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Generated from configure.ac by autoheader. */ /* Define if building universal (internal helper macro) */ #undef AC_APPLE_UNIVERSAL_BUILD /* Width of bits of the FM-index in bits */ #undef FMBITS /* Define to 1 if you have the header file. */ #undef HAVE_BOOST_PROPERTY_MAP_PROPERTY_MAP_HPP /* Define to 1 if you have the header file. */ #undef HAVE_DLFCN_H /* Define to 1 if you don't have `vprintf' but do have `_doprnt.' */ #undef HAVE_DOPRNT /* Define to 1 if you have the `dup2' function. */ #undef HAVE_DUP2 /* Define to 1 if you have the header file. */ #undef HAVE_FCNTL_H /* Define to 1 if you have the header file. */ #undef HAVE_FLOAT_H /* Define to 1 if you have the `fork' function. */ #undef HAVE_FORK /* Define to 1 if you have the `gethostname' function. */ #undef HAVE_GETHOSTNAME /* Define to 1 if you have the `getopt_long' function. */ #undef HAVE_GETOPT_LONG /* Define to 1 if you have the `getpagesize' function. */ #undef HAVE_GETPAGESIZE /* Define to 1 if you have the header 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*/ #undef HAVE_STRINGS_H /* Define to 1 if you have the header file. */ #undef HAVE_STRING_H /* Define to 1 if you have the `strtoul' function. */ #undef HAVE_STRTOUL /* Define to 1 if you have the header file. */ #undef HAVE_SYS_PARAM_H /* Define to 1 if you have the header file. */ #undef HAVE_SYS_STAT_H /* Define to 1 if you have the header file. */ #undef HAVE_SYS_TYPES_H /* Define to 1 if you have the header file. */ #undef HAVE_TR1_UNORDERED_MAP /* Define to 1 if you have the header file. */ #undef HAVE_UNISTD_H /* Define to 1 if you have the header file. */ #undef HAVE_UNORDERED_MAP /* Define to 1 if you have the `vfork' function. */ #undef HAVE_VFORK /* Define to 1 if you have the header file. */ #undef HAVE_VFORK_H /* Define to 1 if you have the `vprintf' function. */ #undef HAVE_VPRINTF /* Define to 1 if `fork' works. */ #undef HAVE_WORKING_FORK /* Define to 1 if `vfork' works. */ #undef HAVE_WORKING_VFORK /* Define to 1 if the system has the type `_Bool'. */ #undef HAVE__BOOL /* Define if the system does not provide HOST_NAME_MAX */ #undef HOST_NAME_MAX /* maximum k-mer length */ #undef MAX_KMER /* Define to disable MPICH C++ bindings */ #undef MPICH_SKIP_MPICXX /* Define to disable OpenMPI C++ bindings */ #undef OMPI_SKIP_MPICXX /* Name of package */ #undef PACKAGE /* Define to the address where bug reports for this package should be sent. */ #undef PACKAGE_BUGREPORT /* Define to the full name of this package. */ #undef PACKAGE_NAME /* Define to the full name and version of this package. */ #undef PACKAGE_STRING /* Define to the one symbol short name of this package. */ #undef PACKAGE_TARNAME /* Define to the home page for this package. */ #undef PACKAGE_URL /* Define to the version of this package. */ #undef PACKAGE_VERSION /* Define to use SAM sequence and quality fields */ #undef SAM_SEQ_QUAL /* Define to 1 if you have the ANSI C header files. */ #undef STDC_HEADERS /* Version number of package */ #undef VERSION /* Define WORDS_BIGENDIAN to 1 if your processor stores words with the most significant byte first (like Motorola and SPARC, unlike Intel). */ #if defined AC_APPLE_UNIVERSAL_BUILD # if defined __BIG_ENDIAN__ # define WORDS_BIGENDIAN 1 # endif #else # ifndef WORDS_BIGENDIAN # undef WORDS_BIGENDIAN # endif #endif /* Define for Solaris 2.5.1 so the uint32_t typedef from , , or is not used. If the typedef were allowed, the #define below would cause a syntax error. */ #undef _UINT32_T /* Define for Solaris 2.5.1 so the uint64_t typedef from , , or is not used. If the typedef were allowed, the #define below would cause a syntax error. */ #undef _UINT64_T /* Define for Solaris 2.5.1 so the uint8_t typedef from , , or is not used. If the typedef were allowed, the #define below would cause a syntax error. */ #undef _UINT8_T /* Define if the system does not provide ceilf */ #undef ceilf /* Define to empty if `const' does not conform to ANSI C. */ #undef const /* Define to `__inline__' or `__inline' if that's what the C compiler calls it, or to nothing if 'inline' is not supported under any name. */ #ifndef __cplusplus #undef inline #endif /* Define to the type of a signed integer type of width exactly 64 bits if such a type exists and the standard includes do not define it. */ #undef int64_t /* Define to rpl_malloc if the replacement function should be used. */ #undef malloc /* Define to `int' if does not define. */ #undef mode_t /* Define to `int' if does not define. */ #undef pid_t /* Define to rpl_realloc if the replacement function should be used. */ #undef realloc /* Define to `unsigned int' if does not define. */ #undef size_t /* Define to `int' if does not define. */ #undef ssize_t /* Define to the type of an unsigned integer type of width exactly 16 bits if such a type exists and the standard includes do not define it. */ #undef uint16_t /* Define to the type of an unsigned integer type of width exactly 32 bits if such a type exists and the standard includes do not define it. */ #undef uint32_t /* Define to the type of an unsigned integer type of width exactly 64 bits if such a type exists and the standard includes do not define it. */ #undef uint64_t /* Define to the type of an unsigned integer type of width exactly 8 bits if such a type exists and the standard includes do not define it. */ #undef uint8_t /* Define as `fork' if `vfork' does not work. */ #undef vfork abyss-1.3.6/ChangeLog000644 002433 001057 00000103771 12176307177 016155 0ustar00traymondassembly000000 000000 2013-07-15 Anthony Raymond * Release version 1.3.6 * Improved documentation for GitHub devs. * ABYSS-P performance improvement. * Various portability and bug fixes. abyss-mergepairs: * Fix program name. abyss-fac: * New option --exp-size to give the expected genome size needed for NG50 calculation. * New option --count-ambig include ambiguities in calculations. ABYSS/ABYSS-P: * Performance improvement. Runtime reduced by ~20%. * Fix support for MPICH. abyss-map: * No longer require POPCNT instruction. * New option --order to force output order the same as input. abyss-filtergraph: * New option --remove to remove specified contigs from graph. PopBubbles: * Bug fix. Setting branches > 2 will now work. abyss-fixmate: * Improved error when first and second read IDs do not match. * New option --cov to compute and store the physical coverage in a Wiggle file. AdjIO: * Bug fix for non-GCC compilers. 2013-03-04 Anthony Raymond * Release version 1.3.5 * Standardized --help message format. * Improve documentation. * Merge overlapping read pairs. * Layout and merge contigs using sequence overlap graph. * Attempt to fill scaffold gap with consensus of all paths between contigs. abyss-pe: * Attempt to fill scaffold gap with consensus of all paths between contigs. AdjList: * Increase the default value of m from 30 to 50. abyss-overlap: * Increase the default value of m from 30 to 50. * New options, --tred and --no-tred. Remove transitive edges. Default --tred. abyss-mergepairs: * New program. Merges overlapping read pairs. ABYSS-P: * Bug fix. Exit when there is a problem reading a file. * Don't store sequences in the rank 0 process when using at least 1000 cores. Improves memory distribution with large number of cores. abyss-fac: * Increase the default value of t from 200 to 500. DistanceEst: * Bug fix. Exit with success if there is only one contig. Fixes this error: DistanceEst: DistanceEst.cpp:534: int main(int, char**): Assertion `in' failed. * Bug fix. Fix the bug causing this error: DistanceEst: error: The observed fragment of size 128 bp is shorter than 2*l (l=71). Decrease l to 64. * Bug fix. Correctly estimate distance using MLE when l=0. abyss-layout: * New program. Layout contigs using the sequence overlap graph. abyss-map: * Return helpful error when query ID starts with '@` * New options, --chastity and --no-chastity. Ignore chastity failed reads. Default --no-chastity. abyss-samtobreak: * New script. Calculate contig and scaffold contiguity and correctness metrics. abyss-fixmate: * New option, l. Minimum alignment length. Set unmapped flag if the CIGAR match length is too small. * Print all alignments when the histogram output file not given. * Print SAM header to the same file when given. 2012-05-30 Shaun Jackman * Release version 1.3.4. * Do not extend paths, which can cause misassemblies. * Increase the default value of m from 30 to 50. * Various portability fixes. abyss-pe: * Increase the default value of m from 30 to 50 to reduce the likelihood of misassemblies. * Integrate with SLURM. Thanks to Timothy Carlson. ABYSS: * Use CityHash64 rather than Bob Jenkins' hashlittle. SimpleGraph: * Do not extend paths. Closes #8. Extending paths can cause misassemblies when the de Bruijn graph is incomplete. MergePaths: * Bug fix. Closes #6. Fix the bug causing the error: Assertion `!m_ambig' failed. abyss-fatoagp: * New script. Create a FASTA file of scaftigs and an AGP file. 2012-03-13 Shaun Jackman * Release version 1.3.3. * New parameter, l. Specify the minimum alignment length when aligning the reads to the contigs. * Improve the scaffolding algorithm that identifies repeats. * Improve the documentation. abyss-pe: * New parameter, l. Specify the minimum alignment length when aligning the reads to the contigs. This option may be specified per library. The default value is k. * New parameter, S. Specify the minimum contig size required for building scaffolds. * New parameter, N. Specify the minimum number of pairs required for building scaffolds. * Integrate with Load Sharing Facility (LSF). * Calculate the assembly contiguity statistics. KAligner, abyss-map: * Rename the minimum alignment length option -k to -l. DistanceEst: * Dual licensed under the GPL and BCCA-Academic licenses. * New options, --fr and --rf. Specify the orientation of the library. The default behaviour is to detect the orientation. * New options, --mind and --maxd. Specify the minimum and maximum distances for the maximum likelihood estimator. * New option, -l, --min-align. Specify the minimum alignment length of the aligner, which can improve distance estimates. * Increase the default minimum mapping quality, -q, to 10, was 1. MergePaths: * Bug fix. Fix the bug causing the error: Assertion `count(it2+1, path2.end(), pivot) == 0' failed. PathConsensus: * Bug fix. Fix the bug causing the error: Assertion `fstSol.size() == sndSol.size()' failed. MergeContigs: * Calculate the assembly contiguity statistics. abyss-scaffold: * Improve the algorithm that identifies repeats. * Remove simple cycles from the scaffold graph. * Calculate the assembly contiguity statistics. * The option -s may specify a range, such as -s200-10000, to find the value of s that maximizes the scaffold N50. abyss-fac: * New option, -m, --mmd. Output MultiMarkdown format. abyss-index: * New option, -a, --alphabet. Specify the alphabet. * New option, --bwt. Output the Burrows-Wheeler transform. abyss-samtoafg: * New script. Convert a SAM file to an AMOS AFG file. README, README.html, abyss-pe.1: * Improve the documentation. 2011-12-13 Shaun Jackman * Release version 1.3.2. * Enable scaffolding by default. * Remove small shim contigs. * Improved distance estimates. * Reduce sequence duplication. * Read compressed files on Mac OS X. abyss-pe: * Enable scaffolding by default. If the mp parameter is not specified, use a default value of ${pe} or ${lib}. * Support using bowtie2 to align reads to contigs by specifying aligner=bowtie2. * The default aligner is abyss-map. * Output the scaffold overlap graph, ${name}-scaffolds.dot. * Set DYLD_FORCE_FLAT_NAMESPACE to read compressed files on OS X. ABYSS: * Can read k-mer count data from a Jellyfish file with extension .jf for k-mer counts or .jfq for q-mer counts. Jellyfish must be installed. * Bug fix. Fix the bug causing the error bool chomp(std::string&, char): Assertion `s.length() > 1' failed. abyss-filtergraph: * New program. Remove small shim contigs that add no useful sequence to the assembly. Thanks to Tony Raymond (tgr). PopBubbles: * New option, -a, --branches. Specify the maximum number of branches of a bubble that may be popped. Default is 2. * Use DIALIGN-TX for multiple sequence alignment. Thanks to tgr. DistanceEst: * Improved distance estimates. abyss-joindist: * Remove this program. Use abyss-todot instead. MergePaths: * Use a non-greedy algorithm that reduces sequence duplication but may reduce contiguity. The greedy algorithm may be used by specifying the option --greedy. abyss-fixmate: * Do not output query names by default. configure: * New option, --enable-samseqqual. Enable SAM sequence and quality fields. 2011-10-24 Shaun Jackman * Release version 1.3.1. * Read sequence files in SRA format. The tool fastq-dump from the sratoolkit must be installed. * Read a contig overlap graph in the ASQG format of SGA. * Fix compile errors for Mac OS X. * Fix the bug that caused the line number of an error in a FASTQ file to be reported incorrectly. abyss-pe: * Support using BWA-SW to align reads to contigs by specifying aligner=bwasw. * The parameter ALIGNER_OPTIONS may be used to specify a different value for k when aligning using abyss-map. * New target, bam, may be used to produce a final BAM file of the reads aligned to the scaffolds. KAligner: * Fix the bug causing the error: Assertion `qstep >= 0 && qstep <= m_hashSize' failed. abyss-scaffold: * The result is independent of the order in which the mate-pair libraries are specified. * Permit scaffolding contigs that have non-numeric identifiers. * The overlap graph is optional. abyss-todot: * Convert adj, dist or ASQG formatted graph files to dot format. * Merge multiple graph files into one. 2011-09-09 Shaun Jackman * Release version 1.3.0. * Use mate-pair libraries to scaffold contigs. * Support CASAVA-formatted FASTQ files. * Bug fix. Do not trim quality 41 bases from the ends of reads. * Boost C++ Libraries are required to compile ABySS. abyss-pe: * New parameter, mp, to specify the mate-pair libraries to be used for scaffolding. * Increase the default value for s from 100 to 200. * Set the default value for n to 10. * Integrate with PBS. abyss-scaffold: * New program. Scaffold using mate-pair libraries. DistanceEst: * Ignore multimapped alignments with a mapping quality of zero. * New option, -q, --min-mapq. Ignore alignments with mapping quality less than this threshold. Default is 1. * Do not use OpenMP 3.0. PopBubbles: * Scaffold over complex bubbles with the option --scaffold. Disabled by default. MergePaths: * Fix a bug that causes PathOverlap to die with the error: Distance get(edge_bundle_t, const Graph&, ContigNode, ContigNode): Assertion `e.second' failed. * New option, --no-greedy. Use a non-greedy algorithm that reduces sequence duplication but reduces contiguity. Disabled by default. KAligner: * Performance improvements. Thanks to Tony Raymond (tgr). * The output is printed in the same order as the input when multithreaded. (tgr) abyss-map: * New program. Use the BWT and FM-index to find the longest common substring. To use it, specify the option aligner=map to abyss-pe. abyss-index: * New program. Build a FM-index of a FASTA file. abyss-bowtie: * Use abyss-tofastq --interleave to speed up abyss-fixmate. abyss-bwa: * Use bwa index -a bwtsw by default. * Use abyss-tofastq --interleave to speed up abyss-fixmate. abyss-fac: * Report N80, N50 and N20. Do not report median and mean. * Increase the default minimum contig size threshold, option -t, from 100 to 200. abyss-fixmate: * Set the mapping quality of both alignments to the minimum mapping quality of the pair of alignments. abyss-tofastq: * New option, -i, --interleave. Interleave the files. configure: * New option, --with-boost. Specify the path for Boost. * New option, --disable-popcnt. Do not use the popcnt instruction. 2011-04-15 Shaun Jackman * Release version 1.2.7. abyss-pe: * Support using bwa or bowtie to align reads to contigs. Specify aligner=bwa or aligner=bowtie. * Integrate with IBM LoadLeveler. PopBubbles: * Use an affine gap penalty. * The default maximum bubble length is 10 kbp. * New option, --scaffold. Scaffold over bubbles with insufficient sequence identity to be popped. SimpleGraph: * New parameter d to specify the acceptable error of a distance estimate. The default is 6 bp. PathConsensus: * Use an affine gap penalty. MergePaths: * Fix a bug that causes PathOverlap to die with the error: Distance get(edge_bundle_t, const Graph&, ContigNode, ContigNode): Assertion `e.second' failed. 2011-02-07 Shaun Jackman * Release version 1.2.6. * Find contigs that overlap by fewer than k-1 bp. * Pop bubbles with sufficient sequence identity. * Merge paths that overlap unambiguously. abyss-pe: * New parameter, m, the minimum number of overlapping bases. The default is 30. * The minimum sequence identity parameter, p, applies to both PopBubbles and PathConsensus. ABYSS: * Support values of k larger than 96. The maximum value of k is set when compiling using `configure --enable-maxk´. AdjList: * Find sequences that overlap by fewer than k-1 bp. The parameter m specifies the minimum number of overlapping bases. PopBubbles: * Align both branches of the bubble and pop bubbles whose sequence identity is sufficient, at least 90% by default. * New parameter, p, the minimum identity required. * The maximum bubble size is unlimited by default. This limit can be changed using the parameter b. SimpleGraph: * Extend each path as long as is unambiguously possible. PathOverlap: * Merge paths that overlap unambiguously. MergeContigs: * Perform an alignment of the two sequences when no simple overlap is found. abyss-fac: * New option, -g. Specify the expected genome size. 2010-11-15 Shaun Jackman * Release version 1.2.5. AdjList: * Fix the colour-space-specific bug causing the error Assertion `seq.length() > (unsigned)opt::overlap' failed. PathConsensus: * Fix the bug causing the error Assertion `fstSol.size() == 1' failed. abyss-fixmate: * Do not output the @RG header record at the end of the output that gives the median fragment size. It breaks `samtools view -S`. * --no-qname: New option. Set the qname to *. 2010-10-13 Shaun Jackman * Release version 1.2.4. ABYSS-P: * Fix the bug causing the error Unexpected sequence extension message. KAligner: * Reduce the amount of memory used by KAligner. PathConsensus: * New program. Replace gaps of Ns that span a region of ambiguous sequence with a consensus sequence of the possible sequences that fill the gap. By default a minimum 90% identity is required. This default can be changed with the parameter, p. The consensus sequence uses IUPAC-IUB ambiguity codes. DIALIGN-TX is used for the multiple sequence alignment. PathOverlap: * Fix the bug causing the error Assertion `back(paths, u) == front(paths, v)' failed. 2010-09-08 Shaun Jackman * Release version 1.2.3. ABYSS-P: * Bug fix. Fix the bug causing the error Assertion `m_comm.receiveEmpty()' failed. PopBubbles: * Bug fix. Fix the bug causing the error error: unexpected ID PathOverlap: * Include the single-end contigs in the overlap graph. abyss-pe: * Output an overlap graph of the paired-end assembly in the file ${name}-contigs.dot. * Do not create the intermediate file ${name}-4.fa. abyss-adjtodot: * Convert an overlap graph in adj format to Graphviz dot format or SAM alignment format. 2010-08-25 Shaun Jackman * Release version 1.2.2. * Merge contigs after popping bubbles. * Handle multi-line FASTA sequences. * Report the amount of memory used. * Most tools can output their results in SAM format, including AdjList, KAligner, ParseAligns and PathOverlap. abyss-pe: * New command, se-dot. Output a Graphviz dot file of the single-end assembly. ABYSS: * Handle multi-line FASTA sequences. * Report the amount of memory used. * Improve error messages for incorrectly-formatted FASTA files. * Bug fix. Improved handling of palindromes. PopBubbles: * Merge contigs after popping bubbles. * Bug fix. Do not pop bubbles resulting from palindromes. KAligner: * Report the amount of memory used. * New option, --sam. Output the alignments in SAM format. ParseAligns, DistanceEst: * Bug fix. The CIGAR string was oriented with respect to the query rather than with respect to the target, which is standard. AdjList, PathOverlap: * New option, --sam. Output the adjacency graph in SAM format. abyss-fixmate: * New program. Similar to samtools fixmate, but does not require that the input be sorted by query ID, although it is faster if it is sorted. 2010-07-12 Shaun Jackman * Release version 1.2.1. * Handle reverse-forward oriented mate pair libraries. * Improved distance estimates, particularly with large fragment libraries. abyss-pe: * New commands: se-contigs: Assemble single-end contigs. pe-contigs: Assemble paired-end contigs (default). se-sam: Output a gzipped SAM file of the single-end assembly. se-bam: Ouptut a BAM file of the single-end assembly. pe-dot: Output a Graphviz dot file of the paired-end assembly. all: Sam as se-bam pe-contigs pe-dot. * Options for one particular library may be specified: lib='lib1 lib2' lib2_s=1000 lib2_n=25 * Input sequence may come from an arbitrary command, which is useful to assemble a region of an aligned BAM file: in='<(samtools view genome.bam chr10)' ABYSS: * Bug fix. When reading SAM/BAM files, the quality format incorrectly defaulted to ASCII-64, when it should be ASCII-33. ABYSS-P: * May use the Intel MPI library. ParseAligns: * Count the number of forward-reverse, reverse-forward and forward-forward oriented alignments. DistanceEst: * Handle reverse-forward oriented mate pair libraries. * Improved distance estimates, particularly with large fragment libraries. * Remove duplicate mate pairs. * Print a pretty UTF-8 bar plot of the fragment-size distribution. * Multithreaded using OpenMP. The -j, --threads option specifies the number of threads to use. * Performance improvment. Overlap: * Handle cases when more than one gap occurs within the mate pair fragment size. SimpleGraph: * Performance improvment. MergePaths: * Handle the case when a circular sequence is assmembled into a single contig. abyss-tofastq: * New program. Convert qseq, export, SAM and BAM files to FASTA or FASTQ format. The files may be compressed with gz, bz2 or xz and may be tarred. 2010-05-25 Shaun Jackman * Release version 1.2.0. * Scaffold over gaps in coverage and unresolved repetitive sequence using Ns. * Read sequence from SAM and BAM files. abyss-pe: * Set q=3 by default. Trim bases from the ends of reads whose quality is less than 3. * Do not store the .pair.gz file. * Generate a BAM file of the mate pairs that align to different contigs of the single-end assembly. Disabled by default. * Output a Graphviz dot file of the paired-end assembly. Disabled by default. * Store the bubbles in ${name}-bubbles.fa rather than bubbles.fa. * Store the indel bubbles in ${name}-indel.fa. * Bug fix for mawk. ABYSS: * Set -E0 when coverage is low (<2). ABYSS-P: * Remove the temporary files contigs-*.fa and snp-*.fa. PopBubbles: * Output in Graphviz dot format using --dot. KAligner: * Do not ignore sequences (reads or contigs) containing N. * Output SAM headers (but not SAM alignments). ParseAligns: * Output in SAM format. DistanceEst: * Input in SAM format. * Output in Graphviz dot format using --dot. Overlap: * Scaffold over gaps in coverage. Scaffolding can be disabled using the option --no-scaffold. * Merge contigs that overlap at simple repeats. These merges can be prevented using the option --no-merge-repeat. SimpleGraph: * Scaffold over repeats. Scaffolding can be disabled using the option --no-scaffold. MergePaths: * Merge paths containing ambiguous sequence. * Multithreaded using OpenMP. The -j, --threads option specifies the number of threads to use. MergeContigs: * Merge paths and contigs containing ambiguous sequence. PathOverlap: * Output in Graphviz dot format using --dot. Consensus: * Output the pileup in samtools format. 2010-02-15 Shaun Jackman * Release version 1.1.2. ABYSS: * Read tar files including compressed tar files. * New parameter -b, --bubble-length=N. Pop bubbles shorter than N bp. The default is b=3*k. AdjList: * Include the contig coverage in the output. * The script abyss-adjtodot converts an ABySS adjacency file to GraphViz dot format. PopBubbles: * Pop bubbles resulting from indels. KAligner: * Synchronize the threads periodically (every ten thousand alignments by default) to ease the computational burden on ParseAligns. This synchronization can be disabled using --sync=0. * Use two threads by default. abyss-pe: * New parameter, b. * Use two threads by default. * The read length argument, l, is deprecated. To emulate the behaviour of ABySS 1.0.14 and older, set t=6*(l-k+1). The default is t=k. 2010-01-19 Shaun Jackman * Release version 1.1.1. ABYSS: * Pop complex bubbles either completely or not at all. Bubble popping now completes in a single round. * Choose better (typically lower) default values for the parameters -e,--erode and -c,--coverage. The default threshold is the square root of the median k-mer coverage. 2009-12-18 Shaun Jackman * Release version 1.1.0. * The output format of AdjList, DistanceEst and SimpleGraph has changed to be more humanly readable. ABYSS: * New options, -q, --trim-quality. Trim bases from the ends of reads whose quality is less than the specified threshold. --standard-quality: zero quality is `!' (33) default for FASTQ files --illumina-quality: zero quality is `@' (64) default for qseq and export files Thanks to Tony Raymond. SimpleGraph: * Multithreaded. The -j, --threads option specifies the number of threads to use. * Expand tandem repeats when it is possible to determine the exact number of the repeat. MergePaths: * Bug fix. A repeat that is larger than the fragment size could be misassembled. Thanks to Tony Raymond. abyss-pe: * Determine the parameter j (number of threads) by finding the number of slots allocated on the head node in the PE_HOSTFILE. * Store the k-mer coverage histogram in coverage.hist. 2009-11-13 Shaun Jackman * Release version 1.0.16. * Improve the performance and memory usage of KAligner and AdjList, particularly for very large data sets. KAligner: * Improve memory usage when maxk is 32 or 96. No change when maxk is the default 64. * New option, -i, --ignore-multimap. Ignore any duplicate k-mer in the target sequence. Thanks to Tony Raymond. AdjList: * Improve performance for very large data sets. ParseAligns: * For reads whose ID begins with `SRR', expect that the forward and reverse read have identical ID and no suffix, such as /1 and /2. 2009-10-19 Shaun Jackman * Release version 1.0.15. ABYSS: * New options, -e, --erode and -E, --erode-strand. The parameter e erodes bases at the ends of blunt contigs with coverage less than the specified threshold. The parameter E erodes bases at the ends of blunt contigs with coverage less than the specified threshold on either strand. * New feature. If the parameters e and c are not specified, attempt to choose appropriate values based on the observed k-mer coverage. This feature will work best for higher coverage data. For lower coverage data, setting e=c=2 is reasonable. * New option, --trim-masked. Removed masked (lower case) sequence at the beginning and end of the read. Disable with --no-trim-masked. * The read length, l, is an optional parameter. If the read length is specified, the trim parameter, t, will default to 6*(l-k+1), as before. If the read length is not specified, t will be set to the same value as k. For longer reads or when k is less than 85% of l, it should not be necessary to specify l. The parameter t may be specified directly if desired. DistanceEst: * Bug fix. The standard deviation could be calculated incorrectly for larger numbers, particularly for libraries with large fragment sizes. Thanks to Tony Raymond. Overlap: * Bug fix. If Overlap found mate pairs on the same contig with incorrect orientation, it would generate a misassembled contig. These misassembled contigs are easily identified in the xxx-3-overlap.fa file. The two contigs IDs, in the fourth and fifth column, will be identical. * New option, --mask-repeat. If two contigs are joined by mate pairs and are found to overlap by a simple repeat so that the exact number of the repeat is unknown, join the contigs estimating the number of the repeat, and mask (lower case) the repeat sequence. This feature is disabled by default. abyss-pe: * Use gunzip -c rather than zcat for portability. configure: * New option, --enable-mpich. Use the MPICH2 MPI library. 2009-09-08 Shaun Jackman * Release version 1.0.14. * Read files compressed with xzip (.xz) and compress (.Z). abyss-pe: * Assemble multiple libraries with different fragment sizes. * New manual page. ABYSS: * Don't necessarily discard reads that contain an N. Keep those k-mer that do not contain an N. ABYSS-P: * Serially renumber the contigs output by ABYSS-P using awk. 2009-08-26 Shaun Jackman * Release version 1.0.13. * Read files compressed with gzip (.gz) or bzip2 (.bz2). ABYSS-P: * Bug fix. Fix a race condition in the erosion algorithm. 2009-08-18 Shaun Jackman * Release version 1.0.12. abyss-pe: * Both ABYSS and KAligner are run only once per assembly, which speeds up the paired-end assembly by nearly a factor of two. * The k-mer coverage information is correct in every contig file. * A new parameter, cs, converts colour-space contigs to nucleotide contigs using Consensus. * A new parameter, ABYSS_OPTIONS, may be used to disable chastity filtering by specifying ABYSS_OPTIONS=--no-chastity. ABYSS: * Read files in export format, which is similar to qseq format. * Discard reads that failed the chastity filter. Use the --no-chastity option to retain these unchaste reads. Chastity filtering affects only qseq- and export formatted-files. * Remove low-coverage contigs within ABYSS rather than filtering using awk and reassembling. * Support big-endian architecture machines. KAligner: * A new option, -m or --multimap, specifies that a duplicate k-mer may be seen in the target sequence. By default, every k-mer in the target sequence must be unique. * A new option, --seq, prints the read sequence of each alignment. Overlap: * A new option, --scaffold, fills the gap between two blunt contigs with Ns. This feature is disabled by default. Consensus: * Call the consensus sequence for each contig based on the alignment of reads to contigs. * Convert colour-space contigs to nucleotide contigs. * Written by Tony Raymond. 2009-07-21 Shaun Jackman * Release version 1.0.11. * Assemble colour-space reads. Read identifiers must be named with the suffixes F3 and R3. * Read files in qseq format. Thanks to Tony Raymond (tgr). * Prevent misassemblies mediated by tandem segmental duplications. A sequence XRRY, where R is a repeat sequence, could have been misassembled as XRY. (tgr) abyss-pe: * Integrate with Sun Grid Engine (SGE). A parallel, paired-end assembly can be run with a single qsub command. The parameters lib, np and k default to the qsub environment variables JOB_NAME (qsub -N), NSLOTS (qsub -pe) and SGE_TASK_ID (qsub -t) respectively. * The .pair file, the largest intermediate file, is now gzipped. ABYSS-P: * Bug fix. At k=19, k-mer would be distributed to even-numbered processes only. KAligner: * Multithreaded. The -j, --threads option specifies the number of threads to use. The order in which the alignments are output will vary from run to run, but the alignments are deterministic and will not vary. Each thread reads and aligns one file, so the reads must be in more than one file to use this feature. (tgr) 2009-06-18 Shaun Jackman * Release version 1.0.10. abyss-pe: * Start an MPI ABySS assembly if the np option is specified. ABYSS: * For a non-parallel assembly, allocate more hash buckets to allow for large single-machine jobs. * Print the hash load during the loading process. KAligner: * Output the IDs of reads that do not align. * Print a progress report of the number of reads aligned. ParseAligns: * To reduce memory usage, do not track reads that did not align. KAligner and ParseAligns should now be able to handle any number of reads in a single run. MergePaths: * Number paired-end contigs so that their IDs do not overlap with the single-end contigs. If a single-end contig is not used in a paired-end contig, its ID will not change. * Merge overlapping paired-end contigs that were previously being missed in some situations. configure: * Print a warning if Google sparsehash was not found. 2009-05-15 Shaun Jackman * Release version 1.0.9. abyss-pe: * Allow multiple input files specified by the parameter `in'. * Support reading FASTA or FASTQ file formats. KAligner: * Support using Google sparsehash to reduce memory usage. Google sparsehash does not provide a multimap, so KAligner built using Google sparsehash cannot handle a duplicate k-mer in the reference sequence. It will print an error message and die if a duplicate k-mer is encountered. If Google sparsehash is not used, the standard STL multimap will be used which does permit duplicate k-mer. * Support reading the query sequence from standard input. ParseAligns: * Significantly reduce memory usage if the mate reads are encountered one after the next in the same file. 2009-04-02 Shaun Jackman * Release version 1.0.8. * Bug fix. Fix the undefined behaviour causing the error Assertion `marked == split' failed. 2009-03-31 Shaun Jackman * Release version 1.0.7. * Use a mark-and-sweep trimming algorithm to remove errors at the ends of blunt contigs. * The parallel (ABYSS-P) trimming algorithm is now deterministic; it will produce the same result every time. In addition, the result of the parallel trimming algorithm is identical to the result of the non-parallel trimming algorithm. * Start trimming branches at length 1, previously 2. * Bug fix in ABYSS-P. Repeat sequences of k-1 bases could potentially be misassembled. Use a mark-and-sweep algorithm to split ambiguous edges before contig generation. The previous algorithm was not deterministic. * Reduce memory usage by 200 MB by removing the MPI transmit buffer. * Bug fix in ABYSS-P. Fix an additional race condition in the erosion algorithm. 2009-03-24 Shaun Jackman * Release version 1.0.6. * Bug fix. Fix a race condition in the erosion algorithm. * For the parallel program (ABYSS-P), after bubble popping perform as many trimming rounds as necessary to remove all the tips, as the non-parallel program does. * New script, abyss2afg, to create an AMOS AFG assembly. 2009-03-11 Shaun Jackman * Release version 1.0.5. * Portability fixes. Tested with g++ 4.3.3. 2009-03-04 Shaun Jackman * Release version 1.0.4. ABYSS: * Remove the need to specify a -e,--erode parameter by improving the erosion algorithm to complete in a single pass. * Remove the default limit on the maximum number of bubble popping rounds. A limit may be specified using -b,--bubbles. * Generate a warning if an input file is empty, but do not die. * When using a Google sparsehash, allocate room for 100 million k-mers. * Increase the maximum FASTA line length from 64 kB to 256 kB. * Require only one of either -l,--read-length or -t,--trim-length to be specified. * Allow read pairs to be named `_forward' and `_reverse'. * Ensure that exactly k-1 bases of context is given on each side of the bubble sequence. Previously, one side would have k bases of context, and the other side would have k-1 bases. * Add command line options to each of the paired-end programs. ABYSS-P: * Use Open MPI as the default MPI library. * Do not link against the Open MPI C++ library. abyss-pe: * Use pipes where possible to avoid intermediate files. * The semantics of the n argument have changed. See DistanceEst -n,--npairs below. SimpleGraph: * If more than one path is found but only one meets all of the constraints, use it. * Allow for some constant error in distance estimates that does not decrease with the number of samples. The expected fragment size seems to vary with genomic coordinate to a certain degree. So, the distribution of fragment size spanning two given contigs may differ from the empirical distribution by a roughly constant offset. DistanceEst: * The semantics of the -n,--npairs option has changed. Require at least NPAIRS pairs between contigs (>= NPAIRS). Previously, required strictly more than NPAIRS pairs between contigs (> NPAIRS). * Give the estimated error to a single decimal place. * When counting the number of pairs that join two contigs, only count pairs that fit the empirical distribution. * When deciding whether the pairs joining two contigs are inconsistent in sense, require NPAIRS read pairs joining two contigs in each sense before considering the pair data to be inconsistent. ParseAligns: * Measure fragments in total size, not alignment distance. * Allow a read that spans two contigs to be used in distance estimates. * Add the -h,--hist option to produce a histogram. * Bug fix. When measuring the empirical fragment size, ensure that the sense of the alignments is correct. Output a negative fragment size if the reverse read aligns ahead of the forward read. * Bug fix. Miscalculated the fragment size estimate between two contigs if they did not have the same sense and one contig required flipping. It was possible to see one distance estimate from contig A to contig B and a differing estimate from contig B to contig A. Typically, the distance estimate would be off by one. 2009-01-23 Shaun Jackman * Release version 1.0.3. * Merge contigs that ended due to a lack of coverage, but which are connected by paired-end reads and overlap unambiguously. * Track the multiplicity the sense and antisense strand separately. Erode the end of a blunt contig until it is represented by both strands. * Ignore the case of the nucleotide sequence of a FASTA file. * Increase the maximum FASTA line length from 1 kB to 64 kB to allow loading contigs. * Output the path through the single-end contigs in the comment field of the paired-end contig. * In the paired-end driver script, abyss-pe, Implement a coverage cutoff, c. Pass the erosion parameter, e, to the single-end assembler. 2008-11-21 Shaun Jackman * Release version 1.0.2. * Terminate contig extension at palindromic k-mers. * If erosion (-e,--erode) is enabled, remove the tips of blunt contigs that are represented only once. 2008-11-07 Shaun Jackman * Release version 1.0.1. * Portability improvements to compile for Mac OS X. 2008-08-07 Shaun Jackman * Release version 1.0. abyss-1.3.6/COPYRIGHT000644 002433 001057 00000044331 12153172224 015656 0ustar00traymondassembly000000 000000 Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Name: ABySS Upstream-Contact: Shaun Jackman Source: http://www.bcgsc.ca/platform/bioinfo/software/abyss License: BCCA-Academic Debian may redistribute this software package. . BC CANCER AGENCY SOFTWARE LICENSE AGREEMENT (ACADEMIC USE) CAREFULLY READ THE FOLLOWING TERMS AND CONDITIONS. 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BCCA, at its sole discretion may assign this Agreement without notice to You. Files: * Copyright: Copyright 2013 Genome Sciences Centre License: BCCA-Academic Files: Common/* DataLayer/* DistanceEst/* FMIndex/* Map/* ParseAligns/* Copyright: Copyright 2013 Genome Sciences Centre License: BCCA-Academic or GPL-3+ Files: Common/cholesky.hpp Copyright: Copyright 2005 Gunter Winkler, Konstantin Kutzkow License: LGPL-2.1+ Files: Common/city.cc Common/city.h Copyright: Copyright 2011 Google, Inc. License: Expat Files: Layout/* Copyright: Copyright 2012 Shaun Jackman License: BCCA-Academic or GPL-3+ Files: dialign/* Copyright: Copyright 2008 Amarendran R. Subramanian License: LGPL-2.1+ License: LGPL-2.1+ On Debian systems, see `/usr/share/common-licenses/LGPL-2.1'. . This library is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version. . This library 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 Lesser General Public License for more details. . You should have received a copy of the GNU Lesser General Public License along with this library; if not, write to the Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA . Amarendran R. Subramanian, hereby disclaims all copyright interest in the DIALIGN-TX (a multiple sequence alignment algorithm) written by Amarendran R. Subramanian. . Amarendran R. Subramanian, 2004-2008 . DIALIGN-TX has been co-authored by Volker Menrad and Dorothea Emig. . Research work using DIALIGN-TX should cite: . DIALIGN-TX: improvement of the segment-based approach for multiple sequence alignment by combining greedy and progressive alignment strategies Amarendran R. Subramanian, Michael Kaufmann, Burkhard Morgenstern, Algorithms for Molecular Biology 3:6, 2008 . DIALIGN-T: An improved algorithm for segment-based multiple sequence alignment Amarendran R. Subramanian, Jan Weyer-Menkhoff, Michael Kaufmann, Burkhard Morgenstern, BMC Bioinformatics 6:66, 2005 Files: FMIndex/bit_array.h Copyright: Copyright 2010 Daisuke Okanohara License: BSD-3-clause Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: . Redistributions of source code must retain the above Copyright notice, this list of conditions and the following disclaimer. . 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ABySS

ABySS is a de novo sequence assembler intended for short paired-end reads and large genomes.

Contents

Quick Start

Install ABySS on Debian or Ubuntu

Run the command

sudo apt-get install abyss

or download and install the Debian package.

Install ABySS on Mac OS X

Download and install the Mac OS X app.

Assemble a small synthetic data set

wget http://www.bcgsc.ca/platform/bioinfo/software/abyss/releases/1.3.4/test-data.tar.gz
tar xzvf test-data.tar.gz
abyss-pe k=25 name=test \
    in='test-data/reads1.fastq test-data/reads2.fastq'

Calculate assembly contiguity statistics

abyss-fac test-unitigs.fa

Dependencies

ABySS requires the following libraries:

ABySS requires a C++ compiler that supports OpenMP such as GCC.

ABySS will receive an error when compiling with Boost 1.51.0 or 1.52.0 since they contain a bug. Later versions of Boost compile without error.

Compiling ABySS from GitHub

When installing ABySS from GitHub source the following tools are required:

To generate the configure script and make files:

./autogen.sh

See “Compiling ABySS from source” for further steps.

Compiling ABySS from source

To compile and install ABySS in /usr/local:

./configure
make
sudo make install

To install ABySS in a specified directory:

./configure --prefix=/opt/abyss
make
sudo make install

ABySS uses OpenMP for parallelization, which requires a modern compiler such as GCC 4.2 or greater. If you have an older compiler, it is best to upgrade your compiler if possible. If you have multiple versions of GCC installed, you can specify a different compiler:

./configure CC=gcc-4.6 CXX=g++-4.6

ABySS requires the Boost C++ libraries. Many systems come with Boost installed. If yours does not, you can download Boost. It is not necessary to compile Boost before installing it. The Boost header file directory should be found at /usr/include/boost, in the ABySS source directory, or its location specified to configure:

./configure --with-boost=/usr/local/include

If you wish to build the parallel assembler with MPI support, MPI should be found in /usr/include and /usr/lib or its location specified to configure:

./configure --with-mpi=/usr/lib/openmpi

ABySS should be built using the sparsehash library to reduce memory usage, although it will build without. sparsehash should be found in /usr/include or its location specified to configure:

./configure CPPFLAGS=-I/usr/local/include

The default maximum k-mer size is 64 and may be decreased to reduce memory usage or increased at compile time:

./configure --enable-maxk=96

If you encounter compiler warnings, you may ignore them like so:

make AM_CXXFLAGS=-Wall

To run ABySS, its executables should be found in your PATH. If you installed ABySS in /opt/abyss, add /opt/abyss/bin to your PATH:

PATH=/opt/abyss/bin:$PATH

Assembling a paired-end library

To assemble paired reads in two files named reads1.fa and reads2.fa into contigs in a file named ecoli-contigs.fa, run the command:

abyss-pe name=ecoli k=64 in='reads1.fa reads2.fa'

The parameter in specifies the input files to read, which may be in FASTA, FASTQ, qseq, export, SRA, SAM or BAM format and compressed with gz, bz2 or xz and may be tarred. The assembled contigs will be stored in ${name}-contigs.fa.

A pair of reads must be named with the suffixes /1 and /2 to identify the first and second read, or the reads may be named identically. The paired reads may be in separate files or interleaved in a single file.

Reads without mates should be placed in a file specified by the parameter se (single-end). Reads without mates in the paired-end files will slow down the paired-end assembler considerably during the abyss-fixmate stage.

Assembling multiple libraries

The distribution of fragment sizes of each library is calculated empirically by aligning paired reads to the contigs produced by the single-end assembler, and the distribution is stored in a file with the extension .hist, such as ecoli-3.hist. The N50 of the single-end assembly must be well over the fragment-size to obtain an accurate empirical distribution.

Here’s an example scenario of assembling a data set with two different fragment libraries and single-end reads:

  • Library pe200 has reads in two files, pe200_1.fa and pe200_2.fa.
  • Library pe500 has reads in two files, pe500_1.fa and pe500_2.fa.
  • Single-end reads are stored in two files, se1.fa and se2.fa.

The command line to assemble this example data set is:

abyss-pe k=64 name=ecoli lib='pe200 pe500' \
    pe200='pe200_1.fa pe200_2.fa' pe500='pe500_1.fa pe500_2.fa' \
    se='se1.fa se2.fa'

The empirical distribution of fragment sizes will be stored in two files named pe200-3.hist and pe500-3.hist. These files may be plotted to check that the empirical distribution agrees with the expected distribution. The assembled contigs will be stored in ${name}-contigs.fa.

Scaffolding

Long-distance mate-pair libraries may be used to scaffold an assembly. Specify the names of the mate-pair libraries using the parameter mp. The scaffolds will be stored in the file ${name}-scaffolds.fa. Here’s an example of assembling a data set with two paired-end libraries and two mate-pair libraries:

abyss-pe k=64 name=ecoli lib='pe1 pe2' mp='mp1 mp2' \
    pe1='pe1_1.fa pe1_2.fa' pe2='pe2_1.fa pe2_2.fa' \
    mp1='mp1_1.fa mp1_2.fa' mp2='mp2_1.fa mp2_2.fa'

The mate-pair libraries are used only for scaffolding and do not contribute towards the consensus sequence.

Optimizing the parameter k

To find the optimal value of k, run multiple assemblies and inspect the assembly contiguity statistics. The following shell snippet will assemble for every value of k from 20 to 40.

export k
for k in {20..40}; do
    mkdir k$k
    abyss-pe -C k$k name=ecoli in=../reads.fa
done
abyss-fac k*/ecoli-contigs.fa

The default maximum value for k is 64. This limit may be changed at compile time using the --enable-maxk option of configure. It may be decreased to 32 to decrease memory usage or increased to 96.

Parallel processing

The np option of abyss-pe specifies the number of processes to use for the parallel MPI job. Without any MPI configuration, this will allow you to use multiple cores on a single machine. To use multiple machines for assembly, you must create a hostfile for mpirun, which is described in the mpirun man page.

Do not run mpirun -np 8 abyss-pe. To run ABySS with 8 threads, use abyss-pe np=8. The abyss-pe driver script will start the MPI process, like so: mpirun -np 8 ABYSS-P.

The paired-end assembly stage is multithreaded, but must run on a single machine. The number of threads to use may be specified with the parameter j. The default value for j is the value of np.

Running ABySS on a cluster

ABySS integrates well with cluster job schedulers, such as:

  • SGE (Sun Grid Engine)
  • Portable Batch System (PBS)
  • Load Sharing Facility (LSF)
  • IBM LoadLeveler

For example, to submit an array of jobs to assemble every odd value of k between 51 and 63 using 64 processes for each job:

mkdir k{51..63}
qsub -N ecoli -pe openmpi 64 -t 51-63:2 \
    <<<'abyss-pe -C k$SGE_TASK_ID in=/data/reads.fa'

Assembly Parameters

Parameters of the driver script, abyss-pe

  • a: maximum number of branches of a bubble [2]
  • b: maximum length of a bubble (bp) [10000]
  • c: minimum mean k-mer coverage of a unitig [sqrt(median)]
  • d: allowable error of a distance estimate (bp) [6]
  • e: minimum erosion k-mer coverage [sqrt(median)]
  • E: minimum erosion k-mer coverage per strand [1]
  • j: number of threads [2]
  • k: size of k-mer (bp)
  • l: minimum alignment length of a read (bp) [k]
  • m: minimum overlap of two unitigs (bp) [30]
  • n: minimum number of pairs required for building contigs [10]
  • N: minimum number of pairs required for building scaffolds [n]
  • p: minimum sequence identity of a bubble [0.9]
  • q: minimum base quality [3]
  • s: minimum unitig size required for building contigs (bp) [200]
  • S: minimum contig size required for building scaffolds (bp) [s]
  • t: minimum tip size (bp) [2k]
  • v: use v=-v to enable verbose logging [disabled]

Please see the abyss-pe manual page for more information on assembly parameters.

ABySS programs

abyss-pe is a driver script implemented as a Makefile. Any option of make may be used with abyss-pe. Particularly useful options are:

  • -C dir, --directory=dir
    Change to the directory dir and store the results there.
  • -n, --dry-run
    Print the commands that would be executed, but do not execute them.

abyss-pe uses the following programs, which must be found in your PATH:

  • ABYSS: de Bruijn graph assembler
  • ABYSS-P: parallel (MPI) de Bruijn graph assembler
  • AdjList: find overlapping sequences
  • DistanceEst: estimate the distance between sequences
  • MergeContigs: merge sequences
  • MergePaths: merge overlapping paths
  • Overlap: find overlapping sequences using paired-end reads
  • PathConsensus: find a consensus sequence of ambiguous paths
  • PathOverlap: find overlapping paths
  • PopBubbles: remove bubbles from the sequence overlap graph
  • SimpleGraph: find paths through the overlap graph
  • abyss-fac: calculate assembly contiguity statistics
  • abyss-filtergraph: remove shim contigs from the overlap graph
  • abyss-fixmate: fill the paired-end fields of SAM alignments
  • abyss-map: map reads to a reference sequence
  • abyss-scaffold: scaffold contigs using distance estimates
  • abyss-todot: convert graph formats and merge graphs

For a flowchart showing the relationship between these programs, see doc/flowchart.pdf.

Mailing List

Subscribe to the [ABySS mailing list] (http://groups.google.com/group/abyss-users), abyss-users@googlegroups.com.

For questions related to transcriptome assembly, contact the [Trans-ABySS mailing list] (http://groups.google.com/group/trans-abyss), trans-abyss@googlegroups.com.

Authors

This document is written by Shaun Jackman.

ABySS is written by Shaun Jackman, Tony Raymond and Jared Simpson.

