m_rootTracker.get(); m_runState = Executing; } void TrackerContext::completeCycle() { m_runState = CompletedCycle; } bool TrackerContext::completedCycle() const { return m_runState == CompletedCycle; } ITracker& TrackerContext::currentTracker() { return *m_currentTracker; } void TrackerContext::setCurrentTracker( ITracker* tracker ) { m_currentTracker = tracker; } TrackerBase::TrackerBase( NameAndLocation const& nameAndLocation, TrackerContext& ctx, ITracker* parent ) : m_nameAndLocation( nameAndLocation ), m_ctx( ctx ), m_parent( parent ) {} NameAndLocation const& TrackerBase::nameAndLocation() const { return m_nameAndLocation; } bool TrackerBase::isComplete() const { return m_runState == CompletedSuccessfully || m_runState == Failed; } bool TrackerBase::isSuccessfullyCompleted() const { return m_runState == CompletedSuccessfully; } bool TrackerBase::isOpen() const { return m_runState != NotStarted && !isComplete(); } bool TrackerBase::hasChildren() const { return !m_children.empty(); } void TrackerBase::addChild( ITrackerPtr const& child ) { m_children.push_back( child ); } ITrackerPtr TrackerBase::findChild( NameAndLocation const& nameAndLocation ) { auto it = std::find_if( m_children.begin(), m_children.end(), [&nameAndLocation]( ITrackerPtr const& tracker ){ return tracker->nameAndLocation().location == nameAndLocation.location && tracker->nameAndLocation().name == nameAndLocation.name; } ); return( it != m_children.end() ) ? *it : nullptr; } ITracker& TrackerBase::parent() { assert( m_parent ); // Should always be non-null except for root return *m_parent; } void TrackerBase::openChild() { if( m_runState != ExecutingChildren ) { m_runState = ExecutingChildren; if( m_parent ) m_parent->openChild(); } } bool TrackerBase::isSectionTracker() const { return false; } bool TrackerBase::isGeneratorTracker() const { return false; } void TrackerBase::open() { m_runState = Executing; moveToThis(); if( m_parent ) m_parent->openChild(); } void TrackerBase::close() { // Close any still open children (e.g. generators) while( &m_ctx.currentTracker() != this ) m_ctx.currentTracker().close(); switch( m_runState ) { case NeedsAnotherRun: break; case Executing: m_runState = CompletedSuccessfully; break; case ExecutingChildren: if( m_children.empty() || m_children.back()->isComplete() ) m_runState = CompletedSuccessfully; break; case NotStarted: case CompletedSuccessfully: case Failed: CATCH_INTERNAL_ERROR( "Illogical state: " << m_runState ); default: CATCH_INTERNAL_ERROR( "Unknown state: " << m_runState ); } moveToParent(); m_ctx.completeCycle(); } void TrackerBase::fail() { m_runState = Failed; if( m_parent ) m_parent->markAsNeedingAnotherRun(); moveToParent(); m_ctx.completeCycle(); } void TrackerBase::markAsNeedingAnotherRun() { m_runState = NeedsAnotherRun; } void TrackerBase::moveToParent() { assert( m_parent ); m_ctx.setCurrentTracker( m_parent ); } void TrackerBase::moveToThis() { m_ctx.setCurrentTracker( this ); } SectionTracker::SectionTracker( NameAndLocation const& nameAndLocation, TrackerContext& ctx, ITracker* parent ) : TrackerBase( nameAndLocation, ctx, parent ) { if( parent ) { while( !parent->isSectionTracker() ) parent = &parent->parent(); SectionTracker& parentSection = static_cast( *parent ); addNextFilters( parentSection.m_filters ); } } bool SectionTracker::isComplete() const { bool complete = true; if ((m_filters.empty() || m_filters[0] == "") || std::find(m_filters.begin(), m_filters.end(), m_nameAndLocation.name) != m_filters.end()) complete = TrackerBase::isComplete(); return complete; } bool SectionTracker::isSectionTracker() const { return true; } SectionTracker& SectionTracker::acquire( TrackerContext& ctx, NameAndLocation const& nameAndLocation ) { std::shared_ptr section; ITracker& currentTracker = ctx.currentTracker(); if( ITrackerPtr childTracker = currentTracker.findChild( nameAndLocation ) ) { assert( childTracker ); assert( childTracker->isSectionTracker() ); section = std::static_pointer_cast( childTracker ); } else { section = std::make_shared( nameAndLocation, ctx, ¤tTracker ); currentTracker.addChild( section ); } if( !ctx.completedCycle() ) section->tryOpen(); return *section; } void SectionTracker::tryOpen() { if( !isComplete() && (m_filters.empty() || m_filters[0].empty() || m_filters[0] == m_nameAndLocation.name ) ) open(); } void SectionTracker::addInitialFilters( std::vector const& filters ) { if( !filters.empty() ) { m_filters.push_back(""); // Root - should never be consulted m_filters.push_back(""); // Test Case - not a section filter m_filters.insert( m_filters.end(), filters.begin(), filters.end() ); } } void SectionTracker::addNextFilters( std::vector const& filters ) { if( filters.size() > 1 ) m_filters.insert( m_filters.end(), ++filters.begin(), filters.end() ); } } // namespace TestCaseTracking using TestCaseTracking::ITracker; using TestCaseTracking::TrackerContext; using TestCaseTracking::SectionTracker; } // namespace Catch #if defined(__clang__) # pragma clang diagnostic pop #endif // end catch_test_case_tracker.cpp // start catch_test_registry.cpp namespace Catch { auto makeTestInvoker( void(*testAsFunction)() ) noexcept -> ITestInvoker* { return new(std::nothrow) TestInvokerAsFunction( testAsFunction ); } NameAndTags::NameAndTags( StringRef const& name_ , StringRef const& tags_ ) noexcept : name( name_ ), tags( tags_ ) {} AutoReg::AutoReg( ITestInvoker* invoker, SourceLineInfo const& lineInfo, StringRef const& classOrMethod, NameAndTags const& nameAndTags ) noexcept { CATCH_TRY { getMutableRegistryHub() .registerTest( makeTestCase( invoker, extractClassName( classOrMethod ), nameAndTags, lineInfo)); } CATCH_CATCH_ALL { // Do not throw when constructing global objects, instead register the exception to be processed later getMutableRegistryHub().registerStartupException(); } } AutoReg::~AutoReg() = default; } // end catch_test_registry.cpp // start catch_test_spec.cpp #include #include #include #include namespace Catch { TestSpec::Pattern::~Pattern() = default; TestSpec::NamePattern::~NamePattern() = default; TestSpec::TagPattern::~TagPattern() = default; TestSpec::ExcludedPattern::~ExcludedPattern() = default; TestSpec::NamePattern::NamePattern( std::string const& name ) : m_wildcardPattern( toLower( name ), CaseSensitive::No ) {} bool TestSpec::NamePattern::matches( TestCaseInfo const& testCase ) const { return m_wildcardPattern.matches( toLower( testCase.name ) ); } TestSpec::TagPattern::TagPattern( std::string const& tag ) : m_tag( toLower( tag ) ) {} bool TestSpec::TagPattern::matches( TestCaseInfo const& testCase ) const { return std::find(begin(testCase.lcaseTags), end(testCase.lcaseTags), m_tag) != end(testCase.lcaseTags); } TestSpec::ExcludedPattern::ExcludedPattern( PatternPtr const& underlyingPattern ) : m_underlyingPattern( underlyingPattern ) {} bool TestSpec::ExcludedPattern::matches( TestCaseInfo const& testCase ) const { return !m_underlyingPattern->matches( testCase ); } bool TestSpec::Filter::matches( TestCaseInfo const& testCase ) const { // All patterns in a filter must match for the filter to be a match for( auto const& pattern : m_patterns ) { if( !pattern->matches( testCase ) ) return false; } return true; } bool TestSpec::hasFilters() const { return !m_filters.empty(); } bool TestSpec::matches( TestCaseInfo const& testCase ) const { // A TestSpec matches if any filter matches for( auto const& filter : m_filters ) if( filter.matches( testCase ) ) return true; return false; } } // end catch_test_spec.cpp // start catch_test_spec_parser.cpp namespace Catch { TestSpecParser::TestSpecParser( ITagAliasRegistry const& tagAliases ) : m_tagAliases( &tagAliases ) {} TestSpecParser& TestSpecParser::parse( std::string const& arg ) { m_mode = None; m_exclusion = false; m_start = std::string::npos; m_arg = m_tagAliases->expandAliases( arg ); m_escapeChars.clear(); for( m_pos = 0; m_pos < m_arg.size(); ++m_pos ) visitChar( m_arg[m_pos] ); if( m_mode == Name ) addPattern(); return *this; } TestSpec TestSpecParser::testSpec() { addFilter(); return m_testSpec; } void TestSpecParser::visitChar( char c ) { if( m_mode == None ) { switch( c ) { case ' ': return; case '~': m_exclusion = true; return; case '[': return startNewMode( Tag, ++m_pos ); case '"': return startNewMode( QuotedName, ++m_pos ); case '\\': return escape(); default: startNewMode( Name, m_pos ); break; } } if( m_mode == Name ) { if( c == ',' ) { addPattern(); addFilter(); } else if( c == '[' ) { if( subString() == "exclude:" ) m_exclusion = true; else addPattern(); startNewMode( Tag, ++m_pos ); } else if( c == '\\' ) escape(); } else if( m_mode == EscapedName ) m_mode = Name; else if( m_mode == QuotedName && c == '"' ) addPattern(); else if( m_mode == Tag && c == ']' ) addPattern(); } void TestSpecParser::startNewMode( Mode mode, std::size_t start ) { m_mode = mode; m_start = start; } void TestSpecParser::escape() { if( m_mode == None ) m_start = m_pos; m_mode = EscapedName; m_escapeChars.push_back( m_pos ); } std::string TestSpecParser::subString() const { return m_arg.substr( m_start, m_pos - m_start ); } void TestSpecParser::addFilter() { if( !m_currentFilter.m_patterns.empty() ) { m_testSpec.m_filters.push_back( m_currentFilter ); m_currentFilter = TestSpec::Filter(); } } TestSpec parseTestSpec( std::string const& arg ) { return TestSpecParser( ITagAliasRegistry::get() ).parse( arg ).testSpec(); } } // namespace Catch // end catch_test_spec_parser.cpp // start catch_timer.cpp #include static const uint64_t nanosecondsInSecond = 1000000000; namespace Catch { auto getCurrentNanosecondsSinceEpoch() -> uint64_t { return std::chrono::duration_cast( std::chrono::high_resolution_clock::now().time_since_epoch() ).count(); } namespace { auto estimateClockResolution() -> uint64_t { uint64_t sum = 0; static const uint64_t iterations = 1000000; auto startTime = getCurrentNanosecondsSinceEpoch(); for( std::size_t i = 0; i < iterations; ++i ) { uint64_t ticks; uint64_t baseTicks = getCurrentNanosecondsSinceEpoch(); do { ticks = getCurrentNanosecondsSinceEpoch(); } while( ticks == baseTicks ); auto delta = ticks - baseTicks; sum += delta; // If we have been calibrating for over 3 seconds -- the clock // is terrible and we should move on. // TBD: How to signal that the measured resolution is probably wrong? if (ticks > startTime + 3 * nanosecondsInSecond) { return sum / ( i + 1u ); } } // We're just taking the mean, here. To do better we could take the std. dev and exclude outliers // - and potentially do more iterations if there's a high variance. return sum/iterations; } } auto getEstimatedClockResolution() -> uint64_t { static auto s_resolution = estimateClockResolution(); return s_resolution; } void Timer::start() { m_nanoseconds = getCurrentNanosecondsSinceEpoch(); } auto Timer::getElapsedNanoseconds() const -> uint64_t { return getCurrentNanosecondsSinceEpoch() - m_nanoseconds; } auto Timer::getElapsedMicroseconds() const -> uint64_t { return getElapsedNanoseconds()/1000; } auto Timer::getElapsedMilliseconds() const -> unsigned int { return static_cast(getElapsedMicroseconds()/1000); } auto Timer::getElapsedSeconds() const -> double { return getElapsedMicroseconds()/1000000.0; } } // namespace Catch // end catch_timer.cpp // start catch_tostring.cpp #if defined(__clang__) # pragma clang diagnostic push # pragma clang diagnostic ignored "-Wexit-time-destructors" # pragma clang diagnostic ignored "-Wglobal-constructors" #endif // Enable specific decls locally #if !defined(CATCH_CONFIG_ENABLE_CHRONO_STRINGMAKER) #define CATCH_CONFIG_ENABLE_CHRONO_STRINGMAKER #endif #include #include namespace Catch { namespace Detail { const std::string unprintableString = "{?}"; namespace { const int hexThreshold = 255; struct Endianness { enum Arch { Big, Little }; static Arch which() { union _{ int asInt; char asChar[sizeof (int)]; } u; u.asInt = 1; return ( u.asChar[sizeof(int)-1] == 1 ) ? Big : Little; } }; } std::string rawMemoryToString( const void *object, std::size_t size ) { // Reverse order for little endian architectures int i = 0, end = static_cast( size ), inc = 1; if( Endianness::which() == Endianness::Little ) { i = end-1; end = inc = -1; } unsigned char const *bytes = static_cast(object); ReusableStringStream rss; rss << "0x" << std::setfill('0') << std::hex; for( ; i != end; i += inc ) rss << std::setw(2) << static_cast(bytes[i]); return rss.str(); } } template std::string fpToString( T value, int precision ) { if (Catch::isnan(value)) { return "nan"; } ReusableStringStream rss; rss << std::setprecision( precision ) << std::fixed << value; std::string d = rss.str(); std::size_t i = d.find_last_not_of( '0' ); if( i != std::string::npos && i != d.size()-1 ) { if( d[i] == '.' ) i++; d = d.substr( 0, i+1 ); } return d; } //// ======================================================= //// // // Out-of-line defs for full specialization of StringMaker // //// ======================================================= //// std::string StringMaker::convert(const std::string& str) { if (!getCurrentContext().getConfig()->showInvisibles()) { return '"' + str + '"'; } std::string s("\""); for (char c : str) { switch (c) { case '\n': s.append("\\n"); break; case '\t': s.append("\\t"); break; default: s.push_back(c); break; } } s.append("\""); return s; } #ifdef CATCH_CONFIG_CPP17_STRING_VIEW std::string StringMaker::convert(std::string_view str) { return ::Catch::Detail::stringify(std::string{ str }); } #endif std::string StringMaker::convert(char const* str) { if (str) { return ::Catch::Detail::stringify(std::string{ str }); } else { return{ "{null string}" }; } } std::string StringMaker::convert(char* str) { if (str) { return ::Catch::Detail::stringify(std::string{ str }); } else { return{ "{null string}" }; } } #ifdef CATCH_CONFIG_WCHAR std::string StringMaker::convert(const std::wstring& wstr) { std::string s; s.reserve(wstr.size()); for (auto c : wstr) { s += (c <= 0xff) ? static_cast(c) : '?'; } return ::Catch::Detail::stringify(s); } # ifdef CATCH_CONFIG_CPP17_STRING_VIEW std::string StringMaker::convert(std::wstring_view str) { return StringMaker::convert(std::wstring(str)); } # endif std::string StringMaker::convert(wchar_t const * str) { if (str) { return ::Catch::Detail::stringify(std::wstring{ str }); } else { return{ "{null string}" }; } } std::string StringMaker::convert(wchar_t * str) { if (str) { return ::Catch::Detail::stringify(std::wstring{ str }); } else { return{ "{null string}" }; } } #endif std::string StringMaker::convert(int value) { return ::Catch::Detail::stringify(static_cast(value)); } std::string StringMaker::convert(long value) { return ::Catch::Detail::stringify(static_cast(value)); } std::string StringMaker::convert(long long value) { ReusableStringStream rss; rss << value; if (value > Detail::hexThreshold) { rss << " (0x" << std::hex << value << ')'; } return rss.str(); } std::string StringMaker::convert(unsigned int value) { return ::Catch::Detail::stringify(static_cast(value)); } std::string StringMaker::convert(unsigned long value) { return ::Catch::Detail::stringify(static_cast(value)); } std::string StringMaker::convert(unsigned long long value) { ReusableStringStream rss; rss << value; if (value > Detail::hexThreshold) { rss << " (0x" << std::hex << value << ')'; } return rss.str(); } std::string StringMaker::convert(bool b) { return b ? "true" : "false"; } std::string StringMaker::convert(signed char value) { if (value == '\r') { return "'\\r'"; } else if (value == '\f') { return "'\\f'"; } else if (value == '\n') { return "'\\n'"; } else if (value == '\t') { return "'\\t'"; } else if ('\0' <= value && value < ' ') { return ::Catch::Detail::stringify(static_cast(value)); } else { char chstr[] = "' '"; chstr[1] = value; return chstr; } } std::string StringMaker::convert(char c) { return ::Catch::Detail::stringify(static_cast(c)); } std::string StringMaker::convert(unsigned char c) { return ::Catch::Detail::stringify(static_cast(c)); } std::string StringMaker::convert(std::nullptr_t) { return "nullptr"; } std::string StringMaker::convert(float value) { return fpToString(value, 5) + 'f'; } std::string StringMaker::convert(double value) { return fpToString(value, 10); } std::string ratio_string::symbol() { return "a"; } std::string ratio_string::symbol() { return "f"; } std::string ratio_string::symbol() { return "p"; } std::string ratio_string::symbol() { return "n"; } std::string ratio_string::symbol() { return "u"; } std::string ratio_string::symbol() { return "m"; } } // end namespace Catch #if defined(__clang__) # pragma clang diagnostic pop #endif // end catch_tostring.cpp // start catch_totals.cpp namespace Catch { Counts Counts::operator - ( Counts const& other ) const { Counts diff; diff.passed = passed - other.passed; diff.failed = failed - other.failed; diff.failedButOk = failedButOk - other.failedButOk; return diff; } Counts& Counts::operator += ( Counts const& other ) { passed += other.passed; failed += other.failed; failedButOk += other.failedButOk; return *this; } std::size_t Counts::total() const { return passed + failed + failedButOk; } bool