Copyright 2012 Canada’s Michael Smith Genome Science Centre

githalytics.com

abyss-1.3.6/README.md000644 002433 001057 00000026706 12176305753 015662 0ustar00traymondassembly000000 000000 Title: ABySS README Author: Shaun Jackman, Anthony Raymond Affiliation: Canada's Michael Smith Genome Science Centre CSS: README.css ABySS ===== ABySS is a *de novo* sequence assembler intended for short paired-end reads and large genomes. Contents ======== * [Quick Start] * [Install ABySS on Debian or Ubuntu] * [Install ABySS on Mac OS X] * [Dependencies] * [Compiling ABySS from source] * [Assembling a paired-end library] * [Assembling multiple libraries] * [Scaffolding] * [Optimizing the parameter k] * [Parallel processing] * [Running ABySS on a cluster] * [Assembly Parameters] * [ABySS programs] * [Mailing List] * [Authors] Quick Start =========== ## Install ABySS on Debian or Ubuntu Run the command sudo apt-get install abyss or download and install the [Debian package](http://www.bcgsc.ca/platform/bioinfo/software/abyss). ## Install ABySS on Mac OS X Download and install the [Mac OS X app](http://www.bcgsc.ca/platform/bioinfo/software/abyss). ## Assemble a small synthetic data set wget http://www.bcgsc.ca/platform/bioinfo/software/abyss/releases/1.3.4/test-data.tar.gz tar xzvf test-data.tar.gz abyss-pe k=25 name=test \ in='test-data/reads1.fastq test-data/reads2.fastq' ## Calculate assembly contiguity statistics abyss-fac test-unitigs.fa Dependencies ============ ABySS requires the following libraries: * [Boost](http://www.boost.org) * [sparsehash](http://code.google.com/p/sparsehash) * [Open MPI](http://www.open-mpi.org) ABySS requires a C++ compiler that supports [OpenMP](http://www.openmp.org) such as [GCC](http://gcc.gnu.org). ABySS will receive an error when compiling with Boost 1.51.0 or 1.52.0 since they contain a bug. Later versions of Boost compile without error. Compiling ABySS from GitHub =========================== When installing ABySS from GitHub source the following tools are required: * [Autoconf](http://www.gnu.org/software/autoconf) * [Automake](http://www.gnu.org/software/automake) To generate the configure script and make files: ./autogen.sh See "Compiling ABySS from source" for further steps. Compiling ABySS from source =========================== To compile and install ABySS in `/usr/local`: ./configure make sudo make install To install ABySS in a specified directory: ./configure --prefix=/opt/abyss make sudo make install ABySS uses OpenMP for parallelization, which requires a modern compiler such as GCC 4.2 or greater. If you have an older compiler, it is best to upgrade your compiler if possible. If you have multiple versions of GCC installed, you can specify a different compiler: ./configure CC=gcc-4.6 CXX=g++-4.6 ABySS requires the Boost C++ libraries. Many systems come with Boost installed. If yours does not, you can download [Boost](http://www.boost.org/users/download). It is not necessary to compile Boost before installing it. The Boost header file directory should be found at `/usr/include/boost`, in the ABySS source directory, or its location specified to `configure`: ./configure --with-boost=/usr/local/include If you wish to build the parallel assembler with MPI support, MPI should be found in `/usr/include` and `/usr/lib` or its location specified to `configure`: ./configure --with-mpi=/usr/lib/openmpi ABySS should be built using the sparsehash library to reduce memory usage, although it will build without. sparsehash should be found in `/usr/include` or its location specified to `configure`: ./configure CPPFLAGS=-I/usr/local/include The default maximum k-mer size is 64 and may be decreased to reduce memory usage or increased at compile time: ./configure --enable-maxk=96 If you encounter compiler warnings, you may ignore them like so: make AM_CXXFLAGS=-Wall To run ABySS, its executables should be found in your `PATH`. If you installed ABySS in `/opt/abyss`, add `/opt/abyss/bin` to your `PATH`: PATH=/opt/abyss/bin:$PATH Assembling a paired-end library =============================== To assemble paired reads in two files named `reads1.fa` and `reads2.fa` into contigs in a file named `ecoli-contigs.fa`, run the command: abyss-pe name=ecoli k=64 in='reads1.fa reads2.fa' The parameter `in` specifies the input files to read, which may be in FASTA, FASTQ, qseq, export, SRA, SAM or BAM format and compressed with gz, bz2 or xz and may be tarred. The assembled contigs will be stored in `${name}-contigs.fa`. A pair of reads must be named with the suffixes `/1` and `/2` to identify the first and second read, or the reads may be named identically. The paired reads may be in separate files or interleaved in a single file. Reads without mates should be placed in a file specified by the parameter `se` (single-end). Reads without mates in the paired-end files will slow down the paired-end assembler considerably during the `abyss-fixmate` stage. Assembling multiple libraries ============================= The distribution of fragment sizes of each library is calculated empirically by aligning paired reads to the contigs produced by the single-end assembler, and the distribution is stored in a file with the extension `.hist`, such as `ecoli-3.hist`. The N50 of the single-end assembly must be well over the fragment-size to obtain an accurate empirical distribution. Here's an example scenario of assembling a data set with two different fragment libraries and single-end reads: * Library `pe200` has reads in two files, `pe200_1.fa` and `pe200_2.fa`. * Library `pe500` has reads in two files, `pe500_1.fa` and `pe500_2.fa`. * Single-end reads are stored in two files, `se1.fa` and `se2.fa`. The command line to assemble this example data set is: abyss-pe k=64 name=ecoli lib='pe200 pe500' \ pe200='pe200_1.fa pe200_2.fa' pe500='pe500_1.fa pe500_2.fa' \ se='se1.fa se2.fa' The empirical distribution of fragment sizes will be stored in two files named `pe200-3.hist` and `pe500-3.hist`. These files may be plotted to check that the empirical distribution agrees with the expected distribution. The assembled contigs will be stored in `${name}-contigs.fa`. Scaffolding =========== Long-distance mate-pair libraries may be used to scaffold an assembly. Specify the names of the mate-pair libraries using the parameter `mp`. The scaffolds will be stored in the file `${name}-scaffolds.fa`. Here's an example of assembling a data set with two paired-end libraries and two mate-pair libraries: abyss-pe k=64 name=ecoli lib='pe1 pe2' mp='mp1 mp2' \ pe1='pe1_1.fa pe1_2.fa' pe2='pe2_1.fa pe2_2.fa' \ mp1='mp1_1.fa mp1_2.fa' mp2='mp2_1.fa mp2_2.fa' The mate-pair libraries are used only for scaffolding and do not contribute towards the consensus sequence. Optimizing the parameter k ========================== To find the optimal value of `k`, run multiple assemblies and inspect the assembly contiguity statistics. The following shell snippet will assemble for every value of `k` from 20 to 40. export k for k in {20..40}; do mkdir k$k abyss-pe -C k$k name=ecoli in=../reads.fa done abyss-fac k*/ecoli-contigs.fa The default maximum value for `k` is 64. This limit may be changed at compile time using the `--enable-maxk` option of configure. It may be decreased to 32 to decrease memory usage or increased to 96. Parallel processing =================== The `np` option of `abyss-pe` specifies the number of processes to use for the parallel MPI job. Without any MPI configuration, this will allow you to use multiple cores on a single machine. To use multiple machines for assembly, you must create a `hostfile` for `mpirun`, which is described in the `mpirun` man page. *Do not* run `mpirun -np 8 abyss-pe`. To run ABySS with 8 threads, use `abyss-pe np=8`. The `abyss-pe` driver script will start the MPI process, like so: `mpirun -np 8 ABYSS-P`. The paired-end assembly stage is multithreaded, but must run on a single machine. The number of threads to use may be specified with the parameter `j`. The default value for `j` is the value of `np`. Running ABySS on a cluster ========================== ABySS integrates well with cluster job schedulers, such as: * SGE (Sun Grid Engine) * Portable Batch System (PBS) * Load Sharing Facility (LSF) * IBM LoadLeveler For example, to submit an array of jobs to assemble every odd value of `k` between 51 and 63 using 64 processes for each job: mkdir k{51..63} qsub -N ecoli -pe openmpi 64 -t 51-63:2 \ <<<'abyss-pe -C k$SGE_TASK_ID in=/data/reads.fa' Assembly Parameters =================== Parameters of the driver script, `abyss-pe` * `a`: maximum number of branches of a bubble [`2`] * `b`: maximum length of a bubble (bp) [`10000`] * `c`: minimum mean k-mer coverage of a unitig [`sqrt(median)`] * `d`: allowable error of a distance estimate (bp) [`6`] * `e`: minimum erosion k-mer coverage [`sqrt(median)`] * `E`: minimum erosion k-mer coverage per strand [`1`] * `j`: number of threads [`2`] * `k`: size of k-mer (bp) * `l`: minimum alignment length of a read (bp) [`k`] * `m`: minimum overlap of two unitigs (bp) [`30`] * `n`: minimum number of pairs required for building contigs [`10`] * `N`: minimum number of pairs required for building scaffolds [`n`] * `p`: minimum sequence identity of a bubble [`0.9`] * `q`: minimum base quality [`3`] * `s`: minimum unitig size required for building contigs (bp) [`200`] * `S`: minimum contig size required for building scaffolds (bp) [`s`] * `t`: minimum tip size (bp) [`2k`] * `v`: use `v=-v` to enable verbose logging [`disabled`] Please see the [abyss-pe](http://manpages.ubuntu.com/abyss-pe.1.html) manual page for more information on assembly parameters. ABySS programs ============== `abyss-pe` is a driver script implemented as a Makefile. Any option of `make` may be used with `abyss-pe`. Particularly useful options are: * `-C dir`, `--directory=dir` Change to the directory `dir` and store the results there. * `-n`, `--dry-run` Print the commands that would be executed, but do not execute them. `abyss-pe` uses the following programs, which must be found in your `PATH`: * `ABYSS`: de Bruijn graph assembler * `ABYSS-P`: parallel (MPI) de Bruijn graph assembler * `AdjList`: find overlapping sequences * `DistanceEst`: estimate the distance between sequences * `MergeContigs`: merge sequences * `MergePaths`: merge overlapping paths * `Overlap`: find overlapping sequences using paired-end reads * `PathConsensus`: find a consensus sequence of ambiguous paths * `PathOverlap`: find overlapping paths * `PopBubbles`: remove bubbles from the sequence overlap graph * `SimpleGraph`: find paths through the overlap graph * `abyss-fac`: calculate assembly contiguity statistics * `abyss-filtergraph`: remove shim contigs from the overlap graph * `abyss-fixmate`: fill the paired-end fields of SAM alignments * `abyss-map`: map reads to a reference sequence * `abyss-scaffold`: scaffold contigs using distance estimates * `abyss-todot`: convert graph formats and merge graphs For a flowchart showing the relationship between these programs, see doc/flowchart.pdf. Mailing List ============ Subscribe to the [ABySS mailing list] (http://groups.google.com/group/abyss-users), . For questions related to transcriptome assembly, contact the [Trans-ABySS mailing list] (http://groups.google.com/group/trans-abyss), . Authors ======= This document is written by Shaun Jackman. ABySS is written by Shaun Jackman, Tony Raymond and Jared Simpson. Copyright 2012 Canada's Michael Smith Genome Science Centre [![githalytics.com](https://cruel-carlota.pagodabox.com/af4811df3b40b7d096f6085db2969f0e "githalytics.com")](http://githalytics.com/sjackman/abyss) abyss-1.3.6/compile000755 002433 001057 00000016245 12171103213 015734 0ustar00traymondassembly000000 000000 #! /bin/sh # Wrapper for compilers which do not understand '-c -o'. scriptversion=2012-10-14.11; # UTC # Copyright (C) 1999-2013 Free Software Foundation, Inc. # Written by Tom Tromey . # # 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 2, 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. 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Options: -h, --help display this help and exit -v, --version output version information and exit Supported PROGRAM values: aclocal autoconf autoheader autom4te automake makeinfo bison yacc flex lex help2man Version suffixes to PROGRAM as well as the prefixes 'gnu-', 'gnu', and 'g' are ignored when checking the name. Send bug reports to ." exit $? ;; -v|--v|--ve|--ver|--vers|--versi|--versio|--version) echo "missing $scriptversion (GNU Automake)" exit $? ;; -*) echo 1>&2 "$0: unknown '$1' option" echo 1>&2 "Try '$0 --help' for more information" exit 1 ;; esac # Run the given program, remember its exit status. "$@"; st=$? # If it succeeded, we are done. test $st -eq 0 && exit 0 # Also exit now if we it failed (or wasn't found), and '--version' was # passed; such an option is passed most likely to detect whether the # program is present and works. case $2 in --version|--help) exit $st;; esac # Exit code 63 means version mismatch. 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Give up. exit $st fi perl_URL=http://www.perl.org/ flex_URL=http://flex.sourceforge.net/ gnu_software_URL=http://www.gnu.org/software program_details () { case $1 in aclocal|automake) echo "The '$1' program is part of the GNU Automake package:" echo "<$gnu_software_URL/automake>" echo "It also requires GNU Autoconf, GNU m4 and Perl in order to run:" echo "<$gnu_software_URL/autoconf>" echo "<$gnu_software_URL/m4/>" echo "<$perl_URL>" ;; autoconf|autom4te|autoheader) echo "The '$1' program is part of the GNU Autoconf package:" echo "<$gnu_software_URL/autoconf/>" echo "It also requires GNU m4 and Perl in order to run:" echo "<$gnu_software_URL/m4/>" echo "<$perl_URL>" ;; esac } give_advice () { # Normalize program name to check for. normalized_program=`echo "$1" | sed ' s/^gnu-//; t s/^gnu//; t s/^g//; t'` printf '%s\n' "'$1' is $msg." configure_deps="'configure.ac' or m4 files included by 'configure.ac'" case $normalized_program in autoconf*) echo "You should only need it if you modified 'configure.ac'," echo "or m4 files included by it." program_details 'autoconf' ;; autoheader*) echo "You should only need it if you modified 'acconfig.h' or" echo "$configure_deps." program_details 'autoheader' ;; automake*) echo "You should only need it if you modified 'Makefile.am' or" echo "$configure_deps." program_details 'automake' ;; aclocal*) echo "You should only need it if you modified 'acinclude.m4' or" echo "$configure_deps." program_details 'aclocal' ;; autom4te*) echo "You might have modified some maintainer files that require" echo "the 'automa4te' program to be rebuilt." program_details 'autom4te' ;; bison*|yacc*) echo "You should only need it if you modified a '.y' file." echo "You may want to install the GNU Bison package:" echo "<$gnu_software_URL/bison/>" ;; lex*|flex*) echo "You should only need it if you modified a '.l' file." echo "You may want to install the Fast Lexical Analyzer package:" echo "<$flex_URL>" ;; help2man*) echo "You should only need it if you modified a dependency" \ "of a man page." echo "You may want to install the GNU Help2man package:" echo "<$gnu_software_URL/help2man/>" ;; makeinfo*) echo "You should only need it if you modified a '.texi' file, or" echo "any other file indirectly affecting the aspect of the manual." echo "You might want to install the Texinfo package:" echo "<$gnu_software_URL/texinfo/>" echo "The spurious makeinfo call might also be the consequence of" echo "using a buggy 'make' (AIX, DU, IRIX), in which case you might" echo "want to install GNU make:" echo "<$gnu_software_URL/make/>" ;; *) echo "You might have modified some files without having the proper" echo "tools for further handling them. Check the 'README' file, it" echo "often tells you about the needed prerequisites for installing" echo "this package. You may also peek at any GNU archive site, in" echo "case some other package contains this missing '$1' program." ;; esac } give_advice "$1" | sed -e '1s/^/WARNING: /' \ -e '2,$s/^/ /' >&2 # Propagate the correct exit status (expected to be 127 for a program # not found, 63 for a program that failed due to version mismatch). exit $st # Local variables: # eval: (add-hook 'write-file-hooks 'time-stamp) # time-stamp-start: "scriptversion=" # time-stamp-format: "%:y-%02m-%02d.%02H" # time-stamp-time-zone: "UTC" # time-stamp-end: "; # UTC" # End: abyss-1.3.6/doxygen.conf000644 002433 001057 00000144125 12176305753 016723 0ustar00traymondassembly000000 000000 # Doxyfile 1.4.7 # This file describes the settings to be used by the documentation system # doxygen (www.doxygen.org) for a project # # All text after a hash (#) is considered a comment and will be ignored # The format is: # TAG = value [value, ...] # For lists items can also be appended using: # TAG += value [value, ...] # Values that contain spaces should be placed between quotes (" ") #--------------------------------------------------------------------------- # Project related configuration options #--------------------------------------------------------------------------- # The PROJECT_NAME tag is a single word (or a sequence of words surrounded # by quotes) that should identify the project. PROJECT_NAME = ABySS # The PROJECT_NUMBER tag can be used to enter a project or revision number. # This could be handy for archiving the generated documentation or # if some version control system is used. PROJECT_NUMBER = # The OUTPUT_DIRECTORY tag is used to specify the (relative or absolute) # base path where the generated documentation will be put. # If a relative path is entered, it will be relative to the location # where doxygen was started. If left blank the current directory will be used. OUTPUT_DIRECTORY = # If the CREATE_SUBDIRS tag is set to YES, then doxygen will create # 4096 sub-directories (in 2 levels) under the output directory of each output # format and will distribute the generated files over these directories. # Enabling this option can be useful when feeding doxygen a huge amount of # source files, where putting all generated files in the same directory would # otherwise cause performance problems for the file system. CREATE_SUBDIRS = NO # The OUTPUT_LANGUAGE tag is used to specify the language in which all # documentation generated by doxygen is written. Doxygen will use this # information to generate all constant output in the proper language. # The default language is English, other supported languages are: # Brazilian, Catalan, Chinese, Chinese-Traditional, Croatian, Czech, Danish, # Dutch, Finnish, French, German, Greek, Hungarian, Italian, Japanese, # Japanese-en (Japanese with English messages), Korean, Korean-en, Norwegian, # Polish, Portuguese, Romanian, Russian, Serbian, Slovak, Slovene, Spanish, # Swedish, and Ukrainian. OUTPUT_LANGUAGE = English # This tag can be used to specify the encoding used in the generated output. # The encoding is not always determined by the language that is chosen, # but also whether or not the output is meant for Windows or non-Windows users. # In case there is a difference, setting the USE_WINDOWS_ENCODING tag to YES # forces the Windows encoding (this is the default for the Windows binary), # whereas setting the tag to NO uses a Unix-style encoding (the default for # all platforms other than Windows). USE_WINDOWS_ENCODING = NO # If the BRIEF_MEMBER_DESC tag is set to YES (the default) Doxygen will # include brief member descriptions after the members that are listed in # the file and class documentation (similar to JavaDoc). # Set to NO to disable this. BRIEF_MEMBER_DESC = YES # If the REPEAT_BRIEF tag is set to YES (the default) Doxygen will prepend # the brief description of a member or function before the detailed description. # Note: if both HIDE_UNDOC_MEMBERS and BRIEF_MEMBER_DESC are set to NO, the # brief descriptions will be completely suppressed. REPEAT_BRIEF = YES # This tag implements a quasi-intelligent brief description abbreviator # that is used to form the text in various listings. Each string # in this list, if found as the leading text of the brief description, will be # stripped from the text and the result after processing the whole list, is # used as the annotated text. Otherwise, the brief description is used as-is. # If left blank, the following values are used ("$name" is automatically # replaced with the name of the entity): "The $name class" "The $name widget" # "The $name file" "is" "provides" "specifies" "contains" # "represents" "a" "an" "the" ABBREVIATE_BRIEF = # If the ALWAYS_DETAILED_SEC and REPEAT_BRIEF tags are both set to YES then # Doxygen will generate a detailed section even if there is only a brief # description. ALWAYS_DETAILED_SEC = NO # If the INLINE_INHERITED_MEMB tag is set to YES, doxygen will show all # inherited members of a class in the documentation of that class as if those # members were ordinary class members. Constructors, destructors and assignment # operators of the base classes will not be shown. INLINE_INHERITED_MEMB = NO # If the FULL_PATH_NAMES tag is set to YES then Doxygen will prepend the full # path before files name in the file list and in the header files. If set # to NO the shortest path that makes the file name unique will be used. FULL_PATH_NAMES = YES # If the FULL_PATH_NAMES tag is set to YES then the STRIP_FROM_PATH tag # can be used to strip a user-defined part of the path. Stripping is # only done if one of the specified strings matches the left-hand part of # the path. The tag can be used to show relative paths in the file list. # If left blank the directory from which doxygen is run is used as the # path to strip. STRIP_FROM_PATH = # The STRIP_FROM_INC_PATH tag can be used to strip a user-defined part of # the path mentioned in the documentation of a class, which tells # the reader which header file to include in order to use a class. # If left blank only the name of the header file containing the class # definition is used. Otherwise one should specify the include paths that # are normally passed to the compiler using the -I flag. STRIP_FROM_INC_PATH = # If the SHORT_NAMES tag is set to YES, doxygen will generate much shorter # (but less readable) file names. This can be useful is your file systems # doesn't support long names like on DOS, Mac, or CD-ROM. SHORT_NAMES = NO # If the JAVADOC_AUTOBRIEF tag is set to YES then Doxygen # will interpret the first line (until the first dot) of a JavaDoc-style # comment as the brief description. If set to NO, the JavaDoc # comments will behave just like the Qt-style comments (thus requiring an # explicit @brief command for a brief description. JAVADOC_AUTOBRIEF = YES # The MULTILINE_CPP_IS_BRIEF tag can be set to YES to make Doxygen # treat a multi-line C++ special comment block (i.e. a block of //! or /// # comments) as a brief description. This used to be the default behaviour. # The new default is to treat a multi-line C++ comment block as a detailed # description. Set this tag to YES if you prefer the old behaviour instead. MULTILINE_CPP_IS_BRIEF = NO # If the DETAILS_AT_TOP tag is set to YES then Doxygen # will output the detailed description near the top, like JavaDoc. # If set to NO, the detailed description appears after the member # documentation. DETAILS_AT_TOP = NO # If the INHERIT_DOCS tag is set to YES (the default) then an undocumented # member inherits the documentation from any documented member that it # re-implements. INHERIT_DOCS = YES # If the SEPARATE_MEMBER_PAGES tag is set to YES, then doxygen will produce # a new page for each member. If set to NO, the documentation of a member will # be part of the file/class/namespace that contains it. SEPARATE_MEMBER_PAGES = NO # The TAB_SIZE tag can be used to set the number of spaces in a tab. # Doxygen uses this value to replace tabs by spaces in code fragments. TAB_SIZE = 4 # This tag can be used to specify a number of aliases that acts # as commands in the documentation. An alias has the form "name=value". # For example adding "sideeffect=\par Side Effects:\n" will allow you to # put the command \sideeffect (or @sideeffect) in the documentation, which # will result in a user-defined paragraph with heading "Side Effects:". # You can put \n's in the value part of an alias to insert newlines. ALIASES = # Set the OPTIMIZE_OUTPUT_FOR_C tag to YES if your project consists of C # sources only. Doxygen will then generate output that is more tailored for C. # For instance, some of the names that are used will be different. The list # of all members will be omitted, etc. OPTIMIZE_OUTPUT_FOR_C = NO # Set the OPTIMIZE_OUTPUT_JAVA tag to YES if your project consists of Java # sources only. Doxygen will then generate output that is more tailored for Java. # For instance, namespaces will be presented as packages, qualified scopes # will look different, etc. OPTIMIZE_OUTPUT_JAVA = NO # If you use STL classes (i.e. std::string, std::vector, etc.) but do not want to # include (a tag file for) the STL sources as input, then you should # set this tag to YES in order to let doxygen match functions declarations and # definitions whose arguments contain STL classes (e.g. func(std::string); v.s. # func(std::string) {}). This also make the inheritance and collaboration # diagrams that involve STL classes more complete and accurate. BUILTIN_STL_SUPPORT = YES # If member grouping is used in the documentation and the DISTRIBUTE_GROUP_DOC # tag is set to YES, then doxygen will reuse the documentation of the first # member in the group (if any) for the other members of the group. By default # all members of a group must be documented explicitly. DISTRIBUTE_GROUP_DOC = NO # Set the SUBGROUPING tag to YES (the default) to allow class member groups of # the same type (for instance a group of public functions) to be put as a # subgroup of that type (e.g. under the Public Functions section). Set it to # NO to prevent subgrouping. Alternatively, this can be done per class using # the \nosubgrouping command. SUBGROUPING = YES #--------------------------------------------------------------------------- # Build related configuration options #--------------------------------------------------------------------------- # If the EXTRACT_ALL tag is set to YES doxygen will assume all entities in # documentation are documented, even if no documentation was available. # Private class members and static file members will be hidden unless # the EXTRACT_PRIVATE and EXTRACT_STATIC tags are set to YES EXTRACT_ALL = NO # If the EXTRACT_PRIVATE tag is set to YES all private members of a class # will be included in the documentation. EXTRACT_PRIVATE = NO # If the EXTRACT_STATIC tag is set to YES all static members of a file # will be included in the documentation. EXTRACT_STATIC = NO # If the EXTRACT_LOCAL_CLASSES tag is set to YES classes (and structs) # defined locally in source files will be included in the documentation. # If set to NO only classes defined in header files are included. EXTRACT_LOCAL_CLASSES = YES # This flag is only useful for Objective-C code. When set to YES local # methods, which are defined in the implementation section but not in # the interface are included in the documentation. # If set to NO (the default) only methods in the interface are included. EXTRACT_LOCAL_METHODS = NO # If the HIDE_UNDOC_MEMBERS tag is set to YES, Doxygen will hide all # undocumented members of documented classes, files or namespaces. # If set to NO (the default) these members will be included in the # various overviews, but no documentation section is generated. # This option has no effect if EXTRACT_ALL is enabled. HIDE_UNDOC_MEMBERS = NO # If the HIDE_UNDOC_CLASSES tag is set to YES, Doxygen will hide all # undocumented classes that are normally visible in the class hierarchy. # If set to NO (the default) these classes will be included in the various # overviews. This option has no effect if EXTRACT_ALL is enabled. HIDE_UNDOC_CLASSES = NO # If the HIDE_FRIEND_COMPOUNDS tag is set to YES, Doxygen will hide all # friend (class|struct|union) declarations. # If set to NO (the default) these declarations will be included in the # documentation. HIDE_FRIEND_COMPOUNDS = NO # If the HIDE_IN_BODY_DOCS tag is set to YES, Doxygen will hide any # documentation blocks found inside the body of a function. # If set to NO (the default) these blocks will be appended to the # function's detailed documentation block. HIDE_IN_BODY_DOCS = NO # The INTERNAL_DOCS tag determines if documentation # that is typed after a \internal command is included. If the tag is set # to NO (the default) then the documentation will be excluded. # Set it to YES to include the internal documentation. INTERNAL_DOCS = NO # If the CASE_SENSE_NAMES tag is set to NO then Doxygen will only generate # file names in lower-case letters. If set to YES upper-case letters are also # allowed. This is useful if you have classes or files whose names only differ # in case and if your file system supports case sensitive file names. Windows # and Mac users are advised to set this option to NO. CASE_SENSE_NAMES = YES # If the HIDE_SCOPE_NAMES tag is set to NO (the default) then Doxygen # will show members with their full class and namespace scopes in the # documentation. If set to YES the scope will be hidden. HIDE_SCOPE_NAMES = NO # If the SHOW_INCLUDE_FILES tag is set to YES (the default) then Doxygen # will put a list of the files that are included by a file in the documentation # of that file. SHOW_INCLUDE_FILES = YES # If the INLINE_INFO tag is set to YES (the default) then a tag [inline] # is inserted in the documentation for inline members. INLINE_INFO = YES # If the SORT_MEMBER_DOCS tag is set to YES (the default) then doxygen # will sort the (detailed) documentation of file and class members # alphabetically by member name. If set to NO the members will appear in # declaration order. SORT_MEMBER_DOCS = YES # If the SORT_BRIEF_DOCS tag is set to YES then doxygen will sort the # brief documentation of file, namespace and class members alphabetically # by member name. If set to NO (the default) the members will appear in # declaration order. SORT_BRIEF_DOCS = NO # If the SORT_BY_SCOPE_NAME tag is set to YES, the class list will be # sorted by fully-qualified names, including namespaces. If set to # NO (the default), the class list will be sorted only by class name, # not including the namespace part. # Note: This option is not very useful if HIDE_SCOPE_NAMES is set to YES. # Note: This option applies only to the class list, not to the # alphabetical list. SORT_BY_SCOPE_NAME = NO # The GENERATE_TODOLIST tag can be used to enable (YES) or # disable (NO) the todo list. This list is created by putting \todo # commands in the documentation. GENERATE_TODOLIST = YES # The GENERATE_TESTLIST tag can be used to enable (YES) or # disable (NO) the test list. This list is created by putting \test # commands in the documentation. GENERATE_TESTLIST = YES # The GENERATE_BUGLIST tag can be used to enable (YES) or # disable (NO) the bug list. This list is created by putting \bug # commands in the documentation. GENERATE_BUGLIST = YES # The GENERATE_DEPRECATEDLIST tag can be used to enable (YES) or # disable (NO) the deprecated list. This list is created by putting # \deprecated commands in the documentation. GENERATE_DEPRECATEDLIST= YES # The ENABLED_SECTIONS tag can be used to enable conditional # documentation sections, marked by \if sectionname ... \endif. ENABLED_SECTIONS = # The MAX_INITIALIZER_LINES tag determines the maximum number of lines # the initial value of a variable or define consists of for it to appear in # the documentation. If the initializer consists of more lines than specified # here it will be hidden. Use a value of 0 to hide initializers completely. # The appearance of the initializer of individual variables and defines in the # documentation can be controlled using \showinitializer or \hideinitializer # command in the documentation regardless of this setting. MAX_INITIALIZER_LINES = 30 # Set the SHOW_USED_FILES tag to NO to disable the list of files generated # at the bottom of the documentation of classes and structs. If set to YES the # list will mention the files that were used to generate the documentation. SHOW_USED_FILES = YES # If the sources in your project are distributed over multiple directories # then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy # in the documentation. The default is NO. SHOW_DIRECTORIES = NO # The FILE_VERSION_FILTER tag can be used to specify a program or script that # doxygen should invoke to get the current version for each file (typically from the # version control system). Doxygen will invoke the program by executing (via # popen()) the command , where is the value of # the FILE_VERSION_FILTER tag, and is the name of an input file # provided by doxygen. Whatever the program writes to standard output # is used as the file version. See the manual for examples. FILE_VERSION_FILTER = #--------------------------------------------------------------------------- # configuration options related to warning and progress messages #--------------------------------------------------------------------------- # The QUIET tag can be used to turn on/off the messages that are generated # by doxygen. Possible values are YES and NO. If left blank NO is used. QUIET = NO # The WARNINGS tag can be used to turn on/off the warning messages that are # generated by doxygen. Possible values are YES and NO. If left blank # NO is used. WARNINGS = YES # If WARN_IF_UNDOCUMENTED is set to YES, then doxygen will generate warnings # for undocumented members. If EXTRACT_ALL is set to YES then this flag will # automatically be disabled. WARN_IF_UNDOCUMENTED = YES # If WARN_IF_DOC_ERROR is set to YES, doxygen will generate warnings for # potential errors in the documentation, such as not documenting some # parameters in a documented function, or documenting parameters that # don't exist or using markup commands wrongly. WARN_IF_DOC_ERROR = YES # This WARN_NO_PARAMDOC option can be abled to get warnings for # functions that are documented, but have no documentation for their parameters # or return value. If set to NO (the default) doxygen will only warn about # wrong or incomplete parameter documentation, but not about the absence of # documentation. WARN_NO_PARAMDOC = NO # The WARN_FORMAT tag determines the format of the warning messages that # doxygen can produce. The string should contain the $file, $line, and $text # tags, which will be replaced by the file and line number from which the # warning originated and the warning text. Optionally the format may contain # $version, which will be replaced by the version of the file (if it could # be obtained via FILE_VERSION_FILTER) WARN_FORMAT = "$file:$line: $text" # The WARN_LOGFILE tag can be used to specify a file to which warning # and error messages should be written. If left blank the output is written # to stderr. WARN_LOGFILE = #--------------------------------------------------------------------------- # configuration options related to the input files #--------------------------------------------------------------------------- # The INPUT tag can be used to specify the files and/or directories that contain # documented source files. You may enter file names like "myfile.cpp" or # directories like "/usr/src/myproject". Separate the files or directories # with spaces. INPUT = # If the value of the INPUT tag contains directories, you can use the # FILE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp # and *.h) to filter out the source-files in the directories. If left # blank the following patterns are tested: # *.c *.cc *.cxx *.cpp *.c++ *.java *.ii *.ixx *.ipp *.i++ *.inl *.h *.hh *.hxx # *.hpp *.h++ *.idl *.odl *.cs *.php *.php3 *.inc *.m *.mm *.py FILE_PATTERNS = # The RECURSIVE tag can be used to turn specify whether or not subdirectories # should be searched for input files as well. Possible values are YES and NO. # If left blank NO is used. RECURSIVE = YES # The EXCLUDE tag can be used to specify files and/or directories that should # excluded from the INPUT source files. This way you can easily exclude a # subdirectory from a directory tree whose root is specified with the INPUT tag. EXCLUDE = # The EXCLUDE_SYMLINKS tag can be used select whether or not files or # directories that are symbolic links (a Unix filesystem feature) are excluded # from the input. EXCLUDE_SYMLINKS = NO # If the value of the INPUT tag contains directories, you can use the # EXCLUDE_PATTERNS tag to specify one or more wildcard patterns to exclude # certain files from those directories. Note that the wildcards are matched # against the file with absolute path, so to exclude all test directories # for example use the pattern */test/* EXCLUDE_PATTERNS = # The EXAMPLE_PATH tag can be used to specify one or more files or # directories that contain example code fragments that are included (see # the \include command). EXAMPLE_PATH = # If the value of the EXAMPLE_PATH tag contains directories, you can use the # EXAMPLE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp # and *.h) to filter out the source-files in the directories. If left # blank all files are included. EXAMPLE_PATTERNS = # If the EXAMPLE_RECURSIVE tag is set to YES then subdirectories will be # searched for input files to be used with the \include or \dontinclude # commands irrespective of the value of the RECURSIVE tag. # Possible values are YES and NO. If left blank NO is used. EXAMPLE_RECURSIVE = NO # The IMAGE_PATH tag can be used to specify one or more files or # directories that contain image that are included in the documentation (see # the \image command). IMAGE_PATH = # The INPUT_FILTER tag can be used to specify a program that doxygen should # invoke to filter for each input file. Doxygen will invoke the filter program # by executing (via popen()) the command , where # is the value of the INPUT_FILTER tag, and is the name of an # input file. Doxygen will then use the output that the filter program writes # to standard output. If FILTER_PATTERNS is specified, this tag will be # ignored. INPUT_FILTER = # The FILTER_PATTERNS tag can be used to specify filters on a per file pattern # basis. Doxygen will compare the file name with each pattern and apply the # filter if there is a match. The filters are a list of the form: # pattern=filter (like *.cpp=my_cpp_filter). See INPUT_FILTER for further # info on how filters are used. If FILTER_PATTERNS is empty, INPUT_FILTER # is applied to all files. FILTER_PATTERNS = # If the FILTER_SOURCE_FILES tag is set to YES, the input filter (if set using # INPUT_FILTER) will be used to filter the input files when producing source # files to browse (i.e. when SOURCE_BROWSER is set to YES). FILTER_SOURCE_FILES = NO #--------------------------------------------------------------------------- # configuration options related to source browsing #--------------------------------------------------------------------------- # If the SOURCE_BROWSER tag is set to YES then a list of source files will # be generated. Documented entities will be cross-referenced with these sources. # Note: To get rid of all source code in the generated output, make sure also # VERBATIM_HEADERS is set to NO. SOURCE_BROWSER = NO # Setting the INLINE_SOURCES tag to YES will include the body # of functions and classes directly in the documentation. INLINE_SOURCES = NO # Setting the STRIP_CODE_COMMENTS tag to YES (the default) will instruct # doxygen to hide any special comment blocks from generated source code # fragments. Normal C and C++ comments will always remain visible. STRIP_CODE_COMMENTS = YES # If the REFERENCED_BY_RELATION tag is set to YES (the default) # then for each documented function all documented # functions referencing it will be listed. REFERENCED_BY_RELATION = YES # If the REFERENCES_RELATION tag is set to YES (the default) # then for each documented function all documented entities # called/used by that function will be listed. REFERENCES_RELATION = YES # If the REFERENCES_LINK_SOURCE tag is set to YES (the default) # and SOURCE_BROWSER tag is set to YES, then the hyperlinks from # functions in REFERENCES_RELATION and REFERENCED_BY_RELATION lists will # link to the source code. Otherwise they will link to the documentstion. REFERENCES_LINK_SOURCE = YES # If the USE_HTAGS tag is set to YES then the references to source code # will point to the HTML generated by the htags(1) tool instead of doxygen # built-in source browser. The htags tool is part of GNU's global source # tagging system (see http://www.gnu.org/software/global/global.html). You # will need version 4.8.6 or higher. USE_HTAGS = NO # If the VERBATIM_HEADERS tag is set to YES (the default) then Doxygen # will generate a verbatim copy of the header file for each class for # which an include is specified. Set to NO to disable this. VERBATIM_HEADERS = YES #--------------------------------------------------------------------------- # configuration options related to the alphabetical class index #--------------------------------------------------------------------------- # If the ALPHABETICAL_INDEX tag is set to YES, an alphabetical index # of all compounds will be generated. Enable this if the project # contains a lot of classes, structs, unions or interfaces. ALPHABETICAL_INDEX = NO # If the alphabetical index is enabled (see ALPHABETICAL_INDEX) then # the COLS_IN_ALPHA_INDEX tag can be used to specify the number of columns # in which this list will be split (can be a number in the range [1..20]) COLS_IN_ALPHA_INDEX = 5 # In case all classes in a project start with a common prefix, all # classes will be put under the same header in the alphabetical index. # The IGNORE_PREFIX tag can be used to specify one or more prefixes that # should be ignored while generating the index headers. IGNORE_PREFIX = #--------------------------------------------------------------------------- # configuration options related to the HTML output #--------------------------------------------------------------------------- # If the GENERATE_HTML tag is set to YES (the default) Doxygen will # generate HTML output. GENERATE_HTML = YES # The HTML_OUTPUT tag is used to specify where the HTML docs will be put. # If a relative path is entered the value of OUTPUT_DIRECTORY will be # put in front of it. If left blank `html' will be used as the default path. HTML_OUTPUT = html # The HTML_FILE_EXTENSION tag can be used to specify the file extension for # each generated HTML page (for example: .htm,.php,.asp). If it is left blank # doxygen will generate files with .html extension. HTML_FILE_EXTENSION = .html # The HTML_HEADER tag can be used to specify a personal HTML header for # each generated HTML page. If it is left blank doxygen will generate a # standard header. HTML_HEADER = # The HTML_FOOTER tag can be used to specify a personal HTML footer for # each generated HTML page. If it is left blank doxygen will generate a # standard footer. HTML_FOOTER = # The HTML_STYLESHEET tag can be used to specify a user-defined cascading # style sheet that is used by each HTML page. It can be used to # fine-tune the look of the HTML output. If the tag is left blank doxygen # will generate a default style sheet. Note that doxygen will try to copy # the style sheet file to the HTML output directory, so don't put your own # stylesheet in the HTML output directory as well, or it will be erased! HTML_STYLESHEET = # If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes, # files or namespaces will be aligned in HTML using tables. If set to # NO a bullet list will be used. HTML_ALIGN_MEMBERS = YES # If the GENERATE_HTMLHELP tag is set to YES, additional index files # will be generated that can be used as input for tools like the # Microsoft HTML help workshop to generate a compressed HTML help file (.chm) # of the generated HTML documentation. GENERATE_HTMLHELP = NO # If the GENERATE_HTMLHELP tag is set to YES, the CHM_FILE tag can # be used to specify the file name of the resulting .chm file. You # can add a path in front of the file if the result should not be # written to the html output directory. CHM_FILE = # If the GENERATE_HTMLHELP tag is set to YES, the HHC_LOCATION tag can # be used to specify the location (absolute path including file name) of # the HTML help compiler (hhc.exe). If non-empty doxygen will try to run # the HTML help compiler on the generated index.hhp. HHC_LOCATION = # If the GENERATE_HTMLHELP tag is set to YES, the GENERATE_CHI flag # controls if a separate .chi index file is generated (YES) or that # it should be included in the master .chm file (NO). GENERATE_CHI = NO # If the GENERATE_HTMLHELP tag is set to YES, the BINARY_TOC flag # controls whether a binary table of contents is generated (YES) or a # normal table of contents (NO) in the .chm file. BINARY_TOC = NO # The TOC_EXPAND flag can be set to YES to add extra items for group members # to the contents of the HTML help documentation and to the tree view. TOC_EXPAND = NO # The DISABLE_INDEX tag can be used to turn on/off the condensed index at # top of each HTML page. The value NO (the default) enables the index and # the value YES disables it. DISABLE_INDEX = NO # This tag can be used to set the number of enum values (range [1..20]) # that doxygen will group on one line in the generated HTML documentation. ENUM_VALUES_PER_LINE = 4 # If the GENERATE_TREEVIEW tag is set to YES, a side panel will be # generated containing a tree-like index structure (just like the one that # is generated for HTML Help). For this to work a browser that supports # JavaScript, DHTML, CSS and frames is required (for instance Mozilla 1.0+, # Netscape 6.0+, Internet explorer 5.0+, or Konqueror). Windows users are # probably better off using the HTML help feature. GENERATE_TREEVIEW = NO # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be # used to set the initial width (in pixels) of the frame in which the tree # is shown. TREEVIEW_WIDTH = 250 #--------------------------------------------------------------------------- # configuration options related to the LaTeX output #--------------------------------------------------------------------------- # If the GENERATE_LATEX tag is set to YES (the default) Doxygen will # generate Latex output. GENERATE_LATEX = NO # The LATEX_OUTPUT tag is used to specify where the LaTeX docs will be put. # If a relative path is entered the value of OUTPUT_DIRECTORY will be # put in front of it. If left blank `latex' will be used as the default path. LATEX_OUTPUT = latex # The LATEX_CMD_NAME tag can be used to specify the LaTeX command name to be # invoked. If left blank `latex' will be used as the default command name. LATEX_CMD_NAME = latex # The MAKEINDEX_CMD_NAME tag can be used to specify the command name to # generate index for LaTeX. If left blank `makeindex' will be used as the # default command name. MAKEINDEX_CMD_NAME = makeindex # If the COMPACT_LATEX tag is set to YES Doxygen generates more compact # LaTeX documents. This may be useful for small projects and may help to # save some trees in general. COMPACT_LATEX = NO # The PAPER_TYPE tag can be used to set the paper type that is used # by the printer. Possible values are: a4, a4wide, letter, legal and # executive. If left blank a4wide will be used. PAPER_TYPE = a4wide # The EXTRA_PACKAGES tag can be to specify one or more names of LaTeX # packages that should be included in the LaTeX output. EXTRA_PACKAGES = # The LATEX_HEADER tag can be used to specify a personal LaTeX header for # the generated latex document. The header should contain everything until # the first chapter. If it is left blank doxygen will generate a # standard header. Notice: only use this tag if you know what you are doing! LATEX_HEADER = # If the PDF_HYPERLINKS tag is set to YES, the LaTeX that is generated # is prepared for conversion to pdf (using ps2pdf). The pdf file will # contain links (just like the HTML output) instead of page references # This makes the output suitable for online browsing using a pdf viewer. PDF_HYPERLINKS = NO # If the USE_PDFLATEX tag is set to YES, pdflatex will be used instead of # plain latex in the generated Makefile. Set this option to YES to get a # higher quality PDF documentation. USE_PDFLATEX = NO # If the LATEX_BATCHMODE tag is set to YES, doxygen will add the \\batchmode. # command to the generated LaTeX files. This will instruct LaTeX to keep # running if errors occur, instead of asking the user for help. # This option is also used when generating formulas in HTML. LATEX_BATCHMODE = NO # If LATEX_HIDE_INDICES is set to YES then doxygen will not # include the index chapters (such as File Index, Compound Index, etc.) # in the output. LATEX_HIDE_INDICES = NO #--------------------------------------------------------------------------- # configuration options related to the RTF output #--------------------------------------------------------------------------- # If the GENERATE_RTF tag is set to YES Doxygen will generate RTF output # The RTF output is optimized for Word 97 and may not look very pretty with # other RTF readers or editors. GENERATE_RTF = NO # The RTF_OUTPUT tag is used to specify where the RTF docs will be put. # If a relative path is entered the value of OUTPUT_DIRECTORY will be # put in front of it. If left blank `rtf' will be used as the default path. RTF_OUTPUT = rtf # If the COMPACT_RTF tag is set to YES Doxygen generates more compact # RTF documents. This may be useful for small projects and may help to # save some trees in general. COMPACT_RTF = NO # If the RTF_HYPERLINKS tag is set to YES, the RTF that is generated # will contain hyperlink fields. The RTF file will # contain links (just like the HTML output) instead of page references. # This makes the output suitable for online browsing using WORD or other # programs which support those fields. # Note: wordpad (write) and others do not support links. RTF_HYPERLINKS = NO # Load stylesheet definitions from file. Syntax is similar to doxygen's # config file, i.e. a series of assignments. You only have to provide # replacements, missing definitions are set to their default value. RTF_STYLESHEET_FILE = # Set optional variables used in the generation of an rtf document. # Syntax is similar to doxygen's config file. RTF_EXTENSIONS_FILE = #--------------------------------------------------------------------------- # configuration options related to the man page output #--------------------------------------------------------------------------- # If the GENERATE_MAN tag is set to YES (the default) Doxygen will # generate man pages GENERATE_MAN = NO # The MAN_OUTPUT tag is used to specify where the man pages will be put. # If a relative path is entered the value of OUTPUT_DIRECTORY will be # put in front of it. If left blank `man' will be used as the default path. MAN_OUTPUT = man # The MAN_EXTENSION tag determines the extension that is added to # the generated man pages (default is the subroutine's section .3) MAN_EXTENSION = .3 # If the MAN_LINKS tag is set to YES and Doxygen generates man output, # then it will generate one additional man file for each entity # documented in the real man page(s). These additional files # only source the real man page, but without them the man command # would be unable to find the correct page. The default is NO. MAN_LINKS = NO #--------------------------------------------------------------------------- # configuration options related to the XML output #--------------------------------------------------------------------------- # If the GENERATE_XML tag is set to YES Doxygen will # generate an XML file that captures the structure of # the code including all documentation. GENERATE_XML = NO # The XML_OUTPUT tag is used to specify where the XML pages will be put. # If a relative path is entered the value of OUTPUT_DIRECTORY will be # put in front of it. If left blank `xml' will be used as the default path. XML_OUTPUT = xml # The XML_SCHEMA tag can be used to specify an XML schema, # which can be used by a validating XML parser to check the # syntax of the XML files. XML_SCHEMA = # The XML_DTD tag can be used to specify an XML DTD, # which can be used by a validating XML parser to check the # syntax of the XML files. XML_DTD = # If the XML_PROGRAMLISTING tag is set to YES Doxygen will # dump the program listings (including syntax highlighting # and cross-referencing information) to the XML output. Note that # enabling this will significantly increase the size of the XML output. XML_PROGRAMLISTING = YES #--------------------------------------------------------------------------- # configuration options for the AutoGen Definitions output #--------------------------------------------------------------------------- # If the GENERATE_AUTOGEN_DEF tag is set to YES Doxygen will # generate an AutoGen Definitions (see autogen.sf.net) file # that captures the structure of the code including all # documentation. Note that this feature is still experimental # and incomplete at the moment. GENERATE_AUTOGEN_DEF = NO #--------------------------------------------------------------------------- # configuration options related to the Perl module output #--------------------------------------------------------------------------- # If the GENERATE_PERLMOD tag is set to YES Doxygen will # generate a Perl module file that captures the structure of # the code including all documentation. Note that this # feature is still experimental and incomplete at the # moment. GENERATE_PERLMOD = NO # If the PERLMOD_LATEX tag is set to YES Doxygen will generate # the necessary Makefile rules, Perl scripts and LaTeX code to be able # to generate PDF and DVI output from the Perl module output. PERLMOD_LATEX = NO # If the PERLMOD_PRETTY tag is set to YES the Perl module output will be # nicely formatted so it can be parsed by a human reader. This is useful # if you want to understand what is going on. On the other hand, if this # tag is set to NO the size of the Perl module output will be much smaller # and Perl will parse it just the same. PERLMOD_PRETTY = YES # The names of the make variables in the generated doxyrules.make file # are prefixed with the string contained in PERLMOD_MAKEVAR_PREFIX. # This is useful so different doxyrules.make files included by the same # Makefile don't overwrite each other's variables. PERLMOD_MAKEVAR_PREFIX = #--------------------------------------------------------------------------- # Configuration options related to the preprocessor #--------------------------------------------------------------------------- # If the ENABLE_PREPROCESSING tag is set to YES (the default) Doxygen will # evaluate all C-preprocessor directives found in the sources and include # files. ENABLE_PREPROCESSING = YES # If the MACRO_EXPANSION tag is set to YES Doxygen will expand all macro # names in the source code. If set to NO (the default) only conditional # compilation will be performed. Macro expansion can be done in a controlled # way by setting EXPAND_ONLY_PREDEF to YES. MACRO_EXPANSION = NO # If the EXPAND_ONLY_PREDEF and MACRO_EXPANSION tags are both set to YES # then the macro expansion is limited to the macros specified with the # PREDEFINED and EXPAND_AS_DEFINED tags. EXPAND_ONLY_PREDEF = NO # If the SEARCH_INCLUDES tag is set to YES (the default) the includes files # in the INCLUDE_PATH (see below) will be search if a #include is found. SEARCH_INCLUDES = YES # The INCLUDE_PATH tag can be used to specify one or more directories that # contain include files that are not input files but should be processed by # the preprocessor. INCLUDE_PATH = # You can use the INCLUDE_FILE_PATTERNS tag to specify one or more wildcard # patterns (like *.h and *.hpp) to filter out the header-files in the # directories. If left blank, the patterns specified with FILE_PATTERNS will # be used. INCLUDE_FILE_PATTERNS = # The PREDEFINED tag can be used to specify one or more macro names that # are defined before the preprocessor is started (similar to the -D option of # gcc). The argument of the tag is a list of macros of the form: name # or name=definition (no spaces). If the definition and the = are # omitted =1 is assumed. To prevent a macro definition from being # undefined via #undef or recursively expanded use the := operator # instead of the = operator. PREDEFINED = # If the MACRO_EXPANSION and EXPAND_ONLY_PREDEF tags are set to YES then # this tag can be used to specify a list of macro names that should be expanded. # The macro definition that is found in the sources will be used. # Use the PREDEFINED tag if you want to use a different macro definition. EXPAND_AS_DEFINED = # If the SKIP_FUNCTION_MACROS tag is set to YES (the default) then # doxygen's preprocessor will remove all function-like macros that are alone # on a line, have an all uppercase name, and do not end with a semicolon. Such # function macros are typically used for boiler-plate code, and will confuse # the parser if not removed. SKIP_FUNCTION_MACROS = YES #--------------------------------------------------------------------------- # Configuration::additions related to external references #--------------------------------------------------------------------------- # The TAGFILES option can be used to specify one or more tagfiles. # Optionally an initial location of the external documentation # can be added for each tagfile. The format of a tag file without # this location is as follows: # TAGFILES = file1 file2 ... # Adding location for the tag files is done as follows: # TAGFILES = file1=loc1 "file2 = loc2" ... # where "loc1" and "loc2" can be relative or absolute paths or # URLs. If a location is present for each tag, the installdox tool # does not have to be run to correct the links. # Note that each tag file must have a unique name # (where the name does NOT include the path) # If a tag file is not located in the directory in which doxygen # is run, you must also specify the path to the tagfile here. TAGFILES = # When a file name is specified after GENERATE_TAGFILE, doxygen will create # a tag file that is based on the input files it reads. GENERATE_TAGFILE = # If the ALLEXTERNALS tag is set to YES all external classes will be listed # in the class index. If set to NO only the inherited external classes # will be listed. ALLEXTERNALS = NO # If the EXTERNAL_GROUPS tag is set to YES all external groups will be listed # in the modules index. If set to NO, only the current project's groups will # be listed. EXTERNAL_GROUPS = YES # The PERL_PATH should be the absolute path and name of the perl script # interpreter (i.e. the result of `which perl'). PERL_PATH = /usr/bin/perl #--------------------------------------------------------------------------- # Configuration options related to the dot tool #--------------------------------------------------------------------------- # If the CLASS_DIAGRAMS tag is set to YES (the default) Doxygen will # generate a inheritance diagram (in HTML, RTF and LaTeX) for classes with base # or super classes. Setting the tag to NO turns the diagrams off. Note that # this option is superseded by the HAVE_DOT option below. This is only a # fallback. It is recommended to install and use dot, since it yields more # powerful graphs. CLASS_DIAGRAMS = YES # If set to YES, the inheritance and collaboration graphs will hide # inheritance and usage relations if the target is undocumented # or is not a class. HIDE_UNDOC_RELATIONS = YES # If you set the HAVE_DOT tag to YES then doxygen will assume the dot tool is # available from the path. This tool is part of Graphviz, a graph visualization # toolkit from AT&T and Lucent Bell Labs. The other options in this section # have no effect if this option is set to NO (the default) HAVE_DOT = YES # If the CLASS_GRAPH and HAVE_DOT tags are set to YES then doxygen # will generate a graph for each documented class showing the direct and # indirect inheritance relations. Setting this tag to YES will force the # the CLASS_DIAGRAMS tag to NO. CLASS_GRAPH = YES # If the COLLABORATION_GRAPH and HAVE_DOT tags are set to YES then doxygen # will generate a graph for each documented class showing the direct and # indirect implementation dependencies (inheritance, containment, and # class references variables) of the class with other documented classes. COLLABORATION_GRAPH = YES # If the GROUP_GRAPHS and HAVE_DOT tags are set to YES then doxygen # will generate a graph for groups, showing the direct groups dependencies GROUP_GRAPHS = YES # If the UML_LOOK tag is set to YES doxygen will generate inheritance and # collaboration diagrams in a style similar to the OMG's Unified Modeling # Language. UML_LOOK = YES # If set to YES, the inheritance and collaboration graphs will show the # relations between templates and their instances. TEMPLATE_RELATIONS = YES # If the ENABLE_PREPROCESSING, SEARCH_INCLUDES, INCLUDE_GRAPH, and HAVE_DOT # tags are set to YES then doxygen will generate a graph for each documented # file showing the direct and indirect include dependencies of the file with # other documented files. INCLUDE_GRAPH = YES # If the ENABLE_PREPROCESSING, SEARCH_INCLUDES, INCLUDED_BY_GRAPH, and # HAVE_DOT tags are set to YES then doxygen will generate a graph for each # documented header file showing the documented files that directly or # indirectly include this file. INCLUDED_BY_GRAPH = YES # If the CALL_GRAPH and HAVE_DOT tags are set to YES then doxygen will # generate a call dependency graph for every global function or class method. # Note that enabling this option will significantly increase the time of a run. # So in most cases it will be better to enable call graphs for selected # functions only using the \callgraph command. CALL_GRAPH = YES # If the CALLER_GRAPH and HAVE_DOT tags are set to YES then doxygen will # generate a caller dependency graph for every global function or class method. # Note that enabling this option will significantly increase the time of a run. # So in most cases it will be better to enable caller graphs for selected # functions only using the \callergraph command. CALLER_GRAPH = YES # If the GRAPHICAL_HIERARCHY and HAVE_DOT tags are set to YES then doxygen # will graphical hierarchy of all classes instead of a textual one. GRAPHICAL_HIERARCHY = YES # If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES # then doxygen will show the dependencies a directory has on other directories # in a graphical way. The dependency relations are determined by the #include # relations between the files in the directories. DIRECTORY_GRAPH = YES # The DOT_IMAGE_FORMAT tag can be used to set the image format of the images # generated by dot. Possible values are png, jpg, or gif # If left blank png will be used. DOT_IMAGE_FORMAT = png # The tag DOT_PATH can be used to specify the path where the dot tool can be # found. If left blank, it is assumed the dot tool can be found in the path. DOT_PATH = # The DOTFILE_DIRS tag can be used to specify one or more directories that # contain dot files that are included in the documentation (see the # \dotfile command). DOTFILE_DIRS = # The MAX_DOT_GRAPH_WIDTH tag can be used to set the maximum allowed width # (in pixels) of the graphs generated by dot. If a graph becomes larger than # this value, doxygen will try to truncate the graph, so that it fits within # the specified constraint. Beware that most browsers cannot cope with very # large images. MAX_DOT_GRAPH_WIDTH = 1024 # The MAX_DOT_GRAPH_HEIGHT tag can be used to set the maximum allows height # (in pixels) of the graphs generated by dot. If a graph becomes larger than # this value, doxygen will try to truncate the graph, so that it fits within # the specified constraint. Beware that most browsers cannot cope with very # large images. MAX_DOT_GRAPH_HEIGHT = 1024 # The MAX_DOT_GRAPH_DEPTH tag can be used to set the maximum depth of the # graphs generated by dot. A depth value of 3 means that only nodes reachable # from the root by following a path via at most 3 edges will be shown. Nodes # that lay further from the root node will be omitted. Note that setting this # option to 1 or 2 may greatly reduce the computation time needed for large # code bases. Also note that a graph may be further truncated if the graph's # image dimensions are not sufficient to fit the graph (see MAX_DOT_GRAPH_WIDTH # and MAX_DOT_GRAPH_HEIGHT). If 0 is used for the depth value (the default), # the graph is not depth-constrained. MAX_DOT_GRAPH_DEPTH = 0 # Set the DOT_TRANSPARENT tag to YES to generate images with a transparent # background. This is disabled by default, which results in a white background. # Warning: Depending on the platform used, enabling this option may lead to # badly anti-aliased labels on the edges of a graph (i.e. they become hard to # read). DOT_TRANSPARENT = YES # Set the DOT_MULTI_TARGETS tag to YES allow dot to generate multiple output # files in one run (i.e. multiple -o and -T options on the command line). This # makes dot run faster, but since only newer versions of dot (>1.8.10) # support this, this feature is disabled by default. DOT_MULTI_TARGETS = YES # If the GENERATE_LEGEND tag is set to YES (the default) Doxygen will # generate a legend page explaining the meaning of the various boxes and # arrows in the dot generated graphs. GENERATE_LEGEND = YES # If the DOT_CLEANUP tag is set to YES (the default) Doxygen will # remove the intermediate dot files that are used to generate # the various graphs. DOT_CLEANUP = YES #--------------------------------------------------------------------------- # Configuration::additions related to the search engine #--------------------------------------------------------------------------- # The SEARCHENGINE tag specifies whether or not a search engine should be # used. If set to NO the values of all tags below this one will be ignored. 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using namespace rel_ops; using namespace boost::lambda; using boost::tie; #define PROGRAM "abyss-filtergraph" static const char VERSION_MESSAGE[] = PROGRAM " (" PACKAGE_NAME ") " VERSION "\n" "Written by Tony Raymond.\n" "\n" "Copyright 2013 Canada's Michael Smith Genome Science Centre\n"; static const char USAGE_MESSAGE[] = "Usage: " PROGRAM " [OPTION]... ADJ\n" "Remove short contigs that do not contribute any relevant\n" "information to the assembly.\n" "\n" " Arguments:\n" "\n" " ADJ contig adjacency graph\n" "\n" " Options:\n" "\n" " -k, --kmer=N k-mer size\n" " -T, --island=N remove islands shorter than N [0]\n" " -t, --tip=N remove tips shorter than N [0]\n" " -l, --length=N remove contigs shorter than N [0]\n" " --shim remove filler contigs that only contribute\n" " to adjacency [default]\n" " --no-shim disable filler contigs removal\n" " -m, --min-overlap=N require a minimum overlap of N bases [10]\n" " --assemble assemble unambiguous paths\n" " --no-assemble disable assembling of paths [default]\n" " -g, --graph=FILE write the contig adjacency graph to FILE\n" " -i, --ignore=FILE ignore contigs seen in FILE\n" " -r, --remove=FILE remove contigs seen in FILE\n" " --adj output the graph in adj format [default]\n" " --asqg output the graph in asqg format\n" " --dot output the graph in dot format\n" " --dot-meancov same as above but give the mean coverage\n" " --sam output the graph in SAM format\n" " -v, --verbose display verbose output\n" " --help display this help and exit\n" " --version output version information and exit\n" "\n" "Report bugs to <" PACKAGE_BUGREPORT ">.\n"; namespace opt { unsigned k; // used by ContigProperties /** Remove island contigs less than this length. */ static unsigned minIslandLen = 0; /** Remove tips less than this length. */ static unsigned minTipLen = 0; /** Remove all contigs less than this length. */ static unsigned minLen = 0; /** Remove short contigs that don't contribute any sequence. */ static int shim = 1; /** Assemble unambiguous paths. */ static int assemble = 0; /** Write the contig adjacency graph to this file. */ static string graphPath; /** Contigs to ignore. */ static string ignorePath; /** Contigs to remove. */ static string removePath; /** The minimum overlap allowed between two contigs. */ static int minOverlap = 10; /** Output graph format. */ int format = ADJ; // used by ContigProperties } static const char shortopts[] = "g:i:r:k:l:m:t:T:v"; enum { OPT_HELP = 1, OPT_VERSION }; static const struct option longopts[] = { { "adj", no_argument, &opt::format, ADJ }, { "asqg", no_argument, &opt::format, ASQG }, { "dot", no_argument, &opt::format, DOT }, { "dot-meancov", no_argument, &opt::format, DOT_MEANCOV }, { "sam", no_argument, &opt::format, SAM }, { "graph", required_argument, NULL, 'g' }, { "ignore", required_argument, NULL, 'i' }, { "remove", required_argument, NULL, 'r' }, { "kmer", required_argument, NULL, 'k' }, { "island", required_argument, NULL, 'T' }, { "tip", required_argument, NULL, 't' }, { "length", required_argument, NULL, 'l' }, { "shim", no_argument, &opt::shim, 1 }, { "no-shim", no_argument, &opt::shim, 0 }, { "assemble", no_argument, &opt::assemble, 1 }, { "no-assemble", no_argument, &opt::assemble, 0 }, { "min-overlap", required_argument, NULL, 'm' }, { "verbose", no_argument, NULL, 'v' }, { "help", no_argument, NULL, OPT_HELP }, { "version", no_argument, NULL, OPT_VERSION }, { NULL, 0, NULL, 0 } }; static vector g_removed; /** Contig adjacency graph. */ typedef ContigGraph > Graph; typedef Graph::vertex_descriptor vertex_descriptor; /** Data for verbose output. */ static struct { unsigned removed; unsigned tails; unsigned too_long; unsigned too_complex; unsigned self_adj; unsigned checked; unsigned parallel_edge; } g_count; /** Returns if the contig can be removed from the graph. */ static bool removable(const Graph* pg, vertex_descriptor v) { typedef graph_traits GTraits; typedef GTraits::out_edge_iterator OEit; typedef GTraits::in_edge_iterator IEit; typedef GTraits::vertex_descriptor V; const Graph& g = *pg; // Check if previously removed if (get(vertex_removed, g, v)) { g_count.removed++; return false; } // Check for tails if (out_degree(v, g) == 0 || in_degree(v, g) == 0) { g_count.tails++; return false; } // Check that the result will be less complex that the original if (!(out_degree(v, g) == 1 && in_degree(v, g) > 1) && !(out_degree(v, g) > 1 && in_degree(v, g) == 1)) { g_count.too_complex++; return false; } // Check if self adjacent OEit oei0, oei1; tie(oei0, oei1) = out_edges(v, g); for (OEit vw = oei0; vw != oei1; ++vw) { V w = target(*vw, g); V vc = get(vertex_complement, g, v); if (v == w || vc == w) { g_count.self_adj++; return false; } } // Check that removing the contig will result in adjacent contigs // overlapping by at least opt::minOverlap. IEit iei0, iei1; tie(iei0, iei1) = in_edges(v, g); IEit maxuv = iei0; for (IEit uv = iei0; uv != iei1; ++uv) if (g[*maxuv].distance < g[*uv].distance) maxuv = uv; OEit maxvw = oei0; for (OEit vw = oei0; vw != oei1; ++vw) if (g[*maxvw].distance < g[*vw].distance) maxvw = vw; if (g[*maxuv].distance + (int)g[v].length + g[*maxvw].distance > -opt::minOverlap) { g_count.too_long++; return false; } return true; } /** Data to store information of an edge. */ struct EdgeInfo { vertex_descriptor u; vertex_descriptor w; edge_bundle_type::type ep; EdgeInfo(vertex_descriptor u, vertex_descriptor w, int ep) : u(u), w(w), ep(ep) {} EdgeInfo() : u(), w(), ep() {} }; /** Returns a list of edges that may be added when the vertex v is * removed. */ static bool findNewEdges(const Graph& g, vertex_descriptor v, vector& eds, vector& markedContigs) { typedef graph_traits GTraits; typedef GTraits::vertex_descriptor V; typedef GTraits::out_edge_iterator OEit; typedef GTraits::in_edge_iterator IEit; IEit iei0, iei1; tie(iei0, iei1) = in_edges(v, g); OEit oei0, oei1; tie(oei0, oei1) = out_edges(v, g); vector marked; // if not marked and longest link LE contig length. // for every edge from u->v and v->w we must add an edge u->w for (IEit uv = iei0; uv != iei1; ++uv) { for (OEit vw = oei0; vw != oei1; ++vw) { int x = g[*uv].distance + (int)g[v].length + g[*vw].distance; assert(x <= 0); EdgeInfo ed(source(*uv, g), target(*vw, g), x); eds.push_back(ed); if (out_degree(v, g) > 1) marked.push_back(ed.u); if (in_degree(v, g) > 1) marked.push_back(ed.w); // Don't remove a vertex if the result is a parallel edge. if (edge(ed.u, ed.w, g).second) { g_count.parallel_edge++; return false; } } } for (vector::const_iterator it = marked.begin(); it != marked.end(); it++) markedContigs[get(vertex_index, g, *it)] = true; return true; } /** Adds all edges described in the vector eds. */ static void addNewEdges(Graph& g, const vector& eds) { for (vector::const_iterator edsit = eds.begin(); edsit != eds.end(); ++edsit) { assert(!edge(edsit->u, edsit->w, g).second); assert(edsit->ep.distance <= -opt::minOverlap); add_edge(edsit->u, edsit->w, edsit->ep, g); } } static void removeContig(vertex_descriptor v, Graph& g) { clear_vertex(v, g); remove_vertex(v, g); g_removed.push_back(get(vertex_contig_index, g, v)); g_count.removed++; } /** Remove the specified contig from the adjacency graph. */ static void removeContigs(Graph& g, vector& sc) { typedef graph_traits GTraits; typedef GTraits::vertex_descriptor V; typedef GTraits::out_edge_iterator OEit; typedef GTraits::in_edge_iterator IEit; vector out; out.reserve(sc.size()); vector markedContigs(g.num_vertices()); for (vector::iterator it = sc.begin(); it != sc.end(); ++it) { V v = *it; if (opt::verbose > 0 && ++g_count.checked % 10000000 == 0) cerr << "Removed " << g_count.removed << "/" << g_count.checked << " vertices that have been checked.\n"; if (markedContigs[get(vertex_index, g, v)]) { out.push_back(v); continue; } if (!removable(&g, v)) continue; vector eds; if (findNewEdges(g, v, eds, markedContigs)) addNewEdges(g, eds); else continue; removeContig(v, g); } sc.swap(out); } /** Return the value of the bit at the specified index. */ struct Marked : unary_function { typedef vector Data; Marked(const Graph& g, const Data& data) : m_g(g), m_data(data) { } bool operator()(vertex_descriptor u) const { return m_data[get(vertex_contig_index, m_g, u)]; } private: const Graph& m_g; const Data& m_data; }; /** Finds all potentially removable contigs in the graph. */ static void findShortContigs(const Graph& g, const vector& seen, vector& sc) { typedef graph_traits GTraits; typedef GTraits::vertex_iterator Vit; Vit first, second; tie(first, second) = vertices(g); copy_if(first, second, back_inserter(sc), !bind(Marked(g, seen), _1) && bind(removable, &g, _1)); } /** Functor used for sorting contigs based on degree, then size, * and then ID. */ struct sortContigs { const Graph& g; sortContigs(const Graph& g) : g(g) {} template bool operator() (V a, V b) { const ContigProperties& ap = g[a]; const ContigProperties& bp = g[b]; unsigned dega = out_degree(a, g) * in_degree(a, g); unsigned degb = out_degree(b, g) * in_degree(b, g); return dega != degb ? dega < degb : ap.length != bp.length ? ap.length < bp.length : a < b; } }; struct ShorterThanX : unary_function { const Graph& g; const vector& seen; size_t x; ShorterThanX(const Graph& g, const vector& seen, size_t x) : g(g), seen(seen), x(x) { } bool operator()(vertex_descriptor y) const { return g[y].length < x && !get(vertex_removed, g, y) && !seen[get(vertex_contig_index, g, y)]; } }; static void removeShims(Graph& g, const vector& seen) { if (opt::verbose > 0) cerr << "Removing shim contigs from the graph...\n"; vector shortContigs; findShortContigs(g, seen, shortContigs); for (unsigned i = 0; !shortContigs.empty(); ++i) { if (opt::verbose > 0) cerr << "Pass " << i + 1 << ": Checking " << shortContigs.size() << " contigs.\n"; sort(shortContigs.begin(), shortContigs.end(), sortContigs(g)); removeContigs(g, shortContigs); } if (opt::verbose > 0) { cerr << "Shim removal stats:\n"; cerr << "Removed: " << g_count.removed/2 << " Too Complex: " << g_count.too_complex/2 << " Tails: " << g_count.tails/2 << " Too Long: " << g_count.too_long/2 << " Self Adjacent: " << g_count.self_adj/2 << " Parallel Edges: " << g_count.parallel_edge/2 << '\n'; } } static void removeShortContigs(Graph& g, const vector& seen) { typedef graph_traits GTraits; typedef GTraits::vertex_iterator Vit; typedef GTraits::vertex_descriptor V; Vit first, second; tie(first, second) = vertices(g); vector sc; copy_if(first, second, back_inserter(sc), ShorterThanX(g, seen, opt::minLen)); remove_vertex_if(g, sc.begin(), sc.end(), True()); transform(sc.begin(), sc.end(), back_inserter(g_removed), mem_fun_ref(&ContigNode::contigIndex)); if (opt::verbose > 0) cerr << "Removed " << sc.size()/2 << " short contigs.\n"; } int main(int argc, char** argv) { string commandLine; { ostringstream ss; char** last = argv + argc - 1; copy(argv, last, ostream_iterator(ss, " ")); ss << *last; commandLine = ss.str(); } bool die = false; for (int c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;) { istringstream arg(optarg != NULL ? optarg : ""); switch (c) { case '?': die = true; break; case 'l': arg >> opt::minLen; break; case 'm': arg >> opt::minOverlap; break; case 'g': arg >> opt::graphPath; break; case 'i': arg >> opt::ignorePath; break; case 'r': arg >> opt::removePath; break; case 'k': arg >> opt::k; break; case 'T': arg >> opt::minIslandLen; break; case 't': arg >> opt::minTipLen; break; case 'v': opt::verbose++; break; case OPT_HELP: cout << USAGE_MESSAGE; exit(EXIT_SUCCESS); case OPT_VERSION: cout << VERSION_MESSAGE; exit(EXIT_SUCCESS); } if (optarg != NULL && !arg.eof()) { cerr << PROGRAM ": invalid option: `-" << (char)c << optarg << "'\n"; exit(EXIT_FAILURE); } } if (opt::minOverlap < 0) { cerr << PROGRAM ": " << "--min-overlap must be a positive integer.\n"; die = true; } if (opt::k <= 0) { cerr << PROGRAM ": " << "missing -k,--kmer option\n"; die = true; } if (argc - optind < 1) { cerr << PROGRAM ": missing arguments\n"; die = true; } if (argc - optind > 1) { cerr << PROGRAM ": too many arguments\n"; die = true; } if (die) { cerr << "Try `" << PROGRAM << " --help' for more information.\n"; exit(EXIT_FAILURE); } Graph g; // Read the contig adjacency graph. { string adjPath(argv[optind++]); if (opt::verbose > 0) cerr << "Loading graph from file: " << adjPath << '\n'; ifstream fin(adjPath.c_str()); assert_good(fin, adjPath); fin >> g; assert(fin.eof()); } // Read the set of contigs to ignore. vector seen(num_vertices(g) / 2); if (!opt::ignorePath.empty()) { ifstream in(opt::ignorePath.c_str()); assert_good(in, opt::ignorePath); markSeenInPath(in, seen); } if (opt::verbose > 0) { cerr << "Graph stats before:\n"; printGraphStats(cerr, g); } // Remove list of contigs if (!opt::removePath.empty()) { ifstream in(opt::removePath.c_str()); assert(in.good()); string s; size_t b = g_removed.size(); while (in >> s) { size_t i = get(g_contigNames, s); removeContig(ContigNode(i,0), g); } assert(in.eof()); if (opt::verbose) cerr << "Removed " << g_removed.size() - b << " contigs.\n"; } // Remove shims. if (opt::shim) removeShims(g, seen); // Remove islands. if (opt::minIslandLen > 0) { size_t s = g_removed.size(); removeIslands_if(g, back_inserter(g_removed), ShorterThanX(g, seen, opt::minIslandLen)); if (opt::verbose) cerr << "Removed " << g_removed.size() - s << " islands.\n"; } // Remove tips. if (opt::minTipLen > 0) { size_t s = g_removed.size(); pruneTips_if(g, back_inserter(g_removed), ShorterThanX(g, seen, opt::minTipLen)); if (opt::verbose) cerr << "Removed " << g_removed.size() - s << " tips.\n"; } // Remove short contigs. if (opt::minLen > 0) removeShortContigs(g, seen); if (opt::verbose > 0) { cerr << "Graph stats after:\n"; printGraphStats(cerr, g); } sort(g_removed.begin(), g_removed.end()); g_removed.erase(unique(g_removed.begin(), g_removed.end()), g_removed.end()); for (vector::const_iterator it = g_removed.begin(); it != g_removed.end(); ++it) cout << get(g_contigNames, *it) << '\n'; // Assemble unambiguous paths. if (opt::assemble) { size_t numContigs = num_vertices(g) / 2; 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A kmer file is a serialized Google sparsehash. * Written by Shaun Jackman . */ #include "Sequence.h" #include "SequenceCollection.h" #include "Uncompress.h" #include #include #include #include #include using namespace std; #define PROGRAM "kmerprint" static const char VERSION_MESSAGE[] = PROGRAM " (" PACKAGE_NAME ") " VERSION "\n" "Written by Shaun Jackman.\n" "\n" "Copyright 2013 Shaun Jackman\n"; static const char USAGE_MESSAGE[] = "Usage: " PROGRAM " [OPTION]... GRAPH...\n" "Convert a binary de Bruijn graph to plain text.\n" "\n" " Arguments:\n" "\n" " GRAPH the binary de Bruijn graph\n" "\n" " Options:\n" "\n" " -k, --kmer=N length of a k-mer\n" " --ray output in Ray Cloud Browser format\n" " --tsv output in TSV format [default]\n" " --help display this help and exit\n" " --version output version information and exit\n" "\n" "Report bugs to <" PACKAGE_BUGREPORT ">.\n"; namespace opt { static unsigned k; static bool strands; /** The output field separator character. */ static int ofsInt = '\t'; static char ofs; } static const char shortopts[] = "k:"; enum { OPT_HELP = 1, OPT_VERSION }; static const struct option longopts[] = { { "kmer", required_argument, NULL, 'k' }, { "ray", no_argument, &opt::ofsInt, ';' }, { "tsv", no_argument, &opt::ofsInt, '\t' }, { "help", no_argument, NULL, OPT_HELP }, { "version", no_argument, NULL, OPT_VERSION }, { NULL, 0, NULL, 0 } }; static void print(const SequenceCollectionHash::value_type& seq) { const KmerData& data = seq.second; 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#define PROGRAM "SimpleGraph" static const char VERSION_MESSAGE[] = PROGRAM " (" PACKAGE_NAME ") " VERSION "\n" "Written by Jared Simpson and Shaun Jackman.\n" "\n" "Copyright 2013 Canada's Michael Smith Genome Science Centre\n"; static const char USAGE_MESSAGE[] = "Usage: " PROGRAM " [OPTION]... ADJ DIST\n" "Find paths through contigs using distance estimates.\n" "\n" " Arguments:\n" "\n" " ADJ adjacency of the contigs\n" " DIST distance estimates between the contigs\n" "\n" " Options:\n" "\n" " -k, --kmer=KMER_SIZE k-mer size\n" " -d, --dist-error=N acceptable error of a distance estimate\n" " default is 6 bp\n" " --max-cost=COST maximum computational cost\n" " -o, --out=FILE write result to FILE\n" " -j, --threads=THREADS use THREADS parallel threads [1]\n" " --extend extend unambiguous paths\n" " --no-extend do not extend unambiguous paths [default]\n" " --scaffold join contigs with Ns [default]\n" " --no-scaffold do not scaffold\n" " -v, --verbose display verbose output\n" " --help display this help and exit\n" " --version output version information and exit\n" "\n" "Report bugs to <" PACKAGE_BUGREPORT ">.\n"; namespace opt { unsigned k; // used by ContigProperties static unsigned threads = 1; static int extend; static int scaffold = 1; static int verbose; static string out; /** The acceptable error of a distance estimate. */ unsigned distanceError = 6; /** Output format */ int format = DIST; // used by Estimate } static const char shortopts[] = "d:j:k:o:v"; enum { OPT_HELP = 1, OPT_VERSION, OPT_MAX_COST }; static const struct option longopts[] = { { "kmer", required_argument, NULL, 'k' }, { "dist-error", required_argument, NULL, 'd' }, { "max-cost", required_argument, NULL, OPT_MAX_COST }, { "out", required_argument, NULL, 'o' }, { "extend", no_argument, &opt::extend, 1 }, { "no-extend", no_argument, &opt::extend, 0 }, { "scaffold", no_argument, &opt::scaffold, 1 }, { "no-scaffold", no_argument, &opt::scaffold, 0 }, { "threads", required_argument, NULL, 'j' }, { "verbose", no_argument, NULL, 'v' }, { "help", no_argument, NULL, OPT_HELP }, { "version", no_argument, NULL, OPT_VERSION }, { NULL, 0, NULL, 0 } }; static void generatePathsThroughEstimates(const Graph& g, const string& estPath); int main(int argc, char** argv) { bool die = false; for (int c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;) { istringstream arg(optarg != NULL ? optarg : ""); switch (c) { case '?': die = true; break; case 'd': arg >> opt::distanceError; break; case 'j': arg >> opt::threads; break; case 'k': arg >> opt::k; break; case OPT_MAX_COST: arg >> opt::maxCost; break; case 'o': arg >> opt::out; break; case 'v': opt::verbose++; break; case OPT_HELP: cout << USAGE_MESSAGE; exit(EXIT_SUCCESS); case OPT_VERSION: cout << VERSION_MESSAGE; exit(EXIT_SUCCESS); } if (optarg != NULL && !arg.eof()) { cerr << PROGRAM ": invalid option: `-" << (char)c << optarg << "'\n"; exit(EXIT_FAILURE); } } if (opt::k <= 0) { cerr << PROGRAM ": missing -k,--kmer option\n"; die = true; } if (opt::out.empty()) { cerr << PROGRAM ": " << "missing -o,--out option\n"; die = true; } if (argc - optind < 2) { cerr << PROGRAM ": missing arguments\n"; die = true; } else if (argc - optind > 2) { cerr << PROGRAM ": too many arguments\n"; die = true; } if (die) { cerr << "Try `" << PROGRAM << " --help' for more information.\n"; exit(EXIT_FAILURE); } string adjFile(argv[optind++]); string estFile(argv[optind++]); // Read the contig adjacency graph. if (opt::verbose > 0) cerr << "Reading `" << adjFile << "'..." << endl; ifstream fin(adjFile.c_str()); assert_good(fin, adjFile); Graph g; fin >> g; assert(fin.eof()); if (opt::verbose > 0) printGraphStats(cout, g); // try to find paths that match the distance estimates generatePathsThroughEstimates(g, estFile); } /** Print a set of constraints. */ static ostream& printConstraints(ostream& out, const Graph& g, const Constraints& s) { for (Constraints::const_iterator it = s.begin(); it != s.end(); ++it) out << ' ' << get(vertex_name, g, it->first) << ',' << it->second; return out; } /** Return the set of contigs that appear more than once in a single * solution. */ static set findRepeats(ContigID seed, const ContigPaths& solutions) { set repeats; for (ContigPaths::const_iterator solIt = solutions.begin(); solIt != solutions.end(); ++solIt) { map count; count[seed]++; for (ContigPath::const_iterator it = solIt->begin(); it != solIt->end(); ++it) count[it->contigIndex()]++; for (map::const_iterator it = count.begin(); it != count.end(); ++it) if (it->second > 1) repeats.insert(it->first); } return repeats; } /** The fewest number of pairs in a distance estimate. */ static unsigned g_minNumPairs = UINT_MAX; /** The fewest number of pairs used in a path. */ static unsigned g_minNumPairsUsed = UINT_MAX; static struct { unsigned totalAttempted; unsigned uniqueEnd; unsigned noPossiblePaths; unsigned noValidPaths; unsigned repeat; unsigned multiEnd; unsigned tooManySolutions; unsigned tooComplex; } stats; typedef graph_traits::vertex_descriptor vertex_descriptor; /** Return the distance from vertex u to v. */ static int getDistance(const Graph& g, vertex_descriptor u, vertex_descriptor v) { typedef graph_traits::edge_descriptor edge_descriptor; pair e = edge(u, v, g); assert(e.second); return g[e.first].distance; } /** Return the length of the specified path in k-mer. */ static unsigned calculatePathLength(const Graph& g, const ContigNode& origin, const ContigPath& path, size_t prefix = 0, size_t suffix = 0) { if (prefix + suffix == path.size()) return 0; assert(prefix + suffix < path.size()); int length = addProp(g, path.begin() + prefix, path.end() - suffix).length; // Account for the overlap on the left. vertex_descriptor u = prefix == 0 ? origin : path[prefix - 1]; length += getDistance(g, u, path[prefix]); assert(length > 0); return length; } /** Compare the lengths of two paths. */ struct ComparePathLength : binary_function { ComparePathLength(const Graph& g, const ContigNode& origin) : m_g(g), m_origin(origin) { } bool operator()(const ContigPath& a, const ContigPath& b) const { unsigned lenA = calculatePathLength(m_g, m_origin, a); unsigned lenB = calculatePathLength(m_g, m_origin, b); return lenA < lenB || lenA == lenB && a.size() < b.size(); } private: const Graph& m_g; const ContigNode& m_origin; }; /** Return an ambiguous path that agrees with all the given paths. */ static ContigPath constructAmbiguousPath(const Graph &g, const ContigNode& origin, const ContigPaths& paths) { assert(!paths.empty()); // Find the size of the smallest path. const ContigPath& firstSol = paths.front(); size_t min_len = firstSol.size(); for (ContigPaths::const_iterator it = paths.begin() + 1; it != paths.end(); ++it) min_len = min(min_len, it->size()); // Find the longest prefix. ContigPath vppath; size_t longestPrefix; bool commonPrefix = true; for (longestPrefix = 0; longestPrefix < min_len; longestPrefix++) { const ContigNode& common_path_node = firstSol[longestPrefix]; for (ContigPaths::const_iterator solIter = paths.begin(); solIter != paths.end(); ++solIter) { const ContigNode& pathnode = (*solIter)[longestPrefix]; if (pathnode != common_path_node) { // Found the longest prefix. commonPrefix = false; break; } } if (!commonPrefix) break; vppath.push_back(common_path_node); } // Find the longest suffix. ContigPath vspath; size_t longestSuffix; bool commonSuffix = true; for (longestSuffix = 0; longestSuffix < min_len-longestPrefix; longestSuffix++) { const ContigNode& common_path_node = firstSol[firstSol.size()-longestSuffix-1]; for (ContigPaths::const_iterator solIter = paths.begin(); solIter != paths.end(); ++solIter) { const ContigNode& pathnode = (*solIter)[solIter->size()-longestSuffix-1]; if (pathnode != common_path_node) { // Found the longest suffix. commonSuffix = false; break; } } if (!commonSuffix) break; vspath.push_back(common_path_node); } ContigPath out; out.reserve(vppath.size() + 1 + vspath.size()); out.insert(out.end(), vppath.begin(), vppath.end()); if (longestSuffix > 0) { const ContigPath& longestPath( *max_element(paths.begin(), paths.end(), ComparePathLength(g, origin))); unsigned length = calculatePathLength(g, origin, longestPath, longestPrefix, longestSuffix); // Account for the overlap on the right. int dist = length + getDistance(g, longestSuffix == longestPath.size() ? origin : *(longestPath.rbegin() + longestSuffix), *(longestPath.rbegin() + longestSuffix - 1)); // Add k-1 because it is the convention. int numN = dist + opt::k - 1; assert(numN > 0); out.push_back(ContigNode(numN, 'N')); out.insert(out.end(), vspath.rbegin(), vspath.rend()); } return out; } /** Return a map of contig IDs to their distance along this path. * Repeat contigs, which would have more than one position, are not * represented in this map. */ map makeDistanceMap(const Graph& g, const ContigNode& origin, const ContigPath& path) { map distances; int distance = 0; for (ContigPath::const_iterator it = path.begin(); it != path.end(); ++it) { vertex_descriptor u = it == path.begin() ? origin : *(it - 1); vertex_descriptor v = *it; distance += getDistance(g, u, v); bool inserted = distances.insert( make_pair(v, distance)).second; if (!inserted) { // Mark this contig as a repeat. distances[v] = INT_MIN; } distance += g[v].length; } // Remove the repeats. for (map::iterator it = distances.begin(); it != distances.end();) if (it->second == INT_MIN) distances.erase(it++); else ++it; return distances; } /** Print a distance map. */ static void printDistanceMap(ostream& out, const Graph& g, const ContigNode& u, const ContigPath& path) { typedef map DistanceMap; DistanceMap distanceMap = makeDistanceMap(g, u, path); for (DistanceMap::const_iterator it = distanceMap.begin(); it != distanceMap.end(); ++it) out << get(edge_name, g, make_pair(u, it->first)) << " [d=" << it->second << "]\n"; } typedef std::vector > Estimates; /** Find a path for the specified distance estimates. * @param out [out] the solution path */ static void handleEstimate(const Graph& g, const EstimateRecord& er, bool dirIdx, ContigPath& out) { if (er.estimates[dirIdx].empty()) return; ContigNode origin(er.refID, dirIdx); ostringstream vout_ss; ostream bitBucket(NULL); ostream& vout = opt::verbose > 0 ? vout_ss : bitBucket; vout << "\n* " << get(vertex_name, g, origin) << '\n'; unsigned minNumPairs = UINT_MAX; // generate the reachable set Constraints constraints; for (Estimates::const_iterator iter = er.estimates[dirIdx].begin(); iter != er.estimates[dirIdx].end(); ++iter) { ContigNode v = iter->first; const DistanceEst& ep = iter->second; minNumPairs = min(minNumPairs, ep.numPairs); constraints.push_back(Constraint(v, ep.distance + allowedError(ep.stdDev))); } vout << "Constraints:"; printConstraints(vout, g, constraints) << '\n'; ContigPaths solutions; unsigned numVisited = 0; constrainedSearch(g, origin, constraints, solutions, numVisited); bool tooComplex = numVisited >= opt::maxCost; bool tooManySolutions = solutions.size() > opt::maxPaths; set repeats = findRepeats(er.refID, solutions); if (!repeats.empty()) { vout << "Repeats:"; for (set::const_iterator it = repeats.begin(); it != repeats.end(); ++it) vout << ' ' << get(g_contigNames, *it); vout << '\n'; } unsigned numPossiblePaths = solutions.size(); if (numPossiblePaths > 0) vout << "Paths: " << numPossiblePaths << '\n'; for (ContigPaths::iterator solIter = solutions.begin(); solIter != solutions.end();) { vout << *solIter << '\n'; // Calculate the path distance to each node and see if // it is within the estimated distance. map distanceMap = makeDistanceMap(g, origin, *solIter); // Remove solutions whose distance estimates are not correct. unsigned validCount = 0, invalidCount = 0, ignoredCount = 0; for (Estimates::const_iterator iter = er.estimates[dirIdx].begin(); iter != er.estimates[dirIdx].end(); ++iter) { ContigNode v = iter->first; const DistanceEst& ep = iter->second; vout << get(vertex_name, g, v) << ',' << ep << '\t'; map::iterator dmIter = distanceMap.find(v); if (dmIter == distanceMap.end()) { // This contig is a repeat. ignoredCount++; vout << "ignored\n"; continue; } // translate distance by -overlap to match // coordinate space used by the estimate int actualDistance = dmIter->second; int diff = actualDistance - ep.distance; unsigned buffer = allowedError(ep.stdDev); bool invalid = (unsigned)abs(diff) > buffer; bool repeat = repeats.count(v.contigIndex()) > 0; bool ignored = invalid && repeat; if (ignored) ignoredCount++; else if (invalid) invalidCount++; else validCount++; vout << "dist: " << actualDistance << " diff: " << diff << " buffer: " << buffer << " n: " << ep.numPairs << (ignored ? " ignored" : invalid ? " invalid" : "") << '\n'; } if (invalidCount == 0 && validCount > 0) ++solIter; else solIter = solutions.erase(solIter); } vout << "Solutions: " << solutions.size(); if (tooComplex) vout << " (too complex)"; if (tooManySolutions) vout << " (too many solutions)"; vout << '\n'; ContigPaths::iterator bestSol = solutions.end(); int minDiff = 999999; for (ContigPaths::iterator solIter = solutions.begin(); solIter != solutions.end(); ++solIter) { map distanceMap = makeDistanceMap(g, origin, *solIter); int sumDiff = 0; for (Estimates::const_iterator iter = er.estimates[dirIdx].begin(); iter != er.estimates[dirIdx].end(); ++iter) { ContigNode v = iter->first; const DistanceEst& ep = iter->second; if (repeats.count(v.contigIndex()) > 0) continue; map::iterator dmIter = distanceMap.find(v); assert(dmIter != distanceMap.end()); int actualDistance = dmIter->second; int diff = actualDistance - ep.distance; sumDiff += abs(diff); } if (sumDiff < minDiff) { minDiff = sumDiff; bestSol = solIter; } vout << *solIter << " length: " << calculatePathLength(g, origin, *solIter) << " sumdiff: " << sumDiff << '\n'; } /** Lock the debugging stream. */ static pthread_mutex_t coutMutex = PTHREAD_MUTEX_INITIALIZER; pthread_mutex_lock(&coutMutex); stats.totalAttempted++; g_minNumPairs = min(g_minNumPairs, minNumPairs); if (tooComplex) { stats.tooComplex++; } else if (tooManySolutions) { stats.tooManySolutions++; } else if (numPossiblePaths == 0) { stats.noPossiblePaths++; } else if (solutions.empty()) { stats.noValidPaths++; } else if (repeats.count(er.refID) > 0) { vout << "Repeat: " << get(vertex_name, g, origin) << '\n'; stats.repeat++; } else if (solutions.size() > 1) { ContigPath path = constructAmbiguousPath(g, origin, solutions); if (!path.empty()) { if (opt::extend) extend(g, path.back(), back_inserter(path)); vout << path << '\n'; if (opt::scaffold) { out.insert(out.end(), path.begin(), path.end()); g_minNumPairsUsed = min(g_minNumPairsUsed, minNumPairs); } } stats.multiEnd++; } else { assert(solutions.size() == 1); assert(bestSol != solutions.end()); ContigPath& path = *bestSol; if (opt::verbose > 1) printDistanceMap(vout, g, origin, path); if (opt::extend) extend(g, path.back(), back_inserter(path)); out.insert(out.end(), path.begin(), path.end()); stats.uniqueEnd++; g_minNumPairsUsed = min(g_minNumPairsUsed, minNumPairs); } cout << vout_ss.str(); if (!out.empty()) assert(!out.back().ambiguous()); pthread_mutex_unlock(&coutMutex); } struct WorkerArg { istream* in; ostream* out; const Graph* graph; WorkerArg(istream* in, ostream* out, const Graph* g) : in(in), out(out), graph(g) { } }; static void* worker(void* pArg) { WorkerArg& arg = *static_cast(pArg); for (;;) { /** Lock the input stream. */ static pthread_mutex_t inMutex = PTHREAD_MUTEX_INITIALIZER; pthread_mutex_lock(&inMutex); EstimateRecord er; bool good = (*arg.in) >> er; pthread_mutex_unlock(&inMutex); if (!good) break; // Flip the anterior distance estimates. for (Estimates::iterator it = er.estimates[1].begin(); it != er.estimates[1].end(); ++it) it->first ^= 1; ContigPath path; handleEstimate(*arg.graph, er, true, path); reverseComplement(path.begin(), path.end()); path.push_back(ContigNode(er.refID, false)); handleEstimate(*arg.graph, er, false, path); if (path.size() > 1) { /** Lock the output stream. */ static pthread_mutex_t outMutex = PTHREAD_MUTEX_INITIALIZER; pthread_mutex_lock(&outMutex); *arg.out << get(g_contigNames, er.refID) << '\t' << path << '\n'; assert(arg.out->good()); pthread_mutex_unlock(&outMutex); } } return NULL; } static void generatePathsThroughEstimates(const Graph& g, const string& estPath) { if (opt::verbose > 0) cerr << "Reading `" << estPath << "'..." << endl; ifstream inStream(estPath.c_str()); assert_good(inStream, estPath); ofstream outStream(opt::out.c_str()); assert(outStream.is_open()); // Create the worker threads. vector threads; threads.reserve(opt::threads); WorkerArg arg(&inStream, &outStream, &g); for (unsigned i = 0; i < opt::threads; i++) { pthread_t thread; pthread_create(&thread, NULL, worker, &arg); threads.push_back(thread); } // Wait for the worker threads to finish. for (vector::const_iterator it = threads.begin(); 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using boost::tie; namespace ublas = boost::numeric::ublas; #define PROGRAM "abyss-drawgraph" static const char VERSION_MESSAGE[] = PROGRAM " (" PACKAGE_NAME ") " VERSION "\n" "Written by Shaun Jackman.\n" "\n" "Copyright 2013 Canada's Michael Smith Genome Science Centre\n"; static const char USAGE_MESSAGE[] = "Usage: " PROGRAM " [OPTION]... FASTA|OVERLAP DIST...\n" "Place each contig on a one-dimesional coordinate system using\n" "distance estimates and output a DOT graph with coordinates.\n" "\n" " Arguments:\n" "\n" " FASTA contigs in FASTA format\n" " OVERLAP the contig overlap graph\n" " DIST estimates of the distance between contigs\n" "\n" " Options:\n" "\n" " -x, --xscale=N set the x scale to N nt/inch [100e3]\n" " -v, --verbose display verbose output\n" " --help display this help and exit\n" " --version output version information and exit\n" "\n" "Report bugs to <" PACKAGE_BUGREPORT ">.\n"; namespace opt { unsigned k; // used by ContigProperties /** The x scale. */ double xscale = 100e3; // nt/inch /** Verbose output. */ int verbose; // used by PopBubbles /** Output format */ int format = DOT; // used by DistanceEst } static const char shortopts[] = "x:v"; enum { OPT_HELP = 1, OPT_VERSION }; static const struct option longopts[] = { { "xscale", required_argument, NULL, 'x' }, { "verbose", no_argument, NULL, 'v' }, { "help", no_argument, NULL, OPT_HELP }, { "version", no_argument, NULL, OPT_VERSION }, { NULL, 0, NULL, 0 } }; /** A distance estimate graph. */ typedef DirectedGraph DG; typedef ContigGraph Graph; /** A matrix. */ typedef ublas::matrix Matrix; /** A vector. */ typedef ublas::vector Vector; /** Read a graph from the specified file. */ static void readGraph(const string& path, Graph& g) { if (opt::verbose > 0) cerr << "Reading `" << path << "'...\n"; ifstream fin(path.c_str()); istream& in = path == "-" ? cin : fin; assert_good(in, path); read_graph(in, g, BetterDistanceEst()); assert(in.eof()); if (opt::verbose > 0) printGraphStats(cerr, g); g_contigNames.lock(); } /** Solve Ax = b for x using Cholesky decomposition. * The matrix A is symmetric and positive-definite. * @param[in,out] a input matrix A, which is clobbered * @param[in,out] b input vector b and output vector x */ static void solve(Matrix& a, Vector& b) { int ret = cholesky_decompose(a); if (ret > 0) { cerr << PROGRAM ": error: " "The graph has multiple connected components.\n"; exit(EXIT_FAILURE); } cholesky_solve(a, b, ublas::lower()); } /** Run abyss-drawgraph. */ int main(int argc, char** argv) { bool die = false; for (int c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;) { istringstream arg(optarg != NULL ? optarg : ""); switch (c) { case '?': die = true; break; case 'x': arg >> opt::xscale; break; case 'v': opt::verbose++; break; case OPT_HELP: cout << USAGE_MESSAGE; exit(EXIT_SUCCESS); case OPT_VERSION: cout << VERSION_MESSAGE; exit(EXIT_SUCCESS); } if (optarg != NULL && !arg.eof()) { cerr << PROGRAM ": invalid option: `-" << (char)c << optarg << "'\n"; exit(EXIT_FAILURE); } } if (argc - optind < 0) { cerr << PROGRAM ": missing arguments\n"; die = true; } if (die) { cerr << "Try `" << PROGRAM << " --help' for more information.\n"; exit(EXIT_FAILURE); } typedef graph_traits::edge_descriptor E; typedef graph_traits::edge_iterator Eit; typedef graph_traits::vertex_descriptor V; typedef graph_traits::vertex_iterator Vit; typedef edge_bundle_type::type EP; Graph g; if (optind < argc) { for (; optind < argc; optind++) readGraph(argv[optind], g); } else readGraph("-", g); // Add any missing complementary edges. addComplementaryEdges(g); size_t n = num_vertices(g); Matrix a(n, n); Vector b = ublas::zero_vector(n); // Set the origin. a(0, 0) = 1; // Build the information matrix. Eit eit, elast; for (tie(eit, elast) = edges(g); eit != elast; ++eit) { E e = *eit; V u = source(e, g); V v = target(e, g); size_t ui = get(vertex_index, g, u); size_t vi = get(vertex_index, g, v); int d = get(edge_weight, g, e); double err = max(0.1, (double)g[e].stdDev); double weight = 1 / err; a(ui, ui) += weight; a(ui, vi) -= weight; a(vi, ui) -= weight; a(vi, vi) += weight; b[ui] -= d * weight; b[vi] += d * weight; } // Solve the equation Ax = b for x. solve(a, b); // Output the coordinates of each contig. if (opt::verbose > 1) { Vit uit, ulast; for (tie(uit, ulast) = vertices(g); uit != ulast; ++uit) { V u = *uit; size_t ui = get(vertex_index, g, u); ssize_t x1 = (ssize_t)b[ui]; ssize_t x0 = x1 - g[u].length; cerr << get(vertex_name, g, u) << '\t' << x0 << '\t' << x1 << '\n'; } } // Sort the contigs by their right coordinate. std::vector< std::pair > sorted; sorted.reserve(n); Vit uit, ulast; for (tie(uit, ulast) = vertices(g); uit != ulast; ++uit) { V u = *uit; size_t ui = get(vertex_index, g, u); sorted.push_back(std::make_pair(b[ui], u)); } sort(sorted.begin(), sorted.end()); // Write the graph. cout << "digraph g {\n" "node [shape=\"box\" height=0.3 fixedsize=1]\n"; assert_good(cout, "stdout"); // Write the vertices. double pos0 = -numeric_limits::max(); size_t yi = 0; for (size_t i = 0; i < n; ++i) { V u = sorted[i].second; double pos = b[get(vertex_index, g, u)]; size_t l = g[u].length; if (pos - l < pos0) yi++; pos0 = pos; double dpi = 72; const double W = dpi / opt::xscale; // pt/nt const double H = 32; // pt double w = l * W; double x = pos * W - w / 2; double y = yi * H; cout << '"' << get(vertex_name, g, u) << "\"" " [pos=\"" << x << ",-" << y << "\"" " width=" << w / dpi << "]\n"; } // Write the edges. for (tie(eit, elast) = edges(g); eit != elast; ++eit) cout << get(edge_name, g, *eit) << '\n'; cout << "}\n"; assert_good(cout, "stdout"); return 0; } abyss-1.3.6/Scaffold/junction.cc000644 002433 001057 00000013452 12116214002 020232 0ustar00traymondassembly000000 000000 #include "config.h" #include "Common/ContigPath.h" #include "Common/IOUtil.h" #include "Graph/ContigGraph.h" #include "Graph/ContigGraphAlgorithms.h" #include "Graph/DirectedGraph.h" #include "Graph/GraphIO.h" #include "Graph/GraphUtil.h" #include "Uncompress.h" #include #include #include #include #include #include #include #include #include #include #include #include #include using namespace std; using namespace boost::lambda; using boost::tie; #if !__GXX_EXPERIMENTAL_CXX0X__ using boost::cref; using boost::ref; #endif #define PROGRAM "abyss-junction" static const char VERSION_MESSAGE[] = PROGRAM " (" PACKAGE_NAME ") " VERSION "\n" "Written by Shaun Jackman.\n" "\n" "Copyright 2013 Canada's Michael Smith Genome Science Centre\n"; static const char USAGE_MESSAGE[] = "Usage: " PROGRAM " [OPTION]... OVERLAP [SCAFFOLD]...\n" "Extend junction contigs that are supported by the scaffold graph.\n" "\n" " Arguments:\n" "\n" " OVERLAP the overlap graph\n" " SCAFFOLD a scaffold graph\n" "\n" " Options:\n" "\n" " -i, --ignore=FILE ignore junctions seen in FILE\n" " -v, --verbose display verbose output\n" " --help display this help and exit\n" " --version output version information and exit\n" "\n" "Report bugs to <" PACKAGE_BUGREPORT ">.\n"; namespace opt { unsigned k; // used by DotIO /** Do not check for evidence in the scaffold graph. */ bool noScaffoldGraph; /** Junction contigs to ignore. */ string ignorePath; /** Verbose output. */ int verbose; // used by PopBubbles /** Output format */ int format = DOT; // used by DistanceEst } static const char shortopts[] = "i:v"; enum { OPT_HELP = 1, OPT_VERSION, }; static const struct option longopts[] = { { "ignore", no_argument, NULL, 'i' }, { "verbose", no_argument, NULL, 'v' }, { "help", no_argument, NULL, OPT_HELP }, { "version", no_argument, NULL, OPT_VERSION }, { NULL, 0, NULL, 0 } }; /** Counts. */ static struct { unsigned junctions; unsigned supported; } g_count; /** An overlap graph. */ typedef DirectedGraph DG; typedef ContigGraph Graph; typedef Graph OverlapGraph; /** A scaffold graph. */ typedef Graph ScaffoldGraph; /** Extend junction contigs. */ void extendJunction( const OverlapGraph& overlapG, const ScaffoldGraph& scaffoldG, graph_traits::vertex_descriptor v) { if (get(vertex_sense, overlapG, v) || in_degree(v, overlapG) != 1 || out_degree(v, overlapG) != 1) return; typedef graph_traits::vertex_descriptor V; V u = source(*in_edges(v, overlapG).first, overlapG); V w = *adjacent_vertices(v, overlapG).first; if (opt::noScaffoldGraph || edge(u, w, scaffoldG).second) { // This junction contig is supported by the scaffold graph. ContigPath path; path.reserve(3); extend(overlapG, get(vertex_complement, overlapG, v), back_inserter(path)); reverseComplement(path.begin(), path.end()); path.push_back(v); extend(overlapG, v, back_inserter(path)); assert(path.size() >= 3); cout << createContigName() << '\t' << path << '\n'; g_count.supported++; } g_count.junctions++; } /** Allow parallel edges. */ struct AllowParallelEdges { template EP operator()(const EP& a, const EP&) const { return a; } }; /** Read a graph from the specified file. */ static void readGraph(const string& path, Graph& g) { if (opt::verbose > 0) cerr << "Reading `" << path << "'...\n"; ifstream fin(path.c_str()); istream& in = path == "-" ? cin : fin; assert_good(in, path); read_graph(in, g, AllowParallelEdges()); assert(in.eof()); if (opt::verbose > 1) printGraphStats(cerr, g); g_contigNames.lock(); } int main(int argc, char** argv) { bool die = false; for (int c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;) { istringstream arg(optarg != NULL ? optarg : ""); switch (c) { case '?': die = true; break; case 'i': arg >> opt::ignorePath; break; case 'v': opt::verbose++; break; case OPT_HELP: cout << USAGE_MESSAGE; exit(EXIT_SUCCESS); case OPT_VERSION: cout << VERSION_MESSAGE; exit(EXIT_SUCCESS); } if (optarg != NULL && !arg.eof()) { cerr << PROGRAM ": invalid option: `-" << (char)c << optarg << "'\n"; exit(EXIT_FAILURE); } } if (argc - optind < 1) { cerr << PROGRAM ": missing arguments\n"; die = true; } if (die) { cerr << "Try `" << PROGRAM << " --help' for more information.\n"; exit(EXIT_FAILURE); } OverlapGraph overlapG; readGraph(argv[optind++], overlapG); ScaffoldGraph scaffoldG(overlapG.num_vertices() / 2); if (optind < argc) { for_each(argv + optind, argv + argc, bind(readGraph, _1, ref(scaffoldG))); // Add any missing complementary edges. size_t numAdded = addComplementaryEdges(scaffoldG); if (opt::verbose > 0) cerr << "Added " << numAdded << " complementary edges.\n"; if (opt::verbose > 1) printGraphStats(cerr, scaffoldG); } else opt::noScaffoldGraph = true; // Read the set of contigs to ignore. vector seen(num_vertices(overlapG) / 2); if (!opt::ignorePath.empty()) { ifstream in(opt::ignorePath.c_str()); assert_good(in, opt::ignorePath); markSeenInPath(in, seen); } // Extend the junction contigs. graph_traits::vertex_iterator uit, ulast; for (tie(uit, ulast) = vertices(overlapG); uit != ulast; ++uit) if (!seen[get(vertex_contig_index, overlapG, *uit)]) extendJunction(overlapG, scaffoldG, *uit); assert_good(cout, "stdout"); if (opt::verbose > 0) { cerr << "Junctions: " << g_count.junctions << '\n'; if (!opt::noScaffoldGraph) cerr << "Supported: " << g_count.supported << '\n'; } return 0; } abyss-1.3.6/Scaffold/scaffold.cc000644 002433 001057 00000047635 12116214002 020174 0ustar00traymondassembly000000 000000 #include "config.h" #include "ContigNode.h" #include "ContigPath.h" #include "ContigProperties.h" #include "Estimate.h" #include "IOUtil.h" #include "Iterator.h" #include "Uncompress.h" #include "Graph/Assemble.h" #include "Graph/ContigGraph.h" #include "Graph/ContigGraphAlgorithms.h" #include "Graph/DirectedGraph.h" #include "Graph/GraphAlgorithms.h" #include "Graph/GraphIO.h" #include "Graph/GraphUtil.h" #include "Graph/PopBubbles.h" #include #include #include #include #include #include #include #include #include #include #include using namespace std; using namespace std::rel_ops; using boost::edge_bundle_type; using boost::tie; #define PROGRAM "abyss-scaffold" static const char VERSION_MESSAGE[] = PROGRAM " (" PACKAGE_NAME ") " VERSION "\n" "Written by Shaun Jackman.\n" "\n" "Copyright 2013 Canada's Michael Smith Genome Science Centre\n"; static const char USAGE_MESSAGE[] = "Usage: " PROGRAM " [OPTION]... FASTA|OVERLAP DIST...\n" "Scaffold contigs using the distance estimate graph.\n" "\n" " Arguments:\n" "\n" " FASTA contigs in FASTA format\n" " OVERLAP the contig overlap graph\n" " DIST estimates of the distance between contigs\n" "\n" " Options:\n" "\n" " -n, --npairs=N minimum number of pairs [0]\n" " -s, --seed-length=N minimum contig length [200]\n" " or -s N0-N1 Find the value of s in [N0,N1]\n" " that maximizes the scaffold N50.\n" " -k, --kmer=N length of a k-mer\n" " --min-gap=N minimum scaffold gap length to output [50]\n" " -o, --out=FILE write the paths to FILE\n" " -g, --graph=FILE write the graph to FILE\n" " -v, --verbose display verbose output\n" " --help display this help and exit\n" " --version output version information and exit\n" "\n" "Report bugs to <" PACKAGE_BUGREPORT ">.\n"; namespace opt { unsigned k; // used by ContigProperties /** Minimum number of pairs. */ static unsigned minNumPairs; /** Minimum contig length. */ static unsigned minContigLength = 200; static unsigned minContigLengthEnd; /** Minimum scaffold gap length to output. */ static int minGap = 50; /** Write the paths to this file. */ static string out; /** Write the graph to this file. */ static string graphPath; /** Verbose output. */ int verbose; // used by PopBubbles /** Output format */ int format = DOT; // used by DistanceEst } static const char shortopts[] = "g:k:n:o:s:v"; enum { OPT_HELP = 1, OPT_VERSION, OPT_MIN_GAP }; static const struct option longopts[] = { { "graph", no_argument, NULL, 'g' }, { "kmer", required_argument, NULL, 'k' }, { "min-gap", required_argument, NULL, OPT_MIN_GAP }, { "npairs", required_argument, NULL, 'n' }, { "out", required_argument, NULL, 'o' }, { "seed-length", required_argument, NULL, 's' }, { "verbose", no_argument, NULL, 'v' }, { "help", no_argument, NULL, OPT_HELP }, { "version", no_argument, NULL, OPT_VERSION }, { NULL, 0, NULL, 0 } }; /** A distance estimate graph. */ typedef DirectedGraph DG; typedef ContigGraph Graph; /** Return whether this edge is invalid. * An edge is invalid when the overlap is larger than the length of * either of its incident sequences. */ struct InvalidEdge { InvalidEdge(Graph& g) : m_g(g) { } bool operator()(graph_traits::edge_descriptor e) const { int d = m_g[e].distance; int ulength = m_g[source(e, m_g)].length; int vlength = m_g[target(e, m_g)].length; return d + ulength <= 0 || d + vlength <= 0; } const Graph& m_g; }; /** Return whether the specified edges has sufficient support. */ struct PoorSupport { PoorSupport(Graph& g) : m_g(g) { } bool operator()(graph_traits::edge_descriptor e) const { return m_g[e].numPairs < opt::minNumPairs; } const Graph& m_g; }; /** Remove short vertices and unsupported edges from the graph. */ static void filterGraph(Graph& g, unsigned minContigLength) { typedef graph_traits GTraits; typedef GTraits::edge_descriptor E; typedef GTraits::edge_iterator Eit; typedef GTraits::vertex_descriptor V; typedef GTraits::vertex_iterator Vit; // Remove short contigs. unsigned numRemovedV = 0; std::pair urange = vertices(g); for (Vit uit = urange.first; uit != urange.second; ++uit) { V u = *uit; if (g[u].length < minContigLength) clear_vertex(u, g); if (out_degree(u, g) == 0 && in_degree(u, g) == 0) { remove_vertex(u, g); numRemovedV++; } } if (opt::verbose > 0) cerr << "Removed " << numRemovedV << " vertices.\n"; // Remove poorly-supported edges. unsigned numBefore = num_edges(g); remove_edge_if(PoorSupport(g), static_cast(g)); unsigned numRemovedE = numBefore - num_edges(g); if (opt::verbose > 0) cerr << "Removed " << numRemovedE << " edges.\n"; } /** Return true if the specified edge is a cycle. */ static bool isCycle(Graph& g, graph_traits::edge_descriptor e) { return edge(target(e, g), source(e, g), g).second; } /** Remove simple cycles of length two from the graph. */ static void removeCycles(Graph& g) { typedef graph_traits::edge_descriptor E; typedef graph_traits::edge_iterator Eit; // Identify the cycles. vector cycles; Eit eit, elast; for (tie(eit, elast) = edges(g); eit != elast; ++eit) { E e = *eit; if (isCycle(g, e)) cycles.push_back(e); } /** Remove the cycles. */ remove_edges(g, cycles.begin(), cycles.end()); if (opt::verbose > 0) { cerr << "Removed " << cycles.size() << " cyclic edges.\n"; printGraphStats(cerr, g); } } /** Find edges in g0 that resolve forks in g. * For a pair of edges (u,v1) and (u,v2) in g, if exactly one of the * edges (v1,v2) or (v2,v1) exists in g0, add that edge to g. */ static void resolveForks(Graph& g, const Graph& g0) { typedef graph_traits::adjacency_iterator Vit; typedef graph_traits::edge_descriptor E; typedef graph_traits::vertex_iterator Uit; typedef graph_traits::vertex_descriptor V; unsigned numEdges = 0; pair urange = vertices(g); for (Uit uit = urange.first; uit != urange.second; ++uit) { V u = *uit; if (out_degree(u, g) < 2) continue; pair vrange = adjacent_vertices(u, g); for (Vit vit1 = vrange.first; vit1 != vrange.second;) { V v1 = *vit1; ++vit1; assert(v1 != u); for (Vit vit2 = vit1; vit2 != vrange.second; ++vit2) { V v2 = *vit2; assert(v2 != u); assert(v1 != v2); if (edge(v1, v2, g).second || edge(v2, v1, g).second) continue; pair e12 = edge(v1, v2, g0); pair e21 = edge(v2, v1, g0); if (e12.second && e21.second) { if (opt::verbose > 1) cerr << "cycle: " << get(vertex_name, g, v1) << ' ' << get(vertex_name, g, v2) << '\n'; } else if (e12.second || e21.second) { E e = e12.second ? e12.first : e21.first; V v = source(e, g0), w = target(e, g0); add_edge(v, w, g0[e], g); numEdges++; if (opt::verbose > 1) cerr << get(vertex_name, g, u) << " -> " << get(vertex_name, g, v) << " -> " << get(vertex_name, g, w) << " [" << g0[e] << "]\n"; } } } } if (opt::verbose > 0) cerr << "Added " << numEdges << " edges to ambiguous vertices.\n"; } /** Remove tips. * For an edge (u,v), remove the vertex v if deg+(u) > 1 * and deg-(v) = 1 and deg+(v) = 0. */ static void pruneTips(Graph& g) { typedef graph_traits::vertex_descriptor V; /** Identify the tips. */ size_t n = 0; pruneTips(g, CountingOutputIterator(n)); if (opt::verbose > 0) { cerr << "Removed " << n << " tips.\n"; printGraphStats(cerr, g); } } /** Remove repetitive vertices from this graph. * input: digraph g { t1->v1 t2->v2 t1->u t2->u u->v1 u->v2 } * operation: remove vertex u * output: digraph g { t1->v1 t2->v2 } */ static void removeRepeats(Graph& g) { typedef graph_traits::adjacency_iterator Ait; typedef graph_traits::edge_descriptor E; typedef graph_traits::vertex_descriptor V; vector repeats; vector transitive; find_transitive_edges(g, back_inserter(transitive)); for (vector::const_iterator it = transitive.begin(); it != transitive.end(); ++it) { // Iterate through the transitive edges, u->w1. V u = source(*it, g), w1 = target(*it, g); Ait vit, vlast; for (tie(vit, vlast) = adjacent_vertices(u, g); vit != vlast; ++vit) { V v = *vit; assert(u != v); // no self loops if (!edge(v, w1, g).second) continue; // u->w1 is a transitive edge spanning u->v->w1. Ait wit, wlast; for (tie(wit, wlast) = adjacent_vertices(v, g); wit != wlast; ++wit) { // For each edge v->w2, check that an edge // w1->w2 or w2->w1 exists. If not, v is a repeat. V w2 = *wit; assert(v != w2); // no self loops if (w1 != w2 && !edge(w1, w2, g).second && !edge(w2, w1, g).second) { repeats.push_back(v); break; } } } } sort(repeats.begin(), repeats.end()); repeats.erase(unique(repeats.begin(), repeats.end()), repeats.end()); if (opt::verbose > 1) { cerr << "Ambiguous:"; for (vector::const_iterator it = repeats.begin(); it != repeats.end(); ++it) cerr << ' ' << get(vertex_name, g, *it); cerr << '\n'; } // Remove the repetitive vertices. unsigned numRemoved = 0; for (vector::const_iterator it = repeats.begin(); it != repeats.end(); ++it) { V u = *it; V uc = get(vertex_complement, g, u); clear_out_edges(u, g); if (it != repeats.begin() && it[-1] == uc) { remove_vertex(u, g); numRemoved++; } } if (opt::verbose > 0) { cerr << "Cleared " << repeats.size() << " ambiguous vertices.\n" << "Removed " << numRemoved << " ambiguous vertices.\n"; printGraphStats(cerr, g); } } /** Remove weak edges from this graph. * input: digraph g { u1->v2 u1->v1 u2->v2 } * (u1,v2).n < (u1,v1).n and (u1,v2).n < (u2,v2).n * operation: remove edge u1->v2 * output: digraph g {u1->v1 u2->v2 } */ static void removeWeakEdges(Graph& g) { typedef graph_traits::edge_descriptor E; typedef graph_traits::edge_iterator Eit; typedef graph_traits::in_edge_iterator Iit; typedef graph_traits::out_edge_iterator Oit; typedef graph_traits::vertex_descriptor V; vector weak; Eit eit, elast; for (tie(eit, elast) = edges(g); eit != elast; ++eit) { E u1v2 = *eit; V u1 = source(u1v2, g), v2 = target(u1v2, g); if (out_degree(u1, g) != 2 || in_degree(v2, g) != 2) continue; Oit oit, olast; tie(oit, olast) = out_edges(u1, g); E u1v1; if (target(*oit, g) == v2) { ++oit; u1v1 = *oit; } else { u1v1 = *oit; ++oit; } assert(++oit == olast); V v1 = target(u1v1, g); assert(v1 != v2); if (in_degree(v1, g) != 1) continue; Iit iit, ilast; tie(iit, ilast) = in_edges(v2, g); E u2v2; if (source(*iit, g) == u1) { ++iit; assert(iit != ilast); u2v2 = *iit; } else { assert(iit != ilast); u2v2 = *iit; ++iit; } assert(++iit == ilast); V u2 = source(u2v2, g); assert(u1 != u2); if (out_degree(u2, g) != 1) continue; unsigned n = g[u1v2].numPairs; if (n < g[u1v1].numPairs && n < g[u2v2].numPairs) weak.push_back(u1v2); } if (opt::verbose > 1) { cerr << "Weak edges:\n"; for (vector::const_iterator it = weak.begin(); it != weak.end(); ++it) { E e = *it; cerr << '\t' << get(edge_name, g, e) << " [" << g[e] << "]\n"; } } /** Remove the weak edges. */ remove_edges(g, weak.begin(), weak.end()); if (opt::verbose > 0) { cerr << "Removed " << weak.size() << " weak edges.\n"; printGraphStats(cerr, g); } } /** Return whether the specified distance estimate is an exact * overlap. */ static bool isOverlap(const DistanceEst& d) { if (d.stdDev == 0) { assert(d.distance < 0); return true; } else return false; } /** Add distance estimates to a path. * @param g0 the original graph * @param g1 the transformed graph */ static ContigPath addDistEst(const Graph& g0, const Graph& g1, const ContigPath& path) { typedef graph_traits::edge_descriptor E; typedef edge_bundle_type::type EP; ContigPath out; out.reserve(2 * path.size()); ContigNode u = path.front(); out.push_back(u); for (ContigPath::const_iterator it = path.begin() + 1; it != path.end(); ++it) { ContigNode v = *it; assert(!v.ambiguous()); pair e0 = edge(u, v, g0); pair e1 = edge(u, v, g1); assert(e0.second || e1.second); const EP& ep = e0.second ? g0[e0.first] : g1[e1.first]; if (!isOverlap(ep)) { int distance = max(ep.distance, (int)opt::minGap); int numN = distance + opt::k - 1; // by convention assert(numN >= 0); numN = max(numN, 1); out.push_back(ContigNode(numN, 'N')); } out.push_back(v); u = v; } return out; } /** Read a graph from the specified file. */ static void readGraph(const string& path, Graph& g) { if (opt::verbose > 0) cerr << "Reading `" << path << "'...\n"; ifstream fin(path.c_str()); istream& in = path == "-" ? cin : fin; assert_good(in, path); read_graph(in, g, BetterDistanceEst()); assert(in.eof()); if (opt::verbose > 0) printGraphStats(cerr, g); g_contigNames.lock(); } /** Return the scaffold length of [first, last), not counting gaps. */ template unsigned addLength(const Graph& g, It first, It last) { typedef typename graph_traits::vertex_descriptor V; assert(first != last); unsigned length = g[*first].length; for (It it = first + 1; it != last; ++it) { V u = *(it - 1); V v = *it; length += min(0, get(edge_bundle, g, u, v).distance); length += g[v].length; } return length; } /** A container of contig paths. */ typedef vector ContigPaths; /** Build the scaffold length histogram. */ static Histogram buildScaffoldLengthHistogram( Graph& g, const ContigPaths& paths) { Histogram h; // Clear the removed flag. typedef graph_traits::vertex_iterator Vit; Vit uit, ulast; for (tie(uit, ulast) = vertices(g); uit != ulast; ++uit) put(vertex_removed, g, *uit, false); // Remove the vertices that are used in paths // and add the lengths of the scaffolds. for (ContigPaths::const_iterator it = paths.begin(); it != paths.end(); ++it) { h.insert(addLength(g, it->begin(), it->end())); remove_vertex_if(g, it->begin(), it->end(), not1(std::mem_fun_ref(&ContigNode::ambiguous))); } // Add the contigs that were not used in paths. for (tie(uit, ulast) = vertices(g); uit != ulast; ++++uit) { typedef graph_traits::vertex_descriptor V; V u = *uit; if (!get(vertex_removed, g, u)) h.insert(g[u].length); } return h; } /** Build scaffold paths. * @param output write the results * @return the scaffold N50 */ unsigned scaffold(const Graph& g0, unsigned minContigLength, bool output) { Graph g(g0); // Filter the graph. filterGraph(g, minContigLength); if (opt::verbose > 0) printGraphStats(cerr, g); // Remove cycles. removeCycles(g); // Resolve forks. resolveForks(g, g0); // Prune tips. pruneTips(g); // Remove repeats. removeRepeats(g); // Remove transitive edges. unsigned numTransitive = remove_transitive_edges(g); if (opt::verbose > 0) { cerr << "Removed " << numTransitive << " transitive edges.\n"; printGraphStats(cerr, g); } // Prune tips. pruneTips(g); // Pop bubbles. typedef graph_traits::vertex_descriptor V; vector popped = popBubbles(g); if (opt::verbose > 0) { cerr << "Removed " << popped.size() << " vertices in bubbles.\n"; printGraphStats(cerr, g); } if (opt::verbose > 1) { cerr << "Popped:"; for (vector::const_iterator it = popped.begin(); it != popped.end(); ++it) cerr << ' ' << get(vertex_name, g, *it); cerr << '\n'; } // Remove weak edges. removeWeakEdges(g); // Assemble the paths. ContigPaths paths; assembleDFS(g, back_inserter(paths)); sort(paths.begin(), paths.end()); if (opt::verbose > 0) { unsigned n = 0; for (ContigPaths::const_iterator it = paths.begin(); it != paths.end(); ++it) n += it->size(); cerr << "Assembled " << n << " contigs in " << paths.size() << " scaffolds.\n"; printGraphStats(cerr, g); } const unsigned STATS_MIN_LENGTH = opt::minContigLength; if (!output) { static bool printHeader = true; Histogram h = buildScaffoldLengthHistogram(g, paths); printContiguityStats(cerr, h, STATS_MIN_LENGTH, printHeader) << "\ts=" << minContigLength << '\n'; if (opt::verbose == 0) printHeader = false; return h.trimLow(STATS_MIN_LENGTH).n50(); } // Output the paths. ofstream fout(opt::out.c_str()); ostream& out = opt::out.empty() || opt::out == "-" ? cout : fout; assert_good(out, opt::out); g_contigNames.unlock(); for (vector::const_iterator it = paths.begin(); it != paths.end(); ++it) out << createContigName() << '\t' << addDistEst(g0, g, *it) << '\n'; assert_good(out, opt::out); // Output the graph. if (!opt::graphPath.empty()) { ofstream out(opt::graphPath.c_str()); assert_good(out, opt::graphPath); write_dot(out, g); assert_good(out, opt::graphPath); } // Print assembly contiguity statistics. Histogram h = buildScaffoldLengthHistogram(g, paths); printContiguityStats(cerr, h, STATS_MIN_LENGTH) << '\n'; return h.trimLow(STATS_MIN_LENGTH).n50(); } /** Run abyss-scaffold. */ int main(int argc, char** argv) { bool die = false; for (int c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;) { istringstream arg(optarg != NULL ? optarg : ""); switch (c) { case '?': die = true; break; case 'k': arg >> opt::k; break; case 'g': arg >> opt::graphPath; break; case 'n': arg >> opt::minNumPairs; break; case 'o': arg >> opt::out; break; case 's': arg >> opt::minContigLength; if (arg.peek() == '-') { opt::minContigLengthEnd = 100 * opt::minContigLength; arg >> expect("-") >> opt::minContigLengthEnd; assert(opt::minContigLength <= opt::minContigLengthEnd); } break; case 'v': opt::verbose++; break; case OPT_MIN_GAP: arg >> opt::minGap; break; case OPT_HELP: cout << USAGE_MESSAGE; exit(EXIT_SUCCESS); case OPT_VERSION: cout << VERSION_MESSAGE; exit(EXIT_SUCCESS); } if (optarg != NULL && !arg.eof()) { cerr << PROGRAM ": invalid option: `-" << (char)c << optarg << "'\n"; 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using namespace boost::lambda; using boost::tie; #if !__GXX_EXPERIMENTAL_CXX0X__ using boost::cref; #endif #define PROGRAM "PopBubbles" static const char VERSION_MESSAGE[] = PROGRAM " (" PACKAGE_NAME ") " VERSION "\n" "Written by Shaun Jackman.\n" "\n" "Copyright 2013 Canada's Michael Smith Genome Science Centre\n"; static const char USAGE_MESSAGE[] = "Usage: " PROGRAM " [OPTION]... FASTA ADJ\n" "Identify and pop simple bubbles.\n" "\n" " Arguments:\n" "\n" " FASTA contigs in FASTA format\n" " ADJ contig adjacency graph\n" "\n" " Options:\n" "\n" " -k, --kmer=N k-mer size\n" " -a, --branches=N maximum number of branches, default: 2\n" " -b, --bubble-length=N pop bubbles shorter than N bp\n" " default is 10000\n" " -p, --identity=REAL minimum identity, default: 0.9\n" " -c, --coverage=REAL remove contigs with mean k-mer coverage\n" " less than this threshold [0]\n" " --scaffold scaffold over bubbles that have\n" " insufficient identity\n" " --no-scaffold disable scaffolding [default]\n" " -g, --graph=FILE write the contig adjacency graph to FILE\n" " --dot output bubbles in dot format\n" " -j, --threads=N use N parallel threads [1]\n" " -v, --verbose display verbose output\n" " --help display this help and exit\n" " --version output version information and exit\n" "\n" "Report bugs to <" PACKAGE_BUGREPORT ">.\n"; namespace opt { unsigned k; // used by ContigProperties /** Maximum number of branches. */ static unsigned maxBranches = 2; /** Pop bubbles shorter than this threshold. */ static unsigned maxLength = 10000; /** Minimum identity. */ static float identity = 0.9; /** Minimum mean k-mer coverage. */ static float minCoverage; /** Scaffold over bubbles that have insufficient identity. */ static int scaffold; /** Write the contig adjacency graph to this file. */ static string graphPath; /** Output bubbles in dot format. */ static int dot; int format; // used by ContigProperties /** Number of threads. */ static int threads = 1; static int dialign_debug; static string dialign_score; static string dialign_prob; } static const char shortopts[] = "a:b:c:g:j:k:p:vD:M:P:"; enum { OPT_HELP = 1, OPT_VERSION }; static const struct option longopts[] = { { "branches", required_argument, NULL, 'a' }, { "bubble-length", required_argument, NULL, 'b' }, { "coverage", required_argument, NULL, 'c' }, { "dot", no_argument, &opt::dot, 1, }, { "graph", required_argument, NULL, 'g' }, { "kmer", required_argument, NULL, 'k' }, { "identity", required_argument, NULL, 'p' }, { "scaffold", no_argument, &opt::scaffold, 1}, { "no-scaffold", no_argument, &opt::scaffold, 0}, { "threads", required_argument, NULL, 'j' }, { "verbose", no_argument, NULL, 'v' }, { "help", no_argument, NULL, OPT_HELP }, { "version", no_argument, NULL, OPT_VERSION }, { "dialign-d", required_argument, NULL, 'D' }, { "dialign-m", required_argument, NULL, 'M' }, { "dialign-p", required_argument, NULL, 'P' }, { NULL, 0, NULL, 0 } }; /** Popped branches. */ static vector g_popped; /** Contig adjacency graph. */ typedef ContigGraph > Graph; typedef Graph::vertex_descriptor vertex_descriptor; typedef Graph::adjacency_iterator adjacency_iterator; /** Return the distance from vertex u to v. */ static int getDistance(const Graph& g, vertex_descriptor u, vertex_descriptor v) { typedef graph_traits::edge_descriptor edge_descriptor; pair e = edge(u, v, g); assert(e.second); return g[e.first].distance; } struct CompareCoverage { const Graph& g; CompareCoverage(const Graph& g) : g(g) { } bool operator()(vertex_descriptor u, vertex_descriptor v) { return g[u].coverage > g[v].coverage; } }; /** Pop the bubble between vertices v and tail. */ static void popBubble(Graph& g, vertex_descriptor v, vertex_descriptor tail) { unsigned nbranches = g.out_degree(v); assert(nbranches > 1); assert(nbranches == g.in_degree(tail)); vector sorted(nbranches); pair adj = g.adjacent_vertices(v); copy(adj.first, adj.second, sorted.begin()); sort(sorted.begin(), sorted.end(), CompareCoverage(g)); if (opt::dot) #pragma omp critical(cout) { cout << '"' << get(vertex_name, g, v) << "\" -> {"; for (vector::const_iterator it = sorted.begin(); it != sorted.end(); ++it) cout << " \"" << get(vertex_name, g, *it) << '"'; cout << " } -> \"" << get(vertex_name, g, tail) << "\"\n"; } #pragma omp critical(g_popped) transform(sorted.begin() + 1, sorted.end(), back_inserter(g_popped), mem_fun_ref(&ContigNode::contigIndex)); } static struct { unsigned bubbles; unsigned popped; unsigned scaffold; unsigned notSimple; unsigned tooLong; unsigned tooMany; unsigned dissimilar; } g_count; /** Contig sequences. */ typedef vector Contigs; static Contigs g_contigs; /** Return the sequence of vertex u. */ static string getSequence(const Graph* g, vertex_descriptor u) { size_t i = get(vertex_contig_index, *g, u); assert(i < g_contigs.size()); string seq(g_contigs[i]); return get(vertex_sense, *g, u) ? reverseComplement(seq) : seq; } /** Return the length of vertex v. */ static unsigned getLength(const Graph* g, vertex_descriptor v) { return (*g)[v].length; } /** Align the specified pair of sequences. * @return the number of matches and size of the consensus */ static pair alignPair( const string& seqa, const string& seqb) { NWAlignment alignment; unsigned matches = alignGlobal(seqa, seqb, alignment); if (opt::verbose > 2) #pragma omp critical(cerr) cerr << alignment; return make_pair(matches, alignment.size()); } /** Align the specified sequences. * @return the number of matches and size of the consensus */ static pair alignMulti(const vector& seqs) { string alignment = seqs[0]; unsigned matches = 0; NWAlignment align; for (unsigned j = 0; j < seqs.size() - 1; j++) { matches = min(matches, alignGlobal(alignment, seqs[j+1], align)); alignment = align.match_align; } if (opt::verbose > 2) #pragma omp critical(cerr) cerr << align; return make_pair(matches, alignment.size()); } /** Align the specified sequences. * @return the number of matches and size of the consensus */ static pair align(const vector& seqs) { assert(seqs.size() > 1); if (seqs.size() == 2) return alignPair(seqs[0], seqs[1]); else return alignMulti(seqs); } /** Align the sequences of [first,last). * @param t the vertex to the left of the bubble * @param v the vertex to the right of the bubble * @return the identity of the global alignment */ template static float getAlignmentIdentity(const Graph& g, vertex_descriptor t, vertex_descriptor v, It first, It last) { unsigned nbranches = distance(first, last); vector inDists(nbranches); transform(first, last, inDists.begin(), bind(getDistance, cref(g), t, _1)); vector outDists(nbranches); transform(first, last, outDists.begin(), bind(getDistance, cref(g), _1, v)); vector insertLens(nbranches); transform(first, last, insertLens.begin(), bind(getDistance, cref(g), t, _1) + bind(getLength, &g, _1) + bind(getDistance, cref(g), _1, v)); int max_in_overlap = -(*min_element(inDists.begin(), inDists.end())); assert(max_in_overlap >= 0); int max_out_overlap = -(*min_element(outDists.begin(), outDists.end())); assert(max_out_overlap >= 0); int min_insert_len = *min_element(insertLens.begin(), insertLens.end()); int max_insert_len = *max_element(insertLens.begin(), insertLens.end()); float max_identity = (float)(min_insert_len + max_in_overlap + max_out_overlap) / (max_insert_len + max_in_overlap + max_out_overlap); if (min_insert_len <= 0 || max_identity < opt::identity) return max_identity; vector seqs(nbranches); transform(first, last, seqs.begin(), bind(getSequence, &g, _1)); for (unsigned i = 0; i < seqs.size(); i++) { // Remove the overlapping sequence. int n = seqs[i].size(); int l = -inDists[i], r = -outDists[i]; assert(n > l + r); seqs[i] = seqs[i].substr(l, n - l - r); } unsigned matches, consensusSize; tie(matches, consensusSize) = align(seqs); return (float)(matches + max_in_overlap + max_out_overlap) / (consensusSize + max_in_overlap + max_out_overlap); } /** Pop the specified bubble if it is a simple bubble. * @return whether the bubble is popped */ static bool popSimpleBubble(Graph* pg, vertex_descriptor v) { Graph& g = *pg; unsigned nbranches = g.out_degree(v); assert(nbranches >= 2); vertex_descriptor v1 = *g.adjacent_vertices(v).first; if (g.out_degree(v1) != 1) { #pragma omp atomic g_count.notSimple++; return false; } vertex_descriptor tail = *g.adjacent_vertices(v1).first; if (v == get(vertex_complement, g, tail) // Palindrome || g.in_degree(tail) != nbranches) { #pragma omp atomic g_count.notSimple++; return false; } // Check that every branch is simple and ends at the same node. pair adj = g.adjacent_vertices(v); for (adjacency_iterator it = adj.first; it != adj.second; ++it) { if (g.out_degree(*it) != 1 || g.in_degree(*it) != 1) { #pragma omp atomic g_count.notSimple++; return false; } if (*g.adjacent_vertices(*it).first != tail) { // The branches do not merge back to the same node. #pragma omp atomic g_count.notSimple++; return false; } } if (opt::verbose > 2) #pragma omp critical(cerr) { cerr << "\n* " << get(vertex_name, g, v) << " ->"; for (adjacency_iterator it = adj.first; it != adj.second; ++it) cerr << ' ' << get(vertex_name, g, *it); cerr << " -> " << get(vertex_name, g, tail) << '\n'; } if (nbranches > opt::maxBranches) { // Too many branches. #pragma omp atomic g_count.tooMany++; if (opt::verbose > 1) #pragma omp critical(cerr) cerr << nbranches << " paths (too many)\n"; return false; } vector lengths(nbranches); transform(adj.first, adj.second, lengths.begin(), bind1st(ptr_fun(getLength), &g)); unsigned minLength = *min_element(lengths.begin(), lengths.end()); unsigned maxLength = *max_element(lengths.begin(), lengths.end()); if (maxLength >= opt::maxLength) { // This branch is too long. #pragma omp atomic g_count.tooLong++; if (opt::verbose > 1) #pragma omp critical(cerr) cerr << minLength << '\t' << maxLength << "\t0\t(too long)\n"; return false; } float identity = opt::identity == 0 ? 0 : getAlignmentIdentity(g, v, tail, adj.first, adj.second); bool dissimilar = identity < opt::identity; if (opt::verbose > 1) #pragma omp critical(cerr) cerr << minLength << '\t' << maxLength << '\t' << identity << (dissimilar ? "\t(dissimilar)" : "") << '\n'; if (dissimilar) { // Insufficient identity. #pragma omp atomic g_count.dissimilar++; return false; } #pragma omp atomic g_count.popped++; popBubble(g, v, tail); return true; } /** Add distances to a path. */ static ContigPath addDistance(const Graph& g, const ContigPath& path) { ContigPath out; out.reserve(path.size()); ContigNode u = path.front(); out.push_back(u); for (ContigPath::const_iterator it = path.begin() + 1; it != path.end(); ++it) { ContigNode v = *it; int distance = getDistance(g, u, v); if (distance >= 0) { int numN = distance + opt::k - 1; // by convention assert(numN >= 0); numN = max(numN, 1); out.push_back(ContigNode(numN, 'N')); } out.push_back(v); u = v; } return out; } /** Return the length of the longest path through the bubble. */ static int longestPath(const Graph& g, const Bubble& topo) { typedef graph_traits::edge_descriptor E; typedef graph_traits::out_edge_iterator Eit; typedef graph_traits::vertex_descriptor V; EdgeWeightMap weight(g); map distance; distance[topo.front()] = 0; for (Bubble::const_iterator it = topo.begin(); it != topo.end(); ++it) { V u = *it; Eit eit, elast; for (tie(eit, elast) = out_edges(u, g); eit != elast; ++eit) { E e = *eit; V v = target(e, g); distance[v] = max(distance[v], distance[u] + weight[e]); } } V v = topo.back(); return distance[v] - g[v].length; } /** Scaffold over the bubble between vertices u and w. * Add an edge (u,w) with the distance property set to the length of * the largest branch of the bubble. */ static void scaffoldBubble(Graph& g, const Bubble& bubble) { typedef graph_traits::adjacency_iterator Ait; typedef graph_traits::vertex_descriptor V; assert(opt::scaffold); assert(bubble.size() > 2); V u = bubble.front(), w = bubble.back(); if (edge(u, w, g).second) { // Already scaffolded. return; } assert(isBubble(g, bubble.begin(), bubble.end())); assert(bubble.size() > 2); size_t n = bubble.size() - 2; g_popped.reserve(g_popped.size() + n); for (Bubble::const_iterator it = bubble.begin() + 1; it != bubble.end() - 1; ++it) g_popped.push_back(it->contigIndex()); add_edge(u, w, max(longestPath(g, bubble), 1), g); } /** Pop the specified bubble if it is simple, otherwise scaffold. */ static void popOrScaffoldBubble(Graph& g, const Bubble& bubble) { #pragma omp atomic g_count.bubbles++; if (!popSimpleBubble(&g, bubble.front()) && opt::scaffold) { #pragma omp atomic g_count.scaffold++; scaffoldBubble(g, bubble); } } /** Return the length of the specified vertex in k-mer. */ static unsigned getKmerLength(const ContigProperties& vp) { assert(vp.length >= opt::k); return vp.length - opt::k + 1; } /** Return the mean k-mer coverage of the specified vertex. */ static float getMeanCoverage(const ContigProperties& vp) { return (float)vp.coverage / getKmerLength(vp); } /** Remove contigs with insufficient coverage. */ static void filterGraph(Graph& g) { typedef graph_traits GTraits; typedef GTraits::vertex_descriptor V; typedef GTraits::vertex_iterator Vit; unsigned removedContigs = 0, removedKmer = 0; std::pair urange = vertices(g); for (Vit uit = urange.first; uit != urange.second; ++uit) { V u = *uit; if (get(vertex_removed, g, u)) continue; const ContigProperties& vp = g[u]; if (getMeanCoverage(vp) < opt::minCoverage) { removedContigs++; removedKmer += getKmerLength(vp); clear_vertex(u, g); remove_vertex(u, g); g_popped.push_back(get(vertex_contig_index, g, u)); } } if (opt::verbose > 0) { cerr << "Removed " << removedKmer << " k-mer in " << removedContigs << " contigs with mean k-mer coverage " "less than " << opt::minCoverage << ".\n"; printGraphStats(cerr, g); } } /** Remove the specified contig from the adjacency graph. */ static void removeContig(Graph* g, ContigID id) { ContigNode v(id, false); g->clear_vertex(v); g->remove_vertex(v); } int main(int argc, char** argv) { string commandLine; { ostringstream ss; char** last = argv + argc - 1; copy(argv, last, ostream_iterator(ss, " ")); ss << *last; commandLine = ss.str(); } bool die = false; for (int c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;) { istringstream arg(optarg != NULL ? optarg : ""); switch (c) { case '?': die = true; break; case 'a': arg >> opt::maxBranches; break; case 'b': arg >> opt::maxLength; break; case 'c': arg >> opt::minCoverage; break; case 'g': arg >> opt::graphPath; break; case 'j': arg >> opt::threads; break; case 'k': arg >> opt::k; break; case 'D': arg >> opt::dialign_debug; break; case 'M': arg >> opt::dialign_score; break; case 'P': arg >> opt::dialign_prob; break; case 'p': arg >> opt::identity; break; case 'v': opt::verbose++; break; case OPT_HELP: cout << USAGE_MESSAGE; exit(EXIT_SUCCESS); case OPT_VERSION: cout << VERSION_MESSAGE; exit(EXIT_SUCCESS); } if (optarg != NULL && !arg.eof()) { cerr << PROGRAM ": invalid option: `-" << (char)c << optarg << "'\n"; exit(EXIT_FAILURE); } } if (opt::k <= 0) { cerr << PROGRAM ": " << "missing -k,--kmer option\n"; die = true; } if (argc - optind < 2) { cerr << PROGRAM ": missing arguments\n"; die = true; } if (argc - optind > 2) { cerr << PROGRAM ": too many arguments\n"; die = true; } if (die) { cerr << "Try `" << PROGRAM << " --help' for more information.\n"; exit(EXIT_FAILURE); } init_parameters(); set_parameters_dna(); para->DEBUG = opt::dialign_debug; para->SCR_MATRIX_FILE_NAME = (char*)opt::dialign_score.c_str(); para->DIAG_PROB_FILE_NAME = (char*)opt::dialign_prob.c_str(); initDialign(); const char* contigsPath(argv[optind++]); string adjPath(argv[optind++]); // Read the contig adjacency graph. if (opt::verbose > 0) cerr << "Reading `" << adjPath << "'...\n"; ifstream fin(adjPath.c_str()); assert_good(fin, adjPath); Graph g; fin >> g; assert(fin.eof()); g_contigNames.lock(); if (opt::verbose > 0) printGraphStats(cerr, g); // Read the contigs. Contigs& contigs = g_contigs; if (opt::identity > 0) { if (opt::verbose > 0) cerr << "Reading `" << contigsPath << "'...\n"; FastaReader in(contigsPath, FastaReader::NO_FOLD_CASE); for (FastaRecord rec; in >> rec;) { if (g_contigNames.count(rec.id) == 0) continue; assert(contigs.size() == get(g_contigNames, rec.id)); contigs.push_back(rec.seq); } assert(in.eof()); assert(!contigs.empty()); opt::colourSpace = isdigit(contigs.front()[0]); } // Remove contigs with insufficient coverage. if (opt::minCoverage > 0) filterGraph(g); if (opt::dot) cout << "digraph bubbles {\n"; Bubbles bubbles = discoverBubbles(g); for (Bubbles::const_iterator it = bubbles.begin(); it != bubbles.end(); ++it) popOrScaffoldBubble(g, *it); // Each bubble should be identified twice. Remove the duplicate. sort(g_popped.begin(), g_popped.end()); g_popped.erase(unique(g_popped.begin(), g_popped.end()), g_popped.end()); if (opt::dot) { cout << "}\n"; } else { for (vector::const_iterator it = g_popped.begin(); it != g_popped.end(); ++it) cout << get(g_contigNames, *it) << '\n'; } free_prob_dist(pdist); free(para); if (opt::verbose > 0) cerr << "Bubbles: " << (g_count.bubbles + 1) / 2 << " Popped: " << (g_count.popped + 1) / 2 << " Scaffolds: " << (g_count.scaffold + 1) / 2 << " Complex: " << (g_count.notSimple + 1) / 2 << " Too long: " << (g_count.tooLong + 1) / 2 << " Too many: " << (g_count.tooMany + 1) / 2 << " Dissimilar: " << (g_count.dissimilar + 1) / 2 << '\n'; if (!opt::graphPath.empty()) { // Remove the popped contigs from the adjacency graph. for_each(g_popped.begin(), g_popped.end(), bind1st(ptr_fun(removeContig), &g)); // Assemble unambiguous paths. g_contigNames.unlock(); typedef vector ContigPaths; ContigPaths paths; size_t numContigs = num_vertices(g) / 2; 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#define PROGRAM "PathOverlap" static const char *VERSION_MESSAGE = PROGRAM " (ABySS) " VERSION "\n" "Written by Shaun Jackman and Tony Raymond.\n" "\n" "Copyright 2013 Canada's Michael Smith Genome Science Centre\n"; static const char *USAGE_MESSAGE = "Usage: " PROGRAM " [OPTION]... ADJ PATH\n" "Find paths that overlap. Either output the graph of overlapping\n" "paths, assemble overlapping paths into larger paths, or trim the\n" "overlapping paths.\n" "\n" " Arguments:\n" "\n" " ADJ contig adjacency graph\n" " PATH sequences of contig IDs\n" "\n" " Options:\n" "\n" " -k, --kmer=N k-mer size\n" " -g, --graph=FILE write the contig adjacency graph to FILE\n" " -r, --repeats=FILE write repeat contigs to FILE\n" " --overlap find overlapping paths [default]\n" " --assemble assemble overlapping paths\n" " --trim trim overlapping paths\n" " --adj output the graph in adj format [default]\n" " --dot output the graph in dot format\n" " --sam output the graph in SAM format\n" " -v, --verbose display verbose output\n" " --help display this help and exit\n" " --version output version information and exit\n" "\n" "Report bugs to <" PACKAGE_BUGREPORT ">.\n"; namespace opt { unsigned k; /** Output format. */ int format; // used by ContigProperties /** Write the contig adjacency graph to this file. */ static string graphPath; /** Output the IDs of contigs in overlaps to this file. */ static string repeatContigs; /** Mode of operation. */ enum { /** Find overlapping paths, do not assemble. */ OVERLAP, /** Assemble overlapping paths. */ ASSEMBLE, /** Trim overlapping paths. */ TRIM, }; static int mode; static int verbose; } static const char* shortopts = "g:k:r:v"; enum { OPT_HELP = 1, OPT_VERSION }; static const struct option longopts[] = { { "graph", required_argument, NULL, 'g' }, { "kmer", required_argument, NULL, 'k' }, { "assemble", no_argument, &opt::mode, opt::ASSEMBLE }, { "overlap", no_argument, &opt::mode, opt::OVERLAP }, { "trim", no_argument, &opt::mode, opt::TRIM }, { "adj", no_argument, &opt::format, ADJ, }, { "dot", no_argument, &opt::format, DOT, }, { "sam", no_argument, &opt::format, SAM, }, { "repeats", required_argument, NULL, 'r' }, { "verbose", no_argument, NULL, 'v' }, { "help", no_argument, NULL, OPT_HELP }, { "version", no_argument, NULL, OPT_VERSION }, { NULL, 0, NULL, 0 } }; /** A vertex of the overlap graph. */ struct Vertex { unsigned id; bool sense; /** The number of single-end contigs. */ static unsigned s_offset; Vertex(unsigned id, bool sense) : id(id), sense(sense) { } bool operator ==(const Vertex& v) const { return id == v.id && sense == v.sense; } ContigNode descriptor() const { return ContigNode(s_offset + id, sense); } }; unsigned Vertex::s_offset; /** An alignment of two overlapping contigs. */ struct Overlap { Vertex source; Vertex target; /** Overlap measured in number of contigs. */ unsigned overlap; /** Overlap measured in bp. */ int distance; Overlap(const Vertex& source, const Vertex& target, unsigned overlap, int distance) : source(source), target(target), overlap(overlap), distance(distance) { } }; /** The contig IDs that have been removed from paths. */ static vector s_trimmedContigs; /** The contig graph. */ typedef DirectedGraph DG; typedef ContigGraph Graph; typedef vector Paths; /** Return whether this vertex is a path or a contig. */ static bool isPath(const ContigNode& u) { return u.id() >= Vertex::s_offset; } /** Return a path, complemented if necessary. */ static ContigPath getPath(const Paths& paths, const ContigNode& u) { if (isPath(u)) { unsigned i = u.id() - Vertex::s_offset; return u.sense() ? reverseComplement(paths[i]) : paths[i]; } else return ContigPath(1, u); } /** Read contig paths from the specified file. * @param g the contig adjacency graph * @param inPath the file of contig paths * @param[out] pathIDs the path IDs * @return the paths */ static Paths readPaths(Graph& g, const string& inPath, vector& pathIDs) { typedef graph_traits::vertex_descriptor V; assert(pathIDs.empty()); ifstream fin(inPath.c_str()); if (opt::verbose > 0) cerr << "Reading `" << inPath << "'..." << endl; if (inPath != "-") assert_good(fin, inPath); istream& in = inPath == "-" ? cin : fin; assert_good(in, inPath); Paths paths; string id; ContigPath path; while (in >> id >> path) { if (path.empty()) { // Remove this contig from the graph. V u = find_vertex(id, false, g); clear_vertex(u, g); remove_vertex(u, g); } else { pathIDs.push_back(id); paths.push_back(path); } } assert(in.eof()); return paths; } typedef multimap SeedMap; /** Index the first and last contig of each path to facilitate finding * overlaps between paths. */ static SeedMap makeSeedMap(const Paths& paths) { SeedMap seedMap; for (Paths::const_iterator it = paths.begin(); it != paths.end(); ++it) { if (it->empty()) continue; assert(!it->front().ambiguous()); seedMap.insert(make_pair(it->front(), Vertex(it - paths.begin(), false))); assert(!it->back().ambiguous()); seedMap.insert(make_pair(it->back() ^ 1, Vertex(it - paths.begin(), true))); } return seedMap; } /** Check whether path starts with the sequence [first, last). */ static bool startsWith(ContigPath path, bool rc, ContigPath::const_iterator first, ContigPath::const_iterator last) { if (rc) reverseComplement(path.begin(), path.end()); assert(*first == path.front()); assert(first < last); return unsigned(last - first) > path.size() ? false : equal(first, last, path.begin()); } /** Check whether path starts with the sequence [first, last). */ static unsigned findOverlap(const Graph& g, const Paths& paths, ContigPath::const_iterator first, ContigPath::const_iterator last, const Vertex& v, int &distance) { if (!startsWith(paths[v.id], v.sense, first, last)) return 0; distance = -addProp(g, first, last).length; return last - first; } typedef vector Overlaps; /** Find every path that overlaps with the specified path. */ static void findOverlaps(const Graph& g, const Paths& paths, const SeedMap& seedMap, const Vertex& v, Overlaps& overlaps) { ContigPath rc; if (v.sense) { rc = paths[v.id]; reverseComplement(rc.begin(), rc.end()); } const ContigPath& path = v.sense ? rc : paths[v.id]; for (ContigPath::const_iterator it = path.begin(); it != path.end(); ++it) { if (it->ambiguous()) continue; pair range = seedMap.equal_range(*it); for (SeedMap::const_iterator seed = range.first; seed != range.second; ++seed) { if (v == seed->second) continue; int distance = 0; unsigned overlap = findOverlap(g, paths, it, path.end(), seed->second, distance); if (overlap > 0) overlaps.push_back(Overlap(v, seed->second, overlap, distance)); } } } /** Find every pair of overlapping paths. */ static Overlaps findOverlaps(const Graph& g, const Paths& paths) { SeedMap seedMap = makeSeedMap(paths); Overlaps overlaps; for (Paths::const_iterator it = paths.begin(); it != paths.end(); ++it) { unsigned i = it - paths.begin(); findOverlaps(g, paths, seedMap, Vertex(i, false), overlaps); findOverlaps(g, paths, seedMap, Vertex(i, true), overlaps); } return overlaps; } /** Record the trimmed contigs. */ static void recordTrimmedContigs( ContigPath::const_iterator first, ContigPath::const_iterator last) { for (ContigPath::const_iterator it = first; it != last; ++it) if (!it->ambiguous()) s_trimmedContigs.push_back(it->contigIndex()); } /** Remove ambiguous contigs from the ends of the path. */ static void removeAmbiguousContigs(ContigPath& path) { if (!path.empty() && path.back().ambiguous()) path.erase(path.end() - 1); if (!path.empty() && path.front().ambiguous()) path.erase(path.begin()); } /** Remove the overlapping portion of the specified contig. */ static void removeContigs(ContigPath& path, unsigned first, unsigned last) { assert(first <= path.size()); assert(last <= path.size()); if (first < last) { recordTrimmedContigs(path.begin(), path.begin() + first); recordTrimmedContigs(path.begin() + last, path.end()); path.erase(path.begin() + last, path.end()); path.erase(path.begin(), path.begin() + first); } else { recordTrimmedContigs(path.begin(), path.end()); path.clear(); } removeAmbiguousContigs(path); } /** Find the largest overlap for each contig and remove it. */ static void trimOverlaps(Paths& paths, const Overlaps& overlaps) { vector removed[2]; removed[0].resize(paths.size()); removed[1].resize(paths.size()); for (Overlaps::const_iterator it = overlaps.begin(); it != overlaps.end(); ++it) { unsigned& a = removed[!it->source.sense][it->source.id]; unsigned& b = removed[it->target.sense][it->target.id]; a = max(a, it->overlap); b = max(b, it->overlap); } for (Paths::iterator it = paths.begin(); it != paths.end(); ++it) removeContigs(*it, removed[0][it - paths.begin()], it->size() - removed[1][it - paths.begin()]); } /** Trim the ends of paths that overlap another path. */ static void trimOverlaps(const Graph& g, Paths& paths) { for (Overlaps overlaps = findOverlaps(g, paths); !overlaps.empty(); overlaps = findOverlaps(g, paths)) { cerr << "Found " << overlaps.size() / 2 << " overlaps.\n"; trimOverlaps(paths, overlaps); } } static inline ContigProperties get(vertex_bundle_t, const Graph& g, ContigNode u) { return u.ambiguous() ? ContigProperties(u.length() + opt::k - 1, 0) : g[u]; } /** Add the path overlap edges to the specified graph. */ static void addPathOverlapEdges(Graph& g, const Paths& paths, const vector& pathIDs, const Overlaps& overlaps) { typedef graph_traits::vertex_descriptor V; const bool allowParallelEdge = opt::mode == opt::ASSEMBLE; // Add the path vertices. g_contigNames.unlock(); for (Paths::const_iterator it = paths.begin(); it != paths.end(); ++it) { const ContigPath& path = *it; const string& id = pathIDs[it - paths.begin()]; if (!path.empty()) { V u = merge(g, path.begin(), path.end()); put(vertex_name, g, u, id); } } g_contigNames.lock(); // Remove the single-end contigs that are in paths. for (Paths::const_iterator it = paths.begin(); it != paths.end(); ++it) remove_vertex_if(g, it->begin(), it->end(), not1(std::mem_fun_ref(&ContigNode::ambiguous))); // Add the path edges. for (Overlaps::const_iterator it = overlaps.begin(); it != overlaps.end(); ++it) { V u = it->source.descriptor(); V v = it->target.descriptor(); if (allowParallelEdge || !edge(u, v, g).second) add_edge(u, v, it->distance, static_cast(g)); else if (opt::verbose > 0) cerr << "ambiguous overlap: " << get(vertex_name, g, u) << " -> " << get(vertex_name, g, v) << '\n'; } } typedef graph_traits::edge_descriptor edge_descriptor; /** A property map giving the number of contigs by which two paths * overlap. */ typedef map OverlapMap; /** Return the number of contigs by which the two paths overlap. */ static unsigned getOverlap(const OverlapMap& pmap, graph_traits::vertex_descriptor u, graph_traits::vertex_descriptor v) { if (isPath(u) && isPath(v)) { // Both vertices are paths. OverlapMap::const_iterator it = pmap.find( edge_descriptor(u, v)); return it == pmap.end() ? 0 : it->second; } else { // One of the two vertices is a contig. return 0; } } /** Merge a sequence of overlapping paths. */ static ContigPath mergePaths(const Paths& paths, const OverlapMap& overlaps, const ContigPath& merge) { assert(!merge.empty()); ContigNode u = merge.front(); ContigPath path(getPath(paths, u)); for (ContigPath::const_iterator it = merge.begin() + 1; it != merge.end(); ++it) { ContigNode v = *it; ContigPath vpath(getPath(paths, v)); unsigned overlap = getOverlap(overlaps, u, v); assert(path.size() > overlap); assert(vpath.size() > overlap); assert(equal(path.end() - overlap, path.end(), vpath.begin())); path.insert(path.end(), vpath.begin() + overlap, vpath.end()); u = v; } return path; } /** Return true if the edge e is a path overlap. */ struct IsPathOverlap : unary_function { IsPathOverlap(const Graph& g, const OverlapMap& pmap) : m_g(g), m_pmap(pmap) { } bool operator()(edge_descriptor e) const { return getOverlap(m_pmap, source(e, m_g), target(e, m_g)); } private: const Graph& m_g; const OverlapMap& m_pmap; }; /** Assemble overlapping paths. */ static void assembleOverlappingPaths(Graph& g, Paths& paths, vector& pathIDs) { if (paths.empty()) return; // Find overlapping paths. Overlaps overlaps = findOverlaps(g, paths); addPathOverlapEdges(g, paths, pathIDs, overlaps); // Create a property map of path overlaps. OverlapMap overlapMap; for (Overlaps::const_iterator it = overlaps.begin(); it != overlaps.end(); ++it) overlapMap.insert(OverlapMap::value_type( OverlapMap::key_type( it->source.descriptor(), it->target.descriptor()), it->overlap)); // Assemble unambiguously overlapping paths. Paths merges; assemble_if(g, back_inserter(merges), IsPathOverlap(g, overlapMap)); // Merge overlapping paths. g_contigNames.unlock(); assert(!pathIDs.empty()); setNextContigName(pathIDs.back()); for (Paths::const_iterator it = merges.begin(); it != merges.end(); ++it) { string name = createContigName(); if (opt::verbose > 0) cerr << name << '\t' << *it << '\n'; Vertex u(paths.size(), false); put(vertex_name, g, u.descriptor(), name); pathIDs.push_back(name); paths.push_back(mergePaths(paths, overlapMap, *it)); // Remove the merged paths. for (ContigPath::const_iterator it2 = it->begin(); it2 != it->end(); ++it2) { if (isPath(*it2)) paths[it2->id() - Vertex::s_offset].clear(); } } g_contigNames.lock(); } int main(int argc, char** argv) { string commandLine; { ostringstream ss; char** last = argv + argc - 1; copy(argv, last, ostream_iterator(ss, " ")); ss << *last; commandLine = ss.str(); } bool die = false; for (int c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;) { istringstream arg(optarg != NULL ? optarg : ""); switch (c) { case '?': die = true; break; case 'g': arg >> opt::graphPath; break; case 'k': arg >> opt::k; break; case 'r': arg >> opt::repeatContigs; break; case 'v': opt::verbose++; break; case OPT_HELP: cout << USAGE_MESSAGE; exit(EXIT_SUCCESS); case OPT_VERSION: cout << VERSION_MESSAGE; exit(EXIT_SUCCESS); } if (optarg != NULL && !arg.eof()) { cerr << PROGRAM ": invalid option: `-" << (char)c << optarg << "'\n"; exit(EXIT_FAILURE); } } if (opt::k <= 0) { cerr << PROGRAM ": missing -k,--kmer option\n"; die = true; } if (argc - optind < 2) { cerr << PROGRAM ": missing arguments\n"; die = true; } else if (argc - optind > 2) { cerr << PROGRAM ": too many arguments\n"; die = true; } if (die) { cerr << "Try `" << PROGRAM << " --help' for more information.\n"; exit(EXIT_FAILURE); } const char *adjPath = argv[optind++]; if (opt::verbose > 0) cerr << "Reading `" << adjPath << "'..." << endl; ifstream fin(adjPath); assert_good(fin, adjPath); Graph g; fin >> g; Vertex::s_offset = g.num_vertices() / 2; string pathsFile(argv[optind++]); vector pathIDs; Paths paths = readPaths(g, pathsFile, pathIDs); switch (opt::mode) { case opt::OVERLAP: // Find overlapping paths, do not assemble. addPathOverlapEdges(g, paths, pathIDs, findOverlaps(g, paths)); paths.clear(); if (opt::graphPath.empty()) opt::graphPath = "-"; break; case opt::ASSEMBLE: // Assemble overlapping paths. assembleOverlappingPaths(g, paths, pathIDs); break; case opt::TRIM: // Trim overlapping paths. trimOverlaps(g, paths); // Remove paths consisting of a single contig. for_each_if(paths.begin(), paths.end(), mem_fun_ref(&ContigPath::clear), compose1( bind2nd(equal_to(), 1), mem_fun_ref(&ContigPath::size))); // Add the paths to the graph. addPathOverlapEdges(g, paths, pathIDs, Overlaps()); break; } // Output the paths. for (Paths::const_iterator it = paths.begin(); it != paths.end(); ++it) { if (it->empty()) continue; assert(it->size() != 1); cout << pathIDs[it - paths.begin()] << '\t' << *it << '\n'; } assert(cout.good()); // Output the graph. if (!opt::graphPath.empty()) { ofstream fout; 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#define PROGRAM "ParseAligns" static const char VERSION_MESSAGE[] = PROGRAM " (" PACKAGE_NAME ") " VERSION "\n" "Written by Jared Simpson and Shaun Jackman.\n" "\n" "Copyright 2013 Canada's Michael Smith Genome Science Centre\n"; static const char USAGE_MESSAGE[] = "Usage: " PROGRAM " [OPTION]... [FILE]...\n" "Write pairs that map to the same contig to the file SAME.\n" "Write pairs that map to different contigs to standard output.\n" "Alignments may be read from FILE(s) or standard input.\n" "\n" " Options:\n" "\n" " -l, --min-align=N minimum alignment length\n" " -d, --dist=DISTANCE write distance estimates to this file\n" " -f, --frag=SAME write fragment sizes to this file\n" " -h, --hist=FILE write the fragment size histogram to FILE\n" " --sam alignments are in SAM format\n" " --kaligner alignments are in KAligner format\n" " -c, --cover=COVERAGE coverage cut-off for distance estimates\n" " -v, --verbose display verbose output\n" " --help display this help and exit\n" " --version output version information and exit\n" "\n" "Report bugs to <" PACKAGE_BUGREPORT ">.\n"; namespace opt { unsigned k; // used by DistanceEst static unsigned c; static int verbose; static string distPath; static string fragPath; static string histPath; /** Input alignment format. */ static int inputFormat; enum { KALIGNER, SAM }; /** Output format */ int format = ADJ; // used by Estimate } static const char shortopts[] = "d:l:f:h:c:v"; enum { OPT_HELP = 1, OPT_VERSION }; static const struct option longopts[] = { { "dist", required_argument, NULL, 'd' }, { "min-align", required_argument, NULL, 'l' }, { "frag", required_argument, NULL, 'f' }, { "hist", required_argument, NULL, 'h' }, { "kaligner",no_argument, &opt::inputFormat, opt::KALIGNER }, { "sam", no_argument, &opt::inputFormat, opt::SAM }, { "cover", required_argument, NULL, 'c' }, { "verbose", no_argument, NULL, 'v' }, { "help", no_argument, NULL, OPT_HELP }, { "version", no_argument, NULL, OPT_VERSION }, { NULL, 0, NULL, 0 } }; static struct { size_t alignments; size_t bothUnaligned; size_t oneUnaligned; size_t numDifferent; size_t numFF; size_t numMulti; size_t numSplit; } stats; static ofstream fragFile; static Histogram histogram; typedef vector AlignmentVector; /** A map of read IDs to alignments. */ typedef unordered_map ReadAlignMap; /** A map of contig IDs to distance estimates. */ typedef unordered_map EstimateMap; static EstimateMap estMap; static bool checkUniqueAlignments(const AlignmentVector& alignVec); static string makePairID(string id); /** * Return the size of the fragment demarcated by the specified * alignments. */ static int fragmentSize(const Alignment& a0, const Alignment& a1) { assert(a0.contig == a1.contig); assert(a0.isRC != a1.isRC); const Alignment& f = a0.isRC ? a1 : a0; const Alignment& r = a0.isRC ? a0 : a1; return r - f; } typedef pair Estimate; typedef vector Estimates; static void addEstimate(EstimateMap& map, const Alignment& a, Estimate& est, bool reverse) { //count up the number of estimates that agree bool placed = false; bool a_isRC = a.isRC != reverse; EstimateMap::iterator estimatesIt = map.find(a.contig); if (estimatesIt != map.end()) { Estimates& estimates = estimatesIt->second.estimates[a_isRC]; for (Estimates::iterator estIt = estimates.begin(); estIt != estimates.end(); ++estIt) { if (estIt->first.id() == est.first.id()) { estIt->second.numPairs++; estIt->second.distance += est.second.distance; placed = true; break; } } } if (!placed) map[a.contig].estimates[a_isRC].push_back(est); } static void doReadIntegrity(const ReadAlignMap::value_type& a) { AlignmentVector::const_iterator refAlignIter = a.second.begin(); unsigned firstStart, lastEnd, largestSize; Alignment first, last, largest; firstStart = refAlignIter->read_start_pos; lastEnd = firstStart + refAlignIter->align_length; largestSize = refAlignIter->align_length; first = last = largest = *refAlignIter; ++refAlignIter; //for each alignment in the vector a.second for (; refAlignIter != a.second.end(); ++refAlignIter) { if ((unsigned)refAlignIter->read_start_pos < firstStart) { firstStart = refAlignIter->read_start_pos; first = *refAlignIter; } if ((unsigned)(refAlignIter->read_start_pos + refAlignIter->align_length) > lastEnd) { lastEnd = refAlignIter->read_start_pos + refAlignIter->align_length; last = *refAlignIter; } if ((unsigned)refAlignIter->align_length > largestSize) { largestSize = refAlignIter->align_length; largest = *refAlignIter; } } if (largest.contig != last.contig) { Estimate est; unsigned largest_end = largest.read_start_pos + largest.align_length - opt::k; int distance = last.read_start_pos - largest_end; est.first = find_vertex( last.contig, largest.isRC != last.isRC, g_contigNames); est.second.distance = distance - opt::k; est.second.numPairs = 1; est.second.stdDev = 0; addEstimate(estMap, largest, est, false); } if (largest.contig != first.contig && largest.contig != last.contig) { Estimate est; unsigned first_end = first.read_start_pos + first.align_length - opt::k; int distance = last.read_start_pos - first_end; est.first = find_vertex( last.contig, first.isRC != last.isRC, g_contigNames); est.second.distance = distance - opt::k; est.second.numPairs = 1; est.second.stdDev = 0; addEstimate(estMap, first, est, false); } if (largest.contig != first.contig) { largest.flipQuery(); first.flipQuery(); Estimate est; unsigned largest_end = largest.read_start_pos + largest.align_length - opt::k; int distance = first.read_start_pos - largest_end; est.first = find_vertex( first.contig, largest.isRC != first.isRC, g_contigNames); est.second.distance = distance - opt::k; est.second.numPairs = 1; est.second.stdDev = 0; addEstimate(estMap, largest, est, false); } #if 0 //for each alignment in the vector a.second for (AlignmentVector::const_iterator refAlignIter = a.second.begin(); refAlignIter != a.second.end(); ++refAlignIter) { //for each alignment after the current one for (AlignmentVector::const_iterator alignIter = a.second.begin(); alignIter != a.second.end(); ++alignIter) { //make sure both alignments aren't for the same contig if (alignIter->contig != refAlignIter->contig) { Estimate est; //Make sure the distance is read as 0 if the two contigs are //directly adjacent to each other. A -ve number suggests an //overlap. assert(refAlignIter->read_start_pos != alignIter->read_start_pos); const Alignment& a = refAlignIter->read_start_pos < alignIter->read_start_pos ? *refAlignIter : *alignIter; const Alignment& b = refAlignIter->read_start_pos > alignIter->read_start_pos ? *refAlignIter : *alignIter; unsigned a_end = a.read_start_pos + a.align_length - opt::k; int distance = b.read_start_pos - a_end; est.nID = ContigID(b.contig); est.distance = distance - opt::k; est.numPairs = 1; est.stdDev = 0; //weird file format... est.isRC = a.isRC != b.isRC; addEstimate(estMap, a, est, false); } } } #endif } static void generateDistFile() { ofstream distFile(opt::distPath.c_str()); assert(distFile.is_open()); for (EstimateMap::iterator mapIt = estMap.begin(); mapIt != estMap.end(); ++mapIt) { //Skip empty iterators assert(!mapIt->second.estimates[0].empty() || !mapIt->second.estimates[1].empty()); distFile << mapIt->first; for (int refIsRC = 0; refIsRC <= 1; refIsRC++) { if (refIsRC) distFile << " ;"; for (Estimates::iterator vecIt = mapIt->second.estimates[refIsRC].begin(); vecIt != mapIt->second.estimates[refIsRC].end(); ++vecIt) { vecIt->second.distance = (int)round((double)vecIt->second.distance / (double)vecIt->second.numPairs); if (vecIt->second.numPairs >= opt::c && vecIt->second.numPairs != 0 /*&& vecIt->distance > 1 - opt::k*/) distFile << ' ' << get(g_contigNames, vecIt->first) << ',' << vecIt->second; } } distFile << '\n'; assert_good(distFile, opt::distPath); } distFile.close(); } static bool isSingleEnd(const string& id); static bool needsFlipping(const string& id); /** * Return an alignment flipped as necessary to produce an alignment * pair whose expected orientation is forward-reverse. If the * expected orientation is forward-forward, then reverse the first * alignment, so that the alignment is forward-reverse, which is * required by DistanceEst. */ static const Alignment flipAlignment(const Alignment& a, const string& id) { return needsFlipping(id) ? a.flipQuery() : a; } static void handleAlignmentPair(const ReadAlignMap::value_type& curr, const ReadAlignMap::value_type& pair) { const string& currID = curr.first; const string& pairID = pair.first; // Both reads must align to a unique location. // The reads are allowed to span more than one contig, but // at least one of the two reads must span no more than // two contigs. const unsigned MAX_SPAN = 2; if (curr.second.empty() && pair.second.empty()) { stats.bothUnaligned++; } else if (curr.second.empty() || pair.second.empty()) { stats.oneUnaligned++; } else if (!checkUniqueAlignments(curr.second) || !checkUniqueAlignments(pair.second)) { stats.numMulti++; } else if (curr.second.size() > MAX_SPAN && pair.second.size() > MAX_SPAN) { stats.numSplit++; } else { // Iterate over the vectors, outputting the aligments bool counted = false; for (AlignmentVector::const_iterator refAlignIter = curr.second.begin(); refAlignIter != curr.second.end(); ++refAlignIter) { for (AlignmentVector::const_iterator pairAlignIter = pair.second.begin(); pairAlignIter != pair.second.end(); ++pairAlignIter) { const Alignment& a0 = flipAlignment(*refAlignIter, currID); const Alignment& a1 = flipAlignment(*pairAlignIter, pairID); bool sameTarget = a0.contig == a1.contig; if (sameTarget && curr.second.size() == 1 && pair.second.size() == 1) { // Same target and the only alignment. if (a0.isRC != a1.isRC) { // Correctly oriented. Add this alignment to // the distribution of fragment sizes. int size = fragmentSize(a0, a1); histogram.insert(size); if (!opt::fragPath.empty()) { fragFile << size << '\n'; assert(fragFile.good()); } } else stats.numFF++; counted = true; } bool outputSameTarget = opt::fragPath.empty() && opt::histPath.empty(); if (!sameTarget || outputSameTarget) { cout << SAMRecord(a0, a1) << '\n' << SAMRecord(a1, a0) << '\n'; assert(cout.good()); } } } if (!counted) stats.numDifferent++; } } static void printProgress(const ReadAlignMap& map) { if (opt::verbose == 0) return; static size_t prevBuckets; if (prevBuckets == 0) prevBuckets = map.bucket_count(); size_t buckets = map.bucket_count(); if (stats.alignments % 1000000 == 0 || buckets != prevBuckets) { prevBuckets = buckets; size_t size = map.size(); cerr << "Read " << stats.alignments << " alignments. " "Hash load: " << size << " / " << buckets << " = " << (float)size / buckets << " using " << toSI(getMemoryUsage()) << "B." << endl; } } static void handleAlignment( const ReadAlignMap::value_type& alignments, ReadAlignMap& out) { if (!isSingleEnd(alignments.first)) { string pairID = makePairID(alignments.first); ReadAlignMap::iterator pairIter = out.find(pairID); if (pairIter != out.end()) { handleAlignmentPair(*pairIter, alignments); out.erase(pairIter); } else if (!out.insert(alignments).second) { cerr << "error: duplicate read ID `" << alignments.first << "'\n"; exit(EXIT_FAILURE); } } if (!opt::distPath.empty() && alignments.second.size() >= 2) doReadIntegrity(alignments); stats.alignments++; printProgress(out); } static void readAlignment(const string& line, ReadAlignMap& out) { istringstream s(line); pair v; switch (opt::inputFormat) { case opt::SAM: { SAMRecord sam; s >> sam; assert(s); v.first = sam.qname; if (sam.isRead1()) v.first += "/1"; else if (sam.isRead2()) v.first += "/2"; if (!sam.isUnmapped()) v.second.push_back(sam); break; } case opt::KALIGNER: { s >> v.first; assert(s); v.second.reserve(count(line.begin(), line.end(), '\t')); v.second.assign( istream_iterator(s), istream_iterator()); assert(s.eof()); break; } } handleAlignment(v, out); } static void readAlignments(istream& in, ReadAlignMap* pout) { for (string line; getline(in, line);) if (line.empty() || line[0] == '@') cout << line << '\n'; else readAlignment(line, *pout); assert(in.eof()); } static void readAlignmentsFile(string path, ReadAlignMap* pout) { if (opt::verbose > 0) cerr << "Reading `" << path << "'..." << endl; ifstream fin(path.c_str()); assert_good(fin, path); readAlignments(fin, pout); fin.close(); } /** Return the specified number formatted as a percent. */ static string percent(size_t x, size_t n) { ostringstream ss; ss << setw((int)log10(n) + 1) << x; if (x > 0) ss << " " << setprecision(3) << (float)100*x/n << '%'; return ss.str(); } int main(int argc, char* const* argv) { bool die = false; for (int c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;) { istringstream arg(optarg != NULL ? optarg : ""); switch (c) { case '?': die = true; break; case 'l': arg >> opt::k; break; case 'c': arg >> opt::c; break; case 'd': arg >> opt::distPath; break; case 'f': arg >> opt::fragPath; break; case 'h': arg >> opt::histPath; break; case 'v': opt::verbose++; break; case OPT_HELP: cout << USAGE_MESSAGE; exit(EXIT_SUCCESS); case OPT_VERSION: cout << VERSION_MESSAGE; exit(EXIT_SUCCESS); } if (optarg != NULL && !arg.eof()) { cerr << PROGRAM ": invalid option: `-" << (char)c << optarg << "'\n"; exit(EXIT_FAILURE); } } if (opt::k <= 0 && opt::inputFormat == opt::KALIGNER) { cerr << PROGRAM ": " << "missing -k,--kmer option\n"; die = true; } if (die) { cerr << "Try `" << PROGRAM << " --help' for more information.\n"; exit(EXIT_FAILURE); } if (!opt::fragPath.empty()) { fragFile.open(opt::fragPath.c_str()); assert(fragFile.is_open()); } ReadAlignMap alignTable(1); if (optind < argc) { for_each(argv + optind, argv + argc, bind2nd(ptr_fun(readAlignmentsFile), &alignTable)); } else { if (opt::verbose > 0) cerr << "Reading from standard input..." << endl; readAlignments(cin, &alignTable); } if (opt::verbose > 0) cerr << "Read " << stats.alignments << " alignments" << endl; unsigned numRF = histogram.count(INT_MIN, 0); unsigned numFR = histogram.count(1, INT_MAX); size_t sum = alignTable.size() + stats.bothUnaligned + stats.oneUnaligned + numFR + numRF + stats.numFF + stats.numDifferent + stats.numMulti + stats.numSplit; cerr << "Mateless " << percent(alignTable.size(), sum) << "\n" "Unaligned " << percent(stats.bothUnaligned, sum) << "\n" "Singleton " << percent(stats.oneUnaligned, sum) << "\n" "FR " << percent(numFR, sum) << "\n" "RF " << percent(numRF, sum) << "\n" "FF " << percent(stats.numFF, sum) << "\n" "Different " << percent(stats.numDifferent, sum) << "\n" "Multimap " << percent(stats.numMulti, sum) << "\n" "Split " << percent(stats.numSplit, sum) << "\n" "Total " << sum << endl; if (!opt::distPath.empty()) generateDistFile(); if (!opt::fragPath.empty()) fragFile.close(); if (!opt::histPath.empty()) { ofstream histFile(opt::histPath.c_str()); assert(histFile.is_open()); histFile << histogram; assert(histFile.good()); histFile.close(); } if (numFR < numRF) histogram = histogram.negate(); histogram.eraseNegative(); histogram.removeNoise(); histogram.removeOutliers(); Histogram h = histogram.trimFraction(0.0001); if (opt::verbose > 0) cerr << "Stats mean: " << setprecision(4) << h.mean() << " " "median: " << setprecision(4) << h.median() << " " "sd: " << setprecision(4) << h.sd() << " " "n: " << h.size() << " " "min: " << h.minimum() << " max: " << h.maximum() << '\n' << h.barplot() << endl; if (stats.numFF > numFR && stats.numFF > numRF) { cerr << "error: The mate pairs of this library are oriented " "forward-forward (FF), which is not supported by ABySS." << endl; exit(EXIT_FAILURE); } return 0; } /** Return whether any k-mer in the query is aligned more than once. */ static bool checkUniqueAlignments(const AlignmentVector& alignVec) { assert(!alignVec.empty()); if (alignVec.size() == 1) return true; unsigned nKmer = alignVec.front().read_length - opt::k + 1; vector coverage(nKmer); for (AlignmentVector::const_iterator iter = alignVec.begin(); iter != alignVec.end(); ++iter) { assert((unsigned)iter->align_length >= opt::k); unsigned end = iter->read_start_pos + iter->align_length - opt::k + 1; assert(end <= nKmer); for (unsigned i = iter->read_start_pos; i < end; i++) coverage[i]++; } for (unsigned i = 0; i < nKmer; ++i) if (coverage[i] > 1) return false; return true; } static bool replaceSuffix(string& s, const string& suffix0, const string& suffix1) { if (endsWith(s, suffix0)) { s.replace(s.length() - suffix0.length(), string::npos, suffix1); return true; } else if (endsWith(s, suffix1)) { s.replace(s.length() - suffix1.length(), string::npos, suffix0); return true; } else return false; } /** Return true if the specified read ID is of a single-end read. */ static bool isSingleEnd(const string& id) { unsigned l = id.length(); return endsWith(id, ".fn") || (l > 6 && id.substr(l-6, 5) == ".part"); } /** Return the mate ID of the specified read ID. */ static string makePairID(string id) { if (equal(id.begin(), id.begin() + 3, "SRR")) return id; assert(!id.empty()); char& c = id[id.length() - 1]; switch (c) { case '1': c = '2'; return id; case '2': c = '1'; return id; case 'A': c = 'B'; return id; case 'B': c = 'A'; return id; case 'F': c = 'R'; return id; case 'R': c = 'F'; return id; case 'f': c = 'r'; return id; case 'r': c = 'f'; return id; } if (replaceSuffix(id, "forward", "reverse") || replaceSuffix(id, "F3", "R3")) return id; cerr << "error: read ID `" << id << "' must end in one of\n" "\t1 and 2 or A and B or F and R or" " F3 and R3 or forward and reverse\n"; exit(EXIT_FAILURE); } static bool needsFlipping(const string& id) { return endsWith(id, "F3"); } abyss-1.3.6/ParseAligns/abyss-fixmate.cc000644 002433 001057 00000025653 12176305753 021676 0ustar00traymondassembly000000 000000 #include "Histogram.h" #include "IOUtil.h" #include "MemoryUtil.h" #include "SAM.h" #include "StringUtil.h" #include "Uncompress.h" #include "UnorderedMap.h" #include "ContigID.h" #include #include #include #include #include #include #include #include #include #include #include using namespace std; #define PROGRAM "abyss-fixmate" static const char VERSION_MESSAGE[] = PROGRAM " (" PACKAGE_NAME ") " VERSION "\n" "Written by Shaun Jackman.\n" "\n" "Copyright 2013 Canada's Michael Smith Genome Science Centre\n"; static const char USAGE_MESSAGE[] = "Usage: " PROGRAM " [OPTION]... [FILE]...\n" "Write read pairs that map to the same contig to the file SAME.\n" "Write read pairs that map to different contigs to stdout.\n" "Alignments may be in FILE(s) or standard input.\n" "\n" " Options:\n" "\n" " --no-qname set the qname to * [default]\n" " --qname do not alter the qname\n" " -l, --min-align=N the minimal alignment size [1]\n" " -s, --same=SAME write properly-paired reads to this file\n" " -h, --hist=FILE write the fragment size histogram to FILE\n" " -c, --cov=FILE write the physical coverage to FILE\n" " -v, --verbose display verbose output\n" " --help display this help and exit\n" " --version output version information and exit\n" "\n" "Report bugs to <" PACKAGE_BUGREPORT ">.\n"; namespace opt { static string fragPath; static string histPath; static string covPath; static int qname; static int verbose; } static const char shortopts[] = "h:c:l:s:v"; enum { OPT_HELP = 1, OPT_VERSION }; static const struct option longopts[] = { { "qname", no_argument, &opt::qname, 1 }, { "no-qname", no_argument, &opt::qname, 0 }, { "min-align", required_argument, NULL, 'l' }, { "hist", required_argument, NULL, 'h' }, { "cov", required_argument, NULL, 'c' }, { "same", required_argument, NULL, 's' }, { "verbose", no_argument, NULL, 'v' }, { "help", no_argument, NULL, OPT_HELP }, { "version", no_argument, NULL, OPT_VERSION }, { NULL, 0, NULL, 0 } }; static struct { size_t alignments; size_t bothUnaligned; size_t oneUnaligned; size_t numDifferent; size_t numFF; } stats; static ofstream g_fragFile; static Histogram g_histogram; static ofstream g_covFile; static vector< vector > g_contigCov; static void incrementRange(SAMRecord& a) { unsigned inx = get(g_contigNames, a.rname); g_contigCov[inx][a.pos]++; assert(a.isize >= 0); unsigned end = a.pos + a.isize; if (end >= g_contigCov[inx].size()) end = g_contigCov[inx].size() - 1; g_contigCov[inx][end]--; } static void handlePair(SAMRecord& a0, SAMRecord& a1) { if ((a0.isRead1() && a1.isRead1()) || (a0.isRead2() && a1.isRead2())) { cerr << "error: duplicate read ID `" << a0.qname << (a0.isRead1() ? "/1" : "") << (a0.isRead2() ? "/2" : "") << "'\n"; exit(EXIT_FAILURE); } if (!opt::qname) a0.qname = a1.qname = "*"; fixMate(a0, a1); if (a0.isUnmapped() && a1.isUnmapped()) { // Both reads are unaligned. stats.bothUnaligned++; } else if (a0.isUnmapped() || a1.isUnmapped()) { // One read is unaligned. stats.oneUnaligned++; } else if (a0.rname != a1.rname) { // Different targets. stats.numDifferent++; // Set the mapping quality of both reads to their minimum. a0.mapq = a1.mapq = min(a0.mapq, a1.mapq); if (!opt::histPath.empty()) cout << a0 << '\n' << a1 << '\n'; } else if (a0.isReverse() == a1.isReverse()) { // Same target, FF orientation. stats.numFF++; } else { // Same target, FR or RF orientation. if (!opt::covPath.empty()) { SAMRecord a = a0.isize >= 0 ? a0 : a1; incrementRange(a); } g_histogram.insert(a0.isReverse() ? a1.isize : a0.isize); if (!opt::fragPath.empty()) { g_fragFile << a0 << '\n' << a1 << '\n'; assert(g_fragFile.good()); } } if (opt::histPath.empty()) { cout << a0 << '\n' << a1 << '\n'; assert(cout.good()); } } #if SAM_SEQ_QUAL typedef unordered_map Alignments; #else typedef unordered_map Alignments; #endif static void printProgress(const Alignments& map) { if (opt::verbose == 0) return; static size_t prevBuckets; if (prevBuckets == 0) prevBuckets = map.bucket_count(); size_t buckets = map.bucket_count(); if (stats.alignments % 1000000 == 0 || buckets != prevBuckets) { prevBuckets = buckets; size_t size = map.size(); cerr << "Read " << stats.alignments << " alignments. " << "Hash load: " << size << " / " << buckets << " = " << (float)size / buckets << " using " << toSI(getMemoryUsage()) << "B." << endl; } } static void handleAlignment(SAMRecord& sam, Alignments& map) { pair it = map.insert( make_pair(sam.qname, sam)); if (!it.second) { #if SAM_SEQ_QUAL SAMRecord& a0 = it.first->second; #else SAMRecord a0(it.first->second, it.first->first); #endif handlePair(a0, sam); map.erase(it.first); } stats.alignments++; printProgress(map); } static void assert_eof(istream& in) { if (in.eof()) return; in.clear(); string line; getline(in, line); cerr << "error: `" << line << "'\n"; exit(EXIT_FAILURE); } /** Print physical coverage in wiggle format. */ static void printCov(string file) { ofstream out(file.c_str()); for (unsigned i = 0; i < g_contigCov.size(); i++) { out << "variableStep\tchrom=" << get(g_contigNames, i) << '\n'; int prev = g_contigCov[i][0]; if (prev != 0) out << "0\t" << prev << '\n'; for (unsigned j = 1; j < g_contigCov[i].size(); j++) { prev += g_contigCov[i][j]; if (prev != 0) out << j << "\t" << prev << '\n'; } } } void parseTag(string line) { stringstream ss(line); string tag; char type[2]; string id; char delim; unsigned length; ss >> tag; if (tag != "@SQ") return; while (ss >> type[0] >> type[1] >> delim) { assert(delim == ':'); if (type[0] == 'S' && type[1] == 'N') ss >> id; else if (type[0] == 'L' && type[1] == 'N') ss >> length; } assert(length > 0); assert(id.size() > 0); put(g_contigNames, g_contigCov.size(), id); g_contigCov.push_back(vector(length)); } static void readAlignments(istream& in, Alignments* pMap) { for (SAMRecord sam; in >> ws;) { if (in.peek() == '@') { string line; getline(in, line); assert(in); if (!opt::covPath.empty()) parseTag(line); cout << line << '\n'; if (!opt::fragPath.empty()) g_fragFile << line << '\n'; } else if (in >> sam) handleAlignment(sam, *pMap); } if (!opt::covPath.empty()) printCov(opt::covPath); assert_eof(in); } static void readAlignmentsFile(string path, Alignments* pMap) { if (opt::verbose > 0) cerr << "Reading `" << path << "'..." << endl; ifstream fin(path.c_str()); assert_good(fin, path); readAlignments(fin, pMap); fin.close(); } /** Return the specified number formatted as a percent. */ static string percent(size_t x, size_t n) { ostringstream ss; ss << setw((int)log10(n) + 1) << x; if (x > 0) ss << " " << setprecision(3) << (float)100*x/n << '%'; return ss.str(); } /** Print statistics of the specified histogram. */ static void printHistogramStats(const Histogram& h) { cerr << "Stats mean: " << setprecision(4) << h.mean() << " " "median: " << setprecision(4) << h.median() << " " "sd: " << setprecision(4) << h.sd() << " " "n: " << h.size() << " " "min: " << h.minimum() << " " "max: " << h.maximum() << '\n' << h.barplot() << endl; } int main(int argc, char* const* argv) { bool die = false; for (int c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;) { istringstream arg(optarg != NULL ? optarg : ""); switch (c) { case '?': die = true; break; case 'l': arg >> opt::minAlign; break; case 's': arg >> opt::fragPath; break; case 'h': arg >> opt::histPath; break; case 'c': arg >> opt::covPath; break; case 'v': opt::verbose++; break; case OPT_HELP: cout << USAGE_MESSAGE; exit(EXIT_SUCCESS); case OPT_VERSION: cout << VERSION_MESSAGE; exit(EXIT_SUCCESS); } if (optarg != NULL && !arg.eof()) { cerr << PROGRAM ": invalid option: `-" << (char)c << optarg << "'\n"; exit(EXIT_FAILURE); } } if (die) { cerr << "Try `" << PROGRAM << " --help' for more information.\n"; exit(EXIT_FAILURE); } if (!opt::fragPath.empty()) { g_fragFile.open(opt::fragPath.c_str()); assert(g_fragFile.is_open()); } Alignments alignments(1); if (optind < argc) { for_each(argv + optind, argv + argc, bind2nd(ptr_fun(readAlignmentsFile), &alignments)); } else { if (opt::verbose > 0) cerr << "Reading from standard input..." << endl; readAlignments(cin, &alignments); } if (opt::verbose > 0) cerr << "Read " << stats.alignments << " alignments" << endl; // Print the unpaired alignments. if (opt::histPath.empty()) { for (Alignments::iterator it = alignments.begin(); it != alignments.end(); it++) { #if SAM_SEQ_QUAL SAMRecord& a0 = it->second; #else SAMRecord a0(it->second, it->first); #endif cout << a0 << '\n'; assert(cout.good()); } } unsigned numRF = g_histogram.count(INT_MIN, 0); unsigned numFR = g_histogram.count(1, INT_MAX); size_t sum = alignments.size() + stats.bothUnaligned + stats.oneUnaligned + numFR + numRF + stats.numFF + stats.numDifferent; cerr << "Mateless " << percent(alignments.size(), sum) << "\n" "Unaligned " << percent(stats.bothUnaligned, sum) << "\n" "Singleton " << percent(stats.oneUnaligned, sum) << "\n" "FR " << percent(numFR, sum) << "\n" "RF " << percent(numRF, sum) << "\n" "FF " << percent(stats.numFF, sum) << "\n" "Different " << percent(stats.numDifferent, sum) << "\n" "Total " << sum << endl; if (alignments.size() == sum) { cerr << PROGRAM ": error: All reads are mateless. 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using namespace boost::lambda; #if !__GXX_EXPERIMENTAL_CXX0X__ using boost::cref; using boost::ref; #endif #define PROGRAM "Overlap" static const char VERSION_MESSAGE[] = PROGRAM " (" PACKAGE_NAME ") " VERSION "\n" "Written by Shaun Jackman.\n" "\n" "Copyright 2013 Canada's Michael Smith Genome Science Centre\n"; static const char USAGE_MESSAGE[] = "Usage: " PROGRAM " [OPTION]... CONTIGS ADJ DIST\n" "Find overlaps between blunt contigs that have negative distance\n" "estimates. Add edges to the overlap graph.\n" "\n" " Options:\n" "\n" " -k, --kmer=KMER_SIZE k-mer size\n" " -m, --min=OVERLAP require a minimum of OVERLAP bases\n" " default is 5 bases\n" " --scaffold join contigs with Ns [default]\n" " --no-scaffold do not scaffold\n" " --mask-repeat join contigs at a simple repeat and mask\n" " the repeat sequence [default]\n" " --no-merge-repeat don't join contigs at a repeat\n" " -g, --graph=FILE write the contig adjacency graph to FILE\n" " -o, --out=FILE write result to FILE\n" " -v, --verbose display verbose output\n" " --help display this help and exit\n" " --version output version information and exit\n" "\n" "Report bugs to <" PACKAGE_BUGREPORT ">.\n"; namespace opt { unsigned k; // used by ContigGraph static unsigned minimum_overlap = 5; static int mask = 1; static int scaffold = 1; /** The acceptable error of a distance estimate. */ unsigned distanceError = 6; /** Write the contig adjacency graph to this file. */ static string graphPath; /** Write the new contigs to this file. */ static string out; /** Output format */ int format = ADJ; // used by ContigProperties } static const char shortopts[] = "g:k:m:o:v"; enum { OPT_HELP = 1, OPT_VERSION }; static const struct option longopts[] = { { "kmer", required_argument, NULL, 'k' }, { "min", required_argument, NULL, 'm' }, { "scaffold", no_argument, &opt::scaffold, 1 }, { "no-scaffold", no_argument, &opt::scaffold, 0 }, { "mask-repeat", no_argument, &opt::mask, 1 }, { "no-merge-repeat", no_argument, &opt::mask, 0 }, { "out", required_argument, NULL, 'o' }, { "verbose", no_argument, NULL, 'v' }, { "help", no_argument, NULL, OPT_HELP }, { "version", no_argument, NULL, OPT_VERSION }, { NULL, 0, NULL, 0 } }; /** Contig sequences. */ static vector g_contigs; /** Contig adjacency graph. */ typedef ContigGraph > Graph; static struct { unsigned overlap; unsigned scaffold; unsigned none; unsigned tooshort; unsigned homopolymer; unsigned motif; unsigned ambiguous; } stats; /** Return the sequence of the specified contig. */ static string sequence(const ContigNode& id) { const string& seq = g_contigs[id.id()]; return id.sense() ? reverseComplement(seq) : seq; } static unsigned findOverlap(const Graph& g, const ContigNode& t_id, const ContigNode& h_id, bool& mask) { mask = false; string t = sequence(t_id); string h = sequence(h_id); unsigned len = min(t.length(), h.length()); vector overlaps; overlaps.reserve(len); for (unsigned overlap = len; overlap >= 1; overlap--) { if (t.substr(t.length()-overlap, overlap) == h.substr(0, overlap)) overlaps.push_back(overlap); } if (opt::verbose > 0) { cout << get(vertex_name, g, t_id) << '\t' << get(vertex_name, g, h_id); for (vector::const_iterator i = overlaps.begin(); i != overlaps.end(); ++i) cout << '\t' << *i; cout << '\n'; } if (overlaps.empty()) { stats.none++; return 0; } if (overlaps[0] < opt::minimum_overlap) { stats.tooshort++; return 0; } if (overlaps.size() >= 3 && overlaps[0]-overlaps[1] == overlaps[1]-overlaps[2]) { // Homopolymer run or motif. if (overlaps[0]-overlaps[1] == 1) stats.homopolymer++; else stats.motif++; mask = true; } return overlaps[0]; } static FastaRecord newContig(const Graph& g, const ContigNode& t, const ContigNode& v, int dist, const string& seq) { ostringstream comment; comment << seq.length() << " 0 " << get(vertex_name, g, t) << ' ' << get(vertex_name, g, v) << ' ' << dist; return FastaRecord(createContigName(), comment.str(), seq); } /** An overlap of two sequences. */ struct Overlap : public DistanceEst { unsigned overlap; bool mask; Overlap() : overlap(UINT_MAX), mask(false) { } Overlap(int) { assert(false); } Overlap(const DistanceEst& est, unsigned overlap, bool mask) : DistanceEst(est), overlap(overlap), mask(mask) { } bool operator==(const Overlap& o) const { return overlap == o.overlap; } operator Distance() const { assert(overlap > 0); return -overlap; } friend ostream& operator<<(ostream& out, const Overlap& o) { return out << "d=" << (o.overlap > 0 ? -(int)o.overlap : o.distance); } }; /** Create a contig representing the gap between contigs u and v. */ static FastaRecord createGapContig(const Graph& g, const ContigNode& u, const ContigNode& v, const Overlap& o) { assert(opt::scaffold); assert(o.overlap == 0); stats.scaffold++; int distance = o.distance; if (opt::verbose > 0) cout << get(vertex_name, g, u) << '\t' << get(vertex_name, g, v) << "\t(" << distance << ")\n"; assert(distance < 100000); string gap = distance <= 0 ? string("n") : string(distance, 'N'); const string& useq = sequence(u); const string& vseq = sequence(v); unsigned overlap = opt::k - 1; // by convention return newContig(g, u, v, distance, useq.substr(useq.length() - overlap) + gap + vseq.substr(0, overlap)); } /** The scaffold graph. Edges join two blunt contigs that are joined * by a distance estimate. */ typedef ContigGraph > OverlapGraph; /** * Check for an overlap between the specified pair of contigs. * Add the size of the overlap to the edge properties. Add the * complementary edge if it does not exist in the graph. * @param goverlap the contig overlap graph * @param g the scaffold graph * @return true if the contigs overlap */ static bool checkEdgeForOverlap(const Graph& goverlap, OverlapGraph& g, graph_traits::edge_descriptor e) { typedef graph_traits::vertex_descriptor V; typedef graph_traits::edge_descriptor E; typedef edge_bundle_type::type EP; V u = source(e, g), v = target(e, g); V uc = get(vertex_complement, g, u); V vc = get(vertex_complement, g, v); assert(u != v); assert(u != vc); EP& ep = g[e]; if (ep.overlap != UINT_MAX) { // Found the complementary overlap. return ep.overlap > 0 || opt::scaffold; } if (ep.distance >= 0 && !opt::scaffold) { // Positive distance estimate and not scaffolding. return false; } if (out_degree(u, goverlap) > 0 || in_degree(v, goverlap) > 0) { // Not blunt. return false; } bool mask = false; unsigned overlap = ep.distance - (int)allowedError(ep.stdDev) <= 0 ? findOverlap(goverlap, u, v, mask) : 0; if (mask && !opt::mask) { // Ambiguous overlap. return false; } if (overlap == 0 && !opt::scaffold) { // No overlap and not scaffolding. return false; } ep.overlap = overlap; ep.mask = mask; pair ecomplement = edge(vc, uc, g); if (ecomplement.second) { // Modify the complementary edge. g[ecomplement.first] = ep; } else { // Add the complementary edge. assert(vc != u); add_edge(vc, uc, ep, static_cast(g)); } return true; } static void findOverlap(const Graph& g, ContigID refID, bool rc, const ContigNode& pair, const DistanceEst& est, OverlapGraph& out) { if (refID == pair.id() || (est.distance >= 0 && !opt::scaffold)) return; ContigNode ref(refID, false); const ContigNode& t = rc ? pair : ref; const ContigNode& h = rc ? ref : pair; if (out_degree(t, g) > 0 || in_degree(h, g) > 0 || edge(t, h, out).second) return; bool mask = false; unsigned overlap = est.distance - (int)allowedError(est.stdDev) <= 0 ? findOverlap(g, t, h, mask) : 0; if (mask && !opt::mask) return; if (overlap > 0 || opt::scaffold) add_edge(t, h, Overlap(est, overlap, mask), out); } static void readContigs(const char *contigPath) { FastaReader in(contigPath, FastaReader::FOLD_CASE); for (FastaRecord rec; in >> rec;) g_contigs.push_back(rec.seq); assert(in.eof()); assert(!g_contigs.empty()); opt::colourSpace = isdigit(g_contigs[0][0]); } int main(int argc, char** argv) { string commandLine; { ostringstream ss; char** last = argv + argc - 1; copy(argv, last, ostream_iterator(ss, " ")); ss << *last; commandLine = ss.str(); } bool die = false; for (int c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;) { istringstream arg(optarg != NULL ? optarg : ""); switch (c) { case '?': die = true; break; case 'g': arg >> opt::graphPath; break; case 'k': arg >> opt::k; break; case 'm': arg >> opt::minimum_overlap; break; case 'o': arg >> opt::out; break; case 'v': opt::verbose++; break; case OPT_HELP: cout << USAGE_MESSAGE; exit(EXIT_SUCCESS); case OPT_VERSION: cout << VERSION_MESSAGE; exit(EXIT_SUCCESS); } if (optarg != NULL && !arg.eof()) { cerr << PROGRAM ": invalid option: `-" << (char)c << optarg << "'\n"; exit(EXIT_FAILURE); } } if (opt::k <= 0) { cerr << PROGRAM ": " << "missing -k,--kmer option\n"; die = true; } if (opt::out.empty()) { cerr << PROGRAM ": " << "missing -o,--out option\n"; die = true; } if (argc - optind < 3) { cerr << PROGRAM ": missing arguments\n"; die = true; } if (argc - optind > 3) { cerr << PROGRAM ": too many arguments\n"; die = true; } if (die) { cerr << "Try `" << PROGRAM << " --help' for more information.\n"; exit(EXIT_FAILURE); } const char* contigPath(argv[optind++]); string adjPath(argv[optind++]); string estPath(argv[optind++]); readContigs(contigPath); // Read the contig adjacency graph. ifstream fin(adjPath.c_str()); assert_good(fin, adjPath); Graph graph; fin >> graph; assert(fin.eof()); g_contigNames.lock(); // Open the output file. ofstream out(opt::out.c_str()); assert_good(out, opt::out); // Read the scaffold graph. ifstream in(estPath.c_str()); assert_good(in, estPath); // Find overlapping contigs. OverlapGraph scaffoldGraph(graph.num_vertices() / 2); if (in.peek() == 'd') { // dot graph format in >> scaffoldGraph; assert(in.eof()); if (opt::verbose > 0) printGraphStats(cout, scaffoldGraph); remove_edge_if( !bind(checkEdgeForOverlap, cref(graph), ref(scaffoldGraph), _1), static_cast(scaffoldGraph)); } else { // dist graph format for (EstimateRecord er; in >> er;) { for (int sense = false; sense <= true; ++sense) { typedef vector< pair > Estimates; const Estimates& ests = er.estimates[sense]; for (Estimates::const_iterator it = ests.begin(); it != ests.end(); ++it) findOverlap(graph, er.refID, sense, it->first, it->second, scaffoldGraph); } } assert(in.eof()); } in.close(); if (opt::verbose > 1) cout << dot_writer(scaffoldGraph); typedef graph_traits::vertex_descriptor vertex_descriptor; typedef graph_traits::vertex_iterator vertex_iterator; typedef graph_traits::edge_descriptor edge_descriptor; typedef graph_traits::out_edge_iterator out_edge_iterator; /** The overlapping edges (d<0) of scaffoldGraph. */ OverlapGraph overlapGraph(num_vertices(graph) / 2); /** The canonical edges of scaffoldGraph. */ unsigned numOverlaps = num_edges(scaffoldGraph) / 2; typedef vector Edges; Edges edges; edges.reserve(numOverlaps); // Create the set of canonical edges and the overlap subgraph. std::pair uit = vertices(scaffoldGraph); for (vertex_iterator u = uit.first; u != uit.second; ++u) { std::pair vit = out_edges(*u, scaffoldGraph); for (out_edge_iterator e = vit.first; e != vit.second; ++e) { vertex_descriptor v = target(*e, scaffoldGraph); assert(*u != v); if (v < *u) continue; edges.push_back(*e); const Overlap& ep = get(edge_bundle, scaffoldGraph, e); if (ep.overlap > 0) add_edge(*u, v, ep, overlapGraph); } } assert(edges.size() == numOverlaps); // First, give priority to overlapping edges (not scaffolded). for (Edges::const_iterator it = edges.begin(); it != edges.end(); ++it) { const ContigNode& t = source(*it, overlapGraph), h = target(*it, overlapGraph); if (!edge(t, h, overlapGraph).second) { // This edge is scaffolded. continue; } const Overlap& overlap = get(edge_bundle, overlapGraph, *it); assert(overlap.overlap > 0); if (contiguous_out(overlapGraph, t)) { stats.overlap++; assert(*adjacent_vertices(t, overlapGraph).first == h); add_edge(t, h, overlap, graph); // Clear the out-edges of t and the in-edges of h. clear_out_edges(t, scaffoldGraph); clear_in_edges(h, scaffoldGraph); } else stats.ambiguous++; } overlapGraph.clear(); // Second, handle scaffolded edges. g_contigNames.unlock(); for (Edges::const_iterator it = edges.begin(); it != edges.end(); ++it) { const ContigNode& t = source(*it, scaffoldGraph), h = target(*it, scaffoldGraph); if (!edge(t, h, scaffoldGraph).second) { // This edge involved a vertex that has already been used // and removed. continue; } const Overlap& overlap = get(edge_bundle, scaffoldGraph, *it); if (overlap.overlap > 0) { // This edge is not scaffolded. } else if (contiguous_out(scaffoldGraph, t)) { assert(*adjacent_vertices(t, scaffoldGraph).first == h); FastaRecord contig = createGapContig(graph, t, h, overlap); out << contig; assert(out.good()); 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Unlike Data.List.groupBy, -- consecutive pairs of elements are compared, and the relation need -- not be transitive. groupBy' rel [] = [] groupBy' rel (x:xs) = (x:ys) : groupBy' rel zs where (ys,zs) = groupByAux x xs groupByAux x0 (x:xs) | rel x0 x = (x:ys, zs) where (ys,zs) = groupByAux x xs groupByAux y xs = ([], xs) -- Return pairs of elements from a list. pairs :: [a] -> [(a, a)] pairs [] = [] pairs (x:y:ys) = (x, y) : pairs ys -- Parse an integer from a ByteString. readS :: ByteString -> Int readS s = x where Just (x, _) = S.readInt s -- Calculate the N50. n50 :: [Int] -> Int n50 ws = x where Just(x, _) = find ((>= g50) . snd) $ zip xs $ scanl1 (+) xs g50 = sum xs `div` 2 xs = sort ws -- A SAM record. -- qname flag rname pos mapq cigar rnext pnext tlen seq qual data SAM = SAM { qname :: ByteString, flag :: Int, rname :: ByteString, pos :: Int, mapq :: Int, cigar :: ByteString, --rnext :: ByteString, --pnext :: Int, --tlen :: Int, --qseq :: ByteString, --qual :: ByteString seqLength :: Int } -- Return whether the unmapped flag is set. isUnmapped :: SAM -> Bool isUnmapped x = flag x .&. 4 /= 0 -- Return whether the reverse complement flag is set. isRC :: SAM -> Bool isRC x = flag x .&. 16 /= 0 -- Parse the CIGAR string. readCigar :: ByteString -> [(Int, Char)] readCigar s = map (readS *** S.head) . pairs . S.groupBy ((==) `on` isDigit) $ s -- Return the left and right soft-clipping. getSoftClip :: SAM -> (Int, Int) getSoftClip sam = ( if snd x == 'S' then fst x else 0, if snd y == 'S' then fst y else 0) where (x, y) = (head xs, last xs) xs = readCigar $ cigar sam -- Return the sum of the specified CIGAR elements. cigarLength :: [Char] -> ByteString -> Int cigarLength ops s = sum [n | (n, op) <- readCigar s, op `elem` ops] -- Return the length of the query alignment. qLength :: SAM -> Int qLength = cigarLength "IM" . cigar -- Return the start position of the query alignment oriented to agree -- with the target. qStart' = fst . getSoftClip -- Return the end position of the query alignment oriented to agree -- with the target. qEnd' x = qStart' x + qLength x -- Return the start position of the query alignment. qStart :: SAM -> Int qStart x = (if isRC x then snd else fst) $ getSoftClip x -- Return the end position of the query alignment. qEnd :: SAM -> Int qEnd x = qStart x + qLength x -- Return the length of the target alignment. tLength :: SAM -> Int tLength = cigarLength "DMN" . cigar -- Return the start of the target alignment. tStart :: SAM -> Int tStart = pos -- Return the end position of the target alignment. tEnd :: SAM -> Int tEnd x = tStart x + tLength x -- Return the start position of the target alignment oriented to agree -- with the query. The coordinate system is [-length, 0). tStart' x = if isRC x then 0 - tEnd x else tStart x -- Return the end position of the target alignment oriented to agree -- with the query. The coordinate system is [-length, 0). tEnd' x = tStart' x + tLength x -- Parse a SAM record. readSAM :: ByteString -> SAM readSAM s = SAM qname (readS flag) rname (readS pos) (readS mapq) cigar lengthQseq where lengthQseq = if S.head qseq == '*' then cigarLength "IMS" cigar else S.length qseq (qname:flag:rname:pos:mapq:cigar:_:_:_:qseq:_) = S.words s -- Print a SAM record. showSAM :: SAM -> String showSAM (SAM qname flag rname pos mapq cigar _) = intercalate "\t" [S.unpack qname, show flag, S.unpack rname, show pos, show mapq, S.unpack cigar, "*", "0", "0", "*", "*"] -- Exclude alignments that overlap a long alignment by 50%. excludeOverlaps :: [SAM] -> [SAM] excludeOverlaps xs = reverse . foldl accum [] $ xs where accum ys x = if any overlapx ys then ys else x:ys where overlapx y = end - start > (qLength x) `div` 2 where start = max (qStart x) (qStart y) end = min (qEnd x) (qEnd y) {- -- Compare the target position. compareTStart :: SAM -> SAM -> Ordering compareTStart a b = compare (rname a, pos a) (rname b, pos b) -- Patch gaps in the alignments that are shorter than 500 bp. patchGaps :: [SAM] -> [SAM] patchGaps ws = (x:) $ map snd . filter (not . isSmallGap) $ zip (x:xs) xs where (x:xs) = sortBy compareTStart ws isSmallGap (q, p) = (rname p, isRC p) == (rname q, isRC q) && max gapt gapq < 500 where gapt = abs (tStart p - tEnd q) gapq = abs (qStart' p - qEnd' q) -} -- Return whether the pair of aligned contigs are colinear. isColinear :: SAM -> SAM -> Bool isColinear a b = (rname a, isRC a) == (rname b, isRC b) && tStart' a < tStart' b && tEnd' a < tEnd' b -- Return pairs of non-colinear alignments. filterNonColinear :: [SAM] -> [(SAM, SAM)] filterNonColinear xs = filter (not . uncurry isColinear) $ zip xs (tail xs) -- The command line options. data Opt = OptLength Int | OptMapq Int | OptPrint | OptHelp deriving Eq options :: [OptDescr Opt] options = [ Option ['l'] ["length"] (ReqArg (OptLength . read) "N") "exclude contigs shorter than N bp [200]", Option ['q'] ["mapq"] (ReqArg (OptMapq . read) "N") "exclude alignments with mapq less than N [10]", Option ['p'] ["print"] (NoArg OptPrint) "print scaffold breakpoints in SAM format", Option [] ["help"] (NoArg OptHelp) "display this help and exit" ] data Options = Options { optLength :: Int, optMapq :: Int, optPrint :: Bool } defaultOptions = Options { optLength = 200, optMapq = 10, optPrint = False } -- Parse the command line options. parseOptions :: [Opt] -> Options parseOptions = foldl parseOption defaultOptions where parseOption opt x = case x of OptLength l -> opt { optLength = l } OptMapq q -> opt { optMapq = q } OptPrint -> opt { optPrint = True } -- Parse the command line arguments. parseArgs :: IO (Options, [String]) parseArgs = do args <- getArgs case getOpt Permute options args of (opts, files, []) -> if OptHelp `elem` opts then help else return (parseOptions opts, files) (_, _, errs) -> error (concat errs ++ tryHelp) where help = putStr (usageInfo usage options) >> exitSuccess tryHelp = "Try 'abyss-samtobreak --help' for more information." usage = "Usage: samtobreak [OPTION]...\n\ \Calculate contig and scaffold contiguity and correctness metrics.\n" -- Calculate contig and scaffold contiguity and correctness metrics. printStats :: Options -> FilePath -> IO () printStats (Options optLength optMapq optPrint) path = do s <- mmapFileByteString path Nothing when (S.null s) $ error $ "`" ++ path ++ "' is empty" let -- Parse the SAM file and discard short contigs. isHeader x = S.head x == '@' (headers, alignments) = span isHeader . S.lines $ s isLong x = seqLength x >= optLength (unmapped, mapped) = partition isUnmapped . filter isLong . map readSAM $ alignments -- Exclude overlapping alignments. excluded = map excludeOverlaps . groupBy ((==) `on` qname) $ mapped concatExcluded = concat excluded qLengths = map qLength concatExcluded -- Kepp long alignments with high mapping quality. isGood x = mapq x >= optMapq && qLength x >= 500 good = filter (not . null) . map (filter isGood) $ excluded -- Group contigs into scaffolds by their name. scaffoldName = S.takeWhile (/= '_') . qname oneHit = concat . filter ((== 1) . length) $ good scaffs = groupBy ((==) `on` scaffoldName) $ oneHit when optPrint (do -- Print scaffold breakpoints. S.putStr $ S.unlines headers putStr $ concat $ map (\(a, b) -> unlines [showSAM a, showSAM b]) $ concatMap filterNonColinear scaffs exitSuccess) -- Calculate contig metrics. putStr "Number of unmapped contigs: " print $ length unmapped putStr "Total length of unmapped contigs: " print $ sum . map seqLength $ unmapped putStr "Number of alignments dropped due to excessive overlaps: " print $ length mapped - length concatExcluded putStr "Mapped contig bases: " print $ sum qLengths putStr "Mapped N50: " print $ n50 qLengths putStr "Number of break points: " print $ length concatExcluded - length excluded putStr "Number of Q10 break points longer than 500 bp: " print $ length (concat good) - length good {- -- Patch small gaps. let patched = map patchGaps excluded concatPatched = concat patched patchedGood = map patchGaps good concatPatchedGood = concat patchedGood putStr "Number of break points after patching gaps shorter than 500 bp: " print $ length concatPatched - length patched putStr "Number of Q10 break points longer than 500 bp after gap patching: " print $ length concatPatchedGood - length patchedGood -} -- Calculate scaffold metrics. let scaffoldLength = sum . map qLength scaffoldLengths = map scaffoldLength colinearScaffs = concatMap (groupBy' isColinear) scaffs putStr "Scaffold N50: " print $ n50 . scaffoldLengths $ scaffs putStr "Aligned scaffold N50: " print $ n50 . scaffoldLengths $ colinearScaffs putStr "Number of Q10 scaffold breakpoints longer than 500 bp: " print $ length colinearScaffs - length scaffs -- Calculate contig and scaffold contiguity and correctness metrics. main :: IO () main = do (opt, files) <- parseArgs case files of [] -> printStats opt "/dev/stdin" [path] -> printStats opt path otherwise -> mapM_ (\path -> do putStr $ "==> " ++ path ++ " <==\n" printStats opt path) files abyss-1.3.6/MergePaths/Makefile.in000644 002433 001057 00000063267 12176317671 020514 0ustar00traymondassembly000000 000000 # Makefile.in generated by automake 1.14 from Makefile.am. # @configure_input@ # Copyright (C) 1994-2013 Free Software Foundation, Inc. # This Makefile.in is free software; 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#define PROGRAM "MergeContigs" static const char VERSION_MESSAGE[] = PROGRAM " (" PACKAGE_NAME ") " VERSION "\n" "Written by Shaun Jackman.\n" "\n" "Copyright 2013 Canada's Michael Smith Genome Science Centre\n"; static const char USAGE_MESSAGE[] = "Usage: " PROGRAM " [OPTION]... FASTA [OVERLAP] PATH\n" "Merge paths of contigs to create larger contigs.\n" "\n" " Arguments:\n" "\n" " FASTA contigs in FASTA format\n" " OVERLAP contig overlap graph\n" " PATH sequences of contig IDs\n" "\n" " Options:\n" "\n" " -k, --kmer=KMER_SIZE k-mer size\n" " -o, --out=FILE output the merged contigs to FILE [stdout]\n" " -g, --graph=FILE write the contig overlap graph to FILE\n" " --merged output only merged contigs\n" " --adj output the graph in adj format\n" " --dot output the graph in dot format [default]\n" " --dot-meancov same as above but give the mean coverage\n" " --sam output the graph in SAM format\n" " -v, --verbose display verbose output\n" " --help display this help and exit\n" " --version output version information and exit\n" "\n" "Report bugs to <" PACKAGE_BUGREPORT ">.\n"; namespace opt { unsigned k; // used by ContigProperties /** Output FASTA path. */ static string out = "-"; /** Output graph path. */ static string graphPath; /** Output graph format. */ int format = DOT; /** Output only merged contigs. */ int onlyMerged; /** Minimum overlap. */ static unsigned minOverlap = 20; /** Minimum alignment identity. */ static float minIdentity = 0.9; } static const char shortopts[] = "g:k:o:v"; enum { OPT_HELP = 1, OPT_VERSION }; static const struct option longopts[] = { { "adj", no_argument, &opt::format, ADJ }, { "dot", no_argument, &opt::format, DOT }, { "dot-meancov", no_argument, &opt::format, DOT_MEANCOV }, { "sam", no_argument, &opt::format, SAM }, { "graph", required_argument, NULL, 'g' }, { "kmer", required_argument, NULL, 'k' }, { "merged", no_argument, &opt::onlyMerged, 1 }, { "out", required_argument, NULL, 'o' }, { "path", required_argument, NULL, 'p' }, { "verbose", no_argument, NULL, 'v' }, { "help", no_argument, NULL, OPT_HELP }, { "version", no_argument, NULL, OPT_VERSION }, { NULL, 0, NULL, 0 } }; /* A contig sequence. */ struct Contig { Contig(const string& comment, const string& seq) : comment(comment), seq(seq) { } Contig(const FastaRecord& o) : comment(o.comment), seq(o.seq) { } string comment; string seq; }; /** The contig sequences. */ typedef vector Contigs; /** Return the sequence of the specified contig node. The sequence * may be ambiguous or reverse complemented. */ static Sequence sequence(const Contigs& contigs, const ContigNode& id) { if (id.ambiguous()) { string s(id.ambiguousSequence()); if (s.length() < opt::k) transform(s.begin(), s.end(), s.begin(), ::tolower); return string(opt::k - 1, 'N') + s; } else { const Sequence& seq = contigs[id.id()].seq; return id.sense() ? reverseComplement(seq) : seq; } } /** Return a consensus sequence of a and b. * @return an empty string if a consensus could not be found */ static string createConsensus(const Sequence& a, const Sequence& b) { assert(a.length() == b.length()); if (a == b) return a; string s; s.reserve(a.length()); for (string::const_iterator ita = a.begin(), itb = b.begin(); ita != a.end(); ++ita, ++itb) { bool mask = islower(*ita) || islower(*itb); char ca = toupper(*ita), cb = toupper(*itb); char c = ca == cb ? ca : ca == 'N' ? cb : cb == 'N' ? ca : ambiguityIsSubset(ca, cb) ? ambiguityOr(ca, cb) : 'x'; if (c == 'x') return string(""); s += mask ? tolower(c) : c; } return s; } typedef ContigGraph > Graph; typedef graph_traits::vertex_descriptor vertex_descriptor; /** Return the properties of the specified vertex, unless u is * ambiguous, in which case return the length of the ambiguous * sequence. */ static inline ContigProperties get(vertex_bundle_t, const Graph& g, ContigNode u) { return u.ambiguous() ? ContigProperties(u.length() + opt::k - 1, 0) : g[u]; } /** Append the sequence of contig v to seq. */ static void mergeContigs(const Graph& g, const Contigs& contigs, vertex_descriptor u, vertex_descriptor v, Sequence& seq, const ContigPath& path) { int d = get(edge_bundle, g, u, v).distance; assert(d < 0); unsigned overlap = -d; const Sequence& s = sequence(contigs, v); assert(s.length() > overlap); Sequence ao; Sequence bo(s, 0, overlap); Sequence o; do { assert(seq.length() > overlap); ao = seq.substr(seq.length() - overlap); o = createConsensus(ao, bo); if (!o.empty()) { seq.resize(seq.length() - overlap); seq += o; seq += Sequence(s, overlap); return; } } while (chomp(seq, 'n')); // Try an overlap alignment. if (opt::verbose > 2) cerr << '\n'; vector overlaps; alignOverlap(ao, bo, 0, overlaps, false, opt::verbose > 2); bool good = false; if (!overlaps.empty()) { assert(overlaps.size() == 1); const overlap_align& o = overlaps.front(); unsigned matches = o.overlap_match; const string& consensus = o.overlap_str; float identity = (float)matches / consensus.size(); good = matches >= opt::minOverlap && identity >= opt::minIdentity; if (opt::verbose > 2) cerr << matches << " / " << consensus.size() << " = " << identity << (matches < opt::minOverlap ? " (too few)" : identity < opt::minIdentity ? " (too low)" : " (good)") << '\n'; } if (good) { assert(overlaps.size() == 1); const overlap_align& o = overlaps.front(); seq.erase(seq.length() - overlap + o.overlap_t_pos); seq += o.overlap_str; seq += Sequence(s, o.overlap_h_pos + 1); } else { cerr << "warning: the head of " << get(vertex_name, g, v) << " does not match the tail of the previous contig\n" << ao << '\n' << bo << '\n' << path << endl; seq += 'n'; seq += s; } } /** Return a FASTA comment for the specified path. */ static void pathToComment(ostream& out, const Graph& g, const ContigPath& path) { assert(path.size() > 1); out << get(vertex_name, g, path.front()); if (path.size() == 3) out << ',' << get(vertex_name, g, path[1]); else if (path.size() > 3) out << ",..."; out << ',' << get(vertex_name, g, path.back()); } /** Merge the specified path. */ static Contig mergePath(const Graph& g, const Contigs& contigs, const ContigPath& path) { Sequence seq; unsigned coverage = 0; for (ContigPath::const_iterator it = path.begin(); it != path.end(); ++it) { if (!it->ambiguous()) coverage += g[*it].coverage; if (seq.empty()) { seq = sequence(contigs, *it); } else { assert(it != path.begin()); mergeContigs(g, contigs, *(it-1), *it, seq, path); } } ostringstream ss; ss << seq.size() << ' ' << coverage << ' '; pathToComment(ss, g, path); return Contig(ss.str(), seq); } /** A container of ContigPath. */ typedef vector ContigPaths; /** Read contig paths from the specified file. * @param ids [out] the string ID of the paths */ static ContigPaths readPaths(const string& inPath, vector* ids = NULL) { if (ids != NULL) assert(ids->empty()); ifstream fin(inPath.c_str()); if (opt::verbose > 0) cerr << "Reading `" << inPath << "'..." << endl; if (inPath != "-") assert_good(fin, inPath); istream& in = inPath == "-" ? cin : fin; unsigned count = 0; ContigPaths paths; string id; ContigPath path; while (in >> id >> path) { paths.push_back(path); if (ids != NULL) ids->push_back(id); ++count; if (opt::verbose > 1 && count % 1000000 == 0) cerr << "Read " << count << " paths. " "Using " << toSI(getMemoryUsage()) << "B of memory.\n"; } if (opt::verbose > 0) cerr << "Read " << count << " paths. " "Using " << toSI(getMemoryUsage()) << "B of memory.\n"; assert(in.eof()); return paths; } /** Finds all contigs used in each path in paths, and * marks them as seen in the vector seen. */ static void seenContigs(vector& seen, const ContigPaths& paths) { for (ContigPaths::const_iterator it = paths.begin(); it != paths.end(); ++it) for (ContigPath::const_iterator itc = it->begin(); itc != it->end(); ++itc) if (itc->id() < seen.size()) seen[itc->id()] = true; } /** Mark contigs for removal. An empty path indicates that a contig * should be removed. */ static void markRemovedContigs(vector& marked, const vector& pathIDs, const ContigPaths& paths) { for (ContigPaths::const_iterator it = paths.begin(); it != paths.end(); ++it) { if (it->empty()) { size_t i = get(g_contigNames, pathIDs[it - paths.begin()]); assert(i < marked.size()); marked[i] = true; } } } /** Output the updated overlap graph. */ static void outputGraph(Graph& g, const vector& pathIDs, const ContigPaths& paths, const string& commandLine) { typedef graph_traits::vertex_descriptor V; // Add the path vertices. g_contigNames.unlock(); for (ContigPaths::const_iterator it = paths.begin(); it != paths.end(); ++it) { const ContigPath& path = *it; const string& id = pathIDs[it - paths.begin()]; if (!path.empty()) { V u = merge(g, path.begin(), path.end()); put(vertex_name, g, u, id); } } g_contigNames.lock(); // Remove the vertices that are used in paths. for (ContigPaths::const_iterator it = paths.begin(); it != paths.end(); ++it) { const ContigPath& path = *it; const string& id = pathIDs[it - paths.begin()]; if (path.empty()) { remove_vertex(find_vertex(id, false, g), g); } else { remove_vertex_if(g, path.begin(), path.end(), not1(std::mem_fun_ref(&ContigNode::ambiguous))); } } // Output the graph. const string& graphPath = opt::graphPath; assert(!graphPath.empty()); if (opt::verbose > 0) cerr << "Writing `" << graphPath << "'..." << endl; ofstream fout(graphPath.c_str()); assert_good(fout, graphPath); write_graph(fout, g, PROGRAM, commandLine); assert_good(fout, graphPath); if (opt::verbose > 0) printGraphStats(cerr, g); } int main(int argc, char** argv) { opt::trimMasked = false; string commandLine; { ostringstream ss; char** last = argv + argc - 1; copy(argv, last, ostream_iterator(ss, " ")); ss << *last; commandLine = ss.str(); } bool die = false; for (int c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;) { istringstream arg(optarg != NULL ? optarg : ""); switch (c) { case '?': die = true; break; case 'g': arg >> opt::graphPath; break; case 'k': arg >> opt::k; break; case 'o': arg >> opt::out; break; case 'v': opt::verbose++; break; case OPT_HELP: cout << USAGE_MESSAGE; exit(EXIT_SUCCESS); case OPT_VERSION: cout << VERSION_MESSAGE; exit(EXIT_SUCCESS); } if (optarg != NULL && !arg.eof()) { cerr << PROGRAM ": invalid option: `-" << (char)c << optarg << "'\n"; exit(EXIT_FAILURE); } } if (opt::k <= 0) { cerr << PROGRAM ": missing -k,--kmer option\n"; die = true; } if (opt::out.empty()) { cerr << PROGRAM ": " << "missing -o,--out option\n"; die = true; } if (argc - optind < 2) { cerr << PROGRAM ": missing arguments\n"; die = true; } if (argc - optind > 3) { cerr << PROGRAM ": too many arguments\n"; die = true; } if (die) { cerr << "Try `" << PROGRAM << " --help' for more information.\n"; exit(EXIT_FAILURE); } const char* contigFile = argv[optind++]; string adjPath, mergedPathFile; Graph g; if (argc - optind > 1) { adjPath = string(argv[optind++]); // Read the contig adjacency graph. if (opt::verbose > 0) cerr << "Reading `" << adjPath << "'..." << endl; ifstream fin(adjPath.c_str()); assert_good(fin, adjPath); fin >> g; assert(fin.eof()); if (opt::verbose > 0) cerr << "Read " << num_vertices(g) << " vertices. " "Using " << toSI(getMemoryUsage()) << "B of memory.\n"; } mergedPathFile = string(argv[optind++]); // Read the contig sequence. Contigs contigs; { if (opt::verbose > 0) cerr << "Reading `" << contigFile << "'..." << endl; unsigned count = 0; FastaReader in(contigFile, FastaReader::NO_FOLD_CASE); for (FastaRecord rec; in >> rec;) { if (!adjPath.empty() && g_contigNames.count(rec.id) == 0) continue; if (adjPath.empty()) put(g_contigNames, contigs.size(), rec.id); else assert(get(g_contigNames, rec.id) == contigs.size()); contigs.push_back(rec); ++count; if (opt::verbose > 1 && count % 1000000 == 0) cerr << "Read " << count << " sequences. " "Using " << toSI(getMemoryUsage()) << "B of memory.\n"; } if (opt::verbose > 0) cerr << "Read " << count << " sequences. " "Using " << toSI(getMemoryUsage()) << "B of memory.\n"; assert(in.eof()); assert(!contigs.empty()); opt::colourSpace = isdigit(contigs[0].seq[0]); g_contigNames.lock(); } vector pathIDs; ContigPaths paths = readPaths(mergedPathFile, &pathIDs); // Record all the contigs that are in a path. vector seen(contigs.size()); seenContigs(seen, paths); markRemovedContigs(seen, pathIDs, paths); // Output those contigs that were not seen in a path. Histogram lengthHistogram; ofstream fout; ostream& out = opt::out == "-" ? cout : (fout.open(opt::out.c_str()), fout); assert_good(out, opt::out); if (!opt::onlyMerged) { for (Contigs::const_iterator it = contigs.begin(); it != contigs.end(); ++it) { ContigID id(it - contigs.begin()); if (!seen[id]) { const Contig& contig = *it; out << '>' << get(g_contigNames, id); if (!contig.comment.empty()) out << ' ' << contig.comment; out << '\n' << contig.seq << '\n'; if (opt::verbose > 0) lengthHistogram.insert( count_if(contig.seq.begin(), contig.seq.end(), isACGT)); } } } if (adjPath.empty()) return 0; unsigned npaths = 0; for (ContigPaths::const_iterator it = paths.begin(); it != paths.end(); ++it) { const ContigPath& path = *it; if (path.empty()) continue; Contig contig = mergePath(g, contigs, path); out << '>' << pathIDs[it - paths.begin()] << ' ' << contig.comment << '\n' << contig.seq << '\n'; assert_good(out, opt::out); npaths++; if (opt::verbose > 0) lengthHistogram.insert( count_if(contig.seq.begin(), contig.seq.end(), isACGT)); } if (npaths == 0) return 0; float minCov = numeric_limits::infinity(), minCovUsed = numeric_limits::infinity(); for (unsigned i = 0; i < contigs.size(); i++) { ContigProperties vp = g[ContigNode(i, false)]; if (vp.coverage == 0 || vp.length < opt::k) continue; float cov = (float)vp.coverage / (vp.length - opt::k + 1); minCov = min(minCov, cov); if (seen[i]) minCovUsed = min(minCovUsed, cov); } if (!opt::graphPath.empty()) outputGraph(g, pathIDs, paths, commandLine); cerr << "The minimum coverage of single-end contigs is " << minCov << ".\n" << "The minimum coverage of merged contigs is " << minCovUsed << ".\n"; if (minCov < minCovUsed) cerr << "Consider increasing the coverage threshold " "parameter, c, to " << minCovUsed << ".\n"; if (opt::verbose > 0) { const unsigned STATS_MIN_LENGTH = 200; // bp printContiguityStats(cerr, lengthHistogram, STATS_MIN_LENGTH) << '\t' << opt::out << '\n'; } return 0; } abyss-1.3.6/MergePaths/MergePaths.cpp000644 002433 001057 00000117047 12116214002 021160 0ustar00traymondassembly000000 000000 #include "config.h" #include "Common/Options.h" #include "ContigID.h" #include "ContigPath.h" #include "Functional.h" // for mem_var #include "IOUtil.h" #include "Uncompress.h" #include "Graph/Assemble.h" #include "Graph/ContigGraph.h" #include "Graph/DirectedGraph.h" #include "Graph/DotIO.h" #include "Graph/GraphAlgorithms.h" #include "Graph/GraphUtil.h" #include #include #include #include // for UINT_MAX #include #include #include #include #include #include #include #include #include #include #include #include #include #include #if _OPENMP # include #endif using namespace std; using boost::tie; #define PROGRAM "MergePaths" static const char VERSION_MESSAGE[] = PROGRAM " (" PACKAGE_NAME ") " VERSION "\n" "Written by Jared Simpson and Shaun Jackman.\n" "\n" "Copyright 2013 Canada's Michael Smith Genome Science Centre\n"; static const char USAGE_MESSAGE[] = "Usage: " PROGRAM " [OPTION]... LEN PATH\n" "Merge sequences of contigs IDs.\n" "\n" " Arguments:\n" "\n" " LEN lengths of the contigs\n" " PATH sequences of contig IDs\n" "\n" " Options:\n" "\n" " -k, --kmer=KMER_SIZE k-mer size\n" " -s, --seed-length=L minimum length of a seed contig [0]\n" " -o, --out=FILE write result to FILE\n" " --no-greedy use the non-greedy algorithm [default]\n" " --greedy use the greedy algorithm\n" " -g, --graph=FILE write the path overlap graph to FILE\n" " -j, --threads=N use N parallel threads [1]\n" " -v, --verbose display verbose output\n" " --help display this help and exit\n" " --version output version information and exit\n" "\n" "Report bugs to <" PACKAGE_BUGREPORT ">.\n"; namespace opt { unsigned k; // used by GraphIO static string out; static int threads = 1; /** Minimum length of a seed contig. */ static unsigned seedLen; /** Use a greedy algorithm. */ static int greedy; /** Write the path overlap graph to this file. */ static string graphPath; } static const char shortopts[] = "g:j:k:o:s:v"; enum { OPT_HELP = 1, OPT_VERSION }; static const struct option longopts[] = { { "graph", no_argument, NULL, 'g' }, { "greedy", no_argument, &opt::greedy, true }, { "no-greedy", no_argument, &opt::greedy, false }, { "kmer", required_argument, NULL, 'k' }, { "out", required_argument, NULL, 'o' }, { "seed-length", required_argument, NULL, 's' }, { "threads", required_argument, NULL, 'j' }, { "verbose", no_argument, NULL, 'v' }, { "help", no_argument, NULL, OPT_HELP }, { "version", no_argument, NULL, OPT_VERSION }, { NULL, 0, NULL, 0 } }; typedef map ContigPathMap; /** Orientation of an edge. */ enum dir_type { DIR_X, // u--v none DIR_F, // u->v forward DIR_R, // u<-v reverse DIR_B, // u<>v both }; /** Lengths of contigs measured in k-mer. */ typedef vector Lengths; static ContigPath align(const Lengths& lengths, const ContigPath& p1, const ContigPath& p2, ContigNode pivot); static ContigPath align(const Lengths& lengths, const ContigPath& p1, const ContigPath& p2, ContigNode pivot, dir_type& orientation); static bool gDebugPrint; /** Return all contigs that are tandem repeats, identified as those * contigs that appear more than once in a single path. */ static set findRepeats(const ContigPathMap& paths) { set repeats; for (ContigPathMap::const_iterator pathIt = paths.begin(); pathIt != paths.end(); ++pathIt) { const ContigPath& path = pathIt->second; map count; for (ContigPath::const_iterator it = path.begin(); it != path.end(); ++it) if (!it->ambiguous()) count[it->contigIndex()]++; for (map::const_iterator it = count.begin(); it != count.end(); ++it) if (it->second > 1) repeats.insert(it->first); } return repeats; } /** Remove tandem repeats from the set of paths. * @return the removed paths */ static set removeRepeats(ContigPathMap& paths) { set repeats = findRepeats(paths); if (gDebugPrint) { cout << "Repeats:"; if (!repeats.empty()) { for (set::const_iterator it = repeats.begin(); it != repeats.end(); ++it) cout << ' ' << get(g_contigNames, *it); } else cout << " none"; cout << '\n'; } unsigned removed = 0; for (set::const_iterator it = repeats.begin(); it != repeats.end(); ++it) if (paths.count(*it) > 0) removed++; if (removed == paths.size()) { // Every path was identified as a repeat. It's most likely a // cyclic sequence. Don't remove anything. repeats.clear(); return repeats; } ostringstream ss; for (set::const_iterator it = repeats.begin(); it != repeats.end(); ++it) if (paths.erase(*it) > 0) ss << ' ' << get(g_contigNames, *it); if (opt::verbose > 0 && removed > 0) cout << "Removing paths in repeats:" << ss.str() << '\n'; return repeats; } static void appendToMergeQ(deque& mergeQ, set& seen, const ContigPath& path) { for (ContigPath::const_iterator it = path.begin(); it != path.end(); ++it) if (!it->ambiguous() && seen.insert(*it).second) mergeQ.push_back(*it); } /** A path overlap graph. */ typedef ContigGraph > PathGraph; /** Add an edge if the two paths overlap. * @param pivot the pivot at which to seed the alignment * @return whether an overlap was found */ static bool addOverlapEdge(const Lengths& lengths, PathGraph& gout, ContigNode pivot, ContigNode seed1, const ContigPath& path1, ContigNode seed2, const ContigPath& path2) { assert(seed1 != seed2); // Determine the orientation of the overlap edge. dir_type orientation = DIR_X; ContigPath consensus = align(lengths, path1, path2, pivot, orientation); if (consensus.empty()) return false; assert(orientation != DIR_X); if (orientation == DIR_B) { // One of the paths subsumes the other. Use the order of the // seeds to determine the orientation of the edge. orientation = find(consensus.begin(), consensus.end(), seed1) < find(consensus.begin(), consensus.end(), seed2) ? DIR_F : DIR_R; } assert(orientation == DIR_F || orientation == DIR_R); // Add the edge. ContigNode u = orientation == DIR_F ? seed1 : seed2; ContigNode v = orientation == DIR_F ? seed2 : seed1; bool added = false; #pragma omp critical(gout) if (!edge(u, v, gout).second) { add_edge(u, v, gout); added = true; } return added; } /** Return the specified path. */ static ContigPath getPath(const ContigPathMap& paths, ContigNode u) { ContigPathMap::const_iterator it = paths.find(u.contigIndex()); assert(it != paths.end()); ContigPath path = it->second; if (u.sense()) reverseComplement(path.begin(), path.end()); return path; } /** Find the overlaps between paths and add edges to the graph. */ static void findPathOverlaps(const Lengths& lengths, const ContigPathMap& paths, const ContigNode& seed1, const ContigPath& path1, PathGraph& gout) { for (ContigPath::const_iterator it = path1.begin(); it != path1.end(); ++it) { ContigNode seed2 = *it; if (seed1 == seed2) continue; if (seed2.ambiguous()) continue; ContigPathMap::const_iterator path2It = paths.find(seed2.contigIndex()); if (path2It == paths.end()) continue; ContigPath path2 = path2It->second; if (seed2.sense()) reverseComplement(path2.begin(), path2.end()); addOverlapEdge(lengths, gout, seed2, seed1, path1, seed2, path2); } } /** Attempt to merge the paths specified in mergeQ with path. * @return the number of paths merged */ static unsigned mergePaths(const Lengths& lengths, ContigPath& path, deque& mergeQ, set& seen, const ContigPathMap& paths) { unsigned merged = 0; deque invalid; for (ContigNode pivot; !mergeQ.empty(); mergeQ.pop_front()) { pivot = mergeQ.front(); ContigPathMap::const_iterator path2It = paths.find(pivot.contigIndex()); if (path2It == paths.end()) continue; ContigPath path2 = path2It->second; if (pivot.sense()) reverseComplement(path2.begin(), path2.end()); ContigPath consensus = align(lengths, path, path2, pivot); if (consensus.empty()) { invalid.push_back(pivot); continue; } appendToMergeQ(mergeQ, seen, path2); path.swap(consensus); if (gDebugPrint) #pragma omp critical(cout) cout << get(g_contigNames, pivot) << '\t' << path2 << '\n' << '\t' << path << '\n'; merged++; } mergeQ.swap(invalid); return merged; } /** Merge the paths of the specified seed path. * @return the merged contig path */ static ContigPath mergePath(const Lengths& lengths, const ContigPathMap& paths, const ContigPath& seedPath) { assert(!seedPath.empty()); ContigNode seed1 = seedPath.front(); ContigPathMap::const_iterator path1It = paths.find(seed1.contigIndex()); assert(path1It != paths.end()); ContigPath path(path1It->second); if (seedPath.front().sense()) reverseComplement(path.begin(), path.end()); if (opt::verbose > 1) #pragma omp critical(cout) cout << "\n* " << seedPath << '\n' << get(g_contigNames, seedPath.front()) << '\t' << path << '\n'; for (ContigPath::const_iterator it = seedPath.begin() + 1; it != seedPath.end(); ++it) { ContigNode seed2 = *it; ContigPathMap::const_iterator path2It = paths.find(seed2.contigIndex()); assert(path2It != paths.end()); ContigPath path2 = path2It->second; if (seed2.sense()) reverseComplement(path2.begin(), path2.end()); ContigNode pivot = find(path.begin(), path.end(), seed2) != path.end() ? seed2 : seed1; ContigPath consensus = align(lengths, path, path2, pivot); if (consensus.empty()) { // This seed could be removed from the seed path. if (opt::verbose > 1) #pragma omp critical(cout) cout << get(g_contigNames, seed2) << '\t' << path2 << '\n' << "\tinvalid\n"; } else { path.swap(consensus); if (opt::verbose > 1) #pragma omp critical(cout) cout << get(g_contigNames, seed2) << '\t' << path2 << '\n' << '\t' << path << '\n'; } seed1 = seed2; } return path; } /** A collection of contig paths. */ typedef vector ContigPaths; /** Merge the specified seed paths. * @return the merged contig paths */ static ContigPaths mergeSeedPaths(const Lengths& lengths, const ContigPathMap& paths, const ContigPaths& seedPaths) { if (opt::verbose > 0) cout << "\nMerging paths\n"; ContigPaths out; out.reserve(seedPaths.size()); for (ContigPaths::const_iterator it = seedPaths.begin(); it != seedPaths.end(); ++it) out.push_back(mergePath(lengths, paths, *it)); return out; } /** Extend the specified path as long as is unambiguously possible and * add the result to the specified container. */ static void extendPaths(const Lengths& lengths, ContigID id, const ContigPathMap& paths, ContigPathMap& out) { ContigPathMap::const_iterator pathIt = paths.find(id); assert(pathIt != paths.end()); pair inserted; #pragma omp critical(out) inserted = out.insert(*pathIt); assert(inserted.second); ContigPath& path = inserted.first->second; if (gDebugPrint) #pragma omp critical(cout) cout << "\n* " << get(g_contigNames, id) << "+\n" << '\t' << path << '\n'; set seen; seen.insert(ContigNode(id, false)); deque mergeQ; appendToMergeQ(mergeQ, seen, path); while (mergePaths(lengths, path, mergeQ, seen, paths) > 0) ; if (!mergeQ.empty() && gDebugPrint) { #pragma omp critical(cout) { cout << "invalid\n"; for (deque::const_iterator it = mergeQ.begin(); it != mergeQ.end(); ++it) cout << get(g_contigNames, *it) << '\t' << paths.find(it->contigIndex())->second << '\n'; } } } /** Return true if the contigs are equal or both are ambiguous. */ static bool equalOrBothAmbiguos(const ContigNode& a, const ContigNode& b) { return a == b || (a.ambiguous() && b.ambiguous()); } /** Return true if both paths are equal, ignoring ambiguous nodes. */ static bool equalIgnoreAmbiguos(const ContigPath& a, const ContigPath& b) { return a.size() == b.size() && equal(a.begin(), a.end(), b.begin(), equalOrBothAmbiguos); } /** Return whether this path is a cycle. */ static bool isCycle(const Lengths& lengths, const ContigPath& path) { return !align(lengths, path, path, path.front()).empty(); } /** Identify paths subsumed by the specified path. * @param overlaps [out] paths that are found to overlap * @return the ID of the subsuming path */ static ContigID identifySubsumedPaths(const Lengths& lengths, ContigPathMap::const_iterator path1It, ContigPathMap& paths, set& out, set& overlaps) { ostringstream vout; out.clear(); ContigID id(path1It->first); const ContigPath& path = path1It->second; if (gDebugPrint) vout << get(g_contigNames, ContigNode(id, false)) << '\t' << path << '\n'; for (ContigPath::const_iterator it = path.begin(); it != path.end(); ++it) { ContigNode pivot = *it; if (pivot.ambiguous() || pivot.id() == id) continue; ContigPathMap::iterator path2It = paths.find(pivot.contigIndex()); if (path2It == paths.end()) continue; ContigPath path2 = path2It->second; if (pivot.sense()) reverseComplement(path2.begin(), path2.end()); ContigPath consensus = align(lengths, path, path2, pivot); if (consensus.empty()) continue; if (equalIgnoreAmbiguos(consensus, path)) { if (gDebugPrint) vout << get(g_contigNames, pivot) << '\t' << path2 << '\n'; out.insert(path2It->first); } else if (equalIgnoreAmbiguos(consensus, path2)) { // This path is larger. Use it as the seed. return identifySubsumedPaths(lengths, path2It, paths, out, overlaps); } else if (isCycle(lengths, consensus)) { // The consensus path is a cycle. bool isCyclePath1 = isCycle(lengths, path); bool isCyclePath2 = isCycle(lengths, path2); if (!isCyclePath1 && !isCyclePath2) { // Neither path is a cycle. if (gDebugPrint) vout << get(g_contigNames, pivot) << '\t' << path2 << '\n' << "ignored\t" << consensus << '\n'; overlaps.insert(id); overlaps.insert(path2It->first); } else { // At least one path is a cycle. if (gDebugPrint) vout << get(g_contigNames, pivot) << '\t' << path2 << '\n' << "cycle\t" << consensus << '\n'; if (isCyclePath1 && isCyclePath2) out.insert(path2It->first); else if (!isCyclePath1) overlaps.insert(id); else if (!isCyclePath2) overlaps.insert(path2It->first); } } else { if (gDebugPrint) vout << get(g_contigNames, pivot) << '\t' << path2 << '\n' << "ignored\t" << consensus << '\n'; overlaps.insert(id); overlaps.insert(path2It->first); } } cout << vout.str(); return id; } /** Remove paths subsumed by the specified path. * @param seed [out] the ID of the subsuming path * @param overlaps [out] paths that are found to overlap * @return the next iterator after path1it */ static ContigPathMap::const_iterator removeSubsumedPaths( const Lengths& lengths, ContigPathMap::const_iterator path1It, ContigPathMap& paths, ContigID& seed, set& overlaps) { if (gDebugPrint) cout << '\n'; set eq; seed = identifySubsumedPaths(lengths, path1It, paths, eq, overlaps); ++path1It; for (set::const_iterator it = eq.begin(); it != eq.end(); ++it) { if (*it == path1It->first) ++path1It; paths.erase(*it); } return path1It; } /** Remove paths subsumed by another path. * @return paths that are found to overlap */ static set removeSubsumedPaths(const Lengths& lengths, ContigPathMap& paths) { set overlaps, seen; for (ContigPathMap::const_iterator iter = paths.begin(); iter != paths.end();) { if (seen.count(iter->first) == 0) { ContigID seed; iter = removeSubsumedPaths(lengths, iter, paths, seed, overlaps); seen.insert(seed); } else ++iter; } return overlaps; } /** Add missing overlap edges. For each vertex u with at least two * outgoing edges, (u,v1) and (u,v2), add the edge (v1,v2) if v1 < v2, * and add the edge (v2,v1) if v2 < v1. */ static void addMissingEdges(const Lengths& lengths, PathGraph& g, const ContigPathMap& paths) { typedef graph_traits::adjacency_iterator Vit; typedef graph_traits::vertex_iterator Uit; typedef graph_traits::vertex_descriptor V; unsigned numAdded = 0; pair urange = vertices(g); for (Uit uit = urange.first; uit != urange.second; ++uit) { V u = *uit; if (out_degree(u, g) < 2) continue; pair vrange = adjacent_vertices(u, g); for (Vit vit1 = vrange.first; vit1 != vrange.second;) { V v1 = *vit1; ++vit1; assert(v1 != u); ContigPath path1 = getPath(paths, v1); if (find(path1.begin(), path1.end(), ContigPath::value_type(u)) == path1.end()) continue; for (Vit vit2 = vit1; vit2 != vrange.second; ++vit2) { V v2 = *vit2; assert(v2 != u); assert(v1 != v2); if (edge(v1, v2, g).second || edge(v2, v1, g).second) continue; ContigPath path2 = getPath(paths, v2); if (find(path2.begin(), path2.end(), ContigPath::value_type(u)) == path2.end()) continue; numAdded += addOverlapEdge(lengths, g, u, v1, path1, v2, path2); } } } if (opt::verbose > 0) cout << "Added " << numAdded << " missing edges.\n"; } /** Remove transitive edges. */ static void removeTransitiveEdges(PathGraph& pathGraph) { unsigned nbefore = num_edges(pathGraph); unsigned nremoved = remove_transitive_edges(pathGraph); unsigned nafter = num_edges(pathGraph); if (opt::verbose > 0) cout << "Removed " << nremoved << " transitive edges of " << nbefore << " edges leaving " << nafter << " edges.\n"; assert(nbefore - nremoved == nafter); } /** Remove ambiguous edges that overlap by only a small amount. * Remove the edge (u,v) if deg+(u) > 1 and deg-(v) > 1 and the * overlap of (u,v) is small. */ static void removeSmallOverlaps(PathGraph& g, const ContigPathMap& paths) { typedef graph_traits::edge_descriptor E; typedef graph_traits::out_edge_iterator Eit; typedef graph_traits::vertex_descriptor V; typedef graph_traits::vertex_iterator Vit; vector edges; pair urange = vertices(g); for (Vit uit = urange.first; uit != urange.second; ++uit) { V u = *uit; if (out_degree(u, g) < 2) continue; ContigPath pathu = getPath(paths, u); pair uvits = out_edges(u, g); for (Eit uvit = uvits.first; uvit != uvits.second; ++uvit) { E uv = *uvit; V v = target(uv, g); assert(v != u); if (in_degree(v, g) < 2) continue; ContigPath pathv = getPath(paths, v); if (pathu.back() == pathv.front() && paths.count(pathu.back().contigIndex()) > 0) edges.push_back(uv); } } remove_edges(g, edges.begin(), edges.end()); if (opt::verbose > 0) cout << "Removed " << edges.size() << " small overlap edges.\n"; } /** Output the path overlap graph. */ static void outputPathGraph(PathGraph& pathGraph) { if (opt::graphPath.empty()) return; ofstream out(opt::graphPath.c_str()); assert_good(out, opt::graphPath); write_dot(out, pathGraph); assert_good(out, opt::graphPath); } /** Sort and output the specified paths. */ static void outputSortedPaths(const ContigPathMap& paths) { // Sort the paths. vector sortedPaths(paths.size()); transform(paths.begin(), paths.end(), sortedPaths.begin(), mem_var(&ContigPathMap::value_type::second)); sort(sortedPaths.begin(), sortedPaths.end()); // Output the paths. ofstream fout(opt::out.c_str()); ostream& out = opt::out.empty() ? cout : fout; assert_good(out, opt::out); for (vector::const_iterator it = sortedPaths.begin(); it != sortedPaths.end(); ++it) out << createContigName() << '\t' << *it << '\n'; assert_good(out, opt::out); } /** Assemble the path overlap graph. */ static void assemblePathGraph(const Lengths& lengths, PathGraph& pathGraph, ContigPathMap& paths) { ContigPaths seedPaths; assembleDFS(pathGraph, back_inserter(seedPaths)); ContigPaths mergedPaths = mergeSeedPaths(lengths, paths, seedPaths); if (opt::verbose > 1) cout << '\n'; // Replace each path with the merged path. for (ContigPaths::const_iterator it1 = seedPaths.begin(); it1 != seedPaths.end(); ++it1) { const ContigPath& path(mergedPaths[it1 - seedPaths.begin()]); ContigPath pathrc(path); reverseComplement(pathrc.begin(), pathrc.end()); for (ContigPath::const_iterator it2 = it1->begin(); it2 != it1->end(); ++it2) { ContigNode seed(*it2); if (find(path.begin(), path.end(), seed) != path.end()) { paths[seed.contigIndex()] = seed.sense() ? pathrc : path; } else { // This seed was not included in the merged path. } } } removeRepeats(paths); // Remove the subsumed paths. if (opt::verbose > 0) cout << "Removing redundant contigs\n"; removeSubsumedPaths(lengths, paths); outputSortedPaths(paths); } /** Read a set of paths from the specified file. */ static ContigPathMap readPaths(const Lengths& lengths, const string& filePath) { if (opt::verbose > 0) cerr << "Reading `" << filePath << "'..." << endl; ifstream in(filePath.c_str()); assert_good(in, filePath); unsigned tooSmall = 0; ContigPathMap paths; std::string name; ContigPath path; while (in >> name >> path) { // Ignore seed contigs shorter than the threshold length. ContigID id(get(g_contigNames, name)); unsigned len = lengths[id] + opt::k - 1; if (len < opt::seedLen) { tooSmall++; continue; } bool inserted = paths.insert( make_pair(id, path)).second; assert(inserted); (void)inserted; } assert(in.eof()); if (opt::seedLen > 0) cout << "Ignored " << tooSmall << " paths whose seeds are shorter than " << opt::seedLen << " bp.\n"; return paths; } /** Store it in out and increment it. * @return true if out != last */ template bool atomicInc(T& it, T last, T& out) { #pragma omp critical(atomicInc) out = it == last ? it : it++; return out != last; } /** Build the path overlap graph. */ static void buildPathGraph(const Lengths& lengths, PathGraph& g, const ContigPathMap& paths) { // Create the vertices of the path overlap graph. PathGraph(lengths.size()).swap(g); // Remove the non-seed contigs. typedef graph_traits::vertex_iterator vertex_iterator; pair vit = g.vertices(); for (vertex_iterator u = vit.first; u != vit.second; ++u) if (paths.count(get(vertex_contig_index, g, *u)) == 0) remove_vertex(*u, g); // Find the overlapping paths. ContigPathMap::const_iterator sharedIt = paths.begin(); #pragma omp parallel for (ContigPathMap::const_iterator it; atomicInc(sharedIt, paths.end(), it);) findPathOverlaps(lengths, paths, ContigNode(it->first, false), it->second, g); if (gDebugPrint) cout << '\n'; addMissingEdges(lengths, g, paths); removeTransitiveEdges(g); removeSmallOverlaps(g, paths); if (opt::verbose > 0) printGraphStats(cout, g); outputPathGraph(g); } /** Read contig lengths. */ static Lengths readContigLengths(istream& in) { assert(in); assert(g_contigNames.empty()); Lengths lengths; string s; unsigned len; while (in >> s >> len) { in.ignore(numeric_limits::max(), '\n'); put(g_contigNames, lengths.size(), s); assert(len >= opt::k); lengths.push_back(len - opt::k + 1); } assert(in.eof()); assert(!lengths.empty()); g_contigNames.lock(); return lengths; } /** Read contig lengths. */ static Lengths readContigLengths(const string& path) { ifstream in(path.c_str()); assert_good(in, path); return readContigLengths(in); } int main(int argc, char** argv) { bool die = false; for (int c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;) { istringstream arg(optarg != NULL ? optarg : ""); switch (c) { case '?': die = true; break; case 'g': arg >> opt::graphPath; break; case 'j': arg >> opt::threads; break; case 'k': arg >> opt::k; break; case 'o': arg >> opt::out; break; case 's': arg >> opt::seedLen; break; case 'v': opt::verbose++; break; case OPT_HELP: cout << USAGE_MESSAGE; exit(EXIT_SUCCESS); case OPT_VERSION: cout << VERSION_MESSAGE; exit(EXIT_SUCCESS); } if (optarg != NULL && !arg.eof()) { cerr << PROGRAM ": invalid option: `-" << (char)c << optarg << "'\n"; exit(EXIT_FAILURE); } } if (opt::k <= 0) { cerr << PROGRAM ": missing -k,--kmer option\n"; die = true; } if (argc - optind < 2) { cerr << PROGRAM ": missing arguments\n"; die = true; } else if (argc - optind > 2) { cerr << PROGRAM ": too many arguments\n"; die = true; } if (die) { cerr << "Try `" << PROGRAM << " --help' for more information.