Counts::allPassed() const { return failed == 0 && failedButOk == 0; } bool Counts::allOk() const { return failed == 0; } Totals Totals::operator - ( Totals const& other ) const { Totals diff; diff.assertions = assertions - other.assertions; diff.testCases = testCases - other.testCases; return diff; } Totals& Totals::operator += ( Totals const& other ) { assertions += other.assertions; testCases += other.testCases; return *this; } Totals Totals::delta( Totals const& prevTotals ) const { Totals diff = *this - prevTotals; if( diff.assertions.failed > 0 ) ++diff.testCases.failed; else if( diff.assertions.failedButOk > 0 ) ++diff.testCases.failedButOk; else ++diff.testCases.passed; return diff; } } // end catch_totals.cpp // start catch_uncaught_exceptions.cpp #include namespace Catch { bool uncaught_exceptions() { #if defined(CATCH_CONFIG_CPP17_UNCAUGHT_EXCEPTIONS) return std::uncaught_exceptions() > 0; #else return std::uncaught_exception(); #endif } } // end namespace Catch // end catch_uncaught_exceptions.cpp // start catch_version.cpp #include namespace Catch { Version::Version ( unsigned int _majorVersion, unsigned int _minorVersion, unsigned int _patchNumber, char const * const _branchName, unsigned int _buildNumber ) : majorVersion( _majorVersion ), minorVersion( _minorVersion ), patchNumber( _patchNumber ), branchName( _branchName ), buildNumber( _buildNumber ) {} std::ostream& operator << ( std::ostream& os, Version const& version ) { os << version.majorVersion << '.' << version.minorVersion << '.' << version.patchNumber; // branchName is never null -> 0th char is \0 if it is empty if (version.branchName[0]) { os << '-' << version.branchName << '.' << version.buildNumber; } return os; } Version const& libraryVersion() { static Version version( 2, 6, 0, "", 0 ); return version; } } // end catch_version.cpp // start catch_wildcard_pattern.cpp #include namespace Catch { WildcardPattern::WildcardPattern( std::string const& pattern, CaseSensitive::Choice caseSensitivity ) : m_caseSensitivity( caseSensitivity ), m_pattern( adjustCase( pattern ) ) { if( startsWith( m_pattern, '*' ) ) { m_pattern = m_pattern.substr( 1 ); m_wildcard = WildcardAtStart; } if( endsWith( m_pattern, '*' ) ) { m_pattern = m_pattern.substr( 0, m_pattern.size()-1 ); m_wildcard = static_cast( m_wildcard | WildcardAtEnd ); } } bool WildcardPattern::matches( std::string const& str ) const { switch( m_wildcard ) { case NoWildcard: return m_pattern == adjustCase( str ); case WildcardAtStart: return endsWith( adjustCase( str ), m_pattern ); case WildcardAtEnd: return startsWith( adjustCase( str ), m_pattern ); case WildcardAtBothEnds: return contains( adjustCase( str ), m_pattern ); default: CATCH_INTERNAL_ERROR( "Unknown enum" ); } } std::string WildcardPattern::adjustCase( std::string const& str ) const { return m_caseSensitivity == CaseSensitive::No ? toLower( str ) : str; } } // end catch_wildcard_pattern.cpp // start catch_xmlwriter.cpp #include using uchar = unsigned char; namespace Catch { namespace { size_t trailingBytes(unsigned char c) { if ((c & 0xE0) == 0xC0) { return 2; } if ((c & 0xF0) == 0xE0) { return 3; } if ((c & 0xF8) == 0xF0) { return 4; } CATCH_INTERNAL_ERROR("Invalid multibyte utf-8 start byte encountered"); } uint32_t headerValue(unsigned char c) { if ((c & 0xE0) == 0xC0) { return c & 0x1F; } if ((c & 0xF0) == 0xE0) { return c & 0x0F; } if ((c & 0xF8) == 0xF0) { return c & 0x07; } CATCH_INTERNAL_ERROR("Invalid multibyte utf-8 start byte encountered"); } void hexEscapeChar(std::ostream& os, unsigned char c) { std::ios_base::fmtflags f(os.flags()); os << "\\x" << std::uppercase << std::hex << std::setfill('0') << std::setw(2) << static_cast(c); os.flags(f); } } // anonymous namespace XmlEncode::XmlEncode( std::string const& str, ForWhat forWhat ) : m_str( str ), m_forWhat( forWhat ) {} void XmlEncode::encodeTo( std::ostream& os ) const { // Apostrophe escaping not necessary if we always use " to write attributes // (see: http://www.w3.org/TR/xml/#syntax) for( std::size_t idx = 0; idx < m_str.size(); ++ idx ) { uchar c = m_str[idx]; switch (c) { case '<': os << "<"; break; case '&': os << "&"; break; case '>': // See: http://www.w3.org/TR/xml/#syntax if (idx > 2 && m_str[idx - 1] == ']' && m_str[idx - 2] == ']') os << ">"; else os << c; break; case '\"': if (m_forWhat == ForAttributes) os << """; else os << c; break; default: // Check for control characters and invalid utf-8 // Escape control characters in standard ascii // see http://stackoverflow.com/questions/404107/why-are-control-characters-illegal-in-xml-1-0 if (c < 0x09 || (c > 0x0D && c < 0x20) || c == 0x7F) { hexEscapeChar(os, c); break; } // Plain ASCII: Write it to stream if (c < 0x7F) { os << c; break; } // UTF-8 territory // Check if the encoding is valid and if it is not, hex escape bytes. // Important: We do not check the exact decoded values for validity, only the encoding format // First check that this bytes is a valid lead byte: // This means that it is not encoded as 1111 1XXX // Or as 10XX XXXX if (c < 0xC0 || c >= 0xF8) { hexEscapeChar(os, c); break; } auto encBytes = trailingBytes(c); // Are there enough bytes left to avoid accessing out-of-bounds memory? if (idx + encBytes - 1 >= m_str.size()) { hexEscapeChar(os, c); break; } // The header is valid, check data // The next encBytes bytes must together be a valid utf-8 // This means: bitpattern 10XX XXXX and the extracted value is sane (ish) bool valid = true; uint32_t value = headerValue(c); for (std::size_t n = 1; n < encBytes; ++n) { uchar nc = m_str[idx + n]; valid &= ((nc & 0xC0) == 0x80); value = (value << 6) | (nc & 0x3F); } if ( // Wrong bit pattern of following bytes (!valid) || // Overlong encodings (value < 0x80) || (0x80 <= value && value < 0x800 && encBytes > 2) || (0x800 < value && value < 0x10000 && encBytes > 3) || // Encoded value out of range (value >= 0x110000) ) { hexEscapeChar(os, c); break; } // If we got here, this is in fact a valid(ish) utf-8 sequence for (std::size_t n = 0; n < encBytes; ++n) { os << m_str[idx + n]; } idx += encBytes - 1; break; } } } std::ostream& operator << ( std::ostream& os, XmlEncode const& xmlEncode ) { xmlEncode.encodeTo( os ); return os; } XmlWriter::ScopedElement::ScopedElement( XmlWriter* writer ) : m_writer( writer ) {} XmlWriter::ScopedElement::ScopedElement( ScopedElement&& other ) noexcept : m_writer( other.m_writer ){ other.m_writer = nullptr; } XmlWriter::ScopedElement& XmlWriter::ScopedElement::operator=( ScopedElement&& other ) noexcept { if ( m_writer ) { m_writer->endElement(); } m_writer = other.m_writer; other.m_writer = nullptr; return *this; } XmlWriter::ScopedElement::~ScopedElement() { if( m_writer ) m_writer->endElement(); } XmlWriter::ScopedElement& XmlWriter::ScopedElement::writeText( std::string const& text, bool indent ) { m_writer->writeText( text, indent ); return *this; } XmlWriter::XmlWriter( std::ostream& os ) : m_os( os ) { writeDeclaration(); } XmlWriter::~XmlWriter() { while( !m_tags.empty() ) endElement(); } XmlWriter& XmlWriter::startElement( std::string const& name ) { ensureTagClosed(); newlineIfNecessary(); m_os << m_indent << '<' << name; m_tags.push_back( name ); m_indent += " "; m_tagIsOpen = true; return *this; } XmlWriter::ScopedElement XmlWriter::scopedElement( std::string const& name ) { ScopedElement scoped( this ); startElement( name ); return scoped; } XmlWriter& XmlWriter::endElement() { newlineIfNecessary(); m_indent = m_indent.substr( 0, m_indent.size()-2 ); if( m_tagIsOpen ) { m_os << "/>"; m_tagIsOpen = false; } else { m_os << m_indent << ""; } m_os << std::endl; m_tags.pop_back(); return *this; } XmlWriter& XmlWriter::writeAttribute( std::string const& name, std::string const& attribute ) { if( !name.empty() && !attribute.empty() ) m_os << ' ' << name << "=\"" << XmlEncode( attribute, XmlEncode::ForAttributes ) << '"'; return *this; } XmlWriter& XmlWriter::writeAttribute( std::string const& name, bool attribute ) { m_os << ' ' << name << "=\"" << ( attribute ? "true" : "false" ) << '"'; return *this; } XmlWriter& XmlWriter::writeText( std::string const& text, bool indent ) { if( !text.empty() ){ bool tagWasOpen = m_tagIsOpen; ensureTagClosed(); if( tagWasOpen && indent ) m_os << m_indent; m_os << XmlEncode( text ); m_needsNewline = true; } return *this; } XmlWriter& XmlWriter::writeComment( std::string const& text ) { ensureTagClosed(); m_os << m_indent << ""; m_needsNewline = true; return *this; } void XmlWriter::writeStylesheetRef( std::string const& url ) { m_os << "\n"; } XmlWriter& XmlWriter::writeBlankLine() { ensureTagClosed(); m_os << '\n'; return *this; } void XmlWriter::ensureTagClosed() { if( m_tagIsOpen ) { m_os << ">" << std::endl; m_tagIsOpen = false; } } void XmlWriter::writeDeclaration() { m_os << "\n"; } void XmlWriter::newlineIfNecessary() { if( m_needsNewline ) { m_os << std::endl; m_needsNewline = false; } } } // end catch_xmlwriter.cpp // start catch_reporter_bases.cpp #include #include #include #include #include namespace Catch { void prepareExpandedExpression(AssertionResult& result) { result.getExpandedExpression(); } // Because formatting using c++ streams is stateful, drop down to C is required // Alternatively we could use stringstream, but its performance is... not good. std::string getFormattedDuration( double duration ) { // Max exponent + 1 is required to represent the whole part // + 1 for decimal point // + 3 for the 3 decimal places // + 1 for null terminator const std::size_t maxDoubleSize = DBL_MAX_10_EXP + 1 + 1 + 3 + 1; char buffer[maxDoubleSize]; // Save previous errno, to prevent sprintf from overwriting it ErrnoGuard guard; #ifdef _MSC_VER sprintf_s(buffer, "%.3f", duration); #else sprintf(buffer, "%.3f", duration); #endif return std::string(buffer); } TestEventListenerBase::TestEventListenerBase(ReporterConfig const & _config) :StreamingReporterBase(_config) {} std::set TestEventListenerBase::getSupportedVerbosities() { return { Verbosity::Quiet, Verbosity::Normal, Verbosity::High }; } void TestEventListenerBase::assertionStarting(AssertionInfo const &) {} bool TestEventListenerBase::assertionEnded(AssertionStats const &) { return false; } } // end namespace Catch // end catch_reporter_bases.cpp // start catch_reporter_compact.cpp namespace { #ifdef CATCH_PLATFORM_MAC const char* failedString() { return "FAILED"; } const char* passedString() { return "PASSED"; } #else const char* failedString() { return "failed"; } const char* passedString() { return "passed"; } #endif // Colour::LightGrey Catch::Colour::Code dimColour() { return Catch::Colour::FileName; } std::string bothOrAll( std::size_t count ) { return count == 1 ? std::string() : count == 2 ? "both " : "all " ; } } // anon namespace namespace Catch { namespace { // Colour, message variants: // - white: No tests ran. // - red: Failed [both/all] N test cases, failed [both/all] M assertions. // - white: Passed [both/all] N test cases (no assertions). // - red: Failed N tests cases, failed M assertions. // - green: Passed [both/all] N tests cases with M assertions. void printTotals(std::ostream& out, const Totals& totals) { if (totals.testCases.total() == 0) { out << "No tests ran."; } else if (totals.testCases.failed == totals.testCases.total()) { Colour colour(Colour::ResultError); const std::string qualify_assertions_failed = totals.assertions.failed == totals.assertions.total() ? bothOrAll(totals.assertions.failed) : std::string(); out << "Failed " << bothOrAll(totals.testCases.failed) << pluralise(totals.testCases.failed, "test case") << ", " "failed " << qualify_assertions_failed << pluralise(totals.assertions.failed, "assertion") << '.'; } else if (totals.assertions.total() == 0) { out << "Passed " << bothOrAll(totals.testCases.total()) << pluralise(totals.testCases.total(), "test case") << " (no assertions)."; } else if (totals.assertions.failed) { Colour colour(Colour::ResultError); out << "Failed " << pluralise(totals.testCases.failed, "test case") << ", " "failed " << pluralise(totals.assertions.failed, "assertion") << '.'; } else { Colour colour(Colour::ResultSuccess); out << "Passed " << bothOrAll(totals.testCases.passed) << pluralise(totals.testCases.passed, "test case") << " with " << pluralise(totals.assertions.passed, "assertion") << '.'; } } // Implementation of CompactReporter formatting class AssertionPrinter { public: AssertionPrinter& operator= (AssertionPrinter const&) = delete; AssertionPrinter(AssertionPrinter const&) = delete; AssertionPrinter(std::ostream& _stream, AssertionStats const& _stats, bool _printInfoMessages) : stream(_stream) , result(_stats.assertionResult) , messages(_stats.infoMessages) , itMessage(_stats.infoMessages.begin()) , printInfoMessages(_printInfoMessages) {} void print() { printSourceInfo(); itMessage = messages.begin(); switch (result.getResultType()) { case ResultWas::Ok: printResultType(Colour::ResultSuccess, passedString()); printOriginalExpression(); printReconstructedExpression(); if (!result.hasExpression()) printRemainingMessages(Colour::None); else printRemainingMessages(); break; case ResultWas::ExpressionFailed: if (result.isOk()) printResultType(Colour::ResultSuccess, failedString() + std::string(" - but was ok")); else printResultType(Colour::Error, failedString()); printOriginalExpression(); printReconstructedExpression(); printRemainingMessages(); break; case ResultWas::ThrewException: printResultType(Colour::Error, failedString()); printIssue("unexpected exception with message:"); printMessage(); printExpressionWas(); printRemainingMessages(); break; case ResultWas::FatalErrorCondition: printResultType(Colour::Error, failedString()); printIssue("fatal error condition with message:"); printMessage(); printExpressionWas(); printRemainingMessages(); break; case ResultWas::DidntThrowException: printResultType(Colour::Error, failedString()); printIssue("expected exception, got none"); printExpressionWas(); printRemainingMessages(); break; case ResultWas::Info: printResultType(Colour::None, "info"); printMessage(); printRemainingMessages(); break; case ResultWas::Warning: printResultType(Colour::None, "warning"); printMessage(); printRemainingMessages(); break; case ResultWas::ExplicitFailure: printResultType(Colour::Error, failedString()); printIssue("explicitly"); printRemainingMessages(Colour::None); break; // These cases are here to prevent compiler warnings case ResultWas::Unknown: case ResultWas::FailureBit: case ResultWas::Exception: printResultType(Colour::Error, "** internal error **"); break; } } private: void printSourceInfo() const { Colour colourGuard(Colour::FileName); stream << result.getSourceInfo() << ':'; } void printResultType(Colour::Code colour, std::string const& passOrFail) const { if (!passOrFail.empty()) { { Colour colourGuard(colour); stream << ' ' << passOrFail; } stream << ':'; } } void printIssue(std::string const& issue) const { stream << ' ' << issue; } void printExpressionWas() { if (result.hasExpression()) { stream << ';'; { Colour colour(dimColour()); stream << " expression was:"; } printOriginalExpression(); } } void printOriginalExpression() const { if (result.hasExpression()) { stream << ' ' << result.getExpression(); } } void printReconstructedExpression() const { if (result.hasExpandedExpression()) { { Colour colour(dimColour()); stream << " for: "; } stream << result.getExpandedExpression(); } } void printMessage() { if (itMessage != messages.end()) { stream << " '" << itMessage->message << '\''; ++itMessage; } } void printRemainingMessages(Colour::Code colour = dimColour()) { if (itMessage == messages.end()) return; // using messages.end() directly yields (or auto) compilation error: std::vector::const_iterator itEnd = messages.end(); const std::size_t N = static_cast(std::distance(itMessage, itEnd)); { Colour colourGuard(colour); stream << " with " << pluralise(N, "message") << ':'; } for (; itMessage != itEnd; ) { // If this assertion is a warning ignore any INFO messages if (printInfoMessages || itMessage->type != ResultWas::Info) { stream << " '" << itMessage->message << '\''; if (++itMessage != itEnd) { Colour colourGuard(dimColour()); stream << " and"; } } } } private: std::ostream& stream; AssertionResult const& result; std::vector messages; std::vector::const_iterator itMessage; bool printInfoMessages; }; } // anon namespace std::string CompactReporter::getDescription() { return "Reports test results on a single line, suitable for IDEs"; } ReporterPreferences CompactReporter::getPreferences() const { return m_reporterPrefs; } void CompactReporter::noMatchingTestCases( std::string const& spec ) { stream << "No test cases matched '" << spec << '\'' << std::endl; } void CompactReporter::assertionStarting( AssertionInfo const& ) {} bool CompactReporter::assertionEnded( AssertionStats const& _assertionStats ) { AssertionResult const& result = _assertionStats.assertionResult; bool printInfoMessages = true; // Drop out if result was successful and we're not printing those if( !m_config->includeSuccessfulResults() && result.isOk() ) { if( result.getResultType() != ResultWas::Warning ) return false; printInfoMessages = false; } AssertionPrinter printer( stream, _assertionStats, printInfoMessages ); printer.print(); stream << std::endl; return true; } void CompactReporter::sectionEnded(SectionStats const& _sectionStats) { if (m_config->showDurations() == ShowDurations::Always) { stream << getFormattedDuration(_sectionStats.durationInSeconds) << " s: " << _sectionStats.sectionInfo.name << std::endl; } } void CompactReporter::testRunEnded( TestRunStats const& _testRunStats ) { printTotals( stream, _testRunStats.totals ); stream << '\n' << std::endl; StreamingReporterBase::testRunEnded( _testRunStats ); } CompactReporter::~CompactReporter() {} CATCH_REGISTER_REPORTER( "compact", CompactReporter ) } // end namespace Catch // end catch_reporter_compact.cpp // start catch_reporter_console.cpp #include #include #if defined(_MSC_VER) #pragma warning(push) #pragma warning(disable:4061) // Not all labels are EXPLICITLY handled in switch // Note that 4062 (not all labels are handled // and default is missing) is enabled #endif namespace Catch { namespace { // Formatter impl for ConsoleReporter class ConsoleAssertionPrinter { public: ConsoleAssertionPrinter& operator= (ConsoleAssertionPrinter const&) = delete; ConsoleAssertionPrinter(ConsoleAssertionPrinter const&) = delete; ConsoleAssertionPrinter(std::ostream& _stream, AssertionStats const& _stats, bool _printInfoMessages) : stream(_stream), stats(_stats), result(_stats.assertionResult), colour(Colour::None), message(result.getMessage()), messages(_stats.infoMessages), printInfoMessages(_printInfoMessages) { switch (result.getResultType()) { case ResultWas::Ok: colour = Colour::Success; passOrFail = "PASSED"; //if( result.hasMessage() ) if (_stats.infoMessages.size() == 1) messageLabel = "with message"; if (_stats.infoMessages.size() > 1) messageLabel = "with messages"; break; case ResultWas::ExpressionFailed: if (result.isOk()) { colour = Colour::Success; passOrFail = "FAILED - but was ok"; } else { colour = Colour::Error; passOrFail = "FAILED"; } if (_stats.infoMessages.size() == 1) messageLabel = "with message"; if (_stats.infoMessages.size() > 1) messageLabel = "with messages"; break; case ResultWas::ThrewException: colour = Colour::Error; passOrFail = "FAILED"; messageLabel = "due to unexpected exception with "; if (_stats.infoMessages.size() == 1) messageLabel += "message"; if (_stats.infoMessages.size() > 1) messageLabel += "messages"; break; case ResultWas::FatalErrorCondition: colour = Colour::Error; passOrFail = "FAILED"; messageLabel = "due to a fatal error condition"; break; case ResultWas::DidntThrowException: colour = Colour::Error; passOrFail = "FAILED"; messageLabel = "because no exception was thrown where one was expected"; break; case ResultWas::Info: messageLabel = "info"; break; case ResultWas::Warning: messageLabel = "warning"; break; case ResultWas::ExplicitFailure: passOrFail = "FAILED"; colour = Colour::Error; if (_stats.infoMessages.size() == 1) messageLabel = "explicitly with message"; if (_stats.infoMessages.size() > 1) messageLabel = "explicitly with messages"; break; // These cases are here to prevent compiler warnings case ResultWas::Unknown: case ResultWas::FailureBit: case ResultWas::Exception: passOrFail = "** internal error **"; colour = Colour::Error; break; } } void print() const { printSourceInfo(); if (stats.totals.assertions.total() > 0) { printResultType(); printOriginalExpression(); printReconstructedExpression(); } else { stream << '\n'; } printMessage(); } private: void printResultType() const { if (!passOrFail.empty()) { Colour colourGuard(colour); stream << passOrFail << ":\n"; } } void printOriginalExpression() const { if (result.hasExpression()) { Colour colourGuard(Colour::OriginalExpression); stream << " "; stream << result.getExpressionInMacro(); stream << '\n'; } } void printReconstructedExpression() const { if (result.hasExpandedExpression()) { stream << "with expansion:\n"; Colour colourGuard(Colour::ReconstructedExpression); stream << Column(result.getExpandedExpression()).indent(2) << '\n'; } } void printMessage() const { if (!messageLabel.empty()) stream << messageLabel << ':' << '\n'; for (auto const& msg : messages) { // If this assertion is a warning ignore any INFO messages if (printInfoMessages || msg.type != ResultWas::Info) stream << Column(msg.message).indent(2) << '\n'; } } void printSourceInfo() const { Colour colourGuard(Colour::FileName); stream << result.getSourceInfo() << ": "; } std::ostream& stream; AssertionStats const& stats; AssertionResult const& result; Colour::Code colour; std::string passOrFail; std::string messageLabel; std::string message; std::vector messages; bool printInfoMessages; }; std::size_t makeRatio(std::size_t number, std::size_t total) { std::size_t ratio = total > 0 ? CATCH_CONFIG_CONSOLE_WIDTH * number / total : 0; return (ratio == 0 && number > 0) ? 1 : ratio; } std::size_t& findMax(std::size_t& i, std::size_t& j, std::size_t& k) { if (i > j && i > k) return i; else if (j > k) return j; else return k; } struct ColumnInfo { enum Justification { Left, Right }; std::string name; int width; Justification justification; }; struct ColumnBreak {}; struct RowBreak {}; class Duration { enum class Unit { Auto, Nanoseconds, Microseconds, Milliseconds, Seconds, Minutes }; static const uint64_t s_nanosecondsInAMicrosecond = 1000; static const uint64_t s_nanosecondsInAMillisecond = 1000 * s_nanosecondsInAMicrosecond; static const uint64_t s_nanosecondsInASecond = 1000 * s_nanosecondsInAMillisecond; static const uint64_t s_nanosecondsInAMinute = 60 * s_nanosecondsInASecond; uint64_t m_inNanoseconds; Unit m_units; public: explicit Duration(uint64_t inNanoseconds, Unit units = Unit::Auto) : m_inNanoseconds(inNanoseconds), m_units(units) { if (m_units == Unit::Auto) { if (m_inNanoseconds < s_nanosecondsInAMicrosecond) m_units = Unit::Nanoseconds; else if (m_inNanoseconds < s_nanosecondsInAMillisecond) m_units = Unit::Microseconds; else if (m_inNanoseconds < s_nanosecondsInASecond) m_units = Unit::Milliseconds; else if (m_inNanoseconds < s_nanosecondsInAMinute) m_units = Unit::Seconds; else m_units = Unit::Minutes; } } auto value() const -> double { switch (m_units) { case Unit::Microseconds: return m_inNanoseconds / static_cast(s_nanosecondsInAMicrosecond); case Unit::Milliseconds: return m_inNanoseconds / static_cast(s_nanosecondsInAMillisecond); case Unit::Seconds: return m_inNanoseconds / static_cast(s_nanosecondsInASecond); case Unit::Minutes: return m_inNanoseconds / static_cast(s_nanosecondsInAMinute); default: return static_cast(m_inNanoseconds); } } auto unitsAsString() const -> std::string { switch (m_units) { case Unit::Nanoseconds: return "ns"; case Unit::Microseconds: return "µs"; case Unit::Milliseconds: return "ms"; case Unit::Seconds: return "s"; case Unit::Minutes: return "m"; default: return "** internal error **"; } } friend auto operator << (std::ostream& os, Duration const& duration) -> std::ostream& { return os << duration.value() << " " << duration.unitsAsString(); } }; } // end anon namespace class TablePrinter { std::ostream& m_os; std::vector m_columnInfos; std::ostringstream m_oss; int m_currentColumn = -1; bool m_isOpen = false; public: TablePrinter( std::ostream& os, std::vector columnInfos ) : m_os( os ), m_columnInfos( std::move( columnInfos ) ) {} auto columnInfos() const -> std::vector const& { return m_columnInfos; } void open() { if (!m_isOpen) { m_isOpen = true; *this << RowBreak(); for (auto const& info : m_columnInfos) *this << info.name << ColumnBreak(); *this << RowBreak(); m_os << Catch::getLineOfChars<'-'>() << "\n"; } } void close() { if (m_isOpen) { *this << RowBreak(); m_os << std::endl; m_isOpen = false; } } template friend TablePrinter& operator << (TablePrinter& tp, T const& value) { tp.m_oss << value; return tp; } friend TablePrinter& operator << (TablePrinter& tp, ColumnBreak) { auto colStr = tp.m_oss.str(); // This takes account of utf8 encodings auto strSize = Catch::StringRef(colStr).numberOfCharacters(); tp.m_oss.str(""); tp.open(); if (tp.m_currentColumn == static_cast(tp.m_columnInfos.size() - 1)) { tp.m_currentColumn = -1; tp.m_os << "\n"; } tp.m_currentColumn++; auto colInfo = tp.m_columnInfos[tp.m_currentColumn]; auto padding = (strSize + 2 < static_cast(colInfo.width)) ? std::string(colInfo.width - (strSize + 2), ' ') : std::string(); if (colInfo.justification == ColumnInfo::Left) tp.m_os << colStr << padding << " "; else tp.m_os << padding << colStr << " "; return tp; } friend TablePrinter& operator << (TablePrinter& tp, RowBreak) { if (tp.m_currentColumn > 0) { tp.m_os << "\n"; tp.m_currentColumn = -1; } return tp; } }; ConsoleReporter::ConsoleReporter(ReporterConfig const& config) : StreamingReporterBase(config), m_tablePrinter(new TablePrinter(config.stream(), { { "benchmark name", CATCH_CONFIG_CONSOLE_WIDTH - 32, ColumnInfo::Left }, { "iters", 8, ColumnInfo::Right }, { "elapsed ns", 14, ColumnInfo::Right }, { "average", 14, ColumnInfo::Right } })) {} ConsoleReporter::~ConsoleReporter() = default; std::string ConsoleReporter::getDescription() { return "Reports test results as plain lines of text"; } void ConsoleReporter::noMatchingTestCases(std::string const& spec) { stream << "No test cases matched '" << spec << '\'' << std::endl; } void ConsoleReporter::assertionStarting(AssertionInfo const&) {} bool ConsoleReporter::assertionEnded(AssertionStats const& _assertionStats) { AssertionResult const& result = _assertionStats.assertionResult; bool includeResults = m_config->includeSuccessfulResults() || !result.isOk(); // Drop out if result was successful but we're not printing them. if (!includeResults && result.getResultType() != ResultWas::Warning) return false; lazyPrint(); ConsoleAssertionPrinter printer(stream, _assertionStats, includeResults); printer.print(); stream << std::endl; return true; } void ConsoleReporter::sectionStarting(SectionInfo const& _sectionInfo) { m_headerPrinted = false; StreamingReporterBase::sectionStarting(_sectionInfo); } void ConsoleReporter::sectionEnded(SectionStats const& _sectionStats) { m_tablePrinter->close(); if (_sectionStats.missingAssertions) { lazyPrint(); Colour colour(Colour::ResultError); if (m_sectionStack.size() > 1) stream << "\nNo assertions in section"; else stream << "\nNo assertions in test case"; stream << " '" << _sectionStats.sectionInfo.name << "'\n" << std::endl; } if (m_config->showDurations() == ShowDurations::Always) { stream << getFormattedDuration(_sectionStats.durationInSeconds) << " s: " << _sectionStats.sectionInfo.name << std::endl; } if (m_headerPrinted) { m_headerPrinted = false; } StreamingReporterBase::sectionEnded(_sectionStats); } void ConsoleReporter::benchmarkStarting(BenchmarkInfo const& info) { lazyPrintWithoutClosingBenchmarkTable(); auto nameCol = Column( info.name ).width( static_cast( m_tablePrinter->columnInfos()[0].width - 2 ) ); bool firstLine = true; for (auto line : nameCol) { if (!firstLine) (*m_tablePrinter) << ColumnBreak() << ColumnBreak() << ColumnBreak(); else firstLine = false; (*m_tablePrinter) << line << ColumnBreak(); } } void ConsoleReporter::benchmarkEnded(BenchmarkStats const& stats) { Duration average(stats.elapsedTimeInNanoseconds / stats.iterations); (*m_tablePrinter) << stats.iterations << ColumnBreak() << stats.elapsedTimeInNanoseconds << ColumnBreak() << average << ColumnBreak(); } void ConsoleReporter::testCaseEnded(TestCaseStats const& _testCaseStats) { m_tablePrinter->close(); StreamingReporterBase::testCaseEnded(_testCaseStats); m_headerPrinted = false; } void ConsoleReporter::testGroupEnded(TestGroupStats const& _testGroupStats) { if (currentGroupInfo.used) { printSummaryDivider(); stream << "Summary for group '" << _testGroupStats.groupInfo.name << "':\n"; printTotals(_testGroupStats.totals); stream << '\n' << std::endl; } StreamingReporterBase::testGroupEnded(_testGroupStats); } void ConsoleReporter::testRunEnded(TestRunStats const& _testRunStats) { printTotalsDivider(_testRunStats.totals); printTotals(_testRunStats.totals); stream << std::endl; StreamingReporterBase::testRunEnded(_testRunStats); } void ConsoleReporter::lazyPrint() { m_tablePrinter->close(); lazyPrintWithoutClosingBenchmarkTable(); } void ConsoleReporter::lazyPrintWithoutClosingBenchmarkTable() { if (!currentTestRunInfo.used) lazyPrintRunInfo(); if (!currentGroupInfo.used) lazyPrintGroupInfo(); if (!m_headerPrinted) { printTestCaseAndSectionHeader(); m_headerPrinted = true; } } void ConsoleReporter::lazyPrintRunInfo() { stream << '\n' << getLineOfChars<'~'>() << '\n'; Colour colour(Colour::SecondaryText); stream << currentTestRunInfo->name << " is a Catch v" << libraryVersion() << " host application.\n" << "Run with -? for options\n\n"; if (m_config->rngSeed() != 0) stream << "Randomness seeded to: " << m_config->rngSeed() << "\n\n"; currentTestRunInfo.used = true; } void ConsoleReporter::lazyPrintGroupInfo() { if (!currentGroupInfo->name.empty() && currentGroupInfo->groupsCounts > 1) { printClosedHeader("Group: " + currentGroupInfo->name); currentGroupInfo.used = true; } } void ConsoleReporter::printTestCaseAndSectionHeader() { assert(!m_sectionStack.empty()); printOpenHeader(currentTestCaseInfo->name); if (m_sectionStack.size() > 1) { Colour colourGuard(Colour::Headers); auto it = m_sectionStack.begin() + 1, // Skip first section (test case) itEnd = m_sectionStack.end(); for (; it != itEnd; ++it) printHeaderString(it->name, 2); } SourceLineInfo lineInfo = m_sectionStack.back().lineInfo; if (!lineInfo.empty()) { stream << getLineOfChars<'-'>() << '\n'; Colour colourGuard(Colour::FileName); stream << lineInfo << '\n'; } stream << getLineOfChars<'.'>() << '\n' << std::endl; } void ConsoleReporter::printClosedHeader(std::string const& _name) { printOpenHeader(_name); stream << getLineOfChars<'.'>() << '\n'; } void ConsoleReporter::printOpenHeader(std::string const& _name) { stream << getLineOfChars<'-'>() << '\n'; { Colour colourGuard(Colour::Headers); printHeaderString(_name); } } // if string has a : in first line will set indent to follow it on // subsequent lines void ConsoleReporter::printHeaderString(std::string const& _string, std::size_t indent) { std::size_t i = _string.find(": "); if (i != std::string::npos) i += 2; else i = 0; stream << Column(_string).indent(indent + i).initialIndent(indent) << '\n'; } struct SummaryColumn { SummaryColumn( std::string _label, Colour::Code _colour ) : label( std::move( _label ) ), colour( _colour ) {} SummaryColumn addRow( std::size_t count ) { ReusableStringStream rss; rss << count; std::string row = rss.str(); for (auto& oldRow : rows) { while (oldRow.size() < row.size()) oldRow = ' ' + oldRow; while (oldRow.size() > row.size()) row = ' ' + row; } rows.push_back(row); return *this; } std::string label; Colour::Code colour; std::vector rows; }; void ConsoleReporter::printTotals( Totals const& totals ) { if (totals.testCases.total() == 0) { stream << Colour(Colour::Warning) << "No tests ran\n"; } else if (totals.assertions.total() > 0 && totals.testCases.allPassed()) { stream << Colour(Colour::ResultSuccess) << "All tests passed"; stream << " (" << pluralise(totals.assertions.passed, "assertion") << " in " << pluralise(totals.testCases.passed, "test case") << ')' << '\n'; } else { std::vector columns; columns.push_back(SummaryColumn("", Colour::None) .addRow(totals.testCases.total()) .addRow(totals.assertions.total())); columns.push_back(SummaryColumn("passed", Colour::Success) .addRow(totals.testCases.passed) .addRow(totals.assertions.passed)); columns.push_back(SummaryColumn("failed", Colour::ResultError) .addRow(totals.testCases.failed) .addRow(totals.assertions.failed)); columns.push_back(SummaryColumn("failed as expected", Colour::ResultExpectedFailure) .addRow(totals.testCases.failedButOk) .addRow(totals.assertions.failedButOk)); printSummaryRow("test cases", columns, 0); printSummaryRow("assertions", columns, 1); } } void ConsoleReporter::printSummaryRow(std::string const& label, std::vector const& cols, std::size_t row) { for (auto col : cols) { std::string value = col.rows[row]; if (col.label.empty()) { stream << label << ": "; if (value != "0") stream << value; else stream << Colour(Colour::Warning) << "- none -"; } else if (value != "0") { stream << Colour(Colour::LightGrey) << " | "; stream << Colour(col.colour) << value << ' ' << col.label; } } stream << '\n'; } void ConsoleReporter::printTotalsDivider(Totals const& totals) { if (totals.testCases.total() > 0) { std::size_t failedRatio = makeRatio(totals.testCases.failed, totals.testCases.total()); std::size_t failedButOkRatio = makeRatio(totals.testCases.failedButOk, totals.testCases.total()); std::size_t passedRatio = makeRatio(totals.testCases.passed, totals.testCases.total()); while (failedRatio + failedButOkRatio + passedRatio < CATCH_CONFIG_CONSOLE_WIDTH - 1) findMax(failedRatio, failedButOkRatio, passedRatio)++; while (failedRatio + failedButOkRatio + passedRatio > CATCH_CONFIG_CONSOLE_WIDTH - 1) findMax(failedRatio, failedButOkRatio, passedRatio)--; stream << Colour(Colour::Error) << std::string(failedRatio, '='); stream << Colour(Colour::ResultExpectedFailure) << std::string(failedButOkRatio, '='); if (totals.testCases.allPassed()) stream << Colour(Colour::ResultSuccess) << std::string(passedRatio, '='); else stream << Colour(Colour::Success) << std::string(passedRatio, '='); } else { stream << Colour(Colour::Warning) << std::string(CATCH_CONFIG_CONSOLE_WIDTH - 1, '='); } stream << '\n'; } void ConsoleReporter::printSummaryDivider() { stream << getLineOfChars<'-'>() << '\n'; } CATCH_REGISTER_REPORTER("console", ConsoleReporter) } // end namespace Catch #if defined(_MSC_VER) #pragma warning(pop) #endif // end catch_reporter_console.cpp // start catch_reporter_junit.cpp #include #include #include #include namespace Catch { namespace { std::string getCurrentTimestamp() { // Beware, this is not reentrant because of backward compatibility issues // Also, UTC only, again because of backward compatibility (%z is C++11) time_t rawtime; std::time(&rawtime); auto const timeStampSize = sizeof("2017-01-16T17:06:45Z"); #ifdef _MSC_VER std::tm timeInfo = {}; gmtime_s(&timeInfo, &rawtime); #else std::tm* timeInfo; timeInfo = std::gmtime(&rawtime); #endif char timeStamp[timeStampSize]; const char * const fmt = "%Y-%m-%dT%H:%M:%SZ"; #ifdef _MSC_VER std::strftime(timeStamp, timeStampSize, fmt, &timeInfo); #else std::strftime(timeStamp, timeStampSize, fmt, timeInfo); #endif return std::string(timeStamp); } std::string fileNameTag(const std::vector &tags) { auto it = std::find_if(begin(tags), end(tags), [] (std::string const& tag) {return tag.front() == '#'; }); if (it != tags.end()) return it->substr(1); return std::string(); } } // anonymous namespace JunitReporter::JunitReporter( ReporterConfig const& _config ) : CumulativeReporterBase( _config ), xml( _config.stream() ) { m_reporterPrefs.shouldRedirectStdOut = true; m_reporterPrefs.shouldReportAllAssertions = true; } JunitReporter::~JunitReporter() {} std::string JunitReporter::getDescription() { return "Reports test results in an XML format that looks like Ant's junitreport target"; } void JunitReporter::noMatchingTestCases( std::string const& /*spec*/ ) {} void JunitReporter::testRunStarting( TestRunInfo const& runInfo ) { CumulativeReporterBase::testRunStarting( runInfo ); xml.startElement( "testsuites" ); } void JunitReporter::testGroupStarting( GroupInfo const& groupInfo ) { suiteTimer.start(); stdOutForSuite.clear(); stdErrForSuite.clear(); unexpectedExceptions = 0; CumulativeReporterBase::testGroupStarting( groupInfo ); } void JunitReporter::testCaseStarting( TestCaseInfo const& testCaseInfo ) { m_okToFail = testCaseInfo.okToFail(); } bool JunitReporter::assertionEnded( AssertionStats const& assertionStats ) { if( assertionStats.assertionResult.getResultType() == ResultWas::ThrewException && !m_okToFail ) unexpectedExceptions++; return CumulativeReporterBase::assertionEnded( assertionStats ); } void JunitReporter::testCaseEnded( TestCaseStats const& testCaseStats ) { stdOutForSuite += testCaseStats.stdOut; stdErrForSuite += testCaseStats.stdErr; CumulativeReporterBase::testCaseEnded( testCaseStats ); } void JunitReporter::testGroupEnded( TestGroupStats const& testGroupStats ) { double suiteTime = suiteTimer.getElapsedSeconds(); CumulativeReporterBase::testGroupEnded( testGroupStats ); writeGroup( *m_testGroups.back(), suiteTime ); } void JunitReporter::testRunEndedCumulative() { xml.endElement(); } void JunitReporter::writeGroup( TestGroupNode const& groupNode, double suiteTime ) { XmlWriter::ScopedElement e = xml.scopedElement( "testsuite" ); TestGroupStats const& stats = groupNode.value; xml.writeAttribute( "name", stats.groupInfo.name ); xml.writeAttribute( "errors", unexpectedExceptions ); xml.writeAttribute( "failures", stats.totals.assertions.failed-unexpectedExceptions ); xml.writeAttribute( "tests", stats.totals.assertions.total() ); xml.writeAttribute( "hostname", "tbd" ); // !TBD if( m_config->showDurations() == ShowDurations::Never ) xml.writeAttribute( "time", "" ); else xml.writeAttribute( "time", suiteTime ); xml.writeAttribute( "timestamp", getCurrentTimestamp() ); // Write test cases for( auto const& child : groupNode.children ) writeTestCase( *child ); xml.scopedElement( "system-out" ).writeText( trim( stdOutForSuite ), false ); xml.scopedElement( "system-err" ).writeText( trim( stdErrForSuite ), false ); } void JunitReporter::writeTestCase( TestCaseNode const& testCaseNode ) { TestCaseStats const& stats = testCaseNode.value; // All test cases have exactly one section - which represents the // test case itself. That section may have 0-n nested sections assert( testCaseNode.children.size() == 1 ); SectionNode const& rootSection = *testCaseNode.children.front(); std::string className = stats.testInfo.className; if( className.empty() ) { className = fileNameTag(stats.testInfo.tags); if ( className.empty() ) className = "global"; } if ( !m_config->name().empty() ) className = m_config->name() + "." + className; writeSection( className, "", rootSection ); } void JunitReporter::writeSection( std::string const& className, std::string const& rootName, SectionNode const& sectionNode ) { std::string name = trim( sectionNode.stats.sectionInfo.name ); if( !rootName.empty() ) name = rootName + '/' + name; if( !sectionNode.assertions.empty() || !sectionNode.stdOut.empty() || !sectionNode.stdErr.empty() ) { XmlWriter::ScopedElement e = xml.scopedElement( "testcase" ); if( className.empty() ) { xml.writeAttribute( "classname", name ); xml.writeAttribute( "name", "root" ); } else { xml.writeAttribute( "classname", className ); xml.writeAttribute( "name", name ); } xml.writeAttribute( "time", ::Catch::Detail::stringify( sectionNode.stats.durationInSeconds ) ); writeAssertions( sectionNode ); if( !sectionNode.stdOut.empty() ) xml.scopedElement( "system-out" ).writeText( trim( sectionNode.stdOut ), false ); if( !sectionNode.stdErr.empty() ) xml.scopedElement( "system-err" ).writeText( trim( sectionNode.stdErr ), false ); } for( auto const& childNode : sectionNode.childSections ) if( className.empty() ) writeSection( name, "", *childNode ); else writeSection( className, name, *childNode ); } void JunitReporter::writeAssertions( SectionNode const& sectionNode ) { for( auto const& assertion : sectionNode.assertions ) writeAssertion( assertion ); } void JunitReporter::writeAssertion( AssertionStats const& stats ) { AssertionResult const& result = stats.assertionResult; if( !result.isOk() ) { std::string elementName; switch( result.getResultType() ) { case ResultWas::ThrewException: case ResultWas::FatalErrorCondition: elementName = "error"; break; case ResultWas::ExplicitFailure: elementName = "failure"; break; case ResultWas::ExpressionFailed: elementName = "failure"; break; case ResultWas::DidntThrowException: elementName = "failure"; break; // We should never see these here: case ResultWas::Info: case ResultWas::Warning: case ResultWas::Ok: case ResultWas::Unknown: case ResultWas::FailureBit: case ResultWas::Exception: elementName = "internalError"; break; } XmlWriter::ScopedElement e = xml.scopedElement( elementName ); xml.writeAttribute( "message", result.getExpandedExpression() ); xml.writeAttribute( "type", result.getTestMacroName() ); ReusableStringStream rss; if( !result.getMessage().empty() ) rss << result.getMessage() << '\n'; for( auto const& msg : stats.infoMessages ) if( msg.type == ResultWas::Info ) rss << msg.message << '\n'; rss << "at " << result.getSourceInfo(); xml.writeText( rss.str(), false ); } } CATCH_REGISTER_REPORTER( "junit", JunitReporter ) } // end namespace Catch // end catch_reporter_junit.cpp // start catch_reporter_listening.cpp #include namespace Catch { ListeningReporter::ListeningReporter() { // We will assume that listeners will always want all assertions m_preferences.shouldReportAllAssertions = true; } void ListeningReporter::addListener( IStreamingReporterPtr&& listener ) { m_listeners.push_back( std::move( listener ) ); } void ListeningReporter::addReporter(IStreamingReporterPtr&& reporter) { assert(!m_reporter && "Listening reporter can wrap only 1 real reporter"); m_reporter = std::move( reporter ); m_preferences.shouldRedirectStdOut = m_reporter->getPreferences().shouldRedirectStdOut; } ReporterPreferences ListeningReporter::getPreferences() const { return m_preferences; } std::set ListeningReporter::getSupportedVerbosities() { return std::set{ }; } void ListeningReporter::noMatchingTestCases( std::string const& spec ) { for ( auto const& listener : m_listeners ) { listener->noMatchingTestCases( spec ); } m_reporter->noMatchingTestCases( spec ); } void ListeningReporter::benchmarkStarting( BenchmarkInfo const& benchmarkInfo ) { for ( auto const& listener : m_listeners ) { listener->benchmarkStarting( benchmarkInfo ); } m_reporter->benchmarkStarting( benchmarkInfo ); } void ListeningReporter::benchmarkEnded( BenchmarkStats const& benchmarkStats ) { for ( auto const& listener : m_listeners ) { listener->benchmarkEnded( benchmarkStats ); } m_reporter->benchmarkEnded( benchmarkStats ); } void ListeningReporter::testRunStarting( TestRunInfo const& testRunInfo ) { for ( auto const& listener : m_listeners ) { listener->testRunStarting( testRunInfo ); } m_reporter->testRunStarting( testRunInfo ); } void ListeningReporter::testGroupStarting( GroupInfo const& groupInfo ) { for ( auto const& listener : m_listeners ) { listener->testGroupStarting( groupInfo ); } m_reporter->testGroupStarting( groupInfo ); } void ListeningReporter::testCaseStarting( TestCaseInfo const& testInfo ) { for ( auto const& listener : m_listeners ) { listener->testCaseStarting( testInfo ); } m_reporter->testCaseStarting( testInfo ); } void ListeningReporter::sectionStarting( SectionInfo const& sectionInfo ) { for ( auto const& listener : m_listeners ) { listener->sectionStarting( sectionInfo ); } m_reporter->sectionStarting( sectionInfo ); } void ListeningReporter::assertionStarting( AssertionInfo const& assertionInfo ) { for ( auto const& listener : m_listeners ) { listener->assertionStarting( assertionInfo ); } m_reporter->assertionStarting( assertionInfo ); } // The return value indicates if the messages buffer should be cleared: bool ListeningReporter::assertionEnded( AssertionStats const& assertionStats ) { for( auto const& listener : m_listeners ) { static_cast( listener->assertionEnded( assertionStats ) ); } return m_reporter->assertionEnded( assertionStats ); } void ListeningReporter::sectionEnded( SectionStats const& sectionStats ) { for ( auto const& listener : m_listeners ) { listener->sectionEnded( sectionStats ); } m_reporter->sectionEnded( sectionStats ); } void ListeningReporter::testCaseEnded( TestCaseStats const& testCaseStats ) { for ( auto const& listener : m_listeners ) { listener->testCaseEnded( testCaseStats ); } m_reporter->testCaseEnded( testCaseStats ); } void ListeningReporter::testGroupEnded( TestGroupStats const& testGroupStats ) { for ( auto const& listener : m_listeners ) { listener->testGroupEnded( testGroupStats ); } m_reporter->testGroupEnded( testGroupStats ); } void ListeningReporter::testRunEnded( TestRunStats const& testRunStats ) { for ( auto const& listener : m_listeners ) { listener->testRunEnded( testRunStats ); } m_reporter->testRunEnded( testRunStats ); } void ListeningReporter::skipTest( TestCaseInfo const& testInfo ) { for ( auto const& listener : m_listeners ) { listener->skipTest( testInfo ); } m_reporter->skipTest( testInfo ); } bool ListeningReporter::isMulti() const { return true; } } // end namespace Catch // end catch_reporter_listening.cpp // start catch_reporter_xml.cpp #if defined(_MSC_VER) #pragma warning(push) #pragma warning(disable:4061) // Not all labels are EXPLICITLY handled in switch // Note that 4062 (not all labels are handled // and default is missing) is enabled #endif namespace Catch { XmlReporter::XmlReporter( ReporterConfig const& _config ) : StreamingReporterBase( _config ), m_xml(_config.stream()) { m_reporterPrefs.shouldRedirectStdOut = true; m_reporterPrefs.shouldReportAllAssertions = true; } XmlReporter::~XmlReporter() = default; std::string XmlReporter::getDescription() { return "Reports test results as an XML document"; } std::string XmlReporter::getStylesheetRef() const { return std::string(); } void XmlReporter::writeSourceInfo( SourceLineInfo const& sourceInfo ) { m_xml .writeAttribute( "filename", sourceInfo.file ) .writeAttribute( "line", sourceInfo.line ); } void XmlReporter::noMatchingTestCases( std::string const& s ) { StreamingReporterBase::noMatchingTestCases( s ); } void XmlReporter::testRunStarting( TestRunInfo const& testInfo ) { StreamingReporterBase::testRunStarting( testInfo ); std::string stylesheetRef = getStylesheetRef(); if( !stylesheetRef.empty() ) m_xml.writeStylesheetRef( stylesheetRef ); m_xml.startElement( "Catch" ); if( !m_config->name().empty() ) m_xml.writeAttribute( "name", m_config->name() ); if( m_config->rngSeed() != 0 ) m_xml.scopedElement( "Randomness" ) .writeAttribute( "seed", m_config->rngSeed() ); } void XmlReporter::testGroupStarting( GroupInfo const& groupInfo ) { StreamingReporterBase::testGroupStarting( groupInfo ); m_xml.startElement( "Group" ) .writeAttribute( "name", groupInfo.name ); } void XmlReporter::testCaseStarting( TestCaseInfo const& testInfo ) { StreamingReporterBase::testCaseStarting(testInfo); m_xml.startElement( "TestCase" ) .writeAttribute( "name", trim( testInfo.name ) ) .writeAttribute( "description", testInfo.description ) .writeAttribute( "tags", testInfo.tagsAsString() ); writeSourceInfo( testInfo.lineInfo ); if ( m_config->showDurations() == ShowDurations::Always ) m_testCaseTimer.start(); m_xml.ensureTagClosed(); } void XmlReporter::sectionStarting( SectionInfo const& sectionInfo ) { StreamingReporterBase::sectionStarting( sectionInfo ); if( m_sectionDepth++ > 0 ) { m_xml.startElement( "Section" ) .writeAttribute( "name", trim( sectionInfo.name ) ); writeSourceInfo( sectionInfo.lineInfo ); m_xml.ensureTagClosed(); } } void XmlReporter::assertionStarting( AssertionInfo const& ) { } bool XmlReporter::assertionEnded( AssertionStats const& assertionStats ) { AssertionResult const& result = assertionStats.assertionResult; bool includeResults = m_config->includeSuccessfulResults() || !result.isOk(); if( includeResults || result.getResultType() == ResultWas::Warning ) { // Print any info messages in tags. for( auto const& msg : assertionStats.infoMessages ) { if( msg.type == ResultWas::Info && includeResults ) { m_xml.scopedElement( "Info" ) .writeText( msg.message ); } else if ( msg.type == ResultWas::Warning ) { m_xml.scopedElement( "Warning" ) .writeText( msg.message ); } } } // Drop out if result was successful but we're not printing them. if( !includeResults && result.getResultType() != ResultWas::Warning ) return true; // Print the expression if there is one. if( result.hasExpression() ) { m_xml.startElement( "Expression" ) .writeAttribute( "success", result.succeeded() ) .writeAttribute( "type", result.getTestMacroName() ); writeSourceInfo( result.getSourceInfo() ); m_xml.scopedElement( "Original" ) .writeText( result.getExpression() ); m_xml.scopedElement( "Expanded" ) .writeText( result.getExpandedExpression() ); } // And... Print a result applicable to each result type. switch( result.getResultType() ) { case ResultWas::ThrewException: m_xml.startElement( "Exception" ); writeSourceInfo( result.getSourceInfo() ); m_xml.writeText( result.getMessage() ); m_xml.endElement(); break; case ResultWas::FatalErrorCondition: m_xml.startElement( "FatalErrorCondition" ); writeSourceInfo( result.getSourceInfo() ); m_xml.writeText( result.getMessage() ); m_xml.endElement(); break; case ResultWas::Info: m_xml.scopedElement( "Info" ) .writeText( result.getMessage() ); break; case ResultWas::Warning: // Warning will already have been written break; case ResultWas::ExplicitFailure: m_xml.startElement( "Failure" ); writeSourceInfo( result.getSourceInfo() ); m_xml.writeText( result.getMessage() ); m_xml.endElement(); break; default: break; } if( result.hasExpression() ) m_xml.endElement(); return true; } void XmlReporter::sectionEnded( SectionStats const& sectionStats ) { StreamingReporterBase::sectionEnded( sectionStats ); if( --m_sectionDepth > 0 ) { XmlWriter::ScopedElement e = m_xml.scopedElement( "OverallResults" ); e.writeAttribute( "successes", sectionStats.assertions.passed ); e.writeAttribute( "failures", sectionStats.assertions.failed ); e.writeAttribute( "expectedFailures", sectionStats.assertions.failedButOk ); if ( m_config->showDurations() == ShowDurations::Always ) e.writeAttribute( "durationInSeconds", sectionStats.durationInSeconds ); m_xml.endElement(); } } void XmlReporter::testCaseEnded( TestCaseStats const& testCaseStats ) { StreamingReporterBase::testCaseEnded( testCaseStats ); XmlWriter::ScopedElement e = m_xml.scopedElement( "OverallResult" ); e.writeAttribute( "success", testCaseStats.totals.assertions.allOk() ); if ( m_config->showDurations() == ShowDurations::Always ) e.writeAttribute( "durationInSeconds", m_testCaseTimer.getElapsedSeconds() ); if( !testCaseStats.stdOut.empty() ) m_xml.scopedElement( "StdOut" ).writeText( trim( testCaseStats.stdOut ), false ); if( !testCaseStats.stdErr.empty() ) m_xml.scopedElement( "StdErr" ).writeText( trim( testCaseStats.stdErr ), false ); m_xml.endElement(); } void XmlReporter::testGroupEnded( TestGroupStats const& testGroupStats ) { StreamingReporterBase::testGroupEnded( testGroupStats ); // TODO: Check testGroupStats.aborting and act accordingly. m_xml.scopedElement( "OverallResults" ) .writeAttribute( "successes", testGroupStats.totals.assertions.passed ) .writeAttribute( "failures", testGroupStats.totals.assertions.failed ) .writeAttribute( "expectedFailures", testGroupStats.totals.assertions.failedButOk ); m_xml.endElement(); } void XmlReporter::testRunEnded( TestRunStats const& testRunStats ) { StreamingReporterBase::testRunEnded( testRunStats ); m_xml.scopedElement( "OverallResults" ) .writeAttribute( "successes", testRunStats.totals.assertions.passed ) .writeAttribute( "failures", testRunStats.totals.assertions.failed ) .writeAttribute( "expectedFailures", testRunStats.totals.assertions.failedButOk ); m_xml.endElement(); } CATCH_REGISTER_REPORTER( "xml", XmlReporter ) } // end namespace Catch #if defined(_MSC_VER) #pragma warning(pop) #endif // end catch_reporter_xml.cpp namespace Catch { LeakDetector leakDetector; } #ifdef __clang__ #pragma clang diagnostic pop #endif // end catch_impl.hpp #endif #ifdef CATCH_CONFIG_MAIN // start catch_default_main.hpp #ifndef __OBJC__ #if defined(CATCH_CONFIG_WCHAR) && defined(WIN32) && defined(_UNICODE) && !defined(DO_NOT_USE_WMAIN) // Standard C/C++ Win32 Unicode wmain entry point extern "C" int wmain (int argc, wchar_t * argv[], wchar_t * []) { #else // Standard C/C++ main entry point int main (int argc, char * argv[]) { #endif return Catch::Session().run( argc, argv ); } #else // __OBJC__ // Objective-C entry point int main (int argc, char * const argv[]) { #if !CATCH_ARC_ENABLED NSAutoreleasePool * pool = [[NSAutoreleasePool alloc] init]; #endif Catch::registerTestMethods(); int result = Catch::Session().run( argc, (char**)argv ); #if !CATCH_ARC_ENABLED [pool drain]; #endif return result; } #endif // __OBJC__ // end catch_default_main.hpp #endif #if !defined(CATCH_CONFIG_IMPL_ONLY) #ifdef CLARA_CONFIG_MAIN_NOT_DEFINED # undef CLARA_CONFIG_MAIN #endif #if !defined(CATCH_CONFIG_DISABLE) ////// // If this config identifier is defined then all CATCH macros are prefixed with CATCH_ #ifdef CATCH_CONFIG_PREFIX_ALL #define CATCH_REQUIRE( ... ) INTERNAL_CATCH_TEST( "CATCH_REQUIRE", Catch::ResultDisposition::Normal, __VA_ARGS__ ) #define CATCH_REQUIRE_FALSE( ... ) INTERNAL_CATCH_TEST( "CATCH_REQUIRE_FALSE", Catch::ResultDisposition::Normal | Catch::ResultDisposition::FalseTest, __VA_ARGS__ ) #define CATCH_REQUIRE_THROWS( ... ) INTERNAL_CATCH_THROWS( "CATCH_REQUIRE_THROWS", Catch::ResultDisposition::Normal, "", __VA_ARGS__ ) #define CATCH_REQUIRE_THROWS_AS( expr, exceptionType ) INTERNAL_CATCH_THROWS_AS( "CATCH_REQUIRE_THROWS_AS", exceptionType, Catch::ResultDisposition::Normal, expr ) #define CATCH_REQUIRE_THROWS_WITH( expr, matcher ) INTERNAL_CATCH_THROWS_STR_MATCHES( "CATCH_REQUIRE_THROWS_WITH", Catch::ResultDisposition::Normal, matcher, expr ) #if !defined(CATCH_CONFIG_DISABLE_MATCHERS) #define CATCH_REQUIRE_THROWS_MATCHES( expr, exceptionType, matcher ) INTERNAL_CATCH_THROWS_MATCHES( "CATCH_REQUIRE_THROWS_MATCHES", exceptionType, Catch::ResultDisposition::Normal, matcher, expr ) #endif// CATCH_CONFIG_DISABLE_MATCHERS #define CATCH_REQUIRE_NOTHROW( ... ) INTERNAL_CATCH_NO_THROW( "CATCH_REQUIRE_NOTHROW", Catch::ResultDisposition::Normal, __VA_ARGS__ ) #define CATCH_CHECK( ... ) INTERNAL_CATCH_TEST( "CATCH_CHECK", Catch::ResultDisposition::ContinueOnFailure, __VA_ARGS__ ) #define CATCH_CHECK_FALSE( ... ) INTERNAL_CATCH_TEST( "CATCH_CHECK_FALSE", Catch::ResultDisposition::ContinueOnFailure | Catch::ResultDisposition::FalseTest, __VA_ARGS__ ) #define CATCH_CHECKED_IF( ... ) INTERNAL_CATCH_IF( "CATCH_CHECKED_IF", Catch::ResultDisposition::ContinueOnFailure, __VA_ARGS__ ) #define CATCH_CHECKED_ELSE( ... ) INTERNAL_CATCH_ELSE( "CATCH_CHECKED_ELSE", Catch::ResultDisposition::ContinueOnFailure, __VA_ARGS__ ) #define CATCH_CHECK_NOFAIL( ... ) INTERNAL_CATCH_TEST( "CATCH_CHECK_NOFAIL", Catch::ResultDisposition::ContinueOnFailure | Catch::ResultDisposition::SuppressFail, __VA_ARGS__ ) #define CATCH_CHECK_THROWS( ... ) INTERNAL_CATCH_THROWS( "CATCH_CHECK_THROWS", Catch::ResultDisposition::ContinueOnFailure, "", __VA_ARGS__ ) #define CATCH_CHECK_THROWS_AS( expr, exceptionType ) INTERNAL_CATCH_THROWS_AS( "CATCH_CHECK_THROWS_AS", exceptionType, Catch::ResultDisposition::ContinueOnFailure, expr ) #define CATCH_CHECK_THROWS_WITH( expr, matcher ) INTERNAL_CATCH_THROWS_STR_MATCHES( "CATCH_CHECK_THROWS_WITH", Catch::ResultDisposition::ContinueOnFailure, matcher, expr ) #if !defined(CATCH_CONFIG_DISABLE_MATCHERS) #define CATCH_CHECK_THROWS_MATCHES( expr, exceptionType, matcher ) INTERNAL_CATCH_THROWS_MATCHES( "CATCH_CHECK_THROWS_MATCHES", exceptionType, Catch::ResultDisposition::ContinueOnFailure, matcher, expr ) #endif // CATCH_CONFIG_DISABLE_MATCHERS #define CATCH_CHECK_NOTHROW( ... ) INTERNAL_CATCH_NO_THROW( "CATCH_CHECK_NOTHROW", Catch::ResultDisposition::ContinueOnFailure, __VA_ARGS__ ) #if !defined(CATCH_CONFIG_DISABLE_MATCHERS) #define CATCH_CHECK_THAT( arg, matcher ) INTERNAL_CHECK_THAT( "CATCH_CHECK_THAT", matcher, Catch::ResultDisposition::ContinueOnFailure, arg ) #define CATCH_REQUIRE_THAT( arg, matcher ) INTERNAL_CHECK_THAT( "CATCH_REQUIRE_THAT", matcher, Catch::ResultDisposition::Normal, arg ) #endif // CATCH_CONFIG_DISABLE_MATCHERS #define CATCH_INFO( msg ) INTERNAL_CATCH_INFO( "CATCH_INFO", msg ) #define CATCH_WARN( msg ) INTERNAL_CATCH_MSG( "CATCH_WARN", Catch::ResultWas::Warning, Catch::ResultDisposition::ContinueOnFailure, msg ) #define CATCH_CAPTURE( ... ) INTERNAL_CATCH_CAPTURE( INTERNAL_CATCH_UNIQUE_NAME(capturer), "CATCH_CAPTURE",__VA_ARGS__ ) #define CATCH_TEST_CASE( ... ) INTERNAL_CATCH_TESTCASE( __VA_ARGS__ ) #define CATCH_TEST_CASE_METHOD( className, ... ) INTERNAL_CATCH_TEST_CASE_METHOD( className, __VA_ARGS__ ) #define CATCH_METHOD_AS_TEST_CASE( method, ... ) INTERNAL_CATCH_METHOD_AS_TEST_CASE( method, __VA_ARGS__ ) #define CATCH_REGISTER_TEST_CASE( Function, ... ) INTERNAL_CATCH_REGISTER_TESTCASE( Function, __VA_ARGS__ ) #define CATCH_SECTION( ... ) INTERNAL_CATCH_SECTION( __VA_ARGS__ ) #define CATCH_DYNAMIC_SECTION( ... ) INTERNAL_CATCH_DYNAMIC_SECTION( __VA_ARGS__ ) #define CATCH_FAIL( ... ) INTERNAL_CATCH_MSG( "CATCH_FAIL", Catch::ResultWas::ExplicitFailure, Catch::ResultDisposition::Normal, __VA_ARGS__ ) #define CATCH_FAIL_CHECK( ... ) INTERNAL_CATCH_MSG( "CATCH_FAIL_CHECK", Catch::ResultWas::ExplicitFailure, Catch::ResultDisposition::ContinueOnFailure, __VA_ARGS__ ) #define CATCH_SUCCEED( ... ) INTERNAL_CATCH_MSG( "CATCH_SUCCEED", Catch::ResultWas::Ok, Catch::ResultDisposition::ContinueOnFailure, __VA_ARGS__ ) #define CATCH_ANON_TEST_CASE() INTERNAL_CATCH_TESTCASE() #ifndef CATCH_CONFIG_TRADITIONAL_MSVC_PREPROCESSOR #define CATCH_TEMPLATE_TEST_CASE( ... ) INTERNAL_CATCH_TEMPLATE_TEST_CASE( __VA_ARGS__ ) #define CATCH_TEMPLATE_TEST_CASE_METHOD( className, ... ) INTERNAL_CATCH_TEMPLATE_TEST_CASE_METHOD( className, __VA_ARGS__ ) #define CATCH_TEMPLATE_PRODUCT_TEST_CASE( ... ) INTERNAL_CATCH_TEMPLATE_PRODUCT_TEST_CASE( __VA_ARGS__ ) #define CATCH_TEMPLATE_PRODUCT_TEST_CASE_METHOD( className, ... ) INTERNAL_CATCH_TEMPLATE_PRODUCT_TEST_CASE_METHOD( className, __VA_ARGS__ ) #else #define CATCH_TEMPLATE_TEST_CASE( ... ) INTERNAL_CATCH_EXPAND_VARGS( INTERNAL_CATCH_TEMPLATE_TEST_CASE( __VA_ARGS__ ) ) #define CATCH_TEMPLATE_TEST_CASE_METHOD( className, ... ) INTERNAL_CATCH_EXPAND_VARGS( INTERNAL_CATCH_TEMPLATE_TEST_CASE_METHOD( className, __VA_ARGS__ ) ) #define CATCH_TEMPLATE_PRODUCT_TEST_CASE( ... ) INTERNAL_CATCH_EXPAND_VARGS( INTERNAL_CATCH_TEMPLATE_PRODUCT_TEST_CASE( __VA_ARGS__ ) ) #define CATCH_TEMPLATE_PRODUCT_TEST_CASE_METHOD( className, ... ) INTERNAL_CATCH_EXPAND_VARGS( INTERNAL_CATCH_TEMPLATE_PRODUCT_TEST_CASE_METHOD( className, __VA_ARGS__ ) ) #endif #if !defined(CATCH_CONFIG_RUNTIME_STATIC_REQUIRE) #define CATCH_STATIC_REQUIRE( ... ) static_assert( __VA_ARGS__ , #__VA_ARGS__ ); CATCH_SUCCEED( #__VA_ARGS__ ) #define CATCH_STATIC_REQUIRE_FALSE( ... ) static_assert( !(__VA_ARGS__), "!(" #__VA_ARGS__ ")" ); CATCH_SUCCEED( #__VA_ARGS__ ) #else #define CATCH_STATIC_REQUIRE( ... ) CATCH_REQUIRE( __VA_ARGS__ ) #define CATCH_STATIC_REQUIRE_FALSE( ... ) CATCH_REQUIRE_FALSE( __VA_ARGS__ ) #endif // "BDD-style" convenience wrappers #define CATCH_SCENARIO( ... ) CATCH_TEST_CASE( "Scenario: " __VA_ARGS__ ) #define CATCH_SCENARIO_METHOD( className, ... ) INTERNAL_CATCH_TEST_CASE_METHOD( className, "Scenario: " __VA_ARGS__ ) #define CATCH_GIVEN( desc ) INTERNAL_CATCH_DYNAMIC_SECTION( " Given: " << desc ) #define CATCH_AND_GIVEN( desc ) INTERNAL_CATCH_DYNAMIC_SECTION( "And given: " << desc ) #define CATCH_WHEN( desc ) INTERNAL_CATCH_DYNAMIC_SECTION( " When: " << desc ) #define CATCH_AND_WHEN( desc ) INTERNAL_CATCH_DYNAMIC_SECTION( " And when: " << desc ) #define CATCH_THEN( desc ) INTERNAL_CATCH_DYNAMIC_SECTION( " Then: " << desc ) #define CATCH_AND_THEN( desc ) INTERNAL_CATCH_DYNAMIC_SECTION( " And: " << desc ) // If CATCH_CONFIG_PREFIX_ALL is not defined then the CATCH_ prefix is not required #else #define REQUIRE( ... ) INTERNAL_CATCH_TEST( "REQUIRE", Catch::ResultDisposition::Normal, __VA_ARGS__ ) #define REQUIRE_FALSE( ... ) INTERNAL_CATCH_TEST( "REQUIRE_FALSE", Catch::ResultDisposition::Normal | Catch::ResultDisposition::FalseTest, __VA_ARGS__ ) #define REQUIRE_THROWS( ... ) INTERNAL_CATCH_THROWS( "REQUIRE_THROWS", Catch::ResultDisposition::Normal, __VA_ARGS__ ) #define REQUIRE_THROWS_AS( expr, exceptionType ) INTERNAL_CATCH_THROWS_AS( "REQUIRE_THROWS_AS", exceptionType, Catch::ResultDisposition::Normal, expr ) #define REQUIRE_THROWS_WITH( expr, matcher ) INTERNAL_CATCH_THROWS_STR_MATCHES( "REQUIRE_THROWS_WITH", Catch::ResultDisposition::Normal, matcher, expr ) #if !defined(CATCH_CONFIG_DISABLE_MATCHERS) #define REQUIRE_THROWS_MATCHES( expr, exceptionType, matcher ) INTERNAL_CATCH_THROWS_MATCHES( "REQUIRE_THROWS_MATCHES", exceptionType, Catch::ResultDisposition::Normal, matcher, expr ) #endif // CATCH_CONFIG_DISABLE_MATCHERS #define REQUIRE_NOTHROW( ... ) INTERNAL_CATCH_NO_THROW( "REQUIRE_NOTHROW", Catch::ResultDisposition::Normal, __VA_ARGS__ ) #define CHECK( ... ) INTERNAL_CATCH_TEST( "CHECK", Catch::ResultDisposition::ContinueOnFailure, __VA_ARGS__ ) #define CHECK_FALSE( ... ) INTERNAL_CATCH_TEST( "CHECK_FALSE", Catch::ResultDisposition::ContinueOnFailure | Catch::ResultDisposition::FalseTest, __VA_ARGS__ ) #define CHECKED_IF( ... ) INTERNAL_CATCH_IF( "CHECKED_IF", Catch::ResultDisposition::ContinueOnFailure, __VA_ARGS__ ) #define CHECKED_ELSE( ... ) INTERNAL_CATCH_ELSE( "CHECKED_ELSE", Catch::ResultDisposition::ContinueOnFailure, __VA_ARGS__ ) #define CHECK_NOFAIL( ... ) INTERNAL_CATCH_TEST( "CHECK_NOFAIL", Catch::ResultDisposition::ContinueOnFailure | Catch::ResultDisposition::SuppressFail, __VA_ARGS__ ) #define CHECK_THROWS( ... ) INTERNAL_CATCH_THROWS( "CHECK_THROWS", Catch::ResultDisposition::ContinueOnFailure, __VA_ARGS__ ) #define CHECK_THROWS_AS( expr, exceptionType ) INTERNAL_CATCH_THROWS_AS( "CHECK_THROWS_AS", exceptionType, Catch::ResultDisposition::ContinueOnFailure, expr ) #define CHECK_THROWS_WITH( expr, matcher ) INTERNAL_CATCH_THROWS_STR_MATCHES( "CHECK_THROWS_WITH", Catch::ResultDisposition::ContinueOnFailure, matcher, expr ) #if !defined(CATCH_CONFIG_DISABLE_MATCHERS) #define CHECK_THROWS_MATCHES( expr, exceptionType, matcher ) INTERNAL_CATCH_THROWS_MATCHES( "CHECK_THROWS_MATCHES", exceptionType, Catch::ResultDisposition::ContinueOnFailure, matcher, expr ) #endif // CATCH_CONFIG_DISABLE_MATCHERS #define CHECK_NOTHROW( ... ) INTERNAL_CATCH_NO_THROW( "CHECK_NOTHROW", Catch::ResultDisposition::ContinueOnFailure, __VA_ARGS__ ) #if !defined(CATCH_CONFIG_DISABLE_MATCHERS) #define CHECK_THAT( arg, matcher ) INTERNAL_CHECK_THAT( "CHECK_THAT", matcher, Catch::ResultDisposition::ContinueOnFailure, arg ) #define REQUIRE_THAT( arg, matcher ) INTERNAL_CHECK_THAT( "REQUIRE_THAT", matcher, Catch::ResultDisposition::Normal, arg ) #endif // CATCH_CONFIG_DISABLE_MATCHERS #define INFO( msg ) INTERNAL_CATCH_INFO( "INFO", msg ) #define WARN( msg ) INTERNAL_CATCH_MSG( "WARN", Catch::ResultWas::Warning, Catch::ResultDisposition::ContinueOnFailure, msg ) #define CAPTURE( ... ) INTERNAL_CATCH_CAPTURE( INTERNAL_CATCH_UNIQUE_NAME(capturer), "CAPTURE",__VA_ARGS__ ) #define TEST_CASE( ... ) INTERNAL_CATCH_TESTCASE( __VA_ARGS__ ) #define TEST_CASE_METHOD( className, ... ) INTERNAL_CATCH_TEST_CASE_METHOD( className, __VA_ARGS__ ) #define METHOD_AS_TEST_CASE( method, ... ) INTERNAL_CATCH_METHOD_AS_TEST_CASE( method, __VA_ARGS__ ) #define REGISTER_TEST_CASE( Function, ... ) INTERNAL_CATCH_REGISTER_TESTCASE( Function, __VA_ARGS__ ) #define SECTION( ... ) INTERNAL_CATCH_SECTION( __VA_ARGS__ ) #define DYNAMIC_SECTION( ... ) INTERNAL_CATCH_DYNAMIC_SECTION( __VA_ARGS__ ) #define FAIL( ... ) INTERNAL_CATCH_MSG( "FAIL", Catch::ResultWas::ExplicitFailure, Catch::ResultDisposition::Normal, __VA_ARGS__ ) #define FAIL_CHECK( ... ) INTERNAL_CATCH_MSG( "FAIL_CHECK", Catch::ResultWas::ExplicitFailure, Catch::ResultDisposition::ContinueOnFailure, __VA_ARGS__ ) #define SUCCEED( ... ) INTERNAL_CATCH_MSG( "SUCCEED", Catch::ResultWas::Ok, Catch::ResultDisposition::ContinueOnFailure, __VA_ARGS__ ) #define ANON_TEST_CASE() INTERNAL_CATCH_TESTCASE() #ifndef CATCH_CONFIG_TRADITIONAL_MSVC_PREPROCESSOR #define TEMPLATE_TEST_CASE( ... ) INTERNAL_CATCH_TEMPLATE_TEST_CASE( __VA_ARGS__ ) #define TEMPLATE_TEST_CASE_METHOD( className, ... ) INTERNAL_CATCH_TEMPLATE_TEST_CASE_METHOD( className, __VA_ARGS__ ) #define TEMPLATE_PRODUCT_TEST_CASE( ... ) INTERNAL_CATCH_TEMPLATE_PRODUCT_TEST_CASE( __VA_ARGS__ ) #define TEMPLATE_PRODUCT_TEST_CASE_METHOD( className, ... ) INTERNAL_CATCH_TEMPLATE_PRODUCT_TEST_CASE_METHOD( className, __VA_ARGS__ ) #else #define TEMPLATE_TEST_CASE( ... ) INTERNAL_CATCH_EXPAND_VARGS( INTERNAL_CATCH_TEMPLATE_TEST_CASE( __VA_ARGS__ ) ) #define TEMPLATE_TEST_CASE_METHOD( className, ... ) INTERNAL_CATCH_EXPAND_VARGS( INTERNAL_CATCH_TEMPLATE_TEST_CASE_METHOD( className, __VA_ARGS__ ) ) #define TEMPLATE_PRODUCT_TEST_CASE( ... ) INTERNAL_CATCH_EXPAND_VARGS( INTERNAL_CATCH_TEMPLATE_PRODUCT_TEST_CASE( __VA_ARGS__ ) ) #define TEMPLATE_PRODUCT_TEST_CASE_METHOD( className, ... ) INTERNAL_CATCH_EXPAND_VARGS( INTERNAL_CATCH_TEMPLATE_PRODUCT_TEST_CASE_METHOD( className, __VA_ARGS__ ) ) #endif #if !defined(CATCH_CONFIG_RUNTIME_STATIC_REQUIRE) #define STATIC_REQUIRE( ... ) static_assert( __VA_ARGS__, #__VA_ARGS__ ); SUCCEED( #__VA_ARGS__ ) #define STATIC_REQUIRE_FALSE( ... ) static_assert( !(__VA_ARGS__), "!(" #__VA_ARGS__ ")" ); SUCCEED( "!(" #__VA_ARGS__ ")" ) #else #define STATIC_REQUIRE( ... ) REQUIRE( __VA_ARGS__ ) #define STATIC_REQUIRE_FALSE( ... ) REQUIRE_FALSE( __VA_ARGS__ ) #endif #endif #define CATCH_TRANSLATE_EXCEPTION( signature ) INTERNAL_CATCH_TRANSLATE_EXCEPTION( signature ) // "BDD-style" convenience wrappers #define SCENARIO( ... ) TEST_CASE( "Scenario: " __VA_ARGS__ ) #define SCENARIO_METHOD( className, ... ) INTERNAL_CATCH_TEST_CASE_METHOD( className, "Scenario: " __VA_ARGS__ ) #define GIVEN( desc ) INTERNAL_CATCH_DYNAMIC_SECTION( " Given: " << desc ) #define AND_GIVEN( desc ) INTERNAL_CATCH_DYNAMIC_SECTION( "And given: " << desc ) #define WHEN( desc ) INTERNAL_CATCH_DYNAMIC_SECTION( " When: " << desc ) #define AND_WHEN( desc ) INTERNAL_CATCH_DYNAMIC_SECTION( " And when: " << desc ) #define THEN( desc ) INTERNAL_CATCH_DYNAMIC_SECTION( " Then: " << desc ) #define AND_THEN( desc ) INTERNAL_CATCH_DYNAMIC_SECTION( " And: " << desc ) using Catch::Detail::Approx; #else // CATCH_CONFIG_DISABLE ////// // If this config identifier is defined then all CATCH macros are prefixed with CATCH_ #ifdef CATCH_CONFIG_PREFIX_ALL #define CATCH_REQUIRE( ... ) (void)(0) #define CATCH_REQUIRE_FALSE( ... ) (void)(0) #define CATCH_REQUIRE_THROWS( ... ) (void)(0) #define CATCH_REQUIRE_THROWS_AS( expr, exceptionType ) (void)(0) #define CATCH_REQUIRE_THROWS_WITH( expr, matcher ) (void)(0) #if !defined(CATCH_CONFIG_DISABLE_MATCHERS) #define CATCH_REQUIRE_THROWS_MATCHES( expr, exceptionType, matcher ) (void)(0) #endif// CATCH_CONFIG_DISABLE_MATCHERS #define CATCH_REQUIRE_NOTHROW( ... ) (void)(0) #define CATCH_CHECK( ... ) (void)(0) #define CATCH_CHECK_FALSE( ... ) (void)(0) #define CATCH_CHECKED_IF( ... ) if (__VA_ARGS__) #define CATCH_CHECKED_ELSE( ... ) if (!