\n"; exit(EXIT_FAILURE); } if (!opt::graphPath.empty()) opt::greedy = false; gDebugPrint = opt::verbose > 1; #if _OPENMP if (opt::threads > 0) omp_set_num_threads(opt::threads); #endif if (opt::verbose > 0) cerr << "Reading `" << argv[optind] << "'..." << endl; Lengths lengths = readContigLengths(argv[optind++]); ContigPathMap originalPathMap = readPaths( lengths, argv[optind++]); removeRepeats(originalPathMap); if (!opt::greedy) { // Assemble the path overlap graph. PathGraph pathGraph; buildPathGraph(lengths, pathGraph, originalPathMap); if (!opt::out.empty()) assemblePathGraph(lengths, pathGraph, originalPathMap); exit(EXIT_SUCCESS); } ContigPathMap resultsPathMap; #if _OPENMP ContigPathMap::iterator sharedIt = originalPathMap.begin(); #pragma omp parallel for (ContigPathMap::iterator it; atomicInc(sharedIt, originalPathMap.end(), it);) extendPaths(lengths, it->first, originalPathMap, resultsPathMap); #else for (ContigPathMap::const_iterator it = originalPathMap.begin(); it != originalPathMap.end(); ++it) extendPaths(lengths, it->first, originalPathMap, resultsPathMap); #endif if (gDebugPrint) cout << '\n'; set repeats = removeRepeats(resultsPathMap); if (gDebugPrint) cout << "\nRemoving redundant contigs\n"; set overlaps = removeSubsumedPaths(lengths, resultsPathMap); if (!overlaps.empty() && !repeats.empty()) { // Remove the newly-discovered repeat contigs from the // original paths. for (set::const_iterator it = repeats.begin(); it != repeats.end(); ++it) originalPathMap.erase(*it); // Reassemble the paths that were found to overlap. if (gDebugPrint) { cout << "\nReassembling overlapping contigs:"; for (set::const_iterator it = overlaps.begin(); it != overlaps.end(); ++it) cout << ' ' << get(g_contigNames, *it); cout << '\n'; } for (set::const_iterator it = overlaps.begin(); it != overlaps.end(); ++it) { if (originalPathMap.count(*it) == 0) continue; // repeat ContigPathMap::iterator oldIt = resultsPathMap.find(*it); if (oldIt == resultsPathMap.end()) continue; // subsumed ContigPath old = oldIt->second; resultsPathMap.erase(oldIt); extendPaths(lengths, *it, originalPathMap, resultsPathMap); if (gDebugPrint) { if (resultsPathMap[*it] == old) cout << "no change\n"; else cout << "was\t" << old << '\n'; } } if (gDebugPrint) cout << '\n'; removeRepeats(resultsPathMap); overlaps = removeSubsumedPaths(lengths, resultsPathMap); if (!overlaps.empty() && gDebugPrint) { cout << "\nOverlapping contigs:"; for (set::const_iterator it = overlaps.begin(); it != overlaps.end(); ++it) cout << ' ' << get(g_contigNames, *it); cout << '\n'; } } originalPathMap.clear(); outputSortedPaths(resultsPathMap); return 0; } /** Return the length of the specified contig in k-mer. */ static unsigned getLength(const Lengths& lengths, const ContigNode& u) { return u.ambiguous() ? u.length() : lengths.at(u.id()); } /** Functor to add the number of k-mer in two contigs. */ struct AddLength { AddLength(const Lengths& lengths) : m_lengths(lengths) { } unsigned operator()(unsigned addend, const ContigNode& u) const { return addend + getLength(m_lengths, u); } private: const Lengths& m_lengths; }; /** Attempt to fill in gaps in one path with the sequence from the * other path and store the consensus at result if an alignment is * found. * @return true if an alignment is found */ template static bool alignCoordinates(const Lengths& lengths, iterator& first1, iterator last1, iterator& first2, iterator last2, oiterator& result) { oiterator out = result; int ambiguous1 = 0, ambiguous2 = 0; iterator it1 = first1, it2 = first2; while (it1 != last1 && it2 != last2) { if (it1->ambiguous()) { ambiguous1 += it1->length(); ++it1; assert(it1 != last1); assert(!it1->ambiguous()); } if (it2->ambiguous()) { ambiguous2 += it2->length(); ++it2; assert(it2 != last2); assert(!it2->ambiguous()); } if (ambiguous1 > 0 && ambiguous2 > 0) { if (ambiguous1 > ambiguous2) { *out++ = ContigNode(ambiguous2, 'N'); ambiguous1 -= ambiguous2; ambiguous2 = 0; } else { *out++ = ContigNode(ambiguous1, 'N'); ambiguous2 -= ambiguous1; ambiguous1 = 0; } } else if (ambiguous1 > 0) { ambiguous1 -= getLength(lengths, *it2); *out++ = *it2++; } else if (ambiguous2 > 0) { ambiguous2 -= getLength(lengths, *it1); *out++ = *it1++; } else assert(false); if (ambiguous1 == 0 && ambiguous2 == 0) break; if (ambiguous1 < 0 || ambiguous2 < 0) return false; } assert(ambiguous1 == 0 || ambiguous2 == 0); int ambiguous = ambiguous1 + ambiguous2; assert(out > result); if (out[-1].ambiguous()) assert(ambiguous == 0); else *out++ = ContigNode(max(1, ambiguous), 'N'); first1 = it1; first2 = it2; result = out; return true; } /** Align the ambiguous region [it1, it1e) to [it2, it2e) and store * the consensus at out if an alignment is found. * @return true if an alignment is found */ template static bool buildConsensus(const Lengths& lengths, iterator it1, iterator it1e, iterator it2, iterator it2e, oiterator& out) { iterator it1b = it1 + 1; assert(!it1b->ambiguous()); if (it1b == it1e) { // path2 completely fills the gap in path1. out = copy(it2, it2e, out); return true; } // The gaps of path1 and path2 overlap. iterator it2a = it2e - 1; if (it2e == it2 || !it2a->ambiguous()) { // The two paths do not agree. No alignment. return false; } unsigned ambiguous1 = it1->length(); unsigned ambiguous2 = it2a->length(); unsigned unambiguous1 = accumulate(it1b, it1e, 0, AddLength(lengths)); unsigned unambiguous2 = accumulate(it2, it2a, 0, AddLength(lengths)); if (ambiguous1 < unambiguous2 || ambiguous2 < unambiguous1) { // Two gaps overlap and either of the gaps is smaller // than the unambiguous sequence that overlaps the // gap. No alignment. return false; } unsigned n = max(1U, max(ambiguous2 - unambiguous1, ambiguous1 - unambiguous2)); out = copy(it2, it2a, out); *out++ = ContigNode(n, 'N'); out = copy(it1b, it1e, out); return true; } /** Align the ambiguous region [it1, last1) to [it2, last2) using it1e * as the seed of the alignment. The end of the alignment is returned * in it1 and it2. * @return true if an alignment is found */ template static bool alignAtSeed(const Lengths& lengths, iterator& it1, iterator it1e, iterator last1, iterator& it2, iterator last2, oiterator& out) { assert(it1 != last1); assert(it1->ambiguous()); assert(it1 + 1 != last1); assert(!it1e->ambiguous()); assert(it2 != last2); // Find the best seeded alignment. The best alignment has the // fewest number of contigs in the consensus sequence. unsigned bestLen = UINT_MAX; iterator bestIt2e; for (iterator it2e = it2; (it2e = find(it2e, last2, *it1e)) != last2; ++it2e) { oiterator myOut = out; if (buildConsensus(lengths, it1, it1e, it2, it2e, myOut) && align(lengths, it1e, last1, it2e, last2, myOut)) { unsigned len = myOut - out; if (len <= bestLen) { bestLen = len; bestIt2e = it2e; } } } if (bestLen != UINT_MAX) { bool good = buildConsensus(lengths, it1, it1e, it2, bestIt2e, out); assert(good); it1 = it1e; it2 = bestIt2e; return good; } else return false; } /** Align the ambiguous region [it1, last1) to [it2, last2). * The end of the alignment is returned in it1 and it2. * @return true if an alignment is found */ template static bool alignAmbiguous(const Lengths& lengths, iterator& it1, iterator last1, iterator& it2, iterator last2, oiterator& out) { assert(it1 != last1); assert(it1->ambiguous()); assert(it1 + 1 != last1); assert(it2 != last2); // Find a seed for the alignment. for (iterator it1e = it1; it1e != last1; ++it1e) { if (it1e->ambiguous()) continue; if (alignAtSeed(lengths, it1, it1e, last1, it2, last2, out)) return true; } // No valid seeded alignment. Check whether path2 fits entirely // within the gap of path1. return alignCoordinates(lengths, it1, last1, it2, last2, out); } /** Align the next pair of contigs. * The end of the alignment is returned in it1 and it2. * @return true if an alignment is found */ template static bool alignOne(const Lengths& lengths, iterator& it1, iterator last1, iterator& it2, iterator last2, oiterator& out) { // Check for a trivial alignment. unsigned n1 = last1 - it1, n2 = last2 - it2; if (n1 <= n2 && equal(it1, last1, it2)) { // [it1,last1) is a prefix of [it2,last2). out = copy(it1, last1, out); it1 += n1; it2 += n1; assert(it1 == last1); return true; } else if (n2 < n1 && equal(it2, last2, it1)) { // [it2,last2) is a prefix of [it1,last1). out = copy(it2, last2, out); it1 += n2; it2 += n2; assert(it2 == last2); return true; } return it1->ambiguous() && it2->ambiguous() ? (it1->length() > it2->length() ? alignAmbiguous(lengths, it1, last1, it2, last2, out) : alignAmbiguous(lengths, it2, last2, it1, last1, out) ) : it1->ambiguous() ? alignAmbiguous(lengths, it1, last1, it2, last2, out) : it2->ambiguous() ? alignAmbiguous(lengths, it2, last2, it1, last1, out) : (*out++ = *it1, *it1++ == *it2++); } /** Align the ambiguous region [it1, last1) to [it2, last2) * and store the consensus at out if an alignment is found. * @return the orientation of the alignment if an alignments is found * or zero otherwise */ template static dir_type align(const Lengths& lengths, iterator it1, iterator last1, iterator it2, iterator last2, oiterator& out) { assert(it1 != last1); assert(it2 != last2); while (it1 != last1 && it2 != last2) if (!alignOne(lengths, it1, last1, it2, last2, out)) return DIR_X; assert(it1 == last1 || it2 == last2); out = copy(it1, last1, out); out = copy(it2, last2, out); return it1 == last1 && it2 == last2 ? DIR_B : it1 == last1 ? DIR_F : it2 == last2 ? DIR_R : DIR_X; } /** Find an equivalent region of the two specified paths, starting the * alignment at pivot1 of path1 and pivot2 of path2. * @param[out] orientation the orientation of the alignment * @return the consensus sequence */ static ContigPath align(const Lengths& lengths, const ContigPath& p1, const ContigPath& p2, ContigPath::const_iterator pivot1, ContigPath::const_iterator pivot2, dir_type& orientation) { assert(*pivot1 == *pivot2); ContigPath::const_reverse_iterator rit1 = ContigPath::const_reverse_iterator(pivot1+1), rit2 = ContigPath::const_reverse_iterator(pivot2+1); ContigPath alignmentr(p1.rend() - rit1 + p2.rend() - rit2); ContigPath::iterator rout = alignmentr.begin(); dir_type alignedr = align(lengths, rit1, p1.rend(), rit2, p2.rend(), rout); alignmentr.erase(rout, alignmentr.end()); ContigPath::const_iterator it1 = pivot1, it2 = pivot2; ContigPath alignmentf(p1.end() - it1 + p2.end() - it2); ContigPath::iterator fout = alignmentf.begin(); dir_type alignedf = align(lengths, it1, p1.end(), it2, p2.end(), fout); alignmentf.erase(fout, alignmentf.end()); ContigPath consensus; if (alignedr != DIR_X && alignedf != DIR_X) { // Found an alignment. assert(!alignmentf.empty()); assert(!alignmentr.empty()); consensus.reserve(alignmentr.size()-1 + alignmentf.size()); consensus.assign(alignmentr.rbegin(), alignmentr.rend()-1); consensus.insert(consensus.end(), alignmentf.begin(), alignmentf.end()); // Determine the orientation of the alignment. unsigned dirs = alignedr << 2 | alignedf; static const dir_type DIRS[16] = { DIR_X, // 0000 XX impossible DIR_X, // 0001 XF impossible DIR_X, // 0010 XR impossible DIR_X, // 0011 XB impossible DIR_X, // 0100 FX impossible DIR_B, // 0101 FF u is subsumed in v DIR_R, // 0110 FR v->u DIR_R, // 0111 FB v->u DIR_X, // 1000 RX impossible DIR_F, // 1001 RF u->v DIR_B, // 1010 RR v is subsumed in u DIR_F, // 1011 RB u->v DIR_X, // 1100 BX impossible DIR_F, // 1101 BF u->v DIR_R, // 1110 BR v->u DIR_B, // 1111 BB u and v are equal }; assert(dirs < 16); orientation = DIRS[dirs]; assert(orientation != DIR_X); } return consensus; } /** Return a pivot suitable for aligning the two paths if one exists, * otherwise return false. */ static pair findPivot( const ContigPath& path1, const ContigPath& path2) { for (ContigPath::const_iterator it = path2.begin(); it != path2.end(); ++it) { if (it->ambiguous()) continue; if (count(path2.begin(), path2.end(), *it) == 1 && count(path1.begin(), path1.end(), *it) == 1) return make_pair(*it, true); } return make_pair(ContigNode(0), false); } /** Find an equivalent region of the two specified paths. * @param[out] orientation the orientation of the alignment * @return the consensus sequence */ static ContigPath align(const Lengths& lengths, const ContigPath& path1, const ContigPath& path2, ContigNode pivot, dir_type& orientation) { if (&path1 == &path2) { // Ignore the trivial alignment when aligning a path to // itself. } else if (path1 == path2) { // These two paths are identical. orientation = DIR_B; return path1; } else { ContigPath::const_iterator it = search(path1.begin(), path1.end(), path2.begin(), path2.end()); if (it != path1.end()) { // path2 is subsumed in path1. // Determine the orientation of the edge. orientation = it == path1.begin() ? DIR_R : it + path2.size() == path1.end() ? DIR_F : DIR_B; return path1; } } // Find a suitable pivot. if (find(path1.begin(), path1.end(), pivot) == path1.end() || find(path2.begin(), path2.end(), pivot) == path2.end()) { bool good; tie(pivot, good) = findPivot(path1, path2); if (!good) return ContigPath(); } assert(find(path1.begin(), path1.end(), pivot) != path1.end()); ContigPath::const_iterator it2 = find(path2.begin(), path2.end(), pivot); assert(it2 != path2.end()); if (&path1 != &path2) { // The seed must be unique in path2, unless we're aligning a // path to itself. assert(count(it2+1, path2.end(), pivot) == 0); } ContigPath consensus; for (ContigPath::const_iterator it1 = find_if( path1.begin(), path1.end(), bind2nd(equal_to(), pivot)); it1 != path1.end(); it1 = find_if(it1+1, path1.end(), bind2nd(equal_to(), pivot))) { if (&*it1 == &*it2) { // We are aligning a path to itself, and this is the // trivial alignment, which we'll ignore. continue; } consensus = align(lengths, path1, path2, it1, it2, orientation); if (!consensus.empty()) return consensus; } return consensus; } /** Find an equivalent region of the two specified paths. * @return the consensus sequence */ static ContigPath align(const Lengths& lengths, const ContigPath& path1, const ContigPath& path2, ContigNode pivot) { dir_type orientation; return align(lengths, path1, path2, pivot, orientation); } abyss-1.3.6/MergePaths/PathConsensus.cpp000644 002433 001057 00000066022 12155671625 021737 0ustar00traymondassembly000000 000000 #include "dialign.h" #include "config.h" #include "Common/Options.h" #include "ConstString.h" #include "ContigNode.h" #include "ContigPath.h" #include "Dictionary.h" #include "FastaReader.h" #include "IOUtil.h" #include "StringUtil.h" #include "Uncompress.h" #include "alignGlobal.h" #include "Graph/ConstrainedSearch.h" #include "Graph/ContigGraph.h" #include "Graph/ContigGraphAlgorithms.h" #include "Graph/GraphIO.h" #include #include #include #include #include #include #include #include #include #include #include #include using namespace std; #define PROGRAM "PathConsensus" static const char VERSION_MESSAGE[] = PROGRAM " (" PACKAGE_NAME ") " VERSION "\n" "Written by Shaun Jackman and Rong She.\n" "\n" "Copyright 2013 Canada's Michael Smith Genome Science Centre\n"; static const char USAGE_MESSAGE[] = "Usage: " PROGRAM " [OPTION]... FASTA ADJ PATH\n" "Align sequences of ambiguous paths and output a consensus\n" "sequence.\n" "\n" " Arguments:\n" "\n" " FASTA contigs in FASTA format\n" " ADJ contig adjacency graph\n" " PATH paths of these contigs\n" "\n" " Options:\n" "\n" " -k, --kmer=N k-mer size\n" " -d, --dist-error=N acceptable error of a distance estimate\n" " default: 6 bp\n" " -o, --out=FILE output contig paths to FILE\n" " -s, --consensus=FILE output consensus sequences to FILE\n" " -g, --graph=FILE output the contig adjacency graph to FILE\n" " -a, --branches=N maximum number of sequences to align\n" " default: 4\n" " -p, --identity=REAL minimum identity, default: 0.9\n" " -v, --verbose display verbose output\n" " --help display this help and exit\n" " --version output version information and exit\n" "\n" " DIALIGN-TX options:\n" " -D, --dialign-d=N dialign debug level, default: 0\n" " -M, --dialign-m=FILE score matrix, default: dna_matrix.scr\n" " -P, --dialign-p=FILE diagonal length probability distribution\n" " default: dna_diag_prob_100_exp_550000\n" "\n" "Report bugs to <" PACKAGE_BUGREPORT ">.\n"; namespace opt { unsigned k; // used by ContigProperties static string out; static string consensusPath; static string graphPath; static float identity = 0.9; static unsigned numBranches = 4; static int dialign_debug; static string dialign_score; static string dialign_prob; /** Output format. */ int format; // used by ContigProperties /** The the number of bases to continue the constrained search of * the graph beyond the size of the ambiguous gap in the path. */ unsigned distanceError = 6; } static const char shortopts[] = "d:k:o:s:g:a:p:vD:M:P:"; enum { OPT_HELP = 1, OPT_VERSION }; static const struct option longopts[] = { { "kmer", required_argument, NULL, 'k' }, { "dist-error", required_argument, NULL, 'd' }, { "out", required_argument, NULL, 'o' }, { "consensus", required_argument, NULL, 's' }, { "graph", required_argument, NULL, 'g' }, { "branches", required_argument, NULL, 'a' }, { "identity", required_argument, NULL, 'p' }, { "verbose", no_argument, NULL, 'v' }, { "help", no_argument, NULL, OPT_HELP }, { "version", no_argument, NULL, OPT_VERSION }, { "dialign-d", required_argument, NULL, 'D' }, { "dialign-m", required_argument, NULL, 'M' }, { "dialign-p", required_argument, NULL, 'P' }, { NULL, 0, NULL, 0 } }; static struct { unsigned numAmbPaths; unsigned numMerged; unsigned numNoSolutions; unsigned numTooManySolutions; unsigned tooComplex; unsigned notMerged; } stats; struct AmbPathConstraint { ContigNode source; ContigNode dest; int dist; AmbPathConstraint(const ContigNode& src, const ContigNode& dst, int d) : source(src), dest(dst), dist(d) {} bool operator ==(const AmbPathConstraint& a) const { return source == a.source && dest == a.dest && dist == a.dist; } bool operator <(const AmbPathConstraint& a) const { return source < a.source || (source == a.source && dest < a.dest) || (source == a.source && dest == a.dest && dist < a.dist); } }; typedef ContigPath Path; typedef vector ContigPaths; typedef map AmbPath2Contig; typedef vector Contigs; static Contigs g_contigs; AmbPath2Contig g_ambpath_contig; /** Return the sequence of the specified contig node. The sequence * may be ambiguous or reverse complemented. */ static const Sequence getSequence(ContigNode id) { if (id.ambiguous()) { string s(id.ambiguousSequence()); if (s.length() < opt::k) transform(s.begin(), s.end(), s.begin(), ::tolower); return string(opt::k - 1, 'N') + s; } else { string seq(g_contigs[id.id()]); return id.sense() ? reverseComplement(seq) : seq; } } /** Return the distance from vertex u to v. */ static int getDistance(const Graph& g, graph_traits::vertex_descriptor u, graph_traits::vertex_descriptor v) { typedef graph_traits::edge_descriptor E; pair e = edge(u, v, g); assert(e.second); return g[e.first].distance; } /** Read contig paths from the specified file. * @param[in] inPath the filename of the contig paths * @param[out] ids the string ID of the paths * @param[out] isAmb whether the path contains a gap */ static ContigPaths readPaths(const string& inPath, vector& ids, vector& isAmb) { typedef graph_traits::vertex_descriptor V; assert(ids.empty()); assert(isAmb.empty()); assert(g_ambpath_contig.empty()); ifstream fin(inPath.c_str()); if (opt::verbose > 0) cerr << "Reading `" << inPath << "'..." << endl; if (inPath != "-") assert_good(fin, inPath); istream& in = inPath == "-" ? cin : fin; ContigPaths paths; string id; Path path; while (in >> id >> path) { paths.push_back(path); ids.push_back(id); isAmb.push_back(false); if (path.size() <= 2) continue; for (Path::iterator it = path.begin() + 2; it != path.end(); ++it) { ContigPath::value_type t = it[-2], u = it[-1], v = it[0]; if (u.ambiguous()) { assert(!t.ambiguous()); assert(!v.ambiguous()); g_ambpath_contig.insert(AmbPath2Contig::value_type( AmbPathConstraint(t, v, u.length()), ContigPath())); isAmb.back() = true; } } } assert(in.eof()); return paths; } /** Mark every contig in path as seen. */ static void markSeen(vector& seen, const ContigPath& path, bool flag) { for (Path::const_iterator it = path.begin(); it != path.end(); ++it) if (!it->ambiguous() && it->id() < seen.size()) seen[it->id()] = flag; } /** Mark every contig in paths as seen. */ static void markSeen(vector& seen, const vector& paths, bool flag) { for (vector::const_iterator it = paths.begin(); it != paths.end(); ++it) markSeen(seen, *it, flag); } /** A new vertex and two edges that will be added to the graph. */ struct NewVertex { typedef graph_traits::vertex_descriptor V; typedef vertex_property::type VP; typedef edge_property::type EP; V t, u, v; VP vpu; EP eptu, epuv; NewVertex(V t, V u, V v, const VP& vpu, const EP& eptu, const EP& epuv) : t(t), u(u), v(v), vpu(vpu), eptu(eptu), epuv(epuv) { } }; typedef vector NewVertices; /** The new vertices that will be added to the graph. */ static NewVertices g_newVertices; /** Output a new contig. */ static ContigNode outputNewContig(const Graph& g, const vector& solutions, size_t longestPrefix, size_t longestSuffix, const Sequence& seq, const unsigned coverage, ofstream& out) { assert(!solutions.empty()); assert(longestPrefix > 0); assert(longestSuffix > 0); size_t numContigs = num_vertices(g) / 2; ContigNode u(numContigs + g_newVertices.size(), false); string name = createContigName(); put(vertex_name, g, u, name); out << '>' << name << ' ' << seq.length() << ' ' << coverage << ' '; int dtu = INT_MAX, duv = INT_MAX; for (vector::const_iterator it = solutions.begin(); it != solutions.end(); it++) { if (it != solutions.begin()) out << ';'; const ContigPath& path = *it; ContigPath::const_iterator first = path.begin() + longestPrefix, last = path.end() - longestSuffix; assert(first <= last); if (first < last) { ContigPath::const_iterator it = first; out << get(vertex_name, g, *it); for (++it; it != last; ++it) out << ',' << get(vertex_name, g, *it); dtu = min(dtu, getDistance(g, first[-1], first[0])); duv = min(duv, getDistance(g, last[-1], last[0])); } else out << '*'; } out << '\n' << seq << '\n'; assert(dtu < INT_MAX); assert(duv < INT_MAX); // Record the newly-created contig to be added to the graph later. g_newVertices.push_back(NewVertex( *(solutions[0].begin() + longestPrefix - 1), u, *(solutions[0].rbegin() + longestSuffix - 1), ContigProperties(seq.length(), coverage), dtu, duv)); return u; } /** Return a consensus sequence of a and b. * @return an empty string if a consensus could not be found */ static string createConsensus(const Sequence& a, const Sequence& b) { assert(a.length() == b.length()); if (a == b) return a; string s; s.reserve(a.length()); for (string::const_iterator ita = a.begin(), itb = b.begin(); ita != a.end(); ++ita, ++itb) { bool mask = islower(*ita) || islower(*itb); char ca = toupper(*ita), cb = toupper(*itb); char c = ca == cb ? ca : ca == 'N' ? cb : cb == 'N' ? ca : 'x'; if (c == 'x') return string(""); s += mask ? tolower(c) : c; } return s; } /** Merge the specified two contigs, default overlap is k-1, * generate a consensus sequence of the overlapping region. The result * is stored in the first argument. */ static void mergeContigs(const Graph& g, unsigned overlap, Sequence& seq, const Sequence& s, const ContigNode& node, const Path& path) { assert(s.length() > overlap); Sequence ao; Sequence bo(s, 0, overlap); Sequence o; do { assert(seq.length() > overlap); ao = seq.substr(seq.length() - overlap); o = createConsensus(ao, bo); } while (o.empty() && chomp(seq, 'n')); if (o.empty()) { cerr << "warning: the head of " << get(vertex_name, g, node) << " does not match the tail of the previous contig\n" << ao << '\n' << bo << '\n' << path << endl; seq += 'n'; seq += s; } else { seq.resize(seq.length() - overlap); seq += o; seq += Sequence(s, overlap); } } static Sequence mergePath(const Graph&g, const Path& path) { Sequence seq; Path::const_iterator prev_it; for (Path::const_iterator it = path.begin(); it != path.end(); ++it) { if (seq.empty()) { seq = getSequence(*it); } else { int d = get(edge_bundle, g, *(it-1), *it).distance; assert(d < 0); unsigned overlap = -d; mergeContigs(g, overlap, seq, getSequence(*it), *it, path); } prev_it = it; } return seq; } /** Calculate the ContigProperties of a path. */ static ContigProperties calculatePathProperties(const Graph& g, const ContigPath& path) { return addProp(g, path.begin(), path.end()); } /* Resolve ambiguous region using pairwise alignment * (Needleman-Wunsch) ('solutions' contain exactly two paths, from a * source contig to a dest contig) */ static ContigPath alignPair(const Graph& g, const ContigPaths& solutions, ofstream& out) { assert(solutions.size() == 2); assert(solutions[0].size() > 1); assert(solutions[1].size() > 1); assert(solutions[0].front() == solutions[1].front()); assert(solutions[0].back() == solutions[1].back()); ContigPath fstSol(solutions[0].begin()+1, solutions[0].end()-1); ContigPath sndSol(solutions[1].begin()+1, solutions[1].end()-1); if (fstSol.empty() || sndSol.empty()) { // This entire sequence may be deleted. const ContigPath& sol(fstSol.empty() ? sndSol : fstSol); assert(!sol.empty()); Sequence consensus(mergePath(g, sol)); assert(consensus.size() > opt::k - 1); string::iterator first = consensus.begin() + opt::k - 1; transform(first, consensus.end(), first, ::tolower); unsigned match = opt::k - 1; float identity = (float)match / consensus.size(); if (opt::verbose > 2) cerr << consensus << '\n'; if (opt::verbose > 1) cerr << identity << (identity < opt::identity ? " (too low)\n" : "\n"); if (identity < opt::identity) return ContigPath(); unsigned coverage = calculatePathProperties(g, sol).coverage; ContigNode u = outputNewContig(g, solutions, 1, 1, consensus, coverage, out); ContigPath path; path.push_back(solutions.front().front()); path.push_back(u); path.push_back(solutions.front().back()); return path; } Sequence fstPathContig(mergePath(g, fstSol)); Sequence sndPathContig(mergePath(g, sndSol)); if (fstPathContig == sndPathContig) { // These two paths have identical sequence. if (fstSol.size() == sndSol.size()) { // A perfect match must be caused by palindrome. typedef ContigPath::const_iterator It; pair it = mismatch( fstSol.begin(), fstSol.end(), sndSol.begin()); assert(it.first != fstSol.end()); assert(it.second != sndSol.end()); assert(*it.first == get(vertex_complement, g, *it.second)); assert(equal(it.first+1, It(fstSol.end()), it.second+1)); if (opt::verbose > 1) cerr << "Palindrome: " << get(vertex_contig_name, g, *it.first) << '\n'; return solutions[0]; } else { // The paths are different lengths. cerr << PROGRAM ": warning: " "Two paths have identical sequence, which may be " "caused by a transitive edge in the overlap graph.\n" << '\t' << fstSol << '\n' << '\t' << sndSol << '\n'; return solutions[fstSol.size() > sndSol.size() ? 0 : 1]; } } unsigned minLength = min( fstPathContig.length(), sndPathContig.length()); unsigned maxLength = max( fstPathContig.length(), sndPathContig.length()); float lengthRatio = (float)minLength / maxLength; if (lengthRatio < opt::identity) { if (opt::verbose > 1) cerr << minLength << '\t' << maxLength << '\t' << lengthRatio << "\t(different length)\n"; return ContigPath(); } NWAlignment align; unsigned match = alignGlobal(fstPathContig, sndPathContig, align); float identity = (float)match / align.size(); if (opt::verbose > 2) cerr << align; if (opt::verbose > 1) cerr << identity << (identity < opt::identity ? " (too low)\n" : "\n"); if (identity < opt::identity) return ContigPath(); unsigned coverage = calculatePathProperties(g, fstSol).coverage + calculatePathProperties(g, sndSol).coverage; ContigNode u = outputNewContig(g, solutions, 1, 1, align.consensus(), coverage, out); ContigPath path; path.push_back(solutions.front().front()); path.push_back(u); path.push_back(solutions.front().back()); return path; } /* Resolve ambiguous region using multiple alignment of all paths in * `solutions'. */ static ContigPath alignMulti(const Graph& g, const vector& solutions, ofstream& out) { // Find the size of the smallest path. const Path& firstSol = solutions.front(); size_t min_len = firstSol.size(); for (vector::const_iterator it = solutions.begin() + 1; it != solutions.end(); ++it) min_len = min(min_len, it->size()); // Find the longest prefix. Path vppath; size_t longestPrefix; bool commonPrefix = true; for (longestPrefix = 0; longestPrefix < min_len; longestPrefix++) { const ContigNode& common_path_node = firstSol[longestPrefix]; for (vector::const_iterator solIter = solutions.begin(); solIter != solutions.end(); ++solIter) { const ContigNode& pathnode = (*solIter)[longestPrefix]; if (pathnode != common_path_node) { // Found the longest prefix. commonPrefix = false; break; } } if (!commonPrefix) break; vppath.push_back(common_path_node); } // Find the longest suffix. Path vspath; size_t longestSuffix; bool commonSuffix = true; for (longestSuffix = 0; longestSuffix < min_len-longestPrefix; longestSuffix++) { const ContigNode& common_path_node = firstSol[firstSol.size()-longestSuffix-1]; for (vector::const_iterator solIter = solutions.begin(); solIter != solutions.end(); ++solIter) { const ContigNode& pathnode = (*solIter)[solIter->size()-longestSuffix-1]; if (pathnode != common_path_node) { // Found the longest suffix. commonSuffix = false; break; } } if (!commonSuffix) break; vspath.push_back(common_path_node); } reverse(vspath.begin(), vspath.end()); if (opt::verbose > 1 && vppath.size() + vspath.size() > 2) cerr << vppath << " * " << vspath << '\n'; // Get sequence of ambiguous region in paths assert(longestPrefix > 0 && longestSuffix > 0); vector amb_seqs; unsigned coverage = 0; for (vector::const_iterator solIter = solutions.begin(); solIter != solutions.end(); solIter++) { assert(longestPrefix + longestSuffix <= solIter->size()); Path path(solIter->begin() + longestPrefix, solIter->end() - longestSuffix); if (!path.empty()) { amb_seqs.push_back(mergePath(g, path)); coverage += calculatePathProperties(g, path).coverage; } else { // The prefix and suffix paths overlap by k-1 bp. Sequence s = getSequence(solutions[0][longestPrefix-1]); amb_seqs.push_back(s.substr(s.length() - opt::k + 1)); } } vector lengths(amb_seqs.size()); transform(amb_seqs.begin(), amb_seqs.end(), lengths.begin(), mem_fun_ref(&string::length)); unsigned minLength = *min_element(lengths.begin(), lengths.end()); unsigned maxLength = *max_element(lengths.begin(), lengths.end()); float lengthRatio = (float)minLength / maxLength; if (lengthRatio < opt::identity) { if (opt::verbose > 1) cerr << minLength << '\t' << maxLength << '\t' << lengthRatio << "\t(different length)\n"; return ContigPath(); } string alignment; unsigned matches; Sequence consensus = dialign(amb_seqs, alignment, matches); if (opt::verbose > 2) cerr << alignment << consensus << '\n'; float identity = (float)matches / consensus.size(); if (opt::verbose > 1) cerr << identity << (identity < opt::identity ? " (too low)\n" : "\n"); if (identity < opt::identity) return ContigPath(); if (identity == 1) { // A perfect match must be caused by two palindromes. ContigID palindrome0 = solutions[0][longestPrefix].contigIndex(); ContigID palindrome1 = solutions[0].rbegin()[longestSuffix].contigIndex(); if (opt::verbose > 1) cerr << "Palindrome: " << get(g_contigNames, palindrome0) << '\n' << "Palindrome: " << get(g_contigNames, palindrome1) << '\n'; #ifndef NDEBUG string s0 = getSequence(ContigNode(palindrome0, false)); string s1 = getSequence(ContigNode(palindrome1, false)); assert(s0 == reverseComplement(s0)); assert(s1 == reverseComplement(s1)); for (vector::const_iterator it = solutions.begin(); it != solutions.end(); ++it) { const ContigPath& path = *it; assert(path[longestPrefix].contigIndex() == palindrome0); assert(path.rbegin()[longestSuffix].contigIndex() == palindrome1); assert(path.size() == solutions[0].size()); } #endif return solutions[0]; } ContigNode u = outputNewContig(g, solutions, longestPrefix, longestSuffix, consensus, coverage, out); ContigPath path(vppath); path.push_back(u); path.insert(path.end(), vspath.begin(), vspath.end()); return path; } /** Align the sequences of the specified paths. * @return the consensus sequence */ static ContigPath align(const Graph& g, const vector& sequences, ofstream& out) { assert(sequences.size() > 1); return sequences.size() == 2 ? alignPair(g, sequences, out) : alignMulti(g, sequences, out); } /** Return the consensus sequence of the specified gap. */ static ContigPath fillGap(const Graph& g, const AmbPathConstraint& apConstraint, vector& seen, ofstream& outFasta) { if (opt::verbose > 1) cerr << "\n* " << get(vertex_name, g, apConstraint.source) << ' ' << apConstraint.dist << "N " << get(vertex_name, g, apConstraint.dest) << '\n'; Constraints constraints; constraints.push_back(Constraint(apConstraint.dest, apConstraint.dist + opt::distanceError)); ContigPaths solutions; unsigned numVisited = 0; constrainedSearch(g, apConstraint.source, constraints, solutions, numVisited); bool tooComplex = numVisited >= opt::maxCost; for (ContigPaths::iterator solIt = solutions.begin(); solIt != solutions.end(); solIt++) solIt->insert(solIt->begin(), apConstraint.source); ContigPath consensus; bool tooManySolutions = solutions.size() > opt::numBranches; if (tooComplex) { stats.tooComplex++; if (opt::verbose > 1) cerr << solutions.size() << " paths (too complex)\n"; } else if (tooManySolutions) { stats.numTooManySolutions++; if (opt::verbose > 1) cerr << solutions.size() << " paths (too many)\n"; } else if (solutions.empty()) { stats.numNoSolutions++; if (opt::verbose > 1) cerr << "no paths\n"; } else if (solutions.size() == 1) { if (opt::verbose > 1) cerr << "1 path\n" << solutions.front() << '\n'; stats.numMerged++; } else { assert(solutions.size() > 1); if (opt::verbose > 2) copy(solutions.begin(), solutions.end(), ostream_iterator(cerr, "\n")); else if (opt::verbose > 1) cerr << solutions.size() << " paths\n"; consensus = align(g, solutions, outFasta); if (!consensus.empty()) { stats.numMerged++; // Mark contigs that are used in a consensus. markSeen(seen, solutions, true); if (opt::verbose > 1) cerr << consensus << '\n'; } else stats.notMerged++; } return consensus; } int main(int argc, char** argv) { string commandLine; { ostringstream ss; char** last = argv + argc - 1; copy(argv, last, ostream_iterator(ss, " ")); ss << *last; commandLine = ss.str(); } bool die = false; for (int c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;) { istringstream arg(optarg != NULL ? optarg : ""); switch (c) { case '?': die = true; break; case 'd': arg >> opt::distanceError; break; case 'k': arg >> opt::k; break; case 'o': arg >> opt::out; break; case 'p': arg >> opt::identity; break; case 'a': arg >> opt::numBranches; break; case 's': arg >> opt::consensusPath; break; case 'g': arg >> opt::graphPath; break; case 'D': arg >> opt::dialign_debug; break; case 'M': arg >> opt::dialign_score; break; case 'P': arg >> opt::dialign_prob; break; case 'v': opt::verbose++; break; case OPT_HELP: cout << USAGE_MESSAGE; exit(EXIT_SUCCESS); case OPT_VERSION: cout << VERSION_MESSAGE; exit(EXIT_SUCCESS); } if (optarg != NULL && !arg.eof()) { cerr << PROGRAM ": invalid option: `-" << (char)c << optarg << "'\n"; exit(EXIT_FAILURE); } } if (opt::k <= 0) { cerr << PROGRAM ": missing -k,--kmer option\n"; die = true; } if (opt::out.empty()) { cerr << PROGRAM ": " << "missing -o,--out option\n"; die = true; } if (opt::consensusPath.empty()) { cerr << PROGRAM ": " << "missing -s,--consensus option\n"; die = true; } if (argc - optind < 3) { cerr << PROGRAM ": missing arguments\n"; die = true; } if (die) { cerr << "Try `" << PROGRAM << " --help' for more information.\n"; exit(EXIT_FAILURE); } const char *contigFile = argv[optind++]; string adjFile(argv[optind++]); string allPaths(argv[optind++]); // Read the contig overlap graph. if (opt::verbose > 0) cerr << "Reading `" << adjFile << "'..." << endl; ifstream fin(adjFile.c_str()); assert_good(fin, adjFile); Graph g; fin >> g; assert(fin.eof()); g_contigNames.lock(); // Read contigs Contigs& contigs = g_contigs; { if (opt::verbose > 0) cerr << "Reading `" << contigFile << "'..." << endl; FastaReader in(contigFile, FastaReader::NO_FOLD_CASE); for (FastaRecord rec; in >> rec;) { assert(contigs.size() == get(g_contigNames, rec.id)); contigs.push_back(rec.seq); } assert(in.eof()); assert(!contigs.empty()); opt::colourSpace = isdigit(contigs[0][0]); } vector pathIDs; vector isAmbPath; ContigPaths paths = readPaths(allPaths, pathIDs, isAmbPath); stats.numAmbPaths = g_ambpath_contig.size(); if (opt::verbose > 0) cerr << "Read " << paths.size() << " paths\n"; // Start numbering new contigs from the last if (!pathIDs.empty()) setNextContigName(pathIDs.back()); // Prepare output fasta file ofstream fa(opt::consensusPath.c_str()); assert_good(fa, opt::consensusPath); init_parameters(); set_parameters_dna(); para->DEBUG = opt::dialign_debug; para->SCR_MATRIX_FILE_NAME = (char*)opt::dialign_score.c_str(); para->DIAG_PROB_FILE_NAME = (char*)opt::dialign_prob.c_str(); initDialign(); // Contigs that were seen in a consensus. vector seen(contigs.size()); // resolve ambiguous paths recorded in g_ambpath_contig g_contigNames.unlock(); for (AmbPath2Contig::iterator ambIt = g_ambpath_contig.begin(); ambIt != g_ambpath_contig.end(); ambIt++) ambIt->second = fillGap(g, ambIt->first, seen, fa); g_contigNames.lock(); assert_good(fa, opt::consensusPath); fa.close(); if (opt::verbose > 1) cerr << '\n'; // Unmark contigs that are used in a path. for (AmbPath2Contig::iterator it = g_ambpath_contig.begin(); it != g_ambpath_contig.end(); it++) markSeen(seen, it->second, false); markSeen(seen, paths, false); ofstream out(opt::out.c_str()); assert_good(out, opt::out); // Output those contigs that were not seen in ambiguous path. for (unsigned id = 0; id < contigs.size(); ++id) if (seen[id]) out << get(g_contigNames, id) << '\n'; for (ContigPaths::const_iterator path = paths.begin(); path != paths.end(); ++path) { unsigned i = path - paths.begin(); if (!isAmbPath[i]) { out << pathIDs[i] << '\t' << *path << '\n'; continue; } assert(path->size() > 2); Path cur_path; cur_path.push_back(path->front()); for (Path::const_iterator prev = path->begin(), it = path->begin() + 1, next = path->begin() + 2; it != path->end(); ++prev, ++it, ++next) { if (!it->ambiguous()) { cur_path.push_back(*it); continue; } //replace Ns by resolved new contig assert(next != path->end()); AmbPath2Contig::iterator ambIt = g_ambpath_contig.find( AmbPathConstraint(*prev, *next, -it->id())); assert(ambIt != g_ambpath_contig.end()); const ContigPath& solution = ambIt->second; if (!solution.empty()) { assert(solution.size() > 1); cur_path.insert(cur_path.end(), solution.begin() + 1, solution.end() - 1); } else cur_path.push_back(*it); } out << pathIDs[i] << '\t' << cur_path << '\n'; } assert_good(out, opt::out); out.close(); free_prob_dist(pdist); free(para); cerr << "Ambiguous paths: " << stats.numAmbPaths << "\n" "Merged: " << stats.numMerged << "\n" "No paths: " << stats.numNoSolutions << "\n" "Too many paths: " << stats.numTooManySolutions << "\n" "Too complex: " << stats.tooComplex << "\n" "Dissimilar: " << stats.notMerged << "\n"; if (!opt::graphPath.empty()) { ofstream fout(opt::graphPath.c_str()); assert_good(fout, opt::graphPath); 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#define PROGRAM "abyss-index" static const char VERSION_MESSAGE[] = PROGRAM " (" PACKAGE_NAME ") " VERSION "\n" "Written by Shaun Jackman.\n" "\n" "Copyright 2013 Canada's Michael Smith Genome Science Centre\n"; static const char USAGE_MESSAGE[] = "Usage: " PROGRAM " [OPTION]... FILE\n" "Build an FM-index of FILE and store it in FILE.fm.\n" "\n" " Options:\n" "\n" " --both build both FAI and FM indexes [default]\n" " --fai build a FAI index\n" " --fm build a FM index\n" " --fa2bwt build the BWT directly without the SA\n" " --bwt2fm build the FM index from the BWT\n" " -a, --alphabet=STRING use the alphabet STRING [-ACGT]\n" " -s, --sample=N sample the suffix array [16]\n" " -d, --decompress decompress the index FILE\n" " -c, --stdout write output to standard output\n" " -v, --verbose display verbose output\n" " --help display this help and exit\n" " --version output version information and exit\n" "\n" "Report bugs to <" PACKAGE_BUGREPORT ">.\n"; namespace opt { /** Sample the suffix array. */ static unsigned sampleSA = 16; /** Which indexes to create. */ enum { NONE, FAI, FM, BOTH }; static int indexes = BOTH; /** Build the BWT directly without the SA. */ static int fa2bwt; /** Build the FM index from the BWT. */ static int bwt2fm; /** The alphabet. */ static string alphabet = "-ACGT"; /** Decompress the index. */ static bool decompress; /** Write output to standard output. */ static bool toStdout; /** Verbose output. */ static int verbose; } static const char shortopts[] = "a:cds:v"; enum { OPT_HELP = 1, OPT_VERSION }; static const struct option longopts[] = { { "both", no_argument, &opt::indexes, opt::BOTH }, { "fai", no_argument, &opt::indexes, opt::FAI }, { "fm", no_argument, &opt::indexes, opt::FM }, { "fa2bwt", no_argument, &opt::fa2bwt, true }, { "bwt2fm", no_argument, &opt::bwt2fm, true }, { "alphabet", optional_argument, NULL, 'a' }, { "decompress", no_argument, NULL, 'd' }, { "sample", required_argument, NULL, 's' }, { "stdout", no_argument, NULL, 'c' }, { "help", no_argument, NULL, OPT_HELP }, { "version", no_argument, NULL, OPT_VERSION }, { NULL, 0, NULL, 0 } }; /** Index the specified FASTA file. */ static void indexFasta(const string& faPath, const string& faiPath) { cerr << "Reading `" << faPath << "'...\n"; FastaIndex fai; fai.index(faPath); if (opt::verbose > 0) cerr << "Read " << fai.size() << " contigs.\n"; cerr << "Writing `" << faiPath << "'...\n"; ofstream out(faiPath.c_str()); assert_good(out, faiPath); out << fai; out.flush(); assert_good(out, faiPath); } /** Build the FM index from the BWT. */ static void buildFMIndexFromBWT(FMIndex& fm, const string& path) { if (opt::verbose > 0) cerr << "Reading `" << path << "'...\n"; std::vector bwt; readFile(path.c_str(), bwt); assert(bwt.size() > 1); if (opt::alphabet.empty()) { fm.setAlphabet(bwt.begin(), bwt.end()); std::cerr << "The alphabet has " << fm.alphabetSize() << " symbols.\n"; } else fm.setAlphabet(opt::alphabet); fm.encode(bwt.begin(), bwt.end()); fm.sampleSA(opt::sampleSA); fm.assignBWT(bwt.begin(), bwt.end()); } /** Build an FM index of the specified file. */ static void buildFMIndex(FMIndex& fm, const string& path) { if (opt::verbose > 0) std::cerr << "Reading `" << path << "'...\n"; std::vector s; readFile(path.c_str(), s); size_t MAX_SIZE = numeric_limits::max(); if (s.size() > MAX_SIZE) { std::cerr << PROGRAM << ": `" << path << "', " << toSI(s.size()) << "B, must be smaller than " << toSI(MAX_SIZE) << "B\n"; exit(EXIT_FAILURE); } // Set the alphabet. transform(s.begin(), s.end(), s.begin(), ::toupper); if (opt::alphabet.empty()) { fm.setAlphabet(s.begin(), s.end()); std::cerr << "The alphabet has " << fm.alphabetSize() << " symbols.\n"; } else fm.setAlphabet(opt::alphabet); if (opt::fa2bwt) { // Build the BWT first. s.push_back(0); fm.buildBWT(s.begin(), s.end() - 1); fm.sampleSA(opt::sampleSA); fm.assignBWT(s.begin(), s.end()); } else { // Construct the suffix array first. fm.assign(s.begin(), s.end()); fm.sampleSA(opt::sampleSA); } } int main(int argc, char **argv) { bool die = false; for (int c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;) { istringstream arg(optarg != NULL ? optarg : ""); switch (c) { case '?': die = true; break; case 'a': opt::alphabet = arg.str(); arg.clear(ios::eofbit); break; case 'c': opt::toStdout = true; break; case 'd': opt::decompress = true; break; case 's': arg >> opt::sampleSA; break; case 'v': opt::verbose++; break; case OPT_HELP: cout << USAGE_MESSAGE; exit(EXIT_SUCCESS); case OPT_VERSION: cout << VERSION_MESSAGE; exit(EXIT_SUCCESS); } if (optarg != NULL && !arg.eof()) { cerr << PROGRAM ": invalid option: `-" << (char)c << optarg << "'\n"; exit(EXIT_FAILURE); } } if (argc - optind < 1) { cerr << PROGRAM ": missing arguments\n"; die = true; } if (argc - optind > 1) { cerr << PROGRAM ": too many arguments\n"; die = true; } if (die) { cerr << "Try `" << PROGRAM << " --help' for more information.\n"; exit(EXIT_FAILURE); } if (opt::decompress) { // Decompress the index. string fmPath(argv[optind]); if (fmPath.size() < 4 || !equal(fmPath.end() - 3, fmPath.end(), ".fm")) fmPath.append(".fm"); string faPath(fmPath, 0, fmPath.size() - 3); ifstream in(fmPath.c_str()); assert_good(in, fmPath); FMIndex fmIndex; in >> fmIndex; assert_good(in, fmPath); in.close(); ofstream fout; if (!opt::toStdout) fout.open(faPath.c_str()); ostream& out = opt::toStdout ? cout : fout; assert_good(out, faPath); fmIndex.decompress( ostream_iterator(out, "")); out.flush(); assert_good(out, faPath); in.open((faPath + ".fai").c_str()); FastaIndex faIndex; if (in) { in >> faIndex; faIndex.writeFASTAHeaders(out); } return 0; } string path = argv[optind]; FMIndex fm; if (opt::bwt2fm) { buildFMIndexFromBWT(fm, path); } else { if (opt::indexes & opt::FAI) indexFasta(path, path + ".fai"); if ((opt::indexes & opt::FM) == 0) return 0; buildFMIndex(fm, path); } if (opt::verbose > 0) { size_t n = fm.size(); ssize_t bytes = getMemoryUsage(); cerr << "Read " << toSI(n) << "B. " "Used " << toSI(bytes) << "B of memory and " << setprecision(3) << (float)bytes / n << " B/bp.\n"; } string fmPath = opt::toStdout ? "-" : path + ".fm"; cerr << "Writing `" << fmPath << "'...\n"; ofstream fout; if (!opt::toStdout) fout.open(fmPath.c_str()); ostream& out = opt::toStdout ? cout : fout; assert_good(out, fmPath); out << fm; out.flush(); assert_good(out, fmPath); return 0; } abyss-1.3.6/Map/map.cc000644 002433 001057 00000031326 12176307445 016176 0ustar00traymondassembly000000 000000 #include "BitUtil.h" #include "DataLayer/Options.h" #include "FMIndex.h" #include "FastaIndex.h" #include "FastaInterleave.h" #include "FastaReader.h" #include "IOUtil.h" #include "MemoryUtil.h" #include "SAM.h" #include "StringUtil.h" #include "Uncompress.h" #include #include #include // for toupper #include #include #include #include #include #include #include #include #if _OPENMP # include #endif using namespace std; #define PROGRAM "abyss-map" static const char VERSION_MESSAGE[] = PROGRAM " (" PACKAGE_NAME ") " VERSION "\n" "Written by Shaun Jackman.\n" "\n" "Copyright 2013 Canada's Michael Smith Genome Science Centre\n"; static const char USAGE_MESSAGE[] = "Usage: " PROGRAM " [OPTION]... QUERY... TARGET\n" "Map the sequences of the files QUERY to those of the file TARGET.\n" "The index files TARGET.fai and TARGET.fm will be used if present.\n" "\n" " Options:\n" "\n" " -l, --min-align=N find matches at least N bp [1]\n" " -j, --threads=N use N parallel threads [1]\n" " -s, --sample=N sample the suffix array [1]\n" " -d, --dup identify and print duplicate sequence\n" " IDs between QUERY and TARGET\n" " --order print alignments in the same order as\n" " read from QUERY\n" " --no-order print alignments ASAP [default]\n" " --chastity discard unchaste reads\n" " --no-chastity do not discard unchaste reads [default]\n" " -v, --verbose display verbose output\n" " --help display this help and exit\n" " --version output version information and exit\n" "\n" "Report bugs to <" PACKAGE_BUGREPORT ">.\n"; namespace opt { /** Find matches at least k bp. */ static unsigned k; /** Sample the suffix array. */ static unsigned sampleSA; /** The number of parallel threads. */ static unsigned threads = 1; /** Identify duplicate and subsumed sequences. */ static bool dup = false; static int order; /** Verbose output. */ static int verbose; } static const char shortopts[] = "j:k:l:s:dv"; enum { OPT_HELP = 1, OPT_VERSION }; static const struct option longopts[] = { { "sample", required_argument, NULL, 's' }, { "min-align", required_argument, NULL, 'l' }, { "dup", no_argument, NULL, 'd' }, { "threads", required_argument, NULL, 'j' }, { "order", no_argument, &opt::order, 1 }, { "no-order", no_argument, &opt::order, 0 }, { "verbose", no_argument, NULL, 'v' }, { "chastity", no_argument, &opt::chastityFilter, 1 }, { "no-chastity", no_argument, &opt::chastityFilter, 0 }, { "help", no_argument, NULL, OPT_HELP }, { "version", no_argument, NULL, OPT_VERSION }, { NULL, 0, NULL, 0 } }; /** Counts. */ static struct { unsigned unique; unsigned multimapped; unsigned unmapped; } g_count; typedef FMIndex::Match Match; /** Return a SAM record of the specified match. */ static SAMRecord toSAM(const FastaIndex& faIndex, const FMIndex& fmIndex, const Match& m, bool rc, unsigned qlength) { SAMRecord a; if (m.size() == 0) { // No hit. a.rname = "*"; a.pos = -1; a.flag = SAMAlignment::FUNMAP; a.mapq = 0; a.cigar = "*"; } else { FastaIndex::SeqPos seqPos = faIndex[fmIndex[m.l]]; a.rname = seqPos.get<0>().id; a.pos = seqPos.get<1>(); a.flag = rc ? SAMAlignment::FREVERSE : 0; // Set the mapq to the alignment score. assert(m.qstart < m.qend); unsigned matches = m.qend - m.qstart; a.mapq = m.size() > 1 ? 0 : min(matches, 255U); ostringstream ss; if (m.qstart > 0) ss << m.qstart << 'S'; ss << matches << 'M'; if (m.qend < qlength) ss << qlength - m.qend << 'S'; a.cigar = ss.str(); } a.mrnm = "*"; a.mpos = -1; a.isize = 0; return a; } /** Return the position of the current contig. */ static size_t getMyPos(const Match& m, const FastaIndex& faIndex, const FMIndex& fmIndex, const string& id) { for (size_t i = m.l; i < m.u; i++) { if (faIndex[fmIndex[i]].get<0>().id == id) return fmIndex[i]; } return fmIndex[m.l]; } /** Return the earlies position of all contigs in m. */ static size_t getMinPos(const Match& m, size_t maxLen, const FastaIndex& faIndex, const FMIndex& fmIndex) { size_t minPos = numeric_limits::max(); for (size_t i = m.l; i < m.u; i++) { size_t pos = fmIndex[i]; if (faIndex[pos].get<0>().size == maxLen && pos < minPos) minPos = fmIndex[i]; } return minPos; } /** Return the largest length of all contig in m. */ static size_t getMaxLen(const Match& m, const FastaIndex& faIndex, const FMIndex& fmIndex) { size_t maxLen = 0; for (size_t i = m.l; i < m.u; i++) { size_t len = faIndex[fmIndex[i]].get<0>().size; if (len > maxLen) maxLen = len; } return maxLen; } /** Print the current contig id if it is not the lartest and earliest * contig in m. */ static void printDuplicates(const Match& m, const Match& rcm, const FastaIndex& faIndex, const FMIndex& fmIndex, const FastqRecord& rec) { size_t myLen = m.qspan(); size_t maxLen = max(getMaxLen(m, faIndex, fmIndex), getMaxLen(rcm, faIndex, fmIndex)); if (myLen < maxLen) { #pragma omp atomic g_count.multimapped++; #pragma omp critical(cout) { cout << rec.id << '\n'; assert_good(cout, "stdout"); } return; } size_t myPos = getMyPos(m, faIndex, fmIndex, rec.id); size_t minPos = min(getMinPos(m, maxLen, faIndex, fmIndex), getMinPos(rcm, maxLen, faIndex, fmIndex)); if (myPos > minPos) { #pragma omp atomic g_count.multimapped++; #pragma omp critical(cout) { cout << rec.id << '\n'; assert_good(cout, "stdout"); } } #pragma omp atomic g_count.unique++; return; } static queue g_pq; /** Return the mapping of the specified sequence. */ static void find(const FastaIndex& faIndex, const FMIndex& fmIndex, const FastqRecord& rec) { if (rec.seq.empty()) { cerr << PROGRAM ": error: " "the sequence `" << rec.id << "' is empty\n"; exit(EXIT_FAILURE); } Match m = fmIndex.find(rec.seq, opt::dup ? rec.seq.length() : opt::k); string rcqseq = reverseComplement(rec.seq); Match rcm = fmIndex.find(rcqseq, opt::dup ? rcqseq.length() : m.qspan()); if (opt::dup) { printDuplicates(m, rcm, faIndex, fmIndex, rec); return; } bool rc = rcm.qspan() > m.qspan(); SAMRecord sam = toSAM(faIndex, fmIndex, rc ? rcm : m, rc, rec.seq.size()); if (rec.id[0] == '@') { cerr << PROGRAM ": error: " "the query ID `" << rec.id << "' is invalid since it " "begins with `@'\n"; exit(EXIT_FAILURE); } sam.qname = rec.id; #if SAM_SEQ_QUAL sam.seq = rc ? rcqseq : rec.seq; sam.qual = rec.qual.empty() ? "*" : rec.qual; if (rc) reverse(sam.qual.begin(), sam.qual.end()); #endif if (m.qstart == rec.seq.size() - rcm.qend && m.qspan() == rcm.qspan()) { // This matching sequence maps to both strands. sam.mapq = 0; } bool print = opt::order == 0; do { #pragma omp critical(cout) { #pragma omp critical(g_pq) if (!print) { print = g_pq.front() == rec.id; if (print) g_pq.pop(); } if (print) { cout << sam << '\n'; assert_good(cout, "stdout"); } } } while (!print); // spinlock :( if (sam.isUnmapped()) #pragma omp atomic g_count.unmapped++; else if (sam.mapq == 0) #pragma omp atomic g_count.multimapped++; else #pragma omp atomic g_count.unique++; } /** Map the sequences of the specified file. */ static void find(const FastaIndex& faIndex, const FMIndex& fmIndex, FastaInterleave& in) { #pragma omp parallel for (FastqRecord rec;;) { bool good; #pragma omp critical(in) { good = in >> rec; if (opt::order) { #pragma omp critical(g_pq) g_pq.push(rec.id); } } if (good) find(faIndex, fmIndex, rec); else break; } assert(in.eof()); } /** Build an FM index of the specified file. */ static void buildFMIndex(FMIndex& fm, const char* path) { if (opt::verbose > 0) std::cerr << "Reading `" << path << "'...\n"; std::vector s; readFile(path, s); size_t MAX_SIZE = numeric_limits::max(); if (s.size() > MAX_SIZE) { std::cerr << PROGRAM << ": `" << path << "', " << toSI(s.size()) << "B, must be smaller than " << toSI(MAX_SIZE) << "B\n"; exit(EXIT_FAILURE); } transform(s.begin(), s.end(), s.begin(), ::toupper); fm.setAlphabet("-ACGT"); fm.assign(s.begin(), s.end()); } /** Return the size of the specified file. */ static streampos fileSize(const string& path) { std::ifstream in(path.c_str()); assert_good(in, path); in.seekg(0, std::ios::end); assert_good(in, path); return in.tellg(); } /** Check that the indexes are up to date. */ static void checkIndexes(const string& path, const FMIndex& fmIndex, const FastaIndex& faIndex) { size_t fastaFileSize = fileSize(path); if (fmIndex.size() != fastaFileSize) { cerr << PROGRAM ": `" << path << "': " "The size of the FM-index, " << fmIndex.size() << " B, does not match the size of the FASTA file, " << fastaFileSize << " B. The index is likely stale.\n"; exit(EXIT_FAILURE); } if (faIndex.fileSize() != fastaFileSize) { cerr << PROGRAM ": `" << path << "': " "The size of the FASTA index, " << faIndex.fileSize() << " B, does not match the size of the FASTA file, " << fastaFileSize << " B. The index is likely stale.\n"; exit(EXIT_FAILURE); } } int main(int argc, char** argv) { string commandLine; { ostringstream ss; char** last = argv + argc - 1; copy(argv, last, ostream_iterator(ss, " ")); ss << *last; commandLine = ss.str(); } opt::chastityFilter = false; opt::trimMasked = false; bool die = false; for (int c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;) { istringstream arg(optarg != NULL ? optarg : ""); switch (c) { case '?': die = true; break; case 'j': arg >> opt::threads; break; case 'k': case 'l': arg >> opt::k; break; case 's': arg >> opt::sampleSA; break; case 'd': opt::dup = true; break; case 'v': opt::verbose++; break; case OPT_HELP: cout << USAGE_MESSAGE; exit(EXIT_SUCCESS); case OPT_VERSION: cout << VERSION_MESSAGE; exit(EXIT_SUCCESS); } if (optarg != NULL && !arg.eof()) { cerr << PROGRAM ": invalid option: `-" << (char)c << optarg << "'\n"; exit(EXIT_FAILURE); } } if (argc - optind < 2) { cerr << PROGRAM ": missing arguments\n"; die = true; } if (die) { cerr << "Try `" << PROGRAM << " --help' for more information.\n"; exit(EXIT_FAILURE); } #if _OPENMP if (opt::threads > 0) omp_set_num_threads(opt::threads); #endif const char* targetFile(argv[--argc]); ostringstream ss; ss << targetFile << ".fm"; string fmPath(ss.str()); ss.str(""); ss << targetFile << ".fai"; string faiPath(ss.str()); ifstream in; // Read the FASTA index. FastaIndex faIndex; in.open(faiPath.c_str()); if (in) { if (opt::verbose > 0) cerr << "Reading `" << faiPath << "'...\n"; in >> faIndex; assert(in.eof()); in.close(); } else { if (opt::verbose > 0) cerr << "Reading `" << targetFile << "'...\n"; faIndex.index(targetFile); } if (opt::verbose > 0) { ssize_t bytes = getMemoryUsage(); if (bytes > 0) cerr << "Using " << toSI(bytes) << "B of memory and " << setprecision(3) << (float)bytes / faIndex.size() << " B/sequence.\n"; } // Read the FM index. FMIndex fmIndex; in.open(fmPath.c_str()); if (in) { if (opt::verbose > 0) cerr << "Reading `" << fmPath << "'...\n"; assert_good(in, fmPath); in >> fmIndex; assert_good(in, fmPath); in.close(); } else buildFMIndex(fmIndex, targetFile); if (opt::sampleSA > 1) fmIndex.sampleSA(opt::sampleSA); if (opt::verbose > 0) { size_t bp = fmIndex.size(); cerr << "Read " << toSI(bp) << "B in " << faIndex.size() << " contigs.\n"; ssize_t bytes = getMemoryUsage(); if (bytes > 0) cerr << "Using " << toSI(bytes) << "B of memory and " << setprecision(3) << (float)bytes / bp << " B/bp.\n"; } // Check that the indexes are up to date. checkIndexes(targetFile, fmIndex, faIndex); if (!opt::dup) { // Write the SAM header. cout << "@HD\tVN:1.4\n" "@PG\tID:" PROGRAM "\tPN:" PROGRAM "\tVN:" VERSION "\t" "CL:" << commandLine << '\n'; faIndex.writeSAMHeader(cout); cout.flush(); assert_good(cout, "stdout"); } else if (opt::verbose > 0) cerr << "Identifying duplicates.\n"; FastaInterleave fa(argv + optind, argv + argc, FastaReader::FOLD_CASE); find(faIndex, fmIndex, fa); if (opt::verbose > 0) { size_t unique = g_count.unique; size_t mapped = unique + g_count.multimapped; size_t total = mapped + g_count.unmapped; cerr << "Mapped " << mapped << " of " << total << " reads (" << (float)100 * mapped / total << "%)\n" << "Mapped " << unique << " of " << total << " reads uniquely (" << (float)100 * unique / total << "%)\n"; } cout.flush(); assert_good(cout, "stdout"); return 0; } abyss-1.3.6/Map/overlap.cc000644 002433 001057 00000031555 12176305753 017075 0ustar00traymondassembly000000 000000 #if __APPLE_CC__ /* Work around a bug in i686-apple-darwin11-llvm-gcc 4.2.1 * Undefined symbols for architecture x86_64: * "___builtin_expect", referenced from: */ #define NDEBUG 1 #endif #include "BitUtil.h" #include "ContigProperties.h" #include "DataLayer/Options.h" #include "FMIndex.h" #include "FastaIndex.h" #include "FastaReader.h" #include "IOUtil.h" #include "MemoryUtil.h" #include "SAM.h" #include "StringUtil.h" #include "Uncompress.h" #include "Graph/ContigGraph.h" #include "Graph/DirectedGraph.h" #include "Graph/GraphAlgorithms.h" #include "Graph/GraphIO.h" #include "Graph/GraphUtil.h" #include #include #include // for toupper #include #include #include #include #include #include #include #if _OPENMP # include #endif using namespace std; #define PROGRAM "abyss-overlap" static const char VERSION_MESSAGE[] = PROGRAM " (" PACKAGE_NAME ") " VERSION "\n" "Written by Shaun Jackman.\n" "\n" "Copyright 2013 Canada's Michael Smith Genome Science Centre\n"; static const char USAGE_MESSAGE[] = "Usage: " PROGRAM " [OPTION]... FILE\n" "Find overlaps of [m,k) bases. Sequences are read from FILE.\n" "Output is written to standard output. The index files FILE.fai\n" "and FILE.fm will be used if present.\n" "\n" " Options:\n" "\n" " -m, --min=N find matches at least N bp [50]\n" " -k, --max=N find matches less than N bp [inf]\n" " -j, --threads=N use N parallel threads [1]\n" " -s, --sample=N sample the suffix array [1]\n" " --tred remove transitive edges [default]\n" " --no-tred do not remove transitive edges\n" " --adj output the results in adj format\n" " --dot output the results in dot format [default]\n" " --sam output the results in SAM format\n" " -v, --verbose display verbose output\n" " --help display this help and exit\n" " --version output version information and exit\n" "\n" "Report bugs to <" PACKAGE_BUGREPORT ">.\n"; namespace opt { /** Find matches at least k bp. */ static unsigned minOverlap = 50; /** Find matches less than k bp. */ static unsigned maxOverlap = UINT_MAX; /** Sample the suffix array. */ static unsigned sampleSA; /** Remove transitive edges. */ static int tred = true; /** The number of parallel threads. */ static unsigned threads = 1; /** Verbose output. */ static int verbose; unsigned k; // used by GraphIO int format = DOT; // used by GraphIO } static const char shortopts[] = "j:k:m:s:v"; enum { OPT_HELP = 1, OPT_VERSION }; static const struct option longopts[] = { { "adj", no_argument, &opt::format, ADJ }, { "dot", no_argument, &opt::format, DOT }, { "sam", no_argument, &opt::format, SAM }, { "help", no_argument, NULL, OPT_HELP }, { "max", required_argument, NULL, 'k' }, { "min", required_argument, NULL, 'm' }, { "sample", required_argument, NULL, 's' }, { "threads", required_argument, NULL, 'j' }, { "tred", no_argument, &opt::tred, true }, { "no-tred", no_argument, &opt::tred, false }, { "verbose", no_argument, NULL, 'v' }, { "version", no_argument, NULL, OPT_VERSION }, { NULL, 0, NULL, 0 } }; /** The overlap graph. */ typedef DirectedGraph DG; typedef ContigGraph Graph; typedef FMIndex::Match Match; /** Add suffix overlaps to the graph. */ static void addSuffixOverlaps(Graph &g, const FastaIndex& faIndex, const FMIndex& fmIndex, const ContigNode& u, const Match& fmi) { typedef edge_property::type EP; typedef graph_traits::edge_descriptor E; typedef graph_traits::vertex_descriptor V; Distance ep(-fmi.qspan()); assert(ep.distance < 0); for (unsigned i = fmi.l; i < fmi.u; ++i) { size_t toffset = fmIndex[i] + 1; FastaIndex::SeqPos seqPos = faIndex[toffset]; const FAIRecord& tseq = seqPos.get<0>(); size_t tstart = seqPos.get<1>(); size_t tend = tstart + fmi.qspan(); assert(tend < tseq.size); (void)tend; if (tstart > 0) { // This match is due to an ambiguity code in the target sequence. continue; } V v = find_vertex(tseq.id, false, g); #pragma omp critical(g) { pair e = edge(u, v, g); if (e.second) { const EP& ep0 = g[e.first]; if (opt::verbose > 1) cerr << "duplicate edge: " << get(edge_name, g, e.first) << ' ' << ep0 << ' ' << ep << '\n'; assert(ep0.distance < ep.distance); } else if(u.sense()) { // Add u- -> v+ add_edge(u, v, ep, static_cast(g)); } else { // Add u+ -> v+ and v- -> u- add_edge(u, v, ep, g); } } } } /** Add prefix overlaps to the graph. */ static void addPrefixOverlaps(Graph &g, const FastaIndex& faIndex, const FMIndex& fmIndex, const ContigNode& v, const Match& fmi) { typedef edge_property::type EP; typedef graph_traits::edge_descriptor E; typedef graph_traits::vertex_descriptor V; assert(v.sense()); assert(fmi.qstart == 0); Distance ep(-fmi.qspan()); assert(ep.distance < 0); for (unsigned i = fmi.l; i < fmi.u; ++i) { size_t toffset = fmIndex[i]; FastaIndex::SeqPos seqPos = faIndex[toffset]; const FAIRecord& tseq = seqPos.get<0>(); size_t tstart = seqPos.get<1>(); size_t tend = tstart + fmi.qspan(); assert(tstart > 0); if (tend < tseq.size) { // This match is due to an ambiguity code in the target sequence. continue; } V u = find_vertex(tseq.id, false, g); #pragma omp critical(g) { pair e = edge(u, v, g); if (e.second) { const EP& ep0 = g[e.first]; if (opt::verbose > 1) cerr << "duplicate edge: " << get(edge_name, g, e.first) << ' ' << ep0 << ' ' << ep << '\n'; assert(ep0.distance < ep.distance); } else { // Add u+ -> v- add_edge(u, v, ep, static_cast(g)); } } } } /** Find suffix overlaps. */ static void findOverlapsSuffix(Graph &g, const FastaIndex& faIndex, const FMIndex& fmIndex, const ContigNode& u, const string& seq) { size_t pos = seq.size() > opt::maxOverlap ? seq.size() - opt::maxOverlap + 1 : 1; string suffix(seq, pos); typedef vector Matches; vector matches; fmIndex.findOverlapSuffix(suffix, back_inserter(matches), opt::minOverlap); for (Matches::reverse_iterator it = matches.rbegin(); it != matches.rend(); ++it) addSuffixOverlaps(g, faIndex, fmIndex, u, *it); } /** Find prefix overlaps. */ static void findOverlapsPrefix(Graph &g, const FastaIndex& faIndex, const FMIndex& fmIndex, const ContigNode& v, const string& seq) { assert(v.sense()); string prefix(seq, 0, min((size_t)opt::maxOverlap, seq.size()) - 1); typedef vector Matches; vector matches; fmIndex.findOverlapPrefix(prefix, back_inserter(matches), opt::minOverlap); for (Matches::reverse_iterator it = matches.rbegin(); it != matches.rend(); ++it) addPrefixOverlaps(g, faIndex, fmIndex, v, *it); } static void findOverlaps(Graph& g, const FastaIndex& faIndex, const FMIndex& fmIndex, const FastqRecord& rec) { typedef graph_traits::vertex_descriptor V; V u = find_vertex(rec.id, false, g); V uc = get(vertex_complement, g, u); // Add edges u+ -> v+ and v- -> u- findOverlapsSuffix(g, faIndex, fmIndex, u, rec.seq); string rcseq = reverseComplement(rec.seq); // Add edges u- -> v+ findOverlapsSuffix(g, faIndex, fmIndex, uc, rcseq); // Add edges v+ -> u- findOverlapsPrefix(g, faIndex, fmIndex, uc, rcseq); } /** Map the sequences of the specified file. */ static void findOverlaps(Graph& g, const FastaIndex& faIndex, const FMIndex& fmIndex, FastaReader& in) { #pragma omp parallel for (FastqRecord rec;;) { bool good; #pragma omp critical(in) good = in >> rec; if (good) findOverlaps(g, faIndex, fmIndex, rec); else break; } assert(in.eof()); } /** Build an FM index of the specified file. */ static void buildFMIndex(FMIndex& fm, const char* path) { if (opt::verbose > 0) std::cerr << "Reading `" << path << "'...\n"; std::vector s; readFile(path, s); size_t MAX_SIZE = numeric_limits::max(); if (s.size() > MAX_SIZE) { std::cerr << PROGRAM << ": `" << path << "', " << toSI(s.size()) << "B, must be smaller than " << toSI(MAX_SIZE) << "B\n"; exit(EXIT_FAILURE); } transform(s.begin(), s.end(), s.begin(), ::toupper); fm.setAlphabet("-ACGT"); fm.assign(s.begin(), s.end()); } /** Read contigs and add vertices to the graph. */ static void addVertices(const string& path, Graph& g) { typedef vertex_property::type VP; if (opt::verbose > 0) cerr << "Reading `" << path << "'...\n"; ifstream in(path.c_str()); assert_good(in, path); in >> g; g_contigNames.lock(); assert(in.eof()); } /** Return the size of the specified file. */ static streampos fileSize(const string& path) { std::ifstream in(path.c_str()); assert_good(in, path); in.seekg(0, std::ios::end); assert_good(in, path); return in.tellg(); } /** Check that the indexes are up to date. */ static void checkIndexes(const string& path, const FMIndex& fmIndex, const FastaIndex& faIndex) { size_t fastaFileSize = fileSize(path); if (fmIndex.size() != fastaFileSize) { cerr << PROGRAM ": `" << path << "': " "The size of the FM-index, " << fmIndex.size() << " B, does not match the size of the FASTA file, " << fastaFileSize << " B. The index is likely stale.\n"; exit(EXIT_FAILURE); } if (faIndex.fileSize() != fastaFileSize) { cerr << PROGRAM ": `" << path << "': " "The size of the FASTA index, " << faIndex.fileSize() << " B, does not match the size of the FASTA file, " << fastaFileSize << " B. The index is likely stale.\n"; exit(EXIT_FAILURE); } } int main(int argc, char** argv) { string commandLine; { ostringstream ss; char** last = argv + argc - 1; copy(argv, last, ostream_iterator(ss, " ")); ss << *last; commandLine = ss.str(); } bool die = false; for (int c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;) { istringstream arg(optarg != NULL ? optarg : ""); switch (c) { case '?': die = true; break; case 'j': arg >> opt::threads; break; case 'm': arg >> opt::minOverlap; break; case 'k': arg >> opt::maxOverlap; break; case 's': arg >> opt::sampleSA; break; case 'v': opt::verbose++; break; case OPT_HELP: cout << USAGE_MESSAGE; exit(EXIT_SUCCESS); case OPT_VERSION: cout << VERSION_MESSAGE; exit(EXIT_SUCCESS); } if (optarg != NULL && !arg.eof()) { cerr << PROGRAM ": invalid option: `-" << (char)c << optarg << "'\n"; exit(EXIT_FAILURE); } } if (argc - optind < 1) { cerr << PROGRAM ": missing arguments\n"; die = true; } else if (argc - optind > 1) { cerr << PROGRAM ": too many arguments\n"; die = true; } if (die) { cerr << "Try `" << PROGRAM << " --help' for more information.\n"; exit(EXIT_FAILURE); } #if _OPENMP if (opt::threads > 0) omp_set_num_threads(opt::threads); #endif if (opt::minOverlap == 0) opt::minOverlap = opt::maxOverlap - 1; opt::minOverlap = min(opt::minOverlap, opt::maxOverlap - 1); if (opt::maxOverlap != UINT_MAX) opt::k = opt::maxOverlap; const char* fastaFile(argv[--argc]); ostringstream ss; ss << fastaFile << ".fm"; string fmPath(ss.str()); ss.str(""); ss << fastaFile << ".fai"; string faiPath(ss.str()); ifstream in; // Read the FASTA index. FastaIndex faIndex; in.open(faiPath.c_str()); if (in) { if (opt::verbose > 0) cerr << "Reading `" << faiPath << "'...\n"; in >> faIndex; assert(in.eof()); in.close(); } else { if (opt::verbose > 0) cerr << "Reading `" << fastaFile << "'...\n"; faIndex.index(fastaFile); } // Read the FM index. 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using boost::tie; #define PROGRAM "abyss-layout" static const char VERSION_MESSAGE[] = PROGRAM " (" PACKAGE_NAME ") " VERSION "\n" "Written by Shaun Jackman.\n" "\n" "Copyright 2012 Shaun Jackman\n"; static const char USAGE_MESSAGE[] = "Usage: " PROGRAM " [OPTION]... OVERLAP\n" "Layout contigs using the sequence overlap graph.\n" "Output sequence paths.\n" "\n" " Arguments:\n" "\n" " OVERLAP the sequence overlap graph\n" "\n" " Options:\n" "\n" " -s, --min-length=N minimum sequence length [0]\n" " -m, --min-overlap=N minimum overlap [0]\n" " -k, --kmer=N length of a k-mer\n" " -o, --out=FILE write the paths to FILE\n" " -g, --graph=FILE write the graph to FILE\n" " --tred remove transitive edges\n" " --no-tred do not remove transitive edges [default]\n" " -v, --verbose display verbose output\n" " --help display this help and exit\n" " --version output version information and exit\n" "\n" "Report bugs to <" PACKAGE_BUGREPORT ">.\n"; namespace opt { unsigned k; // used by ContigProperties /** Minimum sequence length. */ static unsigned minLength; /** Minimum overlap. */ static unsigned minOverlap; /** Write the paths to this file. */ static string out; /** Write the graph to this file. */ static string graphPath; /** Remove transitive edges. */ static int tred; /** Verbose output. */ int verbose; // used by PopBubbles /** Output format */ int format = DOT; } static const char shortopts[] = "g:k:m:o:s:v"; enum { OPT_HELP = 1, OPT_VERSION }; static const struct option longopts[] = { { "graph", required_argument, NULL, 'g' }, { "kmer", required_argument, NULL, 'k' }, { "min-overlap", required_argument, NULL, 'm' }, { "out", required_argument, NULL, 'o' }, { "min-length", required_argument, NULL, 's' }, { "tred", no_argument, &opt::tred, true }, { "no-tred", no_argument, &opt::tred, false }, { "verbose", no_argument, NULL, 'v' }, { "help", no_argument, NULL, OPT_HELP }, { "version", no_argument, NULL, OPT_VERSION }, { NULL, 0, NULL, 0 } }; /** An overlap graph. */ typedef DirectedGraph DG; typedef ContigGraph Graph; /** Remove short vertices. */ static void filterVertices(Graph& g, unsigned minLength) { typedef graph_traits GTraits; typedef GTraits::vertex_descriptor V; typedef GTraits::vertex_iterator Vit; if (minLength == 0) return; // Remove short sequences. unsigned numRemoved = 0; std::pair urange = vertices(g); for (Vit uit = urange.first; uit != urange.second; ++uit) { V u = *uit; if (g[u].length < minLength) clear_vertex(u, g); if (out_degree(u, g) == 0 && in_degree(u, g) == 0) { remove_vertex(u, g); numRemoved++; } } if (opt::verbose > 0) { cerr << "Ignored " << numRemoved << " sequences shorter than " << minLength << " bp.\n"; printGraphStats(cerr, g); } } /** Return true if the edge is a small overlap. */ struct IsSmallOverlap { IsSmallOverlap(Graph& g) : m_g(g) { } bool operator()(graph_traits::edge_descriptor e) const { int maxDistance = -opt::minOverlap; return m_g[e].distance > maxDistance; } const Graph& m_g; }; /** Remove small overlaps. */ static void filterEdges(Graph& g, unsigned minOverlap) { if (minOverlap == 0) return; unsigned numBefore = num_edges(g); remove_edge_if(IsSmallOverlap(g), static_cast(g)); unsigned numRemoved = numBefore - num_edges(g); if (opt::verbose > 0) { cerr << "Removed " << numRemoved << " small overlaps.\n"; printGraphStats(cerr, g); } } /** Read a graph from the specified file. */ static void readGraph(const string& path, Graph& g) { if (opt::verbose > 0) cerr << "Reading `" << path << "'...\n"; ifstream fin(path.c_str()); istream& in = path == "-" ? cin : fin; assert_good(in, path); in >> g; assert(in.eof()); if (opt::verbose > 0) printGraphStats(cerr, g); g_contigNames.lock(); } /** Return the length histogram. */ static Histogram buildLengthHistogram(const Graph& g) { typedef graph_traits::vertex_descriptor V; typedef graph_traits::vertex_iterator Vit; Histogram h; Vit uit, ulast; for (tie(uit, ulast) = vertices(g); uit != ulast; ++++uit) { V u = *uit; if (!get(vertex_removed, g, u)) h.insert(g[u].length); } return h; } /** Run abyss-layout. */ int main(int argc, char** argv) { bool die = false; for (int c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;) { istringstream arg(optarg != NULL ? optarg : ""); switch (c) { case '?': die = true; break; case 'k': arg >> opt::k; break; case 'g': arg >> opt::graphPath; break; case 'm': arg >> opt::minOverlap; break; case 'o': arg >> opt::out; break; case 's': arg >> opt::minLength; break; case 'v': opt::verbose++; break; case OPT_HELP: cout << USAGE_MESSAGE; exit(EXIT_SUCCESS); case OPT_VERSION: cout << VERSION_MESSAGE; exit(EXIT_SUCCESS); } if (optarg != NULL && !arg.eof()) { cerr << PROGRAM ": invalid option: `-" << (char)c << optarg << "'\n"; exit(EXIT_FAILURE); } } if (argc - optind < 1) { cerr << PROGRAM ": missing arguments\n"; die = true; } if (die) { cerr << "Try `" << PROGRAM << " --help' for more information.\n"; exit(EXIT_FAILURE); } Graph g; if (optind < argc) { for (; optind < argc; optind++) readGraph(argv[optind], g); } else readGraph("-", g); // Remove short sequences. filterVertices(g, opt::minLength); // Remove small overlaps. filterEdges(g, opt::minOverlap); // Remove transitive edges. if (opt::tred) { unsigned numTransitive = remove_transitive_edges(g); if (opt::verbose > 0) { cerr << "Removed " << numTransitive << " transitive edges.\n"; printGraphStats(cerr, g); } } /** A container of contig paths. */ typedef vector ContigPaths; // Assemble the paths. ContigPaths paths; assembleDFS(g, back_inserter(paths)); sort(paths.begin(), paths.end()); if (opt::verbose > 0) { unsigned n = 0; for (ContigPaths::const_iterator it = paths.begin(); it != paths.end(); ++it) n += it->size(); cerr << "Assembled " << n << " sequences in " << paths.size() << " contigs.\n"; printGraphStats(cerr, g); } // Output the paths. ofstream fout(opt::out.c_str()); ostream& out = opt::out.empty() || opt::out == "-" ? cout : fout; assert_good(out, opt::out); g_contigNames.unlock(); for (vector::const_iterator it = paths.begin(); it != paths.end(); ++it) out << createContigName() << '\t' << *it << '\n'; assert_good(out, opt::out); // Create the new vertices. for (vector::const_iterator it = paths.begin(); it != paths.end(); ++it) { const ContigPath& path = *it; merge(g, path.begin(), path.end()); remove_vertex_if(g, path.begin(), path.end(), not1(std::mem_fun_ref(&ContigNode::ambiguous))); } if (opt::verbose > 0) printGraphStats(cerr, g); // Output the graph. if (!opt::graphPath.empty()) { ofstream out(opt::graphPath.c_str()); 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#define PROGRAM "KAligner" static const char VERSION_MESSAGE[] = PROGRAM " (" PACKAGE_NAME ") " VERSION "\n" "Written by Jared Simpson and Shaun Jackman.\n" "\n" "Copyright 2013 Canada's Michael Smith Genome Science Centre\n"; static const char USAGE_MESSAGE[] = "Usage: " PROGRAM " [OPTION]... QUERY... TARGET\n" "Align the sequences of the files QUERY to those of TARGET.\n" "All perfect matches of at least k bases will be found.\n" "\n" " Options:\n" "\n" " -k, -l, --kmer=N k-mer size and minimum alignment length\n" " -s, --section=S/N split the target into N sections and align\n" " reads to section S [1/1]\n" " -i, --ignore-multimap ignore duplicate k-mer in the target\n" " [default]\n" " -m, --multimap allow duplicate k-mer in the target\n" " --no-multimap disallow duplicate k-mer in the target\n" " -j, --threads=N use N threads [2] up to one per query file\n" " or if N is 0 use one thread per query file\n" " -v, --verbose display verbose output\n" " --no-sam output the results in KAligner format\n" " --sam output the results in SAM format\n" " --seq print the sequence with the alignments\n" " --help display this help and exit\n" " --version output version information and exit\n" "\n" "Report bugs to <" PACKAGE_BUGREPORT ">.\n"; /** Enumeration of output formats */ enum format { KALIGNER, SAM }; namespace opt { static unsigned k; static int threads = 2; static int printSeq; static unsigned section = 1; static unsigned nsections = 1; /** Output formats */ static int format; } static const char shortopts[] = "ij:k:l:mo:s:v"; enum { OPT_HELP = 1, OPT_VERSION, OPT_SYNC }; static const struct option longopts[] = { { "kmer", required_argument, NULL, 'k' }, { "section", required_argument, NULL, 's' }, { "no-multi", no_argument, &opt::multimap, opt::ERROR }, { "multimap", no_argument, &opt::multimap, opt::MULTIMAP }, { "ignore-multimap", no_argument, &opt::multimap, opt::IGNORE }, { "threads", required_argument, NULL, 'j' }, { "verbose", no_argument, NULL, 'v' }, { "no-sam", no_argument, &opt::format, KALIGNER }, { "sam", no_argument, &opt::format, SAM }, { "no-seq", no_argument, &opt::printSeq, 0 }, { "seq", no_argument, &opt::printSeq, 1 }, { "help", no_argument, NULL, OPT_HELP }, { "version", no_argument, NULL, OPT_VERSION }, { NULL, 0, NULL, 0 } }; /** Return the number of k-mer in the specified file. */ static size_t countKmer(const string& path) { struct stat st; if (stat(path.c_str(), &st) == -1) { perror(path.c_str()); exit(EXIT_FAILURE); } if (!S_ISREG(st.st_mode)) { cerr << "Not calculating k-mer in `" << path << "', because it is not a regular file.\n"; return 500000000; } if (opt::verbose > 0) cerr << "Reading target `" << path << "'..." << endl; ifstream in(path.c_str()); assert(in.is_open()); size_t scaffolds = 0, contigs = 0, bases = 0; enum { ID, SEQUENCE, GAP } state = SEQUENCE; for (char c; in.get(c);) { c = toupper(c); switch (state) { case ID: if (c == '\n') state = SEQUENCE; break; case SEQUENCE: case GAP: switch (c) { case '>': scaffolds++; contigs++; state = ID; break; case 'N': case 'B': case 'D': case 'H': case 'K': case 'M': case 'R': case 'S': case 'V': case 'W': case 'Y': if (state != GAP) contigs++; state = GAP; break; case 'A': case 'C': case 'G': case 'T': case '0': case '1': case '2': case '3': bases++; state = SEQUENCE; break; case '\n': break; default: cerr << "error: unexpected character: " "`" << c << "'\n"; exit(EXIT_FAILURE); } break; } } size_t overlaps = contigs * (opt::k-1); size_t kmer = bases - overlaps; if (opt::verbose > 0) { cerr << "Read " << bases << " bases, " << contigs << " contigs, " << scaffolds << " scaffolds" " from `" << path << "'. " "Expecting " << kmer << " k-mer.\n"; cerr << "Index will use at least " << toSI(kmer * sizeof(pair)) << "B.\n"; } assert(bases > overlaps); return kmer; } template static void readContigsIntoDB(string refFastaFile, Aligner& aligner); static void *alignReadsToDB(void *arg); static void *readFile(void *arg); /** Unique aligner using map */ static Aligner *g_aligner_u; /** Multimap aligner using multimap */ static Aligner *g_aligner_m; /** Number of reads. */ static unsigned g_readCount; /** Number of reads that aligned. */ static unsigned g_alignedCount; /** Guard cerr. */ static pthread_mutex_t g_mutexCerr = PTHREAD_MUTEX_INITIALIZER; /** Stores the output string and the read index number for an * alignment. */ struct OutData { string s; size_t index; OutData(string s = string(), size_t index = 0) : s(s), index(index) { } /** Operator needed for sorting priority queue. */ bool operator<(const OutData& a) const { // Smaller index number has higher priority. return index > a.index; } }; /** Shares data between workers and the output thread. */ static Pipe g_pipeOut(1<<7); /** Shares data between producer and worker threads. */ static PipeMux g_pipeMux(1); /** Notification of the current size of the g_pqueue. */ static size_t g_pqSize; static const size_t MAX_PQ_SIZE = 1000; /** Conditional variable used to block workers until the g_pqueue has * become small enough. */ static pthread_cond_t g_pqSize_cv = PTHREAD_COND_INITIALIZER; static pthread_mutex_t g_mutexPqSize = PTHREAD_MUTEX_INITIALIZER; static void* printAlignments(void*) { priority_queue pqueue; size_t index = 1; for (pair p = g_pipeOut.pop(); p.second > 0; p = g_pipeOut.pop()) { pqueue.push(p.first); while (!pqueue.empty()) { const OutData& rec = pqueue.top(); if (index == rec.index) { // Print the record at the current index. index++; assert(rec.index > 0); cout << rec.s; assert_good(cout, "stdout"); pqueue.pop(); } else if (g_pipeMux.invalidEntry(index)) { // Skip this index since it is invalid. index++; } else { // The record for this index has not been added, get // another record from the pipe. break; } } // Let waiting workers continue if the pqueue is small enough. pthread_mutex_lock(&g_mutexPqSize); g_pqSize = pqueue.size(); if (g_pqSize < MAX_PQ_SIZE) pthread_cond_broadcast(&g_pqSize_cv); pthread_mutex_unlock(&g_mutexPqSize); } return NULL; } /** Store a FastaReader and Pipe. */ struct WorkerArg { FastaReader& in; Pipe& out; WorkerArg(FastaReader& in, Pipe& out) : in(in), out(out) { } ~WorkerArg() { delete ∈ } }; static pthread_t getReadFiles(const char *readsFile) { if (opt::verbose > 0) { pthread_mutex_lock(&g_mutexCerr); cerr << "Reading `" << readsFile << "'...\n"; pthread_mutex_unlock(&g_mutexCerr); } FastaReader* in = new FastaReader( readsFile, FastaReader::FOLD_CASE); WorkerArg* arg = new WorkerArg(*in, *g_pipeMux.addPipe()); pthread_t thread; pthread_create(&thread, NULL, readFile, static_cast(arg)); return thread; } int main(int argc, char** argv) { string commandLine; { ostringstream ss; char** last = argv + argc - 1; copy(argv, last, ostream_iterator(ss, " ")); ss << *last; commandLine = ss.str(); } char delim = '/'; bool die = false; for (int c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;) { istringstream arg(optarg != NULL ? optarg : ""); switch (c) { case '?': die = true; break; case 'k': case 'l': arg >> opt::k; break; case 'm': opt::multimap = opt::MULTIMAP; break; case 'i': opt::multimap = opt::IGNORE; break; case 'j': arg >> opt::threads; break; case 'v': opt::verbose++; break; case 's': arg >> opt::section >> delim >> opt::nsections; break; case OPT_HELP: cout << USAGE_MESSAGE; exit(EXIT_SUCCESS); case OPT_VERSION: cout << VERSION_MESSAGE; exit(EXIT_SUCCESS); } if (optarg != NULL && !arg.eof()) { cerr << PROGRAM ": invalid option: `-" << (char)c << optarg << "'\n"; exit(EXIT_FAILURE); } } if (opt::section == 0 || opt::section > opt::nsections || delim != '/') { cerr << PROGRAM ": -s, --section option is incorrectly set\n"; die = true; } if (opt::k <= 0) { cerr << PROGRAM ": missing -k,--kmer option\n"; die = true; } Kmer::setLength(opt::k); if (argc - optind < 2) { cerr << PROGRAM ": missing arguments\n"; die = true; } if (die) { cerr << "Try `" << PROGRAM << " --help' for more information.\n"; exit(EXIT_FAILURE); } string refFastaFile(argv[--argc]); int numQuery = argc - optind; if (opt::threads <= 0) opt::threads = numQuery; // SAM headers. cout << "@HD\tVN:1.0\n" "@PG\tID:" PROGRAM "\tVN:" VERSION "\t" "CL:" << commandLine << '\n'; size_t numKmer = countKmer(refFastaFile); if (opt::multimap == opt::MULTIMAP) { g_aligner_m = new Aligner(opt::k, numKmer); readContigsIntoDB(refFastaFile, *g_aligner_m); } else { #if HAVE_GOOGLE_SPARSE_HASH_MAP g_aligner_u = new Aligner(opt::k, numKmer, 0.3); #else g_aligner_u = new Aligner(opt::k, numKmer); #endif readContigsIntoDB(refFastaFile, *g_aligner_u); } g_readCount = 0; vector producer_threads; transform(argv + optind, argv + argc, back_inserter(producer_threads), getReadFiles); vector threads; for (int i = 0; i < opt::threads; i++) { pthread_t thread; pthread_create(&thread, NULL, alignReadsToDB, NULL); threads.push_back(thread); } pthread_t out_thread; pthread_create(&out_thread, NULL, printAlignments, NULL); void *status; // Wait for all threads to finish. for (size_t i = 0; i < producer_threads.size(); i++) pthread_join(producer_threads[i], &status); for (size_t i = 0; i < threads.size(); i++) pthread_join(threads[i], &status); g_pipeOut.close(); pthread_join(out_thread, &status); if (opt::verbose > 0) cerr << "Aligned " << g_alignedCount << " of " << g_readCount << " reads (" << (float)100 * g_alignedCount / g_readCount << "%)\n"; if (opt::multimap == opt::MULTIMAP) delete g_aligner_m; else delete g_aligner_u; return 0; } template static void printProgress(const Aligner& align, unsigned count) { size_t size = align.size(); size_t buckets = align.bucket_count(); cerr << "Read " << count << " contigs. " "Hash load: " << size << " / " << buckets << " = " << (float)size / buckets << " using " << toSI(getMemoryUsage()) << "B." << endl; } template static void readContigsIntoDB(string refFastaFile, Aligner& aligner) { if (opt::verbose > 0) cerr << "Reading target `" << refFastaFile << "'..." << endl; unsigned count = 0; FastaReader in(refFastaFile.c_str(), FastaReader::FOLD_CASE); if (opt::nsections > 1) in.split(opt::section, opt::nsections); for (FastaRecord rec; in >> rec;) { if (count == 0) { // Detect colour-space contigs. opt::colourSpace = isdigit(rec.seq[0]); } else { if (opt::colourSpace) assert(isdigit(rec.seq[0])); else assert(isalpha(rec.seq[0])); } cout << "@SQ\tSN:" << rec.id << "\tLN:" << rec.seq.length() << '\n'; aligner.addReferenceSequence(rec.id, rec.seq); count++; if (opt::verbose > 0 && count % 100000 == 0) printProgress(aligner, count); } assert(in.eof()); if (opt::verbose > 0) printProgress(aligner, count); if (opt::multimap == opt::IGNORE) { // Count the number of duplicate k-mer in the target. size_t duplicates = aligner.countDuplicates(); if (duplicates > 0) cerr << "Found " << duplicates << " (" << (float)100 * duplicates / aligner.size() << "%) duplicate k-mer.\n"; } } /** Read each fasta record from 'in', and add it to 'pipe'. */ static void readFile(FastaReader& in, Pipe& pipe) { for (FastaRecord rec; in >> rec;) pipe.push(rec); assert(in.eof()); pipe.close(); } /** Producer thread. */ static void* readFile(void* arg) { WorkerArg* p = static_cast(arg); readFile(p->in, p->out); delete p; return NULL; } /** @Returns the time in seconds between [start, end]. */ static double timeDiff(const timeval& start, const timeval& end) { double result = (double)end.tv_sec + (double)end.tv_usec/1000000.0; result -= (double)start.tv_sec + (double)start.tv_usec/1000000.0; return result; } static void* alignReadsToDB(void*) { opt::chastityFilter = false; opt::trimMasked = false; static timeval start, end; pthread_mutex_lock(&g_mutexCerr); gettimeofday(&start, NULL); pthread_mutex_unlock(&g_mutexCerr); for (pair recPair = g_pipeMux.nextValue(); recPair.second > 0; recPair = g_pipeMux.nextValue()) { const FastaRecord& rec = recPair.first; const Sequence& seq = rec.seq; ostringstream output; if (seq.find_first_not_of("ACGT0123") == string::npos) { if (opt::colourSpace) assert(isdigit(seq[0])); else assert(isalpha(seq[0])); } switch (opt::format) { case KALIGNER: if (opt::multimap == opt::MULTIMAP) g_aligner_m->alignRead(rec.id, seq, affix_ostream_iterator( output, "\t")); else g_aligner_u->alignRead(rec.id, seq, affix_ostream_iterator( output, "\t")); break; case SAM: if (opt::multimap == opt::MULTIMAP) g_aligner_m->alignRead(rec.id, seq, ostream_iterator(output, "\n")); else g_aligner_u->alignRead(rec.id, seq, ostream_iterator(output, "\n")); break; } ostringstream out; string s = output.str(); switch (opt::format) { case KALIGNER: out << rec.id; if (opt::printSeq) { out << ' '; if (opt::colourSpace) out << rec.anchor; out << seq; } out << s << '\n'; break; case SAM: out << s; break; } g_pipeOut.push(OutData(out.str(), recPair.second)); // Prevent the priority_queue from growing too large by // waiting for threads going far too slow. pthread_mutex_lock(&g_mutexPqSize); if (g_pqSize >= MAX_PQ_SIZE) pthread_cond_wait(&g_pqSize_cv, &g_mutexPqSize); pthread_mutex_unlock(&g_mutexPqSize); if (opt::verbose > 0) { pthread_mutex_lock(&g_mutexCerr); if (!s.empty()) g_alignedCount++; if (++g_readCount % 1000000 == 0) { gettimeofday(&end, NULL); double result = timeDiff(start, end); cerr << "Aligned " << g_readCount << " reads at " << (int)(1000000 / result) << " reads/sec.\n"; start = end; } pthread_mutex_unlock(&g_mutexCerr); } } return NULL; } abyss-1.3.6/KAligner/Aligner.cpp000644 002433 001057 00000016010 12104026026 020127 0ustar00traymondassembly000000 000000 #include "Aligner.h" #include "Iterator.h" #include "SAM.h" #include "Sequence.h" #include #include #include #include #include using namespace std; namespace opt { /** For a duplicate k-mer in the target * ERROR: report an error and exit * MULTIMAP: report all alignments * IGNORE: do not report any alignments */ int multimap; } template <> void Aligner::addReferenceSequence( const Kmer& kmer, Position pos) { assert(opt::multimap == opt::MULTIMAP); m_target.insert(make_pair(kmer, pos)); } template void Aligner::addReferenceSequence( const Kmer& kmer, Position pos) { assert(opt::multimap != opt::MULTIMAP); Kmer rc_kmer = reverseComplement(kmer); map_iterator findIt = m_target.find(rc_kmer); if (findIt != m_target.end()) { if (!findIt->second.isDuplicate()) findIt->second.setDuplicate( contigIndexToID(findIt->second.contig), contigIndexToID(pos.contig), kmer.str()); return; } pair inserted = m_target.insert(make_pair(kmer, pos)); if (!inserted.second) if (!inserted.first->second.isDuplicate()) inserted.first->second.setDuplicate( contigIndexToID(inserted.first->second.contig), contigIndexToID(pos.contig), kmer.str()); } /** Create an index of the target sequence. */ template void Aligner::addReferenceSequence( const StringID& idString, const Sequence& seq) { unsigned id = contigIDToIndex(idString); int size = seq.length(); for(int i = 0; i < (size - m_hashSize + 1); ++i) { Sequence subseq(seq, i, m_hashSize); if (subseq.find_first_not_of("ACGT0123") != string::npos) continue; addReferenceSequence(Kmer(subseq), Position(id, i)); } } template template void Aligner::alignRead( const string& qid, const Sequence& seq, oiterator dest) { coalesceAlignments(qid, seq, getAlignmentsInternal(seq, false), dest); Sequence seqrc = reverseComplement(seq); coalesceAlignments(qid, seqrc, getAlignmentsInternal(seqrc, true), dest); } /** Store all alignments for a given Kmer in the parameter aligns. * @param[out] aligns Map of contig IDs to alignment vectors. */ template void Aligner::alignKmer( AlignmentSet& aligns, const Sequence& seq, bool isRC, bool good, int read_ind, int seqLen) { assert(read_ind >= 0); Sequence kmer(seq, read_ind, m_hashSize); if (!good && kmer.find_first_not_of("ACGT0123") != string::npos) return; pair range = m_target.equal_range(Kmer(kmer)); if (range.first != range.second && opt::multimap == opt::IGNORE && range.first->second.isDuplicate()) return; for (map_const_iterator resultIter = range.first; resultIter != range.second; ++resultIter) { assert(opt::multimap != opt::IGNORE || !resultIter->second.isDuplicate()); int read_pos = !isRC ? read_ind : Alignment::calculateReverseReadStart( read_ind, seqLen, m_hashSize); unsigned ctgIndex = resultIter->second.contig; Alignment align(string(), resultIter->second.pos, read_pos, m_hashSize, seqLen, isRC); aligns[ctgIndex].push_back(align); } } template typename Aligner::AlignmentSet Aligner::getAlignmentsInternal( const Sequence& seq, bool isRC) { // The results AlignmentSet aligns; bool good = seq.find_first_not_of("ACGT0123") == string::npos; int seqLen = seq.length(); int last_kmer = seqLen - m_hashSize; if (last_kmer < 0) return aligns; // Align the first kmer alignKmer(aligns, seq, isRC, good, 0, seqLen); if (last_kmer == 0) return aligns; // Align the last kmer alignKmer(aligns, seq, isRC, good, last_kmer, seqLen); // Short-cut logic ignoring the middle alignments if the first // and last kmers overlap, and align to the same contig if (good && seqLen <= 2 * m_hashSize && aligns.size() == 1) { AlignmentSet::const_iterator ctgIter = aligns.begin(); const AlignmentVector& a = ctgIter->second; if (ctgIter->second.size() == 2) { int qstep = isRC ? a[0].read_start_pos - a[1].read_start_pos : a[1].read_start_pos - a[0].read_start_pos; assert(qstep >= 0); // Verify this isn't a kmer aligning to two parts of a // contig, and that the alignments are coalescable. if (qstep == last_kmer && a[1].contig_start_pos == a[0].contig_start_pos + qstep) return aligns; } } // Align middle kmers for(int i = 1; i < last_kmer; ++i) alignKmer(aligns, seq, isRC, good, i, seqLen); return aligns; } static int compareQueryPos(const Alignment& a1, const Alignment& a2) { return a1.read_start_pos < a2.read_start_pos; } /** Coalesce the k-mer alignments into a read alignment. */ template template void Aligner::coalesceAlignments( const string& qid, const string& seq, const AlignmentSet& alignSet, oiterator& dest) { typedef typename output_iterator_traits::value_type value_type; for (AlignmentSet::const_iterator ctgIter = alignSet.begin(); ctgIter != alignSet.end(); ++ctgIter) { AlignmentVector alignVec = ctgIter->second; assert(!alignVec.empty()); sort(alignVec.begin(), alignVec.end(), compareQueryPos); AlignmentVector::iterator prevIter = alignVec.begin(); AlignmentVector::iterator currIter = alignVec.begin() + 1; Alignment currAlign = *prevIter; while (currIter != alignVec.end()) { int qstep = currIter->read_start_pos - prevIter->read_start_pos; assert(qstep >= 0); int tstep = currIter->isRC ? -qstep : qstep; if (currIter->contig_start_pos == prevIter->contig_start_pos + tstep && qstep <= m_hashSize) { currAlign.align_length += qstep; if (currAlign.isRC) currAlign.contig_start_pos -= qstep; } else { currAlign.contig = contigIndexToID(ctgIter->first); *dest++ = value_type(currAlign, qid, seq); currAlign = *currIter; } prevIter = currIter; currIter++; } currAlign.contig = contigIndexToID(ctgIter->first); *dest++ = value_type(currAlign, qid, seq); } } // Explicit instantiation. template void Aligner::addReferenceSequence( const StringID& id, const Sequence& seq); template void Aligner::addReferenceSequence( const StringID& id, const Sequence& seq); template void Aligner:: alignRead >( const string& qid, const Sequence& seq, affix_ostream_iterator dest); template void Aligner:: alignRead >( const string& qid, const Sequence& seq, affix_ostream_iterator dest); template void Aligner:: alignRead >( const string& qid, const Sequence& seq, ostream_iterator dest); template void Aligner:: alignRead >( const string& qid, const Sequence& seq, ostream_iterator dest); abyss-1.3.6/KAligner/Aligner.h000644 002433 001057 00000007201 12104026026 017576 0ustar00traymondassembly000000 000000 #ifndef ALIGNER_H #define ALIGNER_H 1 #include "config.h" #include "KAligner/Options.h" #include "Alignment.h" #include "ConstString.h" #include "Functional.h" #include "Kmer.h" #include "UnorderedMap.h" #include #include #include // for strcpy #include #include #include #include #include #include #include #include typedef std::string StringID; /** A tuple of a target ID and position. */ struct Position { uint32_t contig; uint32_t pos; // 0 indexed Position(uint32_t contig = std::numeric_limits::max(), uint32_t pos = std::numeric_limits::max()) : contig(contig), pos(pos) { } /** Mark this seed as a duplicate. */ void setDuplicate(const char* thisContig, const char* otherContig, const Sequence& kmer) { if (opt::multimap == opt::IGNORE) contig = std::numeric_limits::max(); else { std::cerr << "error: duplicate k-mer in " << thisContig << " also in " << otherContig << ": " << kmer << '\n'; exit(EXIT_FAILURE); } } /** Return whether this seed is a duplciate. */ bool isDuplicate() const { return contig == std::numeric_limits::max(); } }; typedef unordered_multimap SeqPosHashMultiMap; #if HAVE_GOOGLE_SPARSE_HASH_MAP # include typedef google::sparse_hash_map SeqPosHashUniqueMap; #else typedef unordered_map SeqPosHashUniqueMap; #endif typedef std::vector AlignmentVector; /** * Index a target sequence and align query sequences to that indexed * target. */ template class Aligner { public: typedef typename SeqPosHashMap::iterator map_iterator; typedef typename SeqPosHashMap::const_iterator map_const_iterator; Aligner(int hashSize, size_t buckets) : m_hashSize(hashSize), m_target(buckets) { } Aligner(int hashSize, size_t buckets, float factor) : m_hashSize(hashSize) { m_target.max_load_factor(factor); m_target.rehash(buckets); } void addReferenceSequence(const StringID& id, const Sequence& seq); void addReferenceSequence(const Kmer& kmer, Position pos); template void alignRead(const std::string& qid, const Sequence& seq, oiterator dest); size_t size() const { return m_target.size(); } size_t bucket_count() const { return m_target.bucket_count(); } /** Return the number of duplicate k-mer in the target. */ size_t countDuplicates() const { assert(opt::multimap == opt::IGNORE); return count_if(m_target.begin(), m_target.end(), compose1(std::mem_fun_ref(&Position::isDuplicate), mem_var(&SeqPosHashMap::value_type::second))); } private: explicit Aligner(const Aligner&); typedef std::map AlignmentSet; void alignKmer( AlignmentSet& aligns, const Sequence& kmer, bool isRC, bool good, int read_ind, int seqLen); AlignmentSet getAlignmentsInternal( const Sequence& seq, bool isRC); template void coalesceAlignments( const std::string& qid, const std::string& seq, const AlignmentSet& alignSet, oiterator& dest); // The number of bases to hash on int m_hashSize; /** A map of k-mer to contig coordinates. */ SeqPosHashMap m_target; /** A dictionary of contig IDs. */ std::vector m_dict; unsigned contigIDToIndex(const std::string& id) { m_dict.push_back(id); return m_dict.size() - 1; } cstring contigIndexToID(unsigned index) { assert(index < m_dict.size()); return m_dict[index]; } }; #endif abyss-1.3.6/KAligner/Options.h000644 002433 001057 00000000206 12104026026 017646 0ustar00traymondassembly000000 000000 #ifndef ALIGN_OPTIONS_H #define ALIGN_OPTIONS_H 1 namespace opt { enum { IGNORE, MULTIMAP, ERROR }; extern int multimap; } #endif abyss-1.3.6/KAligner/Pipe.h000644 002433 001057 00000004141 12015543262 017121 0ustar00traymondassembly000000 000000 #ifndef PIPE_H #define PIPE_H 1 #include "Semaphore.h" #include #include /** An asynchronous queue for transmitting data from one thread to * another. */ template class Pipe { public: /** Ready to use after constructed. Not thread safe. */ Pipe(unsigned size = 1024) : m_sem_in(size), m_sem_out(0), m_open(true) { assert(size > 0); pthread_mutex_init(&m_mutex_queue, NULL); } /** Destoyr semaphores/mutexs. Not thread safe. */ ~Pipe() { pthread_mutex_destroy(&m_mutex_queue); } /** Add data to the buffer/queue. */ void push(T x) { // Block if pipe is full, or in use. m_sem_in.wait(); pthread_mutex_lock(&m_mutex_queue); assert(m_open); add(x); pthread_mutex_unlock(&m_mutex_queue); m_sem_out.post(); } /** Get data and remove it from the buffer. */ std::pair pop() { // block when pipe is empty and m_open, or in use. m_sem_out.wait(); pthread_mutex_lock(&m_mutex_queue); std::pair temp = remove(); pthread_mutex_unlock(&m_mutex_queue); // If pipe is m_open ensure poping will allow one more push. // Otherwise, let next accessor know pipe is closed. if (temp.second) m_sem_in.post(); else { assert(!m_open); m_sem_out.post(); } return temp; } /** Allows a pop when the pipe is empty to signal the pipe is * closed. */ void close() { pthread_mutex_lock(&m_mutex_queue); m_open = false; pthread_mutex_unlock(&m_mutex_queue); m_sem_out.post(); } private: /** Add an element to the buffer. */ void add(const T& t) { m_queue.push(t); } /** Remove an element from the buffer. */ std::pair remove() { std::pair temp; if (!m_queue.empty()) { temp.first = m_queue.front(); temp.second = 1; m_queue.pop(); } else { temp.second = 0; } return temp; } /** Semaphores to block read on empty, or write on full. */ Semaphore m_sem_in, m_sem_out; /** Mutual exclusion for reading and writing */ pthread_mutex_t m_mutex_queue; /** True if close() has not been called. */ bool m_open; /** Pipe's buffer */ std::queue m_queue; }; #endif abyss-1.3.6/KAligner/PipeMux.h000644 002433 001057 00000007074 12104026026 017614 0ustar00traymondassembly000000 000000 #ifndef PIPEMUX_H #define PIPEMUX_H 1 #include "Pipe.h" #include #include #include template class PipeMux { public: /** Default constructor. */ PipeMux(size_t pipe_size = 1) : m_index(0), m_entry_num(0), m_pipe_size(pipe_size) { pthread_rwlock_init(&m_rwlock_vecs, NULL); pthread_mutex_init(&m_mutex_index, NULL); } /** Destroy remaining pipes, and mutexes. */ ~PipeMux() { pthread_rwlock_destroy(&m_rwlock_vecs); pthread_mutex_destroy(&m_mutex_index); assert(m_pipes.empty()); assert(m_mutex_pipes.empty()); } /** Instantiates a new pipe and adds it to this PipeMux. */ Pipe* addPipe() { Pipe* p = new Pipe(m_pipe_size); pthread_mutex_t* m = new pthread_mutex_t; pthread_mutex_init(m, NULL); pthread_rwlock_wrlock(&m_rwlock_vecs); m_pipes.push_back(p); m_mutex_pipes.push_back(m); pthread_rwlock_unlock(&m_rwlock_vecs); return p; } /** Returns the next value from the appropriate pipe, deletes * closed pipes and returns */ std::pair nextValue() { size_t entry; std::pair t(T(), 0); do { pthread_rwlock_rdlock(&m_rwlock_vecs); pthread_mutex_lock(&m_mutex_index); if (m_pipes.empty() && m_mutex_pipes.empty()) { pthread_rwlock_unlock(&m_rwlock_vecs); pthread_mutex_unlock(&m_mutex_index); return t; } unsigned i = m_index; m_index = m_index + 1 < m_pipes.size() ? m_index + 1 : 0; entry = ++m_entry_num; assert(i < m_mutex_pipes.size()); pthread_mutex_lock(m_mutex_pipes[i]); pthread_mutex_unlock(&m_mutex_index); assert(i < m_pipes.size()); Pipe* p_pipe = m_pipes[i]; t = p_pipe->pop(); // you know you're fed up with race conditions when... assert(i < m_mutex_pipes.size()); pthread_mutex_unlock(m_mutex_pipes[i]); pthread_rwlock_unlock(&m_rwlock_vecs); if (!t.second) removePipe(p_pipe, entry); } while (!t.second); t.second = entry; return t; } bool invalidEntry(size_t e) { pthread_rwlock_rdlock(&m_rwlock_vecs); for (unsigned i = 0; i < m_invalid_entries.size(); i++) { assert(i < m_invalid_entries.size()); if (m_invalid_entries[i] == e) { pthread_rwlock_unlock(&m_rwlock_vecs); return true; } } pthread_rwlock_unlock(&m_rwlock_vecs); return false; } /** Checks that the PipeMux is empty. */ bool empty() { pthread_rwlock_rdlock(&m_rwlock_vecs); bool isEmpty = m_pipes.empty(); pthread_rwlock_unlock(&m_rwlock_vecs); return isEmpty; } private: std::vector*> m_pipes; std::vector m_mutex_pipes; std::vector m_invalid_entries; pthread_rwlock_t m_rwlock_vecs; pthread_mutex_t m_mutex_index; unsigned m_index; size_t m_entry_num; size_t m_pipe_size; /** Removes Pipe p if it is still present in m_pipes. */ void removePipe(Pipe* p, size_t entry) { pthread_rwlock_wrlock(&m_rwlock_vecs); m_invalid_entries.push_back(entry); unsigned i; for (i = 0; i < m_pipes.size(); i++) { assert(i < m_pipes.size()); if (m_pipes[i] == p) break; } if (i >= m_pipes.size()) { pthread_rwlock_unlock(&m_rwlock_vecs); return; } assert(i < m_pipes.size()); delete m_pipes[i]; m_pipes.erase(m_pipes.begin()+i); assert(i < m_mutex_pipes.size()); pthread_mutex_destroy(m_mutex_pipes[i]); delete m_mutex_pipes[i]; m_mutex_pipes.erase(m_mutex_pipes.begin()+i); // Make sure the index points to the next element. pthread_mutex_lock(&m_mutex_index); m_index = m_index == m_pipes.size() ? 0 : m_index; pthread_mutex_unlock(&m_mutex_index); pthread_rwlock_unlock(&m_rwlock_vecs); } }; #endif abyss-1.3.6/KAligner/Semaphore.h000644 002433 001057 00000003443 12015543262 020153 0ustar00traymondassembly000000 000000 #ifndef SEMAPHORE_H #define SEMAPHORE_H 1 /** Semaphore class needed since some OS' do not support unnamed * semaphores. */ #if __APPLE__ # include class Semaphore { public: Semaphore(unsigned value) : m_value(value) { pthread_mutex_init(&m_mutex, NULL); pthread_cond_init(&m_cv, NULL); } ~Semaphore() { pthread_mutex_destroy(&m_mutex); pthread_cond_destroy(&m_cv); } void wait() { pthread_mutex_lock(&m_mutex); // Not a spinlock! 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#define PROGRAM "DistanceEst" static const char VERSION_MESSAGE[] = PROGRAM " (" PACKAGE_NAME ") " VERSION "\n" "Written by Jared Simpson and Shaun Jackman.\n" "\n" "Copyright 2013 Canada's Michael Smith Genome Science Centre\n"; static const char USAGE_MESSAGE[] = "Usage: " PROGRAM " [OPTION]... HIST [PAIR]\n" "Estimate distances between contigs using paired-end alignments.\n" "\n" " Arguments:\n" "\n" " HIST distribution of fragments size\n" " PAIR alignments between contigs\n" "\n" " Options:\n" "\n" " --mind=N minimum distance between contigs [-(k-1)]\n" " --maxd=N maximum distance between contigs\n" " --fr force the orientation to forward-reverse\n" " --rf force the orientation to reverse-forward\n" " -k, --kmer=N set --mind to -(k-1) bp\n" " -l, --min-align=N the minimal alignment size [1]\n" " -n, --npairs=NPAIRS minimum number of pairs\n" " -s, --seed-length=L minimum length of the seed contigs\n" " -q, --min-mapq=N ignore alignments with mapping quality\n" " less than this threshold [10]\n" " -o, --out=FILE write result to FILE\n" " --mle use the MLE [default]\n" " (maximum likelihood estimator)\n" " --mean use the difference of the population mean\n" " and the sample mean\n" " --dist output graph in dist format [default]\n" " --dot output graph in dot format\n" " -j, --threads=N use N parallel threads [1]\n" " -v, --verbose display verbose output\n" " --help display this help and exit\n" " --version output version information and exit\n" "\n" "Report bugs to <" PACKAGE_BUGREPORT ">.\n"; /** Which estimator to use. See opt::method. */ enum { MLE, MEAN }; namespace opt { unsigned k; // used by Estimate.h /** Output graph format. */ int format = DIST; /** Minimum distance between contigs. */ static int minDist = numeric_limits::min(); /** Maximum distance between contigs. */ static int maxDist = numeric_limits::max(); static unsigned seedLen; static unsigned npairs; static unsigned minMapQ = 10; /** Reverse-forward mate pair orientation. */ static int rf = -1; /** Which estimator to use. */ static int method = MLE; static int verbose; static string out; static int threads = 1; } static const char shortopts[] = "j:k:l:n:o:q:s:v"; enum { OPT_HELP = 1, OPT_VERSION, OPT_MIND, OPT_MAXD, OPT_FR, OPT_RF }; static const struct option longopts[] = { { "dist", no_argument, &opt::format, DIST, }, { "dot", no_argument, &opt::format, DOT, }, { "fr", no_argument, &opt::rf, false }, { "rf", no_argument, &opt::rf, true }, { "min-align", required_argument, NULL, 'l' }, { "mind", required_argument, NULL, OPT_MIND }, { "maxd", required_argument, NULL, OPT_MAXD }, { "mle", no_argument, &opt::method, MLE }, { "mean", no_argument, &opt::method, MEAN }, { "kmer", required_argument, NULL, 'k' }, { "npairs", required_argument, NULL, 'n' }, { "out", required_argument, NULL, 'o' }, { "min-mapq", required_argument, NULL, 'q' }, { "seed-length", required_argument, NULL, 's' }, { "threads", required_argument, NULL, 'j' }, { "verbose", no_argument, NULL, 'v' }, { "help", no_argument, NULL, OPT_HELP }, { "version", no_argument, NULL, OPT_VERSION }, { NULL, 0, NULL, 0 } }; /** A collection of aligned read pairs. */ typedef vector Pairs; /** Estimate the distance between two contigs using the difference of * the population mean and the sample mean. * @param numPairs [out] the number of pairs that agree with the * expected distribution * @return the estimated distance */ static int estimateDistanceUsingMean( const std::vector& samples, const PMF& pmf, unsigned& numPairs) { Histogram h(samples.begin(), samples.end()); int d = (int)round(pmf.mean() - h.mean()); // Count the number of samples that agree with the distribution. unsigned n = 0; for (Histogram::const_iterator it = h.begin(); it != h.end(); ++it) if (pmf[it->first + d] > pmf.minProbability()) n += it->second; numPairs = n; return d; } /** Global variable to track a recommended minAlign parameter */ unsigned g_recMA; /** Estimate the distance between two contigs. * @param numPairs [out] the number of pairs that agree with the * expected distribution * @return the estimated distance */ static int estimateDistance(unsigned len0, unsigned len1, const Pairs& pairs, const PMF& pmf, unsigned& numPairs) { // The provisional fragment sizes are calculated as if the contigs // were perfectly adjacent with no overlap or gap. typedef vector > Fragments; Fragments fragments; fragments.reserve(pairs.size()); for (Pairs::const_iterator it = pairs.begin(); it != pairs.end(); ++it) { int a0 = it->targetAtQueryStart(); int a1 = it->mateTargetAtQueryStart(); if (it->isReverse()) a0 = len0 - a0; if (!it->isMateReverse()) a1 = len1 - a1; fragments.push_back(opt::rf ? make_pair(a1, len1 + a0) : make_pair(a0, len0 + a1)); } // Remove duplicate fragments. sort(fragments.begin(), fragments.end()); fragments.erase(unique(fragments.begin(), fragments.end()), fragments.end()); numPairs = fragments.size(); if (numPairs < opt::npairs) return INT_MIN; vector fragmentSizes; fragmentSizes.reserve(fragments.size()); unsigned ma = opt::minAlign; for (Fragments::const_iterator it = fragments.begin(); it != fragments.end(); ++it) { int x = it->second - it->first; if (!opt::rf && opt::method == MLE && x <= 2 * int(ma - 1)) { unsigned align = x / 2; if (opt::verbose > 0) #pragma omp critical(cerr) cerr << PROGRAM ": warning: The observed fragment of " "size " << x << " bp is shorter than 2*l " "(l=" << opt::minAlign << ").\n"; ma = min(ma, align); } fragmentSizes.push_back(x); } #pragma omp critical(g_recMA) g_recMA = min(g_recMA, ma); switch (opt::method) { case MLE: // Use the maximum likelihood estimator. return maximumLikelihoodEstimate(ma, opt::minDist, opt::maxDist, fragmentSizes, pmf, len0, len1, opt::rf, numPairs); case MEAN: // Use the difference of the population mean // and the sample mean. return estimateDistanceUsingMean( fragmentSizes, pmf, numPairs); default: assert(false); abort(); } } static void writeEstimate(ostream& out, const ContigNode& id0, const ContigNode& id1, unsigned len0, unsigned len1, const Pairs& pairs, const PMF& pmf) { if (pairs.size() < opt::npairs) return; DistanceEst est; est.distance = estimateDistance(len0, len1, pairs, pmf, est.numPairs); est.stdDev = pmf.getSampleStdDev(est.numPairs); std::pair e(id0, id1 ^ id0.sense()); if (est.numPairs >= opt::npairs) { if (opt::format == DOT) { #pragma omp critical(out) out << get(g_contigNames, e) << " [" << est << "]\n"; } else out << ' ' << get(g_contigNames, id1) << ',' << est; } else if (opt::verbose > 1) { #pragma omp critical(cerr) cerr << "warning: " << get(g_contigNames, e) << " [d=" << est.distance << "] " << est.numPairs << " of " << pairs.size() << " pairs fit the expected distribution\n"; } } /** Generate distance estimates for the specified alignments. */ static void writeEstimates(ostream& out, const vector& pairs, const vector& lengthVec, const PMF& pmf) { assert(!pairs.empty()); ContigID id0(get(g_contigNames, pairs.front().rname)); assert(id0 < lengthVec.size()); unsigned len0 = lengthVec[id0]; if (len0 < opt::seedLen) return; // Skip contigs shorter than the seed length. ostringstream ss; if (opt::format == DIST) ss << pairs.front().rname; typedef map PairsMap; PairsMap dataMap[2]; for (Pairs::const_iterator it = pairs.begin(); it != pairs.end(); ++it) dataMap[it->isReverse()][find_vertex( it->mrnm, it->isReverse() == it->isMateReverse(), g_contigNames)] .push_back(*it); for (int sense0 = false; sense0 <= true; sense0++) { if (opt::format == DIST && sense0) ss << " ;"; const PairsMap& x = dataMap[sense0 ^ opt::rf]; for (PairsMap::const_iterator it = x.begin(); it != x.end(); ++it) writeEstimate(opt::format == DOT ? out : ss, ContigNode(id0, sense0), it->first, len0, lengthVec[it->first.id()], it->second, pmf); } if (opt::format == DIST) #pragma omp critical(out) out << ss.str() << '\n'; assert(out.good()); } /** Load a histogram from the specified file. */ static Histogram loadHist(const string& path) { ifstream in(path.c_str()); assert_good(in, path); Histogram hist; in >> hist; assert(in.eof()); if (hist.empty()) { cerr << "error: the histogram `" << path << "' is empty\n"; exit(EXIT_FAILURE); } return hist; } /** Read contig lengths from SAM headers. */ static void readContigLengths(istream& in, vector& lengths) { assert(in); assert(lengths.empty()); assert(g_contigNames.empty()); for (string line; in.peek() == '@' && getline(in, line);) { istringstream ss(line); string type; ss >> type; if (type != "@SQ") continue; string s; unsigned len; ss >> expect(" SN:") >> s >> expect(" LN:") >> len; assert(ss); put(g_contigNames, lengths.size(), s); lengths.push_back(len); } if (lengths.empty()) { cerr << PROGRAM ": error: no @SQ records in the SAM header\n"; exit(EXIT_FAILURE); } } /** Copy records from [it, last) to out and stop before alignments to * the next target sequence. * @param[in,out] it an input iterator */ template static void readPairs(It& it, const It& last, vector& out) { assert(out.empty()); for (; it != last; ++it) { if (it->isUnmapped() || it->isMateUnmapped() || !it->isPaired() || it->rname == it->mrnm || it->mapq < opt::minMapQ) continue; if (!out.empty() && out.back().rname != it->rname) break; out.push_back(*it); SAMRecord& sam = out.back(); // Clear unused fields. sam.qname.clear(); #if SAM_SEQ_QUAL sam.seq.clear(); sam.qual.clear(); #endif } // Check that the input is sorted. if (it != last && !out.empty() && get(g_contigNames, it->rname) < get(g_contigNames, out.front().rname)) { cerr << "error: input must be sorted: saw `" << out.front().rname << "' before `" << it->rname << "'\n"; exit(EXIT_FAILURE); } } int main(int argc, char** argv) { bool die = false; for (int c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;) { istringstream arg(optarg != NULL ? optarg : ""); switch (c) { case '?': die = true; break; case OPT_MIND: arg >> opt::minDist; break; case OPT_MAXD: arg >> opt::maxDist; break; case 'l': arg >> opt::minAlign; break; case 'j': arg >> opt::threads; break; case 'k': arg >> opt::k; break; case 'n': arg >> opt::npairs; break; case 'o': arg >> opt::out; break; case 'q': arg >> opt::minMapQ; break; case 's': arg >> opt::seedLen; break; case 'v': opt::verbose++; break; case OPT_HELP: cout << USAGE_MESSAGE; exit(EXIT_SUCCESS); case OPT_VERSION: cout << VERSION_MESSAGE; exit(EXIT_SUCCESS); } if (optarg != NULL && !arg.eof()) { cerr << PROGRAM ": invalid option: `-" << (char)c << optarg << "'\n"; exit(EXIT_FAILURE); } } if (opt::k <= 0) { cerr << PROGRAM ": missing -k,--kmer option\n"; die = true; } if (opt::seedLen <= 0) { cerr << PROGRAM ": missing -s,--seed-length option\n"; die = true; } if (opt::npairs <= 0) { cerr << PROGRAM ": missing -n,--npairs option\n"; die = true; } if (argc - optind < 1) { cerr << PROGRAM ": missing arguments\n"; die = true; } else if (argc - optind > 2) { cerr << PROGRAM ": too many arguments\n"; die = true; } if (die) { cerr << "Try `" << PROGRAM << " --help' for more information.\n"; exit(EXIT_FAILURE); } if (opt::seedLen < 2*opt::k) cerr << "warning: the seed-length should be at least twice k:" " k=" << opt::k << ", s=" << opt::seedLen << '\n'; assert(opt::minAlign > 0); #if _OPENMP if (opt::threads > 0) omp_set_num_threads(opt::threads); #endif string distanceCountFile(argv[optind++]); string alignFile(argv[optind] == NULL ? "-" : argv[optind++]); ifstream inFile(alignFile.c_str()); istream& in(strcmp(alignFile.c_str(), "-") == 0 ? cin : inFile); if (strcmp(alignFile.c_str(), "-") != 0) assert_good(inFile, alignFile); ofstream outFile; if (!opt::out.empty()) { outFile.open(opt::out.c_str()); assert(outFile.is_open()); } ostream& out = opt::out.empty() ? cout : outFile; if (opt::format == DOT) out << "digraph dist {\ngraph [" "k=" << opt::k << " " "s=" << opt::seedLen << " " "n=" << opt::npairs << "]\n"; // The fragment size histogram may not be written out until after // the alignments complete. Wait for the alignments to complete. in.peek(); // Read the fragment size distribution. Histogram distanceHist = loadHist(distanceCountFile); unsigned numRF = distanceHist.count(INT_MIN, 0); unsigned numFR = distanceHist.count(1, INT_MAX); unsigned numTotal = distanceHist.size(); bool libRF = numFR < numRF; if (opt::verbose > 0) { cerr << "Mate orientation FR: " << numFR << setprecision(3) << " (" << (float)100*numFR/numTotal << "%)" << " RF: " << numRF << setprecision(3) << " (" << (float)100*numRF/numTotal << "%)\n" << "The library " << distanceCountFile << " is oriented " << (libRF ? "reverse-forward (RF)" : "forward-reverse (FR)") << ".\n"; } // Determine the orientation of the library. if (opt::rf == -1) opt::rf = libRF; if (opt::rf) distanceHist = distanceHist.negate(); if (opt::rf != libRF) cerr << "warning: The orientation is forced to " << (opt::rf ? "reverse-forward (RF)" : "forward-reverse (FR)") << " which differs from the detected orientation.\n"; distanceHist.eraseNegative(); distanceHist.removeNoise(); distanceHist.removeOutliers(); Histogram h = distanceHist.trimFraction(0.0001); if (opt::verbose > 0) cerr << "Stats mean: " << setprecision(4) << h.mean() << " " "median: " << setprecision(4) << h.median() << " " "sd: " << setprecision(4) << h.sd() << " " "n: " << h.size() << " " "min: " << h.minimum() << " max: " << h.maximum() << '\n' << h.barplot() << endl; PMF pmf(h); if (opt::minDist == numeric_limits::min()) opt::minDist = -opt::k + 1; if (opt::maxDist == numeric_limits::max()) opt::maxDist = pmf.maxValue(); if (opt::verbose > 0) cerr << "Minimum and maximum distance are set to " << opt::minDist << " and " << opt::maxDist << " bp.\n"; assert(opt::minDist < opt::maxDist); // Read the contig lengths. vector contigLens; readContigLengths(in, contigLens); g_contigNames.lock(); // Estimate the distances between contigs. istream_iterator it(in), last; if (contigLens.size() == 1) { // When mapping to a single contig, no alignments spanning // contigs are expected. assert(in.eof()); exit(EXIT_SUCCESS); } assert(in); g_recMA = opt::minAlign; #pragma omp parallel for (vector records;;) { records.clear(); #pragma omp critical(in) readPairs(it, last, records); if (records.empty()) break; writeEstimates(out, records, contigLens, pmf); } if (opt::verbose > 0 && g_recMA != opt::minAlign) cerr << PROGRAM << ": warning: MLE will be more accurate if " "l is decreased to " << g_recMA << ".\n"; assert(in.eof()); if (opt::format == DOT) out << "}\n"; return 0; } abyss-1.3.6/DistanceEst/MLE.cpp000644 002433 001057 00000010476 12104250114 017704 0ustar00traymondassembly000000 000000 #include "MLE.h" #include "PMF.h" #include #include // for swap #include #include // for numeric_limits #include using namespace std; using boost::tie; /** This window function is a triangle with a flat top, or a rectangle * with sloped sides. */ class WindowFunction { public: WindowFunction(int len0, int len1) : x1(len0), x2(len1), x3(len0 + len1) { assert(len0 > 0); assert(len1 > 0); assert(len0 <= len1); } /** Return this window function evaluated at x. */ double operator()(int x) const { return (x <= 0 ? 1 : x < x1 ? x : x < x2 ? x1 : x < x3 ? x3 - x : 1) / (double)x1; } private: /** Parameters of this window function. */ int x1, x2, x3; }; /** Compute the log likelihood that these samples came from the * specified distribution shifted by the parameter theta. * @param theta the parameter of the PMF, f_theta(x) * @param samples the samples * @param pmf the probability mass function * @return the log likelihood */ static pair computeLikelihood(int theta, const Histogram& samples, const PMF& pmf) { double likelihood = 0; unsigned nsamples = 0; for (Histogram::const_iterator it = samples.begin(); it != samples.end(); ++it) { double p = pmf[it->first + theta]; unsigned n = it->second; likelihood += n * log(p); if (p > pmf.minProbability()) nsamples += n; } return make_pair(likelihood, nsamples); } /** Return the most likely distance between two contigs and the number * of pairs that support that estimate. */ static pair maximumLikelihoodEstimate(int first, int last, const Histogram& samples, const PMF& pmf, unsigned len0, unsigned len1) { first = max(first, (int)pmf.minValue() - samples.maximum()); last = min(last, (int)pmf.maxValue() - samples.minimum()); /* When randomly selecting fragments that span a given point, * longer fragments are more likely to be selected than * shorter fragments. */ WindowFunction window(len0, len1); unsigned nsamples = samples.size(); double bestLikelihood = -numeric_limits::max(); int bestTheta = first; unsigned bestn = 0; for (int theta = first; theta <= last; theta++) { // Calculate the normalizing constant of the PMF, f_theta(x). double c = 0; for (int i = pmf.minValue(); i <= (int)pmf.maxValue(); ++i) c += pmf[i] * window(i - theta); double likelihood; unsigned n; tie(likelihood, n) = computeLikelihood(theta, samples, pmf); likelihood -= nsamples * log(c); if (n > 0 && likelihood > bestLikelihood) { bestLikelihood = likelihood; bestTheta = theta; bestn = n; } } return make_pair(bestTheta, bestn); } /** Return the most likely distance between two contigs and the number * of pairs that support that distance estimate. * @param len0 the length of the first contig in bp * @param len1 the length of the second contig in bp * @param rf whether the fragment library is oriented reverse-forward * @param[out] n the number of samples with a non-zero probability */ int maximumLikelihoodEstimate(unsigned l, int first, int last, const vector& samples, const PMF& pmf, unsigned len0, unsigned len1, bool rf, unsigned& n) { assert(first < last); assert(!samples.empty()); // The aligner is unable to map reads to the ends of the sequence. // Correct for this lack of sensitivity by subtracting l-1 bp from // the length of each sequence, where the aligner requires a match // of at least l bp. When the fragment library is oriented // forward-reverse, subtract 2*(l-1) from each sample. assert(l > 0); assert(len0 >= l); assert(len1 >= l); len0 -= l - 1; len1 -= l - 1; if (len0 > len1) swap(len0, len1); if (rf) { // This library is oriented reverse-forward. Histogram h(samples.begin(), samples.end()); int d; tie(d, n) = maximumLikelihoodEstimate( first, last, h, pmf, len0, len1); return d; } else { // This library is oriented forward-reverse. // Subtract 2*(l-1) from each sample. Histogram h; typedef vector Samples; for (Samples::const_iterator it = samples.begin(); it != samples.end(); ++it) { assert(*it > 2 * (int)(l - 1)); h.insert(*it - 2 * (l - 1)); } int d; tie(d, n) = maximumLikelihoodEstimate( first, last, h, pmf, len0, len1); return max(first, d - 2 * (int)(l - 1)); } } abyss-1.3.6/DistanceEst/MLE.h000644 002433 001057 00000000361 12104026026 017344 0ustar00traymondassembly000000 000000 #ifndef MLE_H #define MLE_H 1 #include class PMF; int maximumLikelihoodEstimate(unsigned k, int first, int last, const std::vector& samples, const PMF& pmf, unsigned len0, unsigned len1, bool rf, unsigned& n); #endif abyss-1.3.6/DAssembler/Makefile.in000644 002433 001057 00000053370 12176317671 020470 0ustar00traymondassembly000000 000000 # Makefile.in generated by automake 1.14 from Makefile.am. # @configure_input@ # Copyright (C) 1994-2013 Free Software Foundation, Inc. # This Makefile.in is free software; the Free Software Foundation # gives unlimited permission to copy and/or distribute it, # with or without modifications, as long as this notice is preserved. # This program is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY, to the extent permitted by law; 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#define PROGRAM "DAssembler" static const char VERSION_MESSAGE[] = PROGRAM " (" PACKAGE_NAME ") " VERSION "\n" "Written by Rod Docking.\n" "\n" "Copyright 2013 Canada's Michael Smith Genome Science Centre\n"; namespace opt { static unsigned max_overlap = 10; static unsigned max_mismatch = 2; static unsigned min_coverage = 2; static unsigned read_length = 50; static int verbose = 0; } static const char shortopts[] = "o:m:c:r:v"; enum { OPT_HELP = 1, OPT_VERSION }; static const struct option longopts[] = { { "max_overlap", required_argument, NULL, 'o' }, { "max_mismatch", required_argument, NULL, 'm' }, { "min_coverage", required_argument, NULL, 'c' }, { "read_length", required_argument, NULL, 'r' }, { "verbose", no_argument, NULL, 'v' }, { "help", no_argument, NULL, OPT_HELP }, { "version", no_argument, NULL, OPT_VERSION }, { NULL, 0, NULL, 0 } }; static const char USAGE_MESSAGE[] = "Usage: " PROGRAM " [OPTION]... [READS]\n" "Assemble a single contig from reads in a single orientation.\n" "\n" " Arguments:\n" "\n" " READS fasta-formatted reads file: the first read is used as the seed.\n" "\n" " Options:\n" "\n" " -o, --max_overlap=INT maximum tier overlap for consensus calling" " [10]\n" " -m, --max_mismatch=INT maximum mismatches allowed for consensus" " calling [2]\n" " -c, --min_coverage=INT minimum coverage to call a consensus base" " [2]\n" " -r, --read_length=INT read length\n" " -v, --verbose display verbose output\n" " --help display this help and exit\n" "\n"; /* A small struct for holding overlap information: just a sequence and offset from the focal read */ struct Overlap{ string seq; unsigned offset; Overlap(const string& seq, unsigned offset) : seq(seq), offset(offset) { } }; /* Additional sort of Overlap objects used for pretty-printing alignments*/ static bool offset_sort(const Overlap& x, const Overlap& y) { return x.offset < y.offset; } /* Calculate the tier overlap between two rotated reads */ static int tier_overlap(const string& seq1, const string& seq2, bool allow_mismatch = false); /* From a rotated read, return the original sequence */ static string original_read_from_rotated_read( const string& rotated_read) { size_t dollar_pos = rotated_read.find('$'); string orig_seq = rotated_read.substr( dollar_pos+1,rotated_read.size()-dollar_pos) + rotated_read.substr(0,dollar_pos); return orig_seq; } /* Struct for holding base counts at a given position */ struct BaseCount { unsigned x[4]; BaseCount() { fill(x, x + 4, 0); } /** Return the number of reads at this position. */ unsigned sum() const { return accumulate(x, x+4, 0); } friend ostream& operator <<(ostream& out, const BaseCount& base) { out << base.x[0]; for (int x = 1; x < 4; x++) out << '\t' << base.x[x]; return out; } }; /* Call a consensus base */ static char call_consensus_base(BaseCount counts, char orig_base) { unsigned coverage = accumulate(counts.x, counts.x+4, 0); /*If we're below minimum coverage but have an already-called base (i.e., for the first few bases)*/ if (coverage < opt::min_coverage) return orig_base; // Call a consensus base unsigned *maxIt = max_element(counts.x, counts.x+4); // Very verbose debugging output // char base_to_return = float(*maxIt) <= float(coverage)*0.60 ? orig_base : codeToBase(maxIt - counts.x); // char new_base_to_return = *maxIt < opt::min_coverage ? orig_base : codeToBase(maxIt - counts.x); // float call_threshold = float(coverage)*0.60; // float max_base_percent = float(*maxIt) / float(coverage); // cerr << "Coverage: " << coverage << "\tOriginal: " << orig_base << // "\tReturning: " << base_to_return << "\tBases: " << counts << // "\tCall threshold: " << call_threshold << // "\tMax base percent: " << max_base_percent << // "\tNew base to return: " << new_base_to_return << endl; // Original version with hard-coded coverage frequency of 60% // return float(*maxIt) <= float(coverage)*0.60 ? orig_base // : codeToBase(maxIt - counts.x); // Return the most-frequent base, so long as that base has // coverage >= min_coverage return *maxIt < opt::min_coverage ? orig_base : codeToBase(maxIt - counts.x); } /* Return the frequency of the most-common base*/ static float most_common_base_frequency(BaseCount counts) { // Calculate coverage as before unsigned coverage = accumulate(counts.x, counts.x+4, 0); // Call a consensus base unsigned *maxIt = max_element(counts.x, counts.x+4); // Return the frequency of the most-common base return float(*maxIt) / float(coverage); } typedef vector Rotations; // Find all overlaps with the given focal read and call a consensus sequence static string find_complex_overlap(const RotatedRead& f, const Rotations& r, vector& rl) { // A vector for tracking all the overlaps, seeded with the initial read vector o; o.push_back(Overlap(f.seq, 0)); // The pre-pended string to use to seed the search const string& seq1 = '$' + f.seq; //Find it in the sorted list - NOTE: if the flank read doesn't correspond // to a real read, this iterator will not be used Rotations::const_iterator rt = lower_bound(r.begin(), r.end(), seq1); /* Continue down the sorted list, checking for other matches - for real reads (seq1 == rt->seq), continue from the position of seq1 in the list - otherwise, just start at the beginning */ for(Rotations::const_iterator st = (seq1 == rt->seq) ? rt+1 : r.begin(); st != r.end(); ++st) { // Check for an overlap between the two sequences, // allowing for mismatches const string& seq2 = st->seq; unsigned new_overlap = tier_overlap(seq1, seq2, true); // Continue if there's no match if (new_overlap == 0 || new_overlap > opt::max_overlap) continue; // Add a new overlap object for each appropriate overlap found o.push_back(Overlap( original_read_from_rotated_read(seq2), new_overlap)); } // Counters for calculating coverage // Vector size should be something like "read_length + maximum tier" // THIS WILL BREAK WITH LONGER READS vector counts(300); // Pretty-print the alignment for verbose only if(opt::verbose){ cerr << endl; sort(o.begin(), o.end(), offset_sort); } // Go through each overlap to count bases offset by the appropriate amount for(vector::const_iterator ot = o.begin(); ot != o.end(); ++ot){ // Pretty-print each found read aligned with the focal read if (opt::verbose) cerr << string(ot->offset, ' ') << ot->seq << " t:" << ot->offset; // Retrieve the original RotatedRead object to get the // count for each read vector::const_iterator rt = lower_bound( rl.begin(), rl.end(), ot->seq); if(opt::verbose){cerr << " x" << rt->count << " used: " << rt->used << endl;} // Continue if we've marked this read as used already if(rt->used == true){ continue; } // Increment the coverage lists appropriately for (size_t i = 0; i < opt::read_length; ++i){ if ((ot->seq[i] == 'X') || (ot->seq[i] == 'N')){ continue; } counts[i+ot->offset].x[baseToCode(ot->seq[i])] += rt->count; } } // Call consensus bases until we run out of coverage ostringstream new_contig; char new_base = '*'; float current_consensus_freq = 1.0; float next_consensus_freq = 1.0; for (unsigned i = 0; new_base != 'X'; i++) { // Retrieve the original base, or 'X' if we're past the end // of the original flank char orig_base = i < opt::read_length ? f.seq[i] : 'X'; // Call a new consensus base if possible new_base = call_consensus_base(counts[i], orig_base); // Check the frequency of the most-common base current_consensus_freq = most_common_base_frequency(counts[i]); next_consensus_freq = most_common_base_frequency(counts[i+1]); //cerr << "Current: " << current_consensus_freq << " Next: " << next_consensus_freq << endl; // Bail out if we encounter two SNPs in a row // Set the current base to 'X' and trim the last one if ((current_consensus_freq <= 0.8) && (next_consensus_freq <= 0.8)) new_base = 'X'; // If we've found a new base, add it to the growing consensus if (new_base != 'X') new_contig << new_base; } if (opt::verbose) cerr << new_contig.str() << " (consensus) " << endl; // Mark reads that shouldn't be used again unsigned growth = new_contig.str().size() - opt::read_length; for(vector::const_iterator ot = o.begin(); ot != o.end(); ++ot){ // Reads are used if they don't extend to the end of the consensus if (ot->offset <= (growth-1)){ //Find the correct RotatedRead object and mark it as used vector::iterator rt = lower_bound( rl.begin(), rl.end(), ot->seq); if(rt->seq == ot->seq) rt->used = true; } } /*The sequence returned here contains the original focal read plus any extension The main routine is responsible for trimming back the growing contig */ return new_contig.str(); } // Calculate the tier overlap between two reads static int tier_overlap(const string& seq1, const string& seq2, bool allow_mismatch) { assert(seq1 != seq2); //Find the position of the '$' character in both reads unsigned first_dollar_pos = seq1.find('$'); unsigned second_dollar_pos = seq2.find('$'); unsigned earliest_dollar_pos = first_dollar_pos <= second_dollar_pos ? first_dollar_pos : second_dollar_pos; unsigned latest_dollar_pos = first_dollar_pos > second_dollar_pos ? first_dollar_pos : second_dollar_pos; //If the two strings are equal outside the dollar signs, // return the tier - this is a no-mismatch overlap if( (seq1.substr(0, earliest_dollar_pos) == seq2.substr(0, earliest_dollar_pos)) && (seq1.substr(latest_dollar_pos+1, (opt::read_length+1)-latest_dollar_pos+1) == seq2.substr(latest_dollar_pos+1, (opt::read_length+1)-latest_dollar_pos+1)) ){ return latest_dollar_pos - earliest_dollar_pos; } //Otherwise, if mismatches are allowed, calculate that overlap if (allow_mismatch){ unsigned num_mismatch = 0; for(unsigned i = 0; i < (opt::read_length+1); ++i) { if ((i >= earliest_dollar_pos) && (i <= latest_dollar_pos)){ continue; }else if (seq1[i] != seq2[i]){ num_mismatch++; } } //NOTE: this is also checking that the second read is // DOWNSTREAM from the first if ((num_mismatch <= opt::max_mismatch) && (second_dollar_pos > first_dollar_pos)){ return latest_dollar_pos - earliest_dollar_pos; } } //Otherwise... // NOTE: we're currently defining both "no overlap" // and "no offset but mismatches" as "0" // ==> This could probably be changed return 0; } // From a sorted list of RotatedRead objects, generate a sorted // vector of Rotation objects // This function generates the main vector we traverse when looking // for simple extensions static Rotations generate_rotations_list( const vector& read_list) { // Each rotation has a sequence (string) and overlap (int) // The overlap refers to the overlap between the current sequence // and the next sequence in the list Rotations s; // For each distinct read, add all the rotations to the overlap list for (vector::const_iterator it = read_list.begin(); it != read_list.end(); ++it) for(vector::size_type i = 0; i != (*it).rotations.size(); ++i) // Initialize object with sequence s.push_back(Rotation((*it).rotations[i])); // Sort the list of rotated reads sort(s.begin(), s.end()); // Find the 0-mismatch tier overlap between each pair of reads // in the sorted list for (Rotations::iterator rt = s.begin(); rt != s.end()-1; ++rt) rt->overlap = tier_overlap(rt->seq, rt[1].seq); // Define last entry in the list as 0 s[s.size()-1].overlap = 0; return s; } // Main control flow function int main(int argc, char** argv) { // Parse command-line options bool die = false; for (int c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;) { istringstream arg(optarg != NULL ? optarg : ""); switch (c) { case '?': die = true; break; case 'o': arg >> opt::max_overlap; break; case 'm': arg >> opt::max_mismatch; break; case 'c': arg >> opt::min_coverage; break; case 'r': arg >> opt::read_length; break; case 'v': opt::verbose++; break; case OPT_HELP: cout << USAGE_MESSAGE; exit(EXIT_SUCCESS); case OPT_VERSION: cout << VERSION_MESSAGE; exit(EXIT_SUCCESS); } } if (argc - optind < 1) { cerr << PROGRAM ": missing arguments\n"; die = true; } else if (argc - optind > 1) { cerr << PROGRAM ": too many arguments\n"; die = true; } else if (opt::max_overlap > (opt::read_length-1)){ cerr << PROGRAM ": max_overlap cannot be larger than (read_length-1)\n"; die = true; } if (die) { cerr << "Try `" << PROGRAM << " --help' for more information.\n"; exit(1); } const char* fasta_file = argv[optind++]; if(opt::verbose){ cerr << PROGRAM << "\n max_overlap: " << opt::max_overlap << "\n max_mismatch: " << opt::max_mismatch << "\n min_coverage: " << opt::min_coverage << "\n read_length: " << opt::read_length << endl; } // Use the ABySS FastaReader class to read in a fasta file of reads // Assume the first read in the file is the seed for the assembly if(opt::verbose){cerr << "Reading `" << fasta_file << "'... ";} typedef unordered_map ReadMap; ReadMap read_map; bool first_read = true; string contig; FastaReader in(fasta_file, FastaReader::FOLD_CASE); for (FastaRecord rec; in >> rec;) { string read_seq = rec.seq; if (first_read){ contig = read_seq; first_read = false; } // Count the reads as we collect them here... read_map[read_seq]++; } vector read_list; // ... Then put them into the vector of RotatedRead objects for (ReadMap::iterator i = read_map.begin(); i != read_map.end(); ++i) read_list.push_back(RotatedRead(i->first, i->second)); read_map.clear(); sort(read_list.begin(), read_list.end()); if(opt::verbose){cerr << "finished reading fasta file with " << read_list.size() << " distinct reads.\n\n" << endl;} // Generate the sorted lists Rotations rotation_list = generate_rotations_list(read_list); // Main assembly loop if(opt::verbose){cerr << contig << " (seed)" << endl;} bool time_to_die = false; int hard_cap = 0; while(! time_to_die){ // Temporary hard-cap to prevent runaway execution hard_cap++; if (hard_cap >= 500){ time_to_die = true; //cerr << "Hard cap hit - I give up!" << endl; //cerr << contig.size(); // cout << ">contig (" << contig.size() << "bp)" << endl // << contig << endl; //cout << contig.size(); cout << contig << endl; exit(1); } // Another break if the contig grows too long if (contig.size() >= 1500){ //cerr << contig.size(); cout << contig << endl; exit(1); } // Extract the flanking sequence and fetch rotations of that read string flank = contig.substr(contig.size()-opt::read_length); // Retrieve the flanking read vector::iterator low = lower_bound( read_list.begin(), read_list.end(), flank); //TODO - This search sometimes causes a segfault at higher -o values // Figure out why! RotatedRead flank_read = (*low); // If the flank sequence doesn't correspond to a real read: // - generate a temporary RotatedRead object for the complex search if (flank != flank_read.seq){ if (opt::verbose) cerr << "Flank doesn't correspond to a real read" << endl; flank_read = RotatedRead(flank, 1); } bool found_complex_overlap = false; string read_to_add; string extension_seq = find_complex_overlap( flank_read, rotation_list, read_list); if (! (extension_seq == flank_read.seq)){ found_complex_overlap = true; // The new contig = old contig - flank read + extension sequence // (the extension sequence contains the flank read) contig = contig.substr(0, contig.size()-opt::read_length) + extension_seq; // This is very verbose - prints out a fasta sequence for each // step of the assembly process if(opt::verbose){ cout << ">p" << opt::max_overlap << "_" << contig.size() << "bp_complex\n" << contig << endl; } } // If the search fails, stop extension if (! found_complex_overlap){ time_to_die = true; } } // Output the final contig cout << contig << endl; return 0; } abyss-1.3.6/DAssembler/RotatedRead.cpp000644 002433 001057 00000001043 12015543262 021300 0ustar00traymondassembly000000 000000 #include #include "RotatedRead.h" #include "Sequence.h" using namespace std; //Constructor RotatedRead::RotatedRead(const string& orig_seq, unsigned count) : seq(orig_seq), count(count) { // Add all rotations of the read to the object string appended_seq = orig_seq + '$'; used = false; for(unsigned int i = 0; i < appended_seq.size(); ++i) { string rotated_read = appended_seq.substr(i,(appended_seq.size()-i)) + appended_seq.substr(0,i); rotations.push_back(rotated_read); } } abyss-1.3.6/DAssembler/RotatedRead.h000644 002433 001057 00000001005 12015543262 020743 0ustar00traymondassembly000000 000000 #ifndef ROTATEDREAD_H #define ROTATEDREAD_H 1 #include #include class RotatedRead{ public: RotatedRead(const std::string& orig_seq, unsigned count = 1); bool operator <(const RotatedRead& x) const { return seq < x.seq; } bool operator ==(const RotatedRead& x) const { return seq == x.seq; } std::string seq; std::vector rotations; unsigned count; bool used; }; #endif //ROTATEDREAD_H abyss-1.3.6/DAssembler/Rotation.h000644 002433 001057 00000000741 12015543262 020352 0ustar00traymondassembly000000 000000 #ifndef ROTATION_H #define ROTATION_H 1 #include #include using namespace std; class Rotation { public: Rotation(const string& orig_seq) : seq(orig_seq), overlap(0) { } bool operator <(const Rotation& x) const { return seq < x.seq; 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#define PROGRAM "Consensus" static const char VERSION_MESSAGE[] = PROGRAM " (" PACKAGE_NAME ") " VERSION "\n" "Written by Tony Raymond and Shaun Jackman.\n" "\n" "Copyright 2013 Canada's Michael Smith Genome Science Centre\n"; static const char USAGE_MESSAGE[] = "Usage: " PROGRAM " [OPTION]... CONTIG\n" "\n" "Read alignments from KAligner from standard input.\n" "Ensure that the --seq option was used when running KAligner.\n" "Call a consensus at each position of each contig and write the\n" "consensus in FASTA format to OUTPUT.\n" "\n" " Arguments:\n" "\n" " CONTIG contigs in FASTA format\n" "\n" " Options:\n" "\n" " -o, --out=OUTPUT write the output FASTA file to OUTPUT\n" " -p, --pileup=PILEUP write the pileup to PILEUP\n" " --nt output nucleotide contigs [default]\n" " --cs output colour-space contigs\n" " -V, --variants print only variants in the pileup\n" " -v, --verbose display verbose output\n" " --help display this help and exit\n" " --version output version information and exit\n" "\n" "Report bugs to <" PACKAGE_BUGREPORT ">.\n"; namespace opt { static string outPath; static string pileupPath; static bool csToNt; static int outputCS; static int onlyVariants; } static const char shortopts[] = "o:p:vV"; enum { OPT_HELP = 1, OPT_VERSION }; static const struct option longopts[] = { { "verbose", no_argument, NULL, 'v' }, { "out", required_argument, NULL, 'o' }, { "pileup", required_argument, NULL, 'p' }, { "variants", no_argument, &opt::onlyVariants, 1 }, { "nt", no_argument, &opt::outputCS, 0 }, { "cs", no_argument, &opt::outputCS, 1 }, { "help", no_argument, NULL, OPT_HELP }, { "version", no_argument, NULL, OPT_VERSION }, { NULL, 0, NULL, 0 } }; struct BaseCount { unsigned count[4]; BaseCount() { fill(count, count + 4, 0); } /** Return the number of reads at this position. */ unsigned sum() const { return accumulate(count, count+4, 0); } friend ostream& operator <<(ostream& out, const BaseCount& base) { out << base.count[0]; for (int x = 1; x < 4; x++) out << '\t' << base.count[x]; return out; } }; typedef vector BaseCounts; struct ContigCount { Sequence seq; unsigned coverage; string comment; BaseCounts counts; }; /** A map of contigs. The alignments reference the contig by name. */ typedef unordered_map ContigMap; static ContigMap g_contigs; /** Read all contigs in and store the contigs in g_contigs and make a * g_baseCounts, to store pile-up for each base. */ static void readContigs(const string& contigsPath) { FastaReader contigsFile(contigsPath.c_str(), FastaReader::NO_FOLD_CASE); int count = 0; for (FastaRecord rec; contigsFile >> rec;) { const Sequence& seq = rec.seq; ContigCount& contig = g_contigs[rec.id]; contig.seq = seq; istringstream ss(rec.comment); unsigned length; contig.coverage = 0; ss >> length >> contig.coverage >> ws; getline(ss, contig.comment); if (count == 0) { // Detect colour-space contigs. opt::colourSpace = isdigit(seq[0]); if (!opt::outputCS) opt::csToNt = opt::colourSpace; else if (!opt::colourSpace) { cerr << "error: Cannot convert nucleotide data to " "colour space.\n"; exit(EXIT_FAILURE); } } else { if (opt::colourSpace) assert(isdigit(seq[0])); else assert(isalpha(seq[0])); } contig.counts = BaseCounts(contig.seq.length() + (opt::csToNt ? 1 : 0)); count++; } cerr << "Read " << count << " contigs\n"; assert(contigsFile.eof()); assert(count > 0); } typedef vector AlignmentVector; static void readAlignment(string& line, string& readID, Sequence& seq, AlignmentVector& alignments) { char anchor; istringstream s(line); if (opt::colourSpace || opt::csToNt) s >> readID >> anchor >> seq; else s >> readID >> seq; Alignment alignment; while (s >> alignment) alignments.push_back(alignment); if (!alignments.empty() && opt::csToNt && seq.find_first_not_of("0123") == string::npos) seq = colourToNucleotideSpace(anchor, seq); } /** Builds the pile up of all reads based on the alignments and * read sequence */ static void buildBaseQuality() { if (opt::csToNt) opt::colourSpace = false; // for each read and/or set of alignments. for (string line; getline(cin, line);) { string readID; Sequence seq; AlignmentVector alignments; readAlignment(line, readID, seq, alignments); // If converting to NT space, check that at least one of the // alignments starts at read location 0. Otherwise, it is // likely to introduce a frameshift or erroneous sequence in // the final consensus. if (opt::csToNt) { bool good = false; for (AlignmentVector::const_iterator alignIter = alignments.begin(); alignIter != alignments.end(); ++alignIter) { if (alignIter->read_start_pos == 0) { good = true; break; } } if (!good) continue; } // For each alignment for the read. for (AlignmentVector::const_iterator alignIter = alignments.begin(); alignIter != alignments.end(); ++alignIter) { string seqrc; Alignment a; if (alignIter->isRC) { seqrc = reverseComplement(seq); a = alignIter->flipQuery(); } else { seqrc = seq; a = *alignIter; } const char* s = seqrc.c_str(); ContigMap::iterator contigIt = g_contigs.find(a.contig); if (contigIt == g_contigs.end()) { cerr << "error: unexpected contig ID: `" << a.contig << "'\n"; exit(EXIT_FAILURE); } BaseCounts& countsVec = contigIt->second.counts; int read_min; int read_max; if (!opt::csToNt) { read_min = a.read_start_pos - a.contig_start_pos; read_min = read_min > 0 ? read_min : 0; read_max = a.read_start_pos + countsVec.size() - a.contig_start_pos; read_max = read_max < a.read_length ? read_max : a.read_length; } else { read_min = a.read_start_pos; read_max = read_min + a.align_length + 1; } if ((int)countsVec.size() < a.contig_start_pos - a.read_start_pos + read_max - 1) cerr << countsVec.size() << '\n'; // Assertions to make sure alignment math was done right. assert((int)countsVec.size() >= a.contig_start_pos - a.read_start_pos + read_max - 1); assert(read_max <= (int)seq.length()); assert(read_min >= 0); // Pile-up every base in the read to the contig. for (int x = read_min; x < read_max; x++) { char c = toupper(s[x]); switch (c) { case 'A': case 'C': case 'G': case 'T': case '0': case '1': case '2': case '3': unsigned pos = a.contig_start_pos - a.read_start_pos + x; assert(pos < countsVec.size()); countsVec[pos].count[baseToCode(c)]++; } } } } } /** Returns the most likely base found by the pile up count. */ static char selectBase(const BaseCount& count, unsigned& sumBest, unsigned& sumSecond) { int bestBase = -1; unsigned bestCount = 0; unsigned secondCount = 0; for (int x = 0; x < 4; x++) { if (count.count[x] > bestCount) { bestBase = x; secondCount = bestCount; bestCount = count.count[x]; } } sumBest += bestCount; sumSecond += secondCount; if (bestBase == -1) return 'N'; return codeToBase(bestBase); } /** Convert all 'N' bases to nt's based on local information. */ static void fixUnknown(Sequence& ntSeq, const Sequence& csSeq ) { size_t index = ntSeq.find_first_of('N'); size_t rindex = ntSeq.find_last_of('N'); char base; #if 0 if (index == 0) { #if 0 for (index = ntSeq.find_first_of("ACGT"); index > 0; index--) #endif index = ntSeq.find_first_of("ACGT"); while (index != 0) { base = colourToNucleotideSpace(ntSeq.at(index), csSeq.at(index - 1)); ntSeq.replace(index - 1, 1, 1, base); //ntSeq[index-1] = base; index = ntSeq.find_first_of("ACGT"); } index = ntSeq.find_first_of('N'); } #endif if (index == 0 || rindex == ntSeq.length() - 1) { ntSeq = ntSeq.substr(ntSeq.find_first_of("ACGT"), ntSeq.find_last_of("ACGT") - ntSeq.find_first_of("ACGT") + 1); index = ntSeq.find_first_of('N'); } while (index != string::npos) { // If the base isn't the first or last base in the seq... base = colourToNucleotideSpace(ntSeq.at(index - 1), csSeq.at(index - 1)); ntSeq.replace(index, 1, 1, base); index = ntSeq.find_first_of('N'); } } static void writePileup(ostream& out, const string &id, unsigned pos, char refc, char genotype, const BaseCount& counts) { char foldrefc = toupper(refc); if (opt::onlyVariants && foldrefc == genotype) return; out << id << '\t' // reference sequence name << 1 + pos << '\t' // reference coordinate << refc << '\t' // reference base << genotype << '\t' // genotype << "25\t" // P(genotype is wrong) << "25\t" // P(genotype is the same as the reference) << "25\t" // RMS mapping quality << counts.sum() << '\t'; // number of reads switch (foldrefc) { case 'A': case 'C': case 'G': case 'T': case '0': case '1': case '2': case '3': { uint8_t ref = baseToCode(foldrefc); for (int i = 0; i < 4; i++) if (i != ref) out << string(counts.count[i], codeToBase(i)); out << string(counts.count[ref], '.'); break; } default: for (int i = 0; i < 4; i++) out << string(counts.count[i], codeToBase(i)); } out << '\n'; assert(out.good()); } /** Forms contigs based on the consensus of each base and outputs them * to the file specified by the -o option. */ static void consensus(const string& outPath, const string& pileupPath) { ofstream outFile(outPath.c_str()); assert_good(outFile, outPath); ofstream pileupFile; ostream& pileupOut = pileupPath.empty() || pileupPath == "-" ? cout : (pileupFile.open(pileupPath.c_str()), pileupFile); assert_good(pileupOut, pileupPath); unsigned numIgnored = 0; for (ContigMap::const_iterator it = g_contigs.begin(); it != g_contigs.end(); ++it) { const ContigCount& contig = it->second; unsigned seqLength = it->second.counts.size(); Sequence outSeq(seqLength, 'N'); unsigned sumBest = 0; unsigned sumSecond = 0; for (unsigned x = 0; x < seqLength; x++) { char c = selectBase( it->second.counts[x], sumBest, sumSecond); outSeq[x] = islower(contig.seq[x]) ? tolower(c) : c; } if (outSeq.find_first_of("ACGT") != string::npos) { // Check that the average percent agreement was enough to // write the contig to file. float percentAgreement = sumBest / (float)(sumBest + sumSecond); if (isnan(percentAgreement) || percentAgreement < .9) { numIgnored++; if (opt::csToNt) { if (opt::verbose > 0) cerr << "warning: Contig " << it->first << " has less than 90% agreement " "and will not be converted.\n"; } else continue; } else { if (opt::csToNt) fixUnknown(outSeq, contig.seq); ostringstream comment; comment << outSeq.length() << ' ' << contig.coverage; if (!contig.comment.empty()) comment << ' ' << contig.comment; outFile << FastaRecord( it->first, comment.str(), outSeq); assert(outFile.good()); } if (opt::verbose > 1) { // ID pos reference genotype A C G T if (opt::csToNt) for (unsigned i = 0; i < seqLength - 1; i++) cout << it->first << '\t' << 1+i << '\t' << contig.seq[i] << '\t' << nucleotideToColourSpace( outSeq[i], outSeq[i + 1]) << '\t' << contig.counts[i].sum() << '\t' << contig.counts[i] << '\n'; else for (unsigned i = 0; i < seqLength; i++) cout << it->first << '\t' << 1+i << '\t' << contig.seq[i] << '\t' << outSeq[i] << '\t' << contig.counts[i].sum() << '\t' << contig.counts[i] << '\n'; } if (!pileupPath.empty()) { if (opt::csToNt) for (unsigned i = 0; i < seqLength-1; i++) writePileup(pileupOut, it->first, i, contig.seq[i], nucleotideToColourSpace( outSeq[i], outSeq[i+1]), contig.counts[i]); else for (unsigned i = 0; i < seqLength; i++) writePileup(pileupOut, it->first, i, contig.seq[i], outSeq[i], contig.counts[i]); } } else if (opt::verbose > 0) { cerr << "warning: Contig " << it->first << " was not supported by a complete read " "and was ommited.\n"; } } } int main(int argc, char** argv) { bool die = false; for (int c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;) { istringstream arg(optarg != NULL ? optarg : ""); switch (c) { case '?': die = true; break; case 'v': opt::verbose++; break; case 'o': arg >> opt::outPath; break; case 'p': arg >> opt::pileupPath; 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#define PROGRAM "AdjList" static const char VERSION_MESSAGE[] = PROGRAM " (" PACKAGE_NAME ") " VERSION "\n" "Written by Shaun Jackman.\n" "\n" "Copyright 2013 Canada's Michael Smith Genome Science Centre\n"; static const char USAGE_MESSAGE[] = "Usage: " PROGRAM " [OPTION]... [FILE]...\n" "Find overlaps of [m,k) bases. Contigs may be read from FILE(s)\n" "or standard input. Output is written to standard output.\n" "Overlaps of exactly k-1 bases are found using a hash table.\n" "Overlaps of fewer than k-1 bases are found using a suffix array.\n" "\n" " Options:\n" "\n" " -k, --kmer=K find overlaps of up to K-1 bases\n" " -m, --min-overlap=M require a minimum overlap of M bases [50]\n" " --adj output the results in adj format [default]\n" " --dot output the results in dot format\n" " --sam output the results in SAM format\n" " -v, --verbose display verbose output\n" " --help display this help and exit\n" " --version output version information and exit\n" "\n" "Report bugs to <" PACKAGE_BUGREPORT ">.\n"; namespace opt { unsigned k; // used by GraphIO int format; // used by GraphIO /** The minimum required amount of overlap. */ static unsigned minOverlap = 50; } static const char shortopts[] = "k:m:v"; enum { OPT_HELP = 1, OPT_VERSION }; static const struct option longopts[] = { { "kmer", required_argument, NULL, 'k' }, { "min-overlap", required_argument, NULL, 'm' }, { "adj", no_argument, &opt::format, ADJ }, { "dot", no_argument, &opt::format, DOT }, { "sam", no_argument, &opt::format, SAM }, { "verbose", no_argument, NULL, 'v' }, { "help", no_argument, NULL, OPT_HELP }, { "version", no_argument, NULL, OPT_VERSION }, { NULL, 0, NULL, 0 } }; /** A contig adjacency graph. */ typedef DirectedGraph DG; typedef ContigGraph Graph; /** Parse and return the coverage from the specified FASTA comment. */ static unsigned getCoverage(const string& comment) { istringstream ss(comment); unsigned length, coverage = 0; ss >> length >> coverage; return coverage; } /** Add the overlaps of vseq to the graph. */ static void addOverlapsSA(Graph& g, const SuffixArray& sa, ContigNode v, const string& vseq) { assert(!vseq.empty()); set seen; typedef SuffixArray::const_iterator It; for (string q(vseq, 0, vseq.size() - 1); q.size() >= opt::minOverlap; chop(q)) { pair range = sa.equal_range(q); for (It it = range.first; it != range.second; ++it) { ContigNode u(it->second); if (seen.insert(u).second) { // Add the longest overlap between two vertices. unsigned overlap = it->first.size(); add_edge(u, v, -overlap, static_cast(g)); } } } } /** Add overlaps of fewer than k-1 bp to the graph. */ static void addOverlapsSA(Graph& g, const vector& prefixes) { // Construct a suffix array of the blunt contigs. typedef pair Suffix; typedef vector Suffixes; Suffixes suffixes; SuffixArray sa(opt::minOverlap); typedef graph_traits::vertex_descriptor V; typedef graph_traits::vertex_iterator Vit; pair vertices = g.vertices(); for (Vit it = vertices.first; it != vertices.second; ++it) { ContigNode u(*it); if (out_degree(u, g) > 0) continue; size_t uci = get(vertex_index, g, get(vertex_complement, g, u)); assert(uci < prefixes.size()); string suffix(reverseComplement(prefixes[uci]).str()); suffixes.push_back(Suffix(suffix, u)); sa.insert(suffixes.back()); } sa.construct(); for (Suffixes::const_iterator it = suffixes.begin(); it != suffixes.end(); ++it) { V uc = get(vertex_complement, g, it->second); addOverlapsSA(g, sa, uc, reverseComplement(it->first)); } } /** An index of suffixes of k-1 bp. */ typedef unordered_map, hashKmer> SuffixMap; /** Read contigs. Add contig properties to the graph. Add prefixes to * the collection and add suffixes to their index. */ static void readContigs(const string& path, Graph& g, vector& prefixes, SuffixMap& suffixMap) { if (opt::verbose > 0) cerr << "Reading `" << path << "'...\n"; unsigned count = 0; FastaReader in(path.c_str(), FastaReader::FOLD_CASE); for (FastaRecord rec; in >> rec;) { const Sequence& seq = rec.seq; if (count++ == 0) { // Detect colour-space contigs. opt::colourSpace = isdigit(seq[0]); } else { if (opt::colourSpace) assert(isdigit(seq[0])); else assert(isalpha(seq[0])); } // Add the prefix to the collection. unsigned overlap = opt::k - 1; assert(seq.length() > overlap); Kmer prefix(seq.substr(0, overlap)); Kmer suffix(seq.substr(seq.length() - overlap)); prefixes.push_back(prefix); prefixes.push_back(reverseComplement(suffix)); // Add the suffix to the index. ContigProperties vp(seq.length(), getCoverage(rec.comment)); ContigNode u = add_vertex(vp, g); put(vertex_name, g, u, rec.id); suffixMap[suffix].push_back(u); suffixMap[reverseComplement(prefix)].push_back( get(vertex_complement, g, u)); } assert(in.eof()); } int main(int argc, char** argv) { string commandLine; { ostringstream ss; char** last = argv + argc - 1; copy(argv, last, ostream_iterator(ss, " ")); ss << *last; commandLine = ss.str(); } bool die = false; for (int c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;) { istringstream arg(optarg != NULL ? optarg : ""); switch (c) { case '?': die = true; break; case 'k': arg >> opt::k; break; case 'm': arg >> opt::minOverlap; break; case 'v': opt::verbose++; break; case OPT_HELP: cout << USAGE_MESSAGE; exit(EXIT_SUCCESS); case OPT_VERSION: cout << VERSION_MESSAGE; exit(EXIT_SUCCESS); } if (optarg != NULL && !arg.eof()) { cerr << PROGRAM ": invalid option: `-" << (char)c << optarg << "'\n"; exit(EXIT_FAILURE); } } if (opt::k <= 0) { cerr << PROGRAM ": " << "missing -k,--kmer option\n"; die = true; } if (die) { cerr << "Try `" << PROGRAM << " --help' for more information.\n"; exit(EXIT_FAILURE); } if (opt::minOverlap == 0) opt::minOverlap = opt::k - 1; opt::minOverlap = min(opt::minOverlap, opt::k - 1); opt::trimMasked = false; Kmer::setLength(opt::k - 1); Graph g; vector prefixes; SuffixMap suffixMap(prefixes.size()); if (optind < argc) { for (; optind < argc; optind++) readContigs(argv[optind], g, prefixes, suffixMap); } else readContigs("-", g, prefixes, suffixMap); g_contigNames.lock(); // Add the overlap edges of exactly k-1 bp. typedef graph_traits::vertex_descriptor V; if (opt::verbose > 0) cerr << "Finding overlaps of exactly k-1 bp...\n"; for (vector::const_iterator it = prefixes.begin(); it != prefixes.end(); ++it) { ContigNode v(it - prefixes.begin()); const SuffixMap::mapped_type& edges = suffixMap[*it]; for (SuffixMap::mapped_type::const_iterator itu = edges.begin(); itu != edges.end(); ++itu) { V uc = get(vertex_complement, g, *itu); V vc = get(vertex_complement, g, v); 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/** Execute a shell command and check its return status. */ static void systemx(const string& command) { if (opt::verbose > 0) cout << command << endl; int ret = system(command.c_str()); if (ret == 0) return; cerr << "error: command failed: `" << command << "'\n"; if (ret == -1) cerr << "system() failed: " << strerror(errno) << endl; exit(ret == -1 ? EXIT_FAILURE : ret); } /** Concatenate files using the specified command and remove them. */ static void concatenateFiles(const string& dest, const string& prefix, const string& suffix, const string& command = "cat") { cout << "Concatenating to " << dest << endl; ostringstream s; s << command; for (int i = 0; i < opt::numProc; i++) s << ' ' << prefix << i << suffix; s << " >'" << dest << '\''; systemx(s.str()); bool die = false; for (int i = 0; i < opt::numProc; i++) { s.str(""); s << prefix << i << suffix; const char* path = s.str().c_str(); if (unlink(path) == -1) { cerr << "error: removing `" << path << "': " << strerror(errno) << endl; die = true; } } if (die) exit(EXIT_FAILURE); } int main(int argc, char** argv) { Timer timer("Total"); // Set stdout to be line buffered. setvbuf(stdout, NULL, _IOLBF, 0); MPI_Init(&argc,&argv); MPI_Comm_rank(MPI_COMM_WORLD, &opt::rank); MPI_Comm_size(MPI_COMM_WORLD, &opt::numProc); // OMPI-1.6.1 and later reset the SIGCHLD handler so we need to // reinitialize uncompress. uncompress_init(); opt::parse(argc, argv); if (opt::rank == 0) cout << "Running on " << opt::numProc << " processors\n"; MPI_Barrier(MPI_COMM_WORLD); char hostname[HOST_NAME_MAX]; gethostname(hostname, sizeof hostname); logger(0) << "Running on host " << hostname << endl; MPI_Barrier(MPI_COMM_WORLD); if (opt::rank == 0) { NetworkSequenceCollection networkSeqs; networkSeqs.runControl(); } else { NetworkSequenceCollection networkSeqs; networkSeqs.run(); } MPI_Barrier(MPI_COMM_WORLD); MPI_Finalize(); if (opt::rank == 0) { concatenateFiles(opt::contigsPath, "contigs-", ".fa", "awk '/^>/ { $1=\">\" i++ } { print }'"); if (!opt::snpPath.empty()) concatenateFiles(opt::snpPath, "snp-", ".fa"); cout << "Done." << endl; } return 0; } abyss-1.3.6/Parallel/CommLayer.cpp000644 002433 001057 00000015355 12104026027 020512 0ustar00traymondassembly000000 000000 #include "config.h" #include "CommLayer.h" #include "Common/Options.h" #include "Log.h" #include "MessageBuffer.h" #include #include #include using namespace std; static const unsigned RX_BUFSIZE = 16*1024; CommLayer::CommLayer() : m_msgID(0), m_rxBuffer(new uint8_t[RX_BUFSIZE]), m_request(MPI_REQUEST_NULL), m_rxPackets(0), m_rxMessages(0), m_rxBytes(0), m_txPackets(0), m_txMessages(0), m_txBytes(0) { assert(m_request == MPI_REQUEST_NULL); MPI_Irecv(m_rxBuffer, RX_BUFSIZE, MPI_BYTE, MPI_ANY_SOURCE, MPI_ANY_TAG, MPI_COMM_WORLD, &m_request); } CommLayer::~CommLayer() { MPI_Cancel(&m_request); delete[] m_rxBuffer; logger(1) << "Sent " << m_msgID << " control, " << m_txPackets << " packets, " << m_txMessages << " messages, " << m_txBytes << " bytes. " << "Received " << m_rxPackets << " packets, " << m_rxMessages << " messages, " << m_rxBytes << " bytes.\n"; } /** Return the status of an MPI request. * Wraps MPI_Request_get_status. */ static bool request_get_status(const MPI_Request& req, MPI_Status& status) { int flag; MPI_Request_get_status(req, &flag, &status); // Work around a bug present in Open MPI 1.3.3 and earlier. // MPI_Request_get_status may return false on the first call even // though a message is waiting. The second call should work. if (!flag) MPI_Request_get_status(req, &flag, &status); return flag; } /** Return the tag of the received message or APM_NONE if no message * has been received. If a message has been received, this call should * be followed by a call to either ReceiveControlMessage or * ReceiveBufferedMessage. */ APMessage CommLayer::checkMessage(int& sendID) { MPI_Status status; bool flag = request_get_status(m_request, status); if (flag) sendID = status.MPI_SOURCE; return flag ? (APMessage)status.MPI_TAG : APM_NONE; } /** Return true if no message has been received. */ bool CommLayer::receiveEmpty() { MPI_Status status; return !request_get_status(m_request, status); } /** Block until all processes have reached this routine. */ void CommLayer::barrier() { logger(4) << "entering barrier\n"; MPI_Barrier(MPI_COMM_WORLD); logger(4) << "left barrier\n"; } /** Broadcast a message. */ void CommLayer::broadcast(int message) { assert(opt::rank == 0); MPI_Bcast(&message, 1, MPI_INT, 0, MPI_COMM_WORLD); barrier(); } /** Receive a broadcast message. */ int CommLayer::receiveBroadcast() { assert(opt::rank != 0); int message; MPI_Bcast(&message, 1, MPI_INT, 0, MPI_COMM_WORLD); barrier(); return message; } /** Block until all processes have reached this routine. * @return the sum of count from all processors */ long long unsigned CommLayer::reduce(long long unsigned count) { logger(4) << "entering reduce: " << count << '\n'; long long unsigned sum; MPI_Allreduce(&count, &sum, 1, MPI_UNSIGNED_LONG_LONG, MPI_SUM, MPI_COMM_WORLD); logger(4) << "left reduce: " << sum << '\n'; return sum; } /** Reduce the specified vector. */ vector CommLayer::reduce(const vector& v) { logger(4) << "entering reduce\n"; vector sum(v.size()); MPI_Allreduce(const_cast(&v[0]), &sum[0], v.size(), MPI_UNSIGNED, MPI_SUM, MPI_COMM_WORLD); logger(4) << "left reduce\n"; return sum; } /** Reduce the specified vector. */ vector CommLayer::reduce( const vector& v) { logger(4) << "entering reduce\n"; vector sum(v.size()); MPI_Allreduce(const_cast(&v[0]), &sum[0], v.size(), MPI_UNSIGNED_LONG, MPI_SUM, MPI_COMM_WORLD); logger(4) << "left reduce\n"; return sum; } uint64_t CommLayer::sendCheckPointMessage(int argument) { logger(4) << "checkpoint: " << argument << '\n'; assert(opt::rank != 0); ControlMessage msg; msg.id = m_msgID++; msg.msgType = APC_CHECKPOINT; msg.argument = argument; MPI_Send(&msg, sizeof msg, MPI_BYTE, 0, APM_CONTROL, MPI_COMM_WORLD); return msg.id; } /** Send a control message to every other process. */ void CommLayer::sendControlMessage(APControl m, int argument) { for (int i = 0; i < opt::numProc; i++) if (i != opt::rank) // Don't send the message to myself. sendControlMessageToNode(i, m, argument); } /** Send a control message to a specific node. */ uint64_t CommLayer::sendControlMessageToNode(int nodeID, APControl m, int argument) { assert(opt::rank == 0); ControlMessage msg; msg.id = m_msgID++; msg.msgType = m; msg.argument = argument; MPI_Send(&msg, sizeof msg, MPI_BYTE, nodeID, APM_CONTROL, MPI_COMM_WORLD); return msg.id; } /** Receive a control message. */ ControlMessage CommLayer::receiveControlMessage() { int flag; MPI_Status status; MPI_Test(&m_request, &flag, &status); assert(flag); assert((APMessage)status.MPI_TAG == APM_CONTROL); int count; MPI_Get_count(&status, MPI_BYTE, &count); ControlMessage msg; assert(count == sizeof msg); memcpy(&msg, m_rxBuffer, sizeof msg); assert(m_request == MPI_REQUEST_NULL); MPI_Irecv(m_rxBuffer, RX_BUFSIZE, MPI_BYTE, MPI_ANY_SOURCE, MPI_ANY_TAG, MPI_COMM_WORLD, &m_request); return msg; } /** Send a buffered collection of messages. */ void CommLayer::sendBufferedMessage(int destID, char* msg, size_t size) { MPI_Send(msg, size, MPI_BYTE, destID, APM_BUFFERED, MPI_COMM_WORLD); } /** Receive a buffered message. */ void CommLayer::receiveBufferedMessage(MessagePtrVector& outmessages) { assert(outmessages.empty()); int flag; MPI_Status status; MPI_Test(&m_request, &flag, &status); assert(flag); assert((APMessage)status.MPI_TAG == APM_BUFFERED); int size; MPI_Get_count(&status, MPI_BYTE, &size); int offset = 0; while (offset < size) { MessageType type = Message::readMessageType( (char*)m_rxBuffer + offset); Message* pNewMessage; switch(type) { case MT_ADD: pNewMessage = new SeqAddMessage(); break; case MT_REMOVE: pNewMessage = new SeqRemoveMessage(); break; case MT_SET_FLAG: pNewMessage = new SetFlagMessage(); break; case MT_REMOVE_EXT: pNewMessage = new RemoveExtensionMessage(); break; case MT_SEQ_DATA_REQUEST: pNewMessage = new SeqDataRequest(); break; case MT_SEQ_DATA_RESPONSE: pNewMessage = new SeqDataResponse(); break; case MT_SET_BASE: pNewMessage = new SetBaseMessage(); break; default: assert(false); break; } // Unserialize the new message from the buffer offset += pNewMessage->unserialize( (char*)m_rxBuffer + offset); // Constructed message will be deleted in the // NetworkSequenceCollection calling function. outmessages.push_back(pNewMessage); } assert(offset == size); assert(m_request == MPI_REQUEST_NULL); MPI_Irecv(m_rxBuffer, RX_BUFSIZE, MPI_BYTE, MPI_ANY_SOURCE, MPI_ANY_TAG, MPI_COMM_WORLD, &m_request); m_rxPackets++; m_rxMessages += outmessages.size(); m_rxBytes += size; } abyss-1.3.6/Parallel/CommLayer.h000644 002433 001057 00000004024 12015543262 020154 0ustar00traymondassembly000000 000000 #ifndef COMMLAYER_H #define COMMLAYER_H 1 #include "Messages.h" #include #include enum APMessage { APM_NONE, APM_CONTROL, APM_BUFFERED }; enum APControl { APC_SET_STATE, APC_ERODE_COMPLETE, APC_TRIM, APC_POPBUBBLE, APC_ASSEMBLE, APC_CHECKPOINT, APC_WAIT, APC_BARRIER, }; typedef std::vector MessagePtrVector; struct ControlMessage { int64_t id; APControl msgType; int argument; }; /** Interprocess communication and synchronization primitives. */ class CommLayer { public: CommLayer(); ~CommLayer(); // Check if a message exists, if it does return the type APMessage checkMessage(int &sendID); // Return whether a message has been received. bool receiveEmpty(); // Block until all processes have reached this routine. void barrier(); void broadcast(int message); int receiveBroadcast(); // Block until all processes have reached this routine. long long unsigned reduce(long long unsigned count); std::vector reduce(const std::vector& v); std::vector reduce( const std::vector& v); // Send a control message void sendControlMessage(APControl m, int argument = 0); // Send a control message to a specific node uint64_t sendControlMessageToNode(int nodeID, APControl command, int argument = 0); // Receive a control message ControlMessage receiveControlMessage(); // Send a message that the checkpoint has been reached uint64_t sendCheckPointMessage(int argument = 0); // Send a buffered message void sendBufferedMessage(int destID, char* msg, size_t size); // Receive a buffered sequence of messages void receiveBufferedMessage(MessagePtrVector& outmessages); uint64_t reduceInflight() { return reduce(m_txPackets - m_rxPackets); } private: uint64_t m_msgID; uint8_t* m_rxBuffer; MPI_Request m_request; protected: // Counters uint64_t m_rxPackets; uint64_t m_rxMessages; uint64_t m_rxBytes; uint64_t m_txPackets; uint64_t m_txMessages; uint64_t m_txBytes; }; #endif abyss-1.3.6/Parallel/NetworkSequenceCollection.cpp000644 002433 001057 00000110531 12104250114 023744 0ustar00traymondassembly000000 000000 #include "NetworkSequenceCollection.h" #include "Assembly/Options.h" #include "AssemblyAlgorithms.h" #include "Common/Options.h" #include "FastaWriter.h" #include "Histogram.h" #include "Log.h" #include "StringUtil.h" #include // for UINT_MAX #include #include #include #include using namespace std; // Don't load data into the control process when we have at least // DEDICATE_CONTROL_AT total processes. This is needed because the // control node uses a lot of memory at large NP. const int DEDICATE_CONTROL_AT = 1000; void NetworkSequenceCollection::loadSequences() { Timer timer("LoadSequences"); for (unsigned i = opt::rank; i < opt::inFiles.size(); i += opt::numProc) AssemblyAlgorithms::loadSequences(this, opt::inFiles[i]); } /** Receive, process, send, and synchronize. * @return the number of inflight messages */ size_t NetworkSequenceCollection::pumpFlushReduce() { pumpNetwork(); m_comm.flush(); return m_comm.reduceInflight(); } /** Receive packets and process them until no more work exists for any * slave processor. */ void NetworkSequenceCollection::completeOperation() { Timer timer("completeOperation"); while (pumpFlushReduce() > 0) ; assert(m_comm.transmitBufferEmpty()); // Nothing to send. m_comm.barrier(); // Synchronize. assert(m_comm.receiveEmpty()); // Nothing to receive. assert(m_comm.reduceInflight() == 0); } /** Run the assembly state machine. */ void NetworkSequenceCollection::run() { /** The number of contigs and k-mer assembled. */ pair numAssembled; ofstream bubbleFile; SetState(NAS_LOADING); while (m_state != NAS_DONE) { switch (m_state) { case NAS_LOADING: m_data.setColourSpace( m_comm.receiveBroadcast()); loadSequences(); EndState(); SetState(NAS_WAITING); m_comm.sendCheckPointMessage(); break; case NAS_LOAD_COMPLETE: { m_comm.barrier(); pumpNetwork(); logger(0) << "Loaded " << m_data.size() << " k-mer.\n"; assert(!m_data.empty()); m_data.shrink(); m_comm.reduce(m_data.size()); Histogram myh = AssemblyAlgorithms::coverageHistogram(m_data); Histogram h(m_comm.reduce(myh.toVector())); AssemblyAlgorithms::setCoverageParameters(h); EndState(); SetState(NAS_WAITING); break; } case NAS_GEN_ADJ: m_comm.barrier(); m_numBasesAdjSet = 0; AssemblyAlgorithms::generateAdjacency(this); EndState(); SetState(NAS_WAITING); m_comm.sendCheckPointMessage(); break; case NAS_ADJ_COMPLETE: m_comm.barrier(); pumpNetwork(); logger(0) << "Added " << m_numBasesAdjSet << " edges.\n"; m_comm.reduce(m_numBasesAdjSet); EndState(); SetState(NAS_WAITING); break; case NAS_ERODE: { m_comm.barrier(); size_t numEroded = AssemblyAlgorithms::erodeEnds(this); EndState(); SetState(NAS_ERODE_WAITING); m_comm.sendCheckPointMessage(numEroded); break; } case NAS_ERODE_WAITING: pumpNetwork(); break; case NAS_ERODE_COMPLETE: completeOperation(); m_comm.reduce(AssemblyAlgorithms::getNumEroded()); m_comm.reduce(m_data.cleanup()); m_comm.barrier(); SetState(NAS_WAITING); break; case NAS_TRIM: { assert(m_trimStep != 0); m_comm.barrier(); size_t numRemoved = performNetworkTrim(this); EndState(); SetState(NAS_WAITING); m_comm.sendCheckPointMessage(numRemoved); break; } case NAS_REMOVE_MARKED: { m_comm.barrier(); size_t count = AssemblyAlgorithms::removeMarked(this); EndState(); SetState(NAS_WAITING); m_comm.sendCheckPointMessage(count); break; } case NAS_COVERAGE: { m_comm.reduce(m_data.cleanup()); m_lowCoverageContigs = 0; m_lowCoverageKmer = 0; numAssembled = performNetworkAssembly(this); EndState(); SetState(NAS_WAITING); m_comm.sendCheckPointMessage(); break; } case NAS_COVERAGE_COMPLETE: m_comm.barrier(); pumpNetwork(); m_comm.reduce(numAssembled.first); m_comm.reduce(numAssembled.second); m_comm.reduce(m_lowCoverageContigs); m_comm.reduce(m_lowCoverageKmer); opt::coverage = 0; EndState(); SetState(NAS_WAITING); break; case NAS_DISCOVER_BUBBLES: { size_t numDiscovered = performNetworkDiscoverBubbles(this); EndState(); SetState(NAS_WAITING); m_comm.sendCheckPointMessage(numDiscovered); break; } case NAS_POPBUBBLE: { if (!bubbleFile.is_open()) AssemblyAlgorithms::openBubbleFile(bubbleFile); size_t numPopped = performNetworkPopBubbles(bubbleFile); EndState(); SetState(NAS_WAITING); m_comm.sendCheckPointMessage(numPopped); break; } case NAS_MARK_AMBIGUOUS: { m_comm.barrier(); pumpNetwork(); size_t count = AssemblyAlgorithms::markAmbiguous(this); EndState(); SetState(NAS_WAITING); m_comm.sendCheckPointMessage(count); break; } case NAS_SPLIT_AMBIGUOUS: { m_comm.barrier(); assert(m_comm.receiveEmpty()); m_comm.barrier(); size_t count = AssemblyAlgorithms::splitAmbiguous(this); EndState(); SetState(NAS_WAITING); m_comm.sendCheckPointMessage(count); break; } case NAS_CLEAR_FLAGS: m_comm.barrier(); pumpNetwork(); m_data.wipeFlag( SeqFlag(SF_MARK_SENSE | SF_MARK_ANTISENSE)); m_comm.reduce(m_data.cleanup()); EndState(); SetState(NAS_WAITING); break; case NAS_ASSEMBLE: { m_comm.barrier(); pumpNetwork(); FastaWriter writer(opt::contigsTempPath.c_str()); numAssembled = performNetworkAssembly(this, &writer); EndState(); SetState(NAS_WAITING); m_comm.sendCheckPointMessage(); break; } case NAS_ASSEMBLE_COMPLETE: m_comm.reduce(numAssembled.first); m_comm.reduce(numAssembled.second); EndState(); SetState(NAS_DONE); break; case NAS_WAITING: pumpNetwork(); break; case NAS_DONE: break; } } } size_t NetworkSequenceCollection::controlErode() { SetState(NAS_ERODE); m_comm.sendControlMessage(APC_SET_STATE, NAS_ERODE); m_comm.barrier(); size_t numEroded = AssemblyAlgorithms::erodeEnds(this); EndState(); // Do not call SetState, because it clears the // checkpoint information. //SetState(NAS_ERODE_WAITING); m_state = NAS_ERODE_WAITING; m_numReachedCheckpoint++; while (!checkpointReached()) pumpNetwork(); numEroded += m_checkpointSum; EndState(); if (numEroded == 0) { SetState(NAS_WAITING); m_comm.sendControlMessage(APC_WAIT); m_comm.barrier(); return 0; } SetState(NAS_ERODE_COMPLETE); m_comm.sendControlMessage(APC_ERODE_COMPLETE); completeOperation(); numEroded += m_comm.reduce( AssemblyAlgorithms::getNumEroded()); cout << "Eroded " << numEroded << " tips.\n"; size_t removed = m_comm.reduce(m_data.cleanup()); m_comm.barrier(); assert(removed == numEroded); (void)removed; SetState(NAS_WAITING); return numEroded; } /** Remove marked k-mer. * @return the number of k-mer removed */ size_t NetworkSequenceCollection::controlRemoveMarked() { if (opt::verbose > 0) cout << "Sweeping...\n"; SetState(NAS_REMOVE_MARKED); m_comm.sendControlMessage(APC_SET_STATE, NAS_REMOVE_MARKED); m_comm.barrier(); size_t count = AssemblyAlgorithms::removeMarked(this); m_checkpointSum += count; EndState(); m_numReachedCheckpoint++; while (!checkpointReached()) pumpNetwork(); return m_checkpointSum; } /** Perform a single round of trimming at the specified length. */ size_t NetworkSequenceCollection::controlTrimRound(unsigned trimLen) { assert(trimLen > 0); m_trimStep = trimLen; cout << "Pruning tips shorter than " << trimLen << " bp...\n"; SetState(NAS_TRIM); m_comm.sendControlMessage(APC_TRIM, trimLen); m_comm.barrier(); size_t numRemoved = performNetworkTrim(this); EndState(); m_numReachedCheckpoint++; while (!checkpointReached()) pumpNetwork(); numRemoved += m_checkpointSum; size_t numSweeped = controlRemoveMarked(); if (numRemoved > 0) cout << "Pruned " << numSweeped << " k-mer in " << numRemoved << " tips.\n"; return numRemoved; } /** Perform multiple rounds of trimming until complete. */ void NetworkSequenceCollection::controlTrim(unsigned start) { if (opt::trimLen == 0) return; unsigned rounds = 0, total = 0; for (unsigned trim = start; trim < opt::trimLen; trim *= 2) { rounds++; total += controlTrimRound(trim); } size_t count; while ((count = controlTrimRound(opt::trimLen)) > 0) { rounds++; total += count; } cout << "Pruned " << total << " tips in " << rounds << " rounds.\n"; } /** Remove low-coverage contigs. */ void NetworkSequenceCollection::controlCoverage() { assert(opt::coverage > 0); // Split ambiguous branches. SetState(NAS_MARK_AMBIGUOUS); controlMarkAmbiguous(); // Remove low-coverage contigs. cout << "Removing low-coverage contigs " "(mean k-mer coverage < " << opt::coverage << ")...\n"; SetState(NAS_COVERAGE); m_comm.sendControlMessage(APC_SET_STATE, NAS_COVERAGE); m_comm.reduce(m_data.cleanup()); m_lowCoverageContigs = 0; m_lowCoverageKmer = 0; pair numAssembled = performNetworkAssembly(this); EndState(); m_numReachedCheckpoint++; while (!checkpointReached()) pumpNetwork(); // Count the number of low-coverage contigs. SetState(NAS_COVERAGE_COMPLETE); m_comm.sendControlMessage(APC_SET_STATE, NAS_COVERAGE_COMPLETE); m_comm.barrier(); pumpNetwork(); numAssembled.first = m_comm.reduce(numAssembled.first); numAssembled.second = m_comm.reduce(numAssembled.second); cout << "Found " << numAssembled.second << " k-mer in " << numAssembled.first << " contigs " "before removing low-coverage contigs.\n"; size_t lowCoverageContigs = m_comm.reduce(m_lowCoverageContigs); size_t lowCoverageKmer = m_comm.reduce(m_lowCoverageKmer); cout << "Removed " << lowCoverageKmer << " k-mer in " << lowCoverageContigs << " low-coverage contigs.\n"; EndState(); SetState(NAS_SPLIT_AMBIGUOUS); controlSplitAmbiguous(); SetState(NAS_CLEAR_FLAGS); m_comm.sendControlMessage(APC_SET_STATE, NAS_CLEAR_FLAGS); m_comm.barrier(); pumpNetwork(); m_data.wipeFlag(SeqFlag(SF_MARK_SENSE | SF_MARK_ANTISENSE)); size_t removed = m_comm.reduce(m_data.cleanup()); cout << "Removed " << removed << " marked k-mer.\n"; EndState(); opt::coverage = 0; } /** Run the assembly state machine for the controller (rank = 0). */ void NetworkSequenceCollection::runControl() { SetState(NAS_LOADING); while (m_state != NAS_DONE) { switch (m_state) { case NAS_LOADING: { loadSequences(); EndState(); m_numReachedCheckpoint++; while (!checkpointReached()) pumpNetwork(); SetState(NAS_LOAD_COMPLETE); m_comm.sendControlMessage(APC_SET_STATE, NAS_LOAD_COMPLETE); m_comm.barrier(); pumpNetwork(); logger(0) << "Loaded " << m_data.size() << " k-mer.\n"; assert(!m_data.empty() || opt::numProc >= DEDICATE_CONTROL_AT); m_data.shrink(); size_t numLoaded = m_comm.reduce(m_data.size()); cout << "Loaded " << numLoaded << " k-mer. " "At least " << toSI(numLoaded * sizeof (value_type)) << "B of RAM is required.\n"; Histogram myh = AssemblyAlgorithms::coverageHistogram(m_data); Histogram h(m_comm.reduce(myh.toVector())); AssemblyAlgorithms::setCoverageParameters(h); EndState(); SetState(m_data.isAdjacencyLoaded() ? NAS_ERODE : NAS_GEN_ADJ); break; } case NAS_GEN_ADJ: cout << "Finding adjacenct k-mer...\n"; m_comm.sendControlMessage(APC_SET_STATE, NAS_GEN_ADJ); m_comm.barrier(); m_numBasesAdjSet = 0; AssemblyAlgorithms::generateAdjacency(this); EndState(); m_numReachedCheckpoint++; while (!checkpointReached()) pumpNetwork(); SetState(NAS_ADJ_COMPLETE); m_comm.sendControlMessage(APC_SET_STATE, NAS_ADJ_COMPLETE); m_comm.barrier(); pumpNetwork(); logger(0) << "Added " << m_numBasesAdjSet << " edges.\n"; cout << "Added " << m_comm.reduce(m_numBasesAdjSet) << " edges.\n"; EndState(); SetState(opt::erode > 0 ? NAS_ERODE : NAS_TRIM); break; case NAS_ERODE: assert(opt::erode > 0); cout << "Eroding tips...\n"; controlErode(); SetState(NAS_TRIM); break; case NAS_LOAD_COMPLETE: case NAS_ADJ_COMPLETE: case NAS_REMOVE_MARKED: case NAS_ERODE_WAITING: case NAS_ERODE_COMPLETE: case NAS_COVERAGE_COMPLETE: case NAS_SPLIT_AMBIGUOUS: case NAS_CLEAR_FLAGS: case NAS_DISCOVER_BUBBLES: case NAS_ASSEMBLE_COMPLETE: case NAS_WAITING: // These states are used only by the slaves. assert(false); exit(EXIT_FAILURE); case NAS_TRIM: controlTrim(); SetState(opt::coverage > 0 ? NAS_COVERAGE : opt::bubbleLen > 0 ? NAS_POPBUBBLE : NAS_MARK_AMBIGUOUS); break; case NAS_COVERAGE: controlCoverage(); SetState(opt::erode > 0 ? NAS_ERODE : NAS_TRIM); break; case NAS_POPBUBBLE: { assert(opt::bubbleLen > 0); ofstream out; AssemblyAlgorithms::openBubbleFile(out); cout << "Popping bubbles...\n"; size_t numPopped = controlPopBubbles(out); assert(numPopped == m_numPopped); assert(out.good()); out.close(); cout << "Removed " << numPopped << " bubbles.\n"; SetState(NAS_MARK_AMBIGUOUS); break; } case NAS_MARK_AMBIGUOUS: controlMarkAmbiguous(); SetState(NAS_ASSEMBLE); break; case NAS_ASSEMBLE: { cout << "Assembling...\n"; m_comm.sendControlMessage(APC_ASSEMBLE); m_comm.barrier(); pumpNetwork(); FastaWriter writer(opt::contigsTempPath.c_str()); pair numAssembled = performNetworkAssembly(this, &writer); EndState(); m_numReachedCheckpoint++; while (!checkpointReached()) pumpNetwork(); SetState(NAS_ASSEMBLE_COMPLETE); m_comm.sendControlMessage(APC_SET_STATE, NAS_ASSEMBLE_COMPLETE); numAssembled.first = m_comm.reduce( numAssembled.first); numAssembled.second = m_comm.reduce( numAssembled.second); cout << "Assembled " << numAssembled.second << " k-mer in " << numAssembled.first << " contigs.\n"; SetState(NAS_DONE); break; } case NAS_DONE: break; } } } void NetworkSequenceCollection::EndState() { // Flush the message buffer m_comm.flush(); } // // Set the state // void NetworkSequenceCollection::SetState( NetworkAssemblyState newState) { logger(2) << "SetState " << newState << " (was " << m_state << ")\n"; // Ensure there are no pending messages assert(m_comm.transmitBufferEmpty()); m_state = newState; // Reset the checkpoint counter m_numReachedCheckpoint = 0; m_checkpointSum = 0; } /** Receive and dispatch packets. * @return the number of packets received */ size_t NetworkSequenceCollection::pumpNetwork() { for (size_t count = 0; ; count++) { int senderID; APMessage msg = m_comm.checkMessage(senderID); switch(msg) { case APM_CONTROL: parseControlMessage(senderID); // Deal with the control packet before we continue // processing further packets. return ++count; case APM_BUFFERED: { MessagePtrVector msgs; m_comm.receiveBufferedMessage(msgs); for (MessagePtrVector::iterator iter = msgs.begin(); iter != msgs.end(); iter++) { // Handle each message based on its type (*iter)->handle(senderID, *this); // Delete the message delete (*iter); *iter = 0; } break; } case APM_NONE: return count; } } } /** Call the observers of the specified sequence. */ void NetworkSequenceCollection::notify(const Kmer& key) { switch (m_state) { case NAS_ERODE: case NAS_ERODE_WAITING: case NAS_ERODE_COMPLETE: AssemblyAlgorithms::erode(this, m_data.getSeqAndData(key)); break; default: // Nothing to do. break; } } void NetworkSequenceCollection::handle( int /*senderID*/, const SeqAddMessage& message) { assert(isLocal(message.m_seq)); m_data.add(message.m_seq); } void NetworkSequenceCollection::handle( int /*senderID*/, const SeqRemoveMessage& message) { assert(isLocal(message.m_seq)); m_data.remove(message.m_seq); } void NetworkSequenceCollection::handle( int /*senderID*/, const SetFlagMessage& message) { assert(isLocal(message.m_seq)); m_data.setFlag(message.m_seq, (SeqFlag)message.m_flag); } void NetworkSequenceCollection::handle( int /*senderID*/, const SetBaseMessage& message) { assert(isLocal(message.m_seq)); setBaseExtension(message.m_seq, (extDirection)message.m_dir, message.m_base); } void NetworkSequenceCollection::handle( int /*senderID*/, const RemoveExtensionMessage& message) { assert(isLocal(message.m_seq)); m_data.removeExtension(message.m_seq, (extDirection)message.m_dir, message.m_ext); notify(message.m_seq); } void NetworkSequenceCollection::parseControlMessage(int source) { ControlMessage controlMsg = m_comm.receiveControlMessage(); switch(controlMsg.msgType) { case APC_SET_STATE: SetState(NetworkAssemblyState(controlMsg.argument)); break; case APC_CHECKPOINT: logger(4) << "checkpoint from " << source << ": " << controlMsg.argument << '\n'; m_numReachedCheckpoint++; m_checkpointSum += controlMsg.argument; break; case APC_WAIT: SetState(NAS_WAITING); m_comm.barrier(); break; case APC_BARRIER: assert(m_state == NAS_WAITING); m_comm.barrier(); break; case APC_TRIM: m_trimStep = controlMsg.argument; SetState(NAS_TRIM); break; case APC_ERODE_COMPLETE: assert(m_state == NAS_ERODE_WAITING); m_comm.flush(); SetState(NAS_ERODE_COMPLETE); break; case APC_POPBUBBLE: m_numPopped = controlMsg.argument; SetState(NAS_POPBUBBLE); break; case APC_ASSEMBLE: m_numAssembled = controlMsg.argument; SetState(NAS_ASSEMBLE); break; } } void NetworkSequenceCollection::handle( int senderID, const SeqDataRequest& message) { const Kmer& kmer = message.m_seq; assert(isLocal(kmer)); ExtensionRecord extRec; int multiplicity = -1; bool found = m_data.getSeqData(kmer, extRec, multiplicity); assert(found); (void)found; m_comm.sendSeqDataResponse( senderID, message.m_group, message.m_id, kmer, extRec, multiplicity); } void NetworkSequenceCollection::handle( int /*senderID*/, const SeqDataResponse& message) { processSequenceExtension( message.m_group, message.m_id, message.m_seq, message.m_extRecord, message.m_multiplicity); } /** Distributed trimming function. */ size_t NetworkSequenceCollection::performNetworkTrim( ISequenceCollection* seqCollection) { Timer timer("NetworkTrim"); size_t numBranchesRemoved = 0; // The branch ids uint64_t branchGroupID = 0; for (ISequenceCollection::iterator iter = seqCollection->begin(); iter != seqCollection->end(); ++iter) { if (iter->second.deleted()) continue; extDirection dir; // dir will be set to the trimming direction if the sequence // can be trimmed. SeqContiguity status = AssemblyAlgorithms::checkSeqContiguity( *iter, dir); if (status == SC_CONTIGUOUS) continue; else if(status == SC_ISLAND) { seqCollection->mark(iter->first); numBranchesRemoved++; continue; } bool inserted = m_activeBranchGroups.insert( BranchGroupMap::value_type(branchGroupID, BranchGroup(dir, 1, iter->first, BranchRecord(dir)))) .second; assert(inserted); (void)inserted; generateExtensionRequest(branchGroupID, 0, iter->first); branchGroupID++; numBranchesRemoved += processBranchesTrim(); seqCollection->pumpNetwork(); // Primitive load balancing if(m_activeBranchGroups.size() > MAX_ACTIVE) { while(m_activeBranchGroups.size() > LOW_ACTIVE) { seqCollection->pumpNetwork(); numBranchesRemoved += processBranchesTrim(); } } } // Clear out the remaining branches while(!m_activeBranchGroups.empty()) { numBranchesRemoved += processBranchesTrim(); seqCollection->pumpNetwork(); } logger(0) << "Pruned " << numBranchesRemoved << " tips.\n"; return numBranchesRemoved; } // // Process current branches, removing those that are finished // returns true if the branch list has branches remaining // size_t NetworkSequenceCollection::processBranchesTrim() { size_t numBranchesRemoved = 0; vector removeBranches; // Check if any of the current branches have gone inactive for (BranchGroupMap::iterator iter = m_activeBranchGroups.begin(); iter != m_activeBranchGroups.end(); iter++) { if(!iter->second.isActive()) { assert(iter->second.size() == 1); if (AssemblyAlgorithms::processTerminatedBranchTrim( this, iter->second[0])) numBranchesRemoved++; // Mark the group for removal removeBranches.push_back(iter); } } // Remove all the finished branches for (vector::iterator rmIter = removeBranches.begin(); rmIter != removeBranches.end(); rmIter++) m_activeBranchGroups.erase(*rmIter); return numBranchesRemoved; } /** Discover bubbles to pop. */ size_t NetworkSequenceCollection:: performNetworkDiscoverBubbles(ISequenceCollection* seqCollection) { Timer timer("NetworkDiscoverBubbles"); // The branch ids uint64_t branchGroupID = 0; m_finishedGroups.clear(); // make sure the branch group structure is initially empty assert(m_activeBranchGroups.empty()); size_t count = 0; // Set the cutoffs const unsigned maxNumBranches = 3; for (ISequenceCollection::iterator iter = seqCollection->begin(); iter != seqCollection->end(); ++iter) { if (iter->second.deleted()) continue; if (++count % 100000 == 0) logger(1) << "Popping bubbles: " << count << '\n'; ExtensionRecord extRec = iter->second.extension(); for (extDirection dir = SENSE; dir <= ANTISENSE; ++dir) { if (extRec.dir[dir].isAmbiguous()) { BranchGroupMap::iterator groupIter = m_activeBranchGroups.insert( BranchGroupMap::value_type(branchGroupID, BranchGroup(dir, maxNumBranches, iter->first))).first; BranchGroup& group = groupIter->second; AssemblyAlgorithms::initiateBranchGroup( group, iter->first, extRec.dir[dir]); generateExtensionRequests(branchGroupID++, group.begin(), group.end()); } } // Primitive load balancing if (m_activeBranchGroups.size() > MAX_ACTIVE) { while (m_activeBranchGroups.size() > LOW_ACTIVE) { seqCollection->pumpNetwork(); processBranchesDiscoverBubbles(); } } processBranchesDiscoverBubbles(); seqCollection->pumpNetwork(); } // Wait until the groups finish extending. while (processBranchesDiscoverBubbles()) seqCollection->pumpNetwork(); assert(m_activeBranchGroups.empty()); size_t numDiscovered = m_bubbles.size(); logger(1) << "Discovered " << numDiscovered << " bubbles.\n"; return numDiscovered; } /** Pop bubbles discovered previously. */ size_t NetworkSequenceCollection:: performNetworkPopBubbles(ostream& out) { Timer timer("NetworkPopBubbles"); // Deal with any packets still in the queue. The barrier // synchronization guarantees that the packets have been // delivered, but we may not have dealt with them yet. pumpNetwork(); assert(m_comm.receiveEmpty()); size_t numPopped = 0; for (BranchGroupMap::iterator iter = m_bubbles.begin(); iter != m_bubbles.end(); iter++) { assert(iter->second.getStatus() == BGS_JOINED); // Check whether this bubble has already been popped. if (!iter->second.isAmbiguous(m_data)) continue; numPopped++; AssemblyAlgorithms::writeBubble(out, iter->second, m_numPopped + numPopped); AssemblyAlgorithms::collapseJoinedBranches( this, iter->second); assert(!iter->second.isAmbiguous(m_data)); assert(m_comm.receiveEmpty()); } m_bubbles.clear(); out.flush(); assert(out.good()); logger(0) << "Removed " << numPopped << " bubbles.\n"; return numPopped; } // // Process groups that are finished searching for bubbles // bool NetworkSequenceCollection::processBranchesDiscoverBubbles() { bool active = false; // Check if any of the current branches have gone inactive BranchGroupMap::iterator iter = m_activeBranchGroups.begin(); while (iter != m_activeBranchGroups.end()) { // All branches have been extended one sequence. Check the // stop conditions. updateStatus() is called in // processSequenceExtensionPop(). BranchGroupStatus status = iter->second.isNoExt() ? BGS_NOEXT : iter->second.getStatus(); bool finished = false; switch (status) { case BGS_TOOLONG: case BGS_TOOMANYBRANCHES: case BGS_NOEXT: finished = true; break; case BGS_JOINED: m_bubbles.insert(*iter); finished = true; break; case BGS_ACTIVE: active = true; break; default: assert(false); } if (finished) { m_finishedGroups.insert(iter->first); m_activeBranchGroups.erase(iter++); } else iter++; } return active; } /** Discover bubbles to pop. */ size_t NetworkSequenceCollection::controlDiscoverBubbles() { SetState(NAS_DISCOVER_BUBBLES); m_comm.sendControlMessage(APC_SET_STATE, NAS_DISCOVER_BUBBLES); size_t numDiscovered = performNetworkDiscoverBubbles(this); EndState(); m_numReachedCheckpoint++; while (!checkpointReached()) pumpNetwork(); numDiscovered += m_checkpointSum; if (numDiscovered > 0 && opt::verbose > 0) cout << "Discovered " << numDiscovered << " bubbles.\n"; return numDiscovered; } /** Pop the bubbles discovered previously. */ size_t NetworkSequenceCollection::controlPopBubbles(ostream& out) { controlDiscoverBubbles(); m_comm.sendControlMessage(APC_BARRIER); m_comm.barrier(); pumpNetwork(); // Perform a round-robin bubble pop to avoid concurrency issues SetState(NAS_POPBUBBLE); m_checkpointSum = performNetworkPopBubbles(out); EndState(); // Now tell all the slave nodes to perform the pop one by one for(int i = 1; i < opt::numProc; i++) { m_comm.sendControlMessage(APC_BARRIER); m_comm.barrier(); m_numReachedCheckpoint = 0; m_comm.sendControlMessageToNode(i, APC_POPBUBBLE, m_numPopped + m_checkpointSum); while (!checkpointReached(1)) pumpNetwork(); } size_t numPopped = m_checkpointSum; m_numPopped += numPopped; if (numPopped > 0) cout << "Removed " << numPopped << " bubbles.\n"; return numPopped; } /** Mark ambiguous branches. */ size_t NetworkSequenceCollection::controlMarkAmbiguous() { cout << "Marking ambiguous branches...\n"; m_comm.sendControlMessage(APC_SET_STATE, NAS_MARK_AMBIGUOUS); m_comm.barrier(); pumpNetwork(); size_t count = AssemblyAlgorithms::markAmbiguous(this); m_checkpointSum += count; EndState(); m_numReachedCheckpoint++; while (!checkpointReached()) pumpNetwork(); cout << "Marked " << m_checkpointSum << " ambiguous branches.\n"; return m_checkpointSum; } /** Remove ambiguous branches. */ size_t NetworkSequenceCollection::controlSplitAmbiguous() { cout << "Splitting ambiguous branches...\n"; m_comm.sendControlMessage(APC_SET_STATE, NAS_SPLIT_AMBIGUOUS); m_comm.barrier(); assert(m_comm.receiveEmpty()); m_comm.barrier(); size_t count = AssemblyAlgorithms::splitAmbiguous(this); m_checkpointSum += count; EndState(); m_numReachedCheckpoint++; while (!checkpointReached()) pumpNetwork(); cout << "Split " << m_checkpointSum << " ambiguous branches.\n"; return m_checkpointSum; } /** Assemble a contig. */ void NetworkSequenceCollection::assembleContig( ISequenceCollection* seqCollection, FastaWriter* writer, BranchRecord& branch, unsigned id) { size_t removed = AssemblyAlgorithms::assembleContig( seqCollection, writer, branch, id); if (removed > 0) { m_lowCoverageContigs++; m_lowCoverageKmer += removed; } } namespace std { /** Add a pair of numbers. */ pair& operator+=( pair& a, pair b) { a.first += b.first; a.second += b.second; return a; } } /** Assemble contigs. * @return the number of contigs and k-mer assembled */ pair NetworkSequenceCollection:: performNetworkAssembly(ISequenceCollection* seqCollection, FastaWriter* fileWriter) { Timer timer("NetworkAssembly"); pair numAssembled(0, 0); uint64_t branchGroupID = 0; assert(m_activeBranchGroups.empty()); for (ISequenceCollection::iterator iter = seqCollection->begin(); iter != seqCollection->end(); ++iter) { if (iter->second.deleted()) continue; extDirection dir; // dir will be set to the assembly direction if the sequence // can be assembled. SeqContiguity status = AssemblyAlgorithms::checkSeqContiguity( *iter, dir, true); if (status == SC_CONTIGUOUS) continue; else if(status == SC_ISLAND) { // Output the singleton contig. BranchRecord currBranch(SENSE); currBranch.push_back(*iter); currBranch.terminate(BS_NOEXT); assembleContig(seqCollection, fileWriter, currBranch, m_numAssembled + numAssembled.first); numAssembled.first++; numAssembled.second += currBranch.size(); continue; } BranchGroup group(dir, 1, iter->first); group.addBranch(BranchRecord(dir)); pair inserted = m_activeBranchGroups.insert( BranchGroupMap::value_type(branchGroupID, group)); assert(inserted.second); // Generate the first extension request BranchRecord& branch = inserted.first->second[0]; branch.push_back(*iter); Kmer kmer = iter->first; AssemblyAlgorithms::extendBranch(branch, kmer, iter->second.getExtension(dir)); assert(branch.isActive()); generateExtensionRequest(branchGroupID++, 0, kmer); numAssembled += processBranchesAssembly(seqCollection, fileWriter, numAssembled.first); seqCollection->pumpNetwork(); if(m_activeBranchGroups.size() > MAX_ACTIVE) { while(m_activeBranchGroups.size() > LOW_ACTIVE) { seqCollection->pumpNetwork(); numAssembled += processBranchesAssembly(seqCollection, fileWriter, numAssembled.first); } } } // Clear out the remaining branches while(!m_activeBranchGroups.empty()) { numAssembled += processBranchesAssembly(seqCollection, fileWriter, numAssembled.first); seqCollection->pumpNetwork(); } if (opt::coverage > 0) { logger(0) << "Found " << numAssembled.second << " k-mer in " << numAssembled.first << " contigs before removing low-coverage contigs.\n" "Removed " << m_lowCoverageKmer << " k-mer in " << m_lowCoverageContigs << " low-coverage contigs.\n"; } else logger(0) << "Assembled " << numAssembled.second << " k-mer in " << numAssembled.first << " contigs.\n"; return numAssembled; } /** Processes branches that are in progress, removing those that have * completed. * @return the number of contigs and k-mer assembled */ pair NetworkSequenceCollection:: processBranchesAssembly(ISequenceCollection* seqCollection, FastaWriter* fileWriter, unsigned currContigID) { size_t assembledContigs = 0, assembledKmer = 0; for (BranchGroupMap::iterator it = m_activeBranchGroups.begin(); it != m_activeBranchGroups.end();) { if (!it->second.isActive()) { assert(it->second.size() == 1); BranchRecord& branch = it->second[0]; assert(branch.getState() == BS_NOEXT || branch.getState() == BS_AMBI_SAME || branch.getState() == BS_AMBI_OPP); if (branch.isCanonical()) { assembledContigs++; assembledKmer += branch.size(); assembleContig(seqCollection, fileWriter, branch, m_numAssembled + currContigID++); } m_activeBranchGroups.erase(it++); } else ++it; } return make_pair(assembledContigs, assembledKmer); } /** Send a request for the edges of vertex kmer. */ void NetworkSequenceCollection::generateExtensionRequest( uint64_t groupID, uint64_t branchID, const Kmer& kmer) { if (isLocal(kmer)) { ExtensionRecord extRec; int multiplicity = -1; bool success = m_data.getSeqData(kmer, extRec, multiplicity); assert(success); (void)success; processSequenceExtension(groupID, branchID, kmer, extRec, multiplicity); } else m_comm.sendSeqDataRequest(computeNodeID(kmer), groupID, branchID, kmer); } /** Generate an extension request for each branch of this group. */ void NetworkSequenceCollection::generateExtensionRequests( uint64_t groupID, BranchGroup::const_iterator first, BranchGroup::const_iterator last) { assert(first != last); #if !NDEBUG size_t length = first->size(); #endif unsigned branchID = 0; for (BranchGroup::const_iterator it = first; it != last; ++it) { assert(it->size() == length); generateExtensionRequest(groupID, branchID++, it->back().first); } } void NetworkSequenceCollection::processSequenceExtension( uint64_t groupID, uint64_t branchID, const Kmer& seq, const ExtensionRecord& extRec, int multiplicity) { switch(m_state) { case NAS_TRIM: return processLinearSequenceExtension(groupID, branchID, seq, extRec, multiplicity, m_trimStep); case NAS_ASSEMBLE: case NAS_COVERAGE: return processLinearSequenceExtension(groupID, branchID, seq, extRec, multiplicity, UINT_MAX); case NAS_DISCOVER_BUBBLES: return processSequenceExtensionPop(groupID, branchID, seq, extRec, multiplicity, opt::bubbleLen - opt::kmerSize + 1); case NAS_WAITING: if (m_finishedGroups.count(groupID) == 0) { logger(0) << "error: unexpected seqext message: " "state: " << m_state << " " "gid: " << groupID << " bid: " << branchID << " " "seq: " << seq.str() << '\n'; assert(false); } break; default: logger(0) << "error: unexpected seqext message: " "state: " << m_state << " " "gid: " << groupID << " bid: " << branchID << " " "seq: " << seq.str() << '\n'; assert(false); break; } } /** Process a sequence extension for trimming. */ void NetworkSequenceCollection::processLinearSequenceExtension( uint64_t groupID, uint64_t branchID, const Kmer& seq, const ExtensionRecord& extRec, int multiplicity, unsigned maxLength) { BranchGroupMap::iterator iter = m_activeBranchGroups.find(groupID); assert(iter != m_activeBranchGroups.end()); Kmer currSeq = seq; bool active = AssemblyAlgorithms::processLinearExtensionForBranch( iter->second[branchID], currSeq, extRec, multiplicity, maxLength); if (active) generateExtensionRequest(groupID, branchID, currSeq); } /** Process a sequence extension for popping. */ void NetworkSequenceCollection::processSequenceExtensionPop( uint64_t groupID, uint64_t branchID, const Kmer& seq, const ExtensionRecord& extRec, int multiplicity, unsigned maxLength) { BranchGroupMap::iterator groupIt = m_activeBranchGroups.find(groupID); if (groupIt == m_activeBranchGroups.end()) { // This branch is already complete. Double check that that is // the case. assert(m_finishedGroups.count(groupID) > 0); return; } BranchGroup& group = groupIt->second; bool extendable = AssemblyAlgorithms::processBranchGroupExtension( group, branchID, seq, extRec, multiplicity, maxLength); if (extendable && group.updateStatus(maxLength) == BGS_ACTIVE) generateExtensionRequests(groupID, group.begin(), group.end()); } /** Add a k-mer to this collection. */ void NetworkSequenceCollection::add(const Kmer& seq, unsigned coverage) { if (isLocal(seq)) { m_data.add(seq, coverage); } else { assert(coverage == 1); m_comm.sendSeqAddMessage(computeNodeID(seq), seq); } } /** Remove a k-mer from this collection. */ void NetworkSequenceCollection::remove(const Kmer& seq) { if (isLocal(seq)) m_data.remove(seq); else m_comm.sendSeqRemoveMessage(computeNodeID(seq), seq); } bool NetworkSequenceCollection::checkpointReached() const { return m_numReachedCheckpoint == (unsigned)opt::numProc; } bool NetworkSequenceCollection:: checkpointReached(unsigned numRequired) const { return m_numReachedCheckpoint == numRequired; } void NetworkSequenceCollection::setFlag(const Kmer& seq, SeqFlag flag) { if (isLocal(seq)) m_data.setFlag(seq, flag); else m_comm.sendSetFlagMessage(computeNodeID(seq), seq, flag); } bool NetworkSequenceCollection::setBaseExtension( const Kmer& seq, extDirection dir, uint8_t base) { if (isLocal(seq)) { if (m_data.setBaseExtension(seq, dir, base)) m_numBasesAdjSet++; } else { int nodeID = computeNodeID(seq); m_comm.sendSetBaseExtension(nodeID, seq, dir, base); } // As this call delegates, the return value is meaningless. return false; } /** Remove the specified extensions from this k-mer. */ void NetworkSequenceCollection::removeExtension( const Kmer& seq, extDirection dir, SeqExt ext) { if (isLocal(seq)) { m_data.removeExtension(seq, dir, ext); notify(seq); } else { int nodeID = computeNodeID(seq); m_comm.sendRemoveExtension(nodeID, seq, dir, ext); } } /** Return whether this sequence belongs to this process. */ bool NetworkSequenceCollection::isLocal(const Kmer& seq) const { return computeNodeID(seq) == opt::rank; } /** Return the process ID to which the specified kmer belongs. */ int NetworkSequenceCollection::computeNodeID(const Kmer& seq) const { if (opt::numProc < DEDICATE_CONTROL_AT) { return seq.getCode() % (unsigned)opt::numProc; } else { return seq.getCode() % (unsigned)(opt::numProc - 1) + 1; } } abyss-1.3.6/Parallel/NetworkSequenceCollection.h000644 002433 001057 00000015406 12104026027 023422 0ustar00traymondassembly000000 000000 #ifndef NETWORKSEQUENCECOLLECTION_H #define NETWORKSEQUENCECOLLECTION_H 1 #include "SequenceCollection.h" #include "BranchGroup.h" #include "BranchRecord.h" #include "CommLayer.h" #include "FastaWriter.h" #include "MessageBuffer.h" #include "Timer.h" #include #include #include enum NetworkAssemblyState { NAS_LOADING, // loading sequences NAS_LOAD_COMPLETE, // loading is complete NAS_GEN_ADJ, // generating the sequence data NAS_ADJ_COMPLETE, // adjacency generation is complete NAS_ERODE, // erode the branch ends one sequence at a time NAS_ERODE_WAITING, NAS_ERODE_COMPLETE, NAS_TRIM, // trimming the data NAS_REMOVE_MARKED, // remove marked sequences NAS_COVERAGE, // remove low-coverage contigs NAS_COVERAGE_COMPLETE, NAS_DISCOVER_BUBBLES, // discover read errors/SNPs NAS_POPBUBBLE, // remove read errors/SNPs NAS_MARK_AMBIGUOUS, // mark ambiguous branches NAS_SPLIT_AMBIGUOUS, // split ambiguous branches NAS_CLEAR_FLAGS, // clear the flags NAS_ASSEMBLE, // assembling the data NAS_ASSEMBLE_COMPLETE, // assembling is complete NAS_WAITING, // non-control process is waiting NAS_DONE // finished, clean up and exit }; typedef std::map BranchGroupMap; /** A distributed map of Kmer to KmerData. */ class NetworkSequenceCollection : public ISequenceCollection { public: NetworkSequenceCollection() : m_state(NAS_WAITING), m_trimStep(0), m_numPopped(0), m_numAssembled(0) { } size_t performNetworkTrim(ISequenceCollection* seqCollection); size_t performNetworkDiscoverBubbles(ISequenceCollection* c); size_t performNetworkPopBubbles(std::ostream& out); size_t controlErode(); size_t controlTrimRound(unsigned trimLen); void controlTrim(unsigned start = 1); size_t controlRemoveMarked(); void controlCoverage(); size_t controlDiscoverBubbles(); size_t controlPopBubbles(std::ostream& out); size_t controlMarkAmbiguous(); size_t controlSplitAmbiguous(); size_t controlSplit(); // Perform a network assembly std::pair performNetworkAssembly( ISequenceCollection* seqCollection, FastaWriter* fileWriter = NULL); void add(const Kmer& seq, unsigned coverage = 1); void remove(const Kmer& seq); void setFlag(const Kmer& seq, SeqFlag flag); /** Return true if this container is empty. */ bool empty() const { return m_data.empty(); } void printLoad() const { m_data.printLoad(); } void removeExtension(const Kmer& seq, extDirection dir, SeqExt ext); bool setBaseExtension(const Kmer& seq, extDirection dir, uint8_t base); // Receive and dispatch packets. size_t pumpNetwork(); size_t pumpFlushReduce(); void completeOperation(); // run the assembly void run(); // run the assembly from the controller's point of view void runControl(); // test if the checkpoint has been reached bool checkpointReached() const; bool checkpointReached(unsigned numRequired) const; void handle(int senderID, const SeqAddMessage& message); void handle(int senderID, const SeqRemoveMessage& message); void handle(int senderID, const SetBaseMessage& message); void handle(int senderID, const SetFlagMessage& message); void handle(int senderID, const RemoveExtensionMessage& m); void handle(int senderID, const SeqDataRequest& message); void handle(int senderID, const SeqDataResponse& message); // Observer pattern, not implemented. void attach(SeqObserver f) { (void)f; } void detach(SeqObserver f) { (void)f; } /** Load this collection from disk. */ void load(const char *path) { m_data.load(path); } /** Indicate that this is a colour-space collection. */ void setColourSpace(bool flag) { m_data.setColourSpace(flag); m_comm.broadcast(flag); } iterator begin() { return m_data.begin(); } const_iterator begin() const { return m_data.begin(); } iterator end() { return m_data.end(); } const_iterator end() const { return m_data.end(); } private: // Observer pattern void notify(const Kmer& seq); void loadSequences(); std::pair processBranchesAssembly( ISequenceCollection* seqCollection, FastaWriter* fileWriter, unsigned currContigID); size_t processBranchesTrim(); bool processBranchesDiscoverBubbles(); void generateExtensionRequest( uint64_t groupID, uint64_t branchID, const Kmer& seq); void generateExtensionRequests(uint64_t groupID, BranchGroup::const_iterator first, BranchGroup::const_iterator last); void processSequenceExtension( uint64_t groupID, uint64_t branchID, const Kmer& seq, const ExtensionRecord& extRec, int multiplicity); void processLinearSequenceExtension( uint64_t groupID, uint64_t branchID, const Kmer& seq, const ExtensionRecord& extRec, int multiplicity, unsigned maxLength); void processSequenceExtensionPop( uint64_t groupID, uint64_t branchID, const Kmer& seq, const ExtensionRecord& extRec, int multiplicity, unsigned maxLength); void assembleContig(ISequenceCollection* seqCollection, FastaWriter* fileWriter, BranchRecord& branch, unsigned id); // Check if a branch is redundant with a previously output // branch. bool isBranchRedundant(const BranchRecord& branch); void parseControlMessage(int source); bool isLocal(const Kmer& seq) const; int computeNodeID(const Kmer& seq) const; void EndState(); // Set the state of the network assembly void SetState(NetworkAssemblyState newState); SequenceCollectionHash m_data; // The communications layer implements the functions over the // network. MessageBuffer m_comm; // The number of nodes in the network unsigned m_numDataNodes; // the state of the assembly NetworkAssemblyState m_state; // The number of processes that have sent a checkpoint reached // message, this is used by the control process to determine // the state flow. unsigned m_numReachedCheckpoint; /** The sum of the values returned by the slave nodes in their * checkpoint messages. */ size_t m_checkpointSum; // the number of bases of adjacency set size_t m_numBasesAdjSet; // the current length to trim on (comes from the control node) unsigned m_trimStep; /** The number of low-coverage contigs removed. */ size_t m_lowCoverageContigs; /** The number of low-coverage k-mer removed. */ size_t m_lowCoverageKmer; /** The number of bubbles popped so far. */ size_t m_numPopped; // the number of sequences assembled so far size_t m_numAssembled; // The current branches that are active BranchGroupMap m_activeBranchGroups; /** Bubbles, which are branch groups that have joined. */ BranchGroupMap m_bubbles; // List of IDs of finished groups, used for sanity checking // during bubble popping. std::set m_finishedGroups; static const size_t MAX_ACTIVE = 50; static const size_t LOW_ACTIVE = 10; }; #endif abyss-1.3.6/Parallel/MessageBuffer.cpp000644 002433 001057 00000007413 12104026027 021334 0ustar00traymondassembly000000 000000 #include "MessageBuffer.h" #include "Common/Options.h" #include using namespace std; MessageBuffer::MessageBuffer() : m_msgQueues(opt::numProc) { for (unsigned i = 0; i < m_msgQueues.size(); i++) m_msgQueues[i].reserve(MAX_MESSAGES); } void MessageBuffer::sendSeqAddMessage(int nodeID, const Kmer& seq) { queueMessage(nodeID, new SeqAddMessage(seq), SM_BUFFERED); } void MessageBuffer::sendSeqRemoveMessage(int nodeID, const Kmer& seq) { queueMessage(nodeID, new SeqRemoveMessage(seq), SM_BUFFERED); } // Send a set flag message void MessageBuffer::sendSetFlagMessage(int nodeID, const Kmer& seq, SeqFlag flag) { queueMessage(nodeID, new SetFlagMessage(seq, flag), SM_BUFFERED); } // Send a remove extension message void MessageBuffer::sendRemoveExtension(int nodeID, const Kmer& seq, extDirection dir, SeqExt ext) { queueMessage(nodeID, new RemoveExtensionMessage(seq, dir, ext), SM_BUFFERED); } // Send a sequence data request void MessageBuffer::sendSeqDataRequest(int nodeID, IDType group, IDType id, const Kmer& seq) { queueMessage(nodeID, new SeqDataRequest(seq, group, id), SM_IMMEDIATE); } // Send a sequence data response void MessageBuffer::sendSeqDataResponse(int nodeID, IDType group, IDType id, const Kmer& seq, ExtensionRecord extRec, int multiplicity) { queueMessage(nodeID, new SeqDataResponse(seq, group, id, extRec, multiplicity), SM_IMMEDIATE); } // Send a set base message void MessageBuffer::sendSetBaseExtension(int nodeID, const Kmer& seq, extDirection dir, uint8_t base) { queueMessage(nodeID, new SetBaseMessage(seq, dir, base), SM_BUFFERED); } void MessageBuffer::queueMessage( int nodeID, Message* message, SendMode mode) { if (opt::verbose >= 9) cout << opt::rank << " to " << nodeID << ": " << *message; m_msgQueues[nodeID].push_back(message); checkQueueForSend(nodeID, mode); } void MessageBuffer::checkQueueForSend(int nodeID, SendMode mode) { size_t numMsgs = m_msgQueues[nodeID].size(); // check if the messages should be sent if ((numMsgs == MAX_MESSAGES || mode == SM_IMMEDIATE) && numMsgs > 0) { // Calculate the total size of the message size_t totalSize = 0; for(size_t i = 0; i < numMsgs; i++) { totalSize += m_msgQueues[nodeID][i]->getNetworkSize(); } // Generate a buffer for all the messages char* buffer = new char[totalSize]; // Copy the messages into the buffer size_t offset = 0; for(size_t i = 0; i < numMsgs; i++) offset += m_msgQueues[nodeID][i]->serialize( buffer + offset); assert(offset == totalSize); sendBufferedMessage(nodeID, buffer, totalSize); delete [] buffer; clearQueue(nodeID); m_txPackets++; m_txMessages += numMsgs; m_txBytes += totalSize; } } // Clear a queue of messages void MessageBuffer::clearQueue(int nodeID) { size_t numMsgs = m_msgQueues[nodeID].size(); for(size_t i = 0; i < numMsgs; i++) { // Delete the messages delete m_msgQueues[nodeID][i]; m_msgQueues[nodeID][i] = 0; } m_msgQueues[nodeID].clear(); } // Flush the message buffer by sending all messages that are queued void MessageBuffer::flush() { // Send all messages in all queues for(size_t id = 0; id < m_msgQueues.size(); ++id) { // force the queue to send any pending messages checkQueueForSend(id, SM_IMMEDIATE); } } // Check if all the queues are empty bool MessageBuffer::transmitBufferEmpty() const { bool isEmpty = true; for (MessageQueues::const_iterator it = m_msgQueues.begin(); it != m_msgQueues.end(); ++it) { if (!it->empty()) { cerr << opt::rank << ": error: tx buffer should be empty: " << it->size() << " messages from " << opt::rank << " to " << it - m_msgQueues.begin() << '\n'; for (MsgBuffer::const_iterator j = it->begin(); j != it->end(); ++j) cerr << **j << '\n'; isEmpty = false; } } return isEmpty; } abyss-1.3.6/Parallel/MessageBuffer.h000644 002433 001057 00000003574 12104026027 021005 0ustar00traymondassembly000000 000000 #ifndef MESSAGE_BUFFER_H #define MESSAGE_BUFFER_H 1 class MessageBuffer; #include "CommLayer.h" #include "Messages.h" #include typedef std::vector MsgBuffer; typedef std::vector MessageQueues; enum SendMode { SM_BUFFERED, SM_IMMEDIATE }; /** A buffer of Message. */ class MessageBuffer : public CommLayer { public: MessageBuffer(); void sendCheckPointMessage(int argument = 0) { assert(transmitBufferEmpty()); CommLayer::sendCheckPointMessage(argument); } void sendControlMessage(APControl command, int argument = 0) { assert(transmitBufferEmpty()); CommLayer::sendControlMessage(command, argument); } void sendControlMessageToNode(int dest, APControl command, int argument = 0) { assert(transmitBufferEmpty()); CommLayer::sendControlMessageToNode(dest, command, argument); } void sendSeqAddMessage(int nodeID, const Kmer& seq); void sendSeqRemoveMessage(int nodeID, const Kmer& seq); void sendSetFlagMessage(int nodeID, const Kmer& seq, SeqFlag flag); void sendRemoveExtension(int nodeID, const Kmer& seq, extDirection dir, SeqExt ext); void sendSeqDataRequest(int nodeID, IDType group, IDType id, const Kmer& seq); void sendSeqDataResponse(int nodeID, IDType group, IDType id, const Kmer& seq, ExtensionRecord extRec, int multiplicity); void sendSetBaseExtension(int nodeID, const Kmer& seq, extDirection dir, uint8_t base); void flush(); void queueMessage (int nodeID, Message* message, SendMode mode); // clear out a queue void clearQueue(int nodeID); bool transmitBufferEmpty() const; // check if a queue is full, if so, send the messages if the // immediate mode flag is set, send even if the queue is not // full. void checkQueueForSend(int nodeID, SendMode mode); private: static const size_t MAX_MESSAGES = 100; MessageQueues m_msgQueues; }; #endif abyss-1.3.6/Parallel/Messages.cpp000644 002433 001057 00000011351 12104026027 020361 0ustar00traymondassembly000000 000000 #include "Messages.h" #include "NetworkSequenceCollection.h" #include static size_t serializeData(const void* ptr, char* buffer, size_t size) { memcpy(buffer, ptr, size); return size; } static size_t unserializeData(void* ptr, const char* buffer, size_t size) { memcpy(ptr, buffer, size); return size; } MessageType Message::readMessageType(char* buffer) { return (MessageType)*(uint8_t*)buffer; } size_t Message::unserialize(const char* buffer) { size_t offset = 0; offset++; // MessageType offset += m_seq.unserialize(buffer + offset); return offset; } size_t SeqAddMessage::serialize(char* buffer) { size_t offset = 0; buffer[offset++] = TYPE; offset += m_seq.serialize(buffer + offset); return offset; } void SeqAddMessage::handle(int senderID, NetworkSequenceCollection& handler) { handler.handle(senderID, *this); } size_t SeqRemoveMessage::serialize(char* buffer) { size_t offset = 0; buffer[offset++] = TYPE; offset += m_seq.serialize(buffer + offset); return offset; } void SeqRemoveMessage::handle(int senderID, NetworkSequenceCollection& handler) { handler.handle(senderID, *this); } size_t SetFlagMessage::serialize(char* buffer) { size_t offset = 0; buffer[offset++] = TYPE; offset += m_seq.serialize(buffer + offset); offset += serializeData(&m_flag, buffer + offset, sizeof(m_flag)); return offset; } size_t SetFlagMessage::unserialize(const char* buffer) { size_t offset = 0; offset += Message::unserialize(buffer); offset += unserializeData( &m_flag, buffer + offset, sizeof(m_flag)); return offset; } void SetFlagMessage::handle( int senderID, NetworkSequenceCollection& handler) { handler.handle(senderID, *this); } size_t RemoveExtensionMessage::serialize(char* buffer) { size_t offset = 0; buffer[offset++] = TYPE; offset += m_seq.serialize(buffer + offset); offset += serializeData(&m_dir, buffer + offset, sizeof m_dir); offset += serializeData(&m_ext, buffer + offset, sizeof m_ext); return offset; } size_t RemoveExtensionMessage::unserialize(const char* buffer) { size_t offset = 0; offset += Message::unserialize(buffer); offset += unserializeData(&m_dir, buffer + offset, sizeof m_dir); offset += unserializeData(&m_ext, buffer + offset, sizeof m_ext); return offset; } void RemoveExtensionMessage::handle( int senderID, NetworkSequenceCollection& handler) { handler.handle(senderID, *this); } size_t SetBaseMessage::serialize(char* buffer) { size_t offset = 0; buffer[offset++] = TYPE; offset += m_seq.serialize(buffer + offset); offset += serializeData(&m_dir, buffer + offset, sizeof(m_dir)); offset += serializeData(&m_base, buffer + offset, sizeof(m_base)); return offset; } size_t SetBaseMessage::unserialize(const char* buffer) { size_t offset = 0; offset += Message::unserialize(buffer); offset += unserializeData(&m_dir, buffer + offset, sizeof(m_dir)); offset += unserializeData( &m_base, buffer + offset, sizeof(m_base)); return offset; } void SetBaseMessage::handle( int senderID, NetworkSequenceCollection& handler) { handler.handle(senderID, *this); } size_t SeqDataRequest::serialize(char* buffer) { size_t offset = 0; buffer[offset++] = TYPE; offset += m_seq.serialize(buffer + offset); offset += serializeData( &m_group, buffer + offset, sizeof(m_group)); offset += serializeData(&m_id, buffer + offset, sizeof(m_id)); return offset; } size_t SeqDataRequest::unserialize(const char* buffer) { size_t offset = 0; offset += Message::unserialize(buffer); offset += unserializeData( &m_group, buffer + offset, sizeof(m_group)); offset += unserializeData(&m_id, buffer + offset, sizeof(m_id)); return offset; } void SeqDataRequest::handle( int senderID, NetworkSequenceCollection& handler) { handler.handle(senderID, *this); } size_t SeqDataResponse::serialize(char* buffer) { size_t offset = 0; buffer[offset++] = TYPE; offset += m_seq.serialize(buffer + offset); offset += serializeData( &m_group, buffer + offset, sizeof(m_group)); offset += serializeData( &m_id, buffer + offset, sizeof(m_id)); offset += serializeData( &m_extRecord, buffer + offset, sizeof(m_extRecord)); offset += serializeData( &m_multiplicity, buffer + offset, sizeof(m_multiplicity)); return offset; } size_t SeqDataResponse::unserialize(const char* buffer) { size_t offset = 0; offset += Message::unserialize(buffer); offset += unserializeData( &m_group, buffer + offset, sizeof(m_group)); offset += unserializeData( &m_id, buffer + offset, sizeof(m_id)); offset += unserializeData( &m_extRecord, buffer + offset, sizeof(m_extRecord)); offset += unserializeData( &m_multiplicity, buffer + offset, sizeof(m_multiplicity)); return offset; } void SeqDataResponse::handle( int senderID, NetworkSequenceCollection& handler) { handler.handle(senderID, *this); } abyss-1.3.6/Parallel/Messages.h000644 002433 001057 00000011030 12104026027 020020 0ustar00traymondassembly000000 000000 #ifndef MESSAGES_H #define MESSAGES_H 1 #include "Kmer.h" #include "KmerData.h" #include class NetworkSequenceCollection; enum MessageType { MT_VOID, MT_ADD, MT_REMOVE, MT_SET_FLAG, MT_REMOVE_EXT, MT_SEQ_DATA_REQUEST, MT_SEQ_DATA_RESPONSE, MT_SET_BASE }; enum MessageOp { MO_VOID, MO_ADD, MO_REMOVE, }; typedef uint32_t IDType; /** The base class of all interprocess messages. */ class Message { public: Message() { } Message(const Kmer& seq) : m_seq(seq) { } virtual ~Message() { } virtual void handle( int senderID, NetworkSequenceCollection& handler) = 0; virtual size_t getNetworkSize() const { return sizeof (uint8_t) // MessageType + Kmer::serialSize(); } static MessageType readMessageType(char* buffer); virtual size_t serialize(char* buffer) = 0; virtual size_t unserialize(const char* buffer); friend std::ostream& operator <<(std::ostream& out, const Message& message) { return out << message.m_seq.str() << '\n'; } Kmer m_seq; }; /** Add a Kmer. */ class SeqAddMessage : public Message { public: SeqAddMessage() { } SeqAddMessage(const Kmer& seq) : Message(seq) { } void handle(int senderID, NetworkSequenceCollection& handler); size_t serialize(char* buffer); static const MessageType TYPE = MT_ADD; }; /** Remove a Kmer. */ class SeqRemoveMessage : public Message { public: SeqRemoveMessage() { } SeqRemoveMessage(const Kmer& seq) : Message(seq) { } void handle(int senderID, NetworkSequenceCollection& handler); size_t serialize(char* buffer); static const MessageType TYPE = MT_REMOVE; }; /** Set a flag. */ class SetFlagMessage : public Message { public: SetFlagMessage() { } SetFlagMessage(const Kmer& seq, SeqFlag flag) : Message(seq), m_flag(flag) { } size_t getNetworkSize() const { return Message::getNetworkSize() + sizeof m_flag; } void handle(int senderID, NetworkSequenceCollection& handler); size_t serialize(char* buffer); size_t unserialize(const char* buffer); static const MessageType TYPE = MT_SET_FLAG; uint8_t m_flag; // SeqFlag }; /** Remove an edge. */ class RemoveExtensionMessage : public Message { public: RemoveExtensionMessage() { } RemoveExtensionMessage(const Kmer& seq, extDirection dir, SeqExt ext) : Message(seq), m_dir(dir), m_ext(ext) { } size_t getNetworkSize() const { return Message::getNetworkSize() + sizeof m_dir + sizeof m_ext; } void handle(int senderID, NetworkSequenceCollection& handler); size_t serialize(char* buffer); size_t unserialize(const char* buffer); static const MessageType TYPE = MT_REMOVE_EXT; uint8_t m_dir; // extDirection SeqExt m_ext; }; /** Request vertex properties. */ class SeqDataRequest : public Message { public: SeqDataRequest() { } SeqDataRequest(const Kmer& seq, IDType group, IDType id) : Message(seq), m_group(group), m_id(id) { } size_t getNetworkSize() const { return Message::getNetworkSize() + sizeof m_group + sizeof m_id; } void handle(int senderID, NetworkSequenceCollection& handler); size_t serialize(char* buffer); size_t unserialize(const char* buffer); static const MessageType TYPE = MT_SEQ_DATA_REQUEST; IDType m_group; IDType m_id; }; /** The response to a request for vertex properties. */ class SeqDataResponse : public Message { public: SeqDataResponse() { } SeqDataResponse(const Kmer& seq, IDType group, IDType id, ExtensionRecord& extRecord, int multiplicity) : Message(seq), m_group(group), m_id(id), m_extRecord(extRecord), m_multiplicity(multiplicity) { } size_t getNetworkSize() const { return Message::getNetworkSize() + sizeof m_group + sizeof m_id + sizeof m_extRecord + sizeof m_multiplicity; } void handle(int senderID, NetworkSequenceCollection& handler); size_t serialize(char* buffer); size_t unserialize(const char* buffer); static const MessageType TYPE = MT_SEQ_DATA_RESPONSE; IDType m_group; IDType m_id; ExtensionRecord m_extRecord; uint16_t m_multiplicity; }; /** Add an edge. */ class SetBaseMessage : public Message { public: SetBaseMessage() { } SetBaseMessage(const Kmer& seq, extDirection dir, uint8_t base) : Message(seq), m_dir(dir), m_base(base) { } size_t getNetworkSize() const { return Message::getNetworkSize() + sizeof m_dir + sizeof m_base; 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static void removeLowCoverageContigs(SequenceCollectionHash& g) { AssemblyAlgorithms::markAmbiguous(&g); cout << "Removing low-coverage contigs " "(mean k-mer coverage < " << opt::coverage << ")\n"; AssemblyAlgorithms::assemble(&g); AssemblyAlgorithms::splitAmbiguous(&g); opt::coverage = 0; } static void popBubbles(SequenceCollectionHash& g) { cout << "Popping bubbles" << endl; ofstream out; AssemblyAlgorithms::openBubbleFile(out); unsigned numPopped = AssemblyAlgorithms::popBubbles(&g, out); assert(out.good()); cout << "Removed " << numPopped << " bubbles\n"; } static void write_graph(const string& path, const SequenceCollectionHash& c) { if (path.empty()) return; cout << "Writing graph to `" << path << "'\n"; ofstream out(path.c_str()); DotWriter::write(out, c); } static void assemble(const string& pathIn, const string& pathOut) { Timer timer(__func__); SequenceCollectionHash g; if (!pathIn.empty()) AssemblyAlgorithms::loadSequences(&g, pathIn.c_str()); for_each(opt::inFiles.begin(), opt::inFiles.end(), bind1st(ptr_fun(AssemblyAlgorithms::loadSequences), &g)); size_t numLoaded = g.size(); cout << "Loaded " << numLoaded << " k-mer\n"; g.shrink(); if (g.empty()) { cerr << "error: no usable sequence\n"; exit(EXIT_FAILURE); } AssemblyAlgorithms::setCoverageParameters( AssemblyAlgorithms::coverageHistogram(g)); cout << "Generating adjacency" << endl; AssemblyAlgorithms::generateAdjacency(&g); erode: if (opt::erode > 0) { cout << "Eroding tips" << endl; AssemblyAlgorithms::erodeEnds(&g); assert(AssemblyAlgorithms::erodeEnds(&g) == 0); g.cleanup(); } AssemblyAlgorithms::performTrim(&g); g.cleanup(); if (opt::coverage > 0) { removeLowCoverageContigs(g); g.wipeFlag(SeqFlag(SF_MARK_SENSE | SF_MARK_ANTISENSE)); g.cleanup(); goto erode; } if (opt::bubbleLen > 0) popBubbles(g); write_graph(opt::graphPath, g); AssemblyAlgorithms::markAmbiguous(&g); FastaWriter writer(pathOut.c_str()); unsigned nContigs = AssemblyAlgorithms::assemble(&g, &writer); if (nContigs == 0) { cerr << "error: no contigs assembled\n"; exit(EXIT_FAILURE); } size_t numAssembled = g.size(); 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/** A character representing a gap. */ static const char GAP = '*'; /** The score of a match. */ static const int MATCH = 5; /** The penalty of a mismatch. */ static const int MISMATCH = -4; /** The penalty of opening a gap. */ static const int GAP_OPEN = -12; /** The penalty of extending a gap. */ static const int GAP_EXTEND = -4; /** Return the score of the alignment of a and b. * @param [out] consensus the consensus of a and b * @return the score */ static int score(char a, char b, char& c) { if (a == b) { c = a; return MATCH; } else { c = ambiguityOr(a, b); return c == a || c == b ? MATCH : MISMATCH; } } /** Return the score of the alignment of a and b. */ static int score(char a, char b) { char c; return score(a, b, c); } /** Find the optimal alignment from the score matrices. * @param[out] align the alignment * @return the number of matches */ static unsigned backtrack(int** f, int** g, int** h, const string& seqA, const string& seqB, NWAlignment& align) { string alignmentA, alignmentB, consensus; unsigned matches = 0; unsigned i = seqA.size(), j = seqB.size(); while (i > 0 && j > 0) { int fij = f[i][j]; char a = seqA[i-1], b = seqB[j-1], c; int s = score(a, b, c); if (fij == f[i-1][j-1] + s) { alignmentA += a; alignmentB += b; consensus += c; if (s == MATCH) matches++; i--; j--; } else if (fij == f[i-1][j] + GAP_OPEN || fij == g[i-1][j] + GAP_EXTEND) { while (g[i][j] == g[i-1][j] + GAP_EXTEND) { char a = seqA[i-1]; alignmentA += a; alignmentB += GAP; consensus += tolower(a); i--; assert(i > 0); } assert(g[i][j] == f[i-1][j] + GAP_OPEN); char a = seqA[i-1]; alignmentA += a; alignmentB += GAP; consensus += tolower(a); i--; } else if (fij == f[i][j-1] + GAP_OPEN || fij == h[i][j-1] + GAP_EXTEND) { while (h[i][j] == h[i][j-1] + GAP_EXTEND) { char b = seqB[j-1]; alignmentA += GAP; alignmentB += b; consensus += tolower(b); j--; assert(j > 0); } assert(h[i][j] == f[i][j-1] + GAP_OPEN); char b = seqB[j-1]; alignmentA += GAP; alignmentB += b; consensus += tolower(b); j--; } else { assert(false); abort(); } } while (i > 0) { char a = seqA[i-1]; alignmentA += a; alignmentB += GAP; consensus += tolower(a); i--; } while (j > 0) { char b = seqB[j-1]; alignmentA += GAP; alignmentB += b; consensus += tolower(b); j--; } reverse(alignmentA.begin(), alignmentA.end()); reverse(alignmentB.begin(), alignmentB.end()); reverse(consensus.begin(), consensus.end()); align.query_align = alignmentA; align.target_align = alignmentB; align.match_align = consensus; return matches; } /** Find the optimal global alignment of the two sequences using the * Needleman-Wunsch algorithm and the improvement by Gotoh to use an * affine gap penalty rather than a linear gap penalty. * @param[out] align the alignment * @return the number of matches */ unsigned alignGlobal(const string& seqA, const string& seqB, NWAlignment& align) { unsigned lenA = seqA.size(); unsigned lenB = seqB.size(); int** f = new int*[lenA + 1]; int** g = new int*[lenA + 1]; int** h = new int*[lenA + 1]; for (unsigned i = 0; i <= lenA; i++) { f[i] = new int[lenB + 1]; g[i] = new int[lenB + 1]; h[i] = new int[lenB + 1]; } // Initialize the score matrix. for (unsigned i = 0; i <= lenA; i++) { f[i][0] = g[i][0] = i == 0 ? 0 : GAP_OPEN + GAP_EXTEND * ((int)i - 1); h[i][0] = INT_MIN/2; } for (unsigned j = 0; j <= lenB; j++) { f[0][j] = h[0][j] = j == 0 ? 0 : GAP_OPEN + GAP_EXTEND * ((int)j - 1); g[0][j] = INT_MIN/2; } // Calculate the score matrix. for (unsigned i = 1; i <= lenA; i++) { for (unsigned j = 1; j <= lenB; j++) { g[i][j] = max( f[i-1][j] + GAP_OPEN, g[i-1][j] + GAP_EXTEND); h[i][j] = max( f[i][j-1] + GAP_OPEN, h[i][j-1] + GAP_EXTEND); f[i][j] = max( f[i-1][j-1] + score(seqA[i-1], seqB[j-1]), max(g[i][j], h[i][j])); } } // Find the best alignment. unsigned matches = backtrack(f, g, h, seqA, seqB, align); for (unsigned i = 0; i <= lenA; i++) { delete[] f[i]; delete[] g[i]; delete[] h[i]; } delete[] f; delete[] g; delete[] h; return matches; } abyss-1.3.6/Align/alignGlobal.h000644 002433 001057 00000002016 12015543262 017774 0ustar00traymondassembly000000 000000 #ifndef ALIGNGLOBAL_H #define ALIGNGLOBAL_H #include #include #include #include /** The result of a Needleman-Wunsch alignment. */ struct NWAlignment { std::string query_align; std::string target_align; std::string match_align; //consensus sequence NWAlignment() {} unsigned size() { return match_align.length(); } std::string consensus() { return match_align; } friend std::ostream& operator<<(std::ostream& out, const NWAlignment& o) { const std::string& a = o.query_align; const std::string& b = o.target_align; const std::string& c = o.match_align; assert(a.size() == c.size()); assert(b.size() == c.size()); for (unsigned i = 0; i < c.size(); ++i) out << (toupper(a[i]) == toupper(c[i]) ? '.' : a[i]); out << '\n'; for (unsigned i = 0; i < c.size(); ++i) out << (toupper(b[i]) == toupper(c[i]) ? '.' : b[i]); out << '\n'; return out << c << '\n'; } }; unsigned alignGlobal( const std::string& a, const std::string& b, NWAlignment& align); #endif abyss-1.3.6/Align/dialign.cpp000644 002433 001057 00000026004 12104026025 017516 0ustar00traymondassembly000000 000000 #include "dialign.h" #include "Common/Options.h" #include "Sequence.h" #include "Uncompress.h" #include // for min #include #include // for log #include #include #include #include // for clock #include #include #include using namespace std; /** Score matrix. */ scr_matrix* smatrix; /** Diagonal length probability distribution. */ prob_dist* pdist; /** Return a DNA score matrix. */ static scr_matrix* newDefaultScoreMatrix() { string s("ACGT?#$"); struct scr_matrix* p = (scr_matrix*)calloc(1, sizeof *smatrix); p->length = s.size(); p->num2char = (int*)calloc(256, sizeof(int)); p->char2num = (int*)calloc(256, sizeof(int)); for (unsigned i = 0; i < s.size(); ++i) { unsigned c = s[i]; p->num2char[i] = c; p->char2num[c] = i; } p->data = (int*)calloc(s.size() * s.size(), sizeof(int)); unsigned n = s.size() - 3; // ignore ?#$ // Set the diagonal to 1. for (unsigned i = 0; i < n; i++) p->data[s.size() * i + i] = 1; p->max_score = 1; p->avg_sim_score = para->PROT_SIM_SCORE_THRESHOLD; p->dist = (int*)calloc(2, sizeof(int)); p->dist[0] = n * n - n; p->dist[1] = n; return p; } /** Return a probability distribution for diagonal lengths * for a DNA score matrix. */ static prob_dist* newDefaultDiagProbDist() { prob_dist *o = (prob_dist*)calloc(1, sizeof *o); o->smatrix = smatrix; unsigned length = 100; o->max_dlen = length; o->data = (long double**)calloc( length + 1, sizeof(long double *)); o->log_data = (double**)calloc(length + 1, sizeof(double *)); long double **dist = o->data; double **log_dist = o->log_data; const double* p = dna_diag_prob_100_exp_550000; for (unsigned i = 1; i <= length; i++) { unsigned mxscr = i * smatrix->max_score; dist[i] = (long double*)calloc( mxscr + 1, sizeof(long double)); log_dist[i] = (double*)calloc(mxscr + 1, sizeof(double)); for (unsigned scr = 0; scr <= mxscr; scr++) { double weight = *p++; assert(weight > 0); dist[i][scr] = weight; log_dist[i][scr] = -log(weight); } } return o; } /** Initialize dialign. */ void initDialign() { // Score matrix smatrix = strlen(para->SCR_MATRIX_FILE_NAME) > 0 ? read_scr_matrix(para->SCR_MATRIX_FILE_NAME) : newDefaultScoreMatrix(); if (para->DEBUG > 5) print_scr_matrix(smatrix); // Probability distribution for diagonal lengths pdist = strlen(para->DIAG_PROB_FILE_NAME) > 0 ? read_diag_prob_dist(smatrix, para->DIAG_PROB_FILE_NAME) : newDefaultDiagProbDist(); } static void free_scr_matrix(struct scr_matrix* smatrix) { free(smatrix->dist); free(smatrix->data); free(smatrix->char2num); free(smatrix->num2char); free(smatrix); } void free_prob_dist(struct prob_dist* pdist) { unsigned int length = pdist->max_dlen; unsigned int i; for (i=1; i<=length; i++) { free(pdist->data[i]); free(pdist->log_data[i]); } free(pdist->data); free(pdist->log_data); free_scr_matrix(pdist->smatrix); free(pdist); } static void free_seq_col(struct seq_col* scol) { unsigned int length = scol->length; unsigned int i; for (i=0; iseqs[i]).data); free(scol->seqs); free(scol); } /** Print a dialign alignment. */ static ostream& print(ostream& out, const alignment& o, const string& consensus) { const seq_col& scol = *o.scol; vector proc(scol.length, 0); algn_pos **ap = o.algn; for (int s = 0; s < scol.length; s++) { const seq& sq = scol.seqs[s]; for (int j = 0; j < o.max_pos; j++) { if (proc[s] < sq.length) { const algn_pos& ap1 = *find_eqc(ap, s, proc[s]); assert(j <= *ap1.eqcAlgnPos); if (*ap1.eqcAlgnPos == j) { char c = sq.data[proc[s]]; if (toupper(c) == toupper(consensus[j])) out << '.'; else if (ap1.state & para->STATE_ORPHANE) out << (char)tolower(c); else out << c; proc[s]++; } else out << '*'; } else out << '*'; } out << '\n'; } return out; } /** Return the minimum number of matches. */ static unsigned countMatches(const alignment& o, const string& consensus) { unsigned minMatches = consensus.size(); const seq_col& scol = *o.scol; vector proc(scol.length, 0); algn_pos **ap = o.algn; for (int s = 0; s < scol.length; s++) { unsigned matches = 0; const seq& sq = scol.seqs[s]; for (int j = 0; j < o.max_pos; j++) { if (proc[s] < sq.length) { const algn_pos& ap1 = *find_eqc(ap, s, proc[s]); assert(j <= *ap1.eqcAlgnPos); if (*ap1.eqcAlgnPos == j) { char c = sq.data[proc[s]]; if (toupper(c) == toupper(consensus[j])) matches++; proc[s]++; } } } minMatches = min(minMatches, matches); } return minMatches; } static struct seq_col* read_seqs(const vector& amb_seqs) { struct seq_col* scol = (struct seq_col*)calloc(1, sizeof(struct seq_col)); struct seq* seqs = (scol->seqs = (struct seq*)calloc(amb_seqs.size(), sizeof(struct seq))); if(scol==NULL || seqs==NULL) { cerr << "read_seqs(): Out of memory !\n"; exit(EXIT_FAILURE); } scol->length = amb_seqs.size(); scol->avg_length = 0; seq* seq; for (size_t i=0; iseqs[i]); seq->max_seen = 0; //seq->name = calloc(rlen, sizeof(char)); //do I need this? seq->num = i; seq->orf_frame=0; seq->crick_strand=0; //strncpy(seq->name, &(rline[1]), rlen-2); seq->data = (char*)calloc(amb_seqs[i].length()+1, sizeof(char)); if (seq->data == NULL) { cerr << "seq->data out of memory !\n"; exit(EXIT_FAILURE); } strcpy(seq->data, amb_seqs[i].c_str()); seq->length = amb_seqs[i].length(); scol->avg_length += amb_seqs[i].length(); if(para->DEBUG >1) printf("DEBUG: seq:%s\n", seq->data); } scol->avg_length /= scol->length; if(para->DEBUG >1) printf("DEBUG: total # of amb_seqs: %i, avg_length: %i\n", scol->length, scol->avg_length); return scol; } // assume initial sequences contain only a/c/g/t/n static string get_alignment_consensus(struct alignment *algn) { struct seq_col *scol = algn->scol; unsigned int slen = scol->length; int j; unsigned int s,max; struct seq* sq; struct algn_pos **ap = algn->algn; prepare_alignment(algn); max = algn->max_pos; if (para->DEBUG > 5) printf("slen is %u, max pos is %u\n", slen, max); struct algn_pos *ap1; max = algn->max_pos; int* proc = new int[slen]; for (j=0; j<(int)slen; j++) proc[j] = 0; string consensus; for (j=0; j<(int)max; j++) { char c = 'X'; bool gap = false; for(s=0;sseqs[s]); if(proc[s] < sq->length) { ap1 = find_eqc(ap,s,proc[s]); if(*ap1->eqcAlgnPos==j) { char cur_char = toupper(sq->data[proc[s]]); c = c == 'X' ? cur_char : ambiguityOr(c, cur_char); proc[s]++; } else gap = true; } else gap = true; } consensus += gap ? tolower(c) : c; } delete[] proc; return consensus; } /** Align multiple sequences using DIALIGN-TX. * @param [out] alignment the alignment * @param [out] matches the minimum number of matches * @return the consensus sequence */ string dialign(const vector& amb_seqs, string& alignment, unsigned& matches) { int i; struct seq_col *in_seq_col = NULL; double tim = clock(); in_seq_col = read_seqs(amb_seqs); // fast mode has higher threshold weights struct parameters *dialign_para = para; if(dialign_para->FAST_MODE) dialign_para->PROT_SIM_SCORE_THRESHOLD += 0.25; // Consider Anchors -> default for DNA: DO_ANCHOR = 0; struct alignment *algn = NULL; if (!dialign_para->FAST_MODE) algn = create_empty_alignment(in_seq_col); struct alignment *salgn = create_empty_alignment(in_seq_col); if (dialign_para->DEBUG > 1) printf("empty alignments created\n"); // Compute pairwise diagonals struct diag_col *all_diags = find_all_diags(smatrix, pdist, in_seq_col, salgn, 1); double duration = (clock()-tim)/CLOCKS_PER_SEC; if (dialign_para->DEBUG > 1) printf("Found %i diags in %f secs\n", all_diags->diag_amount, duration); int diag_amount = all_diags->diag_amount; // Compute alignment double tim2 = clock(); if (!dialign_para->FAST_MODE) { vector cp_diags(all_diags->diag_amount); for(i = 0; i < diag_amount; i++) { cp_diags[i] = (diag*)malloc(sizeof(struct diag)); *(cp_diags[i]) = *(all_diags->diags[i]); } guided_aligner(algn, in_seq_col, all_diags, smatrix, pdist, all_diags->gt_root, 1); for(i = 0; i < diag_amount; i++) all_diags->diags[i] = cp_diags[i]; all_diags->diag_amount = diag_amount; } simple_aligner(in_seq_col, all_diags, smatrix, pdist, salgn, 1); duration = (clock()-tim2)/CLOCKS_PER_SEC; if (!dialign_para->FAST_MODE) { if (dialign_para->DEBUG > 1) printf("First alignment after %f secs. " "simple: %f guided: %f\n", duration, salgn->total_weight, algn->total_weight); else if (dialign_para->DEBUG > 1) printf("First alignment after %f secs. simple: %f \n", duration, salgn->total_weight); } free_diag_col(all_diags); dialign_para->DO_ANCHOR = 0; // anchors done // round 2+ int round; char newFound = 0; int type; // consider sensitivity level if (!dialign_para->FAST_MODE) { if (dialign_para->SENS_MODE == 0) { dialign_para->DIAG_THRESHOLD_WEIGHT = 0.0; } else if (dialign_para->SENS_MODE == 1) { dialign_para->DIAG_THRESHOLD_WEIGHT = -log(0.75);//-log(.875+0.125/2.0); } else if (dialign_para->SENS_MODE == 2) { dialign_para->DIAG_THRESHOLD_WEIGHT = -log(0.5);//-log(0.875); } } int stype = (dialign_para->FAST_MODE ? 1 : 0); for (type = stype; type < 2; type++) { for (round = 2; round <= 20; round++) { tim2 = clock(); all_diags = find_all_diags(smatrix, pdist, in_seq_col, (type ? salgn : algn), round); duration = (clock()-tim2)/CLOCKS_PER_SEC; if (dialign_para->DEBUG > 1) printf("Found %i diags after %f secs\n", all_diags->diag_amount, duration); if (all_diags->diag_amount == 0) { free_diag_col(all_diags); break; } else { // round 2 and further we use the simple aligner newFound = simple_aligner(in_seq_col, all_diags, smatrix, pdist, (type ? salgn : algn), round); free_diag_col(all_diags); if (!newFound) break; } } } if (dialign_para->DEBUG > 1) printf("Alignment ready!