(__VA_ARGS__)) #define CATCH_CHECK_NOFAIL( ... ) (void)(0) #define CATCH_CHECK_THROWS( ... ) (void)(0) #define CATCH_CHECK_THROWS_AS( expr, exceptionType ) (void)(0) #define CATCH_CHECK_THROWS_WITH( expr, matcher ) (void)(0) #if !defined(CATCH_CONFIG_DISABLE_MATCHERS) #define CATCH_CHECK_THROWS_MATCHES( expr, exceptionType, matcher ) (void)(0) #endif // CATCH_CONFIG_DISABLE_MATCHERS #define CATCH_CHECK_NOTHROW( ... ) (void)(0) #if !defined(CATCH_CONFIG_DISABLE_MATCHERS) #define CATCH_CHECK_THAT( arg, matcher ) (void)(0) #define CATCH_REQUIRE_THAT( arg, matcher ) (void)(0) #endif // CATCH_CONFIG_DISABLE_MATCHERS #define CATCH_INFO( msg ) (void)(0) #define CATCH_WARN( msg ) (void)(0) #define CATCH_CAPTURE( msg ) (void)(0) #define CATCH_TEST_CASE( ... ) INTERNAL_CATCH_TESTCASE_NO_REGISTRATION(INTERNAL_CATCH_UNIQUE_NAME( ____C_A_T_C_H____T_E_S_T____ )) #define CATCH_TEST_CASE_METHOD( className, ... ) INTERNAL_CATCH_TESTCASE_NO_REGISTRATION(INTERNAL_CATCH_UNIQUE_NAME( ____C_A_T_C_H____T_E_S_T____ )) #define CATCH_METHOD_AS_TEST_CASE( method, ... ) #define CATCH_REGISTER_TEST_CASE( Function, ... ) (void)(0) #define CATCH_SECTION( ... ) #define CATCH_DYNAMIC_SECTION( ... ) #define CATCH_FAIL( ... ) (void)(0) #define CATCH_FAIL_CHECK( ... ) (void)(0) #define CATCH_SUCCEED( ... ) (void)(0) #define CATCH_ANON_TEST_CASE() INTERNAL_CATCH_TESTCASE_NO_REGISTRATION(INTERNAL_CATCH_UNIQUE_NAME( ____C_A_T_C_H____T_E_S_T____ )) #ifndef CATCH_CONFIG_TRADITIONAL_MSVC_PREPROCESSOR #define CATCH_TEMPLATE_TEST_CASE( ... ) INTERNAL_CATCH_TEMPLATE_TEST_CASE_NO_REGISTRATION(INTERNAL_CATCH_UNIQUE_NAME( ____C_A_T_C_H____T_E_M_P_L_A_T_E____T_E_S_T____ ) ) #define CATCH_TEMPLATE_TEST_CASE_METHOD( className, ... ) INTERNAL_CATCH_TEMPLATE_TEST_CASE_METHOD_NO_REGISTRATION(INTERNAL_CATCH_UNIQUE_NAME( ____C_A_T_C_H____T_E_M_P_L_A_T_E____T_E_S_T____ ), className ) #define CATCH_TEMPLATE_PRODUCT_TEST_CASE( ... ) CATCH_TEMPLATE_TEST_CASE( __VA_ARGS__ ) #define CATCH_TEMPLATE_PRODUCT_TEST_CASE_METHOD( className, ... ) CATCH_TEMPLATE_TEST_CASE_METHOD( className, __VA_ARGS__ ) #else #define CATCH_TEMPLATE_TEST_CASE( ... ) INTERNAL_CATCH_EXPAND_VARGS( INTERNAL_CATCH_TEMPLATE_TEST_CASE_NO_REGISTRATION(INTERNAL_CATCH_UNIQUE_NAME( ____C_A_T_C_H____T_E_M_P_L_A_T_E____T_E_S_T____ ) ) ) #define CATCH_TEMPLATE_TEST_CASE_METHOD( className, ... ) INTERNAL_CATCH_EXPAND_VARGS( INTERNAL_CATCH_TEMPLATE_TEST_CASE_METHOD_NO_REGISTRATION(INTERNAL_CATCH_UNIQUE_NAME( ____C_A_T_C_H____T_E_M_P_L_A_T_E____T_E_S_T____ ), className ) ) #define CATCH_TEMPLATE_PRODUCT_TEST_CASE( ... ) CATCH_TEMPLATE_TEST_CASE( __VA_ARGS__ ) #define CATCH_TEMPLATE_PRODUCT_TEST_CASE_METHOD( className, ... ) CATCH_TEMPLATE_TEST_CASE_METHOD( className, __VA_ARGS__ ) #endif // "BDD-style" convenience wrappers #define CATCH_SCENARIO( ... ) INTERNAL_CATCH_TESTCASE_NO_REGISTRATION(INTERNAL_CATCH_UNIQUE_NAME( ____C_A_T_C_H____T_E_S_T____ )) #define CATCH_SCENARIO_METHOD( className, ... ) INTERNAL_CATCH_TESTCASE_METHOD_NO_REGISTRATION(INTERNAL_CATCH_UNIQUE_NAME( ____C_A_T_C_H____T_E_S_T____ ), className ) #define CATCH_GIVEN( desc ) #define CATCH_AND_GIVEN( desc ) #define CATCH_WHEN( desc ) #define CATCH_AND_WHEN( desc ) #define CATCH_THEN( desc ) #define CATCH_AND_THEN( desc ) #define CATCH_STATIC_REQUIRE( ... ) (void)(0) #define CATCH_STATIC_REQUIRE_FALSE( ... ) (void)(0) // If CATCH_CONFIG_PREFIX_ALL is not defined then the CATCH_ prefix is not required #else #define REQUIRE( ... ) (void)(0) #define REQUIRE_FALSE( ... ) (void)(0) #define REQUIRE_THROWS( ... ) (void)(0) #define REQUIRE_THROWS_AS( expr, exceptionType ) (void)(0) #define REQUIRE_THROWS_WITH( expr, matcher ) (void)(0) #if !defined(CATCH_CONFIG_DISABLE_MATCHERS) #define REQUIRE_THROWS_MATCHES( expr, exceptionType, matcher ) (void)(0) #endif // CATCH_CONFIG_DISABLE_MATCHERS #define REQUIRE_NOTHROW( ... ) (void)(0) #define CHECK( ... ) (void)(0) #define CHECK_FALSE( ... ) (void)(0) #define CHECKED_IF( ... ) if (__VA_ARGS__) #define CHECKED_ELSE( ... ) if (!(__VA_ARGS__)) #define CHECK_NOFAIL( ... ) (void)(0) #define CHECK_THROWS( ... ) (void)(0) #define CHECK_THROWS_AS( expr, exceptionType ) (void)(0) #define CHECK_THROWS_WITH( expr, matcher ) (void)(0) #if !defined(CATCH_CONFIG_DISABLE_MATCHERS) #define CHECK_THROWS_MATCHES( expr, exceptionType, matcher ) (void)(0) #endif // CATCH_CONFIG_DISABLE_MATCHERS #define CHECK_NOTHROW( ... ) (void)(0) #if !defined(CATCH_CONFIG_DISABLE_MATCHERS) #define CHECK_THAT( arg, matcher ) (void)(0) #define REQUIRE_THAT( arg, matcher ) (void)(0) #endif // CATCH_CONFIG_DISABLE_MATCHERS #define INFO( msg ) (void)(0) #define WARN( msg ) (void)(0) #define CAPTURE( msg ) (void)(0) #define TEST_CASE( ... ) INTERNAL_CATCH_TESTCASE_NO_REGISTRATION(INTERNAL_CATCH_UNIQUE_NAME( ____C_A_T_C_H____T_E_S_T____ )) #define TEST_CASE_METHOD( className, ... ) INTERNAL_CATCH_TESTCASE_NO_REGISTRATION(INTERNAL_CATCH_UNIQUE_NAME( ____C_A_T_C_H____T_E_S_T____ )) #define METHOD_AS_TEST_CASE( method, ... ) #define REGISTER_TEST_CASE( Function, ... ) (void)(0) #define SECTION( ... ) #define DYNAMIC_SECTION( ... ) #define FAIL( ... ) (void)(0) #define FAIL_CHECK( ... ) (void)(0) #define SUCCEED( ... ) (void)(0) #define ANON_TEST_CASE() INTERNAL_CATCH_TESTCASE_NO_REGISTRATION(INTERNAL_CATCH_UNIQUE_NAME( ____C_A_T_C_H____T_E_S_T____ )) #ifndef CATCH_CONFIG_TRADITIONAL_MSVC_PREPROCESSOR #define TEMPLATE_TEST_CASE( ... ) INTERNAL_CATCH_TEMPLATE_TEST_CASE_NO_REGISTRATION(INTERNAL_CATCH_UNIQUE_NAME( ____C_A_T_C_H____T_E_M_P_L_A_T_E____T_E_S_T____ ) ) #define TEMPLATE_TEST_CASE_METHOD( className, ... ) INTERNAL_CATCH_TEMPLATE_TEST_CASE_METHOD_NO_REGISTRATION(INTERNAL_CATCH_UNIQUE_NAME( ____C_A_T_C_H____T_E_M_P_L_A_T_E____T_E_S_T____ ), className ) #define TEMPLATE_PRODUCT_TEST_CASE( ... ) TEMPLATE_TEST_CASE( __VA_ARGS__ ) #define TEMPLATE_PRODUCT_TEST_CASE_METHOD( className, ... ) TEMPLATE_TEST_CASE_METHOD( className, __VA_ARGS__ ) #else #define TEMPLATE_TEST_CASE( ... ) INTERNAL_CATCH_EXPAND_VARGS( INTERNAL_CATCH_TEMPLATE_TEST_CASE_NO_REGISTRATION(INTERNAL_CATCH_UNIQUE_NAME( ____C_A_T_C_H____T_E_M_P_L_A_T_E____T_E_S_T____ ) ) ) #define TEMPLATE_TEST_CASE_METHOD( className, ... ) INTERNAL_CATCH_EXPAND_VARGS( INTERNAL_CATCH_TEMPLATE_TEST_CASE_METHOD_NO_REGISTRATION(INTERNAL_CATCH_UNIQUE_NAME( ____C_A_T_C_H____T_E_M_P_L_A_T_E____T_E_S_T____ ), className ) ) #define TEMPLATE_PRODUCT_TEST_CASE( ... ) TEMPLATE_TEST_CASE( __VA_ARGS__ ) #define TEMPLATE_PRODUCT_TEST_CASE_METHOD( className, ... ) TEMPLATE_TEST_CASE_METHOD( className, __VA_ARGS__ ) #endif #define STATIC_REQUIRE( ... ) (void)(0) #define STATIC_REQUIRE_FALSE( ... ) (void)(0) #endif #define CATCH_TRANSLATE_EXCEPTION( signature ) INTERNAL_CATCH_TRANSLATE_EXCEPTION_NO_REG( INTERNAL_CATCH_UNIQUE_NAME( catch_internal_ExceptionTranslator ), signature ) // "BDD-style" convenience wrappers #define SCENARIO( ... ) INTERNAL_CATCH_TESTCASE_NO_REGISTRATION(INTERNAL_CATCH_UNIQUE_NAME( ____C_A_T_C_H____T_E_S_T____ ) ) #define SCENARIO_METHOD( className, ... ) INTERNAL_CATCH_TESTCASE_METHOD_NO_REGISTRATION(INTERNAL_CATCH_UNIQUE_NAME( ____C_A_T_C_H____T_E_S_T____ ), className ) #define GIVEN( desc ) #define AND_GIVEN( desc ) #define WHEN( desc ) #define AND_WHEN( desc ) #define THEN( desc ) #define AND_THEN( desc ) using Catch::Detail::Approx; #endif #endif // ! CATCH_CONFIG_IMPL_ONLY // start catch_reenable_warnings.h #ifdef __clang__ # ifdef __ICC // icpc defines the __clang__ macro # pragma warning(pop) # else # pragma clang diagnostic pop # endif #elif defined __GNUC__ # pragma GCC diagnostic pop #endif // end catch_reenable_warnings.h // end catch.hpp #endif // TWOBLUECUBES_SINGLE_INCLUDE_CATCH_HPP_INCLUDED adapterremoval-2.3.1/tests/unit/fastq_enc_test.cpp000066400000000000000000000044141350370616400223620ustar00rootroot00000000000000/*************************************************************************\ * AdapterRemoval - cleaning next-generation sequencing reads * * * * Copyright (C) 2011 by Stinus Lindgreen - stinus@binf.ku.dk * * Copyright (C) 2014 by Mikkel Schubert - mikkelsch@gmail.com * * * * If you use the program, please cite the paper: * * S. Lindgreen (2012): AdapterRemoval: Easy Cleaning of Next Generation * * Sequencing Reads, BMC Research Notes, 5:337 * * http://www.biomedcentral.com/1756-0500/5/337/ * * * * This program is free software: you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation, either version 3 of the License, or * * (at your option) any later version. * * * * This program is distributed in the hope that it will be useful, * * but WITHOUT ANY WARRANTY; without even the implied warranty of * * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * * GNU General Public License for more details. * * * * You should have received a copy of the GNU General Public License * * along with this program. If not, see . * \*************************************************************************/ #include "testing.hpp" #include "fastq.hpp" namespace ar { /////////////////////////////////////////////////////////////////////////////// // Names (default objects) TEST_CASE("Global encodings have expected names", "[fastq_encoding]") { REQUIRE(FASTQ_ENCODING_33.name() == std::string("Phred+33")); REQUIRE(FASTQ_ENCODING_64.name() == std::string("Phred+64")); REQUIRE(FASTQ_ENCODING_SAM.name() == std::string("Phred+33")); REQUIRE(FASTQ_ENCODING_SOLEXA.name() == std::string("Solexa")); } } adapterremoval-2.3.1/tests/unit/fastq_test.cpp000066400000000000000000001114611350370616400215360ustar00rootroot00000000000000/*************************************************************************\ * AdapterRemoval - cleaning next-generation sequencing reads * * * * Copyright (C) 2011 by Stinus Lindgreen - stinus@binf.ku.dk * * Copyright (C) 2014 by Mikkel Schubert - mikkelsch@gmail.com * * * * If you use the program, please cite the paper: * * S. Lindgreen (2012): AdapterRemoval: Easy Cleaning of Next Generation * * Sequencing Reads, BMC Research Notes, 5:337 * * http://www.biomedcentral.com/1756-0500/5/337/ * * * * This program is free software: you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation, either version 3 of the License, or * * (at your option) any later version. * * * * This program is distributed in the hope that it will be useful, * * but WITHOUT ANY WARRANTY; without even the implied warranty of * * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * * GNU General Public License for more details. * * * * You should have received a copy of the GNU General Public License * * along with this program. If not, see . * \*************************************************************************/ #include #include #include "testing.hpp" #include "debug.hpp" #include "fastq.hpp" #include "linereader.hpp" namespace ar { class vec_reader : public line_reader_base { public: vec_reader(const string_vec& lines) : m_lines(lines) , m_it(m_lines.begin()) { } bool getline(std::string& dst) { if (m_it == m_lines.end()) { return false; } dst = *m_it++; return true; } private: string_vec m_lines; string_vec::const_iterator m_it; }; /////////////////////////////////////////////////////////////////////////////// // Helper functions TEST_CASE("ACGT_TO_IDX", "[fastq::*]") { // The exact encoding is unimportant, but it must be unique and 2 bit REQUIRE(ACGT_TO_IDX('A') <= 3); REQUIRE(ACGT_TO_IDX('C') <= 3); REQUIRE(ACGT_TO_IDX('G') <= 3); REQUIRE(ACGT_TO_IDX('T') <= 3); REQUIRE(ACGT_TO_IDX('A') != ACGT_TO_IDX('C')); REQUIRE(ACGT_TO_IDX('A') != ACGT_TO_IDX('G')); REQUIRE(ACGT_TO_IDX('A') != ACGT_TO_IDX('T')); REQUIRE(ACGT_TO_IDX('C') != ACGT_TO_IDX('G')); REQUIRE(ACGT_TO_IDX('C') != ACGT_TO_IDX('T')); REQUIRE(ACGT_TO_IDX('G') != ACGT_TO_IDX('T')); } TEST_CASE("IDX_TO_ACGT", "[fastq::*]") { REQUIRE(IDX_TO_ACGT(ACGT_TO_IDX('A')) == 'A'); REQUIRE(IDX_TO_ACGT(ACGT_TO_IDX('C')) == 'C'); REQUIRE(IDX_TO_ACGT(ACGT_TO_IDX('G')) == 'G'); REQUIRE(IDX_TO_ACGT(ACGT_TO_IDX('T')) == 'T'); } /////////////////////////////////////////////////////////////////////////////// // Default constructor TEST_CASE("default_constructor", "[fastq::fastq]") { const fastq record; REQUIRE(record.header() == ""); REQUIRE(record.sequence() == ""); REQUIRE(record.qualities() == ""); } /////////////////////////////////////////////////////////////////////////////// // Primary constructor TEST_CASE("constructor_empty_fields", "[fastq::fastq]") { const fastq record("", "", ""); REQUIRE(record.header() == ""); REQUIRE(record.sequence() == ""); REQUIRE(record.qualities() == ""); } TEST_CASE("constructor_simple_record_phred_33_encoded", "[fastq::fastq]") { const fastq record("record_1", "ACGAGTCA", "!7BF8DGI"); REQUIRE(record.header() == "record_1"); REQUIRE(record.sequence() == "ACGAGTCA"); REQUIRE(record.qualities() == "!7BF8DGI"); } TEST_CASE("constructor_simple_record_phred_64_encoded", "[fastq::fastq]") { const fastq record("record_2", "ACGAGTCA", "@VaeWcfh", FASTQ_ENCODING_64); REQUIRE(record.header() == "record_2"); REQUIRE(record.sequence() == "ACGAGTCA"); REQUIRE(record.qualities() == "!7BF8DGI"); } TEST_CASE("constructor_simple_record_phred_solexa_encoded", "[fastq::fastq]") { const fastq record("record_3", "AAACGAGTCA", ";h>S\\TCDUJ", FASTQ_ENCODING_SOLEXA); REQUIRE(record.header() == "record_3"); REQUIRE(record.sequence() == "AAACGAGTCA"); REQUIRE(record.qualities() == "\"I#4=5&&6+"); } TEST_CASE("constructor_simple_record_lowercase_to_uppercase", "[fastq::fastq]") { const fastq record("record_1", "AnGaGtcA", "!7BF8DGI"); REQUIRE(record.sequence() == "ANGAGTCA"); } TEST_CASE("constructor_simple_record_dots_to_n", "[fastq::fastq]") { const fastq record("record_1", "AC.AG.C.", "!7BF8DGI"); REQUIRE(record.sequence() == "ACNAGNCN"); } TEST_CASE("constructor_score_boundries_phred_33", "[fastq::fastq]") { REQUIRE_NOTHROW(fastq("Rec", "CAT", "!!\"", FASTQ_ENCODING_33)); REQUIRE_THROWS_AS(fastq("Rec", "CAT", " !\"", FASTQ_ENCODING_33), fastq_error); REQUIRE_NOTHROW(fastq("Rec", "CAT", "IJJ", FASTQ_ENCODING_33)); REQUIRE_THROWS_AS(fastq("Rec", "CAT", "IJK", FASTQ_ENCODING_33), fastq_error); } TEST_CASE("constructor_score_boundries_phred_64", "[fastq::fastq]") { REQUIRE_NOTHROW(fastq("Rec", "CAT", "@@A", FASTQ_ENCODING_64)); REQUIRE_THROWS_AS(fastq("Rec", "CAT", "?@A", FASTQ_ENCODING_64), fastq_error); REQUIRE_NOTHROW(fastq("Rec", "CAT", "ghi", FASTQ_ENCODING_64)); REQUIRE_THROWS_AS(fastq("Rec", "CAT", "ghj", FASTQ_ENCODING_64), fastq_error); } TEST_CASE("constructor_score_boundries_solexa", "[fastq::fastq]") { REQUIRE_NOTHROW(fastq("Rec", "CAT", ";;<", FASTQ_ENCODING_SOLEXA)); REQUIRE_THROWS_AS(fastq("Rec", "CAT", ":;<", FASTQ_ENCODING_SOLEXA), fastq_error); REQUIRE_NOTHROW(fastq("Rec", "CAT", "ghi", FASTQ_ENCODING_SOLEXA)); REQUIRE_THROWS_AS(fastq("Rec", "CAT", "ghj", FASTQ_ENCODING_SOLEXA), fastq_error); } TEST_CASE("constructor_score_boundries_ignored", "[fastq::fastq]") { REQUIRE_NOTHROW(fastq("Rec", "CAT", "!!\"", FASTQ_ENCODING_SAM)); REQUIRE_THROWS_AS(fastq("Rec", "CAT", " !\"", FASTQ_ENCODING_SAM), fastq_error); REQUIRE_NOTHROW(fastq("Rec", "CAT", "gh~", FASTQ_ENCODING_SAM)); REQUIRE_THROWS_AS(fastq("Rec", "CAT", "gh\x7f", FASTQ_ENCODING_SAM), fastq_error); } TEST_CASE("constructor_field_lengths", "[fastq::fastq]") { REQUIRE_NOTHROW(fastq("Name", "CAT", "IJJ")); // A non-empty sequence must be specified REQUIRE_THROWS_AS(fastq("Name", "", "IJJ"), fastq_error); // A non-empty quality string must be specified REQUIRE_THROWS_AS(fastq("Name", "CAT", ""), fastq_error); // And the length of each must be the same REQUIRE_THROWS_AS(fastq("Name", "CA", "IJJ"), fastq_error); REQUIRE_THROWS_AS(fastq("Name", "CAT", "IJ"), fastq_error); } TEST_CASE("constructor_invalid_nucleotides", "[fastq::fastq]") { REQUIRE_NOTHROW(fastq("Name", "CATT", "IJJI")); // Non-alpha characters are not allowed REQUIRE_THROWS_AS(fastq("Name", "CAT!", "IJJI"), fastq_error); // Numeric charecters are not allowed REQUIRE_THROWS_AS(fastq("Name", "CAT7", "IJJI"), fastq_error); // But neither are non acgtn/ACGTN allowed REQUIRE_THROWS_AS(fastq("Name", "CATS", "IJJI"), fastq_error); REQUIRE_THROWS_AS(fastq("Name", "CATs", "IJJI"), fastq_error); } /////////////////////////////////////////////////////////////////////////////// // Constructor without qualities TEST_CASE("constructor_no_qualities", "[fastq::fastq]") { const fastq record("record_1", "ACGT"); REQUIRE(record.header() == "record_1"); REQUIRE(record.sequence() == "ACGT"); REQUIRE(record.qualities() == "!!!!"); } TEST_CASE("constructor_no_qualities_no_sequence", "[fastq::fastq]") { const fastq record("record_1", ""); REQUIRE(record.header() == "record_1"); REQUIRE(record.sequence() == ""); REQUIRE(record.qualities() == ""); } /////////////////////////////////////////////////////////////////////////////// // misc properties TEST_CASE("name", "[fastq::fastq]") { REQUIRE(fastq("name", "", "").name() == "name"); REQUIRE(fastq("name meta", "", "").name() == "name"); REQUIRE(fastq("name meta more", "", "").name() == "name"); } TEST_CASE("length", "[fastq::fastq]") { REQUIRE(fastq("record_1", "", "").length() == 0); REQUIRE(fastq("record_1", "A", "G").length() == 1); REQUIRE(fastq("record_1", "AC", "!B").length() == 2); REQUIRE(fastq("record_1", "ACG", "!7B").length() == 3); } TEST_CASE("count_ns", "[fastq::fastq]") { REQUIRE(fastq("Rec", "ACGTA", "IJIJI").count_ns() == 0); REQUIRE(fastq("Rec", "ANGTA", "IJIJI").count_ns() == 1); REQUIRE(fastq("Rec", "ANGTN", "IJIJI").count_ns() == 2); REQUIRE(fastq("Rec", "ANGNN", "IJIJI").count_ns() == 3); REQUIRE(fastq("Rec", "NNGNN", "IJIJI").count_ns() == 4); REQUIRE(fastq("Rec", "NNNNN", "IJIJI").count_ns() == 5); } /////////////////////////////////////////////////////////////////////////////// // trim_trailing_bases TEST_CASE("trim_trailing_bases__empty_record", "[fastq::fastq]") { fastq record("Empty", "", ""); const fastq::ntrimmed expected(0, 0); REQUIRE(record.trim_trailing_bases(true, 10) == expected); REQUIRE(record == fastq("Empty", "", "")); } TEST_CASE("trim_trailing_bases__trim_nothing", "[fastq::fastq]") { const fastq reference("Rec", "NNNNN", "!!!!!"); const fastq::ntrimmed expected(0, 0); fastq record = reference; // Trim neither Ns nor low Phred score bases REQUIRE(record.trim_trailing_bases(false, -1) == expected); REQUIRE(record == reference); } TEST_CASE("trim_trailing_bases__trim_ns", "[fastq::fastq]") { fastq record("Rec", "NNANT", "23456"); const fastq expected_record("Rec", "ANT", "456"); const fastq::ntrimmed expected_ntrim(2, 0); REQUIRE(record.trim_trailing_bases(true, -1) == expected_ntrim); REQUIRE(record == expected_record); } TEST_CASE("trim_trailing_bases__trim_trailing_bases", "[fastq::fastq]") { const fastq expected_record("Rec", "TN", "%$"); const fastq::ntrimmed expected_ntrim(0, 3); fastq record("Rec", "TNANT", "%$#!