\n"); if (!dialign_para->FAST_MODE) { if (dialign_para->DEBUG > 1) printf("Final alignment simple: %f guided: %f\n", salgn->total_weight, algn->total_weight); } else { if (dialign_para->DEBUG > 1) printf("Final alignment simple: %f \n", salgn->total_weight); } if (dialign_para->FAST_MODE || salgn->total_weight > algn->total_weight) { if (!dialign_para->FAST_MODE) free_alignment(algn); algn = salgn; } else { free_alignment(salgn); } if (opt::verbose > 3) simple_print_alignment_default(algn); string consensus = get_alignment_consensus(algn); matches = countMatches(*algn, consensus); ostringstream ss; print(ss, *algn, consensus); alignment = ss.str(); if (dialign_para->DEBUG > 0) { duration = (clock()-tim)/CLOCKS_PER_SEC; cerr << "Total time: " << duration << " s\n" "Total weight: " << algn->total_weight << '\n'; } free_alignment(algn); free_seq_col(in_seq_col); return consensus; } abyss-1.3.6/Align/dialign.h000644 002433 001057 00000002347 12015543262 017177 0ustar00traymondassembly000000 000000 #ifndef DIALIGN_H #define DIALIGN_H 1 extern "C" { #include "dialign/io.h" #include "dialign/parameters.h" #include "dialign/struct.h" extern struct scr_matrix *smatrix; extern struct prob_dist *pdist; extern const double dna_diag_prob_100_exp_550000[5151]; struct alignment* create_empty_alignment(struct seq_col *scol); struct diag_col *find_all_diags(struct scr_matrix *smatrix, struct prob_dist *pdist, struct seq_col *in_seq_col, struct alignment *algn, int round); struct alignment* guided_aligner(struct alignment *palgn, struct seq_col *scol, struct diag_col *dcol, struct scr_matrix* smatrix, struct prob_dist *pdist, struct gt_node *gtn, int round); char simple_aligner(struct seq_col *scol, struct diag_col *dcol, struct scr_matrix* smatrix, struct prob_dist *pdist, struct alignment *algn, int round); void prepare_alignment(struct alignment *algn); struct algn_pos *find_eqc(struct algn_pos **ap, int seqnum, int pos); void free_alignment(struct alignment* algn); void free_diag_col(struct diag_col* dcol); } #include #include void initDialign(); void free_prob_dist(struct prob_dist* pdist); std::string dialign(const std::vector& amb_seqs, std::string& alignment, unsigned& matches); #endif abyss-1.3.6/Align/dna_diag_prob.cc000644 002433 001057 00000403771 11746352076 020517 0ustar00traymondassembly000000 000000 #include "dialign.h" /* Probability distribution for diagonal lengths. */ const double dna_diag_prob_100_exp_550000[5151] = { /* 1 0 */ 1.000000e+00, /* 1 1 */ 6.730455e-01, /* 2 0 */ 1.000000e+00, /* 2 1 */ 9.670818e-01, /* 2 2 */ 4.120255e-01, /* 3 0 */ 1.000000e+00, /* 3 1 */ 9.979000e-01, /* 3 2 */ 8.519509e-01, /* 3 3 */ 1.974073e-01, /* 4 0 */ 1.000000e+00, /* 4 1 */ 9.998618e-01, /* 4 2 */ 9.809545e-01, /* 4 3 */ 5.966600e-01, /* 4 4 */ 7.885273e-02, /* 5 0 */ 1.000000e+00, /* 5 1 */ 9.999909e-01, /* 5 2 */ 9.982182e-01, /* 5 3 */ 8.905636e-01, /* 5 4 */ 3.229873e-01, /* 5 5 */ 2.844545e-02, /* 6 0 */ 1.000000e+00, /* 6 1 */ 1.000000e+00, /* 6 2 */ 9.998564e-01, /* 6 3 */ 9.827782e-01, /* 6 4 */ 6.597564e-01, /* 6 5 */ 1.446764e-01, /* 6 6 */ 9.710909e-03, /* 7 0 */ 1.000000e+00, /* 7 1 */ 1.000000e+00, /* 7 2 */ 9.999964e-01, /* 7 3 */ 9.980182e-01, /* 7 4 */ 8.957327e-01, /* 7 5 */ 3.821818e-01, /* 7 6 */ 5.771455e-02, /* 7 7 */ 3.210909e-03, /* 8 0 */ 1.000000e+00, /* 8 1 */ 1.000000e+00, /* 8 2 */ 1.000000e+00, /* 8 3 */ 9.998164e-01, /* 8 4 */ 9.798309e-01, /* 8 5 */ 6.726545e-01, /* 8 6 */ 1.831455e-01, /* 8 7 */ 2.081818e-02, /* 8 8 */ 1.034545e-03, /* 9 0 */ 1.000000e+00, /* 9 1 */ 1.000000e+00, /* 9 2 */ 1.000000e+00, /* 9 3 */ 9.999891e-01, /* 9 4 */ 9.971818e-01, /* 9 5 */ 8.838709e-01, /* 9 6 */ 4.005764e-01, /* 9 7 */ 7.684182e-02, /* 9 8 */ 7.283636e-03, /* 9 9 */ 3.327273e-04, /* 10 0 */ 1.000000e+00, /* 10 1 */ 1.000000e+00, /* 10 2 */ 1.000000e+00, /* 10 3 */ 9.999982e-01, /* 10 4 */ 9.996382e-01, /* 10 5 */ 9.730073e-01, /* 10 6 */ 6.584691e-01, /* 10 7 */ 1.977636e-01, /* 10 8 */ 2.972182e-02, /* 10 9 */ 2.398182e-03, /* 10 10 */ 1.127273e-04, /* 11 0 */ 1.000000e+00, /* 11 1 */ 1.000000e+00, /* 11 2 */ 1.000000e+00, /* 11 3 */ 1.000000e+00, /* 11 4 */ 9.999655e-01, /* 11 5 */ 9.953236e-01, /* 11 6 */ 8.598509e-01, /* 11 7 */ 3.929982e-01, /* 11 8 */ 8.693273e-02, /* 11 9 */ 1.099091e-02, /* 11 10 */ 7.872727e-04, /* 11 11 */ 3.272727e-05, /* 12 0 */ 1.000000e+00, /* 12 1 */ 1.000000e+00, /* 12 2 */ 1.000000e+00, /* 12 3 */ 1.000000e+00, /* 12 4 */ 9.999945e-01, /* 12 5 */ 9.993891e-01, /* 12 6 */ 9.605727e-01, /* 12 7 */ 6.266636e-01, /* 12 8 */ 1.981436e-01, /* 12 9 */ 3.510364e-02, /* 12 10 */ 3.932727e-03, /* 12 11 */ 2.781818e-04, /* 12 12 */ 1.007318e-05, /* 13 0 */ 1.000000e+00, /* 13 1 */ 1.000000e+00, /* 13 2 */ 1.000000e+00, /* 13 3 */ 1.000000e+00, /* 13 4 */ 1.000000e+00, /* 13 5 */ 9.999000e-01, /* 13 6 */ 9.921364e-01, /* 13 7 */ 8.258491e-01, /* 13 8 */ 3.724073e-01, /* 13 9 */ 8.930182e-02, /* 13 10 */ 1.366727e-02, /* 13 11 */ 1.394545e-03, /* 13 12 */ 7.818182e-05, /* 13 13 */ 2.920628e-06, /* 14 0 */ 1.000000e+00, /* 14 1 */ 1.000000e+00, /* 14 2 */ 1.000000e+00, /* 14 3 */ 1.000000e+00, /* 14 4 */ 1.000000e+00, /* 14 5 */ 9.999964e-01, /* 14 6 */ 9.987527e-01, /* 14 7 */ 9.410745e-01, /* 14 8 */ 5.849291e-01, /* 14 9 */ 1.902582e-01, /* 14 10 */ 3.750727e-02, /* 14 11 */ 5.054545e-03, /* 14 12 */ 4.563636e-04, /* 14 13 */ 3.454545e-05, /* 14 14 */ 8.381903e-07, /* 15 0 */ 1.000000e+00, /* 15 1 */ 1.000000e+00, /* 15 2 */ 1.000000e+00, /* 15 3 */ 1.000000e+00, /* 15 4 */ 1.000000e+00, /* 15 5 */ 1.000000e+00, /* 15 6 */ 9.998218e-01, /* 15 7 */ 9.857345e-01, /* 15 8 */ 7.810727e-01, /* 15 9 */ 3.435873e-01, /* 15 10 */ 8.694000e-02, /* 15 11 */ 1.504909e-02, /* 15 12 */ 1.870909e-03, /* 15 13 */ 1.400000e-04, /* 15 14 */ 1.096725e-05, /* 15 15 */ 2.384186e-07, /* 16 0 */ 1.000000e+00, /* 16 1 */ 1.000000e+00, /* 16 2 */ 1.000000e+00, /* 16 3 */ 1.000000e+00, /* 16 4 */ 1.000000e+00, /* 16 5 */ 1.000000e+00, /* 16 6 */ 9.999818e-01, /* 16 7 */ 9.972691e-01, /* 16 8 */ 9.120782e-01, /* 16 9 */ 5.356636e-01, /* 16 10 */ 1.751473e-01, /* 16 11 */ 3.724182e-02, /* 16 12 */ 5.770909e-03, /* 16 13 */ 6.545455e-04, /* 16 14 */ 4.363636e-05, /* 16 15 */ 3.297115e-06, /* 16 16 */ 6.728806e-08, /* 17 0 */ 1.000000e+00, /* 17 1 */ 1.000000e+00, /* 17 2 */ 1.000000e+00, /* 17 3 */ 1.000000e+00, /* 17 4 */ 1.000000e+00, /* 17 5 */ 1.000000e+00, /* 17 6 */ 9.999982e-01, /* 17 7 */ 9.996127e-01, /* 17 8 */ 9.740327e-01, /* 17 9 */ 7.278618e-01, /* 17 10 */ 3.094855e-01, /* 17 11 */ 8.132909e-02, /* 17 12 */ 1.516182e-02, /* 17 13 */ 2.134545e-03, /* 17 14 */ 2.309091e-04, /* 17 15 */ 2.406444e-05, /* 17 16 */ 9.806827e-07, /* 17 17 */ 1.885928e-08, /* 18 0 */ 1.000000e+00, /* 18 1 */ 1.000000e+00, /* 18 2 */ 1.000000e+00, /* 18 3 */ 1.000000e+00, /* 18 4 */ 1.000000e+00, /* 18 5 */ 1.000000e+00, /* 18 6 */ 1.000000e+00, /* 18 7 */ 9.999382e-01, /* 18 8 */ 9.941927e-01, /* 18 9 */ 8.733745e-01, /* 18 10 */ 4.831091e-01, /* 18 11 */ 1.582600e-01, /* 18 12 */ 3.553818e-02, /* 18 13 */ 6.020000e-03, /* 18 14 */ 8.090909e-04, /* 18 15 */ 8.000000e-05, /* 18 16 */ 7.522642e-06, /* 18 17 */ 2.889283e-07, /* 18 18 */ 5.253241e-09, /* 19 0 */ 1.000000e+00, /* 19 1 */ 1.000000e+00, /* 19 2 */ 1.000000e+00, /* 19 3 */ 1.000000e+00, /* 19 4 */ 1.000000e+00, /* 19 5 */ 1.000000e+00, /* 19 6 */ 1.000000e+00, /* 19 7 */ 9.999927e-01, /* 19 8 */ 9.989600e-01, /* 19 9 */ 9.548018e-01, /* 19 10 */ 6.672091e-01, /* 19 11 */ 2.747782e-01, /* 19 12 */ 7.364909e-02, /* 19 13 */ 1.470364e-02, /* 19 14 */ 2.361818e-03, /* 19 15 */ 3.127273e-04, /* 19 16 */ 3.454545e-05, /* 19 17 */ 2.323941e-06, /* 19 18 */ 8.440111e-08, /* 19 19 */ 1.455192e-09, /* 20 0 */ 1.000000e+00, /* 20 1 */ 1.000000e+00, /* 20 2 */ 1.000000e+00, /* 20 3 */ 1.000000e+00, /* 20 4 */ 1.000000e+00, /* 20 5 */ 1.000000e+00, /* 20 6 */ 1.000000e+00, /* 20 7 */ 9.999945e-01, /* 20 8 */ 9.998364e-01, /* 20 9 */ 9.880182e-01, /* 20 10 */ 8.238018e-01, /* 20 11 */ 4.288382e-01, /* 20 12 */ 1.396818e-01, /* 20 13 */ 3.265455e-02, /* 20 14 */ 5.916364e-03, /* 20 15 */ 9.327273e-04, /* 20 16 */ 1.145455e-04, /* 20 17 */ 1.305579e-05, /* 20 18 */ 7.103254e-07, /* 20 19 */ 2.446632e-08, /* 20 20 */ 4.010872e-10, /* 21 0 */ 1.000000e+00, /* 21 1 */ 1.000000e+00, /* 21 2 */ 1.000000e+00, /* 21 3 */ 1.000000e+00, /* 21 4 */ 1.000000e+00, /* 21 5 */ 1.000000e+00, /* 21 6 */ 1.000000e+00, /* 21 7 */ 1.000000e+00, /* 21 8 */ 9.999709e-01, /* 21 9 */ 9.974091e-01, /* 21 10 */ 9.260218e-01, /* 21 11 */ 6.026582e-01, /* 21 12 */ 2.398145e-01, /* 21 13 */ 6.590545e-02, /* 21 14 */ 1.380364e-02, /* 21 15 */ 2.380000e-03, /* 21 16 */ 3.672727e-04, /* 21 17 */ 4.363636e-05, /* 21 18 */ 4.166890e-06, /* 21 19 */ 2.150355e-07, /* 21 20 */ 7.043127e-09, /* 21 21 */ 1.100489e-10, /* 22 0 */ 1.000000e+00, /* 22 1 */ 1.000000e+00, /* 22 2 */ 1.000000e+00, /* 22 3 */ 1.000000e+00, /* 22 4 */ 1.000000e+00, /* 22 5 */ 1.000000e+00, /* 22 6 */ 1.000000e+00, /* 22 7 */ 1.000000e+00, /* 22 8 */ 9.999964e-01, /* 22 9 */ 9.995200e-01, /* 22 10 */ 9.760564e-01, /* 22 11 */ 7.642291e-01, /* 22 12 */ 3.756655e-01, /* 22 13 */ 1.211818e-01, /* 22 14 */ 2.931455e-02, /* 22 15 */ 5.654545e-03, /* 22 16 */ 9.218182e-04, /* 22 17 */ 1.345455e-04, /* 22 18 */ 1.913187e-05, /* 22 19 */ 1.314848e-06, /* 22 20 */ 6.453058e-08, /* 22 21 */ 2.014701e-09, /* 22 22 */ 3.007017e-11, /* 23 0 */ 1.000000e+00, /* 23 1 */ 1.000000e+00, /* 23 2 */ 1.000000e+00, /* 23 3 */ 1.000000e+00, /* 23 4 */ 1.000000e+00, /* 23 5 */ 1.000000e+00, /* 23 6 */ 1.000000e+00, /* 23 7 */ 1.000000e+00, /* 23 8 */ 1.000000e+00, /* 23 9 */ 9.999091e-01, /* 23 10 */ 9.939800e-01, /* 23 11 */ 8.861836e-01, /* 23 12 */ 5.363855e-01, /* 23 13 */ 2.062655e-01, /* 23 14 */ 5.769273e-02, /* 23 15 */ 1.282000e-02, /* 23 16 */ 2.223636e-03, /* 23 17 */ 3.818182e-04, /* 23 18 */ 4.909091e-05, /* 23 19 */ 6.281672e-06, /* 23 20 */ 4.106150e-07, /* 23 21 */ 1.921126e-08, /* 23 22 */ 5.729817e-10, /* 23 23 */ 8.185452e-12, /* 24 0 */ 1.000000e+00, /* 24 1 */ 1.000000e+00, /* 24 2 */ 1.000000e+00, /* 24 3 */ 1.000000e+00, /* 24 4 */ 1.000000e+00, /* 24 5 */ 1.000000e+00, /* 24 6 */ 1.000000e+00, /* 24 7 */ 1.000000e+00, /* 24 8 */ 1.000000e+00, /* 24 9 */ 9.999873e-01, /* 24 10 */ 9.987582e-01, /* 24 11 */ 9.557455e-01, /* 24 12 */ 6.970909e-01, /* 24 13 */ 3.241800e-01, /* 24 14 */ 1.044855e-01, /* 24 15 */ 2.595818e-02, /* 24 16 */ 5.249091e-03, /* 24 17 */ 9.036364e-04, /* 24 18 */ 1.381818e-04, /* 24 19 */ 2.497199e-05, /* 24 20 */ 2.038172e-06, /* 24 21 */ 1.270206e-07, /* 24 22 */ 5.677681e-09, /* 24 23 */ 1.620926e-10, /* 24 24 */ 2.220446e-12, /* 25 0 */ 1.000000e+00, /* 25 1 */ 1.000000e+00, /* 25 2 */ 1.000000e+00, /* 25 3 */ 1.000000e+00, /* 25 4 */ 1.000000e+00, /* 25 5 */ 1.000000e+00, /* 25 6 */ 1.000000e+00, /* 25 7 */ 1.000000e+00, /* 25 8 */ 1.000000e+00, /* 25 9 */ 9.999982e-01, /* 25 10 */ 9.997836e-01, /* 25 11 */ 9.863527e-01, /* 25 12 */ 8.327455e-01, /* 25 13 */ 4.696527e-01, /* 25 14 */ 1.758091e-01, /* 25 15 */ 4.943091e-02, /* 25 16 */ 1.134000e-02, /* 25 17 */ 2.156364e-03, /* 25 18 */ 3.509091e-04, /* 25 19 */ 6.727273e-05, /* 25 20 */ 8.405790e-06, /* 25 21 */ 6.541608e-07, /* 25 22 */ 3.895211e-08, /* 25 23 */ 1.666734e-09, /* 25 24 */ 4.563105e-11, /* 25 25 */ 6.004086e-13, /* 26 0 */ 1.000000e+00, /* 26 1 */ 1.000000e+00, /* 26 2 */ 1.000000e+00, /* 26 3 */ 1.000000e+00, /* 26 4 */ 1.000000e+00, /* 26 5 */ 1.000000e+00, /* 26 6 */ 1.000000e+00, /* 26 7 */ 1.000000e+00, /* 26 8 */ 1.000000e+00, /* 26 9 */ 1.000000e+00, /* 26 10 */ 9.999618e-01, /* 26 11 */ 9.967691e-01, /* 26 12 */ 9.239927e-01, /* 26 13 */ 6.252236e-01, /* 26 14 */ 2.766891e-01, /* 26 15 */ 8.827091e-02, /* 26 16 */ 2.257636e-02, /* 26 17 */ 4.838182e-03, /* 26 18 */ 8.618182e-04, /* 26 19 */ 1.400000e-04, /* 26 20 */ 2.909091e-05, /* 26 21 */ 2.795292e-06, /* 26 22 */ 2.078667e-07, /* 26 23 */ 1.184957e-08, /* 26 24 */ 4.862590e-10, /* 26 25 */ 1.278777e-11, /* 26 26 */ 1.618705e-13, /* 27 0 */ 1.000000e+00, /* 27 1 */ 1.000000e+00, /* 27 2 */ 1.000000e+00, /* 27 3 */ 1.000000e+00, /* 27 4 */ 1.000000e+00, /* 27 5 */ 1.000000e+00, /* 27 6 */ 1.000000e+00, /* 27 7 */ 1.000000e+00, /* 27 8 */ 1.000000e+00, /* 27 9 */ 1.000000e+00, /* 27 10 */ 9.999945e-01, /* 27 11 */ 9.993291e-01, /* 27 12 */ 9.726164e-01, /* 27 13 */ 7.696218e-01, /* 27 14 */ 4.050855e-01, /* 27 15 */ 1.481582e-01, /* 27 16 */ 4.218000e-02, /* 27 17 */ 1.004000e-02, /* 27 18 */ 1.972727e-03, /* 27 19 */ 3.290909e-04, /* 27 20 */ 6.727273e-05, /* 27 21 */ 1.031061e-05, /* 27 22 */ 9.192084e-07, /* 27 23 */ 6.544501e-08, /* 27 24 */ 3.578101e-09, /* 27 25 */ 1.410507e-10, /* 27 26 */ 3.568701e-12, /* 27 27 */ 4.352074e-14, /* 28 0 */ 1.000000e+00, /* 28 1 */ 1.000000e+00, /* 28 2 */ 1.000000e+00, /* 28 3 */ 1.000000e+00, /* 28 4 */ 1.000000e+00, /* 28 5 */ 1.000000e+00, /* 28 6 */ 1.000000e+00, /* 28 7 */ 1.000000e+00, /* 28 8 */ 1.000000e+00, /* 28 9 */ 1.000000e+00, /* 28 10 */ 1.000000e+00, /* 28 11 */ 9.999000e-01, /* 28 12 */ 9.922545e-01, /* 28 13 */ 8.798709e-01, /* 28 14 */ 5.509618e-01, /* 28 15 */ 2.333200e-01, /* 28 16 */ 7.442364e-02, /* 28 17 */ 1.933455e-02, /* 28 18 */ 4.320000e-03, /* 28 19 */ 7.781818e-04, /* 28 20 */ 1.381818e-04, /* 28 21 */ 2.727273e-05, /* 28 22 */ 3.504586e-06, /* 28 23 */ 2.991620e-07, /* 28 24 */ 2.042947e-08, /* 28 25 */ 1.073040e-09, /* 28 26 */ 4.069754e-11, /* 28 27 */ 9.920537e-13, /* 28 28 */ 1.167122e-14, /* 29 0 */ 1.000000e+00, /* 29 1 */ 1.000000e+00, /* 29 2 */ 1.000000e+00, /* 29 3 */ 1.000000e+00, /* 29 4 */ 1.000000e+00, /* 29 5 */ 1.000000e+00, /* 29 6 */ 1.000000e+00, /* 29 7 */ 1.000000e+00, /* 29 8 */ 1.000000e+00, /* 29 9 */ 1.000000e+00, /* 29 10 */ 1.000000e+00, /* 29 11 */ 9.999873e-01, /* 29 12 */ 9.982291e-01, /* 29 13 */ 9.487145e-01, /* 29 14 */ 6.981673e-01, /* 29 15 */ 3.453327e-01, /* 29 16 */ 1.235055e-01, /* 29 17 */ 3.544727e-02, /* 29 18 */ 8.707273e-03, /* 29 19 */ 1.783636e-03, /* 29 20 */ 3.090909e-04, /* 29 21 */ 5.090909e-05, /* 29 22 */ 1.183615e-05, /* 29 23 */ 1.177724e-06, /* 29 24 */ 9.643441e-08, /* 29 25 */ 6.326911e-09, /* 29 26 */ 3.197442e-10, /* 29 27 */ 1.168440e-11, /* 29 28 */ 2.747802e-13, /* 29 29 */ 3.122502e-15, /* 30 0 */ 1.000000e+00, /* 30 1 */ 1.000000e+00, /* 30 2 */ 1.000000e+00, /* 30 3 */ 1.000000e+00, /* 30 4 */ 1.000000e+00, /* 30 5 */ 1.000000e+00, /* 30 6 */ 1.000000e+00, /* 30 7 */ 1.000000e+00, /* 30 8 */ 1.000000e+00, /* 30 9 */ 1.000000e+00, /* 30 10 */ 1.000000e+00, /* 30 11 */ 9.999982e-01, /* 30 12 */ 9.996145e-01, /* 30 13 */ 9.822418e-01, /* 30 14 */ 8.227145e-01, /* 30 15 */ 4.789527e-01, /* 30 16 */ 1.952782e-01, /* 30 17 */ 6.181273e-02, /* 30 18 */ 1.640727e-02, /* 30 19 */ 3.714545e-03, /* 30 20 */ 7.036364e-04, /* 30 21 */ 1.200000e-04, /* 30 22 */ 3.611135e-05, /* 30 23 */ 4.102757e-06, /* 30 24 */ 3.916149e-07, /* 30 25 */ 3.080943e-08, /* 30 26 */ 1.944996e-09, /* 30 27 */ 9.471121e-11, /* 30 28 */ 3.339140e-12, /* 30 29 */ 7.585165e-14, /* 30 30 */ 8.335346e-16, /* 31 0 */ 1.000000e+00, /* 31 1 */ 1.000000e+00, /* 31 2 */ 1.000000e+00, /* 31 3 */ 1.000000e+00, /* 31 4 */ 1.000000e+00, /* 31 5 */ 1.000000e+00, /* 31 6 */ 1.000000e+00, /* 31 7 */ 1.000000e+00, /* 31 8 */ 1.000000e+00, /* 31 9 */ 1.000000e+00, /* 31 10 */ 1.000000e+00, /* 31 11 */ 1.000000e+00, /* 31 12 */ 9.999218e-01, /* 31 13 */ 9.951964e-01, /* 31 14 */ 9.121473e-01, /* 31 15 */ 6.207782e-01, /* 31 16 */ 2.910200e-01, /* 31 17 */ 1.022600e-01, /* 31 18 */ 2.944727e-02, /* 31 19 */ 7.225455e-03, /* 31 20 */ 1.632727e-03, /* 31 21 */ 2.781818e-04, /* 31 22 */ 5.454545e-05, /* 31 23 */ 1.289846e-05, /* 31 24 */ 1.405896e-06, /* 31 25 */ 1.289439e-07, /* 31 26 */ 9.761676e-09, /* 31 27 */ 5.938159e-10, /* 31 28 */ 2.789857e-11, /* 31 29 */ 9.501289e-13, /* 31 30 */ 2.087219e-14, /* 31 31 */ 2.220446e-16, /* 32 0 */ 1.000000e+00, /* 32 1 */ 1.000000e+00, /* 32 2 */ 1.000000e+00, /* 32 3 */ 1.000000e+00, /* 32 4 */ 1.000000e+00, /* 32 5 */ 1.000000e+00, /* 32 6 */ 1.000000e+00, /* 32 7 */ 1.000000e+00, /* 32 8 */ 1.000000e+00, /* 32 9 */ 1.000000e+00, /* 32 10 */ 1.000000e+00, /* 32 11 */ 1.000000e+00, /* 32 12 */ 9.999800e-01, /* 32 13 */ 9.989327e-01, /* 32 14 */ 9.638855e-01, /* 32 15 */ 7.548182e-01, /* 32 16 */ 4.098745e-01, /* 32 17 */ 1.615600e-01, /* 32 18 */ 5.084727e-02, /* 32 19 */ 1.364182e-02, /* 32 20 */ 3.136364e-03, /* 32 21 */ 6.763636e-04, /* 32 22 */ 1.345455e-04, /* 32 23 */ 2.363636e-05, /* 32 24 */ 4.550656e-06, /* 32 25 */ 4.766309e-07, /* 32 26 */ 4.206818e-08, /* 32 27 */ 3.068960e-09, /* 32 28 */ 1.801294e-10, /* 32 29 */ 8.175199e-12, /* 32 30 */ 2.692578e-13, /* 32 31 */ 5.726376e-15, /* 32 32 */ 5.903481e-17, /* 33 0 */ 1.000000e+00, /* 33 1 */ 1.000000e+00, /* 33 2 */ 1.000000e+00, /* 33 3 */ 1.000000e+00, /* 33 4 */ 1.000000e+00, /* 33 5 */ 1.000000e+00, /* 33 6 */ 1.000000e+00, /* 33 7 */ 1.000000e+00, /* 33 8 */ 1.000000e+00, /* 33 9 */ 1.000000e+00, /* 33 10 */ 1.000000e+00, /* 33 11 */ 1.000000e+00, /* 33 12 */ 9.999982e-01, /* 33 13 */ 9.997782e-01, /* 33 14 */ 9.881109e-01, /* 33 15 */ 8.623436e-01, /* 33 16 */ 5.440909e-01, /* 33 17 */ 2.428600e-01, /* 33 18 */ 8.408545e-02, /* 33 19 */ 2.426545e-02, /* 33 20 */ 6.121818e-03, /* 33 21 */ 1.385455e-03, /* 33 22 */ 2.618182e-04, /* 33 23 */ 5.818182e-05, /* 33 24 */ 1.347999e-05, /* 33 25 */ 1.587125e-06, /* 33 26 */ 1.599811e-07, /* 33 27 */ 1.360743e-08, /* 33 28 */ 9.578529e-10, /* 33 29 */ 5.431157e-11, /* 33 30 */ 2.383911e-12, /* 33 31 */ 7.601493e-14, /* 33 32 */ 1.566672e-15, /* 33 33 */ 1.566672e-17, /* 34 0 */ 1.000000e+00, /* 34 1 */ 1.000000e+00, /* 34 2 */ 1.000000e+00, /* 34 3 */ 1.000000e+00, /* 34 4 */ 1.000000e+00, /* 34 5 */ 1.000000e+00, /* 34 6 */ 1.000000e+00, /* 34 7 */ 1.000000e+00, /* 34 8 */ 1.000000e+00, /* 34 9 */ 1.000000e+00, /* 34 10 */ 1.000000e+00, /* 34 11 */ 1.000000e+00, /* 34 12 */ 1.000000e+00, /* 34 13 */ 9.999491e-01, /* 34 14 */ 9.967473e-01, /* 34 15 */ 9.345491e-01, /* 34 16 */ 6.803855e-01, /* 34 17 */ 3.466745e-01, /* 34 18 */ 1.326655e-01, /* 34 19 */ 4.164000e-02, /* 34 20 */ 1.138000e-02, /* 34 21 */ 2.674545e-03, /* 34 22 */ 6.127273e-04, /* 34 23 */ 1.236364e-04, /* 34 24 */ 3.272727e-05, /* 34 25 */ 4.832540e-06, /* 34 26 */ 5.476121e-07, /* 34 27 */ 5.319727e-08, /* 34 28 */ 4.366179e-09, /* 34 29 */ 2.969215e-10, /* 34 30 */ 1.628299e-11, /* 34 31 */ 6.919649e-13, /* 34 32 */ 2.138318e-14, /* 34 33 */ 4.274975e-16, /* 34 34 */ 4.150461e-18, /* 35 0 */ 1.000000e+00, /* 35 1 */ 1.000000e+00, /* 35 2 */ 1.000000e+00, /* 35 3 */ 1.000000e+00, /* 35 4 */ 1.000000e+00, /* 35 5 */ 1.000000e+00, /* 35 6 */ 1.000000e+00, /* 35 7 */ 1.000000e+00, /* 35 8 */ 1.000000e+00, /* 35 9 */ 1.000000e+00, /* 35 10 */ 1.000000e+00, /* 35 11 */ 1.000000e+00, /* 35 12 */ 1.000000e+00, /* 35 13 */ 9.999891e-01, /* 35 14 */ 9.993000e-01, /* 35 15 */ 9.741855e-01, /* 35 16 */ 8.002673e-01, /* 35 17 */ 4.693836e-01, /* 35 18 */ 2.005109e-01, /* 35 19 */ 6.863273e-02, /* 35 20 */ 2.008182e-02, /* 35 21 */ 4.994545e-03, /* 35 22 */ 1.203636e-03, /* 35 23 */ 2.509091e-04, /* 35 24 */ 6.909091e-05, /* 35 25 */ 1.361253e-05, /* 35 26 */ 1.712671e-06, /* 35 27 */ 1.870482e-07, /* 35 28 */ 1.753457e-08, /* 35 29 */ 1.390408e-09, /* 35 30 */ 9.145275e-11, /* 35 31 */ 4.855738e-12, /* 35 32 */ 1.999846e-13, /* 35 33 */ 5.994838e-15, /* 35 34 */ 1.163620e-16, /* 35 35 */ 1.097755e-18, /* 36 0 */ 1.000000e+00, /* 36 1 */ 1.000000e+00, /* 36 2 */ 1.000000e+00, /* 36 3 */ 1.000000e+00, /* 36 4 */ 1.000000e+00, /* 36 5 */ 1.000000e+00, /* 36 6 */ 1.000000e+00, /* 36 7 */ 1.000000e+00, /* 36 8 */ 1.000000e+00, /* 36 9 */ 1.000000e+00, /* 36 10 */ 1.000000e+00, /* 36 11 */ 1.000000e+00, /* 36 12 */ 1.000000e+00, /* 36 13 */ 1.000000e+00, /* 36 14 */ 9.998473e-01, /* 36 15 */ 9.916673e-01, /* 36 16 */ 8.920873e-01, /* 36 17 */ 6.013491e-01, /* 36 18 */ 2.898691e-01, /* 36 19 */ 1.085455e-01, /* 36 20 */ 3.413636e-02, /* 36 21 */ 9.327273e-03, /* 36 22 */ 2.260000e-03, /* 36 23 */ 5.000000e-04, /* 36 24 */ 1.254545e-04, /* 36 25 */ 2.727273e-05, /* 36 26 */ 4.951677e-06, /* 36 27 */ 6.004733e-07, /* 36 28 */ 6.328771e-08, /* 36 29 */ 5.732104e-09, /* 36 30 */ 4.396344e-10, /* 36 31 */ 2.799794e-11, /* 36 32 */ 1.440749e-12, /* 36 33 */ 5.756166e-14, /* 36 34 */ 1.675315e-15, /* 36 35 */ 3.159878e-17, /* 36 36 */ 2.898970e-19, /* 37 0 */ 1.000000e+00, /* 37 1 */ 1.000000e+00, /* 37 2 */ 1.000000e+00, /* 37 3 */ 1.000000e+00, /* 37 4 */ 1.000000e+00, /* 37 5 */ 1.000000e+00, /* 37 6 */ 1.000000e+00, /* 37 7 */ 1.000000e+00, /* 37 8 */ 1.000000e+00, /* 37 9 */ 1.000000e+00, /* 37 10 */ 1.000000e+00, /* 37 11 */ 1.000000e+00, /* 37 12 */ 1.000000e+00, /* 37 13 */ 1.000000e+00, /* 37 14 */ 9.999709e-01, /* 37 15 */ 9.978782e-01, /* 37 16 */ 9.506036e-01, /* 37 17 */ 7.282236e-01, /* 37 18 */ 3.987636e-01, /* 37 19 */ 1.646855e-01, /* 37 20 */ 5.604727e-02, /* 37 21 */ 1.618545e-02, /* 37 22 */ 4.296364e-03, /* 37 23 */ 1.007273e-03, /* 37 24 */ 2.272727e-04, /* 37 25 */ 5.272727e-05, /* 37 26 */ 1.335903e-05, /* 37 27 */ 1.780765e-06, /* 37 28 */ 2.084087e-07, /* 37 29 */ 2.122332e-08, /* 37 30 */ 1.859323e-09, /* 37 31 */ 1.380787e-10, /* 37 32 */ 8.522708e-12, /* 37 33 */ 4.254562e-13, /* 37 34 */ 1.650411e-14, /* 37 35 */ 4.667715e-16, /* 37 36 */ 8.561809e-18, /* 37 37 */ 7.644472e-20, /* 38 0 */ 1.000000e+00, /* 38 1 */ 1.000000e+00, /* 38 2 */ 1.000000e+00, /* 38 3 */ 1.000000e+00, /* 38 4 */ 1.000000e+00, /* 38 5 */ 1.000000e+00, /* 38 6 */ 1.000000e+00, /* 38 7 */ 1.000000e+00, /* 38 8 */ 1.000000e+00, /* 38 9 */ 1.000000e+00, /* 38 10 */ 1.000000e+00, /* 38 11 */ 1.000000e+00, /* 38 12 */ 1.000000e+00, /* 38 13 */ 1.000000e+00, /* 38 14 */ 1.000000e+00, /* 38 15 */ 9.995291e-01, /* 38 16 */ 9.810600e-01, /* 38 17 */ 8.353509e-01, /* 38 18 */ 5.225836e-01, /* 38 19 */ 2.401600e-01, /* 38 20 */ 8.822364e-02, /* 38 21 */ 2.739455e-02, /* 38 22 */ 7.583636e-03, /* 38 23 */ 1.885455e-03, /* 38 24 */ 4.309091e-04, /* 38 25 */ 1.000000e-04, /* 38 26 */ 2.909091e-05, /* 38 27 */ 4.924639e-06, /* 38 28 */ 6.335722e-07, /* 38 29 */ 7.164674e-08, /* 38 30 */ 7.057612e-09, /* 38 31 */ 5.986987e-10, /* 38 32 */ 4.309330e-11, /* 38 33 */ 2.580401e-12, /* 38 34 */ 1.250740e-13, /* 38 35 */ 4.714790e-15, /* 38 36 */ 1.296792e-16, /* 38 37 */ 2.314981e-18, /* 38 38 */ 2.013027e-20, /* 39 0 */ 1.000000e+00, /* 39 1 */ 1.000000e+00, /* 39 2 */ 1.000000e+00, /* 39 3 */ 1.000000e+00, /* 39 4 */ 1.000000e+00, /* 39 5 */ 1.000000e+00, /* 39 6 */ 1.000000e+00, /* 39 7 */ 1.000000e+00, /* 39 8 */ 1.000000e+00, /* 39 9 */ 1.000000e+00, /* 39 10 */ 1.000000e+00, /* 39 11 */ 1.000000e+00, /* 39 12 */ 1.000000e+00, /* 39 13 */ 1.000000e+00, /* 39 14 */ 1.000000e+00, /* 39 15 */ 9.998836e-01, /* 39 16 */ 9.940309e-01, /* 39 17 */ 9.138745e-01, /* 39 18 */ 6.495091e-01, /* 39 19 */ 3.354945e-01, /* 39 20 */ 1.346200e-01, /* 39 21 */ 4.504364e-02, /* 39 22 */ 1.313636e-02, /* 39 23 */ 3.481818e-03, /* 39 24 */ 8.290909e-04, /* 39 25 */ 1.836364e-04, /* 39 26 */ 5.636364e-05, /* 39 27 */ 1.279770e-05, /* 39 28 */ 1.794965e-06, /* 39 29 */ 2.231459e-07, /* 39 30 */ 2.441015e-08, /* 39 31 */ 2.328391e-09, /* 39 32 */ 1.914474e-10, /* 39 33 */ 1.336871e-11, /* 39 34 */ 7.772841e-13, /* 39 35 */ 3.661232e-14, /* 39 36 */ 1.342230e-15, /* 39 37 */ 3.593008e-17, /* 39 38 */ 6.246868e-19, /* 39 39 */ 5.293956e-21, /* 40 0 */ 1.000000e+00, /* 40 1 */ 1.000000e+00, /* 40 2 */ 1.000000e+00, /* 40 3 */ 1.000000e+00, /* 40 4 */ 1.000000e+00, /* 40 5 */ 1.000000e+00, /* 40 6 */ 1.000000e+00, /* 40 7 */ 1.000000e+00, /* 40 8 */ 1.000000e+00, /* 40 9 */ 1.000000e+00, /* 40 10 */ 1.000000e+00, /* 40 11 */ 1.000000e+00, /* 40 12 */ 1.000000e+00, /* 40 13 */ 1.000000e+00, /* 40 14 */ 1.000000e+00, /* 40 15 */ 9.999855e-01, /* 40 16 */ 9.985218e-01, /* 40 17 */ 9.615964e-01, /* 40 18 */ 7.668636e-01, /* 40 19 */ 4.470873e-01, /* 40 20 */ 1.971200e-01, /* 40 21 */ 7.127636e-02, /* 40 22 */ 2.214545e-02, /* 40 23 */ 6.107273e-03, /* 40 24 */ 1.563636e-03, /* 40 25 */ 4.000000e-04, /* 40 26 */ 9.818182e-05, /* 40 27 */ 2.727273e-05, /* 40 28 */ 4.775773e-06, /* 40 29 */ 6.472909e-07, /* 40 30 */ 7.784511e-08, /* 40 31 */ 8.246177e-09, /* 40 32 */ 7.624211e-10, /* 40 33 */ 6.081897e-11, /* 40 34 */ 4.123850e-12, /* 40 35 */ 2.330079e-13, /* 40 36 */ 1.067409e-14, /* 40 37 */ 3.808568e-16, /* 40 38 */ 9.929493e-18, /* 40 39 */ 1.682494e-19, /* 40 40 */ 1.390491e-21, /* 41 0 */ 1.000000e+00, /* 41 1 */ 1.000000e+00, /* 41 2 */ 1.000000e+00, /* 41 3 */ 1.000000e+00, /* 41 4 */ 1.000000e+00, /* 41 5 */ 1.000000e+00, /* 41 6 */ 1.000000e+00, /* 41 7 */ 1.000000e+00, /* 41 8 */ 1.000000e+00, /* 41 9 */ 1.000000e+00, /* 41 10 */ 1.000000e+00, /* 41 11 */ 1.000000e+00, /* 41 12 */ 1.000000e+00, /* 41 13 */ 1.000000e+00, /* 41 14 */ 1.000000e+00, /* 41 15 */ 9.999982e-01, /* 41 16 */ 9.996836e-01, /* 41 17 */ 9.854945e-01, /* 41 18 */ 8.630436e-01, /* 41 19 */ 5.692127e-01, /* 41 20 */ 2.783564e-01, /* 41 21 */ 1.091036e-01, /* 41 22 */ 3.642364e-02, /* 41 23 */ 1.052545e-02, /* 41 24 */ 2.803636e-03, /* 41 25 */ 7.127273e-04, /* 41 26 */ 1.727273e-04, /* 41 27 */ 4.363636e-05, /* 41 28 */ 1.200995e-05, /* 41 29 */ 1.762333e-06, /* 41 30 */ 2.310793e-07, /* 41 31 */ 2.691219e-08, /* 41 32 */ 2.763383e-09, /* 41 33 */ 2.478829e-10, /* 41 34 */ 1.920108e-11, /* 41 35 */ 1.265251e-12, /* 41 36 */ 6.952903e-14, /* 41 37 */ 3.100028e-15, /* 41 38 */ 1.077303e-16, /* 41 39 */ 2.737359e-18, /* 41 40 */ 4.523354e-20, /* 41 41 */ 3.647867e-22, /* 42 0 */ 1.000000e+00, /* 42 1 */ 1.000000e+00, /* 42 2 */ 1.000000e+00, /* 42 3 */ 1.000000e+00, /* 42 4 */ 1.000000e+00, /* 42 5 */ 1.000000e+00, /* 42 6 */ 1.000000e+00, /* 42 7 */ 1.000000e+00, /* 42 8 */ 1.000000e+00, /* 42 9 */ 1.000000e+00, /* 42 10 */ 1.000000e+00, /* 42 11 */ 1.000000e+00, /* 42 12 */ 1.000000e+00, /* 42 13 */ 1.000000e+00, /* 42 14 */ 1.000000e+00, /* 42 15 */ 1.000000e+00, /* 42 16 */ 9.999400e-01, /* 42 17 */ 9.956200e-01, /* 42 18 */ 9.298000e-01, /* 42 19 */ 6.904818e-01, /* 42 20 */ 3.770509e-01, /* 42 21 */ 1.607691e-01, /* 42 22 */ 5.732000e-02, /* 42 23 */ 1.790182e-02, /* 42 24 */ 4.956364e-03, /* 42 25 */ 1.287273e-03, /* 42 26 */ 3.236364e-04, /* 42 27 */ 8.909091e-05, /* 42 28 */ 2.870078e-05, /* 42 29 */ 4.532606e-06, /* 42 30 */ 6.434737e-07, /* 42 31 */ 8.171026e-08, /* 42 32 */ 9.224648e-09, /* 42 33 */ 9.190054e-10, /* 42 34 */ 8.005158e-11, /* 42 35 */ 6.026240e-12, /* 42 36 */ 3.862141e-13, /* 42 37 */ 2.065689e-14, /* 42 38 */ 8.970424e-16, /* 42 39 */ 3.038228e-17, /* 42 40 */ 7.528752e-19, /* 42 41 */ 1.214006e-20, /* 42 42 */ 9.559106e-23, /* 43 0 */ 1.000000e+00, /* 43 1 */ 1.000000e+00, /* 43 2 */ 1.000000e+00, /* 43 3 */ 1.000000e+00, /* 43 4 */ 1.000000e+00, /* 43 5 */ 1.000000e+00, /* 43 6 */ 1.000000e+00, /* 43 7 */ 1.000000e+00, /* 43 8 */ 1.000000e+00, /* 43 9 */ 1.000000e+00, /* 43 10 */ 1.000000e+00, /* 43 11 */ 1.000000e+00, /* 43 12 */ 1.000000e+00, /* 43 13 */ 1.000000e+00, /* 43 14 */ 1.000000e+00, /* 43 15 */ 1.000000e+00, /* 43 16 */ 9.999873e-01, /* 43 17 */ 9.989127e-01, /* 43 18 */ 9.693127e-01, /* 43 19 */ 7.987545e-01, /* 43 20 */ 4.900527e-01, /* 43 21 */ 2.294218e-01, /* 43 22 */ 8.803091e-02, /* 43 23 */ 2.904545e-02, /* 43 24 */ 8.496364e-03, /* 43 25 */ 2.352727e-03, /* 43 26 */ 5.927273e-04, /* 43 27 */ 1.581818e-04, /* 43 28 */ 3.454545e-05, /* 43 29 */ 1.107221e-05, /* 43 30 */ 1.691782e-06, /* 43 31 */ 2.326039e-07, /* 43 32 */ 2.863275e-08, /* 43 33 */ 3.136358e-09, /* 43 34 */ 3.034254e-10, /* 43 35 */ 2.568689e-11, /* 43 36 */ 1.880737e-12, /* 43 37 */ 1.173182e-13, /* 43 38 */ 6.111650e-15, /* 43 39 */ 2.586715e-16, /* 43 40 */ 8.544185e-18, /* 43 41 */ 2.066084e-19, /* 43 42 */ 3.252888e-21, /* 43 43 */ 2.502221e-23, /* 44 0 */ 1.000000e+00, /* 44 1 */ 1.000000e+00, /* 44 2 */ 1.000000e+00, /* 44 3 */ 1.000000e+00, /* 44 4 */ 1.000000e+00, /* 44 5 */ 1.000000e+00, /* 44 6 */ 1.000000e+00, /* 44 7 */ 1.000000e+00, /* 44 8 */ 1.000000e+00, /* 44 9 */ 1.000000e+00, /* 44 10 */ 1.000000e+00, /* 44 11 */ 1.000000e+00, /* 44 12 */ 1.000000e+00, /* 44 13 */ 1.000000e+00, /* 44 14 */ 1.000000e+00, /* 44 15 */ 1.000000e+00, /* 44 16 */ 9.999945e-01, /* 44 17 */ 9.997709e-01, /* 44 18 */ 9.887491e-01, /* 44 19 */ 8.835436e-01, /* 44 20 */ 6.091655e-01, /* 44 21 */ 3.144418e-01, /* 44 22 */ 1.304509e-01, /* 44 23 */ 4.616182e-02, /* 44 24 */ 1.412727e-02, /* 44 25 */ 4.100000e-03, /* 44 26 */ 1.101818e-03, /* 44 27 */ 2.872727e-04, /* 44 28 */ 6.545455e-05, /* 44 29 */ 2.580812e-05, /* 44 30 */ 4.222470e-06, /* 44 31 */ 6.248615e-07, /* 44 32 */ 8.328601e-08, /* 44 33 */ 9.947662e-09, /* 44 34 */ 1.058166e-09, /* 44 35 */ 9.949435e-11, /* 44 36 */ 8.192334e-12, /* 44 37 */ 5.838328e-13, /* 44 38 */ 3.547233e-14, /* 44 39 */ 1.801075e-15, /* 44 40 */ 7.434345e-17, /* 44 41 */ 2.396322e-18, /* 44 42 */ 5.657843e-20, /* 44 43 */ 8.702360e-22, /* 44 44 */ 6.543128e-24, /* 45 0 */ 1.000000e+00, /* 45 1 */ 1.000000e+00, /* 45 2 */ 1.000000e+00, /* 45 3 */ 1.000000e+00, /* 45 4 */ 1.000000e+00, /* 45 5 */ 1.000000e+00, /* 45 6 */ 1.000000e+00, /* 45 7 */ 1.000000e+00, /* 45 8 */ 1.000000e+00, /* 45 9 */ 1.000000e+00, /* 45 10 */ 1.000000e+00, /* 45 11 */ 1.000000e+00, /* 45 12 */ 1.000000e+00, /* 45 13 */ 1.000000e+00, /* 45 14 */ 1.000000e+00, /* 45 15 */ 1.000000e+00, /* 45 16 */ 1.000000e+00, /* 45 17 */ 9.999564e-01, /* 45 18 */ 9.966509e-01, /* 45 19 */ 9.415818e-01, /* 45 20 */ 7.239727e-01, /* 45 21 */ 4.167873e-01, /* 45 22 */ 1.870564e-01, /* 45 23 */ 7.046545e-02, /* 45 24 */ 2.312182e-02, /* 45 25 */ 6.969091e-03, /* 45 26 */ 1.892727e-03, /* 45 27 */ 5.000000e-04, /* 45 28 */ 1.309091e-04, /* 45 29 */ 2.363636e-05, /* 45 30 */ 1.005114e-05, /* 45 31 */ 1.592761e-06, /* 45 32 */ 2.285070e-07, /* 45 33 */ 2.955320e-08, /* 45 34 */ 3.427961e-09, /* 45 35 */ 3.544035e-10, /* 45 36 */ 3.241173e-11, /* 45 37 */ 2.597673e-12, /* 45 38 */ 1.803171e-13, /* 45 39 */ 1.067811e-14, /* 45 40 */ 5.287662e-16, /* 45 41 */ 2.129909e-17, /* 45 42 */ 6.703430e-19, /* 45 43 */ 1.546225e-20, /* 45 44 */ 2.324636e-22, /* 45 45 */ 1.709291e-24, /* 46 0 */ 1.000000e+00, /* 46 1 */ 1.000000e+00, /* 46 2 */ 1.000000e+00, /* 46 3 */ 1.000000e+00, /* 46 4 */ 1.000000e+00, /* 46 5 */ 1.000000e+00, /* 46 6 */ 1.000000e+00, /* 46 7 */ 1.000000e+00, /* 46 8 */ 1.000000e+00, /* 46 9 */ 1.000000e+00, /* 46 10 */ 1.000000e+00, /* 46 11 */ 1.000000e+00, /* 46 12 */ 1.000000e+00, /* 46 13 */ 1.000000e+00, /* 46 14 */ 1.000000e+00, /* 46 15 */ 1.000000e+00, /* 46 16 */ 1.000000e+00, /* 46 17 */ 9.999873e-01, /* 46 18 */ 9.991945e-01, /* 46 19 */ 9.749400e-01, /* 46 20 */ 8.239800e-01, /* 46 21 */ 5.291509e-01, /* 46 22 */ 2.600491e-01, /* 46 23 */ 1.046618e-01, /* 46 24 */ 3.656909e-02, /* 46 25 */ 1.147636e-02, /* 46 26 */ 3.390909e-03, /* 46 27 */ 8.654545e-04, /* 46 28 */ 2.163636e-04, /* 46 29 */ 6.363636e-05, /* 46 30 */ 2.291027e-05, /* 46 31 */ 3.870297e-06, /* 46 32 */ 5.946037e-07, /* 46 33 */ 8.277658e-08, /* 46 34 */ 1.039699e-08, /* 46 35 */ 1.172141e-09, /* 46 36 */ 1.178721e-10, /* 46 37 */ 1.049294e-11, /* 46 38 */ 8.191423e-13, /* 46 39 */ 5.542111e-14, /* 46 40 */ 3.200859e-15, /* 46 41 */ 1.546779e-16, /* 46 42 */ 6.083654e-18, /* 46 43 */ 1.870577e-19, /* 46 44 */ 4.217467e-21, /* 46 45 */ 6.200846e-23, /* 46 46 */ 4.461040e-25, /* 47 0 */ 1.000000e+00, /* 47 1 */ 1.000000e+00, /* 47 2 */ 1.000000e+00, /* 47 3 */ 1.000000e+00, /* 47 4 */ 1.000000e+00, /* 47 5 */ 1.000000e+00, /* 47 6 */ 1.000000e+00, /* 47 7 */ 1.000000e+00, /* 47 8 */ 1.000000e+00, /* 47 9 */ 1.000000e+00, /* 47 10 */ 1.000000e+00, /* 47 11 */ 1.000000e+00, /* 47 12 */ 1.000000e+00, /* 47 13 */ 1.000000e+00, /* 47 14 */ 1.000000e+00, /* 47 15 */ 1.000000e+00, /* 47 16 */ 1.000000e+00, /* 47 17 */ 1.000000e+00, /* 47 18 */ 9.998400e-01, /* 47 19 */ 9.908709e-01, /* 47 20 */ 9.002327e-01, /* 47 21 */ 6.445527e-01, /* 47 22 */ 3.496745e-01, /* 47 23 */ 1.514055e-01, /* 47 24 */ 5.606727e-02, /* 47 25 */ 1.855091e-02, /* 47 26 */ 5.649091e-03, /* 47 27 */ 1.465455e-03, /* 47 28 */ 4.400000e-04, /* 47 29 */ 1.018182e-04, /* 47 30 */ 2.181818e-05, /* 47 31 */ 9.001442e-06, /* 47 32 */ 1.474317e-06, /* 47 33 */ 2.197961e-07, /* 47 34 */ 2.971721e-08, /* 47 35 */ 3.627943e-09, /* 47 36 */ 3.978434e-10, /* 47 37 */ 3.894349e-11, /* 47 38 */ 3.376828e-12, /* 47 39 */ 2.569460e-13, /* 47 40 */ 1.695502e-14, /* 47 41 */ 9.556262e-16, /* 47 42 */ 4.509145e-17, /* 47 43 */ 1.732648e-18, /* 47 44 */ 5.207469e-20, /* 47 45 */ 1.148217e-21, /* 47 46 */ 1.651776e-23, /* 47 47 */ 1.163223e-25, /* 48 0 */ 1.000000e+00, /* 48 1 */ 1.000000e+00, /* 48 2 */ 1.000000e+00, /* 48 3 */ 1.000000e+00, /* 48 4 */ 1.000000e+00, /* 48 5 */ 1.000000e+00, /* 48 6 */ 1.000000e+00, /* 48 7 */ 1.000000e+00, /* 48 8 */ 1.000000e+00, /* 48 9 */ 1.000000e+00, /* 48 10 */ 1.000000e+00, /* 48 11 */ 1.000000e+00, /* 48 12 */ 1.000000e+00, /* 48 13 */ 1.000000e+00, /* 48 14 */ 1.000000e+00, /* 48 15 */ 1.000000e+00, /* 48 16 */ 1.000000e+00, /* 48 17 */ 1.000000e+00, /* 48 18 */ 9.999691e-01, /* 48 19 */ 9.972855e-01, /* 48 20 */ 9.503600e-01, /* 48 21 */ 7.527745e-01, /* 48 22 */ 4.519164e-01, /* 48 23 */ 2.128200e-01, /* 48 24 */ 8.375636e-02, /* 48 25 */ 2.908182e-02, /* 48 26 */ 9.198182e-03, /* 48 27 */ 2.627273e-03, /* 48 28 */ 7.218182e-04, /* 48 29 */ 1.927273e-04, /* 48 30 */ 4.545455e-05, /* 48 31 */ 2.010826e-05, /* 48 32 */ 3.497392e-06, /* 48 33 */ 5.558840e-07, /* 48 34 */ 8.048867e-08, /* 48 35 */ 1.057759e-08, /* 48 36 */ 1.256115e-09, /* 48 37 */ 1.340855e-10, /* 48 38 */ 1.278501e-11, /* 48 39 */ 1.080571e-12, /* 48 40 */ 8.019253e-14, /* 48 41 */ 5.164104e-15, /* 48 42 */ 2.842071e-16, /* 48 43 */ 1.310165e-17, /* 48 44 */ 4.920988e-19, /* 48 45 */ 1.446419e-20, /* 48 46 */ 3.120494e-22, /* 48 47 */ 4.394208e-24, /* 48 48 */ 3.030488e-26, /* 49 0 */ 1.000000e+00, /* 49 1 */ 1.000000e+00, /* 49 2 */ 1.000000e+00, /* 49 3 */ 1.000000e+00, /* 49 4 */ 1.000000e+00, /* 49 5 */ 1.000000e+00, /* 49 6 */ 1.000000e+00, /* 49 7 */ 1.000000e+00, /* 49 8 */ 1.000000e+00, /* 49 9 */ 1.000000e+00, /* 49 10 */ 1.000000e+00, /* 49 11 */ 1.000000e+00, /* 49 12 */ 1.000000e+00, /* 49 13 */ 1.000000e+00, /* 49 14 */ 1.000000e+00, /* 49 15 */ 1.000000e+00, /* 49 16 */ 1.000000e+00, /* 49 17 */ 1.000000e+00, /* 49 18 */ 9.999964e-01, /* 49 19 */ 9.993364e-01, /* 49 20 */ 9.790891e-01, /* 49 21 */ 8.448345e-01, /* 49 22 */ 5.628055e-01, /* 49 23 */ 2.895964e-01, /* 49 24 */ 1.218327e-01, /* 49 25 */ 4.456364e-02, /* 49 26 */ 1.467455e-02, /* 49 27 */ 4.443636e-03, /* 49 28 */ 1.227273e-03, /* 49 29 */ 3.490909e-04, /* 49 30 */ 9.090909e-05, /* 49 31 */ 4.327777e-05, /* 49 32 */ 7.965546e-06, /* 49 33 */ 1.344503e-06, /* 49 34 */ 2.075567e-07, /* 49 35 */ 2.921216e-08, /* 49 36 */ 3.734365e-09, /* 49 37 */ 4.316877e-10, /* 49 38 */ 4.488768e-11, /* 49 39 */ 4.171887e-12, /* 49 40 */ 3.439059e-13, /* 49 41 */ 2.490755e-14, /* 49 42 */ 1.566203e-15, /* 49 43 */ 8.421283e-17, /* 49 44 */ 3.794760e-18, /* 49 45 */ 1.393928e-19, /* 49 46 */ 4.008833e-21, /* 49 47 */ 8.466055e-23, /* 49 48 */ 1.167514e-24, /* 49 49 */ 7.888609e-27, /* 50 0 */ 1.000000e+00, /* 50 1 */ 1.000000e+00, /* 50 2 */ 1.000000e+00, /* 50 3 */ 1.000000e+00, /* 50 4 */ 1.000000e+00, /* 50 5 */ 1.000000e+00, /* 50 6 */ 1.000000e+00, /* 50 7 */ 1.000000e+00, /* 50 8 */ 1.000000e+00, /* 50 9 */ 1.000000e+00, /* 50 10 */ 1.000000e+00, /* 50 11 */ 1.000000e+00, /* 50 12 */ 1.000000e+00, /* 50 13 */ 1.000000e+00, /* 50 14 */ 1.000000e+00, /* 50 15 */ 1.000000e+00, /* 50 16 */ 1.000000e+00, /* 50 17 */ 1.000000e+00, /* 50 18 */ 1.000000e+00, /* 50 19 */ 9.998582e-01, /* 50 20 */ 9.925655e-01, /* 50 21 */ 9.130836e-01, /* 50 22 */ 6.745400e-01, /* 50 23 */ 3.807000e-01, /* 50 24 */ 1.719945e-01, /* 50 25 */ 6.671273e-02, /* 50 26 */ 2.311818e-02, /* 50 27 */ 7.265455e-03, /* 50 28 */ 2.103636e-03, /* 50 29 */ 5.945455e-04, /* 50 30 */ 1.854545e-04, /* 50 31 */ 4.363636e-05, /* 50 32 */ 1.747206e-05, /* 50 33 */ 3.120954e-06, /* 50 34 */ 5.116619e-07, /* 50 35 */ 7.677976e-08, /* 50 36 */ 1.051201e-08, /* 50 37 */ 1.308154e-09, /* 50 38 */ 1.473078e-10, /* 50 39 */ 1.493061e-11, /* 50 40 */ 1.353458e-12, /* 50 41 */ 1.088853e-13, /* 50 42 */ 7.700562e-15, /* 50 43 */ 4.730807e-16, /* 50 44 */ 2.486481e-17, /* 50 45 */ 1.095785e-18, /* 50 46 */ 3.938416e-20, /* 50 47 */ 1.108758e-21, /* 50 48 */ 2.293122e-23, /* 50 49 */ 3.098259e-25, /* 50 50 */ 2.051827e-27, /* 51 0 */ 1.000000e+00, /* 51 1 */ 1.000000e+00, /* 51 2 */ 1.000000e+00, /* 51 3 */ 1.000000e+00, /* 51 4 */ 1.000000e+00, /* 51 5 */ 1.000000e+00, /* 51 6 */ 1.000000e+00, /* 51 7 */ 1.000000e+00, /* 51 8 */ 1.000000e+00, /* 51 9 */ 1.000000e+00, /* 51 10 */ 1.000000e+00, /* 51 11 */ 1.000000e+00, /* 51 12 */ 1.000000e+00, /* 51 13 */ 1.000000e+00, /* 51 14 */ 1.000000e+00, /* 51 15 */ 1.000000e+00, /* 51 16 */ 1.000000e+00, /* 51 17 */ 1.000000e+00, /* 51 18 */ 1.000000e+00, /* 51 19 */ 9.999818e-01, /* 51 20 */ 9.977582e-01, /* 51 21 */ 9.574091e-01, /* 51 22 */ 7.771127e-01, /* 51 23 */ 4.843073e-01, /* 51 24 */ 2.370891e-01, /* 51 25 */ 9.729818e-02, /* 51 26 */ 3.544000e-02, /* 51 27 */ 1.151636e-02, /* 51 28 */ 3.529091e-03, /* 51 29 */ 9.763636e-04, /* 51 30 */ 2.963636e-04, /* 51 31 */ 8.727273e-05, /* 51 32 */ 3.700954e-05, /* 51 33 */ 6.974399e-06, /* 51 34 */ 1.210079e-06, /* 51 35 */ 1.928461e-07, /* 51 36 */ 2.815128e-08, /* 51 37 */ 3.752039e-09, /* 51 38 */ 4.548453e-10, /* 51 39 */ 4.992671e-11, /* 51 40 */ 4.935757e-12, /* 51 41 */ 4.366615e-13, /* 51 42 */ 3.430342e-14, /* 51 43 */ 2.370237e-15, /* 51 44 */ 1.423408e-16, /* 51 45 */ 7.316749e-18, /* 51 46 */ 3.155025e-19, /* 51 47 */ 1.110044e-20, /* 51 48 */ 3.060458e-22, /* 51 49 */ 6.201397e-24, /* 51 50 */ 8.212358e-26, /* 51 51 */ 5.332700e-28, /* 52 0 */ 1.000000e+00, /* 52 1 */ 1.000000e+00, /* 52 2 */ 1.000000e+00, /* 52 3 */ 1.000000e+00, /* 52 4 */ 1.000000e+00, /* 52 5 */ 1.000000e+00, /* 52 6 */ 1.000000e+00, /* 52 7 */ 1.000000e+00, /* 52 8 */ 1.000000e+00, /* 52 9 */ 1.000000e+00, /* 52 10 */ 1.000000e+00, /* 52 11 */ 1.000000e+00, /* 52 12 */ 1.000000e+00, /* 52 13 */ 1.000000e+00, /* 52 14 */ 1.000000e+00, /* 52 15 */ 1.000000e+00, /* 52 16 */ 1.000000e+00, /* 52 17 */ 1.000000e+00, /* 52 18 */ 1.000000e+00, /* 52 19 */ 9.999927e-01, /* 52 20 */ 9.994291e-01, /* 52 21 */ 9.819764e-01, /* 52 22 */ 8.613145e-01, /* 52 23 */ 5.942745e-01, /* 52 24 */ 3.165400e-01, /* 52 25 */ 1.389745e-01, /* 52 26 */ 5.301636e-02, /* 52 27 */ 1.834909e-02, /* 52 28 */ 5.754545e-03, /* 52 29 */ 1.683636e-03, /* 52 30 */ 5.000000e-04, /* 52 31 */ 1.636364e-04, /* 52 32 */ 2.909091e-05, /* 52 33 */ 1.504559e-05, /* 52 34 */ 2.754107e-06, /* 52 35 */ 4.645180e-07, /* 52 36 */ 7.201697e-08, /* 52 37 */ 1.023441e-08, /* 52 38 */ 1.328815e-09, /* 52 39 */ 1.570260e-10, /* 52 40 */ 1.681192e-11, /* 52 41 */ 1.622068e-12, /* 52 42 */ 1.401310e-13, /* 52 43 */ 1.075558e-14, /* 52 44 */ 7.264703e-16, /* 52 45 */ 4.266767e-17, /* 52 46 */ 2.146032e-18, /* 52 47 */ 9.058708e-20, /* 52 48 */ 3.121320e-21, /* 52 49 */ 8.431414e-23, /* 52 50 */ 1.674536e-24, /* 52 51 */ 2.174362e-26, /* 52 52 */ 1.384944e-28, /* 53 0 */ 1.000000e+00, /* 53 1 */ 1.000000e+00, /* 53 2 */ 1.000000e+00, /* 53 3 */ 1.000000e+00, /* 53 4 */ 1.000000e+00, /* 53 5 */ 1.000000e+00, /* 53 6 */ 1.000000e+00, /* 53 7 */ 1.000000e+00, /* 53 8 */ 1.000000e+00, /* 53 9 */ 1.000000e+00, /* 53 10 */ 1.000000e+00, /* 53 11 */ 1.000000e+00, /* 53 12 */ 1.000000e+00, /* 53 13 */ 1.000000e+00, /* 53 14 */ 1.000000e+00, /* 53 15 */ 1.000000e+00, /* 53 16 */ 1.000000e+00, /* 53 17 */ 1.000000e+00, /* 53 18 */ 1.000000e+00, /* 53 19 */ 9.999982e-01, /* 53 20 */ 9.998927e-01, /* 53 21 */ 9.935582e-01, /* 53 22 */ 9.235200e-01, /* 53 23 */ 7.005618e-01, /* 53 24 */ 4.099745e-01, /* 53 25 */ 1.929582e-01, /* 53 26 */ 7.798000e-02, /* 53 27 */ 2.814909e-02, /* 53 28 */ 9.010909e-03, /* 53 29 */ 2.787273e-03, /* 53 30 */ 8.090909e-04, /* 53 31 */ 2.509091e-04, /* 53 32 */ 6.363636e-05, /* 53 33 */ 3.140881e-05, /* 53 34 */ 6.048937e-06, /* 53 35 */ 1.076413e-06, /* 53 36 */ 1.766232e-07, /* 53 37 */ 2.665825e-08, /* 53 38 */ 3.690638e-09, /* 53 39 */ 4.671135e-10, /* 53 40 */ 5.384108e-11, /* 53 41 */ 5.625972e-12, /* 53 42 */ 5.300656e-13, /* 53 43 */ 4.474118e-14, /* 53 44 */ 3.356926e-15, /* 53 45 */ 2.217554e-16, /* 53 46 */ 1.274407e-17, /* 53 47 */ 6.274730e-19, /* 53 48 */ 2.593959e-20, /* 53 49 */ 8.756985e-22, /* 53 50 */ 2.318520e-23, /* 53 51 */ 4.515094e-25, /* 53 52 */ 5.750796e-27, /* 53 53 */ 3.594247e-29, /* 54 0 */ 1.000000e+00, /* 54 1 */ 1.000000e+00, /* 54 2 */ 1.000000e+00, /* 54 3 */ 1.000000e+00, /* 54 4 */ 1.000000e+00, /* 54 5 */ 1.000000e+00, /* 54 6 */ 1.000000e+00, /* 54 7 */ 1.000000e+00, /* 54 8 */ 1.000000e+00, /* 54 9 */ 1.000000e+00, /* 54 10 */ 1.000000e+00, /* 54 11 */ 1.000000e+00, /* 54 12 */ 1.000000e+00, /* 54 13 */ 1.000000e+00, /* 54 14 */ 1.000000e+00, /* 54 15 */ 1.000000e+00, /* 54 16 */ 1.000000e+00, /* 54 17 */ 1.000000e+00, /* 54 18 */ 1.000000e+00, /* 54 19 */ 1.000000e+00, /* 54 20 */ 9.999673e-01, /* 54 21 */ 9.980673e-01, /* 54 22 */ 9.630091e-01, /* 54 23 */ 7.965091e-01, /* 54 24 */ 5.125364e-01, /* 54 25 */ 2.606636e-01, /* 54 26 */ 1.116873e-01, /* 54 27 */ 4.187091e-02, /* 54 28 */ 1.438727e-02, /* 54 29 */ 4.538182e-03, /* 54 30 */ 1.352727e-03, /* 54 31 */ 4.254545e-04, /* 54 32 */ 1.200000e-04, /* 54 33 */ 3.090909e-05, /* 54 34 */ 1.285200e-05, /* 54 35 */ 2.406249e-06, /* 54 36 */ 4.165814e-07, /* 54 37 */ 6.654741e-08, /* 54 38 */ 9.785129e-09, /* 54 39 */ 1.320579e-09, /* 54 40 */ 1.630338e-10, /* 54 41 */ 1.834062e-11, /* 54 42 */ 1.871477e-12, /* 54 43 */ 1.722800e-13, /* 54 44 */ 1.421521e-14, /* 54 45 */ 1.043135e-15, /* 54 46 */ 6.742650e-17, /* 54 47 */ 3.793308e-18, /* 54 48 */ 1.829139e-19, /* 54 49 */ 7.408627e-21, /* 54 50 */ 2.451469e-22, /* 54 51 */ 6.364255e-24, /* 54 52 */ 1.215710e-25, /* 54 53 */ 1.519405e-27, /* 54 54 */ 9.321501e-30, /* 55 0 */ 1.000000e+00, /* 55 1 */ 1.000000e+00, /* 55 2 */ 1.000000e+00, /* 55 3 */ 1.000000e+00, /* 55 4 */ 1.000000e+00, /* 55 5 */ 1.000000e+00, /* 55 6 */ 1.000000e+00, /* 55 7 */ 1.000000e+00, /* 55 8 */ 1.000000e+00, /* 55 9 */ 1.000000e+00, /* 55 10 */ 1.000000e+00, /* 55 11 */ 1.000000e+00, /* 55 12 */ 1.000000e+00, /* 55 13 */ 1.000000e+00, /* 55 14 */ 1.000000e+00, /* 55 15 */ 1.000000e+00, /* 55 16 */ 1.000000e+00, /* 55 17 */ 1.000000e+00, /* 55 18 */ 1.000000e+00, /* 55 19 */ 1.000000e+00, /* 55 20 */ 9.999909e-01, /* 55 21 */ 9.995073e-01, /* 55 22 */ 9.845073e-01, /* 55 23 */ 8.751073e-01, /* 55 24 */ 6.197382e-01, /* 55 25 */ 3.424109e-01, /* 55 26 */ 1.563109e-01, /* 55 27 */ 6.148000e-02, /* 55 28 */ 2.202182e-02, /* 55 29 */ 7.229091e-03, /* 55 30 */ 2.185455e-03, /* 55 31 */ 6.818182e-04, /* 55 32 */ 2.054545e-04, /* 55 33 */ 5.818182e-05, /* 55 34 */ 2.647316e-05, /* 55 35 */ 5.201807e-06, /* 55 36 */ 9.475367e-07, /* 55 37 */ 1.597089e-07, /* 55 38 */ 2.485547e-08, /* 55 39 */ 3.562824e-09, /* 55 40 */ 4.690213e-10, /* 55 41 */ 5.651425e-11, /* 55 42 */ 6.208515e-12, /* 55 43 */ 6.189887e-13, /* 55 44 */ 5.570305e-14, /* 55 45 */ 4.495265e-15, /* 55 46 */ 3.227786e-16, /* 55 47 */ 2.042454e-17, /* 55 48 */ 1.125344e-18, /* 55 49 */ 5.316680e-20, /* 55 50 */ 2.110727e-21, /* 55 51 */ 6.848393e-23, /* 55 52 */ 1.743970e-24, /* 55 53 */ 3.268936e-26, /* 55 54 */ 4.010372e-28, /* 55 55 */ 2.415887e-30, /* 56 0 */ 1.000000e+00, /* 56 1 */ 1.000000e+00, /* 56 2 */ 1.000000e+00, /* 56 3 */ 1.000000e+00, /* 56 4 */ 1.000000e+00, /* 56 5 */ 1.000000e+00, /* 56 6 */ 1.000000e+00, /* 56 7 */ 1.000000e+00, /* 56 8 */ 1.000000e+00, /* 56 9 */ 1.000000e+00, /* 56 10 */ 1.000000e+00, /* 56 11 */ 1.000000e+00, /* 56 12 */ 1.000000e+00, /* 56 13 */ 1.000000e+00, /* 56 14 */ 1.000000e+00, /* 56 15 */ 1.000000e+00, /* 56 16 */ 1.000000e+00, /* 56 17 */ 1.000000e+00, /* 56 18 */ 1.000000e+00, /* 56 19 */ 1.000000e+00, /* 56 20 */ 9.999982e-01, /* 56 21 */ 9.998964e-01, /* 56 22 */ 9.944836e-01, /* 56 23 */ 9.311891e-01, /* 56 24 */ 7.227964e-01, /* 56 25 */ 4.365145e-01, /* 56 26 */ 2.129782e-01, /* 56 27 */ 8.882182e-02, /* 56 28 */ 3.311455e-02, /* 56 29 */ 1.130182e-02, /* 56 30 */ 3.514545e-03, /* 56 31 */ 1.089091e-03, /* 56 32 */ 3.145455e-04, /* 56 33 */ 9.636364e-05, /* 56 34 */ 2.545455e-05, /* 56 35 */ 1.089870e-05, /* 56 36 */ 2.083571e-06, /* 56 37 */ 3.695176e-07, /* 56 38 */ 6.067924e-08, /* 56 39 */ 9.206175e-09, /* 56 40 */ 1.287242e-09, /* 56 41 */ 1.653934e-10, /* 56 42 */ 1.946183e-11, /* 56 43 */ 2.089027e-12, /* 56 44 */ 2.036059e-13, /* 56 45 */ 1.792048e-14, /* 56 46 */ 1.415118e-15, /* 56 47 */ 9.947271e-17, /* 56 48 */ 6.164546e-18, /* 56 49 */ 3.327854e-19, /* 56 50 */ 1.541073e-20, /* 56 51 */ 5.999095e-22, /* 56 52 */ 1.909302e-23, /* 56 53 */ 4.771033e-25, /* 56 54 */ 8.778431e-27, /* 56 55 */ 1.057492e-28, /* 56 56 */ 6.257346e-31, /* 57 0 */ 1.000000e+00, /* 57 1 */ 1.000000e+00, /* 57 2 */ 1.000000e+00, /* 57 3 */ 1.000000e+00, /* 57 4 */ 1.000000e+00, /* 57 5 */ 1.000000e+00, /* 57 6 */ 1.000000e+00, /* 57 7 */ 1.000000e+00, /* 57 8 */ 1.000000e+00, /* 57 9 */ 1.000000e+00, /* 57 10 */ 1.000000e+00, /* 57 11 */ 1.000000e+00, /* 57 12 */ 1.000000e+00, /* 57 13 */ 1.000000e+00, /* 57 14 */ 1.000000e+00, /* 57 15 */ 1.000000e+00, /* 57 16 */ 1.000000e+00, /* 57 17 */ 1.000000e+00, /* 57 18 */ 1.000000e+00, /* 57 19 */ 1.000000e+00, /* 57 20 */ 1.000000e+00, /* 57 21 */ 9.999691e-01, /* 57 22 */ 9.982818e-01, /* 57 23 */ 9.670418e-01, /* 57 24 */ 8.133236e-01, /* 57 25 */ 5.386000e-01, /* 57 26 */ 2.829636e-01, /* 57 27 */ 1.253164e-01, /* 57 28 */ 4.860545e-02, /* 57 29 */ 1.748545e-02, /* 57 30 */ 5.656364e-03, /* 57 31 */ 1.780000e-03, /* 57 32 */ 5.363636e-04, /* 57 33 */ 1.690909e-04, /* 57 34 */ 4.727273e-05, /* 57 35 */ 2.217481e-05, /* 57 36 */ 4.439106e-06, /* 57 37 */ 8.262776e-07, /* 57 38 */ 1.427695e-07, /* 57 39 */ 2.285578e-08, /* 57 40 */ 3.382612e-09, /* 57 41 */ 4.616369e-10, /* 57 42 */ 5.792491e-11, /* 57 43 */ 6.659900e-12, /* 57 44 */ 6.988516e-13, /* 57 45 */ 6.661924e-14, /* 57 46 */ 5.737602e-15, /* 57 47 */ 4.435469e-16, /* 57 48 */ 3.053546e-17, /* 57 49 */ 1.854109e-18, /* 57 50 */ 9.810829e-20, /* 57 51 */ 4.454908e-21, /* 57 52 */ 1.701125e-22, /* 57 53 */ 5.312699e-24, /* 57 54 */ 1.303145e-25, /* 57 55 */ 2.354406e-27, /* 57 56 */ 2.785896e-29, /* 57 57 */ 1.619707e-31, /* 58 0 */ 1.000000e+00, /* 58 1 */ 1.000000e+00, /* 58 2 */ 1.000000e+00, /* 58 3 */ 1.000000e+00, /* 58 4 */ 1.000000e+00, /* 58 5 */ 1.000000e+00, /* 58 6 */ 1.000000e+00, /* 58 7 */ 1.000000e+00, /* 58 8 */ 1.000000e+00, /* 58 9 */ 1.000000e+00, /* 58 10 */ 1.000000e+00, /* 58 11 */ 1.000000e+00, /* 58 12 */ 1.000000e+00, /* 58 13 */ 1.000000e+00, /* 58 14 */ 1.000000e+00, /* 58 15 */ 1.000000e+00, /* 58 16 */ 1.000000e+00, /* 58 17 */ 1.000000e+00, /* 58 18 */ 1.000000e+00, /* 58 19 */ 1.000000e+00, /* 58 20 */ 1.000000e+00, /* 58 21 */ 9.999891e-01, /* 58 22 */ 9.996018e-01, /* 58 23 */ 9.863200e-01, /* 58 24 */ 8.862327e-01, /* 58 25 */ 6.426800e-01, /* 58 26 */ 3.667018e-01, /* 58 27 */ 1.722927e-01, /* 58 28 */ 7.062909e-02, /* 58 29 */ 2.618909e-02, /* 58 30 */ 8.863636e-03, /* 58 31 */ 2.780000e-03, /* 58 32 */ 8.654545e-04, /* 58 33 */ 2.836364e-04, /* 58 34 */ 8.363636e-05, /* 58 35 */ 4.389190e-05, /* 58 36 */ 9.181637e-06, /* 58 37 */ 1.789636e-06, /* 58 38 */ 3.245551e-07, /* 58 39 */ 5.467178e-08, /* 58 40 */ 8.537870e-09, /* 58 41 */ 1.233334e-09, /* 58 42 */ 1.643778e-10, /* 58 43 */ 2.015353e-11, /* 58 44 */ 2.265251e-12, /* 58 45 */ 2.324916e-13, /* 58 46 */ 2.168693e-14, /* 58 47 */ 1.828519e-15, /* 58 48 */ 1.384415e-16, /* 58 49 */ 9.338316e-18, /* 58 50 */ 5.557891e-19, /* 58 51 */ 2.883751e-20, /* 58 52 */ 1.284484e-21, /* 58 53 */ 4.813036e-23, /* 58 54 */ 1.475504e-24, /* 58 55 */ 3.553893e-26, /* 58 56 */ 6.306941e-28, /* 58 57 */ 7.332677e-30, /* 58 58 */ 4.190101e-32, /* 59 0 */ 1.000000e+00, /* 59 1 */ 1.000000e+00, /* 59 2 */ 1.000000e+00, /* 59 3 */ 1.000000e+00, /* 59 4 */ 1.000000e+00, /* 59 5 */ 1.000000e+00, /* 59 6 */ 1.000000e+00, /* 59 7 */ 1.000000e+00, /* 59 8 */ 1.000000e+00, /* 59 9 */ 1.000000e+00, /* 59 10 */ 1.000000e+00, /* 59 11 */ 1.000000e+00, /* 59 12 */ 1.000000e+00, /* 59 13 */ 1.000000e+00, /* 59 14 */ 1.000000e+00, /* 59 15 */ 1.000000e+00, /* 59 16 */ 1.000000e+00, /* 59 17 */ 1.000000e+00, /* 59 18 */ 1.000000e+00, /* 59 19 */ 1.000000e+00, /* 59 20 */ 1.000000e+00, /* 59 21 */ 9.999964e-01, /* 59 22 */ 9.999127e-01, /* 59 23 */ 9.950327e-01, /* 59 24 */ 9.379564e-01, /* 59 25 */ 7.414873e-01, /* 59 26 */ 4.604600e-01, /* 59 27 */ 2.318527e-01, /* 59 28 */ 9.998182e-02, /* 59 29 */ 3.844182e-02, /* 59 30 */ 1.356727e-02, /* 59 31 */ 4.440000e-03, /* 59 32 */ 1.414545e-03, /* 59 33 */ 4.527273e-04, /* 59 34 */ 1.290909e-04, /* 59 35 */ 3.636364e-05, /* 59 36 */ 1.846973e-05, /* 59 37 */ 3.761991e-06, /* 59 38 */ 7.144417e-07, /* 59 39 */ 1.263181e-07, /* 59 40 */ 2.075750e-08, /* 59 41 */ 3.164058e-09, /* 59 42 */ 4.463720e-10, /* 59 43 */ 5.813116e-11, /* 59 44 */ 6.967641e-12, /* 59 45 */ 7.660021e-13, /* 59 46 */ 7.693110e-14, /* 59 47 */ 7.025349e-15, /* 59 48 */ 5.801376e-16, /* 59 49 */ 4.303671e-17, /* 59 50 */ 2.845480e-18, /* 59 51 */ 1.660648e-19, /* 59 52 */ 8.452131e-21, /* 59 53 */ 3.694305e-22, /* 59 54 */ 1.358839e-23, /* 59 55 */ 4.090516e-25, /* 59 56 */ 9.677654e-27, /* 59 57 */ 1.687512e-28, /* 59 58 */ 1.928337e-30, /* 59 59 */ 1.083336e-32, /* 60 0 */ 1.000000e+00, /* 60 1 */ 1.000000e+00, /* 60 2 */ 1.000000e+00, /* 60 3 */ 1.000000e+00, /* 60 4 */ 1.000000e+00, /* 60 5 */ 1.000000e+00, /* 60 6 */ 1.000000e+00, /* 60 7 */ 1.000000e+00, /* 60 8 */ 1.000000e+00, /* 60 9 */ 1.000000e+00, /* 60 10 */ 1.000000e+00, /* 60 11 */ 1.000000e+00, /* 60 12 */ 1.000000e+00, /* 60 13 */ 1.000000e+00, /* 60 14 */ 1.000000e+00, /* 60 15 */ 1.000000e+00, /* 60 16 */ 1.000000e+00, /* 60 17 */ 1.000000e+00, /* 60 18 */ 1.000000e+00, /* 60 19 */ 1.000000e+00, /* 60 20 */ 1.000000e+00, /* 60 21 */ 1.000000e+00, /* 60 22 */ 9.999764e-01, /* 60 23 */ 9.984418e-01, /* 60 24 */ 9.702473e-01, /* 60 25 */ 8.273545e-01, /* 60 26 */ 5.613109e-01, /* 60 27 */ 3.040182e-01, /* 60 28 */ 1.385364e-01, /* 60 29 */ 5.582545e-02, /* 60 30 */ 2.043636e-02, /* 60 31 */ 6.976364e-03, /* 60 32 */ 2.280000e-03, /* 60 33 */ 7.400000e-04, /* 60 34 */ 2.327273e-04, /* 60 35 */ 7.272727e-05, /* 60 36 */ 2.363636e-05, /* 60 37 */ 7.688956e-06, /* 60 38 */ 1.525950e-06, /* 60 39 */ 2.825366e-07, /* 60 40 */ 4.873234e-08, /* 60 41 */ 7.816599e-09, /* 60 42 */ 1.163633e-09, /* 60 43 */ 1.604075e-10, /* 60 44 */ 2.042263e-11, /* 60 45 */ 2.394269e-12, /* 60 46 */ 2.575747e-13, /* 60 47 */ 2.532532e-14, /* 60 48 */ 2.265097e-15, /* 60 49 */ 1.832716e-16, /* 60 50 */ 1.332664e-17, /* 60 51 */ 8.640147e-19, /* 60 52 */ 4.946376e-20, /* 60 53 */ 2.470440e-21, /* 60 54 */ 1.059957e-22, /* 60 55 */ 3.828378e-24, /* 60 56 */ 1.132023e-25, /* 60 57 */ 2.631550e-27, /* 60 58 */ 4.510064e-29, /* 60 59 */ 5.066858e-31, /* 60 60 */ 2.799369e-33, /* 61 0 */ 1.000000e+00, /* 61 1 */ 1.000000e+00, /* 61 2 */ 1.000000e+00, /* 61 3 */ 1.000000e+00, /* 61 4 */ 1.000000e+00, /* 61 5 */ 1.000000e+00, /* 61 6 */ 1.000000e+00, /* 61 7 */ 1.000000e+00, /* 61 8 */ 1.000000e+00, /* 61 9 */ 1.000000e+00, /* 61 10 */ 1.000000e+00, /* 61 11 */ 1.000000e+00, /* 61 12 */ 1.000000e+00, /* 61 13 */ 1.000000e+00, /* 61 14 */ 1.000000e+00, /* 61 15 */ 1.000000e+00, /* 61 16 */ 1.000000e+00, /* 61 17 */ 1.000000e+00, /* 61 18 */ 1.000000e+00, /* 61 19 */ 1.000000e+00, /* 61 20 */ 1.000000e+00, /* 61 21 */ 1.000000e+00, /* 61 22 */ 9.999945e-01, /* 61 23 */ 9.995945e-01, /* 61 24 */ 9.874273e-01, /* 61 25 */ 8.950982e-01, /* 61 26 */ 6.628473e-01, /* 61 27 */ 3.880236e-01, /* 61 28 */ 1.881018e-01, /* 61 29 */ 7.946909e-02, /* 61 30 */ 3.018182e-02, /* 61 31 */ 1.063455e-02, /* 61 32 */ 3.509091e-03, /* 61 33 */ 1.150909e-03, /* 61 34 */ 3.527273e-04, /* 61 35 */ 1.309091e-04, /* 61 36 */ 4.545455e-05, /* 61 37 */ 1.530465e-05, /* 61 38 */ 3.168073e-06, /* 61 39 */ 6.130048e-07, /* 61 40 */ 1.107264e-07, /* 61 41 */ 1.864204e-08, /* 61 42 */ 2.920318e-09, /* 61 43 */ 4.248067e-10, /* 61 44 */ 5.725076e-11, /* 61 45 */ 7.129487e-12, /* 61 46 */ 8.179200e-13, /* 61 47 */ 8.614410e-14, /* 61 48 */ 8.295594e-15, /* 61 49 */ 7.269902e-16, /* 61 50 */ 5.765781e-17, /* 61 51 */ 4.111223e-18, /* 61 52 */ 2.614679e-19, /* 61 53 */ 1.468878e-20, /* 61 54 */ 7.201500e-22, /* 61 55 */ 3.034106e-23, /* 61 56 */ 1.076440e-24, /* 61 57 */ 3.127496e-26, /* 61 58 */ 7.145780e-28, /* 61 59 */ 1.204044e-29, /* 61 60 */ 1.330276e-31, /* 61 61 */ 7.229760e-34, /* 62 0 */ 1.000000e+00, /* 62 1 */ 1.000000e+00, /* 62 2 */ 1.000000e+00, /* 62 3 */ 1.000000e+00, /* 62 4 */ 1.000000e+00, /* 62 5 */ 1.000000e+00, /* 62 6 */ 1.000000e+00, /* 62 7 */ 1.000000e+00, /* 62 8 */ 1.000000e+00, /* 62 9 */ 1.000000e+00, /* 62 10 */ 1.000000e+00, /* 62 11 */ 1.000000e+00, /* 62 12 */ 1.000000e+00, /* 62 13 */ 1.000000e+00, /* 62 14 */ 1.000000e+00, /* 62 15 */ 1.000000e+00, /* 62 16 */ 1.000000e+00, /* 62 17 */ 1.000000e+00, /* 62 18 */ 1.000000e+00, /* 62 19 */ 1.000000e+00, /* 62 20 */ 1.000000e+00, /* 62 21 */ 1.000000e+00, /* 62 22 */ 1.000000e+00, /* 62 23 */ 9.999055e-01, /* 62 24 */ 9.954673e-01, /* 62 25 */ 9.430218e-01, /* 62 26 */ 7.576345e-01, /* 62 27 */ 4.823636e-01, /* 62 28 */ 2.498327e-01, /* 62 29 */ 1.111527e-01, /* 62 30 */ 4.388727e-02, /* 62 31 */ 1.600727e-02, /* 62 32 */ 5.414545e-03, /* 62 33 */ 1.745455e-03, /* 62 34 */ 5.872727e-04, /* 62 35 */ 1.963636e-04, /* 62 36 */ 6.000000e-05, /* 62 37 */ 2.971200e-05, /* 62 38 */ 6.403902e-06, /* 62 39 */ 1.292477e-06, /* 62 40 */ 2.439800e-07, /* 62 41 */ 4.301795e-08, /* 62 42 */ 7.073523e-09, /* 62 43 */ 1.082786e-09, /* 62 44 */ 1.539895e-10, /* 62 45 */ 2.029911e-11, /* 62 46 */ 2.473719e-12, /* 62 47 */ 2.778383e-13, /* 62 48 */ 2.866035e-14, /* 62 49 */ 2.704311e-15, /* 62 50 */ 2.323072e-16, /* 62 51 */ 1.806687e-17, /* 62 52 */ 1.263706e-18, /* 62 53 */ 7.886742e-20, /* 62 54 */ 4.349284e-21, /* 62 55 */ 2.093878e-22, /* 62 56 */ 8.665508e-24, /* 62 57 */ 3.020800e-25, /* 62 58 */ 8.626352e-27, /* 62 59 */ 1.937777e-28, /* 62 60 */ 3.211009e-30, /* 62 61 */ 3.489822e-32, /* 62 62 */ 1.866215e-34, /* 63 0 */ 1.000000e+00, /* 63 1 */ 1.000000e+00, /* 63 2 */ 1.000000e+00, /* 63 3 */ 1.000000e+00, /* 63 4 */ 1.000000e+00, /* 63 5 */ 1.000000e+00, /* 63 6 */ 1.000000e+00, /* 63 7 */ 1.000000e+00, /* 63 8 */ 1.000000e+00, /* 63 9 */ 1.000000e+00, /* 63 10 */ 1.000000e+00, /* 63 11 */ 1.000000e+00, /* 63 12 */ 1.000000e+00, /* 63 13 */ 1.000000e+00, /* 63 14 */ 1.000000e+00, /* 63 15 */ 1.000000e+00, /* 63 16 */ 1.000000e+00, /* 63 17 */ 1.000000e+00, /* 63 18 */ 1.000000e+00, /* 63 19 */ 1.000000e+00, /* 63 20 */ 1.000000e+00, /* 63 21 */ 1.000000e+00, /* 63 22 */ 1.000000e+00, /* 63 23 */ 9.999782e-01, /* 63 24 */ 9.985273e-01, /* 63 25 */ 9.728036e-01, /* 63 26 */ 8.386218e-01, /* 63 27 */ 5.818691e-01, /* 63 28 */ 3.231600e-01, /* 63 29 */ 1.519018e-01, /* 63 30 */ 6.306909e-02, /* 63 31 */ 2.366000e-02, /* 63 32 */ 8.256364e-03, /* 63 33 */ 2.745455e-03, /* 63 34 */ 9.290909e-04, /* 63 35 */ 2.745455e-04, /* 63 36 */ 1.036364e-04, /* 63 37 */ 3.090909e-05, /* 63 38 */ 1.262229e-05, /* 63 39 */ 2.652579e-06, /* 63 40 */ 5.222986e-07, /* 63 41 */ 9.624253e-08, /* 63 42 */ 1.657350e-08, /* 63 43 */ 2.663040e-09, /* 63 44 */ 3.985459e-10, /* 63 45 */ 5.544069e-11, /* 63 46 */ 7.151814e-12, /* 63 47 */ 8.532648e-13, /* 63 48 */ 9.386522e-14, /* 63 49 */ 9.487489e-15, /* 63 50 */ 8.775163e-16, /* 63 51 */ 7.391887e-17, /* 63 52 */ 5.639350e-18, /* 63 53 */ 3.870787e-19, /* 63 54 */ 2.371410e-20, /* 63 55 */ 1.284179e-21, /* 63 56 */ 6.072903e-23, /* 63 57 */ 2.469506e-24, /* 63 58 */ 8.461326e-26, /* 63 59 */ 2.375578e-27, /* 63 60 */ 5.247986e-29, /* 63 61 */ 8.554499e-31, /* 63 62 */ 9.148167e-33, /* 63 63 */ 4.814825e-35, /* 64 0 */ 1.000000e+00, /* 64 1 */ 1.000000e+00, /* 64 2 */ 1.000000e+00, /* 64 3 */ 1.000000e+00, /* 64 4 */ 1.000000e+00, /* 64 5 */ 1.000000e+00, /* 64 6 */ 1.000000e+00, /* 64 7 */ 1.000000e+00, /* 64 8 */ 1.000000e+00, /* 64 9 */ 1.000000e+00, /* 64 10 */ 1.000000e+00, /* 64 11 */ 1.000000e+00, /* 64 12 */ 1.000000e+00, /* 64 13 */ 1.000000e+00, /* 64 14 */ 1.000000e+00, /* 64 15 */ 1.000000e+00, /* 64 16 */ 1.000000e+00, /* 64 17 */ 1.000000e+00, /* 64 18 */ 1.000000e+00, /* 64 19 */ 1.000000e+00, /* 64 20 */ 1.000000e+00, /* 64 21 */ 1.000000e+00, /* 64 22 */ 1.000000e+00, /* 64 23 */ 1.000000e+00, /* 64 24 */ 9.995673e-01, /* 64 25 */ 9.884709e-01, /* 64 26 */ 9.025364e-01, /* 64 27 */ 6.803455e-01, /* 64 28 */ 4.089236e-01, /* 64 29 */ 2.032127e-01, /* 64 30 */ 8.823091e-02, /* 64 31 */ 3.457636e-02, /* 64 32 */ 1.244364e-02, /* 64 33 */ 4.245455e-03, /* 64 34 */ 1.403636e-03, /* 64 35 */ 4.454545e-04, /* 64 36 */ 1.563636e-04, /* 64 37 */ 4.363636e-05, /* 64 38 */ 2.429234e-05, /* 64 39 */ 5.307045e-06, /* 64 40 */ 1.088091e-06, /* 64 41 */ 2.091422e-07, /* 64 42 */ 3.764001e-08, /* 64 43 */ 6.334051e-09, /* 64 44 */ 9.950509e-10, /* 64 45 */ 1.456645e-10, /* 64 46 */ 1.982948e-11, /* 64 47 */ 2.504367e-12, /* 64 48 */ 2.926505e-13, /* 64 49 */ 3.154507e-14, /* 64 50 */ 3.125437e-15, /* 64 51 */ 2.834734e-16, /* 64 52 */ 2.342444e-17, /* 64 53 */ 1.753691e-18, /* 64 54 */ 1.181631e-19, /* 64 55 */ 7.108705e-21, /* 64 56 */ 3.781370e-22, /* 64 57 */ 1.757087e-23, /* 64 58 */ 7.022788e-25, /* 64 59 */ 2.365732e-26, /* 64 60 */ 6.531982e-28, /* 64 61 */ 1.419496e-29, /* 64 62 */ 2.276751e-31, /* 64 63 */ 2.396319e-33, /* 64 64 */ 1.241616e-35, /* 65 0 */ 1.000000e+00, /* 65 1 */ 1.000000e+00, /* 65 2 */ 1.000000e+00, /* 65 3 */ 1.000000e+00, /* 65 4 */ 1.000000e+00, /* 65 5 */ 1.000000e+00, /* 65 6 */ 1.000000e+00, /* 65 7 */ 1.000000e+00, /* 65 8 */ 1.000000e+00, /* 65 9 */ 1.000000e+00, /* 65 10 */ 1.000000e+00, /* 65 11 */ 1.000000e+00, /* 65 12 */ 1.000000e+00, /* 65 13 */ 1.000000e+00, /* 65 14 */ 1.000000e+00, /* 65 15 */ 1.000000e+00, /* 65 16 */ 1.000000e+00, /* 65 17 */ 1.000000e+00, /* 65 18 */ 1.000000e+00, /* 65 19 */ 1.000000e+00, /* 65 20 */ 1.000000e+00, /* 65 21 */ 1.000000e+00, /* 65 22 */ 1.000000e+00, /* 65 23 */ 1.000000e+00, /* 65 24 */ 9.999073e-01, /* 65 25 */ 9.958218e-01, /* 65 26 */ 9.467673e-01, /* 65 27 */ 7.717836e-01, /* 65 28 */ 5.023564e-01, /* 65 29 */ 2.667618e-01, /* 65 30 */ 1.216418e-01, /* 65 31 */ 4.977636e-02, /* 65 32 */ 1.856727e-02, /* 65 33 */ 6.527273e-03, /* 65 34 */ 2.114545e-03, /* 65 35 */ 7.218182e-04, /* 65 36 */ 2.127273e-04, /* 65 37 */ 6.909091e-05, /* 65 38 */ 4.570693e-05, /* 65 39 */ 1.036508e-05, /* 65 40 */ 2.209270e-06, /* 65 41 */ 4.421772e-07, /* 65 42 */ 8.301201e-08, /* 65 43 */ 1.459960e-08, /* 65 44 */ 2.402039e-09, /* 65 45 */ 3.691116e-10, /* 65 46 */ 5.287847e-11, /* 65 47 */ 7.047590e-12, /* 65 48 */ 8.717975e-13, /* 65 49 */ 9.982346e-14, /* 65 50 */ 1.054755e-14, /* 65 51 */ 1.024783e-15, /* 65 52 */ 9.117874e-17, /* 65 53 */ 7.393733e-18, /* 65 54 */ 5.433866e-19, /* 65 55 */ 3.595355e-20, /* 65 56 */ 2.124675e-21, /* 65 57 */ 1.110521e-22, /* 65 58 */ 5.071958e-24, /* 65 59 */ 1.993065e-25, /* 65 60 */ 6.602797e-27, /* 65 61 */ 1.793391e-28, /* 65 62 */ 3.834823e-30, /* 65 63 */ 6.053656e-32, /* 65 64 */ 6.272555e-34, /* 65 65 */ 3.200283e-36, /* 66 0 */ 1.000000e+00, /* 66 1 */ 1.000000e+00, /* 66 2 */ 1.000000e+00, /* 66 3 */ 1.000000e+00, /* 66 4 */ 1.000000e+00, /* 66 5 */ 1.000000e+00, /* 66 6 */ 1.000000e+00, /* 66 7 */ 1.000000e+00, /* 66 8 */ 1.000000e+00, /* 66 9 */ 1.000000e+00, /* 66 10 */ 1.000000e+00, /* 66 11 */ 1.000000e+00, /* 66 12 */ 1.000000e+00, /* 66 13 */ 1.000000e+00, /* 66 14 */ 1.000000e+00, /* 66 15 */ 1.000000e+00, /* 66 16 */ 1.000000e+00, /* 66 17 */ 1.000000e+00, /* 66 18 */ 1.000000e+00, /* 66 19 */ 1.000000e+00, /* 66 20 */ 1.000000e+00, /* 66 21 */ 1.000000e+00, /* 66 22 */ 1.000000e+00, /* 66 23 */ 1.000000e+00, /* 66 24 */ 9.999727e-01, /* 66 25 */ 9.986800e-01, /* 66 26 */ 9.743327e-01, /* 66 27 */ 8.483073e-01, /* 66 28 */ 5.999273e-01, /* 66 29 */ 3.415018e-01, /* 66 30 */ 1.643382e-01, /* 66 31 */ 6.988000e-02, /* 66 32 */ 2.721636e-02, /* 66 33 */ 9.720000e-03, /* 66 34 */ 3.261818e-03, /* 66 35 */ 1.074545e-03, /* 66 36 */ 3.327273e-04, /* 66 37 */ 1.018182e-04, /* 66 38 */ 2.909091e-05, /* 66 39 */ 1.978679e-05, /* 66 40 */ 4.377932e-06, /* 66 41 */ 9.109396e-07, /* 66 42 */ 1.780794e-07, /* 66 43 */ 3.267067e-08, /* 66 44 */ 5.617875e-09, /* 66 45 */ 9.041309e-10, /* 66 46 */ 1.359651e-10, /* 66 47 */ 1.907033e-11, /* 66 48 */ 2.489505e-12, /* 66 49 */ 3.017574e-13, /* 66 50 */ 3.387003e-14, /* 66 51 */ 3.509452e-15, /* 66 52 */ 3.344901e-16, /* 66 53 */ 2.920528e-17, /* 66 54 */ 2.324854e-18, /* 66 55 */ 1.677829e-19, /* 66 56 */ 1.090499e-20, /* 66 57 */ 6.332189e-22, /* 66 58 */ 3.253082e-23, /* 66 59 */ 1.460748e-24, /* 66 60 */ 5.645127e-26, /* 66 61 */ 1.839710e-27, /* 66 62 */ 4.916764e-29, /* 66 63 */ 1.034766e-30, /* 66 64 */ 1.608103e-32, /* 66 65 */ 1.640753e-34, /* 66 66 */ 8.244991e-37, /* 67 0 */ 1.000000e+00, /* 67 1 */ 1.000000e+00, /* 67 2 */ 1.000000e+00, /* 67 3 */ 1.000000e+00, /* 67 4 */ 1.000000e+00, /* 67 5 */ 1.000000e+00, /* 67 6 */ 1.000000e+00, /* 67 7 */ 1.000000e+00, /* 67 8 */ 1.000000e+00, /* 67 9 */ 1.000000e+00, /* 67 10 */ 1.000000e+00, /* 67 11 */ 1.000000e+00, /* 67 12 */ 1.000000e+00, /* 67 13 */ 1.000000e+00, /* 67 14 */ 1.000000e+00, /* 67 15 */ 1.000000e+00, /* 67 16 */ 1.000000e+00, /* 67 17 */ 1.000000e+00, /* 67 18 */ 1.000000e+00, /* 67 19 */ 1.000000e+00, /* 67 20 */ 1.000000e+00, /* 67 21 */ 1.000000e+00, /* 67 22 */ 1.000000e+00, /* 67 23 */ 1.000000e+00, /* 67 24 */ 9.999964e-01, /* 67 25 */ 9.996564e-01, /* 67 26 */ 9.892164e-01, /* 67 27 */ 9.085345e-01, /* 67 28 */ 6.953600e-01, /* 67 29 */ 4.264436e-01, /* 67 30 */ 2.178000e-01, /* 67 31 */ 9.685636e-02, /* 67 32 */ 3.918909e-02, /* 67 33 */ 1.462000e-02, /* 67 34 */ 5.047273e-03, /* 67 35 */ 1.730909e-03, /* 67 36 */ 5.400000e-04, /* 67 37 */ 1.727273e-04, /* 67 38 */ 5.454545e-05, /* 67 39 */ 3.696268e-05, /* 67 40 */ 8.477655e-06, /* 67 41 */ 1.831149e-06, /* 67 42 */ 3.721599e-07, /* 67 43 */ 7.109862e-08, /* 67 44 */ 1.275342e-08, /* 67 45 */ 2.145197e-09, /* 67 46 */ 3.378709e-10, /* 67 47 */ 4.974639e-11, /* 67 48 */ 6.834239e-12, /* 67 49 */ 8.742175e-13, /* 67 50 */ 1.038745e-13, /* 67 51 */ 1.143340e-14, /* 67 52 */ 1.162160e-15, /* 67 53 */ 1.087000e-16, /* 67 54 */ 9.316973e-18, /* 67 55 */ 7.283141e-19, /* 67 56 */ 5.163188e-20, /* 67 57 */ 3.297431e-21, /* 67 58 */ 1.881974e-22, /* 67 59 */ 9.505793e-24, /* 67 60 */ 4.197813e-25, /* 67 61 */ 1.595852e-26, /* 67 62 */ 5.117440e-28, /* 67 63 */ 1.346098e-29, /* 67 64 */ 2.788948e-31, /* 67 65 */ 4.267918e-33, /* 67 66 */ 4.288938e-35, /* 67 67 */ 2.123237e-37, /* 68 0 */ 1.000000e+00, /* 68 1 */ 1.000000e+00, /* 68 2 */ 1.000000e+00, /* 68 3 */ 1.000000e+00, /* 68 4 */ 1.000000e+00, /* 68 5 */ 1.000000e+00, /* 68 6 */ 1.000000e+00, /* 68 7 */ 1.000000e+00, /* 68 8 */ 1.000000e+00, /* 68 9 */ 1.000000e+00, /* 68 10 */ 1.000000e+00, /* 68 11 */ 1.000000e+00, /* 68 12 */ 1.000000e+00, /* 68 13 */ 1.000000e+00, /* 68 14 */ 1.000000e+00, /* 68 15 */ 1.000000e+00, /* 68 16 */ 1.000000e+00, /* 68 17 */ 1.000000e+00, /* 68 18 */ 1.000000e+00, /* 68 19 */ 1.000000e+00, /* 68 20 */ 1.000000e+00, /* 68 21 */ 1.000000e+00, /* 68 22 */ 1.000000e+00, /* 68 23 */ 1.000000e+00, /* 68 24 */ 1.000000e+00, /* 68 25 */ 9.999091e-01, /* 68 26 */ 9.960218e-01, /* 68 27 */ 9.500491e-01, /* 68 28 */ 7.830400e-01, /* 68 29 */ 5.190255e-01, /* 68 30 */ 2.823655e-01, /* 68 31 */ 1.322473e-01, /* 68 32 */ 5.526364e-02, /* 68 33 */ 2.137091e-02, /* 68 34 */ 7.643636e-03, /* 68 35 */ 2.589091e-03, /* 68 36 */ 8.781818e-04, /* 68 37 */ 2.727273e-04, /* 68 38 */ 9.818182e-05, /* 68 39 */ 2.181818e-05, /* 68 40 */ 1.606108e-05, /* 68 41 */ 3.596260e-06, /* 68 42 */ 7.587403e-07, /* 68 43 */ 1.507004e-07, /* 68 44 */ 2.814974e-08, /* 68 45 */ 4.939385e-09, /* 68 46 */ 8.130997e-10, /* 68 47 */ 1.253855e-10, /* 68 48 */ 1.808261e-11, /* 68 49 */ 2.434270e-12, /* 68 50 */ 3.052438e-13, /* 68 51 */ 3.556715e-14, /* 68 52 */ 3.840482e-15, /* 68 53 */ 3.830887e-16, /* 68 54 */ 3.517491e-17, /* 68 55 */ 2.960674e-18, /* 68 56 */ 2.273444e-19, /* 68 57 */ 1.583675e-20, /* 68 58 */ 9.941117e-22, /* 68 59 */ 5.578389e-23, /* 68 60 */ 2.771022e-24, /* 68 61 */ 1.203781e-25, /* 68 62 */ 4.503013e-27, /* 68 63 */ 1.421213e-28, /* 68 64 */ 3.680320e-30, /* 68 65 */ 7.508525e-32, /* 68 66 */ 1.131712e-33, /* 68 67 */ 1.120399e-35, /* 68 68 */ 5.465360e-38, /* 69 0 */ 1.000000e+00, /* 69 1 */ 1.000000e+00, /* 69 2 */ 1.000000e+00, /* 69 3 */ 1.000000e+00, /* 69 4 */ 1.000000e+00, /* 69 5 */ 1.000000e+00, /* 69 6 */ 1.000000e+00, /* 69 7 */ 1.000000e+00, /* 69 8 */ 1.000000e+00, /* 69 9 */ 1.000000e+00, /* 69 10 */ 1.000000e+00, /* 69 11 */ 1.000000e+00, /* 69 12 */ 1.000000e+00, /* 69 13 */ 1.000000e+00, /* 69 14 */ 1.000000e+00, /* 69 15 */ 1.000000e+00, /* 69 16 */ 1.000000e+00, /* 69 17 */ 1.000000e+00, /* 69 18 */ 1.000000e+00, /* 69 19 */ 1.000000e+00, /* 69 20 */ 1.000000e+00, /* 69 21 */ 1.000000e+00, /* 69 22 */ 1.000000e+00, /* 69 23 */ 1.000000e+00, /* 69 24 */ 1.000000e+00, /* 69 25 */ 9.999673e-01, /* 69 26 */ 9.987545e-01, /* 69 27 */ 9.754800e-01, /* 69 28 */ 8.571036e-01, /* 69 29 */ 6.147436e-01, /* 69 30 */ 3.579145e-01, /* 69 31 */ 1.770345e-01, /* 69 32 */ 7.712364e-02, /* 69 33 */ 3.093455e-02, /* 69 34 */ 1.142182e-02, /* 69 35 */ 4.003636e-03, /* 69 36 */ 1.376364e-03, /* 69 37 */ 3.981818e-04, /* 69 38 */ 1.436364e-04, /* 69 39 */ 3.818182e-05, /* 69 40 */ 2.980109e-05, /* 69 41 */ 6.908438e-06, /* 69 42 */ 1.510983e-06, /* 69 43 */ 3.115482e-07, /* 69 44 */ 6.050374e-08, /* 69 45 */ 1.105559e-08, /* 69 46 */ 1.898527e-09, /* 69 47 */ 3.059943e-10, /* 69 48 */ 4.621947e-11, /* 69 49 */ 6.531641e-12, /* 69 50 */ 8.619517e-13, /* 69 51 */ 1.059931e-13, /* 69 52 */ 1.211584e-14, /* 69 53 */ 1.283857e-15, /* 69 54 */ 1.257197e-16, /* 69 55 */ 1.133580e-17, /* 69 56 */ 9.372644e-19, /* 69 57 */ 7.071979e-20, /* 69 58 */ 4.842130e-21, /* 69 59 */ 2.988432e-22, /* 69 60 */ 1.649208e-23, /* 69 61 */ 8.059003e-25, /* 69 62 */ 3.444902e-26, /* 69 63 */ 1.268323e-27, /* 69 64 */ 3.940849e-29, /* 69 65 */ 1.004900e-30, /* 69 66 */ 2.019292e-32, /* 69 67 */ 2.998366e-34, /* 69 68 */ 2.924961e-36, /* 69 69 */ 1.406231e-38, /* 70 0 */ 1.000000e+00, /* 70 1 */ 1.000000e+00, /* 70 2 */ 1.000000e+00, /* 70 3 */ 1.000000e+00, /* 70 4 */ 1.000000e+00, /* 70 5 */ 1.000000e+00, /* 70 6 */ 1.000000e+00, /* 70 7 */ 1.000000e+00, /* 70 8 */ 1.000000e+00, /* 70 9 */ 1.000000e+00, /* 70 10 */ 1.000000e+00, /* 70 11 */ 1.000000e+00, /* 70 12 */ 1.000000e+00, /* 70 13 */ 1.000000e+00, /* 70 14 */ 1.000000e+00, /* 70 15 */ 1.000000e+00, /* 70 16 */ 1.000000e+00, /* 70 17 */ 1.000000e+00, /* 70 18 */ 1.000000e+00, /* 70 19 */ 1.000000e+00, /* 70 20 */ 1.000000e+00, /* 70 21 */ 1.000000e+00, /* 70 22 */ 1.000000e+00, /* 70 23 */ 1.000000e+00, /* 70 24 */ 1.000000e+00, /* 70 25 */ 9.999945e-01, /* 70 26 */ 9.996545e-01, /* 70 27 */ 9.895091e-01, /* 70 28 */ 9.136618e-01, /* 70 29 */ 7.081473e-01, /* 70 30 */ 4.425527e-01, /* 70 31 */ 2.320400e-01, /* 70 32 */ 1.058727e-01, /* 70 33 */ 4.385091e-02, /* 70 34 */ 1.680182e-02, /* 70 35 */ 5.967273e-03, /* 70 36 */ 2.050909e-03, /* 70 37 */ 6.600000e-04, /* 70 38 */ 2.145455e-04, /* 70 39 */ 6.727273e-05, /* 70 40 */ 2.000000e-05, /* 70 41 */ 1.299508e-05, /* 70 42 */ 2.942654e-06, /* 70 43 */ 6.290003e-07, /* 70 44 */ 1.268119e-07, /* 70 45 */ 2.409148e-08, /* 70 46 */ 4.308299e-09, /* 70 47 */ 7.243892e-10, /* 70 48 */ 1.143620e-10, /* 70 49 */ 1.692706e-11, /* 70 50 */ 2.344964e-12, /* 70 51 */ 3.034710e-13, /* 70 52 */ 3.660913e-14, /* 70 53 */ 4.106721e-15, /* 70 54 */ 4.272031e-16, /* 70 55 */ 4.108083e-17, /* 70 56 */ 3.638674e-18, /* 70 57 */ 2.956248e-19, /* 70 58 */ 2.192480e-20, /* 70 59 */ 1.475948e-21, /* 70 60 */ 8.958564e-23, /* 70 61 */ 4.863479e-24, /* 70 62 */ 2.338529e-25, /* 70 63 */ 9.838693e-27, /* 70 64 */ 3.566119e-28, /* 70 65 */ 1.091098e-29, /* 70 66 */ 2.740347e-31, /* 70 67 */ 5.424843e-33, /* 70 68 */ 7.937298e-35, /* 70 69 */ 7.631322e-37, /* 70 70 */ 3.616740e-39, /* 71 0 */ 1.000000e+00, /* 71 1 */ 1.000000e+00, /* 71 2 */ 1.000000e+00, /* 71 3 */ 1.000000e+00, /* 71 4 */ 1.000000e+00, /* 71 5 */ 1.000000e+00, /* 71 6 */ 1.000000e+00, /* 71 7 */ 1.000000e+00, /* 71 8 */ 1.000000e+00, /* 71 9 */ 1.000000e+00, /* 71 10 */ 1.000000e+00, /* 71 11 */ 1.000000e+00, /* 71 12 */ 1.000000e+00, /* 71 13 */ 1.000000e+00, /* 71 14 */ 1.000000e+00, /* 71 15 */ 1.000000e+00, /* 71 16 */ 1.000000e+00, /* 71 17 */ 1.000000e+00, /* 71 18 */ 1.000000e+00, /* 71 19 */ 1.000000e+00, /* 71 20 */ 1.000000e+00, /* 71 21 */ 1.000000e+00, /* 71 22 */ 1.000000e+00, /* 71 23 */ 1.000000e+00, /* 71 24 */ 1.000000e+00, /* 71 25 */ 9.999982e-01, /* 71 26 */ 9.999164e-01, /* 71 27 */ 9.961473e-01, /* 71 28 */ 9.527655e-01, /* 71 29 */ 7.929055e-01, /* 71 30 */ 5.340600e-01, /* 71 31 */ 2.971418e-01, /* 71 32 */ 1.422764e-01, /* 71 33 */ 6.150909e-02, /* 71 34 */ 2.423273e-02, /* 71 35 */ 8.849091e-03, /* 71 36 */ 3.105455e-03, /* 71 37 */ 1.063636e-03, /* 71 38 */ 3.072727e-04, /* 71 39 */ 1.236364e-04, /* 71 40 */ 3.090909e-05, /* 71 41 */ 2.395975e-05, /* 71 42 */ 5.610527e-06, /* 71 43 */ 1.241665e-06, /* 71 44 */ 2.595177e-07, /* 71 45 */ 5.118347e-08, /* 71 46 */ 9.516609e-09, /* 71 47 */ 1.666332e-09, /* 71 48 */ 2.744391e-10, /* 71 49 */ 4.245695e-11, /* 71 50 */ 6.160422e-12, /* 71 51 */ 8.369309e-13, /* 71 52 */ 1.062556e-13, /* 71 53 */ 1.257932e-14, /* 71 54 */ 1.385296e-15, /* 71 55 */ 1.415151e-16, /* 71 56 */ 1.336797e-17, /* 71 57 */ 1.163482e-18, /* 71 58 */ 9.291277e-20, /* 71 59 */ 6.775049e-21, /* 71 60 */ 4.485495e-22, /* 71 61 */ 2.678282e-23, /* 71 62 */ 1.430726e-24, /* 71 63 */ 6.771001e-26, /* 71 64 */ 2.804494e-27, /* 71 65 */ 1.000974e-28, /* 71 66 */ 3.016481e-30, /* 71 67 */ 7.463613e-32, /* 71 68 */ 1.455901e-33, /* 71 69 */ 2.099473e-35, /* 71 70 */ 1.989846e-37, /* 71 71 */ 9.298344e-40, /* 72 0 */ 1.000000e+00, /* 72 1 */ 1.000000e+00, /* 72 2 */ 1.000000e+00, /* 72 3 */ 1.000000e+00, /* 72 4 */ 1.000000e+00, /* 72 5 */ 1.000000e+00, /* 72 6 */ 1.000000e+00, /* 72 7 */ 1.000000e+00, /* 72 8 */ 1.000000e+00, /* 72 9 */ 1.000000e+00, /* 72 10 */ 1.000000e+00, /* 72 11 */ 1.000000e+00, /* 72 12 */ 1.000000e+00, /* 72 13 */ 1.000000e+00, /* 72 14 */ 1.000000e+00, /* 72 15 */ 1.000000e+00, /* 72 16 */ 1.000000e+00, /* 72 17 */ 1.000000e+00, /* 72 18 */ 1.000000e+00, /* 72 19 */ 1.000000e+00, /* 72 20 */ 1.000000e+00, /* 72 21 */ 1.000000e+00, /* 72 22 */ 1.000000e+00, /* 72 23 */ 1.000000e+00, /* 72 24 */ 1.000000e+00, /* 72 25 */ 1.000000e+00, /* 72 26 */ 9.999836e-01, /* 72 27 */ 9.987836e-01, /* 72 28 */ 9.770964e-01, /* 72 29 */ 8.636182e-01, /* 72 30 */ 6.278745e-01, /* 72 31 */ 3.720873e-01, /* 72 32 */ 1.881782e-01, /* 72 33 */ 8.431455e-02, /* 72 34 */ 3.458727e-02, /* 72 35 */ 1.306182e-02, /* 72 36 */ 4.589091e-03, /* 72 37 */ 1.563636e-03, /* 72 38 */ 4.781818e-04, /* 72 39 */ 1.800000e-04, /* 72 40 */ 4.727273e-05, /* 72 41 */ 4.334026e-05, /* 72 42 */ 1.048307e-05, /* 72 43 */ 2.399161e-06, /* 72 44 */ 5.191813e-07, /* 72 45 */ 1.061555e-07, /* 72 46 */ 2.049087e-08, /* 72 47 */ 3.730404e-09, /* 72 48 */ 6.398217e-10, /* 72 49 */ 1.032622e-10, /* 72 50 */ 1.566068e-11, /* 72 51 */ 2.228439e-12, /* 72 52 */ 2.970059e-13, /* 72 53 */ 3.700530e-14, /* 72 54 */ 4.300826e-15, /* 72 55 */ 4.651158e-16, /* 72 56 */ 4.667474e-17, /* 72 57 */ 4.332488e-18, /* 72 58 */ 3.706400e-19, /* 72 59 */ 2.910132e-20, /* 72 60 */ 2.086960e-21, /* 72 61 */ 1.359229e-22, /* 72 62 */ 7.986046e-24, /* 72 63 */ 4.198890e-25, /* 72 64 */ 1.956318e-26, /* 72 65 */ 7.979072e-28, /* 72 66 */ 2.804993e-29, /* 72 67 */ 8.327564e-31, /* 72 68 */ 2.030341e-32, /* 72 69 */ 3.903424e-34, /* 72 70 */ 5.548905e-36, /* 72 71 */ 5.185446e-38, /* 72 72 */ 2.389606e-40, /* 73 0 */ 1.000000e+00, /* 73 1 */ 1.000000e+00, /* 73 2 */ 1.000000e+00, /* 73 3 */ 1.000000e+00, /* 73 4 */ 1.000000e+00, /* 73 5 */ 1.000000e+00, /* 73 6 */ 1.000000e+00, /* 73 7 */ 1.000000e+00, /* 73 8 */ 1.000000e+00, /* 73 9 */ 1.000000e+00, /* 73 10 */ 1.000000e+00, /* 73 11 */ 1.000000e+00, /* 73 12 */ 1.000000e+00, /* 73 13 */ 1.000000e+00, /* 73 14 */ 1.000000e+00, /* 73 15 */ 1.000000e+00, /* 73 16 */ 1.000000e+00, /* 73 17 */ 1.000000e+00, /* 73 18 */ 1.000000e+00, /* 73 19 */ 1.000000e+00, /* 73 20 */ 1.000000e+00, /* 73 21 */ 1.000000e+00, /* 73 22 */ 1.000000e+00, /* 73 23 */ 1.000000e+00, /* 73 24 */ 1.000000e+00, /* 73 25 */ 1.000000e+00, /* 73 26 */ 9.999982e-01, /* 73 27 */ 9.996455e-01, /* 73 28 */ 9.902618e-01, /* 73 29 */ 9.175218e-01, /* 73 30 */ 7.185400e-01, /* 73 31 */ 4.565764e-01, /* 73 32 */ 2.443255e-01, /* 73 33 */ 1.140218e-01, /* 73 34 */ 4.873636e-02, /* 73 35 */ 1.892909e-02, /* 73 36 */ 6.830909e-03, /* 73 37 */ 2.400000e-03, /* 73 38 */ 7.636364e-04, /* 73 39 */ 2.490909e-04, /* 73 40 */ 8.727273e-05, /* 73 41 */ 2.545455e-05, /* 73 42 */ 1.921314e-05, /* 73 43 */ 4.542068e-06, /* 73 44 */ 1.016463e-06, /* 73 45 */ 2.151885e-07, /* 73 46 */ 4.306303e-08, /* 73 47 */ 8.139008e-09, /* 73 48 */ 1.451430e-09, /* 73 49 */ 2.439508e-10, /* 73 50 */ 3.859718e-11, /* 73 51 */ 5.740601e-12, /* 73 52 */ 8.013766e-13, /* 73 53 */ 1.048193e-13, /* 73 54 */ 1.282112e-14, /* 73 55 */ 1.463325e-15, /* 73 56 */ 1.554582e-16, /* 73 57 */ 1.532956e-17, /* 73 58 */ 1.398648e-18, /* 73 59 */ 1.176441e-19, /* 73 60 */ 9.084415e-21, /* 73 61 */ 6.408863e-22, /* 73 62 */ 4.107283e-23, /* 73 63 */ 2.375189e-24, /* 73 64 */ 1.229450e-25, /* 73 65 */ 5.640645e-27, /* 73 66 */ 2.265971e-28, /* 73 67 */ 7.847718e-30, /* 73 68 */ 2.295796e-31, /* 73 69 */ 5.516701e-33, /* 73 70 */ 1.045540e-34, /* 73 71 */ 1.465456e-36, /* 73 72 */ 1.350538e-38, /* 73 73 */ 6.138808e-41, /* 74 0 */ 1.000000e+00, /* 74 1 */ 1.000000e+00, /* 74 2 */ 1.000000e+00, /* 74 3 */ 1.000000e+00, /* 74 4 */ 1.000000e+00, /* 74 5 */ 1.000000e+00, /* 74 6 */ 1.000000e+00, /* 74 7 */ 1.000000e+00, /* 74 8 */ 1.000000e+00, /* 74 9 */ 1.000000e+00, /* 74 10 */ 1.000000e+00, /* 74 11 */ 1.000000e+00, /* 74 12 */ 1.000000e+00, /* 74 13 */ 1.000000e+00, /* 74 14 */ 1.000000e+00, /* 74 15 */ 1.000000e+00, /* 74 16 */ 1.000000e+00, /* 74 17 */ 1.000000e+00, /* 74 18 */ 1.000000e+00, /* 74 19 */ 1.000000e+00, /* 74 20 */ 1.000000e+00, /* 74 21 */ 1.000000e+00, /* 74 22 */ 1.000000e+00, /* 74 23 */ 1.000000e+00, /* 74 24 */ 1.000000e+00, /* 74 25 */ 1.000000e+00, /* 74 26 */ 1.000000e+00, /* 74 27 */ 9.999073e-01, /* 74 28 */ 9.963455e-01, /* 74 29 */ 9.545073e-01, /* 74 30 */ 8.003109e-01, /* 74 31 */ 5.471964e-01, /* 74 32 */ 3.100909e-01, /* 74 33 */ 1.521491e-01, /* 74 34 */ 6.699455e-02, /* 74 35 */ 2.708909e-02, /* 74 36 */ 1.015273e-02, /* 74 37 */ 3.541818e-03, /* 74 38 */ 1.196364e-03, /* 74 39 */ 3.690909e-04, /* 74 40 */ 1.345455e-04, /* 74 41 */ 4.181818e-05, /* 74 42 */ 3.457071e-05, /* 74 43 */ 8.433222e-06, /* 74 44 */ 1.949504e-06, /* 74 45 */ 4.268128e-07, /* 74 46 */ 8.843700e-08, /* 74 47 */ 1.732904e-08, /* 74 48 */ 3.208309e-09, /* 74 49 */ 5.606722e-10, /* 74 50 */ 9.238271e-11, /* 74 51 */ 1.433445e-11, /* 74 52 */ 2.091587e-12, /* 74 53 */ 2.865489e-13, /* 74 54 */ 3.679532e-14, /* 74 55 */ 4.419851e-15, /* 74 56 */ 4.955516e-16, /* 74 57 */ 5.173205e-17, /* 74 58 */ 5.014198e-18, /* 74 59 */ 4.498100e-19, /* 74 60 */ 3.720998e-20, /* 74 61 */ 2.826643e-21, /* 74 62 */ 1.962240e-22, /* 74 63 */ 1.237747e-23, /* 74 64 */ 7.046719e-25, /* 74 65 */ 3.591817e-26, /* 74 66 */ 1.623103e-27, /* 74 67 */ 6.423662e-29, /* 74 68 */ 2.192183e-30, /* 74 69 */ 6.320670e-32, /* 74 70 */ 1.497251e-33, /* 74 71 */ 2.797871e-35, /* 74 72 */ 3.867374e-37, /* 74 73 */ 3.515508e-39, /* 74 74 */ 1.576461e-41, /* 75 0 */ 1.000000e+00, /* 75 1 */ 1.000000e+00, /* 75 2 */ 1.000000e+00, /* 75 3 */ 1.000000e+00, /* 75 4 */ 1.000000e+00, /* 75 5 */ 1.000000e+00, /* 75 6 */ 1.000000e+00, /* 75 7 */ 1.000000e+00, /* 75 8 */ 1.000000e+00, /* 75 9 */ 1.000000e+00, /* 75 10 */ 1.000000e+00, /* 75 11 */ 1.000000e+00, /* 75 12 */ 1.000000e+00, /* 75 13 */ 1.000000e+00, /* 75 14 */ 1.000000e+00, /* 75 15 */ 1.000000e+00, /* 75 16 */ 1.000000e+00, /* 75 17 */ 1.000000e+00, /* 75 18 */ 1.000000e+00, /* 75 19 */ 1.000000e+00, /* 75 20 */ 1.000000e+00, /* 75 21 */ 1.000000e+00, /* 75 22 */ 1.000000e+00, /* 75 23 */ 1.000000e+00, /* 75 24 */ 1.000000e+00, /* 75 25 */ 1.000000e+00, /* 75 26 */ 1.000000e+00, /* 75 27 */ 9.999764e-01, /* 75 28 */ 9.987818e-01, /* 75 29 */ 9.776255e-01, /* 75 30 */ 8.685945e-01, /* 75 31 */ 6.387436e-01, /* 75 32 */ 3.855745e-01, /* 75 33 */ 1.986418e-01, /* 75 34 */ 9.116727e-02, /* 75 35 */ 3.802909e-02, /* 75 36 */ 1.482545e-02, /* 75 37 */ 5.290909e-03, /* 75 38 */ 1.870909e-03, /* 75 39 */ 5.854545e-04, /* 75 40 */ 1.963636e-04, /* 75 41 */ 5.454545e-05, /* 75 42 */ 1.818182e-05, /* 75 43 */ 1.536939e-05, /* 75 44 */ 3.666280e-06, /* 75 45 */ 8.291621e-07, /* 75 46 */ 1.776759e-07, /* 75 47 */ 3.604843e-08, /* 75 48 */ 6.919383e-09, /* 75 49 */ 1.255401e-09, /* 75 50 */ 2.150778e-10, /* 75 51 */ 3.475510e-11, /* 75 52 */ 5.290613e-12, /* 75 53 */ 7.576144e-13, /* 75 54 */ 1.018976e-13, /* 75 55 */ 1.284964e-14, /* 75 56 */ 1.516266e-15, /* 75 57 */ 1.670542e-16, /* 75 58 */ 1.714179e-17, /* 75 59 */ 1.633614e-18, /* 75 60 */ 1.441279e-19, /* 75 61 */ 1.172911e-20, /* 75 62 */ 8.767493e-22, /* 75 63 */ 5.990517e-23, /* 75 64 */ 3.720124e-24, /* 75 65 */ 2.085589e-25, /* 75 66 */ 1.047060e-26, /* 75 67 */ 4.661394e-28, /* 75 68 */ 1.817853e-29, /* 75 69 */ 6.114352e-31, /* 75 70 */ 1.737895e-32, /* 75 71 */ 4.059084e-34, /* 75 72 */ 7.480285e-36, /* 75 73 */ 1.019872e-37, /* 75 74 */ 9.146107e-40, /* 75 75 */ 4.046950e-42, /* 76 0 */ 1.000000e+00, /* 76 1 */ 1.000000e+00, /* 76 2 */ 1.000000e+00, /* 76 3 */ 1.000000e+00, /* 76 4 */ 1.000000e+00, /* 76 5 */ 1.000000e+00, /* 76 6 */ 1.000000e+00, /* 76 7 */ 1.000000e+00, /* 76 8 */ 1.000000e+00, /* 76 9 */ 1.000000e+00, /* 76 10 */ 1.000000e+00, /* 76 11 */ 1.000000e+00, /* 76 12 */ 1.000000e+00, /* 76 13 */ 1.000000e+00, /* 76 14 */ 1.000000e+00, /* 76 15 */ 1.000000e+00, /* 76 16 */ 1.000000e+00, /* 76 17 */ 1.000000e+00, /* 76 18 */ 1.000000e+00, /* 76 19 */ 1.000000e+00, /* 76 20 */ 1.000000e+00, /* 76 21 */ 1.000000e+00, /* 76 22 */ 1.000000e+00, /* 76 23 */ 1.000000e+00, /* 76 24 */ 1.000000e+00, /* 76 25 */ 1.000000e+00, /* 76 26 */ 1.000000e+00, /* 76 27 */ 9.999945e-01, /* 76 28 */ 9.996673e-01, /* 76 29 */ 9.903782e-01, /* 76 30 */ 9.195927e-01, /* 76 31 */ 7.270855e-01, /* 76 32 */ 4.693382e-01, /* 76 33 */ 2.551018e-01, /* 76 34 */ 1.216400e-01, /* 76 35 */ 5.298545e-02, /* 76 36 */ 2.116545e-02, /* 76 37 */ 7.898182e-03, /* 76 38 */ 2.785455e-03, /* 76 39 */ 9.236364e-04, /* 76 40 */ 3.054545e-04, /* 76 41 */ 1.000000e-04, /* 76 42 */ 3.454545e-05, /* 76 43 */ 2.751660e-05, /* 76 44 */ 6.766674e-06, /* 76 45 */ 1.579193e-06, /* 76 46 */ 3.495682e-07, /* 76 47 */ 7.334807e-08, /* 76 48 */ 1.457783e-08, /* 76 49 */ 2.742159e-09, /* 76 50 */ 4.877450e-10, /* 76 51 */ 8.195054e-11, /* 76 52 */ 1.299200e-11, /* 76 53 */ 1.940951e-12, /* 76 54 */ 2.728683e-13, /* 76 55 */ 3.604170e-14, /* 76 56 */ 4.464826e-15, /* 76 57 */ 5.177169e-16, /* 76 58 */ 5.606671e-17, /* 76 59 */ 5.656630e-18, /* 76 60 */ 5.301809e-19, /* 76 61 */ 4.601626e-20, /* 76 62 */ 3.684930e-21, /* 76 63 */ 2.711123e-22, /* 76 64 */ 1.823700e-23, /* 76 65 */ 1.115229e-24, /* 76 66 */ 6.158181e-26, /* 76 67 */ 3.045854e-27, /* 76 68 */ 1.336168e-28, /* 76 69 */ 5.135738e-30, /* 76 70 */ 1.702873e-31, /* 76 71 */ 4.772319e-33, /* 76 72 */ 1.099239e-34, /* 76 73 */ 1.998124e-36, /* 76 74 */ 2.687631e-38, /* 76 75 */ 2.378250e-40, /* 76 76 */ 1.038537e-42, /* 77 0 */ 1.000000e+00, /* 77 1 */ 1.000000e+00, /* 77 2 */ 1.000000e+00, /* 77 3 */ 1.000000e+00, /* 77 4 */ 1.000000e+00, /* 77 5 */ 1.000000e+00, /* 77 6 */ 1.000000e+00, /* 77 7 */ 1.000000e+00, /* 77 8 */ 1.000000e+00, /* 77 9 */ 1.000000e+00, /* 77 10 */ 1.000000e+00, /* 77 11 */ 1.000000e+00, /* 77 12 */ 1.000000e+00, /* 77 13 */ 1.000000e+00, /* 77 14 */ 1.000000e+00, /* 77 15 */ 1.000000e+00, /* 77 16 */ 1.000000e+00, /* 77 17 */ 1.000000e+00, /* 77 18 */ 1.000000e+00, /* 77 19 */ 1.000000e+00, /* 77 20 */ 1.000000e+00, /* 77 21 */ 1.000000e+00, /* 77 22 */ 1.000000e+00, /* 77 23 */ 1.000000e+00, /* 77 24 */ 1.000000e+00, /* 77 25 */ 1.000000e+00, /* 77 26 */ 1.000000e+00, /* 77 27 */ 1.000000e+00, /* 77 28 */ 9.999236e-01, /* 77 29 */ 9.962600e-01, /* 77 30 */ 9.555727e-01, /* 77 31 */ 8.066455e-01, /* 77 32 */ 5.586891e-01, /* 77 33 */ 3.216600e-01, /* 77 34 */ 1.601673e-01, /* 77 35 */ 7.201636e-02, /* 77 36 */ 2.981091e-02, /* 77 37 */ 1.142364e-02, /* 77 38 */ 4.109091e-03, /* 77 39 */ 1.452727e-03, /* 77 40 */ 4.763636e-04, /* 77 41 */ 1.436364e-04, /* 77 42 */ 6.545455e-05, /* 77 43 */ 4.843240e-05, /* 77 44 */ 1.226667e-05, /* 77 45 */ 2.951251e-06, /* 77 46 */ 6.741495e-07, /* 77 47 */ 1.461259e-07, /* 77 48 */ 3.003560e-08, /* 77 49 */ 5.850119e-09, /* 77 50 */ 1.078834e-09, /* 77 51 */ 1.881937e-10, /* 77 52 */ 3.102197e-11, /* 77 53 */ 4.826681e-12, /* 77 54 */ 7.079245e-13, /* 77 55 */ 9.773839e-14, /* 77 56 */ 1.268214e-14, /* 77 57 */ 1.543826e-15, /* 77 58 */ 1.759622e-16, /* 77 59 */ 1.873649e-17, /* 77 60 */ 1.859158e-18, /* 77 61 */ 1.714248e-19, /* 77 62 */ 1.464076e-20, /* 77 63 */ 1.153966e-21, /* 77 64 */ 8.358531e-23, /* 77 65 */ 5.536729e-24, /* 77 66 */ 3.334898e-25, /* 77 67 */ 1.814204e-26, /* 77 68 */ 8.842025e-28, /* 77 69 */ 3.822997e-29, /* 77 70 */ 1.448554e-30, /* 77 71 */ 4.735759e-32, /* 77 72 */ 1.308868e-33, /* 77 73 */ 2.973718e-35, /* 77 74 */ 5.332743e-37, /* 77 75 */ 7.077763e-39, /* 77 76 */ 6.180987e-41, /* 77 77 */ 2.664219e-43, /* 78 0 */ 1.000000e+00, /* 78 1 */ 1.000000e+00, /* 78 2 */ 1.000000e+00, /* 78 3 */ 1.000000e+00, /* 78 4 */ 1.000000e+00, /* 78 5 */ 1.000000e+00, /* 78 6 */ 1.000000e+00, /* 78 7 */ 1.000000e+00, /* 78 8 */ 1.000000e+00, /* 78 9 */ 1.000000e+00, /* 78 10 */ 1.000000e+00, /* 78 11 */ 1.000000e+00, /* 78 12 */ 1.000000e+00, /* 78 13 */ 1.000000e+00, /* 78 14 */ 1.000000e+00, /* 78 15 */ 1.000000e+00, /* 78 16 */ 1.000000e+00, /* 78 17 */ 1.000000e+00, /* 78 18 */ 1.000000e+00, /* 78 19 */ 1.000000e+00, /* 78 20 */ 1.000000e+00, /* 78 21 */ 1.000000e+00, /* 78 22 */ 1.000000e+00, /* 78 23 */ 1.000000e+00, /* 78 24 */ 1.000000e+00, /* 78 25 */ 1.000000e+00, /* 78 26 */ 1.000000e+00, /* 78 27 */ 1.000000e+00, /* 78 28 */ 9.999800e-01, /* 78 29 */ 9.987127e-01, /* 78 30 */ 9.779600e-01, /* 78 31 */ 8.725400e-01, /* 78 32 */ 6.480145e-01, /* 78 33 */ 3.979891e-01, /* 78 34 */ 2.073600e-01, /* 78 35 */ 9.732182e-02, /* 78 36 */ 4.155818e-02, /* 78 37 */ 1.637636e-02, /* 78 38 */ 5.943636e-03, /* 78 39 */ 2.210909e-03, /* 78 40 */ 7.527273e-04, /* 78 41 */ 2.290909e-04, /* 78 42 */ 8.727273e-05, /* 78 43 */ 2.727273e-05, /* 78 44 */ 2.185797e-05, /* 78 45 */ 5.416361e-06, /* 78 46 */ 1.275512e-06, /* 78 47 */ 2.853091e-07, /* 78 48 */ 6.058219e-08, /* 78 49 */ 1.220348e-08, /* 78 50 */ 2.330276e-09, /* 78 51 */ 4.214559e-10, /* 78 52 */ 7.212941e-11, /* 78 53 */ 1.166905e-11, /* 78 54 */ 1.782453e-12, /* 78 55 */ 2.567436e-13, /* 78 56 */ 3.482220e-14, /* 78 57 */ 4.440102e-15, /* 78 58 */ 5.312934e-16, /* 78 59 */ 5.954074e-17, /* 78 60 */ 6.235350e-18, /* 78 61 */ 6.086700e-19, /* 78 62 */ 5.522604e-20, /* 78 63 */ 4.642451e-21, /* 78 64 */ 3.602428e-22, /* 78 65 */ 2.569527e-23, /* 78 66 */ 1.676473e-24, /* 78 67 */ 9.948157e-26, /* 78 68 */ 5.332816e-27, /* 78 69 */ 2.561673e-28, /* 78 70 */ 1.091858e-29, /* 78 71 */ 4.079185e-31, /* 78 72 */ 1.315190e-32, /* 78 73 */ 3.585395e-34, /* 78 74 */ 8.036417e-36, /* 78 75 */ 1.422042e-37, /* 78 76 */ 1.862656e-39, /* 78 77 */ 1.605620e-41, /* 78 78 */ 6.832425e-44, /* 79 0 */ 1.000000e+00, /* 79 1 */ 1.000000e+00, /* 79 2 */ 1.000000e+00, /* 79 3 */ 1.000000e+00, /* 79 4 */ 1.000000e+00, /* 79 5 */ 1.000000e+00, /* 79 6 */ 1.000000e+00, /* 79 7 */ 1.000000e+00, /* 79 8 */ 1.000000e+00, /* 79 9 */ 1.000000e+00, /* 79 10 */ 1.000000e+00, /* 79 11 */ 1.000000e+00, /* 79 12 */ 1.000000e+00, /* 79 13 */ 1.000000e+00, /* 79 14 */ 1.000000e+00, /* 79 15 */ 1.000000e+00, /* 79 16 */ 1.000000e+00, /* 79 17 */ 1.000000e+00, /* 79 18 */ 1.000000e+00, /* 79 19 */ 1.000000e+00, /* 79 20 */ 1.000000e+00, /* 79 21 */ 1.000000e+00, /* 79 22 */ 1.000000e+00, /* 79 23 */ 1.000000e+00, /* 79 24 */ 1.000000e+00, /* 79 25 */ 1.000000e+00, /* 79 26 */ 1.000000e+00, /* 79 27 */ 1.000000e+00, /* 79 28 */ 9.999945e-01, /* 79 29 */ 9.996473e-01, /* 79 30 */ 9.902782e-01, /* 79 31 */ 9.217127e-01, /* 79 32 */ 7.343291e-01, /* 79 33 */ 4.810400e-01, /* 79 34 */ 2.647127e-01, /* 79 35 */ 1.285164e-01, /* 79 36 */ 5.689636e-02, /* 79 37 */ 2.329636e-02, /* 79 38 */ 8.629091e-03, /* 79 39 */ 3.203636e-03, /* 79 40 */ 1.160000e-03, /* 79 41 */ 3.763636e-04, /* 79 42 */ 1.272727e-04, /* 79 43 */ 4.909091e-05, /* 79 44 */ 3.831186e-05, /* 79 45 */ 9.769472e-06, /* 79 46 */ 2.369594e-06, /* 79 47 */ 5.464353e-07, /* 79 48 */ 1.197387e-07, /* 79 49 */ 2.491720e-08, /* 79 50 */ 4.920829e-09, /* 79 51 */ 9.215558e-10, /* 79 52 */ 1.635236e-10, /* 79 53 */ 2.746651e-11, /* 79 54 */ 4.362484e-12, /* 79 55 */ 6.544295e-13, /* 79 56 */ 9.260317e-14, /* 79 57 */ 1.234225e-14, /* 79 58 */ 1.546927e-15, /* 79 59 */ 1.820005e-16, /* 79 60 */ 2.006006e-17, /* 79 61 */ 2.066684e-18, /* 79 62 */ 1.985190e-19, /* 79 63 */ 1.772880e-20, /* 79 64 */ 1.467247e-21, /* 79 65 */ 1.121176e-22, /* 79 66 */ 7.876863e-24, /* 79 67 */ 5.063081e-25, /* 79 68 */ 2.960552e-26, /* 79 69 */ 1.564190e-27, /* 79 70 */ 7.407096e-29, /* 79 71 */ 3.112920e-30, /* 79 72 */ 1.146929e-31, /* 79 73 */ 3.647497e-33, /* 79 74 */ 9.809933e-35, /* 79 75 */ 2.169660e-36, /* 79 76 */ 3.788936e-38, /* 79 77 */ 4.898764e-40, /* 79 78 */ 4.168863e-42, /* 79 79 */ 1.751623e-44, /* 80 0 */ 1.000000e+00, /* 80 1 */ 1.000000e+00, /* 80 2 */ 1.000000e+00, /* 80 3 */ 1.000000e+00, /* 80 4 */ 1.000000e+00, /* 80 5 */ 1.000000e+00, /* 80 6 */ 1.000000e+00, /* 80 7 */ 1.000000e+00, /* 80 8 */ 1.000000e+00, /* 80 9 */ 1.000000e+00, /* 80 10 */ 1.000000e+00, /* 80 11 */ 1.000000e+00, /* 80 12 */ 1.000000e+00, /* 80 13 */ 1.000000e+00, /* 80 14 */ 1.000000e+00, /* 80 15 */ 1.000000e+00, /* 80 16 */ 1.000000e+00, /* 80 17 */ 1.000000e+00, /* 80 18 */ 1.000000e+00, /* 80 19 */ 1.000000e+00, /* 80 20 */ 1.000000e+00, /* 80 21 */ 1.000000e+00, /* 80 22 */ 1.000000e+00, /* 80 23 */ 1.000000e+00, /* 80 24 */ 1.000000e+00, /* 80 25 */ 1.000000e+00, /* 80 26 */ 1.000000e+00, /* 80 27 */ 1.000000e+00, /* 80 28 */ 1.000000e+00, /* 80 29 */ 9.999109e-01, /* 80 30 */ 9.962982e-01, /* 80 31 */ 9.565618e-01, /* 80 32 */ 8.112491e-01, /* 80 33 */ 5.686655e-01, /* 80 34 */ 3.323945e-01, /* 80 35 */ 1.681582e-01, /* 80 36 */ 7.708909e-02, /* 80 37 */ 3.264364e-02, /* 80 38 */ 1.276000e-02, /* 80 39 */ 4.596364e-03, /* 80 40 */ 1.734545e-03, /* 80 41 */ 5.927273e-04, /* 80 42 */ 1.800000e-04, /* 80 43 */ 7.818182e-05, /* 80 44 */ 2.000000e-05, /* 80 45 */ 1.733034e-05, /* 80 46 */ 4.325712e-06, /* 80 47 */ 1.027437e-06, /* 80 48 */ 2.321085e-07, /* 80 49 */ 4.984573e-08, /* 80 50 */ 1.016947e-08, /* 80 51 */ 1.969709e-09, /* 80 52 */ 3.619126e-10, /* 80 53 */ 6.302740e-11, /* 80 54 */ 1.039354e-11, /* 80 55 */ 1.621226e-12, /* 80 56 */ 2.389227e-13, /* 80 57 */ 3.322273e-14, /* 80 58 */ 4.352566e-15, /* 80 59 */ 5.363947e-16, /* 80 60 */ 6.206826e-17, /* 80 61 */ 6.730181e-18, /* 80 62 */ 6.823033e-19, /* 80 63 */ 6.450933e-20, /* 80 64 */ 5.671815e-21, /* 80 65 */ 4.622428e-22, /* 80 66 */ 3.479077e-23, /* 80 67 */ 2.408038e-24, /* 80 68 */ 1.525239e-25, /* 80 69 */ 8.790225e-27, /* 80 70 */ 4.578355e-28, /* 80 71 */ 2.137700e-29, /* 80 72 */ 8.859910e-31, /* 80 73 */ 3.219899e-32, /* 80 74 */ 1.010239e-33, /* 80 75 */ 2.680997e-35, /* 80 76 */ 5.851920e-37, /* 80 77 */ 1.008728e-38, /* 80 78 */ 1.287553e-40, /* 80 79 */ 1.081902e-42, /* 80 80 */ 4.489218e-45, /* 81 0 */ 1.000000e+00, /* 81 1 */ 1.000000e+00, /* 81 2 */ 1.000000e+00, /* 81 3 */ 1.000000e+00, /* 81 4 */ 1.000000e+00, /* 81 5 */ 1.000000e+00, /* 81 6 */ 1.000000e+00, /* 81 7 */ 1.000000e+00, /* 81 8 */ 1.000000e+00, /* 81 9 */ 1.000000e+00, /* 81 10 */ 1.000000e+00, /* 81 11 */ 1.000000e+00, /* 81 12 */ 1.000000e+00, /* 81 13 */ 1.000000e+00, /* 81 14 */ 1.000000e+00, /* 81 15 */ 1.000000e+00, /* 81 16 */ 1.000000e+00, /* 81 17 */ 1.000000e+00, /* 81 18 */ 1.000000e+00, /* 81 19 */ 1.000000e+00, /* 81 20 */ 1.000000e+00, /* 81 21 */ 1.000000e+00, /* 81 22 */ 1.000000e+00, /* 81 23 */ 1.000000e+00, /* 81 24 */ 1.000000e+00, /* 81 25 */ 1.000000e+00, /* 81 26 */ 1.000000e+00, /* 81 27 */ 1.000000e+00, /* 81 28 */ 1.000000e+00, /* 81 29 */ 9.999709e-01, /* 81 30 */ 9.987473e-01, /* 81 31 */ 9.785800e-01, /* 81 32 */ 8.746836e-01, /* 81 33 */ 6.568109e-01, /* 81 34 */ 4.079582e-01, /* 81 35 */ 2.168473e-01, /* 81 36 */ 1.029455e-01, /* 81 37 */ 4.495818e-02, /* 81 38 */ 1.837091e-02, /* 81 39 */ 6.714545e-03, /* 81 40 */ 2.478182e-03, /* 81 41 */ 9.290909e-04, /* 81 42 */ 2.872727e-04, /* 81 43 */ 1.018182e-04, /* 81 44 */ 2.909091e-05, /* 81 45 */ 1.272727e-05, /* 81 46 */ 7.765106e-06, /* 81 47 */ 1.898017e-06, /* 81 48 */ 4.416469e-07, /* 81 49 */ 9.778181e-08, /* 81 50 */ 2.058761e-08, /* 81 51 */ 4.119512e-09, /* 81 52 */ 7.828388e-10, /* 81 53 */ 1.411709e-10, /* 81 54 */ 2.413712e-11, /* 81 55 */ 3.909066e-12, /* 81 56 */ 5.990197e-13, /* 81 57 */ 8.675069e-14, /* 81 58 */ 1.185755e-14, /* 81 59 */ 1.527466e-15, /* 81 60 */ 1.851379e-16, /* 81 61 */ 2.107561e-17, /* 81 62 */ 2.248787e-18, /* 81 63 */ 2.243976e-19, /* 81 64 */ 2.088754e-20, /* 81 65 */ 1.808476e-21, /* 81 66 */ 1.451730e-22, /* 81 67 */ 1.076467e-23, /* 81 68 */ 7.342005e-25, /* 81 69 */ 4.583476e-26, /* 81 70 */ 2.604059e-27, /* 81 71 */ 1.337335e-28, /* 81 72 */ 6.158023e-30, /* 81 73 */ 2.517498e-31, /* 81 74 */ 9.026236e-33, /* 81 75 */ 2.794413e-34, /* 81 76 */ 7.318804e-36, /* 81 77 */ 1.576860e-37, /* 81 78 */ 2.683437e-39, /* 81 79 */ 3.382009e-41, /* 81 80 */ 2.806456e-43, /* 81 81 */ 1.150187e-45, /* 82 0 */ 1.000000e+00, /* 82 1 */ 1.000000e+00, /* 82 2 */ 1.000000e+00, /* 82 3 */ 1.000000e+00, /* 82 4 */ 1.000000e+00, /* 82 5 */ 1.000000e+00, /* 82 6 */ 1.000000e+00, /* 82 7 */ 1.000000e+00, /* 82 8 */ 1.000000e+00, /* 82 9 */ 1.000000e+00, /* 82 10 */ 1.000000e+00, /* 82 11 */ 1.000000e+00, /* 82 12 */ 1.000000e+00, /* 82 13 */ 1.000000e+00, /* 82 14 */ 1.000000e+00, /* 82 15 */ 1.000000e+00, /* 82 16 */ 1.000000e+00, /* 82 17 */ 1.000000e+00, /* 82 18 */ 1.000000e+00, /* 82 19 */ 1.000000e+00, /* 82 20 */ 1.000000e+00, /* 82 21 */ 1.000000e+00, /* 82 22 */ 1.000000e+00, /* 82 23 */ 1.000000e+00, /* 82 24 */ 1.000000e+00, /* 82 25 */ 1.000000e+00, /* 82 26 */ 1.000000e+00, /* 82 27 */ 1.000000e+00, /* 82 28 */ 1.000000e+00, /* 82 29 */ 1.000000e+00, /* 82 30 */ 9.996455e-01, /* 82 31 */ 9.905182e-01, /* 82 32 */ 9.231127e-01, /* 82 33 */ 7.410545e-01, /* 82 34 */ 4.910727e-01, /* 82 35 */ 2.746691e-01, /* 82 36 */ 1.353927e-01, /* 82 37 */ 6.124000e-02, /* 82 38 */ 2.562727e-02, /* 82 39 */ 9.823636e-03, /* 82 40 */ 3.667273e-03, /* 82 41 */ 1.350909e-03, /* 82 42 */ 4.418182e-04, /* 82 43 */ 1.581818e-04, /* 82 44 */ 6.000000e-05, /* 82 45 */ 5.201647e-05, /* 82 46 */ 1.371625e-05, /* 82 47 */ 3.447358e-06, /* 82 48 */ 8.255113e-07, /* 82 49 */ 1.882571e-07, /* 82 50 */ 4.086492e-08, /* 82 51 */ 8.438652e-09, /* 82 52 */ 1.656687e-09, /* 82 53 */ 3.089885e-10, /* 82 54 */ 5.470584e-11, /* 82 55 */ 9.186099e-12, /* 82 56 */ 1.461537e-12, /* 82 57 */ 2.200894e-13, /* 82 58 */ 3.133126e-14, /* 82 59 */ 4.210842e-15, /* 82 60 */ 5.334977e-16, /* 82 61 */ 6.361483e-17, /* 82 62 */ 7.126172e-18, /* 82 63 */ 7.484204e-19, /* 82 64 */ 7.352608e-20, /* 82 65 */ 6.739665e-21, /* 82 66 */ 5.747651e-22, /* 82 67 */ 4.545547e-23, /* 82 68 */ 3.321369e-24, /* 82 69 */ 2.232739e-25, /* 82 70 */ 1.374084e-26, /* 82 71 */ 7.697514e-28, /* 82 72 */ 3.898565e-29, /* 82 73 */ 1.770729e-30, /* 82 74 */ 7.141767e-32, /* 82 75 */ 2.526657e-33, /* 82 76 */ 7.719843e-35, /* 82 77 */ 1.995767e-36, /* 82 78 */ 4.245083e-38, /* 82 79 */ 7.133088e-40, /* 82 80 */ 8.878151e-42, /* 82 81 */ 7.276690e-44, /* 82 82 */ 2.946028e-46, /* 83 0 */ 1.000000e+00, /* 83 1 */ 1.000000e+00, /* 83 2 */ 1.000000e+00, /* 83 3 */ 1.000000e+00, /* 83 4 */ 1.000000e+00, /* 83 5 */ 1.000000e+00, /* 83 6 */ 1.000000e+00, /* 83 7 */ 1.000000e+00, /* 83 8 */ 1.000000e+00, /* 83 9 */ 1.000000e+00, /* 83 10 */ 1.000000e+00, /* 83 11 */ 1.000000e+00, /* 83 12 */ 1.000000e+00, /* 83 13 */ 1.000000e+00, /* 83 14 */ 1.000000e+00, /* 83 15 */ 1.000000e+00, /* 83 16 */ 1.000000e+00, /* 83 17 */ 1.000000e+00, /* 83 18 */ 1.000000e+00, /* 83 19 */ 1.000000e+00, /* 83 20 */ 1.000000e+00, /* 83 21 */ 1.000000e+00, /* 83 22 */ 1.000000e+00, /* 83 23 */ 1.000000e+00, /* 83 24 */ 1.000000e+00, /* 83 25 */ 1.000000e+00, /* 83 26 */ 1.000000e+00, /* 83 27 */ 1.000000e+00, /* 83 28 */ 1.000000e+00, /* 83 29 */ 1.000000e+00, /* 83 30 */ 9.999145e-01, /* 83 31 */ 9.963582e-01, /* 83 32 */ 9.573200e-01, /* 83 33 */ 8.156473e-01, /* 83 34 */ 5.770345e-01, /* 83 35 */ 3.419727e-01, /* 83 36 */ 1.758200e-01, /* 83 37 */ 8.197091e-02, /* 83 38 */ 3.548182e-02, /* 83 39 */ 1.419818e-02, /* 83 40 */ 5.261818e-03, /* 83 41 */ 1.983636e-03, /* 83 42 */ 6.890909e-04, /* 83 43 */ 2.363636e-04, /* 83 44 */ 9.454545e-05, /* 83 45 */ 2.909091e-05, /* 83 46 */ 2.385593e-05, /* 83 47 */ 6.160385e-06, /* 83 48 */ 1.516874e-06, /* 83 49 */ 3.559963e-07, /* 83 50 */ 7.959684e-08, /* 83 51 */ 1.694630e-08, /* 83 52 */ 3.433440e-09, /* 83 53 */ 6.615710e-10, /* 83 54 */ 1.211437e-10, /* 83 55 */ 2.106459e-11, /* 83 56 */ 3.474921e-12, /* 83 57 */ 5.433102e-13, /* 83 58 */ 8.042425e-14, /* 83 59 */ 1.125738e-14, /* 83 60 */ 1.488053e-15, /* 83 61 */ 1.854753e-16, /* 83 62 */ 2.176343e-17, /* 83 63 */ 2.399653e-18, /* 83 64 */ 2.481222e-19, /* 83 65 */ 2.400440e-20, /* 83 66 */ 2.167285e-21, /* 83 67 */ 1.820926e-22, /* 83 68 */ 1.419076e-23, /* 83 69 */ 1.021986e-24, /* 83 70 */ 6.772705e-26, /* 83 71 */ 4.109794e-27, /* 83 72 */ 2.270509e-28, /* 83 73 */ 1.134292e-29, /* 83 74 */ 5.082753e-31, /* 83 75 */ 2.022816e-32, /* 83 76 */ 7.062790e-34, /* 83 77 */ 2.130057e-35, /* 83 78 */ 5.436467e-37, /* 83 79 */ 1.141793e-38, /* 83 80 */ 1.894702e-40, /* 83 81 */ 2.329241e-42, /* 83 82 */ 1.885903e-44, /* 83 83 */ 7.543611e-47, /* 84 0 */ 1.000000e+00, /* 84 1 */ 1.000000e+00, /* 84 2 */ 1.000000e+00, /* 84 3 */ 1.000000e+00, /* 84 4 */ 1.000000e+00, /* 84 5 */ 1.000000e+00, /* 84 6 */ 1.000000e+00, /* 84 7 */ 1.000000e+00, /* 84 8 */ 1.000000e+00, /* 84 9 */ 1.000000e+00, /* 84 10 */ 1.000000e+00, /* 84 11 */ 1.000000e+00, /* 84 12 */ 1.000000e+00, /* 84 13 */ 1.000000e+00, /* 84 14 */ 1.000000e+00, /* 84 15 */ 1.000000e+00, /* 84 16 */ 1.000000e+00, /* 84 17 */ 1.000000e+00, /* 84 18 */ 1.000000e+00, /* 84 19 */ 1.000000e+00, /* 84 20 */ 1.000000e+00, /* 84 21 */ 1.000000e+00, /* 84 22 */ 1.000000e+00, /* 84 23 */ 1.000000e+00, /* 84 24 */ 1.000000e+00, /* 84 25 */ 1.000000e+00, /* 84 26 */ 1.000000e+00, /* 84 27 */ 1.000000e+00, /* 84 28 */ 1.000000e+00, /* 84 29 */ 1.000000e+00, /* 84 30 */ 9.999727e-01, /* 84 31 */ 9.987236e-01, /* 84 32 */ 9.785109e-01, /* 84 33 */ 8.772145e-01, /* 84 34 */ 6.635636e-01, /* 84 35 */ 4.174327e-01, /* 84 36 */ 2.249873e-01, /* 84 37 */ 1.084073e-01, /* 84 38 */ 4.819091e-02, /* 84 39 */ 1.998182e-02, /* 84 40 */ 7.518182e-03, /* 84 41 */ 2.838182e-03, /* 84 42 */ 1.054545e-03, /* 84 43 */ 3.472727e-04, /* 84 44 */ 1.327273e-04, /* 84 45 */ 5.090909e-05, /* 84 46 */ 4.087779e-05, /* 84 47 */ 1.083778e-05, /* 84 48 */ 2.741887e-06, /* 84 49 */ 6.616934e-07, /* 84 50 */ 1.522582e-07, /* 84 51 */ 3.338996e-08, /* 84 52 */ 6.974803e-09, /* 84 53 */ 1.386981e-09, /* 84 54 */ 2.623881e-10, /* 84 55 */ 4.718815e-11, /* 84 56 */ 8.060890e-12, /* 84 57 */ 1.306780e-12, /* 84 58 */ 2.008437e-13, /* 84 59 */ 2.923289e-14, /* 84 60 */ 4.024523e-15, /* 84 61 */ 5.233617e-16, /* 84 62 */ 6.419295e-17, /* 84 63 */ 7.414018e-18, /* 84 64 */ 8.048306e-19, /* 84 65 */ 8.195076e-20, /* 84 66 */ 7.809230e-21, /* 84 67 */ 6.946390e-22, /* 84 68 */ 5.751147e-23, /* 84 69 */ 4.417509e-24, /* 84 70 */ 3.136278e-25, /* 84 71 */ 2.049347e-26, /* 84 72 */ 1.226424e-27, /* 84 73 */ 6.683321e-29, /* 84 74 */ 3.293987e-30, /* 84 75 */ 1.456468e-31, /* 84 76 */ 5.720560e-33, /* 84 77 */ 1.971569e-34, /* 84 78 */ 5.870187e-36, /* 84 79 */ 1.479355e-37, /* 84 80 */ 3.068356e-39, /* 84 81 */ 5.029082e-41, /* 84 82 */ 6.107403e-43, /* 84 83 */ 4.885613e-45, /* 84 84 */ 1.931073e-47, /* 85 0 */ 1.000000e+00, /* 85 1 */ 1.000000e+00, /* 85 2 */ 1.000000e+00, /* 85 3 */ 1.000000e+00, /* 85 4 */ 1.000000e+00, /* 85 5 */ 1.000000e+00, /* 85 6 */ 1.000000e+00, /* 85 7 */ 1.000000e+00, /* 85 8 */ 1.000000e+00, /* 85 9 */ 1.000000e+00, /* 85 10 */ 1.000000e+00, /* 85 11 */ 1.000000e+00, /* 85 12 */ 1.000000e+00, /* 85 13 */ 1.000000e+00, /* 85 14 */ 1.000000e+00, /* 85 15 */ 1.000000e+00, /* 85 16 */ 1.000000e+00, /* 85 17 */ 1.000000e+00, /* 85 18 */ 1.000000e+00, /* 85 19 */ 1.000000e+00, /* 85 20 */ 1.000000e+00, /* 85 21 */ 1.000000e+00, /* 85 22 */ 1.000000e+00, /* 85 23 */ 1.000000e+00, /* 85 24 */ 1.000000e+00, /* 85 25 */ 1.000000e+00, /* 85 26 */ 1.000000e+00, /* 85 27 */ 1.000000e+00, /* 85 28 */ 1.000000e+00, /* 85 29 */ 1.000000e+00, /* 85 30 */ 9.999982e-01, /* 85 31 */ 9.996273e-01, /* 85 32 */ 9.903636e-01, /* 85 33 */ 9.249673e-01, /* 85 34 */ 7.449036e-01, /* 85 35 */ 4.995436e-01, /* 85 36 */ 2.830582e-01, /* 85 37 */ 1.419964e-01, /* 85 38 */ 6.502545e-02, /* 85 39 */ 2.749273e-02, /* 85 40 */ 1.094182e-02, /* 85 41 */ 4.189091e-03, /* 85 42 */ 1.532727e-03, /* 85 43 */ 5.381818e-04, /* 85 44 */ 2.000000e-04, /* 85 45 */ 7.454545e-05, /* 85 46 */ 2.363636e-05, /* 85 47 */ 1.878203e-05, /* 85 48 */ 4.878657e-06, /* 85 49 */ 1.209711e-06, /* 85 50 */ 2.862349e-07, /* 85 51 */ 6.460062e-08, /* 85 52 */ 1.389997e-08, /* 85 53 */ 2.849826e-09, /* 85 54 */ 5.564007e-10, /* 85 55 */ 1.033783e-10, /* 85 56 */ 1.826500e-11, /* 85 57 */ 3.066200e-12, /* 85 58 */ 4.886250e-13, /* 85 59 */ 7.384287e-14, /* 85 60 */ 1.057102e-14, /* 85 61 */ 1.431755e-15, /* 85 62 */ 1.832213e-16, /* 85 63 */ 2.212018e-17, /* 85 64 */ 2.515282e-18, /* 85 65 */ 2.688876e-19, /* 85 66 */ 2.696813e-20, /* 85 67 */ 2.531824e-21, /* 85 68 */ 2.219244e-22, /* 85 69 */ 1.810971e-23, /* 85 70 */ 1.371303e-24, /* 85 71 */ 9.599656e-26, /* 85 72 */ 6.186215e-27, /* 85 73 */ 3.651740e-28, /* 85 74 */ 1.963271e-29, /* 85 75 */ 9.548075e-31, /* 85 76 */ 4.166544e-32, /* 85 77 */ 1.615356e-33, /* 85 78 */ 5.496263e-35, /* 85 79 */ 1.615858e-36, /* 85 80 */ 4.021493e-38, /* 85 81 */ 8.238551e-40, /* 85 82 */ 1.333917e-41, /* 85 83 */ 1.600497e-43, /* 85 84 */ 1.265137e-45, /* 85 85 */ 4.941942e-48, /* 86 0 */ 1.000000e+00, /* 86 1 */ 1.000000e+00, /* 86 2 */ 1.000000e+00, /* 86 3 */ 1.000000e+00, /* 86 4 */ 1.000000e+00, /* 86 5 */ 1.000000e+00, /* 86 6 */ 1.000000e+00, /* 86 7 */ 1.000000e+00, /* 86 8 */ 1.000000e+00, /* 86 9 */ 1.000000e+00, /* 86 10 */ 1.000000e+00, /* 86 11 */ 1.000000e+00, /* 86 12 */ 1.000000e+00, /* 86 13 */ 1.000000e+00, /* 86 14 */ 1.000000e+00, /* 86 15 */ 1.000000e+00, /* 86 16 */ 1.000000e+00, /* 86 17 */ 1.000000e+00, /* 86 18 */ 1.000000e+00, /* 86 19 */ 1.000000e+00, /* 86 20 */ 1.000000e+00, /* 86 21 */ 1.000000e+00, /* 86 22 */ 1.000000e+00, /* 86 23 */ 1.000000e+00, /* 86 24 */ 1.000000e+00, /* 86 25 */ 1.000000e+00, /* 86 26 */ 1.000000e+00, /* 86 27 */ 1.000000e+00, /* 86 28 */ 1.000000e+00, /* 86 29 */ 1.000000e+00, /* 86 30 */ 1.000000e+00, /* 86 31 */ 9.999145e-01, /* 86 32 */ 9.961091e-01, /* 86 33 */ 9.578036e-01, /* 86 34 */ 8.183455e-01, /* 86 35 */ 5.846345e-01, /* 86 36 */ 3.503655e-01, /* 86 37 */ 1.828855e-01, /* 86 38 */ 8.655091e-02, /* 86 39 */ 3.789273e-02, /* 86 40 */ 1.547455e-02, /* 86 41 */ 5.954545e-03, /* 86 42 */ 2.240000e-03, /* 86 43 */ 7.836364e-04, /* 86 44 */ 2.745455e-04, /* 86 45 */ 1.054545e-04, /* 86 46 */ 3.454545e-05, /* 86 47 */ 3.208182e-05, /* 86 48 */ 8.549921e-06, /* 86 49 */ 2.176699e-06, /* 86 50 */ 5.291995e-07, /* 86 51 */ 1.228163e-07, /* 86 52 */ 2.719675e-08, /* 86 53 */ 5.743641e-09, /* 86 54 */ 1.156183e-09, /* 86 55 */ 2.217012e-10, /* 86 56 */ 4.046828e-11, /* 86 57 */ 7.026501e-12, /* 86 58 */ 1.159521e-12, /* 86 59 */ 1.816912e-13, /* 86 60 */ 2.700625e-14, /* 86 61 */ 3.803506e-15, /* 86 62 */ 5.069416e-16, /* 86 63 */ 6.385496e-17, /* 86 64 */ 7.589987e-18, /* 86 65 */ 8.499122e-19, /* 86 66 */ 8.949349e-20, /* 86 67 */ 8.843020e-21, /* 86 68 */ 8.180981e-22, /* 86 69 */ 7.067884e-23, /* 86 70 */ 5.685863e-24, /* 86 71 */ 4.245264e-25, /* 86 72 */ 2.930869e-26, /* 86 73 */ 1.863016e-27, /* 86 74 */ 1.084979e-28, /* 86 75 */ 5.755841e-30, /* 86 76 */ 2.762654e-31, /* 86 77 */ 1.189987e-32, /* 86 78 */ 4.554713e-34, /* 86 79 */ 1.530231e-35, /* 86 80 */ 4.442803e-37, /* 86 81 */ 1.092124e-38, /* 86 82 */ 2.210199e-40, /* 86 83 */ 3.535642e-42, /* 86 84 */ 4.191941e-44, /* 86 85 */ 3.274757e-46, /* 86 86 */ 1.264385e-48, /* 87 0 */ 1.000000e+00, /* 87 1 */ 1.000000e+00, /* 87 2 */ 1.000000e+00, /* 87 3 */ 1.000000e+00, /* 87 4 */ 1.000000e+00, /* 87 5 */ 1.000000e+00, /* 87 6 */ 1.000000e+00, /* 87 7 */ 1.000000e+00, /* 87 8 */ 1.000000e+00, /* 87 9 */ 1.000000e+00, /* 87 10 */ 1.000000e+00, /* 87 11 */ 1.000000e+00, /* 87 12 */ 1.000000e+00, /* 87 13 */ 1.000000e+00, /* 87 14 */ 1.000000e+00, /* 87 15 */ 1.000000e+00, /* 87 16 */ 1.000000e+00, /* 87 17 */ 1.000000e+00, /* 87 18 */ 1.000000e+00, /* 87 19 */ 1.000000e+00, /* 87 20 */ 1.000000e+00, /* 87 21 */ 1.000000e+00, /* 87 22 */ 1.000000e+00, /* 87 23 */ 1.000000e+00, /* 87 24 */ 1.000000e+00, /* 87 25 */ 1.000000e+00, /* 87 26 */ 1.000000e+00, /* 87 27 */ 1.000000e+00, /* 87 28 */ 1.000000e+00, /* 87 29 */ 1.000000e+00, /* 87 30 */ 1.000000e+00, /* 87 31 */ 9.999745e-01, /* 87 32 */ 9.987091e-01, /* 87 33 */ 9.785836e-01, /* 87 34 */ 8.782709e-01, /* 87 35 */ 6.693455e-01, /* 87 36 */ 4.258327e-01, /* 87 37 */ 2.328127e-01, /* 87 38 */ 1.138782e-01, /* 87 39 */ 5.116545e-02, /* 87 40 */ 2.156000e-02, /* 87 41 */ 8.500000e-03, /* 87 42 */ 3.220000e-03, /* 87 43 */ 1.178182e-03, /* 87 44 */ 4.272727e-04, /* 87 45 */ 1.490909e-04, /* 87 46 */ 5.454545e-05, /* 87 47 */ 2.000000e-05, /* 87 48 */ 1.476659e-05, /* 87 49 */ 3.857169e-06, /* 87 50 */ 9.628326e-07, /* 87 51 */ 2.296007e-07, /* 87 52 */ 5.228315e-08, /* 87 53 */ 1.136372e-08, /* 87 54 */ 2.356296e-09, /* 87 55 */ 4.658490e-10, /* 87 56 */ 8.775971e-11, /* 87 57 */ 1.574270e-11, /* 87 58 */ 2.686987e-12, /* 87 59 */ 4.360015e-13, /* 87 60 */ 6.719599e-14, /* 87 61 */ 9.826247e-15, /* 87 62 */ 1.361858e-15, /* 87 63 */ 1.786641e-16, /* 87 64 */ 2.215694e-17, /* 87 65 */ 2.593540e-18, /* 87 66 */ 2.860626e-19, /* 87 67 */ 2.967627e-20, /* 87 68 */ 2.889629e-21, /* 87 69 */ 2.634880e-22, /* 87 70 */ 2.244124e-23, /* 87 71 */ 1.780087e-24, /* 87 72 */ 1.310752e-25, /* 87 73 */ 8.926149e-27, /* 87 74 */ 5.597773e-28, /* 87 75 */ 3.216830e-29, /* 87 76 */ 1.684220e-30, /* 87 77 */ 7.979445e-32, /* 87 78 */ 3.393251e-33, /* 87 79 */ 1.282426e-34, /* 87 80 */ 4.254941e-36, /* 87 81 */ 1.220184e-37, /* 87 82 */ 2.963035e-39, /* 87 83 */ 5.924554e-41, /* 87 84 */ 9.365135e-43, /* 87 85 */ 1.097344e-44, /* 87 86 */ 8.473199e-47, /* 87 87 */ 3.234045e-49, /* 88 0 */ 1.000000e+00, /* 88 1 */ 1.000000e+00, /* 88 2 */ 1.000000e+00, /* 88 3 */ 1.000000e+00, /* 88 4 */ 1.000000e+00, /* 88 5 */ 1.000000e+00, /* 88 6 */ 1.000000e+00, /* 88 7 */ 1.000000e+00, /* 88 8 */ 1.000000e+00, /* 88 9 */ 1.000000e+00, /* 88 10 */ 1.000000e+00, /* 88 11 */ 1.000000e+00, /* 88 12 */ 1.000000e+00, /* 88 13 */ 1.000000e+00, /* 88 14 */ 1.000000e+00, /* 88 15 */ 1.000000e+00, /* 88 16 */ 1.000000e+00, /* 88 17 */ 1.000000e+00, /* 88 18 */ 1.000000e+00, /* 88 19 */ 1.000000e+00, /* 88 20 */ 1.000000e+00, /* 88 21 */ 1.000000e+00, /* 88 22 */ 1.000000e+00, /* 88 23 */ 1.000000e+00, /* 88 24 */ 1.000000e+00, /* 88 25 */ 1.000000e+00, /* 88 26 */ 1.000000e+00, /* 88 27 */ 1.000000e+00, /* 88 28 */ 1.000000e+00, /* 88 29 */ 1.000000e+00, /* 88 30 */ 1.000000e+00, /* 88 31 */ 9.999945e-01, /* 88 32 */ 9.996291e-01, /* 88 33 */ 9.903109e-01, /* 88 34 */ 9.251400e-01, /* 88 35 */ 7.494745e-01, /* 88 36 */ 5.065945e-01, /* 88 37 */ 2.911964e-01, /* 88 38 */ 1.479655e-01, /* 88 39 */ 6.874727e-02, /* 88 40 */ 2.957091e-02, /* 88 41 */ 1.206727e-02, /* 88 42 */ 4.640000e-03, /* 88 43 */ 1.761818e-03, /* 88 44 */ 6.236364e-04, /* 88 45 */ 2.127273e-04, /* 88 46 */ 8.363636e-05, /* 88 47 */ 3.272727e-05, /* 88 48 */ 2.514700e-05, /* 88 49 */ 6.735024e-06, /* 88 50 */ 1.724962e-06, /* 88 51 */ 4.223463e-07, /* 88 52 */ 9.882074e-08, /* 88 53 */ 2.208713e-08, /* 88 54 */ 4.713477e-09, /* 88 55 */ 9.599105e-10, /* 88 56 */ 1.864484e-10, /* 88 57 */ 3.451829e-11, /* 88 58 */ 6.086932e-12, /* 88 59 */ 1.021576e-12, /* 88 60 */ 1.630406e-13, /* 88 61 */ 2.472109e-14, /* 88 62 */ 3.557449e-15, /* 88 63 */ 4.853071e-16, /* 88 64 */ 6.268445e-17, /* 88 65 */ 7.655455e-18, /* 88 66 */ 8.826555e-19, /* 88 67 */ 9.591617e-20, /* 88 68 */ 9.805396e-21, /* 88 69 */ 9.410516e-22, /* 88 70 */ 8.459321e-23, /* 88 71 */ 7.104121e-24, /* 88 72 */ 5.557467e-25, /* 88 73 */ 4.036540e-26, /* 88 74 */ 2.711971e-27, /* 88 75 */ 1.678206e-28, /* 88 76 */ 9.517924e-30, /* 88 77 */ 4.918924e-31, /* 88 78 */ 2.300767e-32, /* 88 79 */ 9.660825e-34, /* 88 80 */ 3.605759e-35, /* 88 81 */ 1.181654e-36, /* 88 82 */ 3.347490e-38, /* 88 83 */ 8.031396e-40, /* 88 84 */ 1.586836e-41, /* 88 85 */ 2.478979e-43, /* 88 86 */ 2.871065e-45, /* 88 87 */ 2.191526e-47, /* 88 88 */ 8.269910e-50, /* 89 0 */ 1.000000e+00, /* 89 1 */ 1.000000e+00, /* 89 2 */ 1.000000e+00, /* 89 3 */ 1.000000e+00, /* 89 4 */ 1.000000e+00, /* 89 5 */ 1.000000e+00, /* 89 6 */ 1.000000e+00, /* 89 7 */ 1.000000e+00, /* 89 8 */ 1.000000e+00, /* 89 9 */ 1.000000e+00, /* 89 10 */ 1.000000e+00, /* 89 11 */ 1.000000e+00, /* 89 12 */ 1.000000e+00, /* 89 13 */ 1.000000e+00, /* 89 14 */ 1.000000e+00, /* 89 15 */ 1.000000e+00, /* 89 16 */ 1.000000e+00, /* 89 17 */ 1.000000e+00, /* 89 18 */ 1.000000e+00, /* 89 19 */ 1.000000e+00, /* 89 20 */ 1.000000e+00, /* 89 21 */ 1.000000e+00, /* 89 22 */ 1.000000e+00, /* 89 23 */ 1.000000e+00, /* 89 24 */ 1.000000e+00, /* 89 25 */ 1.000000e+00, /* 89 26 */ 1.000000e+00, /* 89 27 */ 1.000000e+00, /* 89 28 */ 1.000000e+00, /* 89 29 */ 1.000000e+00, /* 89 30 */ 1.000000e+00, /* 89 31 */ 1.000000e+00, /* 89 32 */ 9.999018e-01, /* 89 33 */ 9.961400e-01, /* 89 34 */ 9.579236e-01, /* 89 35 */ 8.207636e-01, /* 89 36 */ 5.906891e-01, /* 89 37 */ 3.584673e-01, /* 89 38 */ 1.897818e-01, /* 89 39 */ 9.075818e-02, /* 89 40 */ 4.045636e-02, /* 89 41 */ 1.669636e-02, /* 89 42 */ 6.596364e-03, /* 89 43 */ 2.523636e-03, /* 89 44 */ 9.290909e-04, /* 89 45 */ 3.272727e-04, /* 89 46 */ 1.145455e-04, /* 89 47 */ 4.727273e-05, /* 89 48 */ 4.224722e-05, /* 89 49 */ 1.159424e-05, /* 89 50 */ 3.044763e-06, /* 89 51 */ 7.649037e-07, /* 89 52 */ 1.837631e-07, /* 89 53 */ 4.220317e-08, /* 89 54 */ 9.261558e-09, /* 89 55 */ 1.941200e-09, /* 89 56 */ 3.883970e-10, /* 89 57 */ 7.413919e-11, /* 89 58 */ 1.349295e-11, /* 89 59 */ 2.339617e-12, /* 89 60 */ 3.862091e-13, /* 89 61 */ 6.064107e-14, /* 89 62 */ 9.048317e-15, /* 89 63 */ 1.281666e-15, /* 89 64 */ 1.721443e-16, /* 89 65 */ 2.189659e-17, /* 89 66 */ 2.634065e-18, /* 89 67 */ 2.992133e-19, /* 89 68 */ 3.204116e-20, /* 89 69 */ 3.228483e-21, /* 89 70 */ 3.054581e-22, /* 89 71 */ 2.707471e-23, /* 89 72 */ 2.242394e-24, /* 89 73 */ 1.730346e-25, /* 89 74 */ 1.239934e-26, /* 89 75 */ 8.220240e-28, /* 89 76 */ 5.020302e-29, /* 89 77 */ 2.810509e-30, /* 89 78 */ 1.433978e-31, /* 89 79 */ 6.622837e-33, /* 89 80 */ 2.746329e-34, /* 89 81 */ 1.012437e-35, /* 89 82 */ 3.277628e-37, /* 89 83 */ 9.173809e-39, /* 89 84 */ 2.174925e-40, /* 89 85 */ 4.246864e-42, /* 89 86 */ 6.557695e-44, /* 89 87 */ 7.507942e-46, /* 89 88 */ 5.666052e-48, /* 89 89 */ 2.114199e-50, /* 90 0 */ 1.000000e+00, /* 90 1 */ 1.000000e+00, /* 90 2 */ 1.000000e+00, /* 90 3 */ 1.000000e+00, /* 90 4 */ 1.000000e+00, /* 90 5 */ 1.000000e+00, /* 90 6 */ 1.000000e+00, /* 90 7 */ 1.000000e+00, /* 90 8 */ 1.000000e+00, /* 90 9 */ 1.000000e+00, /* 90 10 */ 1.000000e+00, /* 90 11 */ 1.000000e+00, /* 90 12 */ 1.000000e+00, /* 90 13 */ 1.000000e+00, /* 90 14 */ 1.000000e+00, /* 90 15 */ 1.000000e+00, /* 90 16 */ 1.000000e+00, /* 90 17 */ 1.000000e+00, /* 90 18 */ 1.000000e+00, /* 90 19 */ 1.000000e+00, /* 90 20 */ 1.000000e+00, /* 90 21 */ 1.000000e+00, /* 90 22 */ 1.000000e+00, /* 90 23 */ 1.000000e+00, /* 90 24 */ 1.000000e+00, /* 90 25 */ 1.000000e+00, /* 90 26 */ 1.000000e+00, /* 90 27 */ 1.000000e+00, /* 90 28 */ 1.000000e+00, /* 90 29 */ 1.000000e+00, /* 90 30 */ 1.000000e+00, /* 90 31 */ 1.000000e+00, /* 90 32 */ 9.999727e-01, /* 90 33 */ 9.985945e-01, /* 90 34 */ 9.783782e-01, /* 90 35 */ 8.799582e-01, /* 90 36 */ 6.740891e-01, /* 90 37 */ 4.329364e-01, /* 90 38 */ 2.400436e-01, /* 90 39 */ 1.191818e-01, /* 90 40 */ 5.422545e-02, /* 90 41 */ 2.318727e-02, /* 90 42 */ 9.343636e-03, /* 90 43 */ 3.709091e-03, /* 90 44 */ 1.358182e-03, /* 90 45 */ 4.909091e-04, /* 90 46 */ 1.563636e-04, /* 90 47 */ 6.000000e-05, /* 90 48 */ 2.545455e-05, /* 90 49 */ 1.968780e-05, /* 90 50 */ 5.297929e-06, /* 90 51 */ 1.364697e-06, /* 90 52 */ 3.364010e-07, /* 90 53 */ 7.932701e-08, /* 90 54 */ 1.788794e-08, /* 90 55 */ 3.855562e-09, /* 90 56 */ 7.939514e-10, /* 90 57 */ 1.561159e-10, /* 90 58 */ 2.929481e-11, /* 90 59 */ 5.242538e-12, /* 90 60 */ 8.941039e-13, /* 90 61 */ 1.452069e-13, /* 90 62 */ 2.243691e-14, /* 90 63 */ 3.295356e-15, /* 90 64 */ 4.595696e-16, /* 90 65 */ 6.078716e-17, /* 90 66 */ 7.616165e-18, /* 90 67 */ 9.026558e-19, /* 90 68 */ 1.010427e-19, /* 90 69 */ 1.066475e-20, /* 90 70 */ 1.059369e-21, /* 90 71 */ 9.883072e-23, /* 90 72 */ 8.639305e-24, /* 90 73 */ 7.058014e-25, /* 90 74 */ 5.373259e-26, /* 90 75 */ 3.799397e-27, /* 90 76 */ 2.485918e-28, /* 90 77 */ 1.498619e-29, /* 90 78 */ 8.282795e-31, /* 90 79 */ 4.172864e-32, /* 90 80 */ 1.903284e-33, /* 90 81 */ 7.795539e-35, /* 90 82 */ 2.838967e-36, /* 90 83 */ 9.080582e-38, /* 90 84 */ 2.511465e-39, /* 90 85 */ 5.884445e-41, /* 90 86 */ 1.135722e-42, /* 90 87 */ 1.733626e-44, /* 90 88 */ 1.962373e-46, /* 90 89 */ 1.464377e-48, /* 90 90 */ 5.403605e-51, /* 91 0 */ 1.000000e+00, /* 91 1 */ 1.000000e+00, /* 91 2 */ 1.000000e+00, /* 91 3 */ 1.000000e+00, /* 91 4 */ 1.000000e+00, /* 91 5 */ 1.000000e+00, /* 91 6 */ 1.000000e+00, /* 91 7 */ 1.000000e+00, /* 91 8 */ 1.000000e+00, /* 91 9 */ 1.000000e+00, /* 91 10 */ 1.000000e+00, /* 91 11 */ 1.000000e+00, /* 91 12 */ 1.000000e+00, /* 91 13 */ 1.000000e+00, /* 91 14 */ 1.000000e+00, /* 91 15 */ 1.000000e+00, /* 91 16 */ 1.000000e+00, /* 91 17 */ 1.000000e+00, /* 91 18 */ 1.000000e+00, /* 91 19 */ 1.000000e+00, /* 91 20 */ 1.000000e+00, /* 91 21 */ 1.000000e+00, /* 91 22 */ 1.000000e+00, /* 91 23 */ 1.000000e+00, /* 91 24 */ 1.000000e+00, /* 91 25 */ 1.000000e+00, /* 91 26 */ 1.000000e+00, /* 91 27 */ 1.000000e+00, /* 91 28 */ 1.000000e+00, /* 91 29 */ 1.000000e+00, /* 91 30 */ 1.000000e+00, /* 91 31 */ 1.000000e+00, /* 91 32 */ 9.999964e-01, /* 91 33 */ 9.995255e-01, /* 91 34 */ 9.901091e-01, /* 91 35 */ 9.248764e-01, /* 91 36 */ 7.525418e-01, /* 91 37 */ 5.127691e-01, /* 91 38 */ 2.985800e-01, /* 91 39 */ 1.536127e-01, /* 91 40 */ 7.255091e-02, /* 91 41 */ 3.156545e-02, /* 91 42 */ 1.297273e-02, /* 91 43 */ 5.234545e-03, /* 91 44 */ 1.960000e-03, /* 91 45 */ 7.527273e-04, /* 91 46 */ 2.472727e-04, /* 91 47 */ 8.727273e-05, /* 91 48 */ 4.000000e-05, /* 91 49 */ 3.299227e-05, /* 91 50 */ 9.091975e-06, /* 91 51 */ 2.399893e-06, /* 91 52 */ 6.065901e-07, /* 91 53 */ 1.467688e-07, /* 91 54 */ 3.398244e-08, /* 91 55 */ 7.526385e-09, /* 91 56 */ 1.593814e-09, /* 91 57 */ 3.225486e-10, /* 91 58 */ 6.234811e-11, /* 91 59 */ 1.150434e-11, /* 91 60 */ 2.024995e-12, /* 91 61 */ 3.397775e-13, /* 91 62 */ 5.430351e-14, /* 91 63 */ 8.259320e-15, /* 91 64 */ 1.194339e-15, /* 91 65 */ 1.640293e-16, /* 91 66 */ 2.137098e-17, /* 91 67 */ 2.638071e-18, /* 91 68 */ 3.081076e-19, /* 91 69 */ 3.399423e-20, /* 91 70 */ 3.537193e-21, /* 91 71 */ 3.464561e-22, /* 91 72 */ 3.187636e-23, /* 91 73 */ 2.748605e-24, /* 91 74 */ 2.215397e-25, /* 91 75 */ 1.664252e-26, /* 91 76 */ 1.161404e-27, /* 91 77 */ 7.500937e-29, /* 91 78 */ 4.464280e-30, /* 91 79 */ 2.436340e-31, /* 91 80 */ 1.212171e-32, /* 91 81 */ 5.460947e-34, /* 91 82 */ 2.209581e-35, /* 91 83 */ 7.950357e-37, /* 91 84 */ 2.512835e-38, /* 91 85 */ 6.868500e-40, /* 91 86 */ 1.590683e-41, /* 91 87 */ 3.034946e-43, /* 91 88 */ 4.580272e-45, /* 91 89 */ 5.126603e-47, /* 91 90 */ 3.783267e-49, /* 91 91 */ 1.380754e-51, /* 92 0 */ 1.000000e+00, /* 92 1 */ 1.000000e+00, /* 92 2 */ 1.000000e+00, /* 92 3 */ 1.000000e+00, /* 92 4 */ 1.000000e+00, /* 92 5 */ 1.000000e+00, /* 92 6 */ 1.000000e+00, /* 92 7 */ 1.000000e+00, /* 92 8 */ 1.000000e+00, /* 92 9 */ 1.000000e+00, /* 92 10 */ 1.000000e+00, /* 92 11 */ 1.000000e+00, /* 92 12 */ 1.000000e+00, /* 92 13 */ 1.000000e+00, /* 92 14 */ 1.000000e+00, /* 92 15 */ 1.000000e+00, /* 92 16 */ 1.000000e+00, /* 92 17 */ 1.000000e+00, /* 92 18 */ 1.000000e+00, /* 92 19 */ 1.000000e+00, /* 92 20 */ 1.000000e+00, /* 92 21 */ 1.000000e+00, /* 92 22 */ 1.000000e+00, /* 92 23 */ 1.000000e+00, /* 92 24 */ 1.000000e+00, /* 92 25 */ 1.000000e+00, /* 92 26 */ 1.000000e+00, /* 92 27 */ 1.000000e+00, /* 92 28 */ 1.000000e+00, /* 92 29 */ 1.000000e+00, /* 92 30 */ 1.000000e+00, /* 92 31 */ 1.000000e+00, /* 92 32 */ 9.999982e-01, /* 92 33 */ 9.998873e-01, /* 92 34 */ 9.959782e-01, /* 92 35 */ 9.570600e-01, /* 92 36 */ 8.220836e-01, /* 92 37 */ 5.950418e-01, /* 92 38 */ 3.650345e-01, /* 92 39 */ 1.957327e-01, /* 92 40 */ 9.528000e-02, /* 92 41 */ 4.273818e-02, /* 92 42 */ 1.803818e-02, /* 92 43 */ 7.307273e-03, /* 92 44 */ 2.823636e-03, /* 92 45 */ 1.096364e-03, /* 92 46 */ 3.727273e-04, /* 92 47 */ 1.236364e-04, /* 92 48 */ 5.272727e-05, /* 92 49 */ 1.454545e-05, /* 92 50 */ 1.090909e-05, /* 92 51 */ 4.161937e-06, /* 92 52 */ 1.077973e-06, /* 92 53 */ 2.674447e-07, /* 92 54 */ 6.353810e-08, /* 92 55 */ 1.444947e-08, /* 92 56 */ 3.144210e-09, /* 92 57 */ 6.543615e-10, /* 92 58 */ 1.301828e-10, /* 92 59 */ 2.474457e-11, /* 92 60 */ 4.490891e-12, /* 92 61 */ 7.777170e-13, /* 92 62 */ 1.284188e-13, /* 92 63 */ 2.020249e-14, /* 92 64 */ 3.025295e-15, /* 92 65 */ 4.308219e-16, /* 92 66 */ 5.828219e-17, /* 92 67 */ 7.481321e-18, /* 92 68 */ 9.100644e-19, /* 92 69 */ 1.047634e-19, /* 92 70 */ 1.139519e-20, /* 92 71 */ 1.169148e-21, /* 92 72 */ 1.129370e-22, /* 92 73 */ 1.024978e-23, /* 92 74 */ 8.719570e-25, /* 92 75 */ 6.935020e-26, /* 92 76 */ 5.141663e-27, /* 92 77 */ 3.541839e-28, /* 92 78 */ 2.258361e-29, /* 92 79 */ 1.327184e-30, /* 92 80 */ 7.152978e-32, /* 92 81 */ 3.515187e-33, /* 92 82 */ 1.564418e-34, /* 92 83 */ 6.254000e-36, /* 92 84 */ 2.223614e-37, /* 92 85 */ 6.945795e-39, /* 92 86 */ 1.876566e-40, /* 92 87 */ 4.296222e-42, /* 92 88 */ 8.104234e-44, /* 92 89 */ 1.209386e-45, /* 92 90 */ 1.338659e-47, /* 92 91 */ 9.770718e-50, /* 92 92 */ 3.527335e-52, /* 93 0 */ 1.000000e+00, /* 93 1 */ 1.000000e+00, /* 93 2 */ 1.000000e+00, /* 93 3 */ 1.000000e+00, /* 93 4 */ 1.000000e+00, /* 93 5 */ 1.000000e+00, /* 93 6 */ 1.000000e+00, /* 93 7 */ 1.000000e+00, /* 93 8 */ 1.000000e+00, /* 93 9 */ 1.000000e+00, /* 93 10 */ 1.000000e+00, /* 93 11 */ 1.000000e+00, /* 93 12 */ 1.000000e+00, /* 93 13 */ 1.000000e+00, /* 93 14 */ 1.000000e+00, /* 93 15 */ 1.000000e+00, /* 93 16 */ 1.000000e+00, /* 93 17 */ 1.000000e+00, /* 93 18 */ 1.000000e+00, /* 93 19 */ 1.000000e+00, /* 93 20 */ 1.000000e+00, /* 93 21 */ 1.000000e+00, /* 93 22 */ 1.000000e+00, /* 93 23 */ 1.000000e+00, /* 93 24 */ 1.000000e+00, /* 93 25 */ 1.000000e+00, /* 93 26 */ 1.000000e+00, /* 93 27 */ 1.000000e+00, /* 93 28 */ 1.000000e+00, /* 93 29 */ 1.000000e+00, /* 93 30 */ 1.000000e+00, /* 93 31 */ 1.000000e+00, /* 93 32 */ 1.000000e+00, /* 93 33 */ 9.999709e-01, /* 93 34 */ 9.984582e-01, /* 93 35 */ 9.776200e-01, /* 93 36 */ 8.802127e-01, /* 93 37 */ 6.768945e-01, /* 93 38 */ 4.390200e-01, /* 93 39 */ 2.459364e-01, /* 93 40 */ 1.235055e-01, /* 93 41 */ 5.715273e-02, /* 93 42 */ 2.466727e-02, /* 93 43 */ 1.020364e-02, /* 93 44 */ 4.041818e-03, /* 93 45 */ 1.576364e-03, /* 93 46 */ 5.490909e-04, /* 93 47 */ 1.854545e-04, /* 93 48 */ 6.909091e-05, /* 93 49 */ 2.181818e-05, /* 93 50 */ 1.090909e-05, /* 93 51 */ 7.121256e-06, /* 93 52 */ 1.888941e-06, /* 93 53 */ 4.802404e-07, /* 93 54 */ 1.169907e-07, /* 93 55 */ 2.729938e-08, /* 93 56 */ 6.099614e-09, /* 93 57 */ 1.304430e-09, /* 93 58 */ 2.668755e-10, /* 93 59 */ 5.220905e-11, /* 93 60 */ 9.760883e-12, /* 93 61 */ 1.742896e-12, /* 93 62 */ 2.970295e-13, /* 93 63 */ 4.827832e-14, /* 93 64 */ 7.477851e-15, /* 93 65 */ 1.102779e-15, /* 93 66 */ 1.546909e-16, /* 93 67 */ 2.061788e-17, /* 93 68 */ 2.608074e-18, /* 93 69 */ 3.127066e-19, /* 93 70 */ 3.548830e-20, /* 93 71 */ 3.806212e-21, /* 93 72 */ 3.851407e-22, /* 93 73 */ 3.669824e-23, /* 93 74 */ 3.285956e-24, /* 93 75 */ 2.758396e-25, /* 93 76 */ 2.165203e-26, /* 93 77 */ 1.584589e-27, /* 93 78 */ 1.077643e-28, /* 93 79 */ 6.784882e-30, /* 93 80 */ 3.937769e-31, /* 93 81 */ 2.096247e-32, /* 93 82 */ 1.017665e-33, /* 93 83 */ 4.474797e-35, /* 93 84 */ 1.767681e-36, /* 93 85 */ 6.211426e-38, /* 93 86 */ 1.917778e-39, /* 93 87 */ 5.122030e-41, /* 93 88 */ 1.159374e-42, /* 93 89 */ 2.162529e-44, /* 93 90 */ 3.191405e-46, /* 93 91 */ 3.493870e-48, /* 93 92 */ 2.522520e-50, /* 93 93 */ 9.008998e-53, /* 94 0 */ 1.000000e+00, /* 94 1 */ 1.000000e+00, /* 94 2 */ 1.000000e+00, /* 94 3 */ 1.000000e+00, /* 94 4 */ 1.000000e+00, /* 94 5 */ 1.000000e+00, /* 94 6 */ 1.000000e+00, /* 94 7 */ 1.000000e+00, /* 94 8 */ 1.000000e+00, /* 94 9 */ 1.000000e+00, /* 94 10 */ 1.000000e+00, /* 94 11 */ 1.000000e+00, /* 94 12 */ 1.000000e+00, /* 94 13 */ 1.000000e+00, /* 94 14 */ 1.000000e+00, /* 94 15 */ 1.000000e+00, /* 94 16 */ 1.000000e+00, /* 94 17 */ 1.000000e+00, /* 94 18 */ 1.000000e+00, /* 94 19 */ 1.000000e+00, /* 94 20 */ 1.000000e+00, /* 94 21 */ 1.000000e+00, /* 94 22 */ 1.000000e+00, /* 94 23 */ 1.000000e+00, /* 94 24 */ 1.000000e+00, /* 94 25 */ 1.000000e+00, /* 94 26 */ 1.000000e+00, /* 94 27 */ 1.000000e+00, /* 94 28 */ 1.000000e+00, /* 94 29 */ 1.000000e+00, /* 94 30 */ 1.000000e+00, /* 94 31 */ 1.000000e+00, /* 94 32 */ 1.000000e+00, /* 94 33 */ 9.999873e-01, /* 94 34 */ 9.994909e-01, /* 94 35 */ 9.895655e-01, /* 94 36 */ 9.249655e-01, /* 94 37 */ 7.539382e-01, /* 94 38 */ 5.178655e-01, /* 94 39 */ 3.043455e-01, /* 94 40 */ 1.588255e-01, /* 94 41 */ 7.545818e-02, /* 94 42 */ 3.347455e-02, /* 94 43 */ 1.406909e-02, /* 94 44 */ 5.674545e-03, /* 94 45 */ 2.172727e-03, /* 94 46 */ 7.963636e-04, /* 94 47 */ 2.690909e-04, /* 94 48 */ 1.036364e-04, /* 94 49 */ 4.181818e-05, /* 94 50 */ 1.272727e-05, /* 94 51 */ 1.202746e-05, /* 94 52 */ 3.265403e-06, /* 94 53 */ 8.502207e-07, /* 94 54 */ 2.122480e-07, /* 94 55 */ 5.078575e-08, /* 94 56 */ 1.164339e-08, /* 94 57 */ 2.556769e-09, /* 94 58 */ 5.375208e-10, /* 94 59 */ 1.081403e-10, /* 94 60 */ 2.080870e-11, /* 94 61 */ 3.827549e-12, /* 94 62 */ 6.725812e-13, /* 94 63 */ 1.128290e-13, /* 94 64 */ 1.805610e-14, /* 94 65 */ 2.754225e-15, /* 94 66 */ 4.000915e-16, /* 94 67 */ 5.529409e-17, /* 94 68 */ 7.262619e-18, /* 94 69 */ 9.055116e-19, /* 94 70 */ 1.070344e-19, /* 94 71 */ 1.197757e-20, /* 94 72 */ 1.266940e-21, /* 94 73 */ 1.264571e-22, /* 94 74 */ 1.188798e-23, /* 94 75 */ 1.050365e-24, /* 94 76 */ 8.702131e-26, /* 94 77 */ 6.742652e-27, /* 94 78 */ 4.871728e-28, /* 94 79 */ 3.271486e-29, /* 94 80 */ 2.034152e-30, /* 94 81 */ 1.166081e-31, /* 94 82 */ 6.132288e-33, /* 94 83 */ 2.941371e-34, /* 94 84 */ 1.278040e-35, /* 94 85 */ 4.989550e-37, /* 94 86 */ 1.732982e-38, /* 94 87 */ 5.289366e-40, /* 94 88 */ 1.396710e-41, /* 94 89 */ 3.126090e-43, /* 94 90 */ 5.766438e-45, /* 94 91 */ 8.416817e-47, /* 94 92 */ 9.114743e-49, /* 94 93 */ 6.510202e-51, /* 94 94 */ 2.300425e-53, /* 95 0 */ 1.000000e+00, /* 95 1 */ 1.000000e+00, /* 95 2 */ 1.000000e+00, /* 95 3 */ 1.000000e+00, /* 95 4 */ 1.000000e+00, /* 95 5 */ 1.000000e+00, /* 95 6 */ 1.000000e+00, /* 95 7 */ 1.000000e+00, /* 95 8 */ 1.000000e+00, /* 95 9 */ 1.000000e+00, /* 95 10 */ 1.000000e+00, /* 95 11 */ 1.000000e+00, /* 95 12 */ 1.000000e+00, /* 95 13 */ 1.000000e+00, /* 95 14 */ 1.000000e+00, /* 95 15 */ 1.000000e+00, /* 95 16 */ 1.000000e+00, /* 95 17 */ 1.000000e+00, /* 95 18 */ 1.000000e+00, /* 95 19 */ 1.000000e+00, /* 95 20 */ 1.000000e+00, /* 95 21 */ 1.000000e+00, /* 95 22 */ 1.000000e+00, /* 95 23 */ 1.000000e+00, /* 95 24 */ 1.000000e+00, /* 95 25 */ 1.000000e+00, /* 95 26 */ 1.000000e+00, /* 95 27 */ 1.000000e+00, /* 95 28 */ 1.000000e+00, /* 95 29 */ 1.000000e+00, /* 95 30 */ 1.000000e+00, /* 95 31 */ 1.000000e+00, /* 95 32 */ 1.000000e+00, /* 95 33 */ 9.999945e-01, /* 95 34 */ 9.998709e-01, /* 95 35 */ 9.957073e-01, /* 95 36 */ 9.568036e-01, /* 95 37 */ 8.226800e-01, /* 95 38 */ 5.988291e-01, /* 95 39 */ 3.702836e-01, /* 95 40 */ 2.010164e-01, /* 95 41 */ 9.868545e-02, /* 95 42 */ 4.486545e-02, /* 95 43 */ 1.930364e-02, /* 95 44 */ 7.840000e-03, /* 95 45 */ 3.081818e-03, /* 95 46 */ 1.209091e-03, /* 95 47 */ 4.290909e-04, /* 95 48 */ 1.490909e-04, /* 95 49 */ 6.363636e-05, /* 95 50 */ 1.818182e-05, /* 95 51 */ 7.272727e-06, /* 95 52 */ 5.571383e-06, /* 95 53 */ 1.484788e-06, /* 95 54 */ 3.796085e-07, /* 95 55 */ 9.308038e-08, /* 95 56 */ 2.188249e-08, /* 95 57 */ 4.930610e-09, /* 95 58 */ 1.064392e-09, /* 95 59 */ 2.200458e-10, /* 95 60 */ 4.354404e-11, /* 95 61 */ 8.243685e-12, /* 95 62 */ 1.492250e-12, /* 95 63 */ 2.581165e-13, /* 95 64 */ 4.263287e-14, /* 95 65 */ 6.718942e-15, /* 95 66 */ 1.009548e-15, /* 95 67 */ 1.444879e-16, /* 95 68 */ 1.967832e-17, /* 95 69 */ 2.547587e-18, /* 95 70 */ 3.131435e-19, /* 95 71 */ 3.649819e-20, /* 95 72 */ 4.028078e-21, /* 95 73 */ 4.202883e-22, /* 95 74 */ 4.138802e-23, /* 95 75 */ 3.839339e-24, /* 95 76 */ 3.347959e-25, /* 95 77 */ 2.737976e-26, /* 95 78 */ 2.094450e-27, /* 95 79 */ 1.494262e-28, /* 95 80 */ 9.909705e-30, /* 95 81 */ 6.086073e-31, /* 95 82 */ 3.446553e-32, /* 95 83 */ 1.790789e-33, /* 95 84 */ 8.487866e-35, /* 95 85 */ 3.644855e-36, /* 95 86 */ 1.406511e-37, /* 95 87 */ 4.829242e-39, /* 95 88 */ 1.457297e-40, /* 95 89 */ 3.805092e-42, /* 95 90 */ 8.422257e-44, /* 95 91 */ 1.536581e-45, /* 95 92 */ 2.218544e-47, /* 95 93 */ 2.376770e-49, /* 95 94 */ 1.679613e-51, /* 95 95 */ 5.872774e-54, /* 96 0 */ 1.000000e+00, /* 96 1 */ 1.000000e+00, /* 96 2 */ 1.000000e+00, /* 96 3 */ 1.000000e+00, /* 96 4 */ 1.000000e+00, /* 96 5 */ 1.000000e+00, /* 96 6 */ 1.000000e+00, /* 96 7 */ 1.000000e+00, /* 96 8 */ 1.000000e+00, /* 96 9 */ 1.000000e+00, /* 96 10 */ 1.000000e+00, /* 96 11 */ 1.000000e+00, /* 96 12 */ 1.000000e+00, /* 96 13 */ 1.000000e+00, /* 96 14 */ 1.000000e+00, /* 96 15 */ 1.000000e+00, /* 96 16 */ 1.000000e+00, /* 96 17 */ 1.000000e+00, /* 96 18 */ 1.000000e+00, /* 96 19 */ 1.000000e+00, /* 96 20 */ 1.000000e+00, /* 96 21 */ 1.000000e+00, /* 96 22 */ 1.000000e+00, /* 96 23 */ 1.000000e+00, /* 96 24 */ 1.000000e+00, /* 96 25 */ 1.000000e+00, /* 96 26 */ 1.000000e+00, /* 96 27 */ 1.000000e+00, /* 96 28 */ 1.000000e+00, /* 96 29 */ 1.000000e+00, /* 96 30 */ 1.000000e+00, /* 96 31 */ 1.000000e+00, /* 96 32 */ 1.000000e+00, /* 96 33 */ 9.999982e-01, /* 96 34 */ 9.999764e-01, /* 96 35 */ 9.984782e-01, /* 96 36 */ 9.773127e-01, /* 96 37 */ 8.798055e-01, /* 96 38 */ 6.793218e-01, /* 96 39 */ 4.432273e-01, /* 96 40 */ 2.516127e-01, /* 96 41 */ 1.279745e-01, /* 96 42 */ 5.969636e-02, /* 96 43 */ 2.622909e-02, /* 96 44 */ 1.099818e-02, /* 96 45 */ 4.398182e-03, /* 96 46 */ 1.745455e-03, /* 96 47 */ 6.236364e-04, /* 96 48 */ 2.218182e-04, /* 96 49 */ 8.363636e-05, /* 96 50 */ 2.545455e-05, /* 96 51 */ 7.272727e-06, /* 96 52 */ 1.818182e-06, /* 96 53 */ 1.818182e-06, /* 96 54 */ 6.696392e-07, /* 96 55 */ 1.681618e-07, /* 96 56 */ 4.051297e-08, /* 96 57 */ 9.360587e-09, /* 96 58 */ 2.073478e-09, /* 96 59 */ 4.401612e-10, /* 96 60 */ 8.950545e-11, /* 96 61 */ 1.742623e-11, /* 96 62 */ 3.246706e-12, /* 96 63 */ 5.785165e-13, /* 96 64 */ 9.852473e-14, /* 96 65 */ 1.602616e-14, /* 96 66 */ 2.487929e-15, /* 96 67 */ 3.683077e-16, /* 96 68 */ 5.194626e-17, /* 96 69 */ 6.973308e-18, /* 96 70 */ 8.900105e-19, /* 96 71 */ 1.078722e-19, /* 96 72 */ 1.239996e-20, /* 96 73 */ 1.349926e-21, /* 96 74 */ 1.389636e-22, /* 96 75 */ 1.350350e-23, /* 96 76 */ 1.236291e-24, /* 96 77 */ 1.064166e-25, /* 96 78 */ 8.592018e-27, /* 96 79 */ 6.489944e-28, /* 96 80 */ 4.572678e-29, /* 96 81 */ 2.995323e-30, /* 96 82 */ 1.817286e-31, /* 96 83 */ 1.016804e-32, /* 96 84 */ 5.220649e-34, /* 96 85 */ 2.445493e-35, /* 96 86 */ 1.037994e-36, /* 96 87 */ 3.959693e-38, /* 96 88 */ 1.344180e-39, /* 96 89 */ 4.010897e-41, /* 96 90 */ 1.035684e-42, /* 96 91 */ 2.267316e-44, /* 96 92 */ 4.091775e-46, /* 96 93 */ 5.844501e-48, /* 96 94 */ 6.194970e-50, /* 96 95 */ 4.331937e-52, /* 96 96 */ 1.498940e-54, /* 97 0 */ 1.000000e+00, /* 97 1 */ 1.000000e+00, /* 97 2 */ 1.000000e+00, /* 97 3 */ 1.000000e+00, /* 97 4 */ 1.000000e+00, /* 97 5 */ 1.000000e+00, /* 97 6 */ 1.000000e+00, /* 97 7 */ 1.000000e+00, /* 97 8 */ 1.000000e+00, /* 97 9 */ 1.000000e+00, /* 97 10 */ 1.000000e+00, /* 97 11 */ 1.000000e+00, /* 97 12 */ 1.000000e+00, /* 97 13 */ 1.000000e+00, /* 97 14 */ 1.000000e+00, /* 97 15 */ 1.000000e+00, /* 97 16 */ 1.000000e+00, /* 97 17 */ 1.000000e+00, /* 97 18 */ 1.000000e+00, /* 97 19 */ 1.000000e+00, /* 97 20 */ 1.000000e+00, /* 97 21 */ 1.000000e+00, /* 97 22 */ 1.000000e+00, /* 97 23 */ 1.000000e+00, /* 97 24 */ 1.000000e+00, /* 97 25 */ 1.000000e+00, /* 97 26 */ 1.000000e+00, /* 97 27 */ 1.000000e+00, /* 97 28 */ 1.000000e+00, /* 97 29 */ 1.000000e+00, /* 97 30 */ 1.000000e+00, /* 97 31 */ 1.000000e+00, /* 97 32 */ 1.000000e+00, /* 97 33 */ 9.999982e-01, /* 97 34 */ 9.999873e-01, /* 97 35 */ 9.994655e-01, /* 97 36 */ 9.893491e-01, /* 97 37 */ 9.243073e-01, /* 97 38 */ 7.551709e-01, /* 97 39 */ 5.215800e-01, /* 97 40 */ 3.095800e-01, /* 97 41 */ 1.632655e-01, /* 97 42 */ 7.875273e-02, /* 97 43 */ 3.541091e-02, /* 97 44 */ 1.515455e-02, /* 97 45 */ 6.174545e-03, /* 97 46 */ 2.432727e-03, /* 97 47 */ 9.418182e-04, /* 97 48 */ 3.345455e-04, /* 97 49 */ 1.290909e-04, /* 97 50 */ 4.545455e-05, /* 97 51 */ 1.272727e-05, /* 97 52 */ 3.636364e-06, /* 97 53 */ 3.636364e-06, /* 97 54 */ 1.165628e-06, /* 97 55 */ 2.996145e-07, /* 97 56 */ 7.392618e-08, /* 97 57 */ 1.750409e-08, /* 97 58 */ 3.975984e-09, /* 97 59 */ 8.660753e-10, /* 97 60 */ 1.808412e-10, /* 97 61 */ 3.618065e-11, /* 97 62 */ 6.932340e-12, /* 97 63 */ 1.271378e-12, /* 97 64 */ 2.230515e-13, /* 97 65 */ 3.741038e-14, /* 97 66 */ 5.994193e-15, /* 97 67 */ 9.168284e-16, /* 97 68 */ 1.337523e-16, /* 97 69 */ 1.859408e-17, /* 97 70 */ 2.460799e-18, /* 97 71 */ 3.096948e-19, /* 97 72 */ 3.701967e-20, /* 97 73 */ 4.197663e-21, /* 97 74 */ 4.508584e-22, /* 97 75 */ 4.579841e-23, /* 97 76 */ 4.392273e-24, /* 97 77 */ 3.969448e-25, /* 97 78 */ 3.373309e-26, /* 97 79 */ 2.689355e-27, /* 97 80 */ 2.006170e-28, /* 97 81 */ 1.396167e-29, /* 97 82 */ 9.034712e-31, /* 97 83 */ 5.415782e-32, /* 97 84 */ 2.994357e-33, /* 97 85 */ 1.519425e-34, /* 97 86 */ 7.035069e-36, /* 97 87 */ 2.951896e-37, /* 97 88 */ 1.113342e-38, /* 97 89 */ 3.737146e-40, /* 97 90 */ 1.102792e-41, /* 97 91 */ 2.816444e-43, /* 97 92 */ 6.099007e-45, /* 97 93 */ 1.088886e-46, /* 97 94 */ 1.538832e-48, /* 97 95 */ 1.614003e-50, /* 97 96 */ 1.116904e-52, /* 97 97 */ 3.825014e-55, /* 98 0 */ 1.000000e+00, /* 98 1 */ 1.000000e+00, /* 98 2 */ 1.000000e+00, /* 98 3 */ 1.000000e+00, /* 98 4 */ 1.000000e+00, /* 98 5 */ 1.000000e+00, /* 98 6 */ 1.000000e+00, /* 98 7 */ 1.000000e+00, /* 98 8 */ 1.000000e+00, /* 98 9 */ 1.000000e+00, /* 98 10 */ 1.000000e+00, /* 98 11 */ 1.000000e+00, /* 98 12 */ 1.000000e+00, /* 98 13 */ 1.000000e+00, /* 98 14 */ 1.000000e+00, /* 98 15 */ 1.000000e+00, /* 98 16 */ 1.000000e+00, /* 98 17 */ 1.000000e+00, /* 98 18 */ 1.000000e+00, /* 98 19 */ 1.000000e+00, /* 98 20 */ 1.000000e+00, /* 98 21 */ 1.000000e+00, /* 98 22 */ 1.000000e+00, /* 98 23 */ 1.000000e+00, /* 98 24 */ 1.000000e+00, /* 98 25 */ 1.000000e+00, /* 98 26 */ 1.000000e+00, /* 98 27 */ 1.000000e+00, /* 98 28 */ 1.000000e+00, /* 98 29 */ 1.000000e+00, /* 98 30 */ 1.000000e+00, /* 98 31 */ 1.000000e+00, /* 98 32 */ 1.000000e+00, /* 98 33 */ 9.999982e-01, /* 98 34 */ 9.999982e-01, /* 98 35 */ 9.998291e-01, /* 98 36 */ 9.954018e-01, /* 98 37 */ 9.559018e-01, /* 98 38 */ 8.228018e-01, /* 98 39 */ 6.024091e-01, /* 98 40 */ 3.748891e-01, /* 98 41 */ 2.062673e-01, /* 98 42 */ 1.021473e-01, /* 98 43 */ 4.720727e-02, /* 98 44 */ 2.056909e-02, /* 98 45 */ 8.587273e-03, /* 98 46 */ 3.423636e-03, /* 98 47 */ 1.374545e-03, /* 98 48 */ 4.818182e-04, /* 98 49 */ 1.836364e-04, /* 98 50 */ 7.090909e-05, /* 98 51 */ 2.363636e-05, /* 98 52 */ 7.272727e-06, /* 98 53 */ 1.818182e-06, /* 98 54 */ 1.818182e-06, /* 98 55 */ 5.267047e-07, /* 98 56 */ 1.330220e-07, /* 98 57 */ 3.225799e-08, /* 98 58 */ 7.508939e-09, /* 98 59 */ 1.677266e-09, /* 98 60 */ 3.593731e-10, /* 98 61 */ 7.382976e-11, /* 98 62 */ 1.453660e-11, /* 98 63 */ 2.741727e-12, /* 98 64 */ 4.950843e-13, /* 98 65 */ 8.554002e-14, /* 98 66 */ 1.413230e-14, /* 98 67 */ 2.231013e-15, /* 98 68 */ 3.362806e-16, /* 98 69 */ 4.835559e-17, /* 98 70 */ 6.627328e-18, /* 98 71 */ 8.648544e-19, /* 98 72 */ 1.073461e-19, /* 98 73 */ 1.265758e-20, /* 98 74 */ 1.416022e-21, /* 98 75 */ 1.500800e-22, /* 98 76 */ 1.504624e-23, /* 98 77 */ 1.424407e-24, /* 98 78 */ 1.270905e-25, /* 98 79 */ 1.066465e-26, /* 98 80 */ 8.396791e-28, /* 98 81 */ 6.186907e-29, /* 98 82 */ 4.253515e-30, /* 98 83 */ 2.719524e-31, /* 98 84 */ 1.610901e-32, /* 98 85 */ 8.802389e-34, /* 98 86 */ 4.414932e-35, /* 98 87 */ 2.020777e-36, /* 98 88 */ 8.383250e-38, /* 98 89 */ 3.126483e-39, /* 98 90 */ 1.037857e-40, /* 98 91 */ 3.029097e-42, /* 98 92 */ 7.652349e-44, /* 98 93 */ 1.639369e-45, /* 98 94 */ 2.895834e-47, /* 98 95 */ 4.049526e-49, /* 98 96 */ 4.203260e-51, /* 98 97 */ 2.878812e-53, /* 98 98 */ 9.758684e-56, /* 99 0 */ 1.000000e+00, /* 99 1 */ 1.000000e+00, /* 99 2 */ 1.000000e+00, /* 99 3 */ 1.000000e+00, /* 99 4 */ 1.000000e+00, /* 99 5 */ 1.000000e+00, /* 99 6 */ 1.000000e+00, /* 99 7 */ 1.000000e+00, /* 99 8 */ 1.000000e+00, /* 99 9 */ 1.000000e+00, /* 99 10 */ 1.000000e+00, /* 99 11 */ 1.000000e+00, /* 99 12 */ 1.000000e+00, /* 99 13 */ 1.000000e+00, /* 99 14 */ 1.000000e+00, /* 99 15 */ 1.000000e+00, /* 99 16 */ 1.000000e+00, /* 99 17 */ 1.000000e+00, /* 99 18 */ 1.000000e+00, /* 99 19 */ 1.000000e+00, /* 99 20 */ 1.000000e+00, /* 99 21 */ 1.000000e+00, /* 99 22 */ 1.000000e+00, /* 99 23 */ 1.000000e+00, /* 99 24 */ 1.000000e+00, /* 99 25 */ 1.000000e+00, /* 99 26 */ 1.000000e+00, /* 99 27 */ 1.000000e+00, /* 99 28 */ 1.000000e+00, /* 99 29 */ 1.000000e+00, /* 99 30 */ 1.000000e+00, /* 99 31 */ 1.000000e+00, /* 99 32 */ 1.000000e+00, /* 99 33 */ 9.999982e-01, /* 99 34 */ 9.999982e-01, /* 99 35 */ 9.999509e-01, /* 99 36 */ 9.982255e-01, /* 99 37 */ 9.766164e-01, /* 99 38 */ 8.793091e-01, /* 99 39 */ 6.818582e-01, /* 99 40 */ 4.474327e-01, /* 99 41 */ 2.563855e-01, /* 99 42 */ 1.315418e-01, /* 99 43 */ 6.242545e-02, /* 99 44 */ 2.772000e-02, /* 99 45 */ 1.168909e-02, /* 99 46 */ 4.869091e-03, /* 99 47 */ 1.847273e-03, /* 99 48 */ 7.490909e-04, /* 99 49 */ 2.781818e-04, /* 99 50 */ 1.109091e-04, /* 99 51 */ 3.454545e-05, /* 99 52 */ 9.090909e-06, /* 99 53 */ 3.636364e-06, /* 99 54 */ 3.399340e-06, /* 99 55 */ 9.139701e-07, /* 99 56 */ 2.361419e-07, /* 99 57 */ 5.861544e-08, /* 99 58 */ 1.397429e-08, /* 99 59 */ 3.198841e-09, /* 99 60 */ 7.028326e-10, /* 99 61 */ 1.481641e-10, /* 99 62 */ 2.995602e-11, /* 99 63 */ 5.805985e-12, /* 99 64 */ 1.078201e-12, /* 99 65 */ 1.917417e-13, /* 99 66 */ 3.263364e-14, /* 99 67 */ 5.312044e-15, /* 99 68 */ 8.264092e-16, /* 99 69 */ 1.227802e-16, /* 99 70 */ 1.740577e-17, /* 99 71 */ 2.352283e-18, /* 99 72 */ 3.027479e-19, /* 99 73 */ 3.706736e-20, /* 99 74 */ 4.312225e-21, /* 99 75 */ 4.760386e-22, /* 99 76 */ 4.979561e-23, /* 99 77 */ 4.927930e-24, /* 99 78 */ 4.605854e-25, /* 99 79 */ 4.057863e-26, /* 99 80 */ 3.362842e-27, /* 99 81 */ 2.615259e-28, /* 99 82 */ 1.903623e-29, /* 99 83 */ 1.293075e-30, /* 99 84 */ 8.169561e-32, /* 99 85 */ 4.782606e-33, /* 99 86 */ 2.583121e-34, /* 99 87 */ 1.280779e-35, /* 99 88 */ 5.796027e-37, /* 99 89 */ 2.377613e-38, /* 99 90 */ 8.769106e-40, /* 99 91 */ 2.879119e-41, /* 99 92 */ 8.312080e-43, /* 99 93 */ 2.077380e-44, /* 99 94 */ 4.403236e-46, /* 99 95 */ 7.696459e-48, /* 99 96 */ 1.065101e-49, /* 99 97 */ 1.094180e-51, /* 99 98 */ 7.417834e-54, /* 99 99 */ 2.489206e-56, /* 100 0 */ 1.000000e+00, /* 100 1 */ 1.000000e+00, /* 100 2 */ 1.000000e+00, /* 100 3 */ 1.000000e+00, /* 100 4 */ 1.000000e+00, /* 100 5 */ 1.000000e+00, /* 100 6 */ 1.000000e+00, /* 100 7 */ 1.000000e+00, /* 100 8 */ 1.000000e+00, /* 100 9 */ 1.000000e+00, /* 100 10 */ 1.000000e+00, /* 100 11 */ 1.000000e+00, /* 100 12 */ 1.000000e+00, /* 100 13 */ 1.000000e+00, /* 100 14 */ 1.000000e+00, /* 100 15 */ 1.000000e+00, /* 100 16 */ 1.000000e+00, /* 100 17 */ 1.000000e+00, /* 100 18 */ 1.000000e+00, /* 100 19 */ 1.000000e+00, /* 100 20 */ 1.000000e+00, /* 100 21 */ 1.000000e+00, /* 100 22 */ 1.000000e+00, /* 100 23 */ 1.000000e+00, /* 100 24 */ 1.000000e+00, /* 100 25 */ 1.000000e+00, /* 100 26 */ 1.000000e+00, /* 100 27 */ 1.000000e+00, /* 100 28 */ 1.000000e+00, /* 100 29 */ 1.000000e+00, /* 100 30 */ 1.000000e+00, /* 100 31 */ 1.000000e+00, /* 100 32 */ 1.000000e+00, /* 100 33 */ 1.000000e+00, /* 100 34 */ 9.999982e-01, /* 100 35 */ 9.999873e-01, /* 100 36 */ 9.993691e-01, /* 100 37 */ 9.888091e-01, /* 100 38 */ 9.235400e-01, /* 100 39 */ 7.562327e-01, /* 100 40 */ 5.248073e-01, /* 100 41 */ 3.143236e-01, /* 100 42 */ 1.679527e-01, /* 100 43 */ 8.159091e-02, /* 100 44 */ 3.699455e-02, /* 100 45 */ 1.610727e-02, /* 100 46 */ 6.689091e-03, /* 100 47 */ 2.636364e-03, /* 100 48 */ 1.078182e-03, /* 100 49 */ 4.018182e-04, /* 100 50 */ 1.472727e-04, /* 100 51 */ 6.000000e-05, /* 100 52 */ 9.090909e-06, /* 100 53 */ 3.636364e-06, /* 100 54 */ 1.818182e-06, /* 100 55 */ 1.566172e-06, /* 100 56 */ 4.137515e-07, /* 100 57 */ 1.050673e-07, /* 100 58 */ 2.563978e-08, /* 100 59 */ 6.011147e-09, /* 100 60 */ 1.353504e-09, /* 100 61 */ 2.925965e-10, /* 100 62 */ 6.070414e-11, /* 100 63 */ 1.208155e-11, /* 100 64 */ 2.305576e-12, /* 100 65 */ 4.216651e-13, /* 100 66 */ 7.386612e-14, /* 100 67 */ 1.238651e-14, /* 100 68 */ 1.986969e-15, /* 100 69 */ 3.046910e-16, /* 100 70 */ 4.462873e-17, /* 100 71 */ 6.238579e-18, /* 100 72 */ 8.315159e-19, /* 100 73 */ 1.055676e-19, /* 100 74 */ 1.275228e-20, /* 100 75 */ 1.463930e-21, /* 100 76 */ 1.594991e-22, /* 100 77 */ 1.646936e-23, /* 100 78 */ 1.609128e-24, /* 100 79 */ 1.485065e-25, /* 100 80 */ 1.292139e-26, /* 100 81 */ 1.057696e-27, /* 100 82 */ 8.125980e-29, /* 100 83 */ 5.844013e-30, /* 100 84 */ 3.922698e-31, /* 100 85 */ 2.449347e-32, /* 100 86 */ 1.417312e-33, /* 100 87 */ 7.567497e-35, /* 100 88 */ 3.709746e-36, /* 100 89 */ 1.660037e-37, /* 100 90 */ 6.734411e-39, /* 100 91 */ 2.456615e-40, /* 100 92 */ 7.978409e-42, /* 100 93 */ 2.278723e-43, /* 100 94 */ 5.634718e-45, /* 100 95 */ 1.181819e-46, /* 100 96 */ 2.044278e-48, /* 100 97 */ 2.799988e-50, /* 100 98 */ 2.847185e-52, /* 100 99 */ 1.910777e-54, /* 100 100 */ 6.348098e-57 }; abyss-1.3.6/Align/smith_waterman.cpp000644 002433 001057 00000017545 12104250113 021140 0ustar00traymondassembly000000 000000 ////////////////////////////////////////////////////////////////////////////// // Smith_waterman implementation, with modification, to find sequence overlap // // Written by Rong She (rshe@bcgsc.ca) // Last modified: Jul 7, 2010 ////////////////////////////////////////////////////////////////////////////// #include "smith_waterman.h" #include "Sequence.h" #include "Align/Options.h" #include #include #include #include // for DBL_MAX #include using namespace std; namespace opt { /** The score of a match. */ int match = 5; /** The score of a mismatch. */ int mismatch = -4; /** gap open penalty */ int gap_open = -12; /** gap extend penalty */ int gap_extend = -4; } /** Print the specified alignment. */ static ostream& printAlignment(ostream& out, const string& aseq, const string& bseq, unsigned alignPos[], SMAlignment align) { unsigned astart = alignPos[0], aend = alignPos[1] + 1; unsigned bstart = alignPos[2], bend = alignPos[3] + 1; assert(aend == aseq.size()); assert(bstart == 0); (void)aend; (void)bstart; out << aseq.substr(0, astart) << align.query_align << '\n' << string(astart, ' '); for (unsigned i = 0; i < align.match_align.size(); i++) { char a = align.query_align[i], b = align.target_align[i], c = align.match_align[i]; out << (c == a || c == b ? '.' : c); } return out << '\n' << string(astart, ' ') << align.target_align << bseq.substr(bend) << '\n'; } /** Index comparison functor. */ template struct index_cmp { const T arr; index_cmp(const T arr) : arr(arr) {} bool operator()(const int a, const int b) const { return arr[a] > arr[b]; } }; /** Return whether the characters a and b match. * @param c [out] the consensus character */ static bool isMatch(char a, char b, char& c) { if (a == b) { c = a; } else if (toupper(a) == toupper(b)) { c = islower(a) || islower(b) ? tolower(a) : a; } else if (a == 'N' || a == 'n') { c = b; } else if (b == 'N' || b == 'n') { c = a; } else { c = ambiguityOr(a, b); return ambiguityIsSubset(a, b); } return true; } /** Return the score of the alignment of a and b. */ static int matchScore(const char a, const char b) { char consensus; return isMatch(a, b, consensus) ? opt::match : opt::mismatch; } /** Return the score of a gap, either newly opened or extended. */ static int gapScore(bool prev_is_gap) { return prev_is_gap ? opt::gap_extend : opt::gap_open; } //the backtrack step in smith_waterman unsigned Backtrack(const int i_max, const int j_max, int** I_i, int** I_j, const string& seq_a, const string& seq_b, SMAlignment& align, unsigned* align_pos) { // Backtracking from H_max int current_i=i_max,current_j=j_max; int next_i=I_i[current_i][current_j]; int next_j=I_j[current_i][current_j]; string consensus_a(""), consensus_b(""), match(""); unsigned num_of_match = 0; while(((current_i!=next_i) || (current_j!=next_j)) && (next_j!=0) && (next_i!=0)){ if(next_i==current_i) { consensus_a += '-'; //deletion in A match += tolower(seq_b[current_j-1]); consensus_b += seq_b[current_j-1]; //b must be some actual char, cannot be '-' aligns with '-'! } else { consensus_a += seq_a[current_i-1]; // match/mismatch in A if(next_j==current_j) { consensus_b += '-'; // deletion in B match += tolower(seq_a[current_i-1]); } else { consensus_b += seq_b[current_j-1]; // match/mismatch in B char consensus_char; if (isMatch(seq_a[current_i-1], seq_b[current_j-1], consensus_char)) { match += consensus_char; num_of_match++; } else { match += ambiguityOr( seq_a[current_i-1], seq_b[current_j-1]); } } } current_i = next_i; current_j = next_j; next_i=I_i[current_i][current_j]; next_j=I_j[current_i][current_j]; } //check whether the alignment is what we want (pinned at the ends), modified version of SW (i_max is already fixed) if (current_j > 1) return 0; //record the last one consensus_a += seq_a[current_i-1]; consensus_b += seq_b[current_j-1]; char consensus_char; if (isMatch(seq_a[current_i-1], seq_b[current_j-1], consensus_char)) { match += consensus_char; num_of_match++; } else { match += ambiguityOr(seq_a[current_i-1], seq_b[current_j-1]); } align_pos[0] = current_i-1; align_pos[2] = current_j-1; align_pos[1] = i_max-1; align_pos[3] = j_max-1; reverse(consensus_a.begin(), consensus_a.end()); reverse(consensus_b.begin(), consensus_b.end()); reverse(match.begin(), match.end()); align.query_align = consensus_a; align.match_align = match; align.target_align = consensus_b; return num_of_match; } /* This is the Smith-Waterman algorithm (a variation of * Needleman-Wunsch algorithm), finds one optimal local alignment * Modified to find overlap of seq_a and seq_b (alignment that is * pinned at the end of seq_a and beginning of seq_b). * Actually, this should be a variation of needleman algorithm, that * looks for a global alignment, but without penalizing overhangs... * and make sure the alignment is end-to-end (end of seqA to beginning * of seqB). */ void alignOverlap(const string& seq_a, const string& seq_b, unsigned seq_a_start_pos, vector& overlaps, bool multi_align, bool verbose) { // get the actual lengths of the sequences int N_a = seq_a.length(); int N_b = seq_b.length(); // initialize H int i, j; double** H; int **I_i, **I_j; H = new double*[N_a+1]; I_i = new int*[N_a+1]; I_j = new int*[N_a+1]; bool** V = new bool*[N_a+1]; for(i=0;i<=N_a;i++){ H[i] = new double[N_b+1]; I_i[i] = new int[N_b+1]; I_j[i] = new int[N_b+1]; H[i][0]=0; //only need to initialize first row and first column I_i[i][0] = i-1; V[i] = new bool[N_b+1]; V[i][0] = true; //valid start } for (j = 0; j <= N_b; j++) { H[0][j] = 0; //initialize first column I_j[0][j] = j-1; V[0][j] = false; //wrong start, not overlap } V[0][0] = true; for(i=1;i<=N_a;i++){ for(j=1;j<=N_b;j++){ char a = seq_a[i-1], b = seq_b[j-1]; double scores[3] = { V[i-1][j-1] ? H[i-1][j-1] + matchScore(a, b) : -DBL_MAX, // match or mismatch V[i-1][j] ? H[i-1][j] + gapScore(I_j[i-1][j] == j) : -DBL_MAX, // deletion in sequence A V[i][j-1] ? H[i][j-1] + gapScore(I_i[i][j-1] == i) : -DBL_MAX // deletion in sequence B }; double* pMax = max_element(scores, scores + 3); H[i][j] = *pMax; switch (pMax - scores) { case 0: // match or mismatch I_i[i][j] = i-1; I_j[i][j] = j-1; break; case 1: // deletion in sequence A I_i[i][j] = i-1; I_j[i][j] = j; break; case 2: // deletion in sequence B I_i[i][j] = i; I_j[i][j] = j-1; break; } V[i][j] = H[i][j] == -DBL_MAX ? false : true; } } // search H for the maximal score unsigned num_of_match = 0; double H_max = 0.; int i_max=N_a, j_max; int* j_max_indexes=new int[N_b]; //this array holds the index of j_max in H[N_a] for (j=0; j(H[N_a])); //find ALL overlap alignments, starting from the highest score j_max j = 0; bool found = false; while (j < N_b) { j_max = j_max_indexes[j]; H_max = H[N_a][j_max]; if (H_max == 0) break; SMAlignment align; unsigned align_pos[4]; num_of_match = Backtrack(i_max, j_max, I_i, I_j, seq_a, seq_b, align, align_pos); if (num_of_match) { overlaps.push_back(overlap_align(seq_a_start_pos+align_pos[0], align_pos[3], align.match_align, num_of_match)); if (!found) { if (verbose) printAlignment(cerr, seq_a, seq_b, align_pos, align); found = true; if (!multi_align || (j+1 < N_b && H[N_a][j_max_indexes[j+1]] < H_max)) break; } } j++; } delete [] j_max_indexes; for(i=0;i<=N_a;i++){ delete [] H[i]; delete [] I_i[i]; delete [] I_j[i]; delete [] V[i]; } delete [] H; delete [] I_i; delete [] I_j; delete [] V; } abyss-1.3.6/Align/smith_waterman.h000644 002433 001057 00000003713 11772724351 020621 0ustar00traymondassembly000000 000000 ////////////////////////////////////////////////////////////////////////////// // Smith_waterman header // // Written by Rong She (rshe@bcgsc.ca) // Last modified: Jul 6, 2010 ////////////////////////////////////////////////////////////////////////////// #ifndef SMITH_WATERMAN_H #define SMITH_WATERMAN_H #include #include #include using namespace std; /* a simple data structure to store alignment sequences */ struct SMAlignment { string query_align; string target_align; string match_align; SMAlignment() {} friend ostream& operator<<(ostream& os, const SMAlignment& align) { os << "query:" << align.query_align << endl; os << "match:" << align.match_align << endl; os << "targt:" << align.target_align << endl; return os; } }; /* overlap alignment between two sequences t and h */ struct overlap_align { unsigned overlap_t_pos; //overlap on t is from this pos to end of sequence t unsigned overlap_h_pos; //overlap on h is from beginning of sequence h to this pos string overlap_str; unsigned overlap_match; overlap_align() : overlap_t_pos(0), overlap_h_pos(0), overlap_str(""), overlap_match(0) {} overlap_align(unsigned t_pos, unsigned h_pos, string& overlap, unsigned num_of_match) : overlap_t_pos(t_pos), overlap_h_pos(h_pos), overlap_str(overlap), overlap_match(num_of_match) {} unsigned length() const { return overlap_str.length(); } double pid() const { return (double)overlap_match / overlap_str.length(); } friend ostream& operator<<(ostream& os, const overlap_align& align) { os << "overlap region:" << align.overlap_str << endl << "t:" << align.overlap_t_pos << ", h:" << align.overlap_h_pos << ";num_of_match:" << align.overlap_match << ";len:" << align.length() << ";pid:" << align.pid() << endl; return os; } }; void alignOverlap(const string& seq_a, const string& seq_b, unsigned seq_a_start_pos, vector& overlaps, bool multi_align, bool verbose); #endif /* SMITH_WATERMAN_H */ abyss-1.3.6/Align/Options.h000644 002433 001057 00000000240 12104250113 017176 0ustar00traymondassembly000000 000000 #ifndef ALIGN_OPTIONS #define ALIGN_OPTIONS 1 namespace opt { extern int match; extern int mismatch; extern int gap_open; extern int gap_extend; } #endif abyss-1.3.6/Align/align.cc000644 002433 001057 00000010523 12116214001 016777 0ustar00traymondassembly000000 000000 #include "dialign.h" #include "config.h" #include "Common/Options.h" #include "FastaReader.h" #include "IOUtil.h" #include "Uncompress.h" #include "alignGlobal.h" #include #include #include #include #include #include #include #include using namespace std; #define PROGRAM "abyss-align" static const char VERSION_MESSAGE[] = PROGRAM " (" PACKAGE_NAME ") " VERSION "\n" "Written by Shaun Jackman.\n" "\n" "Copyright 2013 Canada's Michael Smith Genome Science Centre\n"; static const char USAGE_MESSAGE[] = "Usage: " PROGRAM " [OPTION]... [FASTA]...\n" "Align multiple sequences globally using either Needleman-Wunsch\n" "or DIALIGN-TX. Groups of sequences may be separated using `#.'\n" "\n" " Arguments:\n" "\n" " FASTA sequences in FASTA format\n" "\n" " Options:\n" "\n" " -v, --verbose display verbose output\n" " --help display this help and exit\n" " --version output version information and exit\n" "\n" " DIALIGN-TX options:\n" "\n" " -D, --dialign-d=N dialign debug level, default: 0\n" " -M, --dialign-m=FILE score matrix, default: dna_matrix.scr\n" " -P, --dialign-p=FILE diagonal length probability distribution\n" " default: dna_diag_prob_100_exp_550000\n" "\n" "Report bugs to <" PACKAGE_BUGREPORT ">.\n"; namespace opt { static int dialign_debug; static string dialign_score; static string dialign_prob; } static const char shortopts[] = "v"; enum { OPT_HELP = 1, OPT_VERSION }; static const struct option longopts[] = { { "verbose", no_argument, NULL, 'v' }, { "help", no_argument, NULL, OPT_HELP }, { "version", no_argument, NULL, OPT_VERSION }, { "dialign-d", required_argument, NULL, 'D' }, { "dialign-m", required_argument, NULL, 'M' }, { "dialign-p", required_argument, NULL, 'P' }, { NULL, 0, NULL, 0 } }; /** Align two sequences using the Needlman-Wunsch algorithm. */ static void alignPair(const string& seq0, const string& seq1, ostream& out) { NWAlignment align; unsigned match = alignGlobal(seq0, seq1, align); float identity = (float)match / align.size(); out << align << identity << "\n\n"; } /** Align multiple sequences using DIALIGN-TX. */ static void alignMulti(const vector& seq, ostream& out) { unsigned match; string alignment; string consensus = dialign(seq, alignment, match); float identity = (float)match / consensus.size(); out << alignment << consensus << '\n' << identity << "\n\n"; } /** Align the specified sequences. */ static void align(const vector& seq, ostream& out) { switch (seq.size()) { case 0: return; case 1: out << seq.front() << '\n' << 1 << "\n\n"; return; case 2: return alignPair(seq[0], seq[1], out); default: return alignMulti(seq, out); } } /** Align multiple sequences. */ static void alignFile(const char* path) { if (opt::verbose > 0) cerr << "Aligning `" << path << "'\n"; FastaReader in(path, FastaReader::NO_FOLD_CASE); for (vector seq; in;) { seq.clear(); FastaRecord fa; if (in >> fa) seq.push_back(fa.seq); while (in.peek() == '>' && in >> fa) seq.push_back(fa.seq); align(seq, cout); } assert(in.eof()); } int main(int argc, char** argv) { bool die = false; for (int c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;) { istringstream arg(optarg != NULL ? optarg : ""); switch (c) { case '?': die = true; break; case 'D': arg >> opt::dialign_debug; break; case 'M': arg >> opt::dialign_score; break; case 'P': arg >> opt::dialign_prob; break; case 'v': opt::verbose++; break; case OPT_HELP: cout << USAGE_MESSAGE; exit(EXIT_SUCCESS); case OPT_VERSION: cout << VERSION_MESSAGE; exit(EXIT_SUCCESS); } if (optarg != NULL && !arg.eof()) { cerr << PROGRAM ": invalid option: `-" << (char)c << optarg << "'\n"; exit(EXIT_FAILURE); } } if (die) { cerr << "Try `" << PROGRAM << " --help' for more information.\n"; exit(EXIT_FAILURE); } // Initialize dialign. init_parameters(); set_parameters_dna(); para->DEBUG = opt::dialign_debug; para->SCR_MATRIX_FILE_NAME = (char*)opt::dialign_score.c_str(); para->DIAG_PROB_FILE_NAME = (char*)opt::dialign_prob.c_str(); initDialign(); if (optind < argc) for_each(&argv[optind], &argv[argc], alignFile); else alignFile("-"); return 0; } abyss-1.3.6/Align/mergepairs.cc000644 002433 001057 00000023325 12162364646 020075 0ustar00traymondassembly000000 000000 #include "smith_waterman.h" #include "config.h" #include "DataLayer/Options.h" #include "Align/Options.h" #include "Common/Options.h" #include "FastaReader.h" #include "IOUtil.h" #include "Uncompress.h" #include "alignGlobal.h" #include #include #include #include #include #include #include #include using namespace std; #define PROGRAM "abyss-mergepairs" static const char VERSION_MESSAGE[] = PROGRAM " (" PACKAGE_NAME ") " VERSION "\n" "Written by Anthony Raymond.\n" "\n" "Copyright 2013 Canada's Michael Smith Genome Science Centre\n"; static const char USAGE_MESSAGE[] = "Usage: " PROGRAM " [OPTION]... READS1 READS2\n" "Attempt to merge reads in READS1 with reads in READS2\n" "\n" " Options:\n" "\n" " -o, --prefix=PREFIX the prefix of all output files [out]\n" " -p, --identity=N minimum overlap identity [0.9]\n" " -m, --matches=N minimum number of matches in overlap [10]\n" " -1, --length1=N trim bases from 3' end of first read\n" " down to a maximum of N bp long [inf]\n" " -2, --length2=N trim bases from 3' end of second read\n" " down to a maximum of N bp long [inf]\n" " --chastity discard unchaste reads [default]\n" " --no-chastity do not discard unchaste reads\n" " --trim-masked trim masked bases from the ends of reads\n" " --no-trim-masked do not trim masked bases from the ends\n" " of reads [default]\n" " -q, --trim-quality=N trim bases from the ends of reads whose\n" " quality is less than the threshold\n" " --standard-quality zero quality is `!' (33)\n" " default for FASTQ and SAM files\n" " --illumina-quality zero quality is `@' (64)\n" " default for qseq and export files\n" " -v, --verbose display verbose output\n" " --help display this help and exit\n" " --version output version information and exit\n" "\n" "Report bugs to <" PACKAGE_BUGREPORT ">.\n"; namespace opt { static string prefix = "out"; static float identity = 0.9; static unsigned min_matches = 10; /** Max length of read 1. */ static int max_len_1 = 0; /** Max length of read 2. */ static int max_len_2 = 0; } static struct { unsigned total_reads; unsigned merged_reads; unsigned unmerged_reads; unsigned no_alignment; unsigned too_many_aligns; unsigned low_matches; unsigned has_indel; unsigned pid_low; } stats; static const char shortopts[] = "o:p:m:q:1:2:v"; enum { OPT_HELP = 1, OPT_VERSION }; static const struct option longopts[] = { { "prefix", required_argument, NULL, 'o' }, { "identity", required_argument, NULL, 'p' }, { "matches", required_argument, NULL, 'm' }, { "verbose", no_argument, NULL, 'v' }, { "length1", no_argument, NULL, '1' }, { "length2", no_argument, NULL, '2' }, { "chastity", no_argument, &opt::chastityFilter, 1 }, { "no-chastity", no_argument, &opt::chastityFilter, 0 }, { "trim-masked", no_argument, &opt::trimMasked, 1 }, { "no-trim-masked", no_argument, &opt::trimMasked, 0 }, { "trim-quality", required_argument, NULL, 'q' }, { "standard-quality", no_argument, &opt::qualityOffset, 33 }, { "illumina-quality", no_argument, &opt::qualityOffset, 64 }, { "help", no_argument, NULL, OPT_HELP }, { "version", no_argument, NULL, OPT_VERSION }, { NULL, 0, NULL, 0 } }; char bestBase(char a, char b, char qa, char qb) { return qa > qb ? a : b; } /** Merge the read sequences taking the highest quality base when * there is a dissagreement while reporting the lowest quality * possible. */ static void mergeReads(overlap_align& overlap, FastqRecord& rec1, FastqRecord& rec2, FastqRecord& out) { size_t ol = overlap.length(); Sequence seq1 = rec1.seq; string qual1 = rec1.qual; Sequence rc_seq2 = reverseComplement(rec2.seq); string rc_qual2(rec2.qual); reverse(rc_qual2.begin(), rc_qual2.end()); // Form overhanging portions of the reads. size_t out_len = overlap.overlap_t_pos + ol + rc_seq2.length() - overlap.overlap_h_pos - 1; Sequence out_seq(out_len, 'N'); string out_qual(out_len, '#'); assert(out_seq.length() >= seq1.length() || out_seq.length() >= rc_seq2.length()); copy(seq1.begin(), seq1.begin() + overlap.overlap_t_pos, out_seq.begin()); copy(rc_seq2.begin() + overlap.overlap_h_pos + 1, rc_seq2.end(), out_seq.begin() + overlap.overlap_t_pos + ol); copy(qual1.begin(), qual1.begin() + overlap.overlap_t_pos, out_qual.begin()); copy(rc_qual2.begin() + ol, rc_qual2.end(), out_qual.begin() + seq1.length()); // Fix the sequence and quality inside the overlap. for (unsigned i = 0; i < ol; i++) { assert(int(seq1.length() - ol + i) >= 0); unsigned pos = seq1.length() - ol + i; assert(pos < seq1.length() && i < rc_seq2.length() && pos < out_seq.length()); if (seq1[pos] == rc_seq2[i]) { out_seq[pos] = seq1[pos]; out_qual[pos] = max(qual1[pos], rc_qual2[i]); } else { out_seq[pos] = bestBase(seq1[pos], rc_seq2[i], qual1[pos], rc_qual2[i]); out_qual[pos] = min(qual1[pos], rc_qual2[i]); } } //cout << seq1 << '\n' << rc_seq2 << '\n' << out_seq << '\n'; //cout << qual1 << '\n' << rc_qual2 << '\n' << out_qual << '\n'; out = FastqRecord(rec1.id, rec1.comment, out_seq, out_qual); } bool isGapless(overlap_align& o, Sequence& s) { return o.length() == s.length() - o.overlap_t_pos && o.length() == o.overlap_h_pos + 1; } static void filterAlignments(vector& overlaps, FastaRecord& rec) { if (overlaps.empty()) { stats.no_alignment++; return; } vector::iterator it; for (it = overlaps.begin(); it != overlaps.end(); it++ ) { overlap_align o = *it; if (o.overlap_match < opt::min_matches) overlaps.erase(it--); } if (overlaps.empty()) { stats.low_matches++; return; } for (it = overlaps.begin(); it != overlaps.end(); it++ ) { overlap_align o = *it; if (o.pid() < opt::identity) overlaps.erase(it--); } if (overlaps.empty()) { stats.pid_low++; return; } for (it = overlaps.begin(); it != overlaps.end(); it++ ) { overlap_align o = *it; if (!isGapless(o, rec.seq)) overlaps.erase(it--); } if (overlaps.empty()) { stats.has_indel++; return; } } /** Align read pairs. */ static void alignFiles(const char* reads1, const char* reads2) { if (opt::verbose > 0) cerr << "Merging `" << reads1 << "' with `" << reads2 << "'\n"; FastaReader r1(reads1, FastaReader::NO_FOLD_CASE, opt::max_len_1); FastaReader r2(reads2, FastaReader::NO_FOLD_CASE, opt::max_len_2); // Openning the output files string name(opt::prefix); name.append("_reads_1.fastq"); ofstream unmerged1(name.c_str()); name = string(opt::prefix); name.append("_reads_2.fastq"); ofstream unmerged2(name.c_str()); name = string(opt::prefix); name.append("_merged.fastq"); ofstream merged(name.c_str()); FastqRecord rec1, rec2; int x = 0; while (r1 >> rec1 && r2 >> rec2) { stats.total_reads++; string rc_qual2(rec2.qual); reverse(rc_qual2.begin(), rc_qual2.end()); vector overlaps; alignOverlap(rec1.seq, reverseComplement(rec2.seq), 0, overlaps, true, opt::verbose > 2); filterAlignments(overlaps, rec1); if (overlaps.size() == 1) { // If there is only one good alignment, merge reads and // print to merged file stats.merged_reads++; FastqRecord out; mergeReads(overlaps[0], rec1, rec2, out); merged << out; cout << overlaps[0].length() << ' ' << overlaps[0].overlap_match << '\n'; } else { // print reads to separate files if (overlaps.size() > 1) stats.too_many_aligns++; stats.unmerged_reads++; unmerged1 << rec1; unmerged2 << rec2; } if (opt::verbose > 0 && ++x % 10000 == 0) { cerr << "Aligned " << x << " reads.\n"; } } r2 >> rec2; assert(r1.eof()); assert(r2.eof()); unmerged1.close(); unmerged2.close(); merged.close(); } int main(int argc, char** argv) { bool die = false; //defaults for alignment parameters opt::match = 1; opt::mismatch = -2; opt::gap_open = -10000; opt::gap_extend = -10000; for (int c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;) { istringstream arg(optarg != NULL ? optarg : ""); switch (c) { case '?': die = true; break; case 'o': arg >> opt::prefix; break; case 'p': arg >> opt::identity; break; case 'm': arg >> opt::min_matches; break; case 'q': arg >> opt::qualityThreshold; break; case '1': arg >> opt::max_len_1; break; case '2': arg >> opt::max_len_2; break; case 'v': opt::verbose++; break; case OPT_HELP: cerr << USAGE_MESSAGE; exit(EXIT_SUCCESS); case OPT_VERSION: cerr << VERSION_MESSAGE; exit(EXIT_SUCCESS); } if (optarg != NULL && !arg.eof()) { cerr << PROGRAM ": invalid option: `-" << (char)c << optarg << "'\n"; exit(EXIT_FAILURE); } } if (argc - optind < 2) { cerr << PROGRAM ": missing arguments\n"; die = true; } if (argc - optind > 2) { cerr << PROGRAM ": too many arguments\n"; die = true; } if (die) { cerr << "Try `" << PROGRAM << " --help' for more information.\n"; exit(EXIT_FAILURE); } const char* reads1 = argv[optind++]; const char* reads2 = argv[optind++]; alignFiles(reads1, reads2); cerr << "Read merging stats: total=" << stats.total_reads << " merged=" << stats.merged_reads << " unmerged=" << stats.unmerged_reads << '\n' << "no_alignment=" << stats.no_alignment << " too_many_aligns=" << stats.too_many_aligns << " too_few_matches=" << stats.low_matches << " has_indel=" << stats.has_indel << " low_pid=" << stats.pid_low << '\n'; return 0; } abyss-1.3.6/dialign/Makefile.in000644 002433 001057 00000041243 12176317672 020053 0ustar00traymondassembly000000 000000 # Makefile.in generated by automake 1.14 from Makefile.am. # @configure_input@ # Copyright (C) 1994-2013 Free Software Foundation, Inc. # This Makefile.in is free software; the Free Software Foundation # gives unlimited permission to copy and/or distribute it, # with or without modifications, as long as this notice is preserved. # This program is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY, to the extent permitted by law; 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extern void merror(char *msg1, char *msg2); extern inline void calc_weight(struct diag* dg, struct scr_matrix* smatrix, struct prob_dist *pdist); extern inline void calc_ov_weight(struct diag* dg, struct diag_col *dcol, struct scr_matrix* smatrix, struct prob_dist *pdist); //extern struct seq_part* create_seq_part(int num, struct seq* aSeq, unsigned int startpos); extern struct diag* create_diag(struct seq_part* part1, struct seq_part* part2, int dlength); extern void free_diag(struct diag* dg); // long balance = 0; //unsigned long allocss = 0; //unsigned long freess = 0; long sslen; /** * * alig.c: Takes care of the alignment data structure * * 2003-10-31 A.R.Subramanian * (Initial) */ /** * creates initial empty alignment data structure * * The pointer returned (and the ones included in the struct) * has to be deallocted explicitely from memory. */ struct alignment* create_empty_alignment(struct seq_col *scol) { /* printf("before\n"); sleep(5); */ struct alignment* algn = malloc(sizeof(struct alignment)); sslen = scol->length; //allocss += sizeof(struct alignment); if(algn==NULL) error("create_empty_alignment(): (1) Out of memory !"); //long xsize = sizeof(struct alignment); algn->next = NULL; // algn->prev = NULL; algn->total_weight = 0.0; //algn->pos = 0; algn->max_pos = -1; algn->scol = scol; //algn->aligned_diags_amount=0; //algn->aligned_diags = malloc(sizeof(struct diag*)*diag_amount); //algn->max_aligned_diags_amount = diag_amount; //algn->orig_max_aligned_diags_amount = diag_amount; //algn->backlog_diags = NULL; ////allocss += (sizeof(struct diag*)*diag_amount); //if(algn->aligned_diags==NULL) // error("create_empty_alignment(): (1.5) Out of memory !"); unsigned int slen = scol->length; algn->seq_is_orphane = calloc(slen, sizeof(char)); //allocss += (sizeof(char)*slen); //xsize += slen*sizeof(char); if(algn->seq_is_orphane==NULL) error("create_empty_alignment(): (2) Out of memory !"); // memset(algn->seq_is_orphane, 1, slen*sizeof(char)); algn->algn = malloc(sizeof(struct algn_pos *)*slen); //allocss += sizeof(struct algn_pos *)*slen; //xsize += slen*sizeof(struct algn_pos *); if(algn->algn==NULL) error("create_empty_alignment(): (3) Out of memory !"); //algn->redo_seqs = calloc(slen*slen, sizeof(char)); int i,j; struct seq* sq; for(i=0;iseqs[i]); algn->seq_is_orphane[i]=1; algn->algn[i] = malloc(sizeof(struct algn_pos)*sq->length ); //allocss += sizeof(struct algn_pos )*sq->length; //xsize += sq->length*sizeof(struct algn_pos *); if(algn->algn[i]==NULL) error("create_empty_alignment(): (4) Out of memory !"); for(j=0;jlength;j++) { algn->algn[i][j].state = para->STATE_ORPHANE; // algn->algn[i][j].isInherited = 0; algn->algn[i][j].predFPos = -1; algn->algn[i][j].succFPos = -1; algn->algn[i][j].eqcParent= &(algn->algn[i][j]); //if(j==442) printf(" parent: %i\n", algn->algn[i][j].eqcParent); algn->algn[i][j].eqcRank= 0; algn->algn[i][j].eqcAlgnPos=calloc(1, sizeof(int));; //allocss += sizeof(int); *algn->algn[i][j].eqcAlgnPos=j; algn->algn[i][j].proceed=calloc(1, sizeof(char));; //allocss += sizeof(char); *algn->algn[i][j].proceed = 0; algn->algn[i][j].predF = NULL; algn->algn[i][j].succF = NULL; algn->algn[i][j].row = i; algn->algn[i][j].col = j; algn->algn[i][j].dg_cont = NULL; //xsize += sizeof(char) + sizeof(int); } } /* printf("after\n"); sleep(5); printf("gone\n"); */ // printf(" algnsize=%i\n",xsize); return algn; } /** * free alignment * */ void free_alignment(struct alignment *algn) { struct seq_col *scol = algn->scol; int slen = scol->length; int i,j; struct algn_pos *apos; struct algn_pos *o_apos; struct algn_pos *tpos; struct seq *sq; struct diag_cont *dgc,*ndgc; if(algn->seq_is_orphane!=NULL) { free(algn->seq_is_orphane); //freess += sizeof(char)*slen; } for(i=0;iseqs[i]); for(j=0;jlength;j++) { apos = &(algn->algn[i][j]); if(! (apos->state & para->STATE_INHERITED) && ! (apos->state & para->STATE_ORPHANE)) { //if(! (apos->state & para->STATE_INHERITED) && ! (apos->state & para->STATE_ORPHANE)) { if(apos->predF!=NULL) { free(apos->predF); //freess += sizeof(int)*slen; } if(apos->succF!=NULL) { free(apos->succF); //freess += sizeof(int)*slen; } } if(! (apos->state & para->STATE_INHERITED) || (apos->state & para->STATE_ORPHANE) ) { free(apos->eqcAlgnPos); free(apos->proceed); //freess += sizeof(int)+sizeof(char); } dgc = apos->dg_cont; while(dgc!=NULL) { ndgc = dgc->next; //printf(" free %i %i %i %i\n", i,j,dgc, dgc->next); free(dgc); //freess += sizeof(struct diag_cont); dgc = ndgc; } } free(algn->algn[i]); //freess += sizeof(struct algn_pos)*sq->length; } //dgc = algn->backlog_diags; //while(dgc!=NULL) { // ndgc = dgc->next; // free(dgc); // //freess += sizeof(struct diag_cont); // dgc = ndgc; //} //free(algn->aligned_diags); ////freess += sizeof(struct diag *)*algn->; free(algn->algn); free(algn); ////freess += sizeof(struct algn_pos *)*slen + sizeof(struct alignment); } /** * returnes the representative of the equivalence class */ struct algn_pos *_find_eqc(struct algn_pos *ap) { if(ap!=ap->eqcParent) { // if(doprint) printf(" FIND: %i %i\n", ap, ap->eqcParent); /** if(ap->eqcParent->eqcAlgnPos!=NULL) { if( (ap->eqcAlgnPos!=NULL) && *ap->eqcParent->eqcAlgnPos < *ap->eqcAlgnPos) { // if(doprint) printf(" 1.1 ALGNPOS: %i %i\n", ap, ap->eqcParent); *ap->eqcParent->eqcAlgnPos = *ap->eqcAlgnPos; } } else { // ap->eqcParent->eqcAlgnPos = ap->eqcAlgnPos; } */ ap->eqcParent = _find_eqc(ap->eqcParent); } // if(doprint) printf(" 1.ALGNPOS: %i %i\n", ap, ap->eqcParent); // if(doprint) printf(" 2.ALGNPOS: %i %i\n", ap, ap->eqcParent); return ap->eqcParent; } /** * returnes the representative of the equivalence class */ struct algn_pos *find_eqc(struct algn_pos **ap, int seqnum, int pos) { //if(1) printf("%i %i %i\n", ap, seqnum,pos); struct algn_pos *tap = &ap[seqnum][pos]; struct algn_pos *eq_ap; eq_ap = _find_eqc(tap); struct diag_cont *old_dgc; // if(eq_ap->eqcAlgnPos != tap->eqcAlgnPos) { if(eq_ap != tap) { /* if(tap->state & para->STATE_ORPHANE) { printf(" ALARM ORPHANE %i %i\n", eq_ap->state, tap->state); } if(eq_ap->state & para->STATE_ORPHANE) { printf(" ALARM ORPHANE %i %i\n", eq_ap->state, tap->state); } */ //if((tap->eqcAlgnPos!=NULL) && (*tap->eqcAlgnPos > *eq_ap->eqcAlgnPos)) // *eq_ap->eqcAlgnPos = *tap->eqcAlgnPos; // if(eq_ap->eqcAlgnPos != tap->eqcAlgnPos) if( (!(tap->state & para->STATE_INHERITED))) { //&& !oldparentIsInherited) { if(tap->eqcAlgnPos !=NULL) { //if(pos==175) printf("free eqcAlgnPos: %i\n", tap->eqcAlgnPos); //balance -= sizeof(int); free(tap->eqcAlgnPos); tap->eqcAlgnPos = NULL; //freess += sizeof(int); } if(tap->proceed !=NULL) { //printf("free proceed: %i\n", tap->proceed); //balance -= sizeof(char); free(tap->proceed); //freess += sizeof(char); //printf("after free proceed: %i\n", tap->proceed); tap->proceed = NULL; } //if(tap->predFPos>=0) if( (eq_ap->predF != tap->predF) && (1 || (tap->predFPos<0)) && (tap->predF!=NULL)){ //printf(" free predF: %i %i %i %i\n", tap->predF, tap->isInherited, seqnum, pos); //balance -= sizeof(int)*sslen; //printf (" 3. free: %i %i %i\n",allocs, frees, allocs-frees); //freess += sizeof(int)*sslen; free(tap->predF); //printf(" after free predF: %i\n", tap->predF); tap->predF=NULL; } //if(tap->succFPos>=0) if((eq_ap->succF != tap->succF) && (1 || (tap->succFPos<0)) && (tap->succF!=NULL)) { //printf("free succ: %i\n", tap->succF); //balance -= sizeof(int)*sslen; //printf (" 4. free: %i %i %i\n",allocs, frees, allocs-frees); //freess += sizeof(int)*sslen; free(tap->succF); //printf("after free succ: %i\n", tap->succF); tap->succF=NULL; } } /*else { if(eq_ap->state & para->STATE_INHERITED) { printf(" inherited alarm!\n"); } if(eq_ap->state & para->STATE_ORPHANE) { printf(" orphane alarm!\n"); } }*/ old_dgc = tap->dg_cont; *tap = *eq_ap; tap->dg_cont = old_dgc; tap->row = seqnum; tap->col = pos; tap->state = (tap->state | para->STATE_INHERITED); } //if(seqnum==0 &&pos==175) printf("after !=\n"); // tap = eq_ap; struct algn_pos *ttap; if(tap->predFPos>=0 ) { //if(seqnum==0 && pos==175) printf(" alarm predF: %i %i %i %i\n", tap->predF, tap->predFPos, seqnum, pos); // printf ("PRE Pos %i %i \n", tap->predFPos, pos); if( (tap->predFPos==pos)|| !(tap->state & para->STATE_ORPHANE)) { printf("pred ALARM %i %i\n", tap->predFPos, pos); exit(99); } ttap=find_eqc(ap, seqnum, tap->predFPos); tap->predF = ttap->predF; } if(tap->succFPos>=0) { //if(seqnum==0 && pos==175) printf(" alarm succF: %i %i %i %i\n", tap->succF, tap->succFPos, seqnum, pos); //printf ("2. PRE Pos %i %i \n", tap->predFPos, tap->succFPos); if( (tap->succFPos==pos)|| !(tap->state & para->STATE_ORPHANE)) { printf("succ ALARM %i %i\n", tap->succFPos, pos); exit(99); } ttap = find_eqc(ap, seqnum, tap->succFPos); tap->succF = ttap->succF; } //if(seqnum==0 && pos==175) printf(" end qgc\n"); return tap; } /** * copy alignment * * doDgc = 0: ignore all backlogdiags and position dg_cont's * doDgc = 1: free the target backlogdiags and dg_conts' * doDgc = 2: same as 1 but also copy the original backlog diags and dg_conts to the target struct alignment* copy_alignment( struct alignment *o_algn, struct alignment *algn, char doDgc) { struct seq_col *scol = o_algn->scol; int slen = scol->length; int i,j; struct algn_pos *apos; struct algn_pos *o_apos; struct algn_pos *tpos; struct seq *sq; struct diag_cont *ptdgc, *tdgc, *o_tdgc; if(doDgc>0) { tdgc = algn->backlog_diags; while(tdgc!=NULL) { algn->backlog_diags = algn->backlog_diags->next; free(tdgc); tdgc = algn->backlog_diags; } if(doDgc>1) { o_tdgc = o_algn->backlog_diags; ptdgc = NULL; while(o_tdgc!=NULL) { tdgc = malloc(sizeof(struct diag_cont)); *tdgc = *o_tdgc; if(ptdgc == NULL) { algn->backlog_diags = tdgc; } else { ptdgc->next = tdgc; } ptdgc = tdgc; } } } memcpy(algn->seq_is_orphane, o_algn->seq_is_orphane, sizeof(char)*slen); algn->total_weight = o_algn->total_weight; // printf(" enter copy\n"); for(i=0;iseqs[i]); for(j=0;jlength;j++) { apos = &(algn->algn[i][j]); o_apos = &(o_algn->algn[i][j]); if(doDgc>0) { tdgc = apos->dg_cont; while(tdgc!=NULL) { apos->dg_cont = apos->dg_cont->next; free(tdgc); tdgc = apos->dg_cont; } if(doDgc>1) { o_tdgc = o_apos->dg_cont; ptdgc = NULL; while(o_tdgc!=NULL) { tdgc = malloc(sizeof(struct diag_cont)); *tdgc = *o_tdgc; if(ptdgc == NULL) { apos->dg_cont = tdgc; } else { ptdgc->next = tdgc; } ptdgc = tdgc; } } } if(! (apos->state & para->STATE_ORPHANE)) { if(o_apos->state & para->STATE_ORPHANE) { if(!(apos->state & para->STATE_INHERITED)) { // printf (" free1\n") //frees += sizeof(int)*slen*2; //printf (" 1. frees: %i %i %i\n",allocs, frees, allocs-frees); free(apos->predF); free(apos->succF); //balance -= 2*sizeof(int)*slen; } apos->predF=NULL; apos->succF=NULL; } else { if(apos->state & para->STATE_INHERITED) { if(! (o_apos->state & para->STATE_INHERITED)) { //printf (" 1. malloc: %i %i %i\n",allocs, frees, allocs-frees); apos->predF=malloc(sizeof(int)*slen); apos->succF=malloc(sizeof(int)*slen); //allocss += sizeof(int)*slen*2; //balance += 2*sizeof(int)*slen; if( (apos->predF==NULL) || (apos->succF==NULL)) error("copy_alignment(): (1) Out of memory !"); memcpy(apos->predF, o_apos->predF, sizeof(int)*slen); memcpy(apos->succF, o_apos->succF, sizeof(int)*slen); } else { apos->predF=NULL; apos->succF=NULL; } } else { if(! (o_apos->state & para->STATE_INHERITED)) { memcpy(apos->predF, o_apos->predF, sizeof(int)*slen); memcpy(apos->succF, o_apos->succF, sizeof(int)*slen); } else { // printf (" free2\n") //frees += sizeof(int)*slen*2; //printf (" 2. frees: %i %i %i\n",allocs, frees, allocs-frees); free(apos->predF); free(apos->succF); //freess += sizeof(int)*slen*2; //balance -= 2*sizeof(int)*slen; apos->predF=NULL; apos->succF=NULL; } } } } else { if( !(o_apos->state & para->STATE_ORPHANE)) { if(o_apos->state & para->STATE_INHERITED) { apos->predF=NULL; apos->succF=NULL; } else { //allocs += sizeof(int)*slen*2; //printf (" 2. malloc: %i %i %i\n",allocs, frees, allocs-frees); apos->predF=malloc(sizeof(int)*slen); apos->succF=malloc(sizeof(int)*slen); //allocss += sizeof(int)*slen*2; //balance += 2*sizeof(int)*slen; if( (apos->predF==NULL) || (apos->succF==NULL)) error("copy_alignment(): (2) Out of memory !"); memcpy(apos->predF, o_apos->predF, sizeof(int)*slen); memcpy(apos->succF, o_apos->succF, sizeof(int)*slen); } } else { apos->predF=NULL; apos->succF=NULL; } } apos->predFPos = o_apos->predFPos; apos->succFPos = o_apos->succFPos; //printf(" before %i %i\n", i,j); apos->eqcRank = o_apos->eqcRank; tpos = o_apos->eqcParent; apos->eqcParent = &(algn->algn[tpos->row][tpos->col]); if( (apos->state & para->STATE_INHERITED)) { if( !(o_apos->state & para->STATE_INHERITED)) { //allocs += sizeof(int)+sizeof(char); apos->eqcAlgnPos = malloc(sizeof(int)); *(apos->eqcAlgnPos)=j; apos->proceed = malloc(sizeof(char)); *(apos->proceed)=0; //allocss += sizeof(int)+sizeof(char); } } else { if((o_apos->state & para->STATE_INHERITED)) { //frees += sizeof(int)+sizeof(char); free(apos->eqcAlgnPos); free(apos->proceed); apos->eqcAlgnPos=NULL; apos->proceed=NULL; //balance -= sizeof(int)+sizeof(char); } } //printf(" after %i %i\n", i,j); apos->state = o_apos->state; } } // printf(" leave copy\n"); return algn; } */ /** * adds the given diagional to the given alignment and updates the * datastructure (i.e. frontiers). The given diag must be consistent * to the given alignment ! */ char align_diag(struct alignment *algn, struct scr_matrix *smatrix, struct diag* dg) { char alignedSomething = 0; int i,j,k; char al; if(dg->multi_dg) { //return 0; for(i=0;imulti_length;i++) { if(dg->multi_cont[i]!=NULL) { //printf(" before %f %f\n", dg->total_weight, dg->multi_cont[i]->weight); al = align_diag(algn,smatrix, dg->multi_cont[i]); if(al) algn->total_weight -= dg->multi_cont[i]->total_weight; alignedSomething = alignedSomething || al; //printf(" after \n"); } } return alignedSomething; } //if((dg->length==0) ) return 0; if((dg->length==0) || (!dg->meetsThreshold && !dg->anchor)) return 0; /* printf(" dg %i %i %i\n", dg, dg->multi_dg, dg->length); char adapted = adapt_diag(algn, smatrix, dg); if(adapted) { printf(" dg %i %i %i\n", dg, dg->multi_dg, dg->length); error(" inconsistent diag!\n"); } */ struct seq_col *scol = algn->scol; int s1 = dg->seq_p1.num; int s2 = dg->seq_p2.num; //printf("%i %i\n", s1,s2); //char o1 = algn->seq_is_orphane[s1]; //char o2 = algn->seq_is_orphane[s2]; int length = dg->length; int sp1 = dg->seq_p1.startpos; int sp2 = dg->seq_p2.startpos; struct algn_pos **ap=algn->algn; struct algn_pos *tp; struct algn_pos *apos1, *apos2, *tpos; int p1, p2,plen; int p; struct seq *sq = scol->seqs; int s, slen = scol->length; int *oldpredF, *oldsuccF, *otherpredF, *othersuccF; int pF,sF; int *c2n = smatrix->char2num; int *sdata = smatrix ->data; char *data1 = dg->seq_p1.sq->data; char *data2 = dg->seq_p2.sq->data; int smatrixlen = smatrix->length; int a1,a2; int score1; char seenNonOrphane; int opos; int ms; char skip = 0; char found; struct diag_cont *dgc, *dgc_next; double ttim; /* int nextpos[slen]; int firstpos; int oldpos; char firstRound; */ for(i=0;ilength); skip = 0; //if(sp1==30) printf("%i %i %i %i %i \n", p1,p2,dg->length, dg->seq_p1.sq->length, dg->seq_p2.sq->length); /* // if(dg->onlyOverThres==1) { a1 = c2n[data1[p1]]; a2 = c2n[data2[p2]]; score1 = sdata[smatrixlen*a1+a2]; if( (score1<=3) && (i>length/3)) { skip = 1; } //} */ // printf(" %i %i %i\n",p1,p2,skip); //} else { /* a1 = c2n[data1[p1]]; a2 = c2n[data2[p2]]; score1 = sdata[smatrixlen*a1+a2]; if(score1<=4) { skip = 1; } */ //if( (i==(length-1)) ){ //ttim = clock(); //tim += (clock()-ttim)/CLOCKS_PER_SEC; // printf(" tim %f\n", tim); //printf(" diag n1=%i s1=%i n2=%i s2=%i l=%i\n", s1,sp1,s2,sp2,length); //allocss += 2*sizeof(struct diag_cont ); //} // TODO: tune ration is 1:45 (minor) /* dgc_next = ap[s1][p1].dg_cont; dgc = malloc(sizeof(struct diag_cont)); dgc->dg = dg; dgc->next = dgc_next; ap[s1][p1].dg_cont = dgc; //if((s1==0) && (p1==133)) printf(" dddgc %i %i\n", dgc, dgc->next); dgc_next = ap[s2][p2].dg_cont; dgc = malloc(sizeof(struct diag_cont)); dgc->dg = dg; dgc->next = dgc_next; ap[s2][p2].dg_cont = dgc; */ if(! skip) { //printf("apos1 %i %i\n", s1, p1); apos1 = find_eqc(ap, s1,p1);//&(ap[s1][p1]); //printf("apos2 %i %i %i\n", s2, p2, scol->seqs[s2].length); apos2 = find_eqc(ap, s2,p2); //&(ap[s2][p2]); //printf("after apos2 %i %i\n", s2, p2); oldpredF = apos1->predF; oldsuccF = apos1->succF; if(oldpredF!=NULL && oldsuccF!=NULL) if(oldpredF[s2]==p2 && oldsuccF[s2]==p2) skip = 1; if(para->DEBUG>4) { if(!skip) { if(oldpredF!=NULL) if(oldpredF[s2]>=p2) { printf(" Incons1 %i %i %i\n", s2, p2,oldpredF[p2]); error(" ERROR"); } if(oldsuccF!=NULL) if(oldsuccF[s2]<=p2) { printf(" Incons2 %i %i %i\n",s2, p2,oldsuccF[p2]); error(" ERROR"); } oldpredF=apos2->predF; oldsuccF=apos2->succF; if(oldpredF!=NULL) if(oldpredF[s1]>=p1) { printf(" Incons3 %i %i %i\n", s1, p1,oldpredF[p1]); error(" ERROR"); } if(oldsuccF!=NULL) if(oldsuccF[s1]<=p1) { printf(" Incons4 %i %i %i\n",s1, p1,oldsuccF[p1]); error(" ERROR"); } } } } //} if(! skip) { alignedSomething = 1; for(k=0;k<2;k++) { tpos = (k==0 ? apos1 : apos2); //printf("tpos %i\n", tpos); oldpredF = tpos->predF; oldsuccF = tpos->succF; otherpredF = (k==0 ? apos2->predF : apos1->predF); othersuccF = (k==0 ? apos2->succF : apos1->succF); //printf("pre isorphane %i\n", tpos); if(tpos->state & para->STATE_ORPHANE) { //if(scol->length>21) printf("isorphane %i %i\n", tpos,sizeof(int)*scol->length); //printf("step 1\n"); // printf (" 3. malloc: %i\n",sizeof(int)*slen*2); //allocs += sizeof(int)*slen*2; // printf (" 3. malloc: %i %i %i\n",allocs, frees, allocs-frees); //balance += sizeof(int)*slen*2; tpos->predF = malloc(sizeof(int)*scol->length); //if(k==0) printf(" apos1->predF = %i\n",tpos->predF), //printf("pre succForphane %i %i\n", tpos->succF, scol->length); //printf(" step 2\n"); tpos->succF = malloc(sizeof(int)*scol->length); //allocss += 2*sizeof(int )*scol->length; //printf(" step 3\n"); //printf("succForphane %i\n", tpos); if( (tpos->predF==NULL) || (tpos->succF==NULL)) error("align_diag(): (1) Out of memory !"); } // printf("init loop %i\n", tpos); for(j=0;jlength;j++) { pF = -1; sF = sq[j].length; // propagate predF and succF if(oldpredF!=NULL && oldpredF[j]>pF) pF = oldpredF[j]; //if(j==0) printf("1 pf=%i\n", pF); if(otherpredF!=NULL && otherpredF[j]> pF) pF = otherpredF[j]; //if(j==0) printf("2 pf=%i\n", pF); if(oldsuccF!=NULL && oldsuccF[j] sF) { if(oldpredF!=NULL) printf(" PRE 1. ALARM oldpredF: %i \n",oldpredF[j] ); if(oldsuccF!=NULL) printf(" PRE 1. ALARM oldsuccF: %i \n",oldsuccF[j] ); if(otherpredF!=NULL) printf(" PRE 1. ALARM otherpredF: %i \n",otherpredF[j] ); if(othersuccF!=NULL) printf(" PRE 1. ALARM othersuccF: %i \n",othersuccF[j] ); printf("1. ALARM j=%i %i %i %i %i %i %i %i\n", j, (k==0 ? s1 : s2), (k==0 ? p1 : p2), (k==0 ? p2 : p1), oldpredF!=NULL ? oldpredF[k==0 ? s2 : s1] : -2, oldsuccF!=NULL ? oldsuccF[k==0 ? s2 : s1]: 99999, tpos->predFPos, tpos->succFPos); exit(1); } */ //if(pF==sF && pF==0 && j==0) printf("pf=%i sf=%i j=%i s1=%i s2=%i p1=%i p2=%i iso=%i opf=%i osf=%i otpf=%i otsf=%i\n", pF,sF,j,s1,s2,p1,p2,tpos->isOrphane,oldpredF, oldsuccF, otherpredF, othersuccF); tpos->predF[j]=pF; tpos->succF[j]=sF; } //if(s1==0 && p1==0) printf(" SET IT 1\n"); //if(s2==0 && p2==0) printf(" SET IT 2\n"); //if(tpos->state & para->STATE_ORPHANE) tpos->state = tpos->state & (tpos->state ^ para->STATE_ORPHANE); tpos->predFPos = -1; tpos->succFPos = -1; } //printf("end pre/succ %i\n", tpos); apos1->predF[s1]=p1; apos1->succF[s1]=p1; apos2->predF[s2]=p2; apos2->succF[s2]=p2; apos1->predF[s2]=p2; apos1->succF[s2]=p2; apos2->predF[s1]=p1; apos2->succF[s1]=p1; if(apos2->eqcRank< apos1->eqcRank) { apos2->eqcParent = apos1; } else { apos1->eqcParent = apos2; if(apos2->eqcRank==apos1->eqcRank) apos2->eqcRank++; } //printf("end ranking %i, %i %i\n", s1,p1,apos1->predF); apos1 = find_eqc(ap, s1,p1);//&(ap[s1][p1]); //printf("end first egc %i\n", tpos); apos2 = find_eqc(ap, s2,p2); //&(ap[s2][p2]); //printf("end second egc %i\n", tpos); // update the other affected sites for(ms=0;mspredF[ms]==apos1->succF[ms]) { p = apos1->predF[ms]; // -( (apos1->predF[ms]==apos1->succF[ms]) ? 1 : 0); // GOGOGOGO opos=apos1->predF[ms]; // printf("SUPERPRE WHILE %i %i %i\n",k,s1,s2); tp = ap[ms]; //printf("PRE WHILE %i\n",k); seenNonOrphane=0; found = 1; //firstRound = 1; //firstpos = 0; while( (p>=0)&& found) { // && tp[p].isOrphane) { //printf(" WHILE %i\n",p); if(tp[p].state & para->STATE_ORPHANE) { if( (! seenNonOrphane)) { // if(ms==0 && p==0) printf("setting s1=%i p1=%i iso=%i ms=%i p=%i opos=%i\n",s1,p1, tp[p].isOrphane, ms,p,opos); tp[p].succFPos = opos; } else p = tp[p].predFPos+1; } else { if( (p!=opos) || (apos1->succF[ms]!=apos1->predF[ms])) seenNonOrphane = 1; //if(p==442) printf(" pre find %i %i %i\n",s1, ms,p); tpos = find_eqc(ap, ms,p);//&(ap[s1][p1]); //if(p==442)printf(" post find %i %i\n",ms,p); if(! (tpos->state & para->STATE_ORPHANE) && ! (tpos->state & para->STATE_INHERITED)) { //printf(" %i %i %i %i\n",ms,p,s1,p1); if(seenNonOrphane) found = 0; for(s=0;ssuccF[s]>apos1->succF[s]) { tpos->succF[s]=apos1->succF[s]; found = 1; } } /* oldpos = firstpos; s = firstpos; while(ssuccF[s]>apos1->succF[s]) { tpos->succF[s]=apos1->succF[s]; found = 1; oldpos = s; } else { if(! firstRound) { nextpos[oldpos] = nextpos[s]; if(oldpos==firstpos) { firstpos=nextpos[oldpos]; oldpos = firstpos; } } } if(firstRound) { oldpos = s; s++; } else { s = nextpos[s]; } } */ } } //firstRound = 0; p--; } //printf("END WHILE\n"); //printf(" PRE 2 %i %i %i\n", apos1->predF, apos1->succF,ms ); p = apos1->succF[ms]; // +( (apos1->predF[ms]==apos1->succF[ms]) ? 1 : 0); // GOGOGOGO ; opos= apos1->succF[ms]; plen = scol->seqs[ms].length; seenNonOrphane=0; //printf("2. PRE WHILE %i\n",k); // if(opos>=plen) opos = -1; found = 1; while( (pSTATE_ORPHANE) { if( (! seenNonOrphane)) { /* if(p==opos) { printf("ALARM set predFPos s1=%i s2=%i p1=%i p2=%i ms=%i sF=%i pF=%i p=%i opos=%i iso=%i %i %i %i\n", s1,s2,p1,p2,ms, apos1->succF[ms], apos1->predF[ms],p,opos, tp[p].state,(int) &tp[p],(int) apos1, (int) apos2); exit(98); } */ tp[p].predFPos = opos; } else { if(tp[p].succFPos < 0) p = plen+1; else p = tp[p].succFPos-1; } } else { if( (p!=opos)|| (apos1->succF[ms]!=apos1->predF[ms])) seenNonOrphane = 1; //printf(" pre find %i %i\n",ms,p); tpos = find_eqc(ap, ms,p);//&(ap[s1][p1]); //printf(" end find\n"); if(! (tpos->state & para->STATE_ORPHANE) && !(tpos->state & para->STATE_INHERITED)) { if(seenNonOrphane) found = 0; for(s=0;spredF=%i\n",s,slen,tpos->predF); if( tpos->predF[s]predF[s]) { //printf(" inner before s=%i slen=%i\n",s,slen); tpos->predF[s]=apos1->predF[s]; //printf(" inner after s=%i slen=%i\n",s,slen); found = 1; } } } } p++; } //printf("2. END WHILE %i\n",k); } } } // printf("s1: %i s2: %i\n", algn->seq_is_orphane[s2],s2); algn->seq_is_orphane[s1]=0; algn->seq_is_orphane[s2]=0; int maxposs1 = dg->seq_p1.startpos + dg->length-1; int maxposs2 = dg->seq_p2.startpos + dg->length-1; if(dg->seq_p1.sq->max_seen < maxposs1) dg->seq_p1.sq->max_seen = maxposs1; if(dg->seq_p2.sq->max_seen < maxposs2) dg->seq_p2.sq->max_seen = maxposs2; //if(alignedSomething) { /* if(algn->aligned_diags_amount >= algn->max_aligned_diags_amount) { algn->max_aligned_diags_amount = algn->aligned_diags_amount + 16; algn->aligned_diags = realloc(algn->aligned_diags, sizeof(struct diag*)*algn->max_aligned_diags_amount); if(algn->aligned_diags==NULL) error(" align_diag(): Out of Memory!"); } algn->aligned_diags[algn->aligned_diags_amount++] = dg; */ /* } else { dgc = malloc(sizeof(struct diag_cont)); dgc->dg = dg; dgc->next = NULL; algn->backlog_diags = enter_sorted(algn->backlog_diags, dgc); } */ //printf(" diaglen: %i\n", algn->aligned_diags_amount); if(! dg->anchor) algn->total_weight += dg->weight;//*dg->weight_fac; return(alignedSomething); } /** * * prepares the alignment: calculates the position number of each residue * */ void prepare_alignment(struct alignment *algn) { struct seq_col *scol = algn->scol; unsigned int slen = scol->length; unsigned int i,j,s,ts, hasmore, max; int *predF, *succF; struct seq* sq; struct algn_pos **ap = algn->algn; int tproc[slen]; // char proceed[slen]; for(i=0;iseqs[s]; if(tproc[s]length) { ap1 = find_eqc(ap,s,tproc[s]); *ap1->proceed = 1; } } for(s=0;sseqs[s]; if(tproc[s]length) { //printf(" DO IT %i %i %i %i\n",j,s,tproc[s], *ap1->eqcAlgnPos); ap1 = find_eqc(ap,s,tproc[s]); // printf("alig.c ap1 = %d\tap = %d\n",ap1,ap); if(j>=*ap1->eqcAlgnPos) { predF = ap1->predF; succF = ap1->succF; *ap1->eqcAlgnPos=j;// *tap1->eqcAlgnPos; if(predF!=NULL) { for(ts=0;tseqcAlgnPos=j+1;// *tap1->eqcAlgnPos; //printf(" 2. MIST %i %i %i %i %i %i %i\n",j,s,ts,tproc[s], tproc[ts], predF[ts], succF!=NULL ? succF[ts]: 99999); *ap1->proceed = 0; break; } else { /* *ap1->eqcAlgnPos=j;// *tap1->eqcAlgnPos; *ap1->proceed = 1; */ } } } } else { *ap1->proceed = 0; } /* if(j>=143) { printf("ALARM j=%i s=%i tproc[s]=%i algnPos=%i\n",j,s,tproc[s],*ap[s][tproc[s]].eqcAlgnPos); } */ } } alarmHasProceed=0; for(s=0;sseqs[s]; if(tproc[s]length) { ap1 = find_eqc(ap,s,tproc[s]); if(*ap1->proceed) { alarmHasProceed = 1; tproc[s]++; } } if(tproc[s]length) hasmore = 1; //printf("%i %i\n", sq->length,tproc[s]); } if(! alarmHasProceed && hasmore) { printf("IO ALARM! %i\n",j); exit(1); hasmore=0; } if(!hasmore) max = j+1; } algn->max_pos= max; } abyss-1.3.6/dialign/assemble.c000644 002433 001057 00000112327 11746352100 017732 0ustar00traymondassembly000000 000000 #include #include #include #include #include #include #include "parameters.h" #include "struct.h" extern void error(char *message); extern void merror(char *msg1, char *msg2); extern inline void calc_weight(struct diag* dg, struct scr_matrix* smatrix, struct prob_dist *pdist); extern inline void calc_ov_weight(struct diag* dg, struct diag_col *dcol, struct scr_matrix* smatrix, struct prob_dist *pdist); //extern struct seq_part* create_seq_part(int num, struct seq* aSeq, unsigned int startpos); extern long double** create_tmp_pdist(struct prob_dist *pdist); extern void free_tmp_pdist(long double **dist, int length); extern struct diag* create_diag(int n1, struct seq* sq1, unsigned int sp1, int n2, struct seq* sq2, unsigned int sp2, int dlength); extern void free_diag(struct diag* dg); extern inline struct simple_diag_col* find_diags_guided(struct scr_matrix *smatrix, struct prob_dist *pdist, struct gt_node* n1, struct gt_node* n2, struct alignment *algn, double thres_weight, int *** diag_info); extern struct alignment* create_empty_alignment(struct seq_col *scol); extern void free_alignment(struct alignment *algn); extern inline struct algn_pos *find_eqc(struct algn_pos **ap, int seqnum, int pos); extern struct alignment* copy_alignment( struct alignment *o_algn, struct alignment *algn, char doDgc); //extern char adapt_diag(struct alignment *algn, struct scr_matrix *smatrix, struct diag* dg); extern inline char align_diag(struct alignment *algn, struct scr_matrix *smatrix, struct diag* dg); //extern inline struct diag_cont* enter_sorted(struct diag_cont* backlog_diags, struct diag_cont *cand); //extern inline char fit_fpos_diag(struct alignment *algn, struct diag* dg); //extern unsigned long allocss; //extern unsigned long freess; /** * * assemble.c: assembles the alignment from the diagonals * */ //double tim = 0; /** * enters the candidate in a sorted way to the list and returns pointer to the first element */ inline struct diag_cont* enter_sorted(struct diag_cont* backlog_diags, struct diag_cont *cand) { if(backlog_diags==NULL) { cand->next=NULL; return cand; } struct diag_cont *prev = backlog_diags; struct diag_cont *actual = backlog_diags; //printf(" before %f %i\n", cand->dg->total_weight, backlog_diags->dg); // if( (cand==backlog_diags) || (backlog_diags->next==cand)) error(" enter_sorted(): critical error"); if((cand->dg->total_weight >= backlog_diags->dg->total_weight)) { cand->next = backlog_diags; return cand; } while( (actual!=NULL) && (cand->dg->total_weight < actual->dg->total_weight)) { prev = actual; actual = actual->next; } prev->next = cand; cand->next = actual; //printf(" after\n"); return backlog_diags; } /** * returns whether the given first position of the diag fits intho the given alignment */ inline char fit_fpos_diag(struct alignment *algn, struct diag* dg) { unsigned int s1 = dg->seq_p1.num; unsigned int s2 = dg->seq_p2.num; char o1 = algn->seq_is_orphane[s1]; char o2 = algn->seq_is_orphane[s2]; // if any sequence is orphane the diag is always consistent if( o1 || o2) return 1; int sp1 = dg->seq_p1.startpos; int sp2 = dg->seq_p2.startpos; int ep1 = sp1+dg->length-1; int ep2 = sp2+dg->length-1; struct algn_pos **ap=algn->algn; int predF, succF; struct algn_pos *tap; tap = find_eqc(ap, s1, sp1); if(tap->predF!=NULL) { //&& tap->succF!=NULL) { predF = tap->predF[s2]; } else { predF=-1; } if(tap->succF!=NULL) { succF = tap->succF[s2]; } else { succF = ep2+1; } if( ( (predF>=sp2)|| (succF<=sp2) ) && !(predF==sp2 && succF==sp2)) { //printf(" leave fit_fpos 0 \n"); return 0; } else { // printf(" leave fit_fpos 1 \n"); return 1; } } /** * changes the startpos's and length of the diag such that * it becomes consistent with the given alignment. If the diag * has more than one part that is consistent the leftmost will be chosen * The return value is 1 if any changes were made otherwise 0. * (The weight of the diag is not recalculated !). * */ char adapt_diag(struct alignment *algn, struct scr_matrix *smatrix, struct diag* dg) { //char adapt_diag(struct alignment *algn, struct diag* dg) { //printf(" ENTER adapt\n"); if(dg->multi_dg) { char adapted = 0; int i; for(i=0;imulti_length;i++) { if(dg->multi_cont[i]!=NULL) { if(dg->multi_cont[i]->length > 0) { //printf(" adapted before %i %i\n", adapted, dg->multi_cont[i]->length); adapted = adapted || adapt_diag(algn, smatrix, dg->multi_cont[i]); /* if(dg->multi_cont[i]->length == 0) { dg->multi_cont[i]->meetsThreshold = 0; }*/ //printf(" adapted after %i %i\n", adapted, dg->multi_cont[i]->length); } if(dg->multi_cont[i]->length==0) { free(dg->multi_cont[i]); dg->multi_cont[i]=NULL; } } } return adapted; } unsigned int s1 = dg->seq_p1.num; unsigned int s2 = dg->seq_p2.num; char o1 = algn->seq_is_orphane[s1]; char o2 = algn->seq_is_orphane[s2]; // if any sequence is orphane the diag is always consistent if( o1 || o2) return 0; int sp1 = dg->seq_p1.startpos; int sp2 = dg->seq_p2.startpos; int ep1 = sp1+dg->length-1; int ep2 = sp2+dg->length-1; struct algn_pos **ap=algn->algn; int predF, succF; int rlen; // cut off the beginning of the diag struct algn_pos *tap;// = find_eqc(ap, s1, sp1); sp1--; sp2--; // jump to a consistent position //char included = 1; do { sp1++; sp2++; if(sp1<=ep1) { tap = find_eqc(ap, s1, sp1); if(tap->predF!=NULL) { //&& tap->succF!=NULL) { predF = tap->predF[s2]; } else { predF=-1; } if(tap->succF!=NULL) { succF = tap->succF[s2]; } else { succF = ep2+1; } } //if(predF!=sp2 || succF!=sp2) included = 0; } while( ( (predF>=sp2)|| (succF<=sp2) ) && !(predF==sp2 && succF==sp2) && sp1<=ep1); // cutoff low scoring positions at the beginning /* while( (sp1<=ep1)) { a1 = c2n[data1[sp1]]; a2 = c2n[data2[sp2]]; score1 = sdata[smatrixlen*a1+a2]; if(score1length, score1); sp1++; sp2++; } else { break; } } */ // check whether the diagonal has been cut off to zero length if(sp1>ep1) { // printf(" OUT OF RANGE %i %i %i \n",predF, succF, sp2); //if(included) // dg->weight = 0.0; //else // dg->weight = -1.0; dg->length=0; return 1; } // cut off the end of the diag rlen=0; do { rlen++; //printf(" rlen: %i %i %i %i %i\n", ep1, sp1, sp2, dg->length, sp1+rlen-1); if((sp1+rlen-1)>ep1) { break; }else { tap = find_eqc(ap, s1, sp1+rlen-1); //printf(" after rlen: %i\n", rlen); if(tap->predF!=NULL) { predF = tap->predF[s2]; } else { predF=-1; } if(tap->succF!=NULL) { succF = tap->succF[s2]; } else { succF = sp2+rlen; } } } while( ( ((succF>=(sp2+rlen)) && (predF<(sp2+rlen-1))) || ((succF==(sp2+rlen-1)) && (predF==(sp2+rlen-1)))) && ((sp1+rlen-1)<=ep1)); rlen--; // cutoff low scoring positions at the end /* while(rlen>0) { a1 = c2n[data1[sp1+rlen-1]]; a2 = c2n[data2[sp2+rlen-1]]; //printf(" %i %i %i\n", a1, a2,smatrixlen); score1 = sdata[smatrixlen*a1+a2]; break; if(score1length=0; //printf("sp1: %i\n", sp1); return 1; } int oldlen = dg->length; //printf("sp1: %i\n", sp1); dg->length = rlen; dg->seq_p1.startpos=sp1; dg->seq_p2.startpos=sp2; if(oldlen==rlen) { return 0; } return 1; } /** * heapify void heapify_diag_array(struct diag **diags, int pos, int length, int up) { struct diag *dg = diags[pos]; if(up) { if(pos<=3) return; int parent = (pos-1)/2; struct diag *pdg = diags[parent]; if(pdg->total_weighttotal_weight) { diags[parent]=dg; diags[pos] = pdg; // printf("heapify: %i %i %i %i %i\n", pos,parent, length, dg, pdg); heapify_diag_array(diags, parent,length,up); } } else { int lchild = 2*pos+1; if( (lchild)>=length) return; int rchild = lchild+1; //struct diag *dg = diags[pos]; struct diag *ldg = diags[lchild]; struct diag *rdg = (rchild>=length ? ldg : diags[rchild]); int greatest = pos; if(ldg->total_weight > diags[greatest]->total_weight) greatest = lchild; if( (rchildtotal_weight > diags[greatest]->total_weight)) greatest = rchild; if(greatest != pos) { diags[pos] = diags[greatest]; diags[greatest] = dg; heapify_diag_array(diags, greatest,length,up); } } } */ /** * heapify */ void heapify_diag_array(struct diag **diags, int pos, int length, int up) { struct diag *dg = diags[pos]; if(up) { if(pos<=3) return; int parent = (pos-1)/2; struct diag *pdg = diags[parent]; if( (pdg->total_weight*pdg->weight_fac)< (dg->total_weight*dg->weight_fac)) { //if( (pow(pdg->total_weight,2)*pdg->weight_fac)< (pow(dg->total_weight,2)*dg->weight_fac)) { diags[parent]=dg; diags[pos] = pdg; // printf("heapify: %i %i %i %i %i\n", pos,parent, length, dg, pdg); heapify_diag_array(diags, parent,length,up); } } else { int lchild = 2*pos+1; if( (lchild)>=length) return; int rchild = lchild+1; //struct diag *dg = diags[pos]; struct diag *ldg = diags[lchild]; struct diag *rdg = (rchild>=length ? ldg : diags[rchild]); int greatest = pos; if( (ldg->total_weight*ldg->weight_fac) > (diags[greatest]->total_weight * diags[greatest]->weight_fac)) greatest = lchild; //if( (pow(ldg->total_weight,2)*ldg->weight_fac) > (pow(diags[greatest]->total_weight,2) * diags[greatest]->weight_fac)) greatest = lchild; if( (rchildtotal_weight*rdg->weight_fac) > (diags[greatest]->total_weight*diags[greatest]->weight_fac))) greatest = rchild; //if( (rchildtotal_weight,2)*rdg->weight_fac) > (pow(diags[greatest]->total_weight,2) *diags[greatest]->weight_fac))) greatest = rchild; if(greatest != pos) { diags[pos] = diags[greatest]; diags[greatest] = dg; heapify_diag_array(diags, greatest,length,up); } } } /** *------------------------------------------------------------------------------------------ * SIMPLE ALIGNER SECTION *------------------------------------------------------------------------------------------ */ /** * test function that constructs an arbitrary consistent alignment.this function * is used to check the the correctness of adapt_diag() and align_diag() * * Returns whether something new could be aligned */ char simple_aligner(struct seq_col *scol, struct diag_col *dcol, struct scr_matrix* smatrix, struct prob_dist *pdist, struct alignment *algn, int round) { int dlen = dcol->diag_amount; int i; struct diag * dg,*tdg; char changed; char alignedSomething = 0; // compute counter weights // heapify struct diag **diags = dcol->diags; //calloc(dlen, sizeof(struct diag *)); int alloc_dlen = dlen; for(i= (dlen+1)/2-1;i>=0;i--) { heapify_diag_array(diags, i, dlen,0); } //memset(algn->redo_seqs, 0, sizeof(char)*slen*slen); double oldweight=0.0, prevweight; i=0; double total_weight = 0.0; double alig_time = 0.0; double tclock; struct diag tmp_diag; int tmp_end; int offset; struct diag *hookdg; while(dlen>0) { // printf(" dlen %i\n", dlen); dg = diags[0]; //if(dg->score==217) print_diag(dg); changed = 0; // print_diag(dg); // hookdg = NULL; if(dg!=NULL) { if((dg->length>0) && (dg->meetsThreshold || dg->anchor) ) { /* if(oldweight > 0.0) if(dg->weight > oldweight) { //printf(" ALARM %.20f %.20f\n", oldweight, dg->weight); //print_diag(&odg); //print_diag(dg); //intf(" %i %i \n", odg, dg); } */ //odg = *dg; //printf(" pre changed\n"); prevweight = dg->weight; tmp_diag = *dg; changed= adapt_diag(algn,smatrix, dg); //changed= adapt_diag(algn,NULL, dg); //print_diag(dg); //printf(" after changed %i\n", dg->length); //if(dg!=NULL) printf(" diag %i %i %i %i %.20f %i %i\n", dg, dg->multi_dg, dg->length, dg->meetsThreshold,dg->weight, dg->multi_length,changed); if(changed) { //printf("\nCHANGED\n"); //print_diag(dg); //printf(" pre recalc\n"); calc_weight(dg, smatrix, pdist); if(dg->anchor) { *dg = tmp_diag; } if( (dg->length > 0) && !(dg->anchor)) { tmp_end = tmp_diag.seq_p1.startpos+tmp_diag.length-1; if( ((dg->seq_p1.startpos+dg->length-1)< tmp_end) && !(dg->multi_dg)) { offset = dg->seq_p1.startpos+dg->length-tmp_diag.seq_p1.startpos; tmp_diag.seq_p1.startpos += offset; tmp_diag.seq_p2.startpos += offset; tmp_diag.length -= offset; adapt_diag(algn,smatrix, &tmp_diag); tmp_diag.length = tmp_end - tmp_diag.seq_p1.startpos+1; calc_weight(&tmp_diag, smatrix, pdist); if((tmp_diag.length>0)&& tmp_diag.meetsThreshold) { hookdg = malloc(sizeof(struct diag)); *hookdg = tmp_diag; hookdg->marked = 1; dcol->diag_amount++; if(dcol->diag_amount>alloc_dlen) { //printf("\n\n\nresize %i %i\n\n\n", dlen, alloc_dlen); alloc_dlen += 8; dcol->diags = (diags = realloc(diags, sizeof(struct diag*)*alloc_dlen)); if(diags==NULL) error("Error increasing diag heap durign aligning."); } //print_diag(hookdg); //printf("dlen %i damount %i %i\n", dlen, dcol->diag_amount, hookdg); //free(diags[dcol->diag_amount-1]); dlen++; diags[dcol->diag_amount-1] = diags[dlen-1]; diags[dlen-1]=hookdg; if(dlen>=2) { //printf("heapify: %i\n", dlen-1); heapify_diag_array(diags,dlen-1,dlen,1); } //print_diag(hookdg); } } } else { dg->meetsThreshold=0; } //printf(" \nafter recalc %i %.20f %.20f\n",dg->length, oldweight, dg->weight); //printf("%.20f %.20f\n", oldweight, dg->weight); //if(dg->weightmeetsThreshold = 0; // TODO: reactivate !!! //(dg->weightweight>oldweight) printf(" WEIGHT %e %e\n", dg->weight, oldweight); //algn->redo_seqs[dg->seq_p1.num*slen+dg->seq_p2.num] = 1; //algn->redo_seqs[dg->seq_p2.num*slen+dg->seq_p1.num] = 1; // DELETE THIS: //dg->meetsThreshold = 0; //if(para->DO_OVERLAP) calc_ov_weight(dg, dcol, smatrix, pdist); } else { //printf(" Pre align\n"); //print_diag(dg); if(para->DEBUG >1) tclock = clock(); //if(dg->anchor) printf(" ANCHOR %.20f %.20f\n", dg->weight, dg->total_weight); alignedSomething = align_diag(algn, smatrix, dg) || alignedSomething; if(para->DEBUG >1) alig_time += clock()-tclock; if(para->DEBUG >1) total_weight += dg->total_weight; //printf(" After align\n"); //if(para->DEBUG >2) printf(" aligned diag %i %e\n", i, dg->weight); //dg->length = 0; //dg->weight = 0.0; dg->meetsThreshold = 0; } } else { // printf("ALARM %i %i %Le\n", i, dg->length, dg->weight); oldweight = dg->weight; } } if((dg==NULL) || (!dg->meetsThreshold)) { tdg = diags[dlen-1]; diags[dlen-1]=dg; diags[0] = tdg; dlen--; } heapify_diag_array(diags, 0, dlen,0); } // if(para->DEBUG >1) printf(" Total Weight: %.20f (total %f) with pure alignment time %f \n", total_weight, algn->total_weight, alig_time/CLOCKS_PER_SEC); if(para->DEBUG >1) printf(" Total Weight: %.20f with pure alignment time %f \n", total_weight, alig_time/CLOCKS_PER_SEC); // return algn; return alignedSomething; } /** *------------------------------------------------------------------------------------------ * COMPLEX ALIGNER SECTION *------------------------------------------------------------------------------------------ */ /** * returns a value >0 if the given diags are in conflict within the given alignment * returns a value <0 if there is an non-conflicting overlap * returns 0 in all other non-conflicting cases */ static char confl_diag(struct alignment *algn, char *layer, struct diag *dg1, struct diag *dg2) { // if(dg1->multi_dg || dg2->multi_dg) error(" confl_diag(): cannot accept multi dgs!"); int s1_1 = dg1->seq_p1.num; int s1_2 = dg1->seq_p2.num; int s2_1 = dg2->seq_p1.num; int s2_2 = dg2->seq_p2.num; int ts; int sp1_1 = dg1->seq_p1.startpos; int sp1_2 = dg1->seq_p2.startpos; int sp2_1 = dg2->seq_p1.startpos; int sp2_2 = dg2->seq_p2.startpos; int tsp; int sl1_1 = dg1->seq_p1.sq->length; int sl1_2 = dg1->seq_p2.sq->length; int sl2_1 = dg2->seq_p1.sq->length; int sl2_2 = dg2->seq_p2.sq->length; int tsl; struct algn_pos* ap1_1; struct algn_pos* ap1_2; struct algn_pos* ap2_1; struct algn_pos* ap2_2; int p1_1, p1_2, p2_1, p2_2; int off1, off2; int l1 = dg1->length; int l2 = dg2->length; int pF1, pF2, sF1, sF2; int opF1, opF2, osF1, osF2; int pos2[4]; int lpos2 = 0; int ret = 0; signed char ucmp,lcmp; //l1=1;l2=1; /* int step1 = (l1>10) ? 3 : 1; int step2 = (l2>10) ? 3 : 1;; if(step1==0) step1 = 1; if(step2==0) step2 = 1; */ if(layer[dg1->seq_p1.num]!=1) { ts = s1_2; s1_2 = s1_1; s1_1 = ts; tsl = sl1_2; sl1_2 = sl1_1; sl1_1 = tsl; tsp = sp1_2; sp1_2 = sp1_1; sp1_1 = tsp; } if(layer[dg2->seq_p1.num]!=1) { ts = s2_2; s2_2 = s2_1; s2_1 = ts; tsl = sl2_2; sl2_2 = sl2_1; sl2_1 = tsl; tsp = sp2_2; sp2_2 = sp2_1; sp2_1 = tsp; } // if one is included in the other we define it as a conflict //if( (s1_1==s2_1) && (s1_2==s2_2)) { // //} opF1 = -1; osF1 = sl2_1; opF2 = -1; osF2 = sl2_2; for(off1=0;off1seq_p1.startpos+off1; p1_2 = sp1_2; // dg1->seq_p2.startpos+off1; ap1_1 = find_eqc(algn->algn, s1_1, p1_1); ap1_2 = find_eqc(algn->algn, s1_2, p1_2); // calculate the positions in dg2 that have to be considered for conflicts if(ap1_1->predF!=NULL) { pF1 = ap1_1->predF[s2_1]; } else { pF1 = opF1; } if(ap1_1->succF!=NULL) { sF1 = ap1_1->succF[s2_1]; } else { sF1 = osF1; } if(ap1_2->predF!=NULL) { pF2 = ap1_2->predF[s2_2]; } else { pF2 = opF2; } if(ap1_2->succF!=NULL) { sF1 = ap1_2->succF[s2_2]; } else { sF2 = osF2; } /* //if(ret==0) if( (pF1>=sp2_1) && (pF1!=opF1) && (pF1=sp2_1) && (sF1!=osF1)&& (sF1=sp2_2) && (pF2!=opF2) && (pF2=sp2_2) && (sF2!=osF2)&& (sF2= sp2_1+l2) { pF1 = sp2_1+l2-1; off1 = l1; } if(sF1 < sp2_1) { sF1 = sp2_1; off1 = l1; } if(sF1 >= sp2_1+l2) { sF1 = sp2_1+l2-1; } if(pF2 < sp2_2) { pF2 = sp2_2; } if(pF2 >= sp2_2+l2) { pF2 = sp2_2+l2-1; off1 = l1; } if(sF2 < sp2_2) { sF2 = sp2_2; off1 = l1; } if(sF2 >= sp2_2+l2) { sF2 = sp2_2+l2-1; } lpos2 = 0; if((pF1!=opF1)) { pos2[lpos2++] = pF1-sp2_1; } if((pF2!=opF2)) { pos2[lpos2++] = pF2-sp2_2; } if((sF1!=osF1)) { pos2[lpos2++] = sF1-sp2_1; } if((sF2!=opF2)) { pos2[lpos2++] = sF2-sp2_2; } opF1 = pF1; opF2 = pF2; osF1 = sF1; osF2 = sF2; //for(off2=0;off2algn, s2_1, p2_1); ap2_2 = find_eqc(algn->algn, s2_2, p2_2); ucmp = -1; lcmp = -1; // upper compare if(s1_1==s2_1) { if(p1_1 == p2_1) ucmp = 0; if(p1_1 < p2_1) ucmp = 1; if(p1_1 > p2_1) ucmp = 2; } else if( (ap1_1->succF!=NULL) && (ap1_1->predF!=NULL) && (ap1_1->succF[s2_1]==ap1_1->predF[s2_1]) && (ap1_1->predF[s2_1]==p2_1)) { ucmp = 0; } else if( ( (ap1_1->succF!=NULL) && ( ap1_1->succF[s2_1]<=p2_1))) { ucmp = 1; } else if( ( (ap1_1->predF!=NULL) && ( ap1_1->predF[s2_1]>=p2_1))) { ucmp = 2; } // lower compare if(s1_2==s2_2) { if(p1_2 == p2_2) lcmp = 0; if(p1_2 < p2_2) lcmp = 1; if(p1_2 > p2_2) lcmp = 2; } else if( (ap1_2->succF!=NULL) && (ap1_2->predF!=NULL) && (ap1_2->succF[s2_2]==ap1_2->predF[s2_2]) && (ap1_2->predF[s2_2]==p2_2)) { lcmp = 0; } else if( ( (ap1_2->succF!=NULL) && ( ap1_2->succF[s2_2]<=p2_2))) { lcmp = 1; } else if( ( (ap1_2->predF!=NULL) && ( ap1_2->predF[s2_2]>=p2_2))) { lcmp = 2; } if( (ucmp>=0) && (lcmp>=0)) { if(ucmp!=lcmp) return 1; } } } /* ret = -ret; if((ret<=l1*0.1)&&(ret<=l2*0.1)) { return 0; } else { return -1; } */ return ret; } /** * determine the best diags that fit into the alignment struct simple_diag_col *determine_diags((struct alignment *algn, struct seq_col *scol, struct scr_matrix *smatrix, struct prob_dist *pdist, char *layer, struct diag **diags, int diag_amount) { struct simple_diag_col scol; // TODO return scol; } */ /** * guided aligner recursion * * doHigher: >0 - only higher and equal than threshold weight * doHigher: 0 - only lower than threshold weight */ struct alignment* guided_aligner_rec(struct alignment *palgn, struct seq_col *scol, struct diag_col *dcol, struct scr_matrix* smatrix, struct prob_dist *pdist, struct gt_node *gtn, double thres_weight, char doHigher, int round) { if(palgn==NULL) { palgn = create_empty_alignment(scol); } // recursion as per the guide tree if(gtn->isLeaf) return palgn; palgn = guided_aligner_rec(palgn,scol,dcol,smatrix,pdist, gtn->succ1, thres_weight,doHigher,round); palgn = guided_aligner_rec(palgn,scol,dcol,smatrix,pdist, gtn->succ2, thres_weight,doHigher,round); // now align the fragments that are between succ1 and succ2 of gtn int scol_len = scol->length; struct diag *dg, *tdg, *sdg, *stdg; int i,j,si,sj,k,l, l1,l2; struct gt_node *n1, *n2; n1 = gtn->succ1; n2 = gtn->succ2; int diag_amount = dcol->diag_amount;//n1->seq_num_length + n2->seq_num_length; double multi_weight_fac = 0.0; int diag_p=0; struct diag **all_diags = malloc(sizeof( struct diag*)*diag_amount); //struct diag *looser_diags[diag_amount]; int diag_l=0; struct simple_diag_col *sdcol; //char crossing[scol_len*scol_len]; char changed; char layer[scol_len]; // memset(crossing, 0, sizeof(char)*scol_len*scol_len); memset(layer, 0, sizeof(char)*scol_len); for(i=0;iseq_num_length;i++) { si = n1->seq_num[i]; layer[si]=1; for(j=0;jseq_num_length;j++) { sj = n2->seq_num[j]; if(i==0) layer[sj]=2; //printf(" %i %i %i %i\n", i,j,si,sj); //crossing[si*scol_len+sj] = 1; //crossing[sj*scol_len+si] = 1; if(sj>si) { sdcol = dcol->diag_matrix[scol_len*si+sj]; } else { sdcol = dcol->diag_matrix[scol_len*sj+si]; } multi_weight_fac += pow(sdcol->weight_fac,0.5); for(k=0;klength;k++) { dg = (sdcol->data[k]); //changed = adapt_diag(palgn, smatrix, dg); //if(changed) { //calc_weight(dg, smatrix, pdist); //} if(dg->meetsThreshold) { if(doHigher>0) { if((dg->total_weight) >= thres_weight) { all_diags[diag_p++] = dg; } } else { if((dg->total_weight) < thres_weight) { all_diags[diag_p++] = dg; } } } } } } multi_weight_fac = pow(multi_weight_fac/((double)n1->seq_num_length*n2->seq_num_length),2.0); struct diag_col tdcol; int survive; /* tdcol.diags = all_diags; tdcol.diag_amount = diag_p; simple_aligner(scol, &tdcol, smatrix, pdist, palgn, 0); return palgn; */ /* struct simple_diag_col ssdcol = split_diags(palgn, scol, smatrix, pdist, all_diags, diag_p); struct diag **sall_diags = ssdcol.data; int sdiag_p = ssdcol.length; printf(" diags split before:%i after:%i\n", diag_p, sdiag_p); */ int sdiag_p = diag_p; struct diag **sall_diags = all_diags; // if both successor nodes are leaf align directly if(n1->isLeaf && n2->isLeaf) { tdcol.diags = all_diags; tdcol.diag_amount = diag_p; //printf(" before inner rec %i %i %i\n",all_diags,diag_p,diag_amount); simple_aligner(scol, &tdcol, smatrix, pdist, palgn, 0); //printf(" after inner rec %i\n",all_diags); free(all_diags); //printf(" after inner rec\n"); return palgn; } //if( (n1->seq_num_length > 1) && (n2->seq_num_length > 1)) { // OMIT for the time being /* if( ((n1->seq_num_length>1) || (n2->seq_num_length>1)) && ((n1->seq_num_length*n2->seq_num_length)>=4.0) && ((n1->seq_num_length > sqrt(scol->length)) || (n2->seq_num_length > sqrt(scol->length)))) { int ***diag_info; diag_info = malloc(sizeof(int **)*n1->seq_num_length); for(i=0;iseq_num_length;i++) { diag_info[i] = malloc(sizeof(int *)*n2->seq_num_length); } struct seq *seq1, *seq2; int maxk; for(i=0;iseq_num_length;i++) { si = n1->seq_num[i]; for(j=0;jseq_num_length;j++) { sj = n2->seq_num[j]; seq1 = &(scol->seqs[si]); seq2 = &(scol->seqs[sj]); // prepare diag info diag_info[i][j] = malloc(sizeof(int)*seq1->length); for(k=0;klength;k++) { diag_info[i][j][k] = -1; } if(sj>si) { sdcol = dcol->diag_matrix[scol_len*si+sj]; } else { sdcol = dcol->diag_matrix[scol_len*sj+si]; } for(k=0;klength;k++) { dg = (sdcol->data[k]); if(dg->meetsThreshold) { for(l=0;llength;l++) { if( (dg->weight >= thres_weight)) { if(dg->seq_p1.num==si) { //printf(" 1) %i %i %i\n",dg->seq_p1.startpos+l, dg->length, seq1->length); diag_info[i][j][dg->seq_p1.startpos+l] = dg->seq_p2.startpos+l; } else { //printf(" 2) %i %i %i \n",dg->seq_p2.startpos+l,dg->length, seq1->length); diag_info[i][j][dg->seq_p2.startpos+l] = dg->seq_p1.startpos+l; } } } } } } } //printf(" before guided diags\n"); struct simple_diag_col *mscol = find_diags_guided(smatrix, pdist,n1, n2, palgn, thres_weight, diag_info); //printf(" after guided diags\n"); for(i=0;iseq_num_length;i++) { si = n1->seq_num[i]; for(j=0;jseq_num_length;j++) { sj = n2->seq_num[j]; free(diag_info[i][j]); // free_tmp_pdist(tmp_dist[sj][si], pdist->max_dlen); } free(diag_info[i]); } free(diag_info); diag_amount += mscol->length; all_diags = realloc(all_diags, sizeof( struct diag*)*diag_amount); sall_diags = all_diags; for(i=0;ilength;i++) { //printf(" multi dg %i %i %.20f\n", mscol->length,mscol->data[i], mscol->data[i]->weight); //survive = 1; dg = mscol->data[i]; survive = 0; dg->weight = 0.0; for(j=0;jmulti_length;j++) { if( (dg->multi_cont[j]!=NULL) && (dg->multi_cont[j]->weight >= thres_weight)) { survive++; dg->weight += dg->multi_cont[j]->weight; } else { free_diag(dg->multi_cont[j]); dg->multi_cont[j]=NULL; } } dg->total_weight = dg->weight; if(survive>1) { sall_diags[sdiag_p++] = mscol->data[i]; mscol->data[i]->weight_fac = multi_weight_fac; mscol->data[i]->pred_diag = NULL; } else { free_diag(mscol->data[i]); } } // free data free(mscol->data); free(mscol); } if(para->DEBUG>1) printf(" Found %i relevant multi diags\n", sdiag_p - diag_p); */ diag_p = sdiag_p; struct diag **looser_diags = malloc(sizeof( struct diag*)*diag_amount); /* // sort diags for(i=0;itotal_weight*dg->weight_fac) > (dg->total_weight*dg->weight_fac)) { if( (tdg->total_weight) > (dg->total_weight)) { sall_diags[i] = tdg; sall_diags[j]= dg; } } } // align the good diags first diag_l=0; for(i=0;iDEBUG>2) printf(" BEGIN: calc conflict of #diags: %i\n", sdiag_p); // build vertex cover graph char confl; int multilen1; int multipos1; int multilen2; int multipos2; char multi1, multi2; for(i=0;iweight_fac = 1.0; dg->weight_sum = dg->total_weight;//*dg->weight_fac; multilen1 = 1; multipos1 = 0; multi1 = dg->multi_dg; if(multi1) multilen1 = dg->multi_length; //dg->weight_sum = dg->total_weight; //printf(" degree %i\n", dg->degree); sdg = dg; while(multipos1multi_cont[multipos1]; if(dg!=NULL) { for(j=i+1;jmulti_dg; if(multi2) multilen2 = tdg->multi_length; stdg = tdg; while(multipos2multi_cont[multipos2]; if(tdg!=NULL) { confl = confl_diag(palgn, layer, dg, tdg) ; if( (confl>0) ) { //printf(" conflict %i %i !\n",i,j); sdg->degree++; if(sdg->degree > sdg->max_degree) { sdg->max_degree += 64; sdg->neighbours = realloc(sdg->neighbours, sizeof(struct diag *)*sdg->max_degree); } sdg->neighbours[sdg->degree - 1] = stdg; stdg->degree++; if(stdg->degree > stdg->max_degree) { stdg->max_degree += 64; stdg->neighbours = realloc(stdg->neighbours, sizeof(struct diag *)*stdg->max_degree); } stdg->neighbours[stdg->degree - 1] = sdg; //printf(" CONFLICT FOUND %i %i!\n", i,j); } } multipos2++; } } } multipos1++; } } // if(para->DEBUG>2) printf(" END: calc conflict of #diags: %i\n", sdiag_p); // perform clarkson vertex cover int max_n; double max_d; double t_d; while(1) { max_n = -1; max_d = -1.0; for(i=0;idegree); //printf(" before %i %i %i\n",i,sdiag_p,dg); //printf(" degree %i\n", dg->degree); //printf(" after\n"); if(dg->degree > 0) { t_d = dg->degree / dg->weight_sum; if((max_dmulti_dg, dg->total_weight); //printf(" 0sall[0] %i \n",sall_diags[0]); //i=11; //printf(" 00sall[0] %i \n",sall_diags[0]); for(i=0; i < dg->degree; i++) { //printf(" 1sall[0] %i i=%i\n",sall_diags[0],i); //printf(" %i %i\n",i,dg->degree); dg->neighbours[i]->weight_sum -= max_d; tdg = dg->neighbours[i]; //printf(" before loop %i %i\n",i,dg->degree); for(j=0;jdegree;j++) { if(tdg->neighbours[j]==dg) { //printf(" MATCH \n"); tdg->neighbours[j]=tdg->neighbours[tdg->degree-1]; tdg->degree--; j=tdg->degree;//break; } } //printf(" 2sall[0] %i\n",sall_diags[0]); } free(dg->neighbours); dg->neighbours=NULL; dg->degree = 0; dg->max_degree=0; } /* struct algn_pos *ap1 = find_eqc(palgn->algn,4,19); if(ap1->predF!=NULL)printf(" 4-19 predF-0 %i\n", ap1->predF[0]); ap1 = find_eqc(palgn->algn,0,4); if(ap1->succF!=NULL)printf(" 0-4 succF-4 %i\n", ap1->succF[4]); */ //if( (sdiag_p>60) && (sall_diags[60]!=NULL)) sall_diags[0]=sall_diags[60]; /* if((sdiag_p>60) && (sall_diags[60]!=NULL) && (sall_diags[52]!=NULL)) { printf(" conflict pre %i\n", confl_diag(palgn, layer, sall_diags[52], sall_diags[60])); } */ /* for(i=0;iseq_p1.num, dg->seq_p1.startpos, dg->length); //printf(" b) %i %i %i\n\n", dg->seq_p2.num, dg->seq_p2.startpos, dg->length); //rdg = *dg; //printf(" before adapt %i %i\n", i, sdiag_p); changed = adapt_diag(palgn, smatrix, dg); //printf(" after adapt %i %i %i %i %i\n", changed, i, sdiag_p, rdg.length,dg->length); if(changed) { calc_weight(dg, smatrix, pdist); looser_diags[diag_l++] = dg; } else { //if(dg->meetsThreshold) { align_diag(palgn, smatrix, dg); //} dg->meetsThreshold = 0; } if(dg->neighbours!=NULL) { free(dg->neighbours); dg->neighbours = NULL; } } else { } } */ // align the winners first tdcol.diags = all_diags; tdcol.diag_amount = 0; for(i=0;imulti_dg, sall_diags[i]->total_weight); all_diags[tdcol.diag_amount++] = sall_diags[i]; } } simple_aligner(scol, &tdcol, smatrix, pdist, palgn, 0); all_diags = tdcol.diags; for(i=0;imarked ) { //printf(" free %i %i %i\n", all_diags[i], all_diags[i]->multi_dg, looser_diags[0]); free_diag(all_diags[i]); //printf(" free end%i\n", all_diags[i]); } else { if(all_diags[i]->neighbours!=NULL) { free(all_diags[i]->neighbours); all_diags[i]->neighbours=NULL; } all_diags[i]->meetsThreshold = 0; } } // align the loosers afterwards tdcol.diags = looser_diags; tdcol.diag_amount = diag_l; simple_aligner(scol, &tdcol, smatrix, pdist, palgn, 0); looser_diags = tdcol.diags; for(i=0;imarked ) { //printf(" lfree %i %i %i %i %i %i\n", i, diag_l, tdcol.diag_amount, looser_diags[i], all_diags[i]->multi_dg, looser_diags[0]); free_diag(looser_diags[i]); //printf(" lfree end%i\n", all_diags[i]); } else { if(looser_diags[i]->neighbours!=NULL) { free(looser_diags[i]->neighbours); looser_diags[i]->neighbours=NULL; } looser_diags[i]->meetsThreshold = 0; } } //printf("-----------------END GUIDED ALIGNER RECURSION STEP-------------------\n"); // TODO: free/remove used diags //free(sall_diags); free(all_diags); free(looser_diags); return palgn; } /** * guided aligner method * NOTE: all diags are freeded within this routine */ struct alignment* guided_aligner(struct alignment *palgn, struct seq_col *scol, struct diag_col *dcol, struct scr_matrix* smatrix, struct prob_dist *pdist, struct gt_node *gtn, int round) { struct diag **all_diags = dcol->diags; int diag_p = dcol->diag_amount; struct diag *dg, *tdg; int i,j,k; /* // sort diags for(i=0;itotal_weight*dg->weight_fac) > (dg->total_weight*dg->weight_fac)) { if( (tdg->total_weight) > (dg->total_weight)) { all_diags[i] = tdg; all_diags[j]= dg; } } } */ int slen = scol->length; double tavg, ttavg; double avg_weight = 0.0; struct simple_diag_col *sdcol; int tsdlen=0; ttavg = 0; for(i=0;idiag_matrix[slen*i+j]; for(k=0; klength; k++) { tavg +=sdcol->data[k]->total_weight; ttavg += sdcol->data[k]->total_weight; tsdlen++; } if(sdcol->length >0) { tavg = (tavg/sdcol->length); } /* tavg = 0.0; tsdlen = 0; for(k=0; klength; k++) { if(sdcol->data[k]->total_weight >= ttavg) { tavg +=sdcol->data[k]->total_weight; tsdlen++; } } tavg = tavg / tsdlen; */ avg_weight += tavg; } } avg_weight = avg_weight/ (slen*(slen-1)/2.0); double thres_weight = ttavg/tsdlen;//1.0*avg_weight; //all_diags[ 0]->total_weight*0.05; palgn = guided_aligner_rec(palgn,scol,dcol,smatrix,pdist,gtn,thres_weight,1,round); //palgn = guided_aligner_rec(palgn,scol,dcol,smatrix,pdist,gtn,thres_weight,0,round); //printf(" intermediate alignment weight %f %f\n",palgn->total_weight, thres_weight); struct diag_col tdcol; struct diag **sall_diags = malloc(sizeof(struct diag*)*diag_p); int sdiag_p=0; for(i=0;imeetsThreshold && (all_diags[i]->total_weight < thres_weight)) { sall_diags[sdiag_p++] = all_diags[i]; } else { free(all_diags[i]); } } tdcol.diags = sall_diags; tdcol.diag_amount = sdiag_p; simple_aligner(scol, &tdcol, smatrix, pdist, palgn, 0); sall_diags = tdcol.diags; for(i=0;idiag_amount = diag_p; return palgn; } abyss-1.3.6/dialign/diag.c000644 002433 001057 00000162311 12104572373 017046 0ustar00traymondassembly000000 000000 #include #include #include #include #include #include #include "parameters.h" #include "struct.h" #include "io.h" extern void error(char *message); extern void merror(char *msg1, char *msg2); extern struct algn_pos *find_eqc(struct algn_pos **ap, int seqnum, int pos); extern void prepare_alignment(struct alignment *algn); /** * * diag.c: Creation of diagonals & calculation of scores and weights * */ /** * factory method that creates a diagonal from the given sequence parts * * The pointer returned has to be deallocted explicitely from memory. */ struct diag* create_diag(int n1, struct seq* sq1, unsigned int sp1, int n2, struct seq* sq2, unsigned int sp2, int dlength) { struct diag* dg = malloc(sizeof(struct diag)); if(dg==NULL) error("create_diag(): Out of Memory !"); if(sq1->length < sp1+dlength) { printf(" startpos=%i diaglength=%i seqlength=%i\n",sp1,dlength,sq1->length); merror("create_diag(): startpos+diaglength exceeds sequence length in diag ", sq1->name); } if(sq2->length < sp2+dlength) { printf(" startpos=%i diaglength=%i seqlength=%i\n",sp2,dlength,sq2->length); merror("create_diag(): startpos+diaglength exceeds sequence length in diag ", sq2->name); } dg->seq_p1.num = n1; dg->seq_p1.sq = sq1; dg->seq_p1.startpos = sp1; //dg->seq_p1.leftmargin = sp1; //dg->seq_p1.rightmargin = sq1->length - dlength - sp1; dg->seq_p2.num = n2; dg->seq_p2.sq = sq2; dg->seq_p2.startpos = sp2; //dg->seq_p1.leftmargin = sp2; //dg->seq_p1.rightmargin = sq2->length - dlength - sp2; dg->pred_diag = NULL; dg->col_pred_diag = NULL; dg->length = dlength; //dg->onlyOverThres= 0; dg->score= -1; dg->orig_score= -1; dg->weight = 0.0; dg->weight_sum = 0.0; dg->ov_weight = 0.0; dg->weight_fac = 1.0; dg->anchor = 0; dg->marked = 0; dg->multi_dg = 0; dg->multi_cont = NULL; dg->multi_length = 0; dg->meetsThreshold = 0; dg->neighbours = NULL; dg->degree = 0; dg->max_degree= 0; return dg; } /** * frees the memory of the given diagonal and the included seq_parts */ void free_diag(struct diag* dg) { if(dg->multi_dg) { int i; for(i=0;imulti_length;i++) { if(dg->multi_cont[i]!=NULL) free_diag(dg->multi_cont[i]); } free(dg->multi_cont); } free(dg); } /** * frees the (sub) tree of the given gt_node */ void free_gt_node(struct gt_node *gtn) { if(! gtn->isLeaf) { free_gt_node(gtn->succ1); free_gt_node(gtn->succ2); } free(gtn->seq_num); free(gtn); } /** * calculuates "m over n" */ unsigned long binomial(long m, long n) { double result=1.0; long i; for(i=0;imax_dlen; struct scr_matrix *smatrix = pdist->smatrix; long double **dist = calloc(length+1, sizeof(long double *)); if(dist==NULL) error("create_tmp_pdist(): (1) Out of memory when allocating data !"); int i; long mxscr, sm_max_scr=smatrix->max_score; for(i=0;i<=length;i++) { mxscr = i *sm_max_scr; dist[i] = calloc(mxscr+1, sizeof(long double )); if(dist[i]==NULL) error("create_tmp_pdist(): (3) Out of memory at iteration" ); } return dist; } /** * frees temporary probability distribution */ void free_tmp_pdist(long double **dist, int length) { int i; for(i=0;i<=length;i++) { free(dist[i]); } free(dist); } void fill_tmp_pdist(struct prob_dist *pdist, long double **tmp_dist, int slen1, int slen2) { unsigned int length = pdist->max_dlen; struct scr_matrix * smatrix = pdist->smatrix; unsigned int i; long mxscr, sm_max_scr=smatrix->max_score,scr; long double factor, np, np2,prob; long double seq_factor= (((long double)slen1)*(slen2)); for(i=1;i<=length;i++) { mxscr = i *sm_max_scr; factor = (long double)(seq_factor)/(long double)(4.0*i*i); // original ! for(scr=0;scr<=mxscr;scr++) { prob = pdist->data[i][scr]; np2 =prob * (factor); if(np2>=para->DIAG_CALC_WEIGHT_THRESHOLD) { // curent np = (long double)1.0- pow(1.0-prob,factor); // current } else { np = np2; } tmp_dist[i][scr] = -log(np); } } } /** * calculates the score of the given diag by using the given score matrix. the * resulting score is stored within the diag * omitScore = -1: score calculation but weight interpolation with seqlen = 100 * omitScore = 0: normal * omitScore = 1: no score calculation */ static void real_calc_weight(struct diag* dg, struct scr_matrix* smatrix, struct prob_dist *pdist, char omitScore, long double **tmp_dist, struct alignment *algn ) { if(dg->multi_dg) { int i; dg->weight = 0.0; dg->meetsThreshold = 0; dg->length = 0; for(i=0;imulti_length;i++) { if(dg->multi_cont[i]!=NULL) { //printf(" before real calc %i %i %f\n", dg->length, dg->score, dg->weight); real_calc_weight(dg->multi_cont[i],smatrix, pdist, omitScore, tmp_dist, algn); if(dg->multi_cont[i]->length > dg->length) dg->length = dg->multi_cont[i]->length; //printf(" real calc %i %i %f\n", dg->length, dg->score,dg->weight); dg->weight += dg->multi_cont[i]->weight; dg->meetsThreshold = dg->meetsThreshold | dg->multi_cont[i]->meetsThreshold; //printf(" readjusted %i %i %i %i %i %i %f %f %i\n", dg, dg->multi_cont[i],dg->multi_cont[i], dg->multi_dg, dg->multi_length, dg->weight, dg->multi_cont[i]->weight, dg->length); } } if(dg->length<=0) dg->meetsThreshold = 0; dg->total_weight = dg->weight; return; } if(dg->length==0) { dg->score = 0; dg->weight = 0.0; dg->meetsThreshold = 0; return; } unsigned int len = dg->length; int pos; long double np=0.0,np2; if(omitScore<=0) { unsigned int sp1=dg->seq_p1.startpos; unsigned int sp2=dg->seq_p2.startpos; char *data1 = dg->seq_p1.sq->data; char *data2 = dg->seq_p2.sq->data; int a1, a2; int *c2n = smatrix->char2num; int *sdata = smatrix ->data; int slen = smatrix->length; dg->score = 0; for(pos=0;posscore+=(long)sdata[slen*a1+a2]; } } long double prob; long double factor; dg->meetsThreshold = 0; if(dg->score <= pdist->smatrix->avg_sim_score*dg->length) { dg->total_weight = 0.0; dg->ov_weight = 0.0; dg->weight_fac = 1.0; dg->weight = 0.0; return; } // interpolate only for splitted diags that fall beyond the threshold /* if( (dg->orig_score>0)) { //if( (dg->weight<=0.0) && (dg->orig_score>0)) { dg->weight = ((double)dg->score)/((double)dg->orig_score)*dg->weight_sum; // printf(" ws %.20f %.20f \n", dg->weight, dg->weight_sum); //if(dg->weight_sum>0.0) dg->weight = dg->weight_sum; }else */ if(len<=pdist->max_dlen) { if(tmp_dist==NULL) { prob =pdist->data[len][dg->score]; /* if(omitScore>=0) { factor = (long double)((len + dg->seq_p1.leftmargin + dg->seq_p1.rightmargin )* (len + dg->seq_p2.leftmargin + dg->seq_p2.rightmargin ))/(long double)(4.0*len*len); // original } else { factor = (long double)(10000.0)/(long double)(4.0*len*len); } */ //printf(" %i %i\n", dg->seq_p1.sq->length, len+dg->seq_p1.leftmargin+dg->seq_p1.rightmargin); if(omitScore>=0) { factor = (long double)((dg->seq_p1.sq->length )* (dg->seq_p2.sq->length ))/(long double)(4.0*len*len); // original } else { factor = (long double)(10000.0)/(long double)(4.0*len*len); } np2 =prob * (factor); if(np2>=para->DIAG_CALC_WEIGHT_THRESHOLD) { np = (long double)1.0- pow(1.0-prob,factor); // current } else { np = np2; } dg->weight = -log(np); } else { dg->weight = tmp_dist[len][dg->score]; } } dg->total_weight = (dg->weight);//+dg->ov_weight);//* dg->weight_fac; if( (dg->length >= para->DIAG_MIN_LENGTH) && (dg->weight > para->DIAG_THRESHOLD_WEIGHT)) { dg->meetsThreshold = 1; } else { } } void calc_weight(struct diag* dg, struct scr_matrix* smatrix, struct prob_dist *pdist) { real_calc_weight(dg, smatrix, pdist, 0,NULL,NULL); } /** * calculates the overlap weight for the given diag */ void calc_ov_weight(struct diag* dg, struct diag_col *dcol, struct scr_matrix* smatrix, struct prob_dist *pdist) { int sn1 = dg->seq_p1.num; int sn2 = dg->seq_p2.num; int snt, sn; struct seq *seq1 = dg->seq_p1.sq; struct seq *seq2 = dg->seq_p1.sq; struct diag* tdg = create_diag(sn1, seq1,0, 1, seq2,0,0); struct diag* dg2; struct simple_diag_col *sdcol; int i,j, slen=dcol->seq_amount, dlen; int sp1 = dg->seq_p2.startpos,tsp1; int tep1,t; double w; struct seq_part *seq_p, *d_seq_p1, *d_seq_p2; dg->ov_weight = 0.0; int tstartpos; if(dg->length >0) { for(sn=0;sn<2;sn++) { tstartpos = (sn==0 ? dg->seq_p1.startpos : dg->seq_p2.startpos); tdg->seq_p1.sq = (sn==0 ? seq1 : seq2); tdg->seq_p1.num = (sn==0 ? sn1 : sn2);; // other way seq_p = (sn==0 ? &dg->seq_p2 : &dg->seq_p1); tsp1 = seq_p->startpos; tep1 = seq_p->startpos+dg->length-1; snt = (sn==0 ? sn2 : sn1); //printf(" slen %i\n", slen); for(i=0; idiag_matrix[(snt < i) ? (snt*slen + i) : (i*slen+snt)]; tdg->seq_p2.num=i; dlen = sdcol->length; for(j=0;jdata[j]; if(sntseq_p1; d_seq_p2 = &dg2->seq_p2; } else { d_seq_p1 = &dg2->seq_p2; d_seq_p2 = &dg2->seq_p1; } if(j==0) { tdg->seq_p2.sq = d_seq_p2->sq; } if(dg2->length >0) { if(d_seq_p1->startpos>tsp1) tsp1 = d_seq_p1->startpos; t=d_seq_p1->startpos+dg2->length-1; if(tseq_p2.sq=dg2->seq_p2.sq; tdg->seq_p1.startpos = tstartpos + tsp1- sp1; tdg->seq_p2.startpos = d_seq_p2->startpos + tsp1- d_seq_p1->startpos; tdg->length = tep1-tsp1+1; //real_calc_weight(tdg, smatrix, pdist,-1,NULL,NULL); real_calc_weight(tdg, smatrix, pdist,0,NULL,NULL); if(tdg->meetsThreshold ) { w = tdg->weight; //printf("add %.20f\n",w); dg->ov_weight += w/2.0; //dg2->ov_weight += w; } } } } } } } } dg->total_weight = (dg->weight);//+dg->ov_weight)*dg->weight_fac;// + dg->ov_weight; free_diag(tdg); } /** * creates the collection of all diags * * The pointer returned (and the ones included in the struct) * has to be deallocted explicitely from memory. */ struct diag_col* create_diag_col(int seq_amount) { struct diag_col *dc = calloc(1, sizeof(struct diag_col)); if(dc==NULL) error("create_diag_col(): (1) Out of memory !"); //printf("go for k\n"); dc->diag_matrix = malloc(seq_amount*seq_amount* sizeof(struct simple_diag_col *)); //printf("2go for k\n"); dc->gt_root = NULL; if(dc->diag_matrix==NULL) error("create_diag_col(): (2) Out of memory !"); return dc; } /** * frees a diagcol and all data included in it */ void free_diag_col(struct diag_col* dcol) { int s1,s2,sl=dcol->seq_amount; // printf("damount: %i\n", dcol->diag_amount); //printf("--------------------------------\n"); for(s1 =0;s1diag_amount;s1++) { // print_diag(dcol->diags[s1]); //printf(" NO FREEEEEEEEEE %i %i\n", s1,dcol->diags[s1]); free_diag(dcol->diags[s1]); } free(dcol->diags); for(s1=0;s1diag_matrix[s1+sl*s2]->data); free(dcol->diag_matrix[s1+sl*s2]); } } free(dcol->diag_matrix); if(dcol->gt_root!=NULL) free_gt_node(dcol->gt_root); free(dcol); } /** * finds all relevant multi diags with respect to the given alignment * and two groups of sequences that come from the guided method * * The pointer returned (and the ones included in the struct) * has to be deallocted explicitely from memory. */ inline struct simple_diag_col* find_diags_guided(struct scr_matrix *smatrix, struct prob_dist *pdist, struct gt_node* n1, struct gt_node* n2, struct alignment *algn, double thres_weight, int*** diag_info) { struct simple_diag_col* dcol = calloc(1, sizeof(struct simple_diag_col)); if(dcol==NULL) error("find_diags_guided(): (1) Out of memory !"); prepare_alignment(algn); struct seq_col *scol = algn->scol; struct seq *seq1 = &(scol->seqs[n1->seq_num[0]]); struct seq *seq2 = &(scol->seqs[n2->seq_num[0]]); int slen = scol->length; int ni1, ni2; struct seq *seq_n1, *seq_n2; unsigned int size = 16; int length = 0; struct diag **data = calloc(size, sizeof(struct diag* )); // printf("go for k\n"); if(data==NULL) error("find_diags_guided(): (2) Out of memory !"); struct algn_pos *tap;// = find_eqc(algn->algn, seq1->num, seq1->length-1); long slen1 = algn->max_pos; long slen2 = slen1; unsigned int max_dlen = pdist->max_dlen; struct diag *sdg, *tsdg; struct diag *dg = create_diag(seq1->num, seq1,0, seq2->num, seq2,0,0); struct diag* tdg,*tdg2; int i,j,k,l,kposi,kposj,jmin=0,jmax=slen2; int sn1 = seq1->num; int sn2 = seq2->num; int *c2n = smatrix->char2num; int *sdata = smatrix ->data; char *data1;// = seq1->data; char *data2;// = seq2->data; int smatrixlen = smatrix->length; int a1,a2; int maxslen = slen1; if(slen2>maxslen) maxslen = slen2; //long double **tmp_dist = create_tmp_pdist(pdist); //fill_tmp_pdist(pdist, tmp_dist, slen1, slen1); int max_pool = (slen1+slen2-1); struct diag **diag_col = malloc(sizeof(struct diag*)*(slen1+1)); struct diag **diag_row = malloc(sizeof(struct diag*)*(slen2+1)); struct diag **pool_diags=malloc(sizeof(struct diag *)*max_pool); int pooled = 0; double thres_sim_score =para->PROT_SIM_SCORE_THRESHOLD; char hasAli = (algn!=NULL); double diag_thres = para->DIAG_THRESHOLD_WEIGHT; double avg_sim_score = pdist->smatrix->avg_sim_score; int maxd,maxd2,cons_maxd; int score1=0,score2 = 0; char prevail; int extended,passed;//,actuals; int passed2; int max_under = 0;//para->PROT_DIAG_MAX_UNDER_THRESHOLD_POS; int max_under_inner =0;//2*para->PROT_DIAG_MAX_UNDER_THRESHOLD_POS; double dg_thres_weight = thres_weight;// * n1->seq_num_length*n2->seq_num_length; //int min_motives = n1->seq_num_length; //if(n2->seq_num_length > min_motives) min_motives = n2->seq_num_length; //min_motives++; int min_motives = sqrt(n1->seq_num_length * n2->seq_num_length); if(min_motives<2) min_motives = 2; // if(min_motives>(n1->seq_num_length*n2->seq_num_length)) min_motives = (n1->seq_num_length * n2->seq_num_length); char stst; char mstatus; int slensq = slen*slen; int sqind; char startstop[slensq]; char startstop_pre[slen]; int c_klen[slensq]; int c_kscore[slensq]; int rev_pos[slen][slen1]; struct gt_node *tgtn; // build reverse algn pos int iterlen = 0; int iter[slen*slen]; for(ni1=0;ni1seq_num_length;ni1++) { sn1 = n1->seq_num[ni1]; for(ni2=0;ni2seq_num_length;ni2++) { //printf(" begin MARKER MARKER MARKER %i %i %i\n",i,j,k); sn2 = n2->seq_num[ni2]; sqind = sn1*slen+sn2; iter[iterlen++] = sqind; } } dg->multi_dg = 1; dg->marked = 1; dg->multi_length = slensq; dg->multi_cont = malloc(sizeof(struct diag *)*slensq); memset(dg->multi_cont, 0, sizeof(struct diag *)*slensq); for(i=0;imulti_cont[i]=NULL; } maxd = n1->seq_num_length + n2->seq_num_length; for(i=0;i=n1->seq_num_length) { k-=n1->seq_num_length; tgtn = n2; } ni1 = tgtn->seq_num[k]; seq_n1 = &(scol->seqs[ni1]); for(j=0;jlength;j++) { tap = find_eqc(algn->algn, seq_n1->num, j); rev_pos[ni1][*(tap->eqcAlgnPos)] = j; } } // DIALIGN for(k=0;k<=slen1;k++) { //printf(" begin %i %i %i %i\n",k,slen, seq1->num, seq2->num); diag_col[k]=create_diag(seq1->num, seq1,0, seq2->num, seq2,0,0); //printf(" middle\n"); diag_col[k]->multi_dg = 1; diag_col[k]->marked = 1; diag_col[k]->multi_length = 0; //diag_col[k]->length = 1; diag_col[k]->weight_sum = 0.0; diag_col[k]->weight = 0.0; diag_col[k]->meetsThreshold = 0; pool_diags[pooled] = diag_col[k]; pool_diags[pooled]->pool_pos = pooled; pooled++; //printf(" end %i %i\n",k,slen); } for(k=0;k<=slen2;k++) { diag_row[k] = diag_col[0]; } double old_weight; if(max_dlen> slen1/2.0) max_dlen = slen1/2.0; if(max_dlen> slen2/2.0) max_dlen = slen2/2.0; for(i=0;i<=slen1;i++) { // merge row/col //printf("before \n"); if(i>0) { tdg = diag_col[i]; while(tdg!=NULL) { kposi = tdg->seq_p2.startpos+tdg->length; //printf(" kposi %i %i %i\n", diag_row[kposi], kposi, slen2); if(tdg->weight_sum > diag_row[kposi]->weight_sum) { diag_row[kposi] = tdg; prevail = 1; } else { prevail = 0; } tdg2 = tdg; tdg = tdg->col_pred_diag; if(! prevail) { pool_diags[tdg2->pool_pos]=NULL; //printf(" BEFORE\n"); free_diag(tdg2); //printf(" AFTER\n"); } } } //printf("after \n"); for(j=1;j<=slen2;j++) { if(diag_row[j-1]->weight_sum > diag_row[j]->weight_sum) { diag_row[j] = diag_row[j-1]; } } if(i==slen1) break; for(j=jmin;jslen1) maxd = slen1-i; if( (j+maxd)>slen1) maxd = slen1-j; /* for(l=0;lmulti_cont[iter[l]]; if(sdg!=NULL) { free_diag(sdg); dg->multi_cont[iter[l]]=NULL; } } */ dg->seq_p1.startpos = i; dg->seq_p2.startpos = j; passed = 0; passed2 = 0; // actuals = 0; for(k=1;k<=maxd;k++) { //printf(" %i %i %i %i\n",i,j,k,slen1); kposi = i+k-1; kposj = j+k-1; maxd2 = maxd; maxd = 0; //printf(" k= %i\n",k); extended = 0; //mstatus = 0; for(ni1=0;ni1seq_num_length;ni1++) { sn1 = n1->seq_num[ni1]; seq_n1 = &(scol->seqs[sn1]); if( (rev_pos[sn1][kposi]>=0)&& (startstop_pre[sn1]!=2) ) { data1 = seq_n1->data; startstop_pre[sn1]=2; for(ni2=0;ni2seq_num_length;ni2++) { //printf(" begin MARKER MARKER MARKER %i %i %i\n",i,j,k); sn2 = n2->seq_num[ni2]; seq_n2 = &(scol->seqs[sn2]); sqind = sn1*slen+sn2; stst = startstop[sqind]; //if(stst==1) mstatus += stst; //printf(" end MARKER MARKER MARKER %i %i\n",sn2, kpos); if( (rev_pos[sn2][kposj]>=0) && (stst!=2) && (diag_info[ni1][ni2][rev_pos[sn1][kposi]]==rev_pos[sn2][kposj]) ) { dg->length = k; data2 = seq_n2->data; a1 = c2n[(int) data1[rev_pos[sn1][kposi]]]; a2 = c2n[(int) data2[rev_pos[sn2][kposj]]]; score2 = sdata[smatrixlen*a1+a2]; sdg = NULL; if( (stst==0) && (score2 >= thres_sim_score)) { //if(rev_pos[sn1][kpos]>1000) printf(" %i %i %i\n", sn1,kpos, rev_pos[sn1][kpos]); sdg = dg->multi_cont[sqind]; if(sdg==NULL) { sdg = create_diag(sn1, seq_n1, rev_pos[sn1][kposi], sn2, seq_n2, rev_pos[sn2][kposj],0); } else { sdg->seq_p1.num = sn1; sdg->seq_p1.sq = seq_n1; sdg->seq_p1.startpos = rev_pos[sn1][kposi]; sdg->seq_p2.num = sn2; sdg->seq_p2.sq = seq_n2; sdg->seq_p2.startpos = rev_pos[sn2][kposj]; sdg->length = 0; } sdg->score = 0; dg->multi_cont[sqind] = sdg; startstop[sqind] = 1; passed++; c_klen[sqind] = 0; c_kscore[sqind] = 0; } else if(stst==1) { sdg = dg->multi_cont[sqind]; } else { //startstop[sqind]=2; if(k>max_under) startstop[sqind] = 2; sdg == NULL; } if(sdg!=NULL) { maxd = maxd2; // reallow next k //printf(" length compare %i %i %i %i\n",sqind, sdg->length+1,k,sdg); c_klen[sqind]++; c_kscore[sqind]+=score2; // if( (sdg->seq_p1.startpos==20) && (sdg->seq_p2.startpos==2) ) printf(" %i %i %i %i %i\n", k, c_klen[sqind], sdg->seq_p1.startpos, sdg->seq_p2.startpos); if(((sdg->score+c_kscore[sqind]) < (avg_sim_score*(sdg->length+c_klen[sqind])))) { if( (sdg->length+c_klen[sqind])>max_under_inner) startstop[sqind]=2; } /* if( (c_klen[sqind]>=1) && (c_kscore[sqind]< (para->PROT_DIAG_AVG_SCORE_THRESHOLD*c_klen[sqind]))) { passed--; startstop[sqind]=2; } */ if( (c_klen[sqind]>=para->PROT_DIAG_MAX_UNDER_THRESHOLD_POS) && (c_kscore[sqind]< (para->PROT_DIAG_AVG_SCORE_THRESHOLD*c_klen[sqind]))) { if ( ((sdg->length+c_klen[sqind])>para->PROT_DIAG_MIN_LENGTH_THRESHOLD)) { passed--; startstop[sqind]=2; } } //printf(" diag length %i %i %i %i %i\n", sn1, sn2, i,j, sdg->length); if( (score2 >= thres_sim_score) && (startstop[sqind]==1)) { //printf(" very before score %i\n", sdg->score); sdg->score += c_kscore[sqind]; sdg->length += c_klen[sqind]; //printf(" begin CONSIDER SDG %i %i %i %f %f\n",sn1,sn2,sdg->length,sdg->weight, diag_thres); //sdg->weight = tmp_dist[sdg->length][sdg->score]; calc_weight(sdg, smatrix, pdist); //printf(" before score %i %i %.20f %i %i\n", sdg->score, sdg->length, sdg->weight, c_kscore[sqind], c_klen[sqind]); /* score1 = sdg->score; if(score1!=sdg->score) { print_diag(sdg); printf(" score %i %i %i %.20f sc %i %i len %i %i %i \n", score1, sdg->score, sdg->length, sdg->weight, c_kscore[sqind],score2, c_klen[sqind],a1,a2); error(" score changed!\n"); } */ //printf(" after score %i %i %.20f\n", sdg->score, sdg->length, sdg->weight); //printf(" END\n"); //if(sdg->weight>0.0) printf(" end CONSIDER SDG %i %i %i %i %f %f\n",sn1, sn2, sdg->length, sdg->score, sdg->weight, diag_thres); c_klen[sqind]=0; c_kscore[sqind]=0; sdg->meetsThreshold = (sdg->weight>diag_thres ? 1 : 0); extended++; } } } else { if(startstop[sqind]==1) { startstop[sqind]=2; passed--; } } if(startstop[sqind]!=2) startstop_pre[sn1]=0; } } else { for(ni2=0;ni2seq_num_length;ni2++) { sn2 = n2->seq_num[ni2]; sqind = sn1*slen+sn2; if(startstop[sqind]==1) { startstop[sqind]=2; passed--; } } } } // if no inner starting diag break if( (k==1) && !extended) maxd = 0; // if only one inner diag and proceeded max_under further then break if( (passed2>=0) && (passed=max_under)) { //printf(" break %i\n"); maxd = 0; } // find the last k where >=2 inner diags where active if(passed >= min_motives) passed2 = k; if( ((extended) && (passed>=min_motives))) { // && (passed>1)){// && (mstatus>1)) { dg->weight = 0.0; extended = 0; for(l=0;lmulti_cont[iter[l]]; if( (sdg!=NULL) && (startstop[iter[l]]>0) && (sdg->weight >= thres_weight)) { extended++; dg->weight += sdg->weight; } } dg->meetsThreshold = (dg->weight>diag_thres ? 1 : 0); if(dg->meetsThreshold && (extended >=min_motives) && (dg->weight>=old_weight) && (dg->weight>=dg_thres_weight)) { old_weight = dg->weight; if(max_pool<=pooled) { max_pool += maxslen; pool_diags = realloc(pool_diags, sizeof(struct diag*)*max_pool); //printf(" pool size %i %.20f %.20f\n", max_pool, dg->weight, old_weight); } tdg = malloc(sizeof(struct diag)); pool_diags[pooled] = tdg; dg->pool_pos = pooled; pooled++; *tdg = *dg; tdg->pred_diag = diag_row[j]; tdg->weight_sum = diag_row[j]->weight_sum+tdg->weight; tdg->col_pred_diag = diag_col[i+k]; diag_col[i+k] = tdg; dg->multi_cont = malloc(sizeof(struct diag *)*slensq); memset(dg->multi_cont, 0, sizeof(struct diag *)*slensq); for(l=0;lmulti_cont[iter[l]]; if((tsdg!=NULL)) { // && (startstop[iter[l]]==1)){ sdg = malloc(sizeof(struct diag)); if(startstop[iter[l]]==0) { tsdg->length = 0; tsdg->score = 0; tsdg->weight = 0.0; tsdg->total_weight = 0.0; } *sdg = *tsdg; dg->multi_cont[iter[l]]=sdg; } else { dg->multi_cont[iter[l]]=NULL; } //dg->multi_cont[iter[l]]=NULL; } } } //if(k > 20) printf(" maxk= %i\n",k); } } } //printf(" after main %i\n",k); tdg = diag_row[slen2]; dcol->total_weight = 0; double lencomp = (log(slen1)+log(slen2)); length = 0; while((tdg!=NULL)) { //if (tdg->weight <=0.0) break; if(tdg->meetsThreshold) { // printf(" add tdg %i %i %i\n", tdg, tdg->length, tdg->meetsThreshold); dcol->total_weight += tdg->weight+lencomp; data[length] = tdg; l = 0; tdg->weight = 0.0; for(i=0;imulti_cont[i]; if(sdg!=NULL) { calc_weight(sdg, smatrix, pdist); if ((sdg->length>0) && (sdg->meetsThreshold) && (sdg->weight > thres_weight)){ tdg->multi_cont[l++] = sdg; tdg->weight += sdg->weight; //printf (" tdg %i %f %f\n", tdg, tdg->weight, sdg->weight); } } } tdg->multi_length = l; if( (tdg->multi_length>=min_motives) && (tdg->weight >= dg_thres_weight)) { tdg->marked = 1; tdg->total_weight = tdg->weight; tdg->weight_sum = -1.0; length++; } else { // TODO free ?? } if(length >= size) { size += 64; data = realloc(data, sizeof(struct diag *)*size); if(data==NULL) error("find_diags(): (3) Out of memory !"); } } tdg = tdg->pred_diag; } for(k=0;kweight_sum>-1.0) { free_diag(pool_diags[k]); } } free(pool_diags); free(diag_col); free(diag_row); free_diag(dg); //free_tmp_pdist(tmp_dist, pdist->max_dlen); dcol->length = length; data = realloc(data, sizeof(struct diag *)*length); dcol->data = data; return dcol; } /** * finds all relevant diags by the DIALIGN METHOD * * The pointer returned (and the ones included in the struct) * has to be deallocted explicitely from memory. */ struct simple_diag_col* find_diags_dialign(struct scr_matrix *smatrix, struct prob_dist *pdist, struct seq* seq1, struct seq* seq2, struct alignment *algn, long double **tmp_dist, int round) { struct simple_diag_col* dcol = calloc(1, sizeof(struct simple_diag_col)); if(dcol==NULL) error("find_diags_dialign(): (1) Out of memory !"); unsigned int size = 16; int length = 0; struct diag **data = calloc(size, sizeof(struct diag* )); // printf("go for k\n"); if(data==NULL) error("find_diags_dialign(): (2) Out of memory !"); long slen1 = seq1->length; long slen2 = seq2->length; unsigned int max_dlen = pdist->max_dlen; struct diag *dg = create_diag(seq1->num, seq1,0, seq2->num, seq2,0,0); struct diag* tdg,*tdg2; int i,j,k,kpos,jmin=0,jmax=slen2; int sn1 = seq1->num; int sn2 = seq2->num; int *c2n = smatrix->char2num; int *sdata = smatrix ->data; char *data1 = seq1->data; char *data2 = seq2->data; int smatrixlen = smatrix->length; int a1,a2; int c_klen,c_kscore; int maxslen = slen1; if(slen2>maxslen) maxslen = slen2; int max_pool = (slen1+slen2-1); struct diag **diag_col = malloc(sizeof(struct diag*)*(slen1+1)); struct diag **diag_row = malloc(sizeof(struct diag*)*(slen2+1)); struct diag **pool_diags=malloc(sizeof(struct diag *)*max_pool); int pooled = 0; double thres_sim_score =para->PROT_SIM_SCORE_THRESHOLD; char hasAli = (round>1); //(algn!=NULL); struct algn_pos **ap,*tap; double diag_thres = para->DIAG_THRESHOLD_WEIGHT; double avg_sim_score = pdist->smatrix->avg_sim_score; int maxd,maxd2,cons_maxd; double score1=0,score2 = 0; char prevail; if(hasAli || para->DO_ANCHOR) { ap = algn->algn; } // DIALIGN for(k=0;k<=slen1;k++) { diag_col[k]=create_diag(seq1->num, seq1,0, seq2->num, seq2,0,1); //diag_col[k]->length = 1; diag_col[k]->weight_sum = 0.0; diag_col[k]->weight = 0.0; pool_diags[pooled] = diag_col[k]; pool_diags[pooled]->pool_pos = pooled; pooled++; } for(k=0;k<=slen2;k++) { diag_row[k] = diag_col[0]; } double old_weight; if(max_dlen> slen1/2.0) max_dlen = slen1/2.0; if(max_dlen> slen2/2.0) max_dlen = slen2/2.0; for(i=0;i<=slen1;i++) { // merge row/col if(i>0) { tdg = diag_col[i]; while(tdg!=NULL) { kpos = tdg->seq_p2.startpos+tdg->length; if(tdg->weight_sum > diag_row[kpos]->weight_sum) { diag_row[kpos] = tdg; prevail = 1; } else { prevail = 0; } tdg2 = tdg; tdg = tdg->col_pred_diag; if(! prevail) { pool_diags[tdg2->pool_pos]=NULL; free_diag(tdg2); } } } for(j=1;j<=slen2;j++) { if(diag_row[j-1]->weight_sum > diag_row[j]->weight_sum) { diag_row[j] = diag_row[j-1]; } } if(i==slen1) break; if(hasAli || para->DO_ANCHOR) { tap = find_eqc(ap, sn1, i); if(tap->predF!=NULL) { jmin = tap->predF[sn2]+1; } else { jmin = 0; } if(tap->succF!=NULL) { jmax = tap->succF[sn2]; }else { jmax = slen2; } if(jmin<0) jmin = 0; } if(para->DO_ANCHOR) { if( (jmin-1)==jmax) { jmin--; jmax++; } } for(j=jmin;j=thres_sim_score) { maxd = slen1 - i; maxd2 = slen2 - j; if(maxd >maxd2) maxd = maxd2; if(maxd > max_dlen) maxd = max_dlen; dg->seq_p1.startpos = i; dg->seq_p2.startpos = j; dg->score = score1; cons_maxd = maxd+1; old_weight = 0.0; c_klen = 0; c_kscore = 0; for(k=1;k<=maxd;k++) { dg->length = k; kpos = i+k; if(hasAli || para->DO_ANCHOR) { a1 = i+k-1; a2 = j+k-1; tap = find_eqc(ap, sn1, a1); if (! ( (para->DO_ANCHOR) && (tap->predF!=NULL) && (tap->succF!=NULL) && (tap->predF[sn2]==tap->succF[sn2]) && (tap->predF[sn2]==a2) ) ) { if(tap->predF!=NULL) { if( (tap->predF[sn2] - a2)>0) break; /* if(tap->predF[sn2]==a2) { if( (tap->succF==NULL) || (tap->predF[sn2]!=tap->succF[sn2])) break; } */ } if(tap->succF!=NULL) { if((a2 - tap->succF[sn2])>0) break; /* if(tap->succF[sn2]==a2) { if( (tap->predF==NULL) || (tap->predF[sn2]!=tap->succF[sn2])) break; } */ } } } if(k>1) { a1 = c2n[(int) data1[kpos-1]]; a2 = c2n[(int) data2[j+k-1]]; score2 = sdata[smatrixlen*a1+a2]; dg->score += score2; } else { score2 = score1; } if( dg->score < (avg_sim_score*(double)k)) { break; } c_klen++; c_kscore+=score2; if( (c_klen>=para->PROT_DIAG_MAX_UNDER_THRESHOLD_POS) && (c_kscore< (para->PROT_DIAG_AVG_SCORE_THRESHOLD*c_klen))) { if ( (k>para->PROT_DIAG_MIN_LENGTH_THRESHOLD)) { break; } else { if(maxd>para->PROT_DIAG_MIN_LENGTH_THRESHOLD) maxd = para->PROT_DIAG_MIN_LENGTH_THRESHOLD; } } if(score2 >= thres_sim_score) { c_klen=0; c_kscore=0; if(1) { if(!hasAli) { dg->weight = tmp_dist[k][dg->score]; dg->meetsThreshold = (dg->weight>diag_thres ? 1 : 0); } else { real_calc_weight(dg, smatrix, pdist,1,tmp_dist,algn); } if(dg->meetsThreshold && (dg->weight>=old_weight)) { old_weight = dg->weight; if(max_pool<=pooled) { max_pool += maxslen; pool_diags = realloc(pool_diags, sizeof(struct diag*)*max_pool); //printf(" old pool size %i\n", max_pool); } tdg = malloc(sizeof(struct diag)); pool_diags[pooled] = tdg; dg->pool_pos = pooled; pooled++; *tdg = *dg; tdg->pred_diag = diag_row[j]; tdg->weight_sum = diag_row[j]->weight_sum+tdg->weight; tdg->col_pred_diag = diag_col[kpos]; diag_col[kpos] = tdg; } } } } } } } tdg = diag_row[slen2]; dcol->total_weight = 0; double lencomp = (log(slen1)+log(slen2)); while((tdg!=NULL)) { if (tdg->weight <=0.0) break; if(1) { dcol->total_weight += tdg->weight+lencomp; data[length] = tdg; tdg->weight_sum = -1.0; length++; if(length >= size) { size += 64; data = realloc(data, sizeof(struct diag *)*size); if(data==NULL) error("find_diags(): (3) Out of memory !"); } } tdg = tdg->pred_diag; } for(k=0;kweight_sum>-1.0) { free(pool_diags[k]); } } free(pool_diags); free(diag_col); free(diag_row); free_diag(dg); dcol->length = length; data = realloc(data, sizeof(struct diag *)*length); dcol->data = data; if(para->DEBUG>5) { for(i=0;ilength; int slen2 = seq2->length; unsigned int max_dlen = pdist->max_dlen; struct diag* dg = create_diag(seq1->num, seq1,0, seq2->num, seq2,0,0); struct diag* tdg; int i,j,d; int sn1 = seq1->num; int sn2 = seq2->num; // printf("%i\n",slen2); int *c2n = smatrix->char2num; int *sdata = smatrix ->data; char *data1 = seq1->data; char *data2 = seq2->data; int slen = smatrix->length; int a1,a2; int score1=0,score2 = 0; int maxslen = slen1; if(slen2>maxslen) maxslen = slen2; double avslen = ((double)slen1+slen2)/2.0; int delta; int sim_thr_pred_pos[maxslen]; //int sim_thr_succ_pos[maxslen]; int scores[maxslen]; long score_sum[maxslen]; long s_sum; int old_thr_pos; //double *dyn_weight = calloc(maxslen, sizeof(double)); double weight; struct diag **dyn_diags=malloc(sizeof(struct diag *)*maxslen); int max_pool = maxslen; struct diag **pool_diags=malloc(sizeof(struct diag *)*max_pool); int pooled = 0; int thres_sim_score = para->PROT_SIM_SCORE_THRESHOLD; int kscore, klen; char hasAli = (algn!=NULL); double diag_thres = para->DIAG_THRESHOLD_WEIGHT; double avg_sim_score = pdist->smatrix->avg_sim_score; struct algn_pos **ap,*tap; if(hasAli) { ap = algn->algn; thres_sim_score =thres_sim_score/2; if(thres_sim_score<4) thres_sim_score = 4; diag_thres = 0.0; } for(d=-slen1+1;dpredF!=NULL) { if( (tap->predF[sn2] - a2)>0) break; } if(tap->succF!=NULL) { if((a2 - tap->succF[sn2])>0) break; } } a1 = c2n[(int) data1[i+k]]; a2 = c2n[(int) data2[j+k]]; score1 = sdata[slen*a1+a2]; scores[k] = score1; s_sum+= score1; score_sum[k] = s_sum; if(score1 < thres_sim_score) { sim_thr_pred_pos[k] = old_thr_pos; } else { //if(old_thr_pos>=0) sim_thr_succ_pos[old_thr_pos] = k; old_thr_pos = k; } } maxl = k; //if(old_thr_pos>=0) sim_thr_succ_pos[old_thr_pos] = maxl; dyn_diags[0] = create_diag(seq1->num, seq1,0, seq2->num, seq2,0,0); dyn_diags[0]->weight_sum = 0.0; dyn_diags[0]->weight = 0.0; pool_diags[0] = dyn_diags[0]; pooled = 1; lastk=0; for(k=0;k0) { dyn_diags[k] = dyn_diags[lastk]; //dyn_weight[k] = dyn_weight[lastk]; } if(hasAli) { a1 = i+k; a2 = j+k; //printf("pre %i\n", a1); tap = find_eqc(ap, sn1, a1); //printf("after %i\n", a1); if(tap->predF!=NULL) { if( (tap->predF[sn2] - a2)>0) break; } if(tap->succF!=NULL) { if((a2 - tap->succF[sn2])>0) break; } } score1 = scores[k]; if(score1>=thres_sim_score) { for(l=para->DIAG_MIN_LENGTH;l<=max_dlen; l++) { delta = k-l+1; dg->seq_p1.startpos = i+delta; dg->seq_p2.startpos = j+delta; kscore = 0; klen = 0; if((dg->seq_p1.startpos<0) || (dg->seq_p2.startpos<0)) { break; } else { dg->length = l; //printf("%i %i \n", i-l+1, j-l+1); score2 = scores[delta]; klen++; kscore += score2; if( (kscore < avg_sim_score*klen)) { // && (dg->score>1.2*k*avg_sim_score)) { /* experiment */ if( ( (k>=0.2*avslen) || (k>=20) || ( (i-j)>0.3*avslen)) && klen>=4) break; } if(kscore >= avg_sim_score*klen ) { //if(score2 >= thres_sim_score) { kscore = 0; klen = 0; dg->score = score_sum[k] - (delta > 0 ? score_sum[delta-1] : 0); if(dg->score <= avg_sim_score*dg->length) break; if(!hasAli) { dg->weight = tmp_dist[dg->length][dg->score]; dg->meetsThreshold = (dg->weight>diag_thres ? 1 : 0); } else { real_calc_weight(dg, smatrix, pdist,1,tmp_dist,algn); } if(dg->meetsThreshold) { if(max_pool<=pooled) { max_pool += maxslen; pool_diags = realloc(pool_diags, sizeof(struct diag*)*max_pool); } if(delta==0) { if(dg->weight > dyn_diags[k]->weight_sum) { dg->weight_sum = dg->weight; dyn_diags[k] = malloc(sizeof(struct diag)); pool_diags[pooled] = dyn_diags[k]; pooled++; *dyn_diags[k] = *dg; dyn_diags[k]->pred_diag = NULL; } } else { weight = dg->weight + dyn_diags[delta-1]->weight_sum; if( (weight) >= dyn_diags[k]->weight_sum) { dg->weight_sum = weight; dyn_diags[k] = malloc(sizeof(struct diag)); pool_diags[pooled] = dyn_diags[k]; pooled++; *dyn_diags[k] = *dg; if(dyn_diags[delta-1]->weight >0) { dyn_diags[k]->pred_diag = dyn_diags[delta-1]; } else { dyn_diags[k]->pred_diag = NULL; } } } lastk = k; } } else { l += (delta - sim_thr_pred_pos[delta])-1; } } } } } tdg = dyn_diags[lastk]; while((tdg!=NULL)) { if (tdg->weight <=0.0) break; data[length] = tdg; tdg->weight_sum = -1.0; length++; if(length >= size) { size += 64; data = realloc(data, sizeof(struct diag *)*size); if(data==NULL) error("find_diags(): (3) Out of memory !"); } tdg = tdg->pred_diag; } for(k=0;kweight_sum>-1.0) free(pool_diags[k]); } } data = realloc(data, sizeof(struct diag *)*length); free(pool_diags); free(dyn_diags); free_diag(dg); dcol->length = length; dcol->data = data; if(para->DEBUG>5) { for(i=0;ilength; unsigned int dl, d, si,k; unsigned int odgpos1[sl]; unsigned int odgpos2[sl]; int min,max,xpos,txpos1, txpos2; unsigned int odglen; char next; char hasSplit=1; while(hasSplit) { //printf("hasSplit %i\n",hasSplit); hasSplit = 0; for(s1=0;s1diag_matrix[s1+sl*s2]; dl = sdcol->length; data = sdcol->data; memset(odgpos1,0,sl*sizeof(int)); memset(odgpos2,0,sl*sizeof(int)); pdg=NULL; for(d=0;dweight_sum = dg->weight; dg->orig_score = dg->score; if(pdg!=NULL) pdg->pred_diag = dg; pdg = dg; dg->pred_diag=NULL; next=0; while(! next) { next = 1; xpos = -1; // round 1 //print_diag(dg); //printf(" %i %i min=%i max=%i\n", s1,s2, min,max); min = dg->seq_p1.startpos; max = dg->seq_p1.startpos+dg->length-1; for(si=0;sidiag_matrix[s1+sl*si]->length; n_data = all_diags->diag_matrix[s1+sl*si]->data; } else { odglen = all_diags->diag_matrix[si+sl*s1]->length; n_data = all_diags->diag_matrix[si+sl*s1]->data; } //printf(" %i %i %i\n", si, odglen, odgpos1[si]); while( (odgpos1[si]seq_p2.num) ? sdg->seq_p2.startpos : sdg->seq_p1.startpos; txpos2 = txpos1 + sdg->length-1; //if( (s1==0) && (s2==2) && (si==3)) printf(" pppp %i %i %i %i\n", min,max,txpos1, txpos2); if(txpos2min) && (txpos1<=max) && ((txpos1seq_p2.startpos; max = dg->seq_p2.startpos+dg->length-1; if(xpos>=0) xpos = dg->seq_p2.startpos + (xpos-dg->seq_p1.startpos); for(si=0;sidiag_matrix[s2+sl*si]->length; n_data = all_diags->diag_matrix[s2+sl*si]->data; } else { odglen = all_diags->diag_matrix[si+sl*s2]->length; n_data = all_diags->diag_matrix[si+sl*s2]->data; } while( (odgpos2[si]seq_p2.num) ? sdg->seq_p2.startpos : sdg->seq_p1.startpos; txpos2 = txpos1 + sdg->length-1; if(txpos2min) && (txpos1<=max) && ((txpos1=0) && (xpos<=max) && (xpos>min)) { hasSplit = 1; next = 0; //print_diag(dg); tdg = create_diag(dg->seq_p1.num, dg->seq_p1.sq, xpos-min+dg->seq_p1.startpos, dg->seq_p2.num, dg->seq_p2.sq, xpos, max-xpos+1); tdg->weight_sum = dg->weight_sum; tdg->orig_score = dg->score; dg->length = xpos - min; //print_diag(dg); //print_diag(tdg); //if( (s1==0) && (s2==2)) printf(" SPLIT %i %i %i %i %i !\n", dg, dg->seq_p1.startpos, dg->length, tdg->seq_p1.startpos, tdg->length); //printf(" 2SPLIT %i !\n", dg->length); sdcol->length++; dg->pred_diag = tdg; tdg->pred_diag=NULL; dg = tdg; pdg = dg; } else { //if(s1==0) printf(" ELSE %i %i %i !\n", dg, dg->seq_p1.startpos, dg->length); } } } dl = sdcol->length; if(dl>0) dg=sdcol->data[0]; //printf(" before realloc %i\n", sdcol->length); sdcol->data=realloc(sdcol->data, sdcol->length*sizeof(struct diag*)); //printf(" after realloc %i\n", sdcol->length); if( (dl>0)&& (sdcol->data==NULL)) { error(" split_diags: Out of Memory - reallocating!\n"); } for(k=0;kseq_p1.num, dg->seq_p2.num, dg->seq_p1.startpos, dg->length); sdcol->data[k] = dg; dg = dg->pred_diag; } } } } } */ /** * builds the upgma guide tree in the given diag_col */ void build_guide_tree(struct diag_col *dcol) { int slen = dcol->seq_amount; double weights[slen][slen]; struct gt_node *nodes[slen]; struct gt_node *gtn, *gtn1, *gtn2; int max1=0, max2=1; int i,j,k; for(i=0;iisLeaf = 1; gtn->seq_num = malloc(sizeof(int)*1); gtn->seq_num[0] = i; gtn->seq_num_length = 1; gtn->succ1 = NULL; gtn->succ2 = NULL; nodes[i] = gtn; for(j=i+1;jdiag_matrix[slen*i+j]->total_weight; weights[j][i] = weights[i][j]; if(weights[i][j] > weights[max1][max2]) { max1 = i; max2 = j; } } } for(k=0;k<(slen-1);k++) { gtn1 = nodes[max1]; gtn2 = nodes[max2]; gtn = malloc(sizeof(struct gt_node )); gtn->isLeaf = 0; gtn->seq_num_length = gtn1->seq_num_length + gtn2->seq_num_length; gtn->seq_num = malloc(sizeof(int)*gtn->seq_num_length); for(i=0;iseq_num_length;i++) { gtn->seq_num[i] = gtn1->seq_num[i]; } for(i=0;iseq_num_length;i++) { gtn->seq_num[gtn1->seq_num_length+i] = gtn2->seq_num[i]; } gtn->succ1 = gtn1; gtn->succ2 = gtn2; nodes[max1] = gtn; nodes[max2] = NULL; for(i=0;i weights[i][max2]) ? weights[i][max1] : weights[i][max2]); //weights[i][max1] = 1.0*(weights[i][max1]+weights[i][max2]) + 0.0* ( (weights[i][max1] > weights[i][max2]) ? weights[i][max1] : weights[i][max2]); weights[max1][i] = weights[i][max1]; } } max1 = -1; max2 = -1; for(i=0;igt_root = nodes[0]; /* printf(" root %i\n", nodes[0]); printf(" left1 %i\n", nodes[0]->succ1->succ1->seq_num); printf(" left2 %i\n", nodes[0]->succ1->succ2->seq_num); printf(" right %i\n", nodes[0]->succ2->seq_num); */ } /** * Finds all diags of each pair of sequences in in_seq_col by using * the function above * * The pointer returned (and the ones included in the struct) * has to be deallocted explicitely from memory. */ struct diag_col *find_all_diags(struct scr_matrix *smatrix, struct prob_dist *pdist, struct seq_col *in_seq_col, struct alignment *algn, int round) { unsigned int s1, s2, rs2, sl = in_seq_col->length, sp, ap; struct diag_col *all_diags = create_diag_col(sl); struct simple_diag_col *sdcol; unsigned int diag_amount = 0; struct diag *dg; char hasAli = (round >1);//(algn!=NULL); long double **tmp_dist = NULL; if(!hasAli) tmp_dist = create_tmp_pdist(pdist); int s2max = sl; int s2width =(int) sqrt(sl); double total=0.0; //double imp[sl]; // for(s1=0;s1FAST_PAIRWISE_ALIGNMENT && s2width+1seqs[s1].length,in_seq_col->seqs[rs2].length ); } if(para->DEBUG>5) printf("%i %i\n", s1,s2); //time1 = clock(); //sdcol=find_diags_dyn(smatrix, pdist, &in_seq_col->seqs[s1], // &in_seq_col->seqs[s2],algn,tmp_dist); /* doAlign = 1; if(hasAli) { if(algn->redo_seqs[s1*sl+s2]==0) doAlign = 0; } if(doAlign) { */ if(in_seq_col->seqs[s1].length > 0 && in_seq_col->seqs[s2].length > 0) { //if(para->DEBUG>1) printf(" %i %i %i\n", s1, rs2,sl-1); // printf("find diags %i %i\n",s1,s2); sdcol=find_diags_dialign(smatrix, pdist, &in_seq_col->seqs[s1], &in_seq_col->seqs[rs2],algn,tmp_dist, round); // imp[s1] += sdcol->total_weight; //imp[s2] += sdcol->total_weight; total += sdcol->total_weight; //totala[s1] +=sdcol->total_weight; //totala[s2] +=sdcol->total_weight; //printf(" num of diags:%i\n ", sdcol->length); /* } else { sdcol = calloc(1, sizeof(struct simple_diag_col)); sdcol->length = 0; } */ //printf("%i %i %f\n", s1,s2, (clock()-time1)/CLOCKS_PER_SEC); all_diags->diag_matrix[s1+sl*rs2] = sdcol; all_diags->diag_matrix[rs2+sl*s1] = sdcol; diag_amount += sdcol->length; } } } if(!hasAli) free_tmp_pdist(tmp_dist, pdist->max_dlen); all_diags->diags= calloc(diag_amount, sizeof(struct diag*)); if(all_diags->diags==NULL) error("find_all_diags(): (1) Out of memory !"); ap=0; for(s1=0;s1diag_matrix[s1+sl*s2]; if(sdcol!=NULL) { for(sp=0;splength;sp++) { // if(hasAli || (sdcol->data[sp]->weight >0.01*(sdcol->total_weight/sdcol->length))) { sdcol->data[sp]->pred_diag = NULL; all_diags->diags[ap]=sdcol->data[sp]; ap++; //} else { // free(sdcol->data[sp]); //diag_amount--; // } } } } } all_diags->seq_amount = sl; for(s1=0;s1diag_matrix[sl*s1+s2]; if(sdcol!=NULL) { sdcol->weight_fac =pow(sdcol->total_weight/total,2.0); for(sp=0;splength;sp++) { dg = sdcol->data[sp]; // if(hasAli) print_diag(dg); dg->weight_fac = sdcol->weight_fac; // dg->ov_weight = sdcol->total_weight; /* if(1 || !hasAli) { dg->weight_fac = sdcol->total_weight*totala[s1]/(sl-1)*sdcol->total_weight*totala[s2]/(sl-1); } */ //dg->weight_fac =pow(sdcol->total_weight*(sl-1),2.0)/(totala[s1]*totala[s2]); if(!hasAli) { if(para->DO_OVERLAP) { //printf(" do overlap\n"); //dg->weight_fac = 1.0; calc_ov_weight(dg,all_diags, smatrix,pdist); } dg->total_weight = (dg->weight);//+dg->ov_weight);// *dg->weight_fac; } else { // changed in TX 1.0.0 if(para->FAST_MODE) dg->weight_fac = 1.0; dg->total_weight = (dg->weight);//+dg->ov_weight);// *dg->weight_fac; } //if(sp==sdcol->length-1) sdcol->total_weight *= dg->weight_fac; } } } } all_diags->diag_amount = diag_amount; if(! hasAli) build_guide_tree(all_diags); return all_diags; } /** * Finds all diags of each pair of sequences in in_seq_col by using * the function above * * The pointer returned (and the ones included in the struct) * has to be deallocted explicitely from memory. */ struct diag_col *old_find_all_diags(struct scr_matrix *smatrix, struct prob_dist *pdist, struct seq_col *in_seq_col, struct alignment *algn, int round ) { unsigned int s1, s2, rs2, sl = in_seq_col->length, sp, ap; struct diag_col *all_diags = create_diag_col(sl); struct simple_diag_col *sdcol; unsigned int diag_amount = 0; struct diag *dg; char hasAli = (round >1);//(algn!=NULL); long double **tmp_dist = NULL; if(!hasAli) tmp_dist = create_tmp_pdist(pdist); int s2max = sl; int s2width =(int) sqrt(sl); double total=0.0; //double imp[sl]; // for(s1=0;s1FAST_PAIRWISE_ALIGNMENT && s2width+1seqs[s1].length,in_seq_col->seqs[rs2].length ); } if(para->DEBUG>5) printf("%i %i\n", s1,s2); //time1 = clock(); //sdcol=find_diags_dyn(smatrix, pdist, &in_seq_col->seqs[s1], // &in_seq_col->seqs[s2],algn,tmp_dist); /* doAlign = 1; if(hasAli) { if(algn->redo_seqs[s1*sl+s2]==0) doAlign = 0; } if(doAlign) { */ if(in_seq_col->seqs[s1].length > 0 && in_seq_col->seqs[s2].length > 0) { //if(para->DEBUG>1) printf(" %i %i %i\n", s1, rs2,sl-1); // printf("find diags %i %i\n",s1,s2); sdcol=find_diags_dialign(smatrix, pdist, &in_seq_col->seqs[s1], &in_seq_col->seqs[rs2],algn,tmp_dist, round); // imp[s1] += sdcol->total_weight; //imp[s2] += sdcol->total_weight; total += sdcol->total_weight; //totala[s1] +=sdcol->total_weight; //totala[s2] +=sdcol->total_weight; //printf(" num of diags:%i\n ", sdcol->length); /* } else { sdcol = calloc(1, sizeof(struct simple_diag_col)); sdcol->length = 0; } */ //printf("%i %i %f\n", s1,s2, (clock()-time1)/CLOCKS_PER_SEC); all_diags->diag_matrix[s1+sl*rs2] = sdcol; all_diags->diag_matrix[rs2+sl*s1] = sdcol; diag_amount += sdcol->length; } } } // new: call of split function //printf("before split\n"); /* if(! hasAli) { diag_amount = 0; split_diags(in_seq_col, all_diags); //total=0.0; for(s1=0;s1diag_matrix[s1+sl*s2]; if(sdcol!=NULL) { //sdcol->total_weight = 0.0; for(sp=0;splength;sp++) { dg = sdcol->data[sp]; real_calc_weight(dg, smatrix, pdist, 0, NULL,algn); //sdcol->total_weight += dg->weight; //total += dg->weight; } diag_amount +=sdcol->length; } } } } */ //all_diags->diag_amount = diag_amount; // printf("after split\n"); //double max = 0.0; all_diags->diags= calloc(diag_amount, sizeof(struct diag*)); if(all_diags->diags==NULL) error("find_all_diags(): (1) Out of memory !"); double sdtotal; ap=0; for(s1=0;s1diag_matrix[s1+sl*s2]; if(sdcol!=NULL) { for(sp=0;splength;sp++) { // if(hasAli || (sdcol->data[sp]->weight >0.01*(sdcol->total_weight/sdcol->length))) { all_diags->diags[ap]=sdcol->data[sp]; ap++; //} else { // free(sdcol->data[sp]); //diag_amount--; // } } } } } all_diags->seq_amount = sl; all_diags->total_weight = 0.0; for(s1=0;s1diag_matrix[sl*s1+s2]; sdcol->total_weight = 0.0; sdtotal = 0.0; if(sdcol!=NULL) { for(sp=0;splength;sp++) { dg = sdcol->data[sp]; // if(hasAli) print_diag(dg); dg->weight_fac = pow(sdcol->total_weight/total,2.0); //dg->weight_fac = 1.0; // dg->ov_weight = sdcol->total_weight; /* if(1 || !hasAli) { dg->weight_fac = sdcol->total_weight*totala[s1]/(sl-1)*sdcol->total_weight*totala[s2]/(sl-1); } */ // dg->weight_fac =pow(sdcol->total_weight*(sl-1),2.0)/(totala[s1]*totala[s2]); if(!hasAli) { if(para->DO_OVERLAP) { //dg->weight_fac = 1.0; //error("calc ov\n"); calc_ov_weight(dg,all_diags, smatrix,pdist); } //dg->total_weight = (dg->weight+dg->ov_weight) *dg->weight_fac; } else { dg->weight_fac = 1.0; } dg->total_weight = (dg->weight+dg->ov_weight);//*dg->weight_fac; //if(dg->total_weight > max) max = dg->total_weight; //dg->weight = dg->score; // print_diag(dg); sdtotal += dg->weight; all_diags->total_weight += dg->total_weight; } sdcol->total_weight = sdtotal; } } } all_diags->average_weight = all_diags->total_weight / all_diags->diag_amount; //printf(" max %f\n", max); if(!hasAli) free_tmp_pdist(tmp_dist, pdist->max_dlen); all_diags->diag_amount = diag_amount; if(! hasAli) build_guide_tree(all_diags); return all_diags; } abyss-1.3.6/dialign/io.c000644 002433 001057 00000073017 12015543263 016552 0ustar00traymondassembly000000 000000 /** * * io.c: IO operations, e.g. read input files, console output etc. * * A.R.Subramanian */ #include #include #include #include #include #include #include "parameters.h" #include "struct.h" #include "translate.h" #include "io.h" // alig.c extern struct algn_pos *find_eqc(struct algn_pos **ap, int seqnum, int pos); extern void prepare_alignment(struct alignment *algn); extern struct diag* create_diag(int n1, struct seq* sq1, unsigned int sp1, int n2, struct seq* sq2, unsigned int sp2, int dlength); extern int errno; /** * print version */ void version() { printf(" This is DIALIGN-TX Version %s - A Multiple Sequence alignment program.\n",para->VERSION ); printf(" Author: Amarendran R. Subramanian, 2004-2008 \n"); printf(" subraman@informatik.uni-tuebingen.de\n\n"); printf(" \n"); printf(" Research work using DIALIGN-TX should cite:\n\n"); printf(" DIALIGN-TX: improvement of the segment-based approach for multiple\n"); printf(" sequence alignment by combining greedy and progressive alignment strategies\n"); printf(" Amarendran R. Subramanian, Michael Kaufmann, Burkhard Morgenstern,\n"); printf(" Algorithms for Molecular Biology 3:6, 2008\n\n"); printf(" DIALIGN-T: An improved algorithm for segment-based multiple sequence alignment\n"); printf(" Amarendran R. Subramanian, Jan Weyer-Menkhoff, Michael Kaufmann,\n"); printf(" Burkhard Morgenstern, BMC Bioinformatics 6:66, 2005\n"); // printf(" Special Thanks to:\n"); //printf(" Burkhard Morgenstern\n"); //printf(" Michael Kaufmann\n"); //printf(" David Mathog\n"); //printf(" Numereous DIALIGN-T/X Users\n"); } /** * print error message and exit */ void error(char *message) { printf("ERROR: %s\n", message); // if(errno) perror("perror()"); exit(1); } /** * print error message and exit */ void merror(char *msg1, char *msg2) { printf("ERROR: %s %s\n", msg1, msg2); // if(errno) perror("perror()"); exit(1); } /** * strips off leading whitespace characters */ void strip_leading_ws( char *str ) { int s,d; for(s=d=0; str[s]==' ' || str[s]=='\t'; s++){} for(;;s++,d++){ str[d]=str[s]; if( str[s] == '\0')break; } } /** * builds a pathname from a dir-name and a filename. * * The pointer returned (and the ones included in the struct) * has to be deallocted explicitely from memory. */ char* build_pathname(char *dir, char *file) { int dirslen = strlen(dir); char *pathn = calloc(dirslen+strlen(file)+2, sizeof(char)); if(pathn==NULL) error("build_pathname(): out of memory !"); strcpy(pathn, dir); if(dirslen>0 && dir[dirslen-1]!