\""); REQUIRE(record.trim_trailing_bases(false, 2) == expected_ntrim); REQUIRE(record == expected_record); } TEST_CASE("trim_trailing_bases__trim_mixed", "[fastq::fastq]") { const fastq expected_record("Rec", "TAG", "$12"); const fastq::ntrimmed expected_ntrim(3, 2); fastq record("Rec", "NTNTAGNT", "1!#$12#\""); REQUIRE(record.trim_trailing_bases(true, 2) == expected_ntrim); REQUIRE(record == expected_record); } TEST_CASE("trim_trailing_bases__trim_mixed__no_low_quality_bases", "[fastq::fastq]") { const fastq expected_record("Rec", "ACTTAG", "12I$12"); const fastq::ntrimmed expected_ntrim(0, 0); fastq record = expected_record; REQUIRE(record.trim_trailing_bases(true, 2) == expected_ntrim); REQUIRE(record == expected_record); } TEST_CASE("trim_trailing_bases__trim_everything", "[fastq::fastq]") { fastq record("Rec", "TAG", "!!!"); const fastq expected_record = fastq("Rec", "", ""); const fastq::ntrimmed expected_ntrim(0, 3); REQUIRE(record.trim_trailing_bases(true, 2) == expected_ntrim); REQUIRE(record == expected_record); } TEST_CASE("trim_trailing_bases__trim_3p__trim_ns", "[fastq::fastq]") { fastq record("Rec", "NNATN", "23456"); const fastq expected_record("Rec", "NNAT", "2345"); const fastq::ntrimmed expected_ntrim(0, 1); REQUIRE(record.trim_trailing_bases(true, -1, true) == expected_ntrim); REQUIRE(record == expected_record); } TEST_CASE("trim_trailing_bases__trim_3p__trim_trailing_bases", "[fastq::fastq]") { const fastq expected_record("Rec", "TN", "!$"); const fastq::ntrimmed expected_ntrim(0, 3); fastq record("Rec", "TNANT", "!$#!\""); REQUIRE(record.trim_trailing_bases(false, 2, true) == expected_ntrim); REQUIRE(record == expected_record); } /////////////////////////////////////////////////////////////////////////////// // trim_windowed_bases TEST_CASE("Window trimming with invalid parameters", "[fastq::windows]") { const std::vector values = {-1.0, std::numeric_limits::quiet_NaN()}; for (const auto& value : values) { fastq record("Rec", "TAGTGACAT", "111111111"); REQUIRE_THROWS_AS(record.trim_windowed_bases(false, -1, value), assert_failed); } } TEST_CASE("Window trimming empty reads", "[fastq::windows]") { const std::vector values = {1, 0.1, 3}; for (const auto& value : values) { fastq record("Empty", "", ""); const fastq::ntrimmed expected(0, 0); REQUIRE(record.trim_windowed_bases(true, 10, value) == expected); REQUIRE(record == fastq("Empty", "", "")); } } TEST_CASE("Window trimming entire read", "[fastq::windows]") { const std::vector values = {1, 0.2, 4, 10}; for (const auto& value : values) { fastq record("Rec", "TAGTGACAT", "111111111"); const fastq expected_record = fastq("Rec", "", ""); const fastq::ntrimmed expected_ntrim(9, 0); REQUIRE(record.trim_windowed_bases(false, '2' - '!', value) == expected_ntrim); REQUIRE(record == expected_record); } } TEST_CASE("Window trimming nothing", "[fastq::windows]") { const std::vector values = {0, 1, 0.2, 3, 4, 5, 6, 7, 8, 9, 10, 11}; for (const auto& value : values) { fastq record("Rec", "TAGTGACAT", "111111111"); const fastq expected_record = record; const fastq::ntrimmed expected_ntrim(0, 0); REQUIRE(record.trim_windowed_bases(false, -1, value) == expected_ntrim); REQUIRE(record == expected_record); } } TEST_CASE("Window trimming of Ns", "[fastq::windows]") { const std::vector values = {1, 0.2}; for (const auto& value : values) { fastq record("Rec", "NNATNT", "234567"); const fastq expected_record("Rec", "ATNT", "4567"); const fastq::ntrimmed expected_ntrim(2, 0); REQUIRE(record.trim_windowed_bases(true, -1, value) == expected_ntrim); REQUIRE(record == expected_record); } } TEST_CASE("Window trimming of Ns, final window contains Ns", "[fastq::windows]") { const std::vector values = {2, 3, 4}; for (const auto& value : values) { fastq record("Rec", "NNATNT", "234567"); const fastq expected_record("Rec", "AT", "45"); const fastq::ntrimmed expected_ntrim(2, 2); REQUIRE(record.trim_windowed_bases(true, -1, value) == expected_ntrim); REQUIRE(record == expected_record); } } TEST_CASE("Window trimming of Ns, no valid window found", "[fastq::fastq]") { fastq record("Rec", "NNATNT", "234567"); const fastq expected_record("Rec", "", ""); const fastq::ntrimmed expected_ntrim(6, 0); REQUIRE(record.trim_windowed_bases(true, -1, 5) == expected_ntrim); REQUIRE(record == expected_record); } TEST_CASE("Window trimming 5p only, 1bp", "[fastq::windows]") { const std::vector values = {1, 0.1}; for (const auto& value : values) { fastq record("Rec", "TAACGATCCG", "0123456789"); const fastq expected_record("Rec", "CGATCCG", "3456789"); const fastq::ntrimmed expected_ntrim(3, 0); REQUIRE(record.trim_windowed_bases(false, '2' - '!', value) == expected_ntrim); REQUIRE(record == expected_record); } } TEST_CASE("Window trimming 5p only, 2bp", "[fastq::windows]") { const std::vector values = {2, 0.2}; for (const auto& value : values) { fastq record("Rec", "TAACGATCCG", "0123456789"); const fastq expected_record("Rec", "CGATCCG", "3456789"); const fastq::ntrimmed expected_ntrim(3, 0); REQUIRE(record.trim_windowed_bases(false, '2' - '!', value) == expected_ntrim); REQUIRE(record == expected_record); } } TEST_CASE("Window trimming 5p only, inclusive lower bound", "[fastq::windows]") { const std::vector values = {2, 3}; for (const auto& value : values) { fastq record("Rec", "TAACGATCCG", "0123126789"); const fastq expected_record("Rec", "TCCG", "6789"); const fastq::ntrimmed expected_ntrim(6, 0); REQUIRE(record.trim_windowed_bases(false, '2' - '!', value) == expected_ntrim); REQUIRE(record == expected_record); } } TEST_CASE("Window trimming 3p only, inclusive lower bound", "[fastq::windows]") { const std::vector values = {3}; for (const auto& value : values) { fastq record("Rec", "TAACGATCCG", "9876312333"); const fastq expected_record("Rec", "TAACG", "98763"); const fastq::ntrimmed expected_ntrim(0, 5); REQUIRE(record.trim_windowed_bases(false, '2' - '!', value) == expected_ntrim); REQUIRE(record == expected_record); } } TEST_CASE("Window trimming big and small windows #1", "[fastq::windows]") { const std::vector values = {0, 0.01, 20}; for (const auto& value : values) { fastq record("Rec", "TAACGATC", "23456789"); const fastq expected_record("Rec", "", ""); const fastq::ntrimmed expected_ntrim(8, 0); CHECK(record.trim_windowed_bases(false, '2' - '!', value) == expected_ntrim); REQUIRE(record == expected_record); } } TEST_CASE("Window trimming big and small windows #2", "[fastq::windows]") { const std::vector values = {0, 0.01, 20}; for (const auto& value : values) { fastq record("Rec", "TAACGATC", "23456780"); const fastq expected_record("Rec", "TAACGAT", "2345678"); const fastq::ntrimmed expected_ntrim(0, 1); REQUIRE(record.trim_windowed_bases(false, '1' - '!', value) == expected_ntrim); REQUIRE(record == expected_record); } } TEST_CASE("Window trimming last trailing window", "[fastq::windows]") { const std::vector values = {1, 2, 3, 4, 5, 6, 7, 8, 9}; for (const auto& value : values) { fastq record("Rec", "TAACGATCC", "234567811"); const fastq expected_record("Rec", "TAACGAT", "2345678"); const fastq::ntrimmed expected_ntrim(0, 2); REQUIRE(record.trim_windowed_bases(false, '1' - '!', value) == expected_ntrim); REQUIRE(record == expected_record); } } TEST_CASE("trim_windowed_bases__trim_window", "[fastq::fastq]") { // Should trim starting at the window of low quality bases in the middle // even with high qual bases at the end. fastq record("Rec", "NNAAAAAAAAATNNNNNNNA", "##EEEEEEEEEE#######E"); const fastq expected_record = fastq("Rec", "AAAAAAAAAT", "EEEEEEEEEE"); const fastq::ntrimmed expected_ntrim(2, 8); REQUIRE(record.trim_windowed_bases(true, 10, 5) == expected_ntrim); REQUIRE(record == expected_record); } TEST_CASE("trim_windowed_bases__trim_3p", "[fastq::fastq]") { fastq record("Rec", "NNAAAAAAAAATNNNNNNN", "##EEEEEEEEEE#######"); const fastq expected_record = fastq("Rec", "NNAAAAAAAAAT", "##EEEEEEEEEE"); const fastq::ntrimmed expected_ntrim(0, 7); REQUIRE(record.trim_windowed_bases(false, 10, 5, true) == expected_ntrim); REQUIRE(record == expected_record); } TEST_CASE("trim_windowed_bases__trim_3p__trim_ns", "[fastq::fastq]") { fastq record("Rec", "NNAAAAAAAAATNNNNNNN", "##EEEEEEEEEE#######"); const fastq expected_record = fastq("Rec", "NNAAAAAAAAAT", "##EEEEEEEEEE"); const fastq::ntrimmed expected_ntrim(0, 7); REQUIRE(record.trim_windowed_bases(true, 10, 5, true) == expected_ntrim); REQUIRE(record == expected_record); } TEST_CASE("trim_windowed_bases__trim_3p__reversed", "[fastq::fastq]") { fastq record("Rec", "NNNNNNNTAAAAAAAAANN", "#######EEEEEEEEEE##"); const fastq expected_record = fastq("Rec", "NNNNNNNTAAAAAAAAA", "#######EEEEEEEEEE"); const fastq::ntrimmed expected_ntrim(0, 2); REQUIRE(record.trim_windowed_bases(true, 10, 5, true) == expected_ntrim); REQUIRE(record == expected_record); } /////////////////////////////////////////////////////////////////////////////// // Truncate TEST_CASE("truncate_empty", "[fastq::fastq]") { fastq record("Empty", "", ""); record.truncate(0, 10); REQUIRE(record == fastq("Empty", "", "")); } TEST_CASE("truncate_zero_bases", "[fastq::fastq]") { const fastq expected_record("Rec", "ACTTAG", "12I$12"); fastq current_record = expected_record; current_record.truncate(); REQUIRE(current_record == expected_record); } TEST_CASE("truncate_all_bases", "[fastq::fastq]") { const fastq expected_record("Rec", "", ""); fastq current_record("Rec", "ACTTAG", "12I$12"); current_record.truncate(1, 0); REQUIRE(current_record == expected_record); } TEST_CASE("truncate_5p", "[fastq::fastq]") { const fastq expected_record("Rec", "TTAG", "I$12"); fastq current_record("Rec", "ACTTAG", "12I$12"); current_record.truncate(2); REQUIRE(current_record == expected_record); } TEST_CASE("truncate_3p", "[fastq::fastq]") { const fastq expected_record("Rec", "ACT", "12I"); fastq current_record("Rec", "ACTTAG", "12I$12"); current_record.truncate(0, 3); REQUIRE(current_record == expected_record); } TEST_CASE("truncate_middle", "[fastq::fastq]") { const fastq expected_record("Rec", "TTA", "I$1"); fastq current_record("Rec", "ACTTAG", "12I$12"); current_record.truncate(2, 3); REQUIRE(current_record == expected_record); } TEST_CASE("truncate_len_higher_than_n_bases", "[fastq::fastq]") { const fastq expected_record("Rec", "TTAG", "I$12"); fastq current_record("Rec", "ACTTAG", "12I$12"); current_record.truncate(2, 1024); REQUIRE(current_record == expected_record); } TEST_CASE("truncate_pos_after_last_base", "[fastq::fastq]") { // Same behavior as string::substr fastq current_record("Rec", "ACTTAG", "12I$12"); REQUIRE_NOTHROW(current_record.truncate(6)); REQUIRE_THROWS_AS(current_record.truncate(7), assert_failed); } /////////////////////////////////////////////////////////////////////////////// // Reverse complement TEST_CASE("reverse_complement__empty", "[fastq::fastq]") { const fastq expected = fastq("Empty", "", ""); fastq result = fastq("Empty", "", ""); result.reverse_complement(); REQUIRE(result == expected); } TEST_CASE("reverse_complement", "[fastq::fastq]") { const fastq expected = fastq("Rec", "TACAGANGTN", "0123456789"); fastq result = fastq("Rec", "NACNTCTGTA", "9876543210"); result.reverse_complement(); REQUIRE(result == expected); } /////////////////////////////////////////////////////////////////////////////// // Adding prefixes to the header TEST_CASE("add_prefix_to_header", "[fastq::fastq]") { const fastq expected("not_my_header", "ACGTA", "12345"); fastq record("my_header", "ACGTA", "12345"); record.add_prefix_to_header("not_"); REQUIRE(record == expected); } TEST_CASE("add_prefix_to_header__empty_prefix", "[fastq::fastq]") { const fastq expected("my_header", "ACGTA", "12345"); fastq record = expected; record.add_prefix_to_header(""); REQUIRE(record == expected); } TEST_CASE("add_prefix_to_header__header", "[fastq::fastq]") { const fastq expected("new_header", "ACGTA", "12345"); fastq record("", "ACGTA", "12345"); record.add_prefix_to_header("new_header"); REQUIRE(record == expected); } /////////////////////////////////////////////////////////////////////////////// // Adding postfixes to the header TEST_CASE("add_postfix_to_header", "[fastq::fastq]") { const fastq expected("my_header new postfix", "ACGTA", "12345"); fastq record("my_header", "ACGTA", "12345"); record.add_postfix_to_header(" new postfix"); REQUIRE(record == expected); } TEST_CASE("add_postfix_to_header__empty_prefix", "[fastq::fastq]") { const fastq expected("my_header", "ACGTA", "12345"); fastq record = expected; record.add_postfix_to_header(""); REQUIRE(record == expected); } TEST_CASE("add_postfix_to_header__header", "[fastq::fastq]") { const fastq expected("new_header", "ACGTA", "12345"); fastq record("", "ACGTA", "12345"); record.add_postfix_to_header("new_header"); REQUIRE(record == expected); } /////////////////////////////////////////////////////////////////////////////// // Discarding read, setting seq to N and qual to '!' TEST_CASE("discard_read", "[fastq::fastq]") { const fastq expected("my_header", "N", "!"); fastq record("my_header", "ACGTA", "12345"); record.discard(); REQUIRE(record == expected); } TEST_CASE("discard_discarded_read", "[fastq::fastq]") { const fastq expected("my_header", "N", "!"); fastq record("my_header", "N", "!"); record.discard(); REQUIRE(record == expected); } TEST_CASE("discard_empty_read", "[fastq::fastq]") { const fastq expected("my_header", "N", "!"); fastq record("my_header", "", ""); record.discard(); REQUIRE(record == expected); } /////////////////////////////////////////////////////////////////////////////// // Reading from stream TEST_CASE("simple_fastq_record_1", "[fastq::fastq]") { string_vec lines; lines.push_back("@record_1"); lines.push_back("ACGAGTCA"); lines.push_back("+"); lines.push_back("!7BF8DGI"); vec_reader reader(lines); fastq record; CHECK(record.read(reader, FASTQ_ENCODING_33)); REQUIRE(record.header() == "record_1"); REQUIRE(record.sequence() == "ACGAGTCA"); REQUIRE(record.qualities() == "!7BF8DGI"); } TEST_CASE("simple_fastq_record_2", "[fastq::fastq]") { string_vec lines; lines.push_back("@record_1"); lines.push_back("ACGAGTCA"); lines.push_back("+"); lines.push_back("!7BF8DGI"); lines.push_back("@record_2"); lines.push_back("GTCAGGAT"); lines.push_back("+"); lines.push_back("D7BIG!F8"); vec_reader reader(lines); fastq record; CHECK(record.read(reader, FASTQ_ENCODING_33)); REQUIRE(record.header() == "record_1"); REQUIRE(record.sequence() == "ACGAGTCA"); REQUIRE(record.qualities() == "!7BF8DGI"); CHECK(record.read(reader, FASTQ_ENCODING_33)); REQUIRE(record.header() == "record_2"); REQUIRE(record.sequence() == "GTCAGGAT"); REQUIRE(record.qualities() == "D7BIG!F8"); CHECK(!record.read(reader, FASTQ_ENCODING_33)); } TEST_CASE("simple_fastq_record__with_extra_header_1", "[fastq::fastq]") { string_vec lines; lines.push_back("@record_1 Extra header here"); lines.push_back("ACGAGTCA"); lines.push_back("+"); lines.push_back("!7BF8DGI"); vec_reader reader(lines); fastq record; CHECK(record.read(reader, FASTQ_ENCODING_33)); REQUIRE(record.header() == "record_1 Extra header here"); REQUIRE(record.sequence() == "ACGAGTCA"); REQUIRE(record.qualities() == "!7BF8DGI"); CHECK(!record.read(reader, FASTQ_ENCODING_33)); } TEST_CASE("simple_fastq_record__with_extra_header_2", "[fastq::fastq]") { string_vec lines; lines.push_back("@record_1"); lines.push_back("ACGAGTCA"); lines.push_back("+Extra header here"); lines.push_back("!7BF8DGI"); vec_reader reader(lines); fastq record; CHECK(record.read(reader, FASTQ_ENCODING_33)); REQUIRE(record.header() == "record_1"); REQUIRE(record.sequence() == "ACGAGTCA"); REQUIRE(record.qualities() == "!7BF8DGI"); CHECK(!record.read(reader, FASTQ_ENCODING_33)); } TEST_CASE("simple_fastq_record__no_header", "[fastq::fastq]") { string_vec lines; lines.push_back("@"); lines.push_back("ACGAGTCA"); lines.push_back("+"); lines.push_back("!7BF8DGI"); vec_reader reader(lines); fastq record; REQUIRE_THROWS_AS(record.read(reader, FASTQ_ENCODING_33), fastq_error); } TEST_CASE("simple_fastq_record__no_sequence", "[fastq::fastq]") { string_vec lines; lines.push_back("@record_1"); lines.push_back(""); lines.push_back("+"); lines.push_back("!7BF8DGI"); vec_reader reader(lines); fastq record; REQUIRE_THROWS_AS(record.read(reader, FASTQ_ENCODING_33), fastq_error); } TEST_CASE("simple_fastq_record__no_qualities", "[fastq::fastq]") { string_vec lines; lines.push_back("@"); lines.push_back("ACGAGTCA"); lines.push_back("+"); lines.push_back(""); vec_reader reader(lines); fastq record; REQUIRE_THROWS_AS(record.read(reader, FASTQ_ENCODING_33), fastq_error); } TEST_CASE("simple_fastq_record__no_qualities_or_sequence", "[fastq::fastq]") { string_vec lines; lines.push_back("@"); lines.push_back(""); lines.push_back("+"); lines.push_back(""); vec_reader reader(lines); fastq record; REQUIRE_THROWS_AS(record.read(reader, FASTQ_ENCODING_33), fastq_error); } TEST_CASE("eof_when_starting_to_read_record", "[fastq::fastq]") { string_vec lines; vec_reader reader(lines); fastq record; CHECK(!record.read(reader)); } TEST_CASE("eof_after_header", "[fastq::fastq]") { string_vec lines; lines.push_back("@record"); vec_reader reader(lines); fastq record; REQUIRE_THROWS_AS(record.read(reader), fastq_error); } TEST_CASE("eof_after_sequence_1", "[fastq::fastq]") { string_vec lines; lines.push_back("@record"); lines.push_back("ACGTA"); vec_reader reader(lines); fastq record; REQUIRE_THROWS_AS(record.read(reader), fastq_error); } TEST_CASE("eof_after_sequence_2", "[fastq::fastq]") { string_vec lines; lines.push_back("@record"); lines.push_back("ACGTA"); lines.push_back(""); vec_reader reader(lines); fastq record; REQUIRE_THROWS_AS(record.read(reader), fastq_error); } TEST_CASE("eof_after_sep_1", "[fastq::fastq]") { string_vec lines; lines.push_back("@record"); lines.push_back("ACGTA"); lines.push_back("+"); vec_reader reader(lines); fastq record; REQUIRE_THROWS_AS(record.read(reader), fastq_error); } TEST_CASE("eof_after_sep_2", "[fastq::fastq]") { string_vec lines; lines.push_back("@record"); lines.push_back("ACGTA"); lines.push_back("+"); lines.push_back(""); vec_reader reader(lines); fastq record; REQUIRE_THROWS_AS(record.read(reader), fastq_error); } TEST_CASE("eof_after_qualities_following_previous_read_1", "[fastq::fastq]") { string_vec lines; lines.push_back("@record_1"); lines.push_back("ACGTA"); lines.push_back("+"); lines.push_back("!!!!!"); lines.push_back("@record_2"); lines.push_back("ACGTA"); lines.push_back("+"); vec_reader reader(lines); fastq record; REQUIRE_NOTHROW(record.read(reader)); REQUIRE_THROWS_AS(record.read(reader), fastq_error); } TEST_CASE("eof_after_qualities_following_previous_read_2", "[fastq::fastq]") { string_vec lines; lines.push_back("@record_1"); lines.push_back("ACGTA"); lines.push_back("+"); lines.push_back("!!!!!"); lines.push_back("@record_2"); lines.push_back("ACGTA"); lines.push_back("+"); lines.push_back(""); vec_reader reader(lines); fastq record; REQUIRE_NOTHROW(record.read(reader)); REQUIRE_THROWS_AS(record.read(reader), fastq_error); } /////////////////////////////////////////////////////////////////////////////// // Writing to stream TEST_CASE("Writing_to_stream_phred_33", "[fastq::fastq]") { const fastq record = fastq("record_1", "ACGTACGATA", "!$#$*68CGJ"); REQUIRE(record.to_str() == "@record_1\nACGTACGATA\n+\n!$#$*68CGJ\n"); } TEST_CASE("Writing_to_stream_phred_33_explicit", "[fastq::fastq]") { const fastq record = fastq("record_1", "ACGTACGATA", "!$#$*68CGJ"); REQUIRE(record.to_str() == "@record_1\nACGTACGATA\n+\n!$#$*68CGJ\n"); } TEST_CASE("Writing_to_stream_phred_64_explicit", "[fastq::fastq]") { const fastq record = fastq("record_1", "ACGTACGATA", "!$#$*68CGJ"); REQUIRE(record.to_str(FASTQ_ENCODING_64) == "@record_1\nACGTACGATA\n+\n@CBCIUWbfi\n"); } /////////////////////////////////////////////////////////////////////////////// // Validating pairs TEST_CASE("validate_paired_reads__throws_if_order_or_number_is_wrong", "[fastq::fastq]") { const fastq ref_mate0 = fastq("Mate/0", "ACGT", "!!#$"); const fastq ref_mate1 = fastq("Mate/1", "ACGT", "!!#$"); const fastq ref_mate2 = fastq("Mate/2", "ACGT", "!!#$"); const fastq ref_mate3 = fastq("Mate/3", "ACGT", "!!#$"); const fastq ref_matea = fastq("Mate/A", "ACGT", "!!#$"); const fastq ref_mateb = fastq("Mate/B", "ACGT", "!!#$"); { fastq mate0 = ref_mate0; fastq mate1 = ref_mate1; REQUIRE_THROWS_AS(fastq::validate_paired_reads(mate0, mate1), fastq_error); } { fastq mate0 = ref_mate0; fastq mate1 = ref_mate1; REQUIRE_THROWS_AS(fastq::validate_paired_reads(mate1, mate0), fastq_error); } { fastq mate1 = ref_mate1; fastq mate2 = ref_mate2; fastq::validate_paired_reads(mate1, mate2); } { fastq mate1 = ref_mate1; fastq mate2 = ref_mate2; REQUIRE_THROWS_AS(fastq::validate_paired_reads(mate2, mate1), fastq_error); } { fastq mate2 = ref_mate2; fastq mate3 = ref_mate3; REQUIRE_THROWS_AS(fastq::validate_paired_reads(mate2, mate3), fastq_error); } { fastq mate2 = ref_mate2; fastq mate3 = ref_mate3; REQUIRE_THROWS_AS(fastq::validate_paired_reads(mate3, mate2), fastq_error); } { fastq matea = ref_matea; fastq mateb = ref_mateb; REQUIRE_THROWS_AS(fastq::validate_paired_reads(matea, mateb), fastq_error); } { fastq matea = ref_matea; fastq mateb = ref_mateb; REQUIRE_THROWS_AS(fastq::validate_paired_reads(mateb, matea), fastq_error); } } TEST_CASE("validate_paired_reads__allows_other_separators", "[fastq::fastq]") { const fastq ref_mate1 = fastq("Mate:1", "ACGT", "!!#$"); const fastq ref_mate2 = fastq("Mate:2", "GCTAA", "$!@#$"); { fastq mate1 = ref_mate1; fastq mate2 = ref_mate2; fastq::validate_paired_reads(mate1, mate2, ':'); } { fastq mate1 = ref_mate1; fastq mate2 = ref_mate2; REQUIRE_THROWS_AS(fastq::validate_paired_reads(mate2, mate1), fastq_error); } } TEST_CASE("validate_paired_reads__mate_separator_is_updated", "[fastq::fastq]") { const fastq ref_mate_1 = fastq("Mate/1", "ACGT", "!!#$"); const fastq ref_mate_2 = fastq("Mate/2", "GCTAA", "$!@#$"); fastq mate1 = fastq("Mate:1", "ACGT", "!!#$"); fastq mate2 = fastq("Mate:2", "GCTAA", "$!@#$"); fastq::validate_paired_reads(mate1, mate2, ':'); REQUIRE(ref_mate_1 == mate1); REQUIRE(ref_mate_2 == mate2); } TEST_CASE("validate_paired_reads__throws_if_mate_is_empty", "[fastq::fastq]") { const fastq ref_mate1 = fastq("Mate", "", ""); const fastq ref_mate2 = fastq("Mate", "ACGT", "!!#$"); { fastq mate1 = ref_mate1; fastq mate2 = ref_mate2; REQUIRE_THROWS_AS(fastq::validate_paired_reads(mate1, mate2), fastq_error); } { fastq mate1 = ref_mate1; fastq mate2 = ref_mate2; REQUIRE_THROWS_AS(fastq::validate_paired_reads(mate2, mate1), fastq_error); } { fastq mate1 = ref_mate1; fastq mate2 = ref_mate2; REQUIRE_THROWS_AS(fastq::validate_paired_reads(mate1, mate1), fastq_error); } } TEST_CASE("validate_paired_reads__throws_if_only_mate_1_is_numbered", "[fastq::fastq]") { const fastq ref_mate2 = fastq("Mate/1", "GCTAA", "$!@#$"); const fastq ref_mate1 = fastq("Mate", "ACGT", "!!#$"); { fastq mate1 = ref_mate1; fastq mate2 = ref_mate2; REQUIRE_THROWS_AS(fastq::validate_paired_reads(mate1, mate2), fastq_error); } { fastq mate1 = ref_mate1; fastq mate2 = ref_mate2; REQUIRE_THROWS_AS(fastq::validate_paired_reads(mate2, mate1), fastq_error); } } TEST_CASE("validate_paired_reads__throws_if_only_mate_2_is_numbered", "[fastq::fastq]") { const fastq ref_mate1 = fastq("Mate", "GCTAA", "$!@#$"); const fastq ref_mate2 = fastq("Mate/2", "ACGT", "!!#$"); { fastq mate1 = ref_mate1; fastq mate2 = ref_mate2; REQUIRE_THROWS_AS(fastq::validate_paired_reads(mate1, mate2), fastq_error); } { fastq mate1 = ref_mate1; fastq mate2 = ref_mate2; REQUIRE_THROWS_AS(fastq::validate_paired_reads(mate2, mate1), fastq_error); } } TEST_CASE("validate_paired_reads__throws_if_mate_is_misnumbered", "[fastq::fastq]") { fastq mate1 = fastq("Mate/1", "GCTAA", "$!@#$"); fastq mate2 = fastq("Mate/3", "ACGT", "!!#$"); REQUIRE_THROWS_AS(fastq::validate_paired_reads(mate1, mate2), fastq_error); } TEST_CASE("validate_paired_reads__throws_if_same_mate_numbers", "[fastq::fastq]") { fastq mate1 = fastq("Mate/1", "GCTAA", "$!@#$"); fastq mate2 = fastq("Mate/1", "ACGT", "!!#$"); REQUIRE_THROWS_AS(fastq::validate_paired_reads(mate1, mate2), fastq_error); } TEST_CASE("validate_paired_reads__throws_if_name_differs", "[fastq::fastq]") { fastq mate1 = fastq("Mate/1", "GCTAA", "$!@#$"); fastq mate2 = fastq("WrongName/2", "ACGT", "!!#$"); REQUIRE_THROWS_AS(fastq::validate_paired_reads(mate1, mate2), fastq_error); } } // namespace ar adapterremoval-2.3.1/tests/unit/main_test.cpp000077500000000000000000000000611350370616400213400ustar00rootroot00000000000000#define CATCH_CONFIG_MAIN #include "catch.hpp" adapterremoval-2.3.1/tests/unit/strutils_test.cpp000066400000000000000000000173611350370616400223150ustar00rootroot00000000000000/*************************************************************************\ * AdapterRemoval - cleaning next-generation sequencing reads * * * * Copyright (C) 2011 by Stinus Lindgreen - stinus@binf.ku.dk * * Copyright (C) 2014 by Mikkel Schubert - mikkelsch@gmail.com * * * * If you use the program, please cite the paper: * * S. Lindgreen (2012): AdapterRemoval: Easy Cleaning of Next Generation * * Sequencing Reads, BMC Research Notes, 5:337 * * http://www.biomedcentral.com/1756-0500/5/337/ * * * * This program is free software: you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation, either version 3 of the License, or * * (at your option) any later version. * * * * This program is distributed in the hope that it will be useful, * * but WITHOUT ANY WARRANTY; without even the implied warranty of * * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * * GNU General Public License for more details. * * * * You should have received a copy of the GNU General Public License * * along with this program. If not, see . * \*************************************************************************/ #include #include #include "testing.hpp" #include "strutils.hpp" namespace ar { /////////////////////////////////////////////////////////////////////////////// // Tests for 'toupper' TEST_CASE("ASCII letters are uppercased", "[strutils::toupper]") { REQUIRE(toupper("") == ""); REQUIRE(toupper("a1{2BZ`zAdeK") == "A1{2BZ`ZADEK"); } /////////////////////////////////////////////////////////////////////////////// // Tests for 'indent_lines' TEST_CASE("Empty lines are not indented", "[strutils::indent_lines]") { REQUIRE(indent_lines("") == ""); REQUIRE(indent_lines("\n") == "\n"); REQUIRE(indent_lines("\n\n") == "\n\n"); REQUIRE(indent_lines("\n\n\n") == "\n\n\n"); } TEST_CASE("Singular lines are indented", "[strutils::indent_lines]") { REQUIRE(indent_lines("this is a test") == " this is a test"); REQUIRE(indent_lines("this is a test\n") == " this is a test\n"); } TEST_CASE("Multiple lines are indented", "[strutils::indent_lines]") { REQUIRE(indent_lines("this is a test\nline #2") == " this is a test\n line #2"); REQUIRE(indent_lines("this is a test\nline #2\n") == " this is a test\n line #2\n"); } TEST_CASE("Mixed lines are partially indented", "[strutils::indent_lines]") { REQUIRE(indent_lines("this is a test\nline #2\n\n") == " this is a test\n line #2\n\n"); REQUIRE(indent_lines("this is a test\n\nline #2\n") == " this is a test\n\n line #2\n"); REQUIRE(indent_lines("this is a test\nline #2\n\n\n") == " this is a test\n line #2\n\n\n"); } /////////////////////////////////////////////////////////////////////////////// // Tests for 'columnize_text' TEST_CASE("Whitespace only is stripped", "[strutils::columnize_text]") { REQUIRE(columnize_text("") == ""); REQUIRE(columnize_text(" ") == ""); REQUIRE(columnize_text("\n") == ""); REQUIRE(columnize_text("\n\n") == ""); REQUIRE(columnize_text("\n \n") == ""); REQUIRE(columnize_text("\n ") == ""); REQUIRE(columnize_text(" \n") == ""); REQUIRE(columnize_text(" \n ") == ""); } TEST_CASE("Whitespace between words is stripped", "[strutils::columnize_text]") { REQUIRE(columnize_text("foo bar") == "foo bar"); REQUIRE(columnize_text("foo bar") == "foo bar"); REQUIRE(columnize_text("foo\nbar") == "foo bar"); REQUIRE(columnize_text("foo\nbar\n") == "foo bar"); REQUIRE(columnize_text("\nfoo\nbar") == "foo bar"); REQUIRE(columnize_text("foo\nbar\n\n") == "foo bar"); REQUIRE(columnize_text("\nfoo\nbar\n") == "foo bar"); REQUIRE(columnize_text("\n \n foo \n bar \n") == "foo bar"); } TEST_CASE("Linebreaks are added by max width", "[strutils::columnize_text]") { REQUIRE(columnize_text("foo bar\nzood", 12) == "foo bar zood"); REQUIRE(columnize_text("foo bar\nzood", 11) == "foo bar\nzood"); REQUIRE(columnize_text("foo bar\nzood", 7) == "foo bar\nzood"); REQUIRE(columnize_text("foo bar\nzood", 6) == "foo\nbar\nzood"); REQUIRE(columnize_text("foo bar\nzood", 3) == "foo\nbar\nzood"); REQUIRE(columnize_text("foo bar\nzood", 1) == "foo\nbar\nzood"); REQUIRE(columnize_text("foo bar\nzood", 0) == "foo\nbar\nzood"); } TEST_CASE("Subsequent lines are indented", "[strutils::columnize_text]") { REQUIRE(columnize_text("foo bar\nzood", 12, 2) == "foo bar zood"); REQUIRE(columnize_text("foo bar\nzood", 11, 0) == "foo bar\nzood"); REQUIRE(columnize_text("foo bar\nzood", 11, 1) == "foo bar\n zood"); REQUIRE(columnize_text("foo bar\nzood", 11, 2) == "foo bar\n zood"); REQUIRE(columnize_text("foo bar\nzood", 7, 2) == "foo bar\n zood"); REQUIRE(columnize_text("foo bar\nzood", 6, 2) == "foo\n bar\n zood"); REQUIRE(columnize_text("foo bar\nzood", 3, 2) == "foo\n bar\n zood"); REQUIRE(columnize_text("foo bar\nzood", 1, 2) == "foo\n bar\n zood"); REQUIRE(columnize_text("foo bar\nzood", 0, 2) == "foo\n bar\n zood"); } TEST_CASE("Proper numbers are converted", "[strutils::str_to_unsigned]") { REQUIRE(str_to_unsigned("0") == 0); REQUIRE(str_to_unsigned("1") == 1); REQUIRE(str_to_unsigned("2") == 2); REQUIRE(str_to_unsigned("2147483647") == 2147483647); REQUIRE(str_to_unsigned("2147483648") == 2147483648); REQUIRE(str_to_unsigned("2147483649") == 2147483649); REQUIRE(str_to_unsigned("4294967293") == 4294967293); REQUIRE(str_to_unsigned("4294967294") == 4294967294); REQUIRE(str_to_unsigned("4294967295") == 4294967295); } TEST_CASE("Whitespace is ignored", "[strutils::str_to_unsigned]") { REQUIRE(str_to_unsigned(" 123") == 123); REQUIRE(str_to_unsigned("123 ") == 123); REQUIRE(str_to_unsigned(" 123 ") == 123); REQUIRE(str_to_unsigned("\n123\n") == 123); } TEST_CASE("Numbers outside range are rejected", "[strutils::str_to_unsigned]") { REQUIRE_THROWS_AS(str_to_unsigned("-2"), std::invalid_argument); REQUIRE_THROWS_AS(str_to_unsigned("-1"), std::invalid_argument); REQUIRE_THROWS_AS(str_to_unsigned("4294967296"), std::invalid_argument); REQUIRE_THROWS_AS(str_to_unsigned("4294967297"), std::invalid_argument); } TEST_CASE("Non numeric strings are rejected", "[strutils::str_to_unsigned]") { REQUIRE_THROWS_AS(str_to_unsigned(" "), std::invalid_argument); REQUIRE_THROWS_AS(str_to_unsigned("x"), std::invalid_argument); REQUIRE_THROWS_AS(str_to_unsigned("a b c"), std::invalid_argument); REQUIRE_THROWS_AS(str_to_unsigned("\n"), std::invalid_argument); } TEST_CASE("Mixed strings are rejected", "[strutils::str_to_unsigned]") { REQUIRE_THROWS_AS(str_to_unsigned("1a"), std::invalid_argument); REQUIRE_THROWS_AS(str_to_unsigned("123x"), std::invalid_argument); REQUIRE_THROWS_AS(str_to_unsigned("123 x"), std::invalid_argument); REQUIRE_THROWS_AS(str_to_unsigned("x123"), std::invalid_argument); REQUIRE_THROWS_AS(str_to_unsigned("x 123"), std::invalid_argument); } TEST_CASE("Base 10 is assumed", "[strutils::str_to_unsigned]") { REQUIRE(str_to_unsigned("010") == 10); } } // namespace ar adapterremoval-2.3.1/tests/unit/testing.hpp000066400000000000000000000041661350370616400210460ustar00rootroot00000000000000/*************************************************************************\ * AdapterRemoval - cleaning next-generation sequencing reads * * * * Copyright (C) 2011 by Stinus Lindgreen - stinus@binf.ku.dk * * Copyright (C) 2014 by Mikkel Schubert - mikkelsch@gmail.com * * * * If you use the program, please cite the paper: * * S. Lindgreen (2012): AdapterRemoval: Easy Cleaning of Next Generation * * Sequencing Reads, BMC Research Notes, 5:337 * * http://www.biomedcentral.com/1756-0500/5/337/ * * * * This program is free software: you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation, either version 3 of the License, or * * (at your option) any later version. * * * * This program is distributed in the hope that it will be useful, * * but WITHOUT ANY WARRANTY; without even the implied warranty of * * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * * GNU General Public License for more details. * * * * You should have received a copy of the GNU General Public License * * along with this program. If not, see . * \*************************************************************************/ #ifndef TESTING_H #define TESTING_H #include #include "catch.hpp" #include "fastq.hpp" namespace ar { inline std::ostream& operator<<(std::ostream& stream, const fastq& record) { return stream << "'@" << record.header() << "\\n" << record.sequence() << "\\n+\\n" << record.qualities() << "\\n'"; } } #endif