='/') strcat(pathn, "/"); strcat(pathn, file); // if(para->DEBUG) // printf("DEBUG build_pathname(): Created filename: %s from dir=%s and file=%s\n", pathn, dir, file); return pathn; } /** * prints a sequence */ void print_seq(struct seq * aSeq) { int row; int slen = aSeq->length; int maxrow = slen/para->PRINT_SEQ_LINE_LENGTH; int row_residue = slen % para->PRINT_SEQ_LINE_LENGTH; printf("Sequence: %s\nLength: %i\n", aSeq->name, slen); char line[para->PRINT_SEQ_LINE_LENGTH+1]; for(row=0;row <=maxrow; row++) { if(rowdata[row*para->PRINT_SEQ_LINE_LENGTH]), para->PRINT_SEQ_LINE_LENGTH); line[para->PRINT_SEQ_LINE_LENGTH]='\0'; } else{ if(row_residue==0) break; strncpy(line, &(aSeq->data[row*para->PRINT_SEQ_LINE_LENGTH]), row_residue); line[row_residue]='\0'; } printf("%s\n", line); } } /** * prints a diagional */ void print_diag(struct diag *aDiag) { int row; int slen = aDiag->length; int maxrow = slen/para->PRINT_SEQ_LINE_LENGTH; int row_residue = slen % para->PRINT_SEQ_LINE_LENGTH; printf("Diag: %s\n %s\nLength: %i startpos1: %i startpos2: %i\n", aDiag->seq_p1.sq->name, aDiag->seq_p2.sq->name, slen, aDiag->seq_p1.startpos,aDiag->seq_p2.startpos ); char *data1 =aDiag->seq_p1.sq->data; char *data2 =aDiag->seq_p2.sq->data; char *data; int startpos1 = aDiag->seq_p1.startpos; int startpos2 = aDiag->seq_p2.startpos; int snum, startpos; char line[para->PRINT_SEQ_LINE_LENGTH+1]; for(row=0;row <=maxrow; row++) { for (snum=0;snum<2;snum++) { startpos = (snum==0 ? startpos1 : startpos2); data = (snum==0 ? data1 : data2); if(rowPRINT_SEQ_LINE_LENGTH]), para->PRINT_SEQ_LINE_LENGTH); line[para->PRINT_SEQ_LINE_LENGTH]='\0'; } else{ if(row_residue==0) break; strncpy(line, &(data[startpos+row*para->PRINT_SEQ_LINE_LENGTH]), row_residue); line[row_residue]='\0'; } printf("%s\n", line); } if(rowscore, aDiag->weight); } /** * prints a score matrix */ void print_scr_matrix(struct scr_matrix *aSmatrix) { int len =aSmatrix->length; printf("Length: %i, maximal score: %i\n", len, aSmatrix->max_score); int r, c; for (r=-1; rnum2char[c]); } else if(cdata[len*r+c]); } else { printf(" %c ", aSmatrix->num2char[r]); } } printf("\n"); } } /** * reads score matrix from the file * indicated by filename parameter. * * The pointer returned (and the ones included in the struct) * has to be deallocted explicitely from memory. */ struct scr_matrix* read_scr_matrix(char *filename) { if(para->DEBUG) printf("DEBUG read_scr_matrix(): Processing input file: %s\n", filename); int length = 0; struct scr_matrix *smatrix = calloc(1, sizeof(struct scr_matrix)); int *char2num = (smatrix->char2num =calloc(256, sizeof(int))); int *num2char = (smatrix->num2char =calloc(256, sizeof(int))); if(smatrix==NULL || char2num==NULL) error("read_scr_matrix(): Out of memory !"); FILE *fp; char rline[100]; if( (fp = fopen( filename , "r")) == NULL) { merror("read_scr_matrix(): Cannot open input score matrix file", filename ); } int sret; char amino; while( (sret=fscanf(fp, " %c ", &amino))!=EOF && sret>0) { if(amino=='#') { break; } else { num2char[length]=amino; char2num[(int)amino]=length++; } } num2char[length]='?'; char2num[(int)'?']=length++; num2char[length]='#'; char2num[(int)'#']=length++; num2char[length]='$'; char2num[(int)'$']=length++; int additional=3; if(sret==EOF) merror("read_scr_matrix(): Unexpected end of file ",filename); if(length==0) merror("read_scr_matrix(): Invalid format of file ",filename); smatrix->length = length; int *data = (smatrix->data = calloc(length*length, sizeof(int))); if(data==NULL) error("read_scr_matrix(): Out of memory when allocating data !"); // read the matrix entries int r,c; int is;//,tis; long double frac = (long double)2.0/(long double)(length*length); long double avg_score = 0.0; // generate Array from Matrix for( r=0; rSCR_MATRIX_ADD; if(smatrix->max_scoremax_score =is; avg_score += (long double)is*frac; data[length*r+c] = is; // ensure symmetry of the weight matrix data[length*c+r] = is; } fscanf(fp, "%s\n", rline); } fclose(fp); // Array is a symmetric Matrix /************************************ vvv Vorsicht !!! ***********/ smatrix->avg_sim_score = para->PROT_SIM_SCORE_THRESHOLD; int ms = smatrix->max_score; int *dist = (smatrix->dist=calloc(ms+1, sizeof(int))); for(r=0;r='A') && (num2char[r]<='Z')) if(num2char[c]!='X' && (num2char[c] >='A') && (num2char[c]<='Z')) dist[data[length*r+c]]++; } } return smatrix; } /** * reads the probability distribution for diagonal lengths from the file * indicated by filename parameter. * * The pointer returned (and the ones included in the struct) * has to be deallocted explicitely from memory. */ struct prob_dist* read_diag_prob_dist(struct scr_matrix* smatrix, char *filename) { if(para->DEBUG>1) printf("DEBUG read_diag_prob_dist(): Processing input file: %s\n", filename); int length = 0; struct prob_dist *pdist = calloc(1, sizeof(struct prob_dist)); pdist->smatrix = smatrix; if(pdist==NULL) error("read_diag_prob_dist(): Out of memory !"); FILE *fp; if( (fp = fopen( filename , "r")) == NULL) { merror("read_diag_prob_dist(): Cannot open input file", filename ); } int sret; sret=fscanf(fp, "%i\n", &length); if(sret<=0) merror("read_diag_prob_dist(): Invalid format in file", filename ); if(length==0) merror("read_scr_matrix(): Invalid format of file ",filename); // fscanf(fp, "%s\n", rline); // printf("rline:%s %i\n",rline, length); // length=40; pdist->max_dlen = length; pdist->data = calloc(length+1, sizeof(long double *)); long double **dist =pdist->data; if(dist==NULL) error("read_diag_prob_dist(): (1) Out of memory when allocating data !"); pdist->log_data = calloc(length+1, sizeof(double *)); double **log_dist =pdist->log_data; if(log_dist==NULL) error("read_diag_prob_dist(): (1.1) Out of memory when allocating data !"); // read the entries unsigned long i, scr, mxscr, sm_max_scr=smatrix->max_score; unsigned long ti, tscr; long double weight; long size=0; for( i=1; i<=length; i++) { mxscr = i*sm_max_scr; size += mxscr+1; dist[i] = calloc(mxscr+1, sizeof(long double )); log_dist[i] = calloc(mxscr+1, sizeof(long double )); if(dist[i]==NULL) error("read_diag_prob_dist(): (3) Out of memory at iteration" ); for(scr=0;scr<=mxscr;scr++) { dist[i][scr]=1.0; } for(scr=0;scr<=mxscr;scr++) { dist[i][scr]=1.0; fscanf( fp, "%li %li %Le\n", &ti,&tscr,&weight ); //if(i!=ti || tscr!=scr) merror("read_scr_matrix(): (4) Invalid format of file ",filename); scr = tscr; if(weight==0.0) weight = 1.0; dist[i][scr]=weight; log_dist[i][scr]=-log(weight); if(para->DEBUG>5)printf("%li %li %Le\n", i, scr,dist[i][scr] ); } } if(para->DEBUG >1) printf("DEBUG: PROB DIST SIZE: %li bytes\n", size*sizeof(long double)+length*sizeof(long double *)); //pdist->avg_sim_score = 4; return pdist; } /** * reads sequence collection (seq_col) from the file * indicated by filename parameter. * * The pointer returned (and the ones included in the struct) * has to be deallocted explicitely from memory. */ struct seq_col* read_fasta(char *filename) { if(para->DEBUG) printf("DEBUG read_seq_col(): Processing input file: %s\n", filename); struct seq_col *scol = calloc(1, sizeof(struct seq_col)); struct seq* seqs = (scol->seqs = calloc(para->MAX_SEQ_AMOUNT, sizeof(struct seq))); struct seq* seq; if(scol==NULL || seqs==NULL) error("read_fasta(): Out of memory !"); FILE *fp; char rline[para->MAX_FASTA_LINE_LENGTH]; if( (fp = fopen( filename , "r")) == NULL) { merror("read_fasta(): Cannot open input FASTA file", filename ); } scol->length = 0; char *data; char ch; unsigned int *slen; int data_maxlen; int c, rlen; int valid =0; char long_name=0; int name_length; while( fgets( rline , para->MAX_FASTA_LINE_LENGTH+1, fp ) != NULL ) { // if(para->DEBUG) // printf(rline); strip_leading_ws(rline); rlen = strlen(rline); if(rline[0] == '>') { valid = 1; long_name=1; seq = &(scol->seqs[scol->length]); seq->max_seen = 0; seq->name = calloc(rlen, sizeof(char)); seq->num = scol->length; seq->orf_frame=0; seq->crick_strand=0; strncpy(seq->name, &(rline[1]), rlen-2); slen = (unsigned int *) &(seq->length); *slen = 0; data_maxlen = 1024; seq->data = (data = calloc(data_maxlen, sizeof(char))); if(data==NULL) error("read_fasta(): Out of memory: seq->data alloc"); scol->length++; if(rlen < para->MAX_FASTA_LINE_LENGTH) { long_name = 0; // if relen = then line is longer } } else if(long_name) { long_name=1; if(rlen < para->MAX_FASTA_LINE_LENGTH) { long_name = 0; // if relen = then line is longer rline[rlen-1]='\0'; } name_length = strlen(seq->name); if(NULL == (seq->name = realloc(seq->name,rlen + name_length) ) ) { error("read_fasta(): Out of memory: seq->data realloc"); } strcat(seq->name, rline); } else { for( c=0;c= 65 && ch < 91) || (ch >= 97 && ch < 123)) { if(! valid) merror("read_fasta(): File is not in FASTA format:", filename); // realloc memory when necessary if(*slen >= data_maxlen) { data_maxlen += 1024; seq->data = (data = realloc(data, data_maxlen*sizeof(char))); if(data==NULL) error("read_fasta(): Out of memory: seq->data alloc"); } data[(*slen)++] = ((ch >= 97) ? toupper(ch) : ch); } } } } int avg=0; for(c=0;clength;c++) { avg += scol->seqs[c].length; } scol->avg_length = avg/scol->length; if(para->DEBUG) printf("\n"); fclose(fp); return scol; } /** * reads the given anchor file and returns the accordingly created * simple_diag_col structure pointer */ struct simple_diag_col* read_anchors(char *filename, struct seq_col* scol) { if(para->DEBUG) printf("DEBUG read_anchors(): Processing anchor file: %s\n", filename); struct simple_diag_col *sdcol = malloc(sizeof(struct simple_diag_col)); FILE *fp; if( (fp = fopen( filename , "r")) == NULL) { merror("read_anchros(): Cannot open input anchor file", filename ); } //fscanf( fp, "%li %li %Le\n", &ti,&tscr,&weight ); long int s1,s2,sp1,sp2,len; double score; int alloc_size = 64; sdcol->data = malloc(sizeof (struct diag*)*alloc_size); sdcol->length=0; while( fscanf(fp,"%li %li %li %li %li %le\n",&s1,&s2,&sp1,&sp2,&len,&score ) == 6) { if(sdcol->length >= alloc_size) { alloc_size+=16; sdcol->data = realloc(sdcol->data,sizeof (struct diag*)*alloc_size); } sdcol->data[sdcol->length]= create_diag(s1-1,&(scol->seqs[s1-1]),sp1-1, s2-1,&(scol->seqs[s2-1]),sp2-1,len); sdcol->data[sdcol->length]->anchor = 1; sdcol->data[sdcol->length]->meetsThreshold = 1; //printf(" total weight %e\n", score); sdcol->data[sdcol->length++]->total_weight = score; } if(para->DEBUG) printf("DEBUG read_anchors(): Read %i anchors from file\n", sdcol->length); fclose(fp); return sdcol; } /** * prints the given alignment in a simple way. */ void simple_print_alignment_default(struct alignment *algn) { struct seq_col *scol = algn->scol; unsigned int slen = scol->length; unsigned int i,j,s,pos,max,tmax; struct seq* sq; struct algn_pos **ap = algn->algn; int proc[slen]; // char proceed[slen]; for(i=0;imax_pos; struct algn_pos *ap1; // // print block // WARNING! print_info reallocates memory, this loses the algn pointer // since the new one is not stored when it is returned here, so it cannot // be freed later. In the present version the leak is relatively minor and // should not crash anything. // printf("%s",print_info(algn)); printf("\n ALIGNMENT OUTPUT:\n"); printf(" -----------------\n\n"); // printf("%i\n", max); for(pos=0;posmax) tmax = max; for(s=0;sseqs[s]; for(j=pos;jname, proc[s]+1); } else if( (j%10)==0) { printf(" "); } if(proc[s]length) { ap1 = find_eqc(ap,s,proc[s]); if( (*ap1->eqcAlgnPos) < j) { printf ("\nALARM %i %i %i %i\n", s,j, proc[s], *ap1->eqcAlgnPos); } // if(proc[0]==244 && s==0) printf("\nMOVE FORWARD: %i %i %i\n",j, *ap[0][244].eqcAlgnPos, *ap[1][241].eqcAlgnPos); if( (*ap1->eqcAlgnPos) == j) { if(ap1->state & para->STATE_ORPHANE) { printf("%c", tolower(sq->data[proc[s]])); } else { printf("%c", toupper(sq->data[proc[s]])); } proc[s]++; } else { printf("-"); //printf("%i",*ap[s][proc[s]].maxpos); } } else { printf("-"); //printf("%i",*ap[s][proc[s]].maxpos); // printf("\n%i %i %i\n", s, j,proc[s]); } } printf("\n"); } printf("\n"); printf("\n"); } } void simple_print_alignment_dna_retranslate(struct alignment *algn) { char *tmp = "000"; struct seq_col *scol = algn->scol; unsigned int slen = scol->length; unsigned int i,j,s,pos,max,tmax; struct seq* sq; struct algn_pos **ap = algn->algn; int proc[slen]; // char proceed[slen]; for(i=0;imax_pos; struct algn_pos *ap1; // // print block // printf("%s",print_info(algn)); printf("\n ALIGNMENT OUTPUT:\n"); printf(" -----------------\n\n"); // printf("%i\n", max); for(pos=0;posmax) tmax = max; for(s=0;sseqs[s]; for(j=pos;jname, ((proc[s])*3)+1); } else if( (j%4)==0) { printf(" "); } if(proc[s]length) { ap1 = find_eqc(ap,s,proc[s]); if( (*ap1->eqcAlgnPos) < j) { printf ("\nALARM %i %i %i %i\n", s,j, proc[s], *ap1->eqcAlgnPos); } // if(proc[0]==244 && s==0) printf("\nMOVE FORWARD: %i %i %i\n",j, *ap[0][244].eqcAlgnPos, *ap[1][241].eqcAlgnPos); if( (*ap1->eqcAlgnPos) == j) { tmp = retranslate(sq->dna_num[proc[s]]); if(ap1->state & para->STATE_ORPHANE) { printf("%c%c%c", tolower(tmp[0]),tolower(tmp[1]), tolower(tmp[2]) ); } else { printf("%c%c%c", toupper(tmp[0]), toupper(tmp[1]), toupper(tmp[2]) ); } proc[s]++; } else { printf("---"); //printf("%i",*ap[s][proc[s]].maxpos); } } else { printf("---"); //printf("%i",*ap[s][proc[s]].maxpos); // printf("\n%i %i %i\n", s, j,proc[s]); } } printf("\n"); } printf("\n"); printf("\n"); } } /** * prints the given alignment in fasta format * to the given file. */ void fasta_print_alignment_default(struct alignment *algn, char *filename) { struct seq_col *scol = algn->scol; unsigned int slen = scol->length; unsigned int j,s,proc, max; struct seq* sq; struct algn_pos **ap = algn->algn; prepare_alignment(algn); max = algn->max_pos; struct algn_pos *ap1; FILE *fp; if( (fp = fopen( filename , "w")) == NULL) { merror("fasta_print_alignment(): Cannot open file", filename ); } // fprintf(fp,"%s",print_info(algn)); max = algn->max_pos; for(s=0;sseqs[s]); fprintf(fp, ">%s",sq->name); proc = 0; for(j=0;jlength) { if( (j%60)==0) fprintf(fp,"\n"); ap1 = find_eqc(ap,s,proc); if(*ap1->eqcAlgnPos==j) { if(ap1->state & para->STATE_ORPHANE) { fprintf(fp, "%c", tolower(sq->data[proc])); } else { fprintf(fp, "%c", toupper(sq->data[proc])); } proc++; } else { fprintf(fp,"-"); } } else { if( (j%60)==0) fprintf(fp,"\n"); fprintf(fp,"-"); } } fprintf(fp,"\n"); } fclose(fp); } void fasta_print_alignment_dna_retranslate(struct alignment *algn, char *filename) { char *tmp = "000"; struct seq_col *scol = algn->scol; unsigned int slen = scol->length; unsigned int j,s,proc, max; struct seq* sq; struct algn_pos **ap = algn->algn; prepare_alignment(algn); max = algn->max_pos; struct algn_pos *ap1; FILE *fp; if( (fp = fopen( filename , "w")) == NULL) { merror("fasta_print_alignment(): Cannot open file", filename ); } // fprintf(fp,"%s",print_info(algn)); max = algn->max_pos; for(s=0;sseqs[s]); fprintf(fp, ">%s",sq->name); proc = 0; for(j=0;jlength) { if( (j%20)==0) fprintf(fp,"\n"); ap1 = find_eqc(ap,s,proc); if(*ap1->eqcAlgnPos==j) { tmp = retranslate(sq->dna_num[proc]); // printf(fp,"%c,\n",sq->dna_num[proc]); if(ap1->state & para->STATE_ORPHANE) { fprintf(fp, "%c%c%c", tolower(tmp[0]),tolower(tmp[1]), tolower(tmp[2])); } else { fprintf(fp, "%c%c%c", toupper(tmp[0]), toupper(tmp[1]), toupper(tmp[2])); } proc++; } else { fprintf(fp,"---"); } } else { if( (j%20)==0) fprintf(fp,"\n"); fprintf(fp,"---"); } } fprintf(fp,"\n"); } fclose(fp); } char* print_info(struct alignment *algn) { int i; char *output; char *line, *line2; if(NULL == ( output = (calloc(63,sizeof(char))))) { error("print_info(): Out of memory !"); } strcat(output, "\n"); for(i=0;i!=60; ++i) { strcat(output, "*"); } strcat(output, "\n"); if (para->DNA_TRANSLATION) { if(para->FIND_ORF){ if(!para->ORF_FRAME){ // -L : if(NULL == ( line = (calloc(62, sizeof(char))))) { error("print_info(): Out of memory !"); } if(NULL == ( output = (realloc(output,strlen(output)+15*61)))) { error("print_info(): Out of memory !"); } line = "Multiple Sequence Alignment (with translation)"; line = output_line(line); strcat(output, line); line = "Input sequences in DNA"; line = output_line(line); strcat(output, line); if(!para->OUTPUT) line = "Alignment output in aminoacids"; else line = "Alignment output in DNA"; line = output_line(line); strcat(output, line); line = "Sequences translated into aminoacids"; line = output_line(line); strcat(output, line); line = "Only longest open reading frames aligned"; line = output_line(line); strcat(output, line); line = "Sequence lengths cut mod 3 = 0"; line = output_line(line); strcat(output, line); strcat(output,blank_line()); line = "reading frame 1 : 123 123 123 123 ..."; line = output_line_left(line); strcat(output, line); line = "reading frame 2 : X 123 123 123 123 ..."; line = output_line_left(line); strcat(output, line); line = "reading frame 3 : XX 123 123 123 123 ..."; line = output_line_left(line); strcat(output, line); line = "reading frame 4 : ... 321 321 321 321 XX"; line = output_line_left(line); strcat(output, line); line = "reading frame 5 : ... 321 321 321 321 X"; line = output_line_left(line); strcat(output, line); line = "reading frame 6 : ... 321 321 321 321"; line = output_line_left(line); strcat(output, line); strcat(output,blank_line()); strcat(output,blank_line()); for (i = 0; i != algn->scol->length; ++i) { int k; char *tmp; int tmp2; tmp = " : reading frame = "; line[0] = algn->scol->seqs[i].name[0]; for(k=1; k!=12 ; ++k) { line[k]=algn->scol->seqs[i].name[k]; tmp2=algn->scol->seqs[i].orf_frame+48; } line[12]='\0'; strcat(line, tmp); line[strlen(line)-1]=tmp2; line[strlen(line)]='\0'; if(NULL == ( output = (realloc(output,strlen(output)+62)))) { error("print_info(): Out of memory !"); } line = output_line(line); strcat(output, line); } free(line); } else{ // -O : if(NULL == ( line = (calloc(62, sizeof(char))))) { error("print_info(): Out of memory !"); } if(NULL == ( output = (realloc(output,strlen(output)+15*61)))) { error("print_info(): Out of memory !"); } line = "Multiple Sequence Alignment (with translation)"; line = output_line(line); strcat(output, line); line = "Input sequences in DNA"; line = output_line(line); strcat(output, line); if(!para->OUTPUT) line = "Alignment output in aminoacids"; else line = "Alignment output in DNA"; line = output_line(line); strcat(output, line); line = "Sequences translated into aminoacids"; line = output_line(line); strcat(output, line); line = "reading frames found due to longest ORF"; line = output_line(line); strcat(output, line); line = "Sequence lengths cut mod 3 = 0"; line = output_line(line); strcat(output, line); strcat(output,blank_line()); line = "reading frame 1 : 123 123 123 123 ..."; line = output_line_left(line); strcat(output, line); line = "reading frame 2 : X 123 123 123 123 ..."; line = output_line_left(line); strcat(output, line); line = "reading frame 3 : XX 123 123 123 123 ..."; line = output_line_left(line); strcat(output, line); line = "reading frame 4 : ... 321 321 321 321 XX"; line = output_line_left(line); strcat(output, line); line = "reading frame 5 : ... 321 321 321 321 X"; line = output_line_left(line); strcat(output, line); line = "reading frame 6 : ... 321 321 321 321"; line = output_line_left(line); strcat(output, line); strcat(output,blank_line()); strcat(output,blank_line()); for (i = 0; i != algn->scol->length; ++i) { int k; char *tmp; int tmp2; tmp = " : reading frame = "; line[0] = algn->scol->seqs[i].name[0]; for(k=1; k!=12 ; ++k) { line[k]=algn->scol->seqs[i].name[k]; tmp2=algn->scol->seqs[i].orf_frame+48; } line[12]='\0'; strcat(line, tmp); line[strlen(line)-1]=tmp2; line[strlen(line)]='\0'; if(NULL == ( output = (realloc(output,strlen(output)+62)))) { error("print_info(): Out of memory !"); } line = output_line(line); strcat(output, line); } free(line); } } else{ // -T : if(NULL == ( line = (calloc(62, sizeof(char))))) { error("print_info(): Out of memory !"); } if(NULL == ( output = (realloc(output,strlen(output)+5*61)))) { error("print_info(): Out of memory !"); } line = "Multiple Sequence Alignment (with translation)"; line = output_line(line); strcat(output, line); line = "Input sequences in DNA"; line = output_line(line); strcat(output, line); if(!para->OUTPUT) line = "Alignment output in aminoacids"; else line = "Alignment output in DNA"; line = output_line(line); strcat(output, line); line = "Sequences translated into aminoacids"; line = output_line(line); strcat(output, line); line = "Sequence lengths cut mod 3 = 0"; line = output_line(line); strcat(output, line); free(line); } } else{ // -D : if(NULL == ( line = (calloc(62, sizeof(char))))) { error("print_info(): Out of memory !"); } if(NULL == ( line2 = (calloc(62, sizeof(char))))) { error("print_info(): Out of memory !"); } if(NULL == ( output = (realloc(output,strlen(output)+3*61+1)))) { error("print_info(): Out of memory !"); } (void) strcpy(line,"Multiple Sequence Alignment"); line = output_line(line); strcat(output, line); if(para->DNA_PARAMETERS) (void) strcpy(line2,"in DNA"); else (void) strcpy(line2,"in aminoacids"); sprintf(line,"Input sequences %s", line2); line = output_line(line); strcat(output, line); if(para->DNA_PARAMETERS) (void) strcpy(line2,"in DNA"); else (void) strcpy(line2,"in aminoacids"); sprintf(line,"Alignment output %s", line2); line = output_line(line); strcat(output, line); free(line); free(line2); } if(NULL == ( output = (realloc(output,strlen(output)+63)))) { error("print_info(): Out of memory !"); } for(i=0;i!=60; ++i) { strcat(output, "*"); } strcat(output, "\n\n"); return output; } /*SIDE EFFECT, releases original memory held by string */ char* output_line(char *string) { char *tmp; if(NULL == ( tmp = (calloc(62, sizeof(char))))) { error("print_info(): Out of memory !"); } int x, i, y; y = 0; if (strlen(string) %2 == 0) y = 1; x = (60 - strlen(string)) /2 ; strcat(tmp, "*"); for (i = 0; i != x-y; ++i) { strcat(tmp, " "); } strcat(tmp,string); for (i = 0; i != x-1; ++i) { strcat(tmp, " "); } strcat(tmp, "*\n"); free(string); string=&(tmp[0]); return string; } /*SIDE EFFECT, releases original memory held by string */ char* output_line_left(char *string) { char *tmp; if(NULL == ( tmp = (calloc(62, sizeof(char))))) { error("print_info(): Out of memory !"); } int x, i, y; y = 0; x = (60 - strlen(string)-3) ; strcat(tmp, "* "); strcat(tmp,string); for (i = 0; i != x; ++i) { strcat(tmp, " "); } strcat(tmp, "*\n"); free(string); string=&(tmp[0]); return string; } char* blank_line() { int i; char *string; if(NULL == ( string = (calloc(62,sizeof(char))))) { error("print_info(): Out of memory !"); } strcat(string, "*"); for (i = 0; i != 58; ++i) { strcat(string, " "); } strcat(string, "*\n"); return string; } void print_pdist_matrix(struct prob_dist *sdist, char *filename) { int lh, scr, mxscr; FILE *fp; if( (fp = fopen( filename , "w")) == NULL) { merror("fasta_print_alignment(): Cannot open file", filename ); } fprintf(fp,"%d\n",sdist->max_dlen); for(lh=1; lh!=sdist->max_dlen+1; ++lh) { mxscr = lh * sdist->smatrix->max_score; for(scr=0; scr!=mxscr+1; ++scr) { fprintf(fp,"%d %d %Le\n",lh,scr,sdist->data[lh][scr]); } } } abyss-1.3.6/dialign/io.h000644 002433 001057 00000003667 11746352100 016561 0ustar00traymondassembly000000 000000 /** * * io.h: * * 2004-08-30 Dorothea Emig Volker Menrad * */ /************************************************/ /* */ /* structs */ /* */ /************************************************/ /************************************************/ /* */ /* global variable */ /* */ /************************************************/ /*********************************************/ /* */ /* functions from io.c */ /* */ /*********************************************/ void version(); // prints version on stdout void print_scr_matrix(struct scr_matrix* aSmatrix); struct scr_matrix* read_scr_matrix(char *filename); void print_seq(struct seq* aSeq); struct seq_col* read_fasta(char *filename); void print_diag(struct diag* aDiag); struct prob_dist* read_diag_prob_dist(struct scr_matrix* smatrix, char *filename); void simple_print_alignment_default(struct alignment *algn); void simple_print_alignment_dna_retranslate(struct alignment *algn); //void simple_print_alignment_dna(struct alignment *algn); void fasta_print_alignment_default(struct alignment *algn, char *filename); void fasta_print_alignment_dna_retranslate(struct alignment *algn, char *filename); //void fasta_print_alignment_dna(struct alignment *algn, char *filename); char *print_info(struct alignment *align); char *output_line(char *string); char *output_line_left(char *string); char *blank_line(); void print_pdist_matrix(struct prob_dist *sdist,char *filename); void error(char *message); void merror(char *msg1, char *msg2); char* build_pathname(char *dir, char *file); abyss-1.3.6/dialign/orf.c000644 002433 001057 00000112123 11746352100 016717 0ustar00traymondassembly000000 000000 /** * * orf.c: find the longest Open Reading Frame * * 2004-08-24 Dorothea Emig Volker Menrad * */ #include #include #include "parameters.h" #include "struct.h" #include "translate.h" #include "orf.h" #include "io.h" struct seq_col* set_longest_orf(struct seq_col *in_seq_col) { int i; struct seq_col *ret_seq_col; struct seq *seq, *input_seq; if((ret_seq_col = calloc(1,sizeof(struct seq_col)))==NULL) { error("set_longest_orf(): Out of memory "); } if((ret_seq_col->seqs = calloc((in_seq_col->length),sizeof(struct seq)))==NULL) { error("set_longest_orf(): Out of memory "); } input_seq = &(in_seq_col->seqs[0]); for(i=0; i!= in_seq_col->length; ++i) { seq = orf_finder(input_seq); ++input_seq; ret_seq_col->seqs[i].dna_num = seq->dna_num; ret_seq_col->seqs[i].orf_frame = seq->orf_frame; ret_seq_col->seqs[i].data = seq->data; ret_seq_col->seqs[i].name = seq->name; ret_seq_col->seqs[i].num = seq->num; ret_seq_col->seqs[i].length = seq->length; ++seq; } ret_seq_col->length=in_seq_col->length; return ret_seq_col; } struct seq* orf_finder(struct seq *in_seq) { char flag_no_start = 1; struct seq *ret_seq; struct orf **orfs; int i, max_length, max_orf; char a,b,c,d,e,f; // first three possible reading frames and last three int help, j, x; // XXX........XXX j = (in_seq->length)/3; help = in_seq->length-1; // index of last element in sequence a=0;b=0;c=0;d=0;e=0;f=0; if((orfs = (calloc (12, sizeof(struct orf *)))) == NULL) // We need 12 because we look for the longest orf in every reading frame // and save the longest for every reading frame = 6 // orf[0] && orf[1] for reading frame a // orf[2] && orf[3] for reading frame b // orf[4] && orf[5] for reading frame c // orf[6] && orf[7] for reading frame d // orf[8] && orf[9] for reading frame e // orf[10] && orf[11] for reading frame f { error("orf_finder(): Out of memory !"); } for (x = 0; x != 12; ++x) { if((orfs[x] = (calloc(1,sizeof(struct orf))))==NULL) { error("orf_finder(): Out of memory !"); } if((orfs[x]->sequence = (calloc(j+1,sizeof(char))))==NULL) { error("orf_finder(2): Out of memory !"); } if((orfs[x]->dna_num = (calloc(j+1,sizeof(char))))==NULL) { error("orf_finder(3): Out of memory !"); } orfs[x]->finish = 0; } for (i = 0; i < (j*3)-3; ++i) { /****************************************************************************************/ if (a == 1) { if(!(orfs[0]->finish)) { if((in_seq->data[i] == 'T' && in_seq->data[i+1] == 'A' && in_seq->data[i+2] == 'A') || (in_seq->data[i] == 'U' && in_seq->data[i+1] == 'A' && in_seq->data[i+2] == 'A') || (in_seq->data[i] == 'T' && in_seq->data[i+1] == 'A' && in_seq->data[i+2] == 'G') || (in_seq->data[i] == 'U' && in_seq->data[i+1] == 'A' && in_seq->data[i+2] == 'G') || (in_seq->data[i] == 'T' && in_seq->data[i+1] == 'G' && in_seq->data[i+2] == 'A') || (in_seq->data[i] == 'U' && in_seq->data[i+1] == 'G' && in_seq->data[i+2] == 'A') ) //Stop-Codon then end orf { orfs[0]->finish = 1; // end orf a=0; // wait for new ATG-Start-Codon } orfs[0]->sequence[(orfs[0]->length)] = translate(in_seq->data[i], in_seq->data[i+1], in_seq->data[i+2], &(orfs[0]->dna_num[(orfs[0]->length)]) ); // translate in aminoacid and safe in orf ++orfs[0]->length; } else { if((in_seq->data[i] == 'T' && in_seq->data[i+1] == 'A' && in_seq->data[i+2] == 'A') || (in_seq->data[i] == 'U' && in_seq->data[i+1] == 'A' && in_seq->data[i+2] == 'A') || (in_seq->data[i] == 'T' && in_seq->data[i+1] == 'A' && in_seq->data[i+2] == 'G') || (in_seq->data[i] == 'U' && in_seq->data[i+1] == 'A' && in_seq->data[i+2] == 'G') || (in_seq->data[i] == 'T' && in_seq->data[i+1] == 'G' && in_seq->data[i+2] == 'A') || (in_seq->data[i] == 'U' && in_seq->data[i+1] == 'G' && in_seq->data[i+2] == 'A') ) { orfs[1]->finish = 1; a=0; } orfs[1]->sequence[(orfs[1]->length)] = translate(in_seq->data[i], in_seq->data[i+1], in_seq->data[i+2],&(orfs[1]->dna_num[(orfs[1]->length)])); ++orfs[1]->length; } } /****************************************************************************************/ if (b == 1) { if(!(orfs[2]->finish)) { if((in_seq->data[i+1] == 'T' && in_seq->data[i+2] == 'A' && in_seq->data[i+3] == 'A') || (in_seq->data[i+1] == 'U' && in_seq->data[i+2] == 'A' && in_seq->data[i+3] == 'A') || (in_seq->data[i+1] == 'T' && in_seq->data[i+2] == 'A' && in_seq->data[i+3] == 'G') || (in_seq->data[i+1] == 'U' && in_seq->data[i+2] == 'A' && in_seq->data[i+3] == 'G') || (in_seq->data[i+1] == 'T' && in_seq->data[i+2] == 'G' && in_seq->data[i+3] == 'A') || (in_seq->data[i+1] == 'U' && in_seq->data[i+2] == 'G' && in_seq->data[i+3] == 'A') ) //Stop-Codon then end orf { orfs[2]->finish = 1; // end orf b=0; // wait for new ATG-Start-Codon } orfs[2]->sequence[(orfs[2]->length)] = translate(in_seq->data[i+1], in_seq->data[i+2], in_seq->data[i+3],&(orfs[2]->dna_num[(orfs[2]->length)]) ); // translate in aminoacid and safe in orf ++orfs[2]->length; } else { if((in_seq->data[i+1] == 'T' && in_seq->data[i+2] == 'A' && in_seq->data[i+3] == 'A') || (in_seq->data[i+1] == 'U' && in_seq->data[i+2] == 'A' && in_seq->data[i+3] == 'A') || (in_seq->data[i+1] == 'T' && in_seq->data[i+2] == 'A' && in_seq->data[i+3] == 'G') || (in_seq->data[i+1] == 'U' && in_seq->data[i+2] == 'A' && in_seq->data[i+3] == 'G') || (in_seq->data[i+1] == 'T' && in_seq->data[i+2] == 'G' && in_seq->data[i+3] == 'A') || (in_seq->data[i+1] == 'U' && in_seq->data[i+2] == 'G' && in_seq->data[i+3] == 'A') ) { orfs[3]->finish = 1; b=0; } orfs[3]->sequence[(orfs[3]->length)] = translate(in_seq->data[i+1], in_seq->data[i+2], in_seq->data[i+3],&(orfs[3]->dna_num[(orfs[3]->length)]) ); ++orfs[3]->length; } } /****************************************************************************************/ if (c == 1) { if(!(orfs[4]->finish)) { if((in_seq->data[i+2] == 'T' && in_seq->data[i+3] == 'A' && in_seq->data[i+4] == 'A') || (in_seq->data[i+2] == 'U' && in_seq->data[i+3] == 'A' && in_seq->data[i+4] == 'A') || (in_seq->data[i+2] == 'T' && in_seq->data[i+3] == 'A' && in_seq->data[i+4] == 'G') || (in_seq->data[i+2] == 'U' && in_seq->data[i+3] == 'A' && in_seq->data[i+4] == 'G') || (in_seq->data[i+2] == 'T' && in_seq->data[i+3] == 'G' && in_seq->data[i+4] == 'A') || (in_seq->data[i+2] == 'U' && in_seq->data[i+3] == 'G' && in_seq->data[i+4] == 'A') ) //Stop-Codon then end orf { orfs[4]->finish = 1; // end orf c=0; // wait for new ATG-Start-Codon } orfs[4]->sequence[(orfs[4]->length)] = translate(in_seq->data[i+2], in_seq->data[i+3], in_seq->data[i+4],&(orfs[4]->dna_num[(orfs[4]->length)])); // translate in aminoacid and safe in orf ++orfs[4]->length; } else { if((in_seq->data[i+2] == 'T' && in_seq->data[i+3] == 'A' && in_seq->data[i+4] == 'A') || (in_seq->data[i+2] == 'U' && in_seq->data[i+3] == 'A' && in_seq->data[i+4] == 'A') || (in_seq->data[i+2] == 'T' && in_seq->data[i+3] == 'A' && in_seq->data[i+4] == 'G') || (in_seq->data[i+2] == 'U' && in_seq->data[i+3] == 'A' && in_seq->data[i+4] == 'G') || (in_seq->data[i+2] == 'T' && in_seq->data[i+3] == 'G' && in_seq->data[i+4] == 'A') || (in_seq->data[i+2] == 'U' && in_seq->data[i+3] == 'G' && in_seq->data[i+4] == 'A') ) { orfs[5]->finish = 1; c=0; } orfs[5]->sequence[(orfs[5]->length)] = translate(in_seq->data[i+2], in_seq->data[i+3], in_seq->data[i+4],&(orfs[5]->dna_num[(orfs[5]->length)]) ); ++orfs[5]->length; } } /****************************************************************************************/ /****************************************************************************************/ if (d == 1) { if(!(orfs[6]->finish)) /* Da Crick-Strand : TAA -> ATT UAA -> AUU TAG -> ATC UAG -> AUC TGA -> ACT UGA -> ACU */ { if((in_seq->data[help-(i+2)] == 'A' && in_seq->data[help-(i+3)] == 'T' && in_seq->data[help-(i+4)] == 'T') || (in_seq->data[help-(i+2)] == 'A' && in_seq->data[help-(i+3)] == 'U' && in_seq->data[help-(i+4)] == 'U') || (in_seq->data[help-(i+2)] == 'A' && in_seq->data[help-(i+3)] == 'T' && in_seq->data[help-(i+4)] == 'C') || (in_seq->data[help-(i+2)] == 'A' && in_seq->data[help-(i+3)] == 'U' && in_seq->data[help-(i+4)] == 'C') || (in_seq->data[help-(i+2)] == 'A' && in_seq->data[help-(i+3)] == 'C' && in_seq->data[help-(i+4)] == 'T') || (in_seq->data[help-(i+2)] == 'A' && in_seq->data[help-(i+3)] == 'C' && in_seq->data[help-(i+4)] == 'U') ) //Stop-Codon then end orf { orfs[6]->finish = 1; // end orf d=0; // wait for new ATG-Start-Codon } orfs[6]->sequence[(orfs[6]->length)] = translate(inverse(in_seq->data[help-(i+2)]), inverse(in_seq->data[help-(i+3)]), inverse(in_seq->data[help-(i+4)]),&(orfs[6]->dna_num[(orfs[6]->length)]) ); // translate in aminoacid and safe in orf ++orfs[6]->length; } else { if((in_seq->data[help-(i+2)] == 'A' && in_seq->data[help-(i+3)] == 'T' && in_seq->data[help-(i+4)] == 'T') || (in_seq->data[help-(i+2)] == 'A' && in_seq->data[help-(i+3)] == 'U' && in_seq->data[help-(i+4)] == 'U') || (in_seq->data[help-(i+2)] == 'A' && in_seq->data[help-(i+3)] == 'T' && in_seq->data[help-(i+4)] == 'C') || (in_seq->data[help-(i+2)] == 'A' && in_seq->data[help-(i+3)] == 'U' && in_seq->data[help-(i+4)] == 'C') || (in_seq->data[help-(i+2)] == 'A' && in_seq->data[help-(i+3)] == 'C' && in_seq->data[help-(i+4)] == 'T') || (in_seq->data[help-(i+2)] == 'A' && in_seq->data[help-(i+3)] == 'C' && in_seq->data[help-(i+4)] == 'U') ) { orfs[7]->finish = 1; d=0; } orfs[7]->sequence[(orfs[7]->length)] = translate(inverse(in_seq->data[help-(i+2)]), inverse(in_seq->data[help-(i+3)]), inverse(in_seq->data[help-(i+4)]),&(orfs[7]->dna_num[(orfs[7]->length)]) ); ++orfs[7]->length; } } /****************************************************************************************/ if (e == 1) { if(!(orfs[8]->finish)) { if((in_seq->data[help-(i+1)] == 'A' && in_seq->data[help-(i+2)] == 'T' && in_seq->data[help-(i+3)] == 'T') || (in_seq->data[help-(i+1)] == 'A' && in_seq->data[help-(i+2)] == 'U' && in_seq->data[help-(i+3)] == 'U') || (in_seq->data[help-(i+1)] == 'A' && in_seq->data[help-(i+2)] == 'T' && in_seq->data[help-(i+3)] == 'C') || (in_seq->data[help-(i+1)] == 'A' && in_seq->data[help-(i+2)] == 'U' && in_seq->data[help-(i+3)] == 'C') || (in_seq->data[help-(i+1)] == 'A' && in_seq->data[help-(i+2)] == 'C' && in_seq->data[help-(i+3)] == 'T') || (in_seq->data[help-(i+1)] == 'A' && in_seq->data[help-(i+2)] == 'C' && in_seq->data[help-(i+3)] == 'U') ) //Stop-Codon then end orf { orfs[8]->finish = 1; // end orf e=0; // wait for new ATG-Start-Codon } orfs[8]->sequence[(orfs[8]->length)] = translate(inverse(in_seq->data[help-(i+1)]), inverse(in_seq->data[help-(i+2)]), inverse(in_seq->data[help-(i+3)]),&(orfs[8]->dna_num[(orfs[8]->length)]) ); // translate in aminoacid and safe in orf ++orfs[8]->length; } else { if((in_seq->data[help-(i+1)] == 'A' && in_seq->data[help-(i+2)] == 'T' && in_seq->data[help-(i+3)] == 'T') || (in_seq->data[help-(i+1)] == 'A' && in_seq->data[help-(i+2)] == 'U' && in_seq->data[help-(i+3)] == 'U') || (in_seq->data[help-(i+1)] == 'A' && in_seq->data[help-(i+2)] == 'T' && in_seq->data[help-(i+3)] == 'C') || (in_seq->data[help-(i+1)] == 'A' && in_seq->data[help-(i+2)] == 'U' && in_seq->data[help-(i+3)] == 'C') || (in_seq->data[help-(i+1)] == 'A' && in_seq->data[help-(i+2)] == 'C' && in_seq->data[help-(i+3)] == 'T') || (in_seq->data[help-(i+1)] == 'A' && in_seq->data[help-(i+2)] == 'C' && in_seq->data[help-(i+3)] == 'U') ) { orfs[9]->finish = 1; e=0; } orfs[9]->sequence[(orfs[9]->length)] = translate(inverse(in_seq->data[help-(i+1)]), inverse(in_seq->data[help-(i+2)]), inverse(in_seq->data[help-(i+3)]), &(orfs[9]->dna_num[(orfs[9]->length)]) ); ++orfs[9]->length; } } /****************************************************************************************/ if (f == 1) { if(!(orfs[10]->finish)) { if((in_seq->data[help-(i)] == 'A' && in_seq->data[help-(i+1)] == 'T' && in_seq->data[help-(i+2)] == 'T') || (in_seq->data[help-(i)] == 'A' && in_seq->data[help-(i+1)] == 'U' && in_seq->data[help-(i+2)] == 'U') || (in_seq->data[help-(i)] == 'A' && in_seq->data[help-(i+1)] == 'T' && in_seq->data[help-(i+2)] == 'C') || (in_seq->data[help-(i)] == 'A' && in_seq->data[help-(i+1)] == 'U' && in_seq->data[help-(i+2)] == 'C') || (in_seq->data[help-(i)] == 'A' && in_seq->data[help-(i+1)] == 'C' && in_seq->data[help-(i+2)] == 'T') || (in_seq->data[help-(i)] == 'A' && in_seq->data[help-(i+1)] == 'C' && in_seq->data[help-(i+2)] == 'U') ) //Stop-Codon then end orf { orfs[10]->finish = 1; // end orf f=0; // wait for new ATG-Start-Codon } orfs[10]->sequence[(orfs[10]->length)] = translate(inverse(in_seq->data[help-(i)]), inverse(in_seq->data[help-(i+1)]), inverse(in_seq->data[help-(i+2)]), &(orfs[10]->dna_num[(orfs[10]->length)])); // translate in aminoacid and safe in orf ++orfs[10]->length; } else { if((in_seq->data[help-(i)] == 'A' && in_seq->data[help-(i+1)] == 'T' && in_seq->data[help-(i+2)] == 'T') || (in_seq->data[help-(i)] == 'A' && in_seq->data[help-(i+1)] == 'U' && in_seq->data[help-(i+2)] == 'T') || (in_seq->data[help-(i)] == 'A' && in_seq->data[help-(i+1)] == 'T' && in_seq->data[help-(i+2)] == 'C') || (in_seq->data[help-(i)] == 'A' && in_seq->data[help-(i+1)] == 'U' && in_seq->data[help-(i+2)] == 'C') || (in_seq->data[help-(i)] == 'A' && in_seq->data[help-(i+1)] == 'C' && in_seq->data[help-(i+2)] == 'T') || (in_seq->data[help-(i)] == 'A' && in_seq->data[help-(i+1)] == 'C' && in_seq->data[help-(i+2)] == 'U') ) { orfs[11]->finish = 1; f=0; } orfs[11]->sequence[(orfs[11]->length)] = translate(inverse(in_seq->data[help-(i)]), inverse(in_seq->data[help-(i+1)]), inverse(in_seq->data[help-(i+2)]), &(orfs[11]->dna_num[(orfs[11]->length)])); ++orfs[11]->length; } } /****************************************************************************************/ /****************************************************************************************/ if(((in_seq->data[i] == 'A' && in_seq->data[i+1] == 'T' && in_seq->data[i+2] == 'G') && (a==0)) || ( (in_seq->data[i] == 'A' && in_seq->data[i+1] == 'U' && in_seq->data[i+2] == 'G') && (a==0))) { a=1; // start found in first reading frame flag_no_start=0; if(!(orfs[0]->finish)) // orf not yet started in orfs[0] { orfs[0]->length=0; orfs[0]->sequence[(orfs[0]->length)] = translate(in_seq->data[i],in_seq->data[i+1],in_seq->data[i+2], &(orfs[0]->dna_num[(orfs[0]->length)]) ); ++orfs[0]->length; } else if(!(orfs[1]->finish))// orf not yet started in orfs[1] { orfs[1]->length=0; orfs[1]->sequence[(orfs[1]->length)] = translate(in_seq->data[i],in_seq->data[i+1],in_seq->data[i+2], &(orfs[1]->dna_num[(orfs[1]->length)]) ); ++orfs[1]->length; } else // orf finished in orfs[1] and orfs[0], so find the max and delete the min { if((orfs[0]->length) >= (orfs[1]->length)) // orfs[0] = Max { free(orfs[1]->sequence); free(orfs[1]->dna_num); free(orfs[1]); if((orfs[1] = calloc(1, sizeof(struct orf))) == NULL) // free memory error("orf_finder(): Out of memory!"); if((orfs[1]->sequence = calloc(j+1, sizeof(char))) == NULL) error("orf_finder(): Out of memory!"); if((orfs[1]->dna_num = calloc(j+1, sizeof(char))) == NULL) error("orf_finder(): Out of memory!"); orfs[1]->length=0; // new init orfs[1]->finish = 0; orfs[1]->sequence[(orfs[1]->length)] = translate(in_seq->data[i],in_seq->data[i+1],in_seq->data[i+2], &(orfs[1]->dna_num[(orfs[1]->length)]) ); ++orfs[1]->length; } else { free(orfs[0]->dna_num); free(orfs[0]->sequence); free(orfs[0]); if((orfs[0] = calloc(1, sizeof(struct orf))) == NULL) // free memory error("orf_finder(): Out of memory!"); if((orfs[0]->sequence = calloc(j+1, sizeof(char))) == NULL) error("orf_finder(): Out of memory!"); if((orfs[0]->dna_num = calloc(j+1, sizeof(char))) == NULL) error("orf_finder(): Out of memory!"); orfs[0]->length = 0; // new init orfs[0]->finish = 0; orfs[0]->sequence[(orfs[0]->length)] = translate(in_seq->data[i],in_seq->data[i+1],in_seq->data[i+2], &(orfs[0]->dna_num[(orfs[0]->length)]) ); ++orfs[0]->length; } } } /****************************************************************************************/ if(((in_seq->data[i+1] == 'A' && in_seq->data[i+2] == 'T' && in_seq->data[i+3] == 'G') && (b==0)) || ( (in_seq->data[i+1] == 'A' && in_seq->data[i+2] == 'U' && in_seq->data[i+3] == 'G') && (b==0))) { b=1; // start found in second reading frame flag_no_start=0; if(!(orfs[2]->finish)) // orf not yet started in orfs[2] { orfs[2]->length=0; orfs[2]->sequence[(orfs[2]->length)] = translate(in_seq->data[i+1],in_seq->data[i+2],in_seq->data[i+3], &(orfs[2]->dna_num[(orfs[2]->length)]) ); ++orfs[2]->length; } else if(!(orfs[3]->finish))// orf not yet started in orfs[3] { orfs[3]->length=0; orfs[3]->sequence[(orfs[3]->length)] = translate(in_seq->data[i+1],in_seq->data[i+2],in_seq->data[i+3], &(orfs[3]->dna_num[(orfs[3]->length)]) ); ++orfs[3]->length; } else // orf finished in orfs[3] and orfs[2], so find the max and delete the min { if((orfs[2]->length) >= (orfs[3]->length)) // orfs[2] = Max { free(orfs[3]->dna_num); free(orfs[3]->sequence); free(orfs[3]); if((orfs[3] = calloc(1, sizeof(struct orf))) == NULL) // free memory error("orf_finder(): Out of memory!"); if((orfs[3]->sequence = calloc(j+1, sizeof(char))) == NULL) error("orf_finder(): Out of memory!"); if((orfs[3]->dna_num = calloc(j+1, sizeof(char))) == NULL) error("orf_finder(): Out of memory!"); orfs[3]->length=0; // new init orfs[3]->finish = 0; orfs[3]->sequence[(orfs[3]->length)] = translate(in_seq->data[i+1],in_seq->data[i+2],in_seq->data[i+3], &(orfs[3]->dna_num[(orfs[3]->length)]) ); ++orfs[3]->length; } else { free(orfs[2]->dna_num); free(orfs[2]->sequence); free(orfs[2]); if((orfs[2] = calloc(1, sizeof(struct orf))) == NULL) // free memory error("orf_finder(): Out of memory!"); if((orfs[2]->sequence = calloc(j+1, sizeof(char))) == NULL) error("orf_finder(): Out of memory!"); if((orfs[2]->dna_num = calloc(j+1, sizeof(char))) == NULL) error("orf_finder(): Out of memory!"); orfs[2]->length = 0; // new init orfs[2]->finish = 0; orfs[2]->sequence[(orfs[2]->length)] = translate(in_seq->data[i+1],in_seq->data[i+2],in_seq->data[i+3], &(orfs[2]->dna_num[(orfs[2]->length)]) ); ++orfs[2]->length; } } } /****************************************************************************************/ if(((in_seq->data[i+2] == 'A' && in_seq->data[i+3] == 'T' && in_seq->data[i+4] == 'G') && (c==0)) || ( (in_seq->data[i+2] == 'A' && in_seq->data[i+3] == 'U' && in_seq->data[i+4] == 'G') && (c==0) )) { c=1; // start found in third reading frame flag_no_start=0; if(!(orfs[4]->finish)) // orf not yet started in orfs[4] { orfs[4]->length=0; orfs[4]->sequence[(orfs[4]->length)] = translate(in_seq->data[i+2],in_seq->data[i+3],in_seq->data[i+4], &(orfs[4]->dna_num[(orfs[4]->length)]) ); ++orfs[4]->length; } else if(!(orfs[5]->finish))// orf not yet started in orfs[5] { orfs[5]->length=0; orfs[5]->sequence[(orfs[5]->length)] = translate(in_seq->data[i+2],in_seq->data[i+3],in_seq->data[i+4], &(orfs[5]->dna_num[(orfs[5]->length)]) ); ++orfs[5]->length; } else // orf finished in orfs[5] and orfs[4], so find the max and delete the min { if((orfs[4]->length) >= (orfs[5]->length)) // orfs[4] = Max { free(orfs[5]->dna_num); free(orfs[5]->sequence); free(orfs[5]); if((orfs[5] = calloc(1, sizeof(struct orf))) == NULL) // free memory error("orf_finder(): Out of memory!"); if((orfs[5]->sequence = calloc(j+1, sizeof(char))) == NULL) error("orf_finder(): Out of memory!"); if((orfs[5]->dna_num = calloc(j+1, sizeof(char))) == NULL) error("orf_finder(): Out of memory!"); orfs[5]->length=0; // new init orfs[5]->finish = 0; orfs[5]->sequence[(orfs[5]->length)] = translate(in_seq->data[i+2],in_seq->data[i+3],in_seq->data[i+4], &(orfs[5]->dna_num[(orfs[5]->length)]) ); ++orfs[5]->length; } else { free(orfs[4]->dna_num); free(orfs[4]->sequence); free(orfs[4]); if((orfs[4] = calloc(1, sizeof(struct orf))) == NULL) // free memory error("orf_finder(): Out of memory!"); if((orfs[4]->sequence = calloc(j+1, sizeof(char))) == NULL) error("orf_finder(): Out of memory!"); if((orfs[4]->dna_num = calloc(j+1, sizeof(char))) == NULL) error("orf_finder(): Out of memory!"); orfs[4]->length = 0; // new init orfs[4]->finish = 0; orfs[4]->sequence[(orfs[4]->length)] = translate(in_seq->data[i+2],in_seq->data[i+3],in_seq->data[i+4], &(orfs[4]->dna_num[(orfs[4]->length)]) ); ++orfs[4]->length; } } } /****************************************************************************************/ /****************************************************************************************/ if(((in_seq->data[help-(i+2)] == 'T' && in_seq->data[help-(i+3)] == 'A' && in_seq->data[help-(i+4)] == 'C') && (d==0)) || ( (in_seq->data[help-(i+2)] == 'U' && in_seq->data[help-(i+3)] == 'A' && in_seq->data[help-(i+4)] == 'C') && (d==0) )) { d=1; // start found in last but two reading frame flag_no_start=0; if(!(orfs[6]->finish)) // orf not yet started in orfs[6] { orfs[6]->length=0; orfs[6]->sequence[(orfs[6]->length)] = translate(in_seq->data[help-(i+2)],in_seq->data[help-(i+3)],in_seq->data[help-(i+4)], &(orfs[6]->dna_num[(orfs[6]->length)]) ); ++orfs[6]->length; } else if(!(orfs[7]->finish))// orf not yet started in orfs[7] { orfs[7]->length=0; orfs[7]->sequence[(orfs[7]->length)] = translate(in_seq->data[help-(i+2)],in_seq->data[help-(i+3)],in_seq->data[help-(i+4)], &(orfs[7]->dna_num[(orfs[7]->length)]) ); ++orfs[7]->length; } else // orf finished in orfs[7] and orfs[6], so find the max and delete the min { if((orfs[6]->length) >= (orfs[7]->length)) // orfs[6] = Max { free(orfs[7]->dna_num); free(orfs[7]->sequence); free(orfs[7]); if((orfs[7] = calloc(1, sizeof(struct orf))) == NULL) // free memory error("orf_finder(): Out of memory!"); if((orfs[7]->sequence = calloc(j+1, sizeof(char))) == NULL) error("orf_finder(): Out of memory!"); if((orfs[7]->dna_num = calloc(j+1, sizeof(char))) == NULL) error("orf_finder(): Out of memory!"); orfs[7]->length=0; // new init orfs[7]->finish = 0; orfs[7]->sequence[(orfs[7]->length)] = translate(in_seq->data[help-(i+2)],in_seq->data[help-(i+3)],in_seq->data[help-(i+4)], &(orfs[7]->dna_num[(orfs[7]->length)]) ); ++orfs[7]->length; } else { free(orfs[6]->dna_num); free(orfs[6]->sequence); free(orfs[6]); if((orfs[6] = calloc(1, sizeof(struct orf))) == NULL) // free memory error("orf_finder(): Out of memory!"); if((orfs[6]->sequence = calloc(j+1, sizeof(char))) == NULL) error("orf_finder(): Out of memory!"); if((orfs[6]->dna_num = calloc(j+1, sizeof(char))) == NULL) error("orf_finder(): Out of memory!"); orfs[6]->length = 0; // new init orfs[6]->finish = 0; orfs[6]->sequence[(orfs[6]->length)] = translate(in_seq->data[help-(i+2)],in_seq->data[help-(i+3)],in_seq->data[help-(i+4)], &(orfs[6]->dna_num[(orfs[6]->length)]) ); ++orfs[6]->length; } } } /****************************************************************************************/ if(((in_seq->data[help-(i+1)] == 'T' && in_seq->data[help-(i+2)] == 'A' && in_seq->data[help-(i+3)] == 'C') && (e==0)) || ( (in_seq->data[help-(i+1)] == 'U' && in_seq->data[help-(i+2)] == 'A' && in_seq->data[help-(i+3)] == 'C') && (e==0))) { e=1; // start found in last but one reading frame flag_no_start=0; if(!(orfs[8]->finish)) // orf not yet started in orfs[8] { orfs[8]->length=0; orfs[8]->sequence[(orfs[8]->length)] = translate(in_seq->data[help-(i+1)],in_seq->data[help-(i+2)],in_seq->data[help-(i+3)], &(orfs[8]->dna_num[(orfs[8]->length)]) ); ++orfs[8]->length; } else if(!(orfs[9]->finish))// orf not yet started in orfs[9] { orfs[9]->length=0; orfs[9]->sequence[(orfs[9]->length)] = translate(in_seq->data[help-(i+1)],in_seq->data[help-(i+2)],in_seq->data[help-(i+3)], &(orfs[9]->dna_num[(orfs[9]->length)]) ); ++orfs[9]->length; } else // orf finished in orfs[9] and orfs[8], so find the max and delete the min { if((orfs[8]->length) >= (orfs[9]->length)) // orfs[8] = Max { free(orfs[9]->dna_num); free(orfs[9]->sequence); free(orfs[9]); if((orfs[9] = calloc(1, sizeof(struct orf))) == NULL) // free memory error("orf_finder(): Out of memory!"); if((orfs[9]->sequence = calloc(j+1, sizeof(char))) == NULL) error("orf_finder(): Out of memory!"); if((orfs[9]->dna_num = calloc(j+1, sizeof(char))) == NULL) error("orf_finder(): Out of memory!"); orfs[9]->length=0; // new init orfs[9]->finish = 0; orfs[9]->sequence[(orfs[9]->length)] = translate(in_seq->data[help-(i+1)],in_seq->data[help-(i+2)],in_seq->data[help-(i+3)], &(orfs[9]->dna_num[(orfs[9]->length)]) ); ++orfs[9]->length; } else { // printf(" im else also orf[0]dna_num); free(orfs[8]->sequence); free(orfs[8]); if((orfs[8] = calloc(1, sizeof(struct orf))) == NULL) // free memory error("orf_finder(): Out of memory!"); if((orfs[8]->sequence = calloc(j+1, sizeof(char))) == NULL) error("orf_finder(): Out of memory!"); if((orfs[8]->dna_num = calloc(j+1, sizeof(char))) == NULL) error("orf_finder(): Out of memory!"); orfs[8]->length = 0; // new init orfs[8]->finish = 0; orfs[8]->sequence[(orfs[8]->length)] = translate(in_seq->data[help-(i+1)],in_seq->data[help-(i+2)],in_seq->data[help-(i+3)], &(orfs[8]->dna_num[(orfs[8]->length)]) ); ++orfs[8]->length; } } } /****************************************************************************************/ if(((in_seq->data[help-i] == 'T' && in_seq->data[help-(i+1)] == 'A' && in_seq->data[help-(i+2)] == 'C') && (f==0)) || ( (in_seq->data[help-i] == 'U' && in_seq->data[help-(i+1)] == 'A' && in_seq->data[help-(i+2)] == 'C') && (f==0))) { f=1; // start found in last reading frame flag_no_start=0; if(!(orfs[10]->finish)) // orf not yet started in orfs[10] { orfs[10]->length=0; orfs[10]->sequence[(orfs[10]->length)] = translate(in_seq->data[help-(i)],in_seq->data[help-(i+1)],in_seq->data[help-(i+2)], &(orfs[10]->dna_num[(orfs[10]->length)]) ); ++orfs[10]->length; } else if(!(orfs[11]->finish))// orf not yet started in orfs[11] { orfs[11]->length=0; orfs[11]->sequence[(orfs[11]->length)] = translate(in_seq->data[help-(i)],in_seq->data[help-(i+1)],in_seq->data[help-(i+2)], &(orfs[11]->dna_num[(orfs[11]->length)]) ); ++orfs[11]->length; } else // orf finished in orfs[11] and orfs[10], so find the max and delete the min { if((orfs[10]->length) >= (orfs[11]->length)) // orfs[10] = Max { free(orfs[11]->dna_num); free(orfs[11]->sequence); free(orfs[11]); if((orfs[11] = calloc(1, sizeof(struct orf))) == NULL) // free memory error("orf_finder(): Out of memory!"); if((orfs[11]->sequence = calloc(j+1, sizeof(char))) == NULL) error("orf_finder(): Out of memory!"); if((orfs[11]->dna_num = calloc(j+1, sizeof(char))) == NULL) error("orf_finder(): Out of memory!"); orfs[11]->length=0; // new init orfs[11]->finish = 0; orfs[11]->sequence[(orfs[11]->length)] = translate(in_seq->data[help-(i)],in_seq->data[help-(i+1)],in_seq->data[help-(i+2)], &(orfs[11]->dna_num[(orfs[11]->length)]) ); ++orfs[11]->length; } else { free(orfs[10]->dna_num); free(orfs[10]->sequence); free(orfs[10]); if((orfs[10] = calloc(1, sizeof(struct orf))) == NULL) // free memory error("orf_finder(): Out of memory!"); if((orfs[10]->sequence = calloc(j+1, sizeof(char))) == NULL) error("orf_finder(): Out of memory!"); if((orfs[10]->dna_num = calloc(j+1, sizeof(char))) == NULL) error("orf_finder(): Out of memory!"); orfs[10]->length = 0; // new init orfs[10]->finish = 0; orfs[10]->sequence[(orfs[10]->length)] = translate(in_seq->data[help-(i)],in_seq->data[help-(i+1)],in_seq->data[help-(i+2)], &(orfs[10]->dna_num[(orfs[10]->length)]) ); ++orfs[10]->length; } } } /****************************************************************************************/ /****************************************************************************************/ i = i+2; } // if last codon in reading frame is no stop codon -> translate last codon if available if (((help+1) % 3) == 0) // length = last index + 1 ;translate last codon for orf 1 and orf 6 { // a: if (!orfs[0]->finish && orfs[0]->length) // open orf && already started before { orfs[0]->sequence[(orfs[0]->length)] = translate(in_seq->data[help-2], in_seq->data[help-1], in_seq->data[help], &(orfs[0]->dna_num[(orfs[0]->length)])); ++orfs[0]->length; } else if (!orfs[1]->finish && orfs[1]->length) { orfs[1]->sequence[(orfs[1]->length)] = translate(in_seq->data[help-2], in_seq->data[help-1], in_seq->data[help], &(orfs[1]->dna_num[(orfs[1]->length)])); ++orfs[1]->length; } // f: if (!(orfs[10]->finish) && orfs[10]->length ) { orfs[10]->sequence[(orfs[10]->length)] = translate(inverse(in_seq->data[2]), inverse(in_seq->data[1]), inverse(in_seq->data[0]), &(orfs[10]->dna_num[(orfs[10]->length)]) ); ++orfs[10]->length; } else if (!orfs[11]->finish && orfs[11]->length ) { orfs[11]->sequence[(orfs[11]->length)] = translate(inverse(in_seq->data[2]), inverse(in_seq->data[1]), inverse(in_seq->data[0]), &(orfs[11]->dna_num[(orfs[11]->length)]) ); ++orfs[11]->length; } } else if (((help+1) % 3) == 1) { // a: if (!orfs[0]->finish && orfs[0]->length) // open orf && already started before { orfs[0]->sequence[(orfs[0]->length)] = translate(in_seq->data[help-3], in_seq->data[help-2], in_seq->data[help-1], &(orfs[0]->dna_num[(orfs[0]->length)]) ); ++orfs[0]->length; } else if (!orfs[1]->finish && orfs[1]->length) { orfs[1]->sequence[(orfs[1]->length)] = translate(in_seq->data[help-3], in_seq->data[help-2], in_seq->data[help-1], &(orfs[1]->dna_num[(orfs[1]->length)]) ); ++orfs[1]->length; } // b: if (!orfs[2]->finish && orfs[2]->length) // open orf && already started before { orfs[2]->sequence[(orfs[2]->length)] = translate(in_seq->data[help-2], in_seq->data[help-1], in_seq->data[help], &(orfs[2]->dna_num[(orfs[2]->length)]) ); ++orfs[2]->length; } else if (!orfs[3]->finish && orfs[3]->length) { orfs[3]->sequence[(orfs[3]->length)] = translate(in_seq->data[help-2], in_seq->data[help-1], in_seq->data[help], &(orfs[3]->dna_num[(orfs[3]->length)]) ); ++orfs[3]->length; } // e: if (!(orfs[8]->finish) && orfs[8]->length ) { orfs[8]->sequence[(orfs[8]->length)] = translate(inverse(in_seq->data[2]), inverse(in_seq->data[1]), inverse(in_seq->data[0]), &(orfs[8]->dna_num[(orfs[8]->length)]) ); ++orfs[8]->length; } else if (!orfs[9]->finish && orfs[9]->length ) { orfs[9]->sequence[(orfs[9]->length)] = translate(inverse(in_seq->data[2]), inverse(in_seq->data[1]), inverse(in_seq->data[0]), &(orfs[9]->dna_num[(orfs[9]->length)]) ); ++orfs[9]->length; } // f: if (!(orfs[10]->finish) && orfs[10]->length ) { orfs[10]->sequence[(orfs[10]->length)] = translate(inverse(in_seq->data[3]), inverse(in_seq->data[2]), inverse(in_seq->data[1]), &(orfs[10]->dna_num[(orfs[10]->length)]) ); ++orfs[10]->length; } else if (!orfs[11]->finish && orfs[11]->length ) { orfs[11]->sequence[(orfs[11]->length)] = translate(inverse(in_seq->data[3]), inverse(in_seq->data[2]), inverse(in_seq->data[1]), &(orfs[11]->dna_num[(orfs[11]->length)]) ); ++orfs[11]->length; } } else { // a: if (!orfs[0]->finish && orfs[0]->length) // open orf && already started before { orfs[0]->sequence[(orfs[0]->length)] = translate(in_seq->data[help-4], in_seq->data[help-3], in_seq->data[help-2], &(orfs[0]->dna_num[(orfs[0]->length)]) ); ++orfs[0]->length; } else if (!orfs[1]->finish && orfs[1]->length) { orfs[1]->sequence[(orfs[1]->length)] = translate(in_seq->data[help-4], in_seq->data[help-3], in_seq->data[help-2], &(orfs[1]->dna_num[(orfs[1]->length)])); ++orfs[1]->length; } // b: if (!orfs[2]->finish && orfs[2]->length) // open orf && already started before { orfs[2]->sequence[(orfs[2]->length)] = translate(in_seq->data[help-3], in_seq->data[help-2], in_seq->data[help-1], &(orfs[2]->dna_num[(orfs[2]->length)]) ); ++orfs[2]->length; } else if (!orfs[3]->finish && orfs[3]->length) { orfs[3]->sequence[(orfs[3]->length)] = translate(in_seq->data[help-3], in_seq->data[help-2], in_seq->data[help-1], &(orfs[3]->dna_num[(orfs[3]->length)]) ); ++orfs[3]->length; } // c: if (!orfs[4]->finish && orfs[4]->length) // open orf && already started before { orfs[4]->sequence[(orfs[4]->length)] = translate(in_seq->data[help-2], in_seq->data[help-1], in_seq->data[help],&(orfs[4]->dna_num[(orfs[4]->length)]) ); ++orfs[4]->length; } else if (!orfs[5]->finish && orfs[5]->length) { orfs[5]->sequence[(orfs[5]->length)] = translate(in_seq->data[help-2], in_seq->data[help-1], in_seq->data[help],&(orfs[5]->dna_num[(orfs[5]->length)]) ); ++orfs[5]->length; } // d: if (!(orfs[6]->finish) && orfs[6]->length ) { orfs[6]->sequence[(orfs[6]->length)] = translate(inverse(in_seq->data[2]), inverse(in_seq->data[1]), inverse(in_seq->data[0]), &(orfs[6]->dna_num[(orfs[6]->length)]) ); ++orfs[6]->length; } else if (!orfs[7]->finish && orfs[7]->length ) { orfs[7]->sequence[(orfs[7]->length)] = translate(inverse(in_seq->data[2]), inverse(in_seq->data[1]), inverse(in_seq->data[0]), &(orfs[7]->dna_num[(orfs[7]->length)]) ); ++orfs[7]->length; } // e: if (!(orfs[8]->finish) && orfs[8]->length ) { orfs[8]->sequence[(orfs[8]->length)] = translate(inverse(in_seq->data[3]), inverse(in_seq->data[2]), inverse(in_seq->data[1]), &(orfs[8]->dna_num[(orfs[8]->length)]) ); ++orfs[8]->length; } else if (!orfs[9]->finish && orfs[9]->length ) { orfs[9]->sequence[(orfs[9]->length)] = translate(inverse(in_seq->data[3]), inverse(in_seq->data[2]), inverse(in_seq->data[1]), &(orfs[9]->dna_num[(orfs[9]->length)]) ); ++orfs[9]->length; } // f: if (!(orfs[10]->finish) && orfs[10]->length ) { orfs[10]->sequence[(orfs[10]->length)] = translate(inverse(in_seq->data[4]), inverse(in_seq->data[3]), inverse(in_seq->data[2]), &(orfs[10]->dna_num[(orfs[10]->length)]) ); ++orfs[10]->length; } else if (!orfs[11]->finish && orfs[11]->length ) { orfs[11]->sequence[(orfs[11]->length)] = translate(inverse(in_seq->data[4]), inverse(in_seq->data[3]), inverse(in_seq->data[2]), &(orfs[11]->dna_num[(orfs[11]->length)]) ); ++orfs[11]->length; } } // now we got 12 orfs and we search for the longest if((ret_seq = calloc(1,sizeof(struct seq)))==NULL) { error("orf_finder(): Out of memory"); } max_length=orfs[0]->length; max_orf=0; for (i=1; i != 12; ++i) { if(max_lengthlength) { max_length=orfs[i]->length; max_orf=i; } } if((ret_seq->data = calloc(max_length+1, sizeof(char)))==NULL) { error("orf_finder(): Out of memory"); } if((ret_seq->dna_num = calloc(max_length+1, sizeof(char)))==NULL) { error("orf_finder(): Out of memory"); } if(max_orf >5)ret_seq->crick_strand=1; ret_seq->name=in_seq->name; ret_seq->length = max_length; ret_seq->num=in_seq->num; ret_seq->orf_frame=max_orf/2; // As orf[1] && orf[0] = Reading frame 0 ,... for(i=0; i!= max_length; i++) { ret_seq->dna_num[i]=orfs[max_orf]->dna_num[i]; ret_seq->data[i]=orfs[max_orf]->sequence[i]; } // free memory for (x = 0; x != 12; ++x) { free(orfs[x]->dna_num); free(orfs[x]->sequence); free(orfs[x]); } free(orfs); if(flag_no_start){ char tmp[300]; sprintf(tmp,"orf_finder(): No Startcodon found in Sequence %s !\n", in_seq->name ); if(para->ORF_FRAME) printf("\n%sStarting translation for Sequence %s in reading frame 0\n\n", tmp,in_seq->name); else error(tmp); } return ret_seq; } abyss-1.3.6/dialign/orf.h000644 002433 001057 00000002424 11746352100 016726 0ustar00traymondassembly000000 000000 /** * * orf.h: * * 2004-08-24 Dorothea Emig Volker Menrad * */ /************************************************/ /* */ /* structs */ /* */ /************************************************/ struct orf { int length; // length of found orf char *sequence; // part of the sequence in the orf char finish; char *dna_num; // retranslation }; /************************************************/ /* */ /* global variable */ /* */ /************************************************/ /*********************************************/ /* */ /* functions from parameters.c */ /* */ /*********************************************/ struct seq_col* set_longest_orf(struct seq_col *in_seq_col); struct seq* orf_finder(struct seq *in_seq_col); //char inverse(char base); //char translate(char first_base, char second_base, char third_base,char* dna_number_for_retranslate); abyss-1.3.6/dialign/parameters.c000644 002433 001057 00000024041 11746352100 020275 0ustar00traymondassembly000000 000000 /** * * parameters.c: Read from stdin * * */ #include #include #include #include #include #include #include #include "parameters.h" #include "struct.h" #include "io.h" #ifdef __unix__ #include #include #else #include #endif extern char *optarg; extern int optind, opterr, optopt; struct parameters* para; /**************************** * PROTEIN DEFAULT VALUES! * ****************************/ void init_parameters() { if((para =(struct parameters *) malloc(sizeof(struct parameters)) ) == NULL) { error("init_parameters(): Out of memory when allocating data !"); } para->VERSION = "1.0.2"; para->DEBUG = 0; para->MAX_SEQ_AMOUNT = 5000; para->MAX_FASTA_LINE_LENGTH = 100; para->PRINT_SEQ_LINE_LENGTH = 80; para->SCR_MATRIX_FILE_NAME="BLOSUM.scr"; para->DIAG_CALC_WEIGHT_THRESHOLD = 0.000000065; para->DIAG_PROB_FILE_NAME="BLOSUM.diag_prob_t10"; para->SCR_MATRIX_ADD = 0; para->PROT_SIM_SCORE_THRESHOLD = 4.0; //para->PROT_DIAG_MAX_UNDER_THRESHOLD_POS = 4; //para->PROT_DIAG_MIN_LENGTH_THRESHOLD = 10.0; para->PROT_DIAG_MAX_UNDER_THRESHOLD_POS = 4; para->PROT_DIAG_MIN_LENGTH_THRESHOLD = 40.0; para->PROT_DIAG_AVG_SCORE_THRESHOLD = 4.0; para->DO_ANCHOR = 0; para->ANCHOR_FILE_NAME = NULL; para->DO_OVERLAP = 0; para->DIAG_MIN_LENGTH = 1; para->FAST_MODE = 0; para->SENS_MODE = 0; para->DIAG_THRESHOLD_WEIGHT = -log(0.5); para->FAST_PAIRWISE_ALIGNMENT = 0; para->conf_dir = NULL; para->in_file = NULL; para->out_file = NULL; para->COMPUTE_PROB=0; para->STATE_ORPHANE=1; para->STATE_INHERITED=2; para->DNA_PARAMETERS = 0; para->DNA_TRANSLATION = 0; para->FIND_ORF = 0; para->ORF_FRAME = 0; para->OUTPUT = 0; } /**************************** * DNA DEFAULT VALUES! * ****************************/ void set_parameters_dna() { para->VERSION = "1.0.2"; para->DEBUG = 0; para->MAX_SEQ_AMOUNT = 5000; para->MAX_FASTA_LINE_LENGTH = 100; para->PRINT_SEQ_LINE_LENGTH = 80; para->SCR_MATRIX_FILE_NAME="dna_matrix.scr"; para->DIAG_CALC_WEIGHT_THRESHOLD = 0.000000065; para->DIAG_PROB_FILE_NAME="dna_diag_prob_100_exp_550000"; para->SCR_MATRIX_ADD = 0; para->PROT_SIM_SCORE_THRESHOLD = 0.25; para->PROT_DIAG_MAX_UNDER_THRESHOLD_POS = 4; // 1 para->PROT_DIAG_MIN_LENGTH_THRESHOLD = 40.0;//40.0; // 1 para->PROT_DIAG_AVG_SCORE_THRESHOLD = 0.25; //1.0 para->DO_ANCHOR = 0; para->ANCHOR_FILE_NAME = NULL; para->DO_OVERLAP = 0; para->DIAG_MIN_LENGTH = 1; para->FAST_MODE = 0; para->SENS_MODE = 0; para->DIAG_THRESHOLD_WEIGHT = -log(0.5);//-log(0.875); para->FAST_PAIRWISE_ALIGNMENT = 0; para->conf_dir = NULL; para->in_file = NULL; para->out_file = NULL; para->COMPUTE_PROB=0; para->STATE_ORPHANE=1; para->STATE_INHERITED=2; para->DNA_PARAMETERS = 1; para->DNA_TRANSLATION = 0; para->FIND_ORF = 0; para->ORF_FRAME = 0; para->OUTPUT = 1; } void check_input(int argc, char** argv) { int flag_protein_output = 0; opterr = 1; optind = 0; int opt, only_config_dir = 0; while((opt = getopt(argc, argv,"PDTLOCFHhA:d:s:a:c:l:m:w:p:v:t:n:g:o:r:u"))!= -1){ switch(opt){ case 'd': para->DEBUG = atoi(optarg); break; case 's': para->MAX_SEQ_AMOUNT = atoi(optarg); break; case 'a': para->MAX_FASTA_LINE_LENGTH = atoi(optarg); break; case 'c': para->PRINT_SEQ_LINE_LENGTH = atoi(optarg); break; case 'l': para->SENS_MODE = atoi(optarg); break; case 'A': para->ANCHOR_FILE_NAME = optarg; para->DO_ANCHOR = 1; break; case 'm': para->SCR_MATRIX_FILE_NAME = optarg; break; case 'w': para->DIAG_CALC_WEIGHT_THRESHOLD = atof(optarg); break; case 'p': para->DIAG_PROB_FILE_NAME = optarg; break; case 'v': para->SCR_MATRIX_ADD = atoi(optarg); break; case 't': para->PROT_SIM_SCORE_THRESHOLD = atoi(optarg); break; case 'n': para->PROT_DIAG_MAX_UNDER_THRESHOLD_POS = atoi(optarg); break; case 'g': para->PROT_DIAG_MIN_LENGTH_THRESHOLD = atof(optarg); break; case 'r': para->PROT_DIAG_AVG_SCORE_THRESHOLD = atof(optarg); break; case 'o': para->DO_OVERLAP = atoi(optarg); break; case 'u': para->DIAG_MIN_LENGTH = atoi(optarg); break; case 'h': wrong_input(); case 'H': wrong_input(); case 'C': only_config_dir = 1; para->COMPUTE_PROB = 1; break; case 'F': para->DIAG_THRESHOLD_WEIGHT = 0.0; para->FAST_MODE = 1; break; case 'O': para->DNA_PARAMETERS = 0; para->DNA_TRANSLATION = 1; para->FIND_ORF = 1; para->ORF_FRAME = 1; para->OUTPUT = 1; break; case 'L': para->DNA_PARAMETERS = 0; para->DNA_TRANSLATION = 1; para->FIND_ORF = 1; para->ORF_FRAME = 0; para->OUTPUT = 1; break; case 'T': para->DNA_PARAMETERS = 0; para->DNA_TRANSLATION = 1; para->FIND_ORF = 0; para->ORF_FRAME = 0; para->OUTPUT = 1; break; case 'D': break; case 'P': flag_protein_output = 1; break; case '?': break; } } if(flag_protein_output){ para->OUTPUT = 0; } if(argc-optind == 0 ){ wrong_input(); error("conf-directory and infile needed !"); } else if(argc-optind > 3){ wrong_input(); error("too many arguments -> conf-directory, infile, [outfile] !"); } else{ struct stat attribut_dir; if(only_config_dir){ if(stat(argv[optind],&attribut_dir)==-1){ wrong_input(); error("conf-directory doesn't exist"); } else { if(attribut_dir.st_mode & S_IFDIR){ para->conf_dir = argv[optind++]; } else { wrong_input(); error("conf-directory is no directory"); } } } else{ struct stat attribut_file; if(stat(argv[optind],&attribut_dir)==-1){ wrong_input(); error("conf-directory doesn't exist"); } else{ if(attribut_dir.st_mode & S_IFDIR){ para->conf_dir = argv[optind++]; if(stat(argv[optind],&attribut_file)==-1){ wrong_input(); error("infile doesn't exist"); } else{ if(attribut_file.st_mode & S_IFREG){ para->in_file = argv[optind++]; } else{ wrong_input(); error("infile isn't a regular file!"); } } } else{ wrong_input(); error("conf-directory is no directory"); } } if(argv-optind >0) para->out_file = argv[optind]; } } return; } void wrong_input() { printf("Usage: dialign-t [OPTIONS] []\n"); printf("\n -d\tDebug-Mode [DEFAULT 0]\n"); printf(" \t\t 0 no debug statements\n"); printf(" \t\t 1 debugs the current phase of the processing\n"); printf(" \t\t 2 very loquacious debugging\n"); printf(" \t\t 5 hardcore debugging\n"); printf(" -s\tmaximum amount of input sequences [DEFAULT 5000]\n"); printf(" -a\tmaximum number of characters per line in a FASTA file [DEFAULT 100]\n"); printf(" -c\tmaximum amount of characters per line when printing a sequence\n \t[DEFAULT 80]\n"); printf(" -l\tsensitivity mode, the higher the level the less likely\n"); printf(" \tspurious random fragments are aligned in local alignments \n \t[DEFAULT 0]\n"); printf(" \t\t 0 switched off \n"); printf(" \t\t 1 level-1, reduced sensitivity\n"); printf(" \t\t 2 level-2, strongly reduced sensitivity\n"); printf(" -m\tscore matrix file name (in the configuration directory)\n \t\t[DEFAULT PROTEIN: BLOSUM.scr]\n \t\t[DEFAULT DNA: dna_matrix.scr]\n"); printf(" -w\tdefines the minimum weight when the weight formula is changed\n \tto 1-pow(1-prob, factor) [DEFAULT 0.000000065]\n"); printf(" -p\tprobability distribution file name (in the configuration\n \tdirectory) \n \t\t[DEFAULT PROTEIN: BLOSUM.diag_prob_t10]\n\t\t[DEFAULT DNA: dna_diag_prob_100_exp_550000]\n"); printf(" -v\tadd to each score (to prevent negative values) [DEFAULT 0]\n"); printf(" -t\t\"even\" threshold for low score for sequences alignment \n \t\t[DEFAULT PROTEIN: 4]\n\t\t[DEFAULT DNA: 0]\n"); printf(" -n\tmaximum number of consecutive positions for window containing\n \tlow scoring positions \n \t\t[DEFAULT PROTEIN: 4]\n\t\t[DEFAULT DNA: 4]\n"); printf(" -g\tglobal minimum fragment length for stop criterion \n \t\t[DEFAULT PROTEIN: 40] \n\t\t[DEFAULT DNA: 40]\n"); printf(" -m\tminimal allowed average score in frag window containing low \n \tscoring positions \n \t\t[DEFAULT PROTEIN: 4.0]\n\t\t[DEFAULT DNA: 0.25]\n"); printf(" -o\twether overlap weights are calculated or not [DEFAULT 0]\n"); printf(" -f\tminimum fragment length [DEFAULT 1]\n"); printf(" -r\tthreshold weight to consider the fragment at all [DEFAULT 0.0]\n"); printf(" -u\t[DEFAULT 0]\n"); printf(" \t\t1: only use a sqrt(amount_of_seqs) stripe of neighbour\n \t\t sequences to calculate pairwise alignments (increase performance)\n"); printf(" \t\t0: all pairwise alignments will be calculated\n"); printf(" -A\toptional anchor file [DEFAULT none]\n"); printf(" -D\tinput is DNA-sequence\n"); printf(" -T\ttranslate DNA into aminoacids from begin to end (length will be cut to mod 3 = 0)\n\tWARNING: Do not use -D with this option \n\t(Default values for PROTEIN input will be loaded)\n"); printf(" -L\tcompare only longest Open Reading Frame\n\tWARNING: Do not use -D with this option \n\t(Default values for PROTEIN input will be loaded)\n"); printf(" -O\ttranslate DNA to aminoacids, reading frame for each sequence calculated due to its longest ORF\n\tWARNING: Do not use -D with this option \n\t(Default values for PROTEIN input will be loaded)\n"); printf(" -P\toutput in aminoacids, no retranslation of DNA sequences\n\t[DEFAULT: input = output]\n"); printf(" -F\tfast mode (implies -l0, since it already significantly reduces sensitivity)\n"); printf(" -C\tgenerate probability table saved in /prob_table and exit\n"); printf(" -H -h\tprint this message\n\n"); exit(1); } void parameters(int argc, char** argv) { init_parameters(); int opt_flag = 0; int opt; opterr = 0; while((opt = getopt(argc, argv, "D") )!=-1){ switch(opt){ case 'D': opt_flag = 1; break; case '?': break; } } if(opt_flag) set_parameters_dna(); check_input(argc, argv); } abyss-1.3.6/dialign/parameters.h000644 002433 001057 00000011414 11746352100 020302 0ustar00traymondassembly000000 000000 /** * * parameters.h: * * 2004-08-13 Dorothea Emig Volker Menrad * */ /************************************************/ /* */ /* structs */ /* */ /************************************************/ struct parameters { char *VERSION; // 0 no debug statements // 1 debugs the current phase of the processing // 2 very loquacious debugging // 5 hardcore debugging int DEBUG; // = 0; // maximum amount of input sequences int MAX_SEQ_AMOUNT; // = 5000; // maximum number of characters per line in a FASTA file int MAX_FASTA_LINE_LENGTH; // = 100; // maximum amount of characters per line when printing a sequence int PRINT_SEQ_LINE_LENGTH; // = 80; /******************************* * * PROTEIN SCORING/WEIGHTING SECTION * *****************************/ // score matrix (e.g. BLOSUM) file name (in the configuration directory) //#define SCR_MATRIX_FILE_NAME "BLOSUM75.scr" char *SCR_MATRIX_FILE_NAME; // = "BLOSUM.scr"; //#define SCR_MATRIX_FILE_NAME "BLOSUM90.scr" // defines the minimum weight when the weight is changed to // 1-pow(1-prob, factor) double DIAG_CALC_WEIGHT_THRESHOLD; // = 0.000000065; //#define DIAG_CALC_WEIGHT_THRESHOLD 0.0000002 // diag prob. distribution file name (in the configuration directory) char *DIAG_PROB_FILE_NAME; // = "BLOSUM.diag_prob_t10"; //#define DIAG_PROB_FILE_NAME "BLOSUM.diag_prob_t7" // current //#define DIAG_PROB_FILE_NAME "BLOSUM75.diag_prob_t2" // //#define DIAG_PROB_FILE_NAME "BLOSUM75.diag_prob_t1" //#define DIAG_PROB_FILE_NAME "BLOSUM90.diag_prob" //#define DIAG_PROB_FILE_NAME "BLOSUM75.diag_prob" //#define DIAG_PROB_FILE_NAME "tp400_prot" // add to each score (to prevent negative values) int SCR_MATRIX_ADD; // = 0; // BLOSUM(62) //#define SCR_MATRIX_ADD 5 // BLOSUM75 //#define SCR_MATRIX_ADD 6 // BLOSUM90 /******************************* * * PROTEIN QUALITY SECTION * *****************************/ // "even" sim score threshold for protein sequences alignment //#define PROT_SIM_SCORE_THRESHOLD 6 //BLOSUM90 //#define PROT_SIM_SCORE_THRESHOLD 5 //BLOSUM75 double PROT_SIM_SCORE_THRESHOLD; // = 4; // BLOSUM62 // maximum number of consecutive positions for frag-window int PROT_DIAG_MAX_UNDER_THRESHOLD_POS; // = 4; // old was 4 // minimum diagonal length for breaking double PROT_DIAG_MIN_LENGTH_THRESHOLD; // = 40.0; // old was 40 // minimal allowed average csore in frag window double PROT_DIAG_AVG_SCORE_THRESHOLD; // = 4.0; // BLOSUM62 //#define PROT_DIAG_AVG_SCORE_THRESHOLD 5.0 // BLOSUM75 /******************************* * * GLOBAL QUALITY/SPEED SECTION * *****************************/ // wether overlap weights are calculated or not int DO_OVERLAP; // = 0; // minimum diag length int DIAG_MIN_LENGTH;// = 1; // diag threshold weight double DIAG_THRESHOLD_WEIGHT;// = -log(0.5); // if there are anchors char DO_ANCHOR; // = 0; // name of optional anchor file char *ANCHOR_FILE_NAME; // = NULL; // sensitivity mode, does not set // DIAG_THRESHOLD_WEIGHT to 0 four rounds >1 char SENS_MODE;// = 0; // fast mode - behaves like dialign t 0.2.2 char FAST_MODE;// = 0; // 1: only use a sqrt(amount_of_seqs) stripe of neighbour sequences to // calculate pairwise alignments // 0: all pairwise alignments will be calculated int FAST_PAIRWISE_ALIGNMENT;// = 0; char *conf_dir ; char *in_file ; char *out_file ; char COMPUTE_PROB; int DNA_PARAMETERS; // default Einstellungen fr DNA holen int DNA_TRANSLATION; // Vergleich auf Proteinebene, input DNA int FIND_ORF; // Vergleich auf Proteinebene, input DNA, mit ORF Finder int ORF_FRAME; // Vergleich auf Proteinebene, input DNA, nur longest ORF wird aligned int OUTPUT; // fr DNA = 1, fr Aminosuren = 0 int STATE_ORPHANE; int STATE_INHERITED; }; /************************************************/ /* */ /* global variable */ /* */ /************************************************/ extern struct parameters* para; /*********************************************/ /* */ /* functions from parameters.c */ /* */ /*********************************************/ //struct parameters* //initialises the parameters with default values void init_parameters(); // check, whether there are enough arguments and if options are used void check_input(int length, char** arguments); //error message void wrong_input(); void parameters(int argc, char** argv); void set_parameters_dna(); abyss-1.3.6/dialign/prob.c000644 002433 001057 00000016542 12015543263 017105 0ustar00traymondassembly000000 000000 #include #include #include #include #include #include #include #include "struct.h" #include "parameters.h" extern void error(char *message); extern void merror(char *msg1, char *msg2); // io.c# extern void print_diag(struct diag* aDiag); // diag.c //extern struct seq_part* create_seq_part(int num, struct seq* aSeq, // long startpos); extern struct diag* create_diag(struct seq_part* part1, struct seq_part* part2, int dlength); /** * * prob.c: Probability measurement (Creation of random sequences, diags,...) * * 2003-10-14 A.R.Subramanian * (Initial) */ /** * auxiliary method that fills random data into the sequence (see next func.) */ void fill_random_seq(struct seq* sq, struct scr_matrix *smatrix) { long length = sq->length; char *data = sq->data; int *n2c = smatrix->num2char; float slen = (float)smatrix->length; int pos, rnd; for(pos=0; pos'Z')); } } /** * create random squence of the given length using the characters * of the given score matrix * * The pointer returned (and the ones included in the struct) * has to be deallocted explicitely from memory. */ struct seq* create_random_seq(struct scr_matrix *smatrix, int length) { struct seq* sq = calloc(1, sizeof(struct seq)); sq->length=length; sq->data = calloc(length, sizeof(char)); sq->name = calloc(strlen("random")+1, sizeof(char)); strcpy(sq->name, "random"); fill_random_seq(sq, smatrix); return sq; } /** * calculates the score distribution up to the given maximum diaglen * * The pointer returned and the included dist pointer has to be deallocted * explicitely from memory. */ struct prob_dist* calc_score_dist(struct scr_matrix *smatrix, int mxdlen) { long sm_max_scr = smatrix->max_score; long maxdlen = mxdlen; struct prob_dist *sdist = calloc(1, sizeof(struct prob_dist)); long **edist = (calloc(maxdlen+1, sizeof(long *))); long **tdist = (calloc(maxdlen+1, sizeof(long *))); long double **dist = (sdist->data=calloc(maxdlen+1, sizeof(long double *))); if(sdist==NULL || dist==NULL || edist==NULL|| tdist==NULL) error("calc_score_dist(): Out of memory !"); sdist->max_dlen = maxdlen; int *sdata = smatrix->data; int *smdist = smatrix->dist; sdist->smatrix = smatrix; sdist->max_dlen = maxdlen; int reduce = 3; // special characters '?', '#', '%', we don't account for if(smatrix->char2num['X']>0) reduce++; // don't account for 'X' long double square = (smatrix->length-reduce) * (smatrix->length-reduce); long scr; unsigned long i,j, scr2, mxscr, omxscr; for(i=1;i<=maxdlen;i++) { mxscr = i*sm_max_scr; dist[i] = calloc(mxscr+1, sizeof(long double )); edist[i] = calloc(mxscr+1, sizeof(long )); tdist[i] = calloc(mxscr+1, sizeof(long )); if(dist[i]==NULL) error("calc_score_dist(): Out of memory at iteration" ); if(i==1) { for(j=0;j<=mxscr;j++) { dist[i][j] = smdist[j]; //static, wie oft kommt ein score j in der scr-Matrix vor, nur fr Fragmentlnge 1, ansonsten initialisiere mit Null edist[i][j]=0; tdist[i][j]=0; } } else { for(scr=0;scr<=mxscr;scr++) { dist[i][scr]=0.0; edist[i][scr]=0; tdist[i][scr]=0; omxscr = (i-1)*sm_max_scr; for(j=0;j<=sm_max_scr;j++) { if((scr-j)<=omxscr) dist[i][scr] += dist[1][j]*dist[i-1][scr-j]; // statisch wenn grer eins } } } } struct seq *sq1, *sq2; long max_experiment=550000, ex, found; struct diag dg; char *data1; char *data2; int *c2n = smatrix->char2num; int a1, a2,pos,dpos1,dpos2; long double experiment,oldprob,opf,opf2; int dlen = 100; // int maxdlen=100; long double factor = (long double)dlen*dlen; //long double expect; for(i=1;i<=maxdlen;i++) { // printf(" Diag of length %i\n", i); mxscr = i*sm_max_scr; //expect =0.0; dlen = i; factor = (long double)dlen*dlen; for(scr=0;scr<=mxscr;scr++) { //expect += ((long double)scr) * dist[i][scr]*pow(1.0/square,i);; //printf(" max %i\n", mxscr); for(scr2=scr+1;scr2<=mxscr;scr2++) { dist[i][scr] += dist[i][scr2]; } dist[i][scr] = dist[i][scr]*pow(1.0/square,i); } } // EXPERIMENTS: srandom((int)time(NULL)); sq1 = create_random_seq(smatrix, 2*maxdlen); sq2 = create_random_seq(smatrix, 2*maxdlen); dg.seq_p1.sq = sq1; dg.seq_p2.sq = sq2; dg.length =2*maxdlen; //printf(" pre random\n"); // for(ex=0;(exdata; data2 = sq2->data; for(dpos1=0;dpos1<=maxdlen;dpos1++) { for(dpos2=0;dpos2<=maxdlen;dpos2++) { dg.seq_p1.startpos = dpos1;//(int)( (100*random())/(RAND_MAX+1.0)); dg.seq_p2.startpos = dpos2; //(int)( (100*random())/(RAND_MAX+1.0)); dg.score = 0; for(pos=0;poslength*a1+a2]; if(dpos1<=pos+1 && dpos2<=pos+1) // t6 tdist[pos+1][dg.score]=1; // kann mehrmals dasselbe sein?? kann immer wieder berschrieben werden, warum? } } } for(i=1;i<=maxdlen;i++) { //printf(" Diag of length %i\n", i); mxscr = i*sm_max_scr; seenmax =0; for(scr=mxscr;scr>=0;scr--) { if(!seenmax) { if(tdist[i][scr]==1) { edist[i][scr]=edist[i][scr]+1; //fr jedes Exp. maximalen score der jeweiligen Fragmentlnge hochzhlen seenmax = 1; } } tdist[i][scr]=0; // alles wieder auf Null setzen ! } } } free(sq1); free(sq2); for(i=1;i<=maxdlen;i++) { // printf(" Diag of length %i\n", i); mxscr = i*sm_max_scr; //expect =0.0; dlen = i; factor = (long double)(dlen+1)*(dlen+1); // t6 //factor = (long double)10201.0; for(scr=0;scr<=mxscr;scr++) { for(scr2=scr+1;scr2<=mxscr;scr2++) { edist[i][scr] += edist[i][scr2]; // da in scr2 ja auch schon der scr1 beinhaltet ist; durch aufsummieren bekommen wir die Anzahl, wie viele Fragmente der Lnge i min. den score scr haben (oder mehr) } found = edist[i][scr]; // random exp. oldprob = dist[i][scr]; // statisch opf2 = (long double)oldprob*factor; opf = (long double)1.0-pow(1.0-oldprob,factor); experiment =((long double)found)/ ( ((long double)(max_experiment))); //if(switcher==0 && oldprob<0.000001) { // old 0.00001 t3 //if(found==0) //printf ("%Le %Le %Le %Le %Le %Le %i\n",experiment,opf,opf2,oldprob,factor,square,found); if(scr>0 && (found==0 || (experiment>opf || experiment>opf2 || experiment<10.0/max_experiment))) { if( (opf<=dist[i][scr-1]) && ( (opf > opf2) || (opf2 > dist[i][scr-1]))) { experiment = opf; } if( ( (opf2 <= dist[i][scr-1]))) { experiment = opf2; } } if(experiment == 0.0) { experiment = dist[i][scr-1]; } dist[i][scr] = experiment; //if(isnan(dist[i][scr]) || isinf(dist[i][scr])) dist[i][scr]=1.0; if(para->DEBUG>1)printf("%li %li %Le\n", i, scr,dist[i][scr] ); } // printf("%i %Le\n", i, expect); } return sdist; } abyss-1.3.6/dialign/struct.h000644 002433 001057 00000015357 11746352100 017475 0ustar00traymondassembly000000 000000 /** * * struct.h: Basic data structures * * Author: A.R.Subramanian */ /** * score matrix (e.g. BLOSUM62) */ struct scr_matrix { int length; // number of amino acids int max_score; // maximum among all entries in the data array int *char2num; // resolves the character of an amino acid to its number int *num2char; // resolves the number of an amino acid to its character int *data; // contains the matrix indexed by the number of the particular amino acid int *dist; // number of pairs of amino acids (i,j) having score at equal to // the value of the index long double **raw_dist; double avg_sim_score; }; /** * raw sequence */ struct seq { char *data; // sequence data char *name; // name/description of the sequence int num; // number of the sequence int length; // length of sequence int max_seen; char *dna_num; // Numbers fo retranslation from Protein to DNA int orf_frame; // reading frame of the longest orf char crick_strand; // orf translation or sequence translation on crickstrand }; /** * sequence collection */ struct seq_col { struct seq *seqs; // array of the sequences int avg_length; // average length of sequences int length; // number of sequences }; /** * probability distribution of scores in diagonals */ struct prob_dist { struct scr_matrix *smatrix; // pointer to the associated score matrix long double **data; // distribution of scores dist[i][j] contains the // probability of a diags of length i having score >=j double **log_data; // distribution of scores dist[i][j] contains the // -log(probability of a diags of length i having score >=j) // long double *expect; // score expectancy for each diaglen unsigned int max_dlen; // maximum diaglength in dist }; /** * part of a sequence (auxiliary data structure) */ struct seq_part { int num; // a number that indicates a position in an array struct seq* sq; // the pointer to the sequence int startpos; // startpos in the sequence //int leftmargin; //int rightmargin; }; /** * diagonal in the dotmatrix */ struct diag { struct seq_part seq_p1; // first sequence part struct seq_part seq_p2; // seconde sequence part unsigned int length; // length of the diag long score; // score of the diag long orig_score; // orig score of the diag struct diag *pred_diag; // predecessor diag for dynamic programming struct diag *col_pred_diag; // col predecessor diag for dynamic programming int pool_pos; // position in diag pool char meetsThreshold; // whether diag meets threshold // for vertex cover int degree; int max_degree; struct diag **neighbours; char anchor; // if this is an anchor diag char marked; // marking flag for arbitrary use char multi_dg; // is >0 if this is a multi dg struct diag **multi_cont; // the contained dgs of this is a multi dg int multi_length; // size of multi_cont // char onlyOverThres; double weight; // weight of the diag = -log(prob) double weight_sum; // weight sum for dialign double weight_fac; // weight factor double ov_weight; // overlap weight double total_weight; // total_weight = weight+o_weight }; /** * collection of diag */ struct simple_diag_col { unsigned int length; // number of diags double total_weight; // total weight double weight_fac; // weight factor struct diag** data; // the array of diags }; /** * guide tree node */ struct gt_node { char isLeaf; // whether it is leaf int *seq_num; // the sequence numbers int seq_num_length; // length of sequence numbers array struct gt_node *succ1; // successor nodes struct gt_node *succ2; }; /** * vertex cover node struct vc_node { double weight; struct diag *dg; int degree; struct vc_node *adjacents; } */ /** * collection of all diagonals sorted by the sequences */ struct diag_col { int seq_amount; // number of sequences involved struct simple_diag_col** diag_matrix; // diag_matrix[i +seq_amount *j] contains // all diags found involving the sequences i and j double total_weight; // total weight double average_weight; // average_weight struct diag** diags; // all diags unordered unsigned int diag_amount; // number of diags found struct gt_node *gt_root; }; /** * diag container */ struct diag_cont { struct diag* dg; struct diag_cont *next; }; /** * alignment position */ struct algn_pos { // int seq_num; // sequence number // unsigned long pos_in_seq; // position in the sequence char state; // orphane: not aligned to any pos, struct diag_cont *dg_cont; // diags that are aligned with that position int row; int col; // unsigned int succFPos; // if orphane, the position holding the succF // unsigned int predFPos; // analogous to succFPos // char* isAli; // if alignemnt at the positions exist int* predF; // predecessor frontier, only filled if non-orphane int* succF; // successor frontier, only filled if non-orphane char *proceed; // for output //char isInherited; // whether the pointers are inherited int predFPos; // in case of orphane, where to find the predF or succF int succFPos; int *eqcAlgnPos; // equivalence class minimum alignment position (for output) struct algn_pos *eqcParent; // equivalence class parent int eqcRank; // equivalence class rank (>= maximum number of children) // unsigned int *maxpos; // needed for output of the alignment }; /** * alignment */ struct alignment { //int seq_amount; // number of sequences involved //char *redo_seqs; // which pairs of sequences are to be aligned again char *seq_is_orphane; // boolean array indicating for each sequence // whether it is orphane or not int max_pos; // the greatest position in the alignment (including all -'s) // if <0: the alignment has not yet been prepared struct seq_col *scol; // all the sequences involved struct algn_pos **algn; // the alignment double total_weight; // the total weight of the alignment struct alignment *next; // pointer to next alignment in the sorted linked list //struct alignment *prev; // pointer to previous alignment in the sorted linked list //unsigned long pos; // position in the sorted linked list //struct diag** aligned_diags; // all aligned diags //int aligned_diags_amount; //int max_aligned_diags_amount; //int orig_max_aligned_diags_amount; //struct diag_cont* backlog_diags; // all backlog diags }; abyss-1.3.6/dialign/translate.c000644 002433 001057 00000043154 12015543263 020137 0ustar00traymondassembly000000 000000 /** * * translate.c: * * 2004-08-30 Dorothea Emig Volker Menrad * */ #include #include #include #include "struct.h" #include "translate.h" #include "parameters.h" #include "orf.h" #include "io.h" void translate_sequence_collection_orf_frame(struct seq_col *in_seq_col) { int i; struct seq_col* tmp; tmp = set_longest_orf(in_seq_col); /************** reading frames : 0: 123 123 123 123 123 ... 1: X 123 123 123 123 123 ... 2: XX 123 123 123 123 123 ... 3: ... 321 321 321 321 321 XX 4: ... 321 321 321 321 321 X 5: ... 321 321 321 321 321 **************/ for(i=0; i!= in_seq_col->length; ++i){ in_seq_col->seqs[i].orf_frame = tmp->seqs[i].orf_frame; translate_sequence( &(in_seq_col->seqs[i]) ); free(tmp->seqs[i].data); free(tmp->seqs[i].dna_num); } free(tmp); } void translate_sequence_collection_default(struct seq_col *in_seq_col) { int i; for(i=0; i!= in_seq_col->length; ++i) translate_sequence( &(in_seq_col->seqs[i]) ); } void translate_sequence(struct seq *in_seq) { int i, rest; // printf("%d\t%s\n%s\n%d\n\n\n",in_seq->num, in_seq->name, in_seq->data, in_seq->orf_frame ); switch(in_seq->orf_frame) { case 0: break; case 1: --in_seq->length; in_seq->data=&(in_seq->data[1]); break; case 2: in_seq->length= in_seq->length-2; in_seq->data=&(in_seq->data[2]); break; case 3: in_seq->crick_strand=1; in_seq->length= in_seq->length-2; in_seq->data[in_seq->length]='\0'; break; case 4: in_seq->crick_strand=1; --in_seq->length; in_seq->data[in_seq->length]='\0'; break; case 5: in_seq->crick_strand=1; break; } struct seq* new; if(NULL == ( new = (calloc(1,sizeof(struct seq))))) { error("translate_sequence: Out of memory! "); } if(NULL == (new->data = (calloc(in_seq->length/3+1, sizeof(char))))) { error("translate_sequence: Out of memory! "); } if(NULL == (new->dna_num = (calloc(in_seq->length/3+1, sizeof(char))))) { error("translate_sequence: Out of memory! "); } rest = in_seq->length%3; for(i=0; i < (in_seq->length) - rest ; ++i) { int help = in_seq->length-1; if(in_seq->crick_strand==0) { new->data[new->length] = translate(in_seq->data[i], in_seq->data[i+1], in_seq->data[i+2], &(new->dna_num[new->length]) ); ++new->length; } else { new->data[new->length] = translate(inverse(in_seq->data[help - i]), inverse(in_seq->data[help - (i+1)]), inverse(in_seq->data[help - (i+2)]), &(new->dna_num[new->length]) ); ++new->length; } i=i+2; } switch(in_seq->orf_frame) { case 1: --in_seq->data; free(in_seq->data); break; case 2: in_seq->data = in_seq->data-2; free(in_seq->data); break; default: free(in_seq->data); } in_seq->data = &(new->data[0]); in_seq->length = new->length; in_seq->dna_num = new->dna_num; } char translate(char first_base, char second_base, char third_base, char *dna_number) { switch(first_base) { case 'A': switch(second_base) { case 'A': switch(third_base) { case 'A': *dna_number = 0; // AAA return('K'); // Lysin = K case 'T': *dna_number = 1; // AAT return('N'); // Asparagin = N case 'U': *dna_number = 2; // AAU return('N'); // Asparagin = N case 'G': *dna_number = 3; // AAG return('K'); //Lysin = K case 'C': *dna_number = 4; // AAC return('N'); //Asparagin = N default: error("No regular aminoacid !"); } case 'T': switch(third_base) { case 'A': *dna_number = 5; // ATA return('I'); // Isoleucin = I case 'T': *dna_number = 6; // ATT return('I'); // Isoleucin = I case 'G': *dna_number = 7; // ATG return('M'); // Methionin = M case 'C': *dna_number = 8; // ATC return('I'); // Isoleucin = I default: error("No regular aminoacid !"); } case 'U': switch(third_base) { case 'A': *dna_number = 9; // AUA return('I'); // Isoleucin = I case 'U': *dna_number = 10; // AUU return('I'); // Isoleucin = I case 'G': *dna_number = 11; // AUG return('M'); // Methionin= M case 'C': *dna_number = 12; // AUC return('I'); // Isoleucin = I default: error("No regular aminoacid !"); } case 'G': switch(third_base) { case 'A': *dna_number = 13; // AGA return('R'); // Arginin = R case 'T': *dna_number = 14; // AGT return('S'); // Serin = S case 'U': *dna_number = 15; // AGU return('S'); // Serin = S case 'G': *dna_number = 16; // AGG return('R'); // Arginin = R case 'C': *dna_number = 17; // AGC return('S'); // Serin = S default: error("No regular aminoacid !"); } case 'C': switch(third_base) { case 'A': *dna_number = 18; // ACA return('T'); // Threonin = T case 'T': *dna_number = 19; // ACT return('T'); // Threonin = T case 'U': *dna_number = 20; // ACU return('T'); // Threonin = T case 'G': *dna_number = 21; // ACG return('T'); // Threonin = T case 'C': *dna_number = 22; // ACC return('T'); // Threonin = T default: error("No regular aminoacid !"); } default: error("No regular aminoacid !"); } case 'T': switch(second_base) { case 'A': switch(third_base) { case 'A': *dna_number = 23; // TAA return('X'); // Stop case 'T': *dna_number = 24; // TAT return('Y'); // Tyrosin case 'G': *dna_number = 25; // TAG return('X'); // Stop case 'C': *dna_number = 26; // TAC return('Y'); // Tyrosin default: error("No regular aminoacid !"); } case 'T': switch(third_base) { case 'A': *dna_number = 27; // TTA return('L'); // Leucin case 'T': *dna_number = 28; // TTT return('F'); // Phenylalanin case 'G': *dna_number = 29; // TTG return('L'); // Leucin case 'C': *dna_number = 30; // TTC return('F'); // Phenylalanin default: error("No regular aminoacid !"); } case 'G': switch(third_base) { case 'A': *dna_number = 31; // TGA return('X'); // Stop case 'T': *dna_number = 32; // TGT return('C'); // Cystein case 'G': *dna_number = 33; // TGG return('W'); // Tryptophan case 'C': *dna_number = 34; // TGC return('C'); // Cystein default: error("No regular aminoacid !"); } case 'C': switch(third_base) { case 'A': *dna_number = 35; // TCA return('S'); // Serin case 'T': *dna_number = 36; // TCT return('S'); // Serin case 'G': *dna_number = 37; // TCG return('S'); // Serin case 'C': *dna_number = 38; // TCC return('S'); // Serin default: error("No regular aminoacid !"); } default: error("no regular Aminoacid !"); } case 'U': switch(second_base) { case 'A': switch(third_base) { case 'A': *dna_number = 39; // UAA return('X'); // Stop case 'U': *dna_number = 40; // UAU return('Y'); // Tyrosin case 'G': *dna_number = 41; // UAG return('X'); // Stop case 'C': *dna_number = 42; // UAC return('Y'); // Tyrosin default: error("No regular aminoacid !"); } case 'U': switch(third_base) { case 'A': *dna_number = 43; // UUA return('L'); // Leucin case 'U': *dna_number = 44; // UUU return('F'); // Phenylalanin case 'G': *dna_number = 45; // UUG return('L'); // Leucin case 'C': *dna_number = 46; // UUC return('F'); // Phenylalanin default: error("No regular aminoacid !"); } case 'G': switch(third_base) { case 'A': *dna_number = 47; // UGA return('X'); // Stop case 'U': *dna_number = 48; // UGU return('C'); // Cystein case 'G': *dna_number = 49; // UGG return('W'); // Tryptophan case 'C': *dna_number = 50; // UGC return('C'); // Cystein default: error("No regular aminoacid !"); } case 'C': switch(third_base) { case 'A': *dna_number = 51; // UCA return('S'); // Serin case 'U': *dna_number = 52; // UCU return('S'); // Serin case 'G': *dna_number = 53; // UCG return('S'); // Serin case 'C': *dna_number = 54; // UCC return('S'); // Serin default: error("No regular aminoacid !"); } default: error("no regular Aminoacid !"); } case 'G': switch(second_base) { case 'A': switch(third_base) { case 'A': *dna_number = 55; // GAA return('E'); // Glutaminsaeure case 'T': *dna_number = 56; // GAT return('D'); // Asparaginsaeure case 'U': *dna_number = 57; // GAU return('D'); // Asparaginsaeure case 'G': *dna_number = 58; // GAG return('E'); // Glutaminsaeure case 'C': *dna_number = 59; // GAC return('D'); // Asparaginsaeure default: error("No regular aminoacid !"); } case 'T': switch(third_base) { case 'A': *dna_number = 60; // GTA return('V'); // Valin case 'T': *dna_number = 61; // GTT return('V'); // Valin case 'G': *dna_number = 62; // GTG return('V'); // Valin case 'C': *dna_number = 63; // GTC return('V'); // Valin default: error("No regular aminoacid !"); } case 'U': switch(third_base) { case 'A': *dna_number = 64; // GUA return('V'); // Valin case 'U': *dna_number = 65; // GUU return('V'); // Valin case 'G': *dna_number = 66; // GUG return('V'); // Valin case 'C': *dna_number = 67; // GUC return('V'); // Valin default: error("No regular aminoacid !"); } case 'G': switch(third_base) { case 'A': *dna_number = 68; // GGA return('G'); // Glycin case 'T': *dna_number = 69; // GGT return('G'); // Glycin case 'U': *dna_number = 70; // GGU return('G'); // Glycin case 'G': *dna_number = 71; // GGG return('G'); // Glycin case 'C': *dna_number = 72; // GGC return('G'); // Glycin default: error("No regular aminoacid !"); } case 'C': switch(third_base) { case 'A': *dna_number = 73; // GCA return('A'); // Alanin case 'T': *dna_number = 74; // GCT return('A'); // Alanin case 'U': *dna_number = 75; // GCU return('A'); // Alanin case 'G': *dna_number = 76; // GCG return('A'); // Alanin case 'C': *dna_number = 77; // GCC return('A'); // Alanin default: error("No regular aminoacid !"); } default: error("No regular aminoacid !"); } case 'C': switch(second_base) { case 'A': switch(third_base) { case 'A': *dna_number = 78; // CAA return('Q'); // Glutamin case 'T': *dna_number = 79; // CAT return('H'); // Histidin case 'U': *dna_number = 80; // CAU return('H'); // Histidin case 'G': *dna_number = 81; // CAG return('Q'); // Glutamin case 'C': *dna_number = 82; // CAC return('H'); // Histidin default: error("No regular aminoacid !"); } case 'T': switch(third_base) { case 'A': *dna_number = 83; // CTA return('L'); // Leucin case 'T': *dna_number = 84; // CTT return('L'); // Leucin case 'G': *dna_number = 85; // CTG return('L'); // Leucin case 'C': *dna_number = 86; // CTC return('L'); // Leucin default: error("No regular aminoacid !"); } case 'U': switch(third_base) { case 'A': *dna_number = 87; // CUA return('L'); // Leucin case 'U': *dna_number = 88; // CUU return('L'); // Leucin case 'G': *dna_number = 89; // CUG return('L'); // Leucin case 'C': *dna_number = 90; // CUC return('L'); // Leucin default: error("No regular aminoacid !"); } case 'G': switch(third_base) { case 'A': *dna_number = 91; // CGA return('R'); // Arginin case 'T': *dna_number = 92; // CGT return('R'); // Arginin case 'U': *dna_number = 93; // CGU return('R'); // Arginin case 'G': *dna_number = 94; // CGG return('R'); // Arginin case 'C': *dna_number = 95; // CGC return('R'); // Arginin default: error("No regular aminoacid !"); } case 'C': switch(third_base) { case 'A': *dna_number = 96; // CCA return('P'); // Prolin case 'T': *dna_number = 97; // CCT return('P'); // Prolin case 'U': *dna_number = 98; // CCU return('P'); // Prolin case 'G': *dna_number = 99; // CCG return('P'); // Prolin case 'C': *dna_number = 100; // CCC return('P'); // Prolin default: error("No regular aminoacid !"); } default: error("No regular aminoacid !"); } default: error("No regular aminoacid !"); } abort(); } char inverse(char base) { switch(base) { case 'A': return('T'); case 'T': return('A'); case 'U': return('A'); case 'C': return('G'); case 'G': return('C'); } abort(); } void retranslate_sequence(struct seq *in_seq) { char *tmp_char= "000"; int i; struct seq* tmp; if(NULL == ( tmp =(calloc(1,sizeof(struct seq))))) { error("retranslate_sequence(): Out of memory !"); } if(NULL == ( tmp->data =(calloc((in_seq->length)*3+1,sizeof(char))))) { error("retranslate_sequence(): Out of memory !"); } for(i=0; i!=in_seq->length; ++i) { tmp_char = retranslate(in_seq->dna_num[i]); strcat(tmp->data,tmp_char); } in_seq->length = strlen(tmp->data); free(in_seq->data); free(in_seq->dna_num); in_seq->data = tmp->data; } char* retranslate(char amino) { switch(amino) { case 0: return "AAA"; case 1: return "AAT"; case 2: return "AAU"; case 3: return "AAG"; case 4: return "AAC"; case 5: return "ATA"; case 6: return "ATT"; case 7: return "ATG"; case 8: return "ATC"; case 9: return "AUA"; case 10: return "AUU"; case 11: return "AUG"; case 12: return "AUC"; case 13: return "AGA"; case 14: return "AGT"; case 15: return "AGU"; case 16: return "AGG"; case 17: return "AGC"; case 18: return "ACA"; case 19: return "ACT"; case 20: return "ACU"; case 21: return "ACG"; case 22: return "ACC"; case 23: return "TAA"; case 24: return "TAT"; case 25: return "TAG"; case 26: return "TAC"; case 27: return "TTA"; case 28: return "TTT"; case 29: return "TTG"; case 30: return "TTC"; case 31: return "TGA"; case 32: return "TGT"; case 33: return "TGG"; case 34: return "TGC"; case 35: return "TCA"; case 36: return "TCT"; case 37: return "TCG"; case 38: return "TCC"; case 39: return "UAA"; case 40: return "UAU"; case 41: return "UAG"; case 42: return "UAC"; case 43: return "UUA"; case 44: return "UUU"; case 45: return "UUG"; case 46: return "UUC"; case 47: return "UGA"; case 48: return "UGU"; case 49: return "UGG"; case 50: return "UGC"; case 51: return "UCA"; case 52: return "UCU"; case 53: return "UCG"; case 54: return "UCC"; case 55: return "GAA"; case 56: return "GAT"; case 57: return "GAU"; case 58: return "GAG"; case 59: return "GAC"; case 60: return "GTA"; case 61: return "GTT"; case 62: return "GTG"; case 63: return "GTC"; case 64: return "GUA"; case 65: return "GUU"; case 66: return "GUG"; case 67: return "GUC"; case 68: return "GGA"; case 69: return "GGT"; case 70: return "GGU"; case 71: return "GGG"; case 72: return "GGC"; case 73: return "GCA"; case 74: return "GCT"; case 75: return "GCU"; case 76: return "GCG"; case 77: return "GCC"; case 78: return "CAA"; case 79: return "CAT"; case 80: return "CAU"; case 81: return "CAG"; case 82: return "CAC"; case 83: return "CTA"; case 84: return "CTT"; case 85: return "CTG"; case 86: return "CTC"; case 87: return "CUA"; case 88: return "CUU"; case 89: return "CUG"; case 90: return "CUC"; case 91: return "CGA"; case 92: return "CGT"; case 93: return "CGU"; case 94: return "CGG"; case 95: return "CGC"; case 96: return "CCA"; case 97: return "CCT"; case 98: return "CCU"; case 99: return "CCG"; case 100: return "CCC"; default: error("Sorry something wrong while retranslation !"); } abort(); } abyss-1.3.6/dialign/translate.h000644 002433 001057 00000002533 11746352100 020136 0ustar00traymondassembly000000 000000 /** * * translate.h: * * 2004-08-30 Dorothea Emig Volker Menrad * */ /************************************************/ /* */ /* structs */ /* */ /************************************************/ /************************************************/ /* */ /* global variable */ /* */ /************************************************/ /*********************************************/ /* */ /* functions from translate.c */ /* */ /*********************************************/ void translate_sequence_collection(struct seq_col *in_sequence_collection); void translate_sequence(struct seq *in_sequence); char translate(char first_base, char second_base, char third_base, char *dna_number); char inverse(char base); void retranslate_sequence(struct seq *in_sequence); char* retranslate(char amino); void translate_sequence_collection_orf_frame(struct seq_col *in_seq_col); void translate_sequence_collection_default(struct seq_col *in_seq_col); abyss-1.3.6/dialign/museq.c000644 002433 001057 00000022270 11746352100 017266 0ustar00traymondassembly000000 000000 /** * * museq.c: Main program control * Author: A.R.Subramanian * */ /** * TODO LIST: * - option: multi diags as optional argument */ #include #include #include #include #include #include #include "parameters.h" #include "struct.h" #include "translate.h" #include "orf.h" #include "io.h" /** * external functions definitions */ // diag.c //extern struct seq_part* create_seq_part(int num, struct seq* aSeq, // unsigned int startpos); //extern struct diag* create_diag(struct seq_part* part1, struct seq_part* part2, // int dlength); //extern void calc_weight(struct diag* dg, struct scr_matrix* smatrix, // struct prob_dist *pdist); //extern struct diag_col *create_diag_col(int seq_amount); extern void free_diag_col(struct diag_col* dcol); extern struct diag_col *find_all_diags(struct scr_matrix *smatrix, struct prob_dist *pdist, struct seq_col *in_seq_col, struct alignment *algn, int round); // prob.c //extern struct seq* create_random_seq(struct scr_matrix *smatrix, int length); //extern double* approx_prob(struct scr_matrix *smatrix, struct prob_dist *sdist, // int diaglen, int seqlen); extern struct prob_dist* calc_score_dist(struct scr_matrix *smatrix, int mxdlen); // alig.c extern struct alignment* create_empty_alignment(struct seq_col *scol); //extern char adapt_diag(struct alignment *algn, struct scr_matrix *smatrix, struct diag* dg); extern int simple_aligner(struct seq_col *scol, struct diag_col *dcol, struct scr_matrix* smatrix, struct prob_dist *pdist, struct alignment *algn, int round); extern struct simple_diag_col* read_anchors(char *filename, struct seq_col* scol); extern struct alignment* guided_aligner(struct alignment *palgn, struct seq_col *scol, struct diag_col *dcol, struct scr_matrix* smatrix, struct prob_dist *pdist, struct gt_node *gtn, int round); /** * main program routine */ int main(int argc, char **argv) { parameters(argc, argv); version(); // read similarity matrix char *smatrixfile = (char *)build_pathname(para->conf_dir,para->SCR_MATRIX_FILE_NAME); struct scr_matrix *smatrix = read_scr_matrix(smatrixfile); // print the score matrix if( para->DEBUG >5) { print_scr_matrix(smatrix); } // read the probability distribution for diagonals char *pdistfilename = (char *)build_pathname(para->conf_dir,para->DIAG_PROB_FILE_NAME); int i; struct seq_col *in_seq_col; struct prob_dist *pdist; if(!para->COMPUTE_PROB){ pdist = read_diag_prob_dist(smatrix, pdistfilename); in_seq_col = read_fasta(para->in_file); if(para->DNA_TRANSLATION){ if(para->FIND_ORF){ if(para->ORF_FRAME){ translate_sequence_collection_orf_frame(in_seq_col); } else { in_seq_col = set_longest_orf(in_seq_col); } } else{ translate_sequence_collection_default(in_seq_col); } } } // print read input sequences if(para->DEBUG>5) { int sc,scl = in_seq_col->length; for(sc=0; sc < scl;sc++) { print_seq(&(in_seq_col->seqs[sc])); printf("\n"); } } // ---------------------------------------------------------------------- // probability table generation area // ---------------------------------------------------------------------- if(para->COMPUTE_PROB) { char *prob_table_output_file = (char *)build_pathname(para->conf_dir,"prob_table"); struct prob_dist *sdist = calc_score_dist(smatrix, 100); print_pdist_matrix(sdist, prob_table_output_file); exit(0); } double tim = clock(),tim2; // fast mode has higher threshold weights if(para->FAST_MODE) { para->PROT_SIM_SCORE_THRESHOLD += 0.25; } // ---------------------------------------------------------------------- // Consider Anchors // ---------------------------------------------------------------------- struct simple_diag_col *anchors = NULL; struct diag_col adcol; struct alignment *algn= NULL; if(! para->FAST_MODE) { algn = create_empty_alignment(in_seq_col); } struct alignment *salgn = create_empty_alignment(in_seq_col); if(para->DO_ANCHOR>0) { anchors = read_anchors(para->ANCHOR_FILE_NAME, in_seq_col); adcol.diags = anchors->data; adcol.diag_amount = anchors->length; simple_aligner(in_seq_col, &adcol,smatrix,pdist,salgn,1); if(! para->FAST_MODE) simple_aligner(in_seq_col, &adcol,smatrix,pdist,algn,1); if(anchors!=NULL) { for(i=0;iDNA_PARAMETERS && (para->SENS_MODE>0)) { // para->DIAG_THRESHOLD_WEIGHT = -log(0.875); //} struct diag_col *all_diags = find_all_diags(smatrix, pdist, in_seq_col,salgn,1); double duration = (clock()-tim)/CLOCKS_PER_SEC; if(para->DEBUG >1) printf("Found %i diags in %f secs\n", all_diags->diag_amount, duration); int diag_amount = all_diags->diag_amount; // ---------------------------------------------------------------------- // Compute alignment // ---------------------------------------------------------------------- tim2=clock(); if(! para->FAST_MODE) { struct diag *cp_diags[all_diags->diag_amount]; for(i=0;idiags[i]); } guided_aligner(algn, in_seq_col, all_diags,smatrix,pdist,all_diags->gt_root, 1); for(i=0;idiags[i] = cp_diags[i]; } all_diags->diag_amount = diag_amount; } //struct alignment *algn = salgn; simple_aligner(in_seq_col, all_diags,smatrix,pdist,salgn,1); duration = (clock()-tim2)/CLOCKS_PER_SEC; if(! para->FAST_MODE) { if(para->DEBUG >1) printf("First alignment after %f secs. simple: %f guided: %f\n", duration, salgn->total_weight, algn->total_weight); } else { if(para->DEBUG >1) printf("First alignment after %f secs. simple: %f \n", duration, salgn->total_weight); } //if(para->DEBUG >1) printf("First alignment after %f secs. guided: %f\n", duration, algn->total_weight); free_diag_col(all_diags); para->DO_ANCHOR = 0; // anchors done // round 2+ int round; char newFound = 0; int type; //printf(" SENS %i\n", para->SENS_MODE); // consider sensitivity level if(! para->FAST_MODE) { if(para->SENS_MODE==0) { para->DIAG_THRESHOLD_WEIGHT = 0.0; } else if(para->SENS_MODE==1) { if(para->DNA_PARAMETERS) para->DIAG_THRESHOLD_WEIGHT = -log(0.75);//-log(.875+0.125/2.0); else para->DIAG_THRESHOLD_WEIGHT = -log(0.75); }else if(para->SENS_MODE==2) { if(para->DNA_PARAMETERS) para->DIAG_THRESHOLD_WEIGHT = -log(0.5);//-log(0.875); else para->DIAG_THRESHOLD_WEIGHT = -log(0.5); } } int stype = (para->FAST_MODE ? 1 : 0); for(type=stype;type<2;type++) { for(round=2;round<=20;round++) { //for(round=2;round<=1;round++) { tim2=clock(); all_diags = find_all_diags(smatrix, pdist, in_seq_col,(type ? salgn : algn), round); //all_diags = find_all_diags(smatrix, pdist, in_seq_col, algn); duration = (clock()-tim2)/CLOCKS_PER_SEC; if(para->DEBUG >1) printf("Found %i diags after %f secs\n", all_diags->diag_amount, duration); if(all_diags->diag_amount ==0) { free_diag_col(all_diags); break; } else { // round 2 and further we use the simple aligner newFound = simple_aligner(in_seq_col, all_diags,smatrix,pdist,(type ? salgn : algn),round); //newFound = simple_aligner(in_seq_col, all_diags,smatrix,pdist,algn,round); // newFound = complex_aligner(in_seq_col, all_diags,smatrix,pdist,algn,round); free_diag_col(all_diags); if(!newFound) break; } } } if(para->DEBUG >1) printf("Alignment ready!\n"); if(! para->FAST_MODE) { if(para->DEBUG >1) printf("Final alignment simple: %f guided: %f\n", salgn->total_weight, algn->total_weight); } else { if(para->DEBUG >1) printf("Final alignment simple: %f \n", salgn->total_weight); } //if(para->DEBUG >1) printf("Final alignment guided: %f\n", algn->total_weight); if( ( para->FAST_MODE) || (salgn->total_weight > algn->total_weight)) { if(! para->FAST_MODE) free_alignment(algn); 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using boost::graph_traits; template void write_edge_prop(std::ostream& out, const EdgeProp& ep) { if (ep != EdgeProp()) out << " [" << ep << ']'; } static inline void write_edge_prop(std::ostream&, const no_property&) { } /** Output a contig adjacency graph. */ template std::ostream& write_adj(std::ostream& out, const Graph& g) { typedef typename graph_traits::vertex_descriptor vertex_descriptor; typedef typename graph_traits::vertex_iterator vertex_iterator; typedef typename graph_traits::out_edge_iterator out_edge_iterator; std::pair vit = vertices(g); bool sense = false; for (vertex_iterator u = vit.first; u != vit.second; ++u, sense = !sense) { if (get(vertex_removed, g, *u)) continue; if (!sense) out << get(vertex_contig_name, g, *u) << get(vertex_bundle, g, *u); out << "\t;"; std::pair adj = out_edges(*u, g); for (out_edge_iterator e = adj.first; e != adj.second; ++e) { vertex_descriptor v = target(*e, g); assert(!get(vertex_removed, g, v)); out << ' ' << get(vertex_name, g, v ^ sense); write_edge_prop(out, get(edge_bundle, g, e)); } if (sense) out << '\n'; } return out; } /** Read the edges of a graph in dist format. */ template std::istream& readDistEdges(std::istream& in, ContigGraph& g, typename graph_traits::vertex_descriptor u, BetterEP betterEP) { typedef typename graph_traits::vertex_descriptor V; typedef typename graph_traits::edge_descriptor E; typedef typename Graph::edge_property_type EP; for (std::string vname; getline(in >> std::ws, vname, ',');) { assert(!vname.empty()); V v = find_vertex(vname, g); v = v ^ get(vertex_sense, g, u); EP ep; in >> ep; assert(in); if (in.peek() != ' ') in >> Ignore(' '); E e; bool found; boost::tie(e, found) = edge(u, v, g); if (found) { // Parallel edge EP& ref = g[e]; ref = betterEP(ref, ep); } else g.Graph::add_edge(u, v, ep); } assert(in.eof()); return in; } /** Read a contig adjacency graph. * @param betterEP handle parallel edges */ template std::istream& read_adj(std::istream& in, ContigGraph& g, BetterEP betterEP) { if (in.eof()) { // Allow reading an empty file if the graph is not empty. assert(num_vertices(g) > 0); return in; } assert(in); typedef typename Graph::vertex_descriptor vertex_descriptor; typedef typename Graph::vertex_property_type vertex_property_type; typedef typename Graph::edge_property_type edge_property_type; // Check for ADJ or DIST format. std::string line; getline(in, line); assert(in); unsigned numSemicolons = std::count(line.begin(), line.end(), ';'); if (numSemicolons > 2) { std::cerr << "error: expected 0, 1 or 2 semicolons and saw " << numSemicolons << '\n'; exit(EXIT_FAILURE); } bool faiFormat = numSemicolons == 0; bool adjFormat = numSemicolons == 2; // Read the vertex properties. if (adjFormat || faiFormat) { assert(num_vertices(g) == 0); in.clear(); in.seekg(0, std::ios::beg); assert(in); for (std::string uname; in >> uname;) { vertex_property_type vp; if (faiFormat) { unsigned length; in >> length; put(vertex_length, vp, length); } else in >> vp; in >> Ignore('\n'); assert(in); vertex_descriptor u = add_vertex(vp, g); put(vertex_name, g, u, uname); } assert(in.eof()); } assert(num_vertices(g) > 0); g_contigNames.lock(); if (faiFormat) return in; // Read the edges. in.clear(); in.seekg(0, std::ios::beg); assert(in); for (std::string name; in >> name;) { if (adjFormat) in >> Ignore(';'); vertex_descriptor u = find_vertex(name, false, g); for (int sense = false; sense <= true; ++sense) { std::string s; getline(in, s, !sense ? ';' : '\n'); assert(in.good()); std::istringstream ss(s); if (!adjFormat) { readDistEdges(ss, g, u ^ sense, betterEP); } else for (std::string vname; ss >> vname;) { ss >> std::ws; vertex_descriptor v = find_vertex(vname, g); assert(!edge(u ^ sense, v ^ sense, g).second); if (ss.peek() == '[') { ss.get(); edge_property_type ep; ss >> ep >> Ignore(']'); g.Graph::add_edge(u ^ sense, v ^ sense, ep); } else g.Graph::add_edge(u ^ sense, v ^ sense); } assert(ss.eof()); } } assert(in.eof()); return in; } template class AdjWriter { const Graph& m_g; public: AdjWriter(const Graph& g) : m_g(g) { } friend std::ostream& operator<<(std::ostream& out, const AdjWriter& o) { return write_adj(out, o.m_g); } }; template AdjWriter adj_writer(const Graph& g) { return AdjWriter(g); } #endif abyss-1.3.6/Graph/AsqgIO.h000644 002433 001057 00000007631 12104026026 016714 0ustar00traymondassembly000000 000000 #ifndef ASQGIO_H #define ASQGIO_H 1 #include "Common/IOUtil.h" #include "Graph/Properties.h" #include #include #include #include #include using boost::graph_traits; /** Write a graph in ASQG format. */ template std::ostream& write_asqg(std::ostream& out, Graph& g) { typedef typename graph_traits::edge_descriptor E; typedef typename graph_traits::edge_iterator Eit; typedef typename graph_traits::vertex_descriptor V; typedef typename graph_traits::vertex_iterator Vit; typedef typename vertex_bundle_type::type VP; out << "HT\tVN:i:1\n"; assert(out); std::pair vrange = vertices(g); for (Vit uit = vrange.first; uit != vrange.second; ++uit, ++uit) { V u = *uit; if (get(vertex_removed, g, u)) continue; const VP& vp = g[u]; out << "VT\t" << get(vertex_contig_name, g, u) << "\t*\tLN:i:" << vp.length; if (vp.coverage > 0) out << "\tXC:i:" << vp.coverage; out << '\n'; } std::pair erange = edges(g); for (Eit eit = erange.first; eit != erange.second; ++eit) { E e = *eit; V u = source(e, g); V v = target(e, g); if (v < u || get(vertex_removed, g, u)) continue; assert(!get(vertex_removed, g, v)); int distance = g[e].distance; assert(distance < 0); unsigned overlap = -distance; unsigned ulen = g[u].length; unsigned vlen = g[v].length; bool usense = get(vertex_sense, g, u); bool vsense = get(vertex_sense, g, v); out << "ED\t" << get(vertex_contig_name, g, u) << ' ' << get(vertex_contig_name, g, v) << ' ' << (usense ? 0 : ulen - overlap) << ' ' << (usense ? overlap : ulen) - 1 << ' ' << ulen << ' ' << (!vsense ? 0 : vlen - overlap) << ' ' << (!vsense ? overlap : vlen) - 1 << ' ' << vlen << ' ' << (usense != vsense) << " -1\n"; // number of mismatches } return out; } /** Read a graph in ASQG format. */ template std::istream& read_asqg(std::istream& in, Graph& g) { assert(in); typedef typename graph_traits::vertex_descriptor V; typedef typename graph_traits::edge_descriptor E; typedef typename vertex_property::type VP; typedef typename edge_property::type EP; // Add vertices if this graph is empty. bool addVertices = num_vertices(g) == 0; while (in && in.peek() != EOF) { switch (in.peek()) { case 'H': in >> expect("HT") >> Ignore('\n'); assert(in); break; case 'V': { std::string uname, seq; in >> expect("VT") >> uname >> seq; assert(in); assert(!seq.empty()); unsigned length = 0; if (seq == "*") { in >> expect(" LN:i:") >> length; assert(in); } else length = seq.size(); in >> Ignore('\n'); if (addVertices) { VP vp; put(vertex_length, vp, length); V u = add_vertex(vp, g); put(vertex_name, g, u, uname); } else { V u = find_vertex(uname, false, g); assert(get(vertex_index, g, u) < num_vertices(g)); (void)u; } break; } case 'E': { std::string uname, vname; unsigned s1, e1, l1, s2, e2, l2; bool rc; int nd; in >> expect("ED") >> uname >> vname >> s1 >> e1 >> l1 >> s2 >> e2 >> l2 >> rc >> nd >> Ignore('\n'); assert(in); assert(s1 < e1 && e1 < l1 && s2 < e2 && e2 < l2); assert(e1 - s1 == e2 - s2); assert(e1 - s1 + 1 < l1 && e2 - s2 + 1 < l2); assert(((s1 > 0) == (s2 > 0)) == rc); int d = -(e1 - s1 + 1); assert(d < 0); EP ep(d); V u = find_vertex(uname, s1 == 0, g); V v = find_vertex(vname, s2 > 0, g); std::pair e = edge(u, v, g); if (e.second) { // Ignore duplicate edges that are self loops. assert(g[e.first] == ep); assert(u == v); } else add_edge(u, v, ep, g); break; } default: { std::string s; in >> s; std::cerr << "error: unknown record type: `" << s << "'\n"; exit(EXIT_FAILURE); } } } assert(in.eof()); return in; } #endif abyss-1.3.6/Graph/Assemble.h000644 002433 001057 00000003013 12104026026 017312 0ustar00traymondassembly000000 000000 #ifndef ASSEMBLE_H #define ASSEMBLE_H 1 #include "Common/ContigNode.h" // for ContigIndexMap #include "Common/Iterator.h" // for output_iterator_traits #include "Graph/DepthFirstSearch.h" using boost::graph_traits; /** Return true if this edge is contiguous. */ template bool isContiguous(const Graph &g, typename graph_traits::edge_descriptor e) { return out_degree(source(e, g), g) == 1 && in_degree(target(e, g), g) == 1; } /** Assemble contigous paths. Write the paths to out. */ template class AssembleVisitor : public boost::default_dfs_visitor { public: AssembleVisitor(OutIt it) : m_it(it) { } template void discover_vertex(const Vertex& u, Graph&) { m_path.push_back(u); } template void finish_vertex(const Vertex&, Graph&) { finishContig(); } template void examine_edge(const Edge& e, const Graph& g) { if (!isContiguous(g, e)) finishContig(); } private: void finishContig() { if (m_path.size() > 1) *m_it++ = m_path; m_path.clear(); } OutIt m_it; typename output_iterator_traits::value_type m_path; }; /** Assemble unambiguous paths. Write the paths to out. */ template void assembleDFS(const Graph& g, OutIt out) { typedef boost::vector_property_map< boost::default_color_type, ContigIndexMap> ColorMap; depthFirstSearch(g, AssembleVisitor(out), ColorMap(num_vertices(g) / 2)); } #endif abyss-1.3.6/Graph/ConstrainedSearch.cpp000644 002433 001057 00000007310 12015543262 021524 0ustar00traymondassembly000000 000000 #include "ConstrainedSearch.h" #include "ContigGraph.h" #include "DirectedGraph.h" #include "Graph/Properties.h" #include #include // for INT_MIN #include using namespace std; namespace opt { /** Abort the search after visiting maxCost vertices. */ unsigned maxCost = 100000; } /** Compare the distance of two constraints. */ static inline bool compareDistance( const Constraint& a, const Constraint& b) { return a.second < b.second; } /** Compare the ID of a constraint. */ static inline bool compareID(const Constraint& constraint, const ContigNode& key) { return constraint.first < key; } /** Find a constraint by ID. */ static inline Constraints::iterator findConstraint( Constraints& constraints, const ContigNode& key) { Constraints::iterator it = lower_bound( constraints.begin(), constraints.end(), key, compareID); return it != constraints.end() && it->first == key ? it : constraints.end(); } typedef graph_traits::vertex_descriptor vertex_descriptor; typedef graph_traits::out_edge_iterator out_edge_iterator; /** Find paths through the graph that satisfy the constraints. * @return false if the search exited early */ bool constrainedSearch(const Graph& g, vertex_descriptor u, Constraints& constraints, Constraints::const_iterator nextConstraint, unsigned satisfied, ContigPath& path, ContigPaths& solutions, int distance, unsigned& visitedCount) { assert(satisfied < constraints.size()); static const int SATISFIED = INT_MAX; if (!path.empty()) { vertex_descriptor v = path.back(); Constraints::iterator it = findConstraint(constraints, v); if (it != constraints.end() && it->second != SATISFIED) { if (distance > it->second) return true; // This constraint cannot be met. if (++satisfied == constraints.size()) { // All the constraints have been satisfied. solutions.push_back(path); return solutions.size() <= opt::maxPaths; } // This constraint has been satisfied. int constraint = it->second; it->second = SATISFIED; if (!constrainedSearch(g, u, constraints, nextConstraint, satisfied, path, solutions, distance, visitedCount)) return false; it->second = constraint; return true; } if (++visitedCount >= opt::maxCost) return false; // Too complex. // Check that the next constraint has not been violated. while (distance > nextConstraint->second && findConstraint(constraints, nextConstraint->first)->second == SATISFIED) ++nextConstraint; // This constraint is satisfied. if (distance > nextConstraint->second) return true; // This constraint cannot be met. distance += g[v].length; u = v; } path.push_back(vertex_descriptor()); pair adj = g.out_edges(u); for (out_edge_iterator it = adj.first; it != adj.second; ++it) { path.back() = target(*it, g); if (!constrainedSearch(g, u, constraints, nextConstraint, satisfied, path, solutions, distance + g[*it].distance, visitedCount)) return false; } assert(!path.empty()); path.pop_back(); return true; } /** Find paths through the graph that satisfy the constraints. * @return false if the search exited early */ bool constrainedSearch(const Graph& g, vertex_descriptor v, Constraints& constraints, ContigPaths& paths, unsigned& cost) { if (constraints.empty()) return false; // Sort the constraints by ID. sort(constraints.begin(), constraints.end()); // Sort the constraints by distance. Constraints queue(constraints); sort(queue.begin(), queue.end(), compareDistance); ContigPath path; constrainedSearch(g, v, constraints, queue.begin(), 0, path, paths, 0, cost); return cost >= opt::maxCost ? false : !paths.empty(); } abyss-1.3.6/Graph/ConstrainedSearch.h000644 002433 001057 00000001377 12104026026 021171 0ustar00traymondassembly000000 000000 #ifndef CONSTRAINEDSEARCH_H #define CONSTRAINEDSEARCH_H 1 #include "ContigGraph.h" #include "ContigPath.h" #include "ContigProperties.h" #include "DirectedGraph.h" #include #include #include #include namespace opt { extern unsigned maxCost; /** Abort the search after visiting maxPaths solutions. */ static const unsigned maxPaths = 200; } typedef ContigGraph > Graph; typedef std::pair Constraint; typedef std::vector Constraints; typedef std::vector ContigPaths; bool constrainedSearch(const Graph& g, graph_traits::vertex_descriptor origin, Constraints& constraints, ContigPaths& superPaths, unsigned& compCost); #endif abyss-1.3.6/Graph/ContigGraph.h000644 002433 001057 00000026774 12104026026 020007 0ustar00traymondassembly000000 000000 #ifndef CONTIGGRAPH_H #define CONTIGGRAPH_H 1 #include "ContigID.h" #include "Graph/Properties.h" #include #include #include using boost::graph_traits; /** A contig graph is a directed graph with the property that * the edge (u,v) implies the existence of the edge (~v,~u). */ template class ContigGraph : public G { public: typedef G base_type; // Graph typedef typename graph_traits::vertex_descriptor vertex_descriptor; typedef typename graph_traits::directed_category directed_category; typedef typename graph_traits::traversal_category traversal_category; typedef typename graph_traits::edge_parallel_category edge_parallel_category; // IncidenceGraph typedef typename graph_traits::edge_descriptor edge_descriptor; typedef typename graph_traits::out_edge_iterator out_edge_iterator; typedef typename graph_traits::degree_size_type degree_size_type; // AdjacencyGraph typedef typename graph_traits::adjacency_iterator adjacency_iterator; // VertexListGraph typedef typename graph_traits::vertex_iterator vertex_iterator; typedef typename graph_traits::vertices_size_type vertices_size_type; // EdgeListGraph typedef typename graph_traits::edge_iterator edge_iterator; typedef typename graph_traits::edges_size_type edges_size_type; // VertexMutablePropertyGraph typedef typename vertex_property::type vertex_property_type; // EdgeMutablePropertyGraph typedef typename edge_property::type edge_property_type; // BidirectionalGraph /** Iterate through the in-edges. */ class in_edge_iterator : public std::iterator { /** Return the complement (~v, ~u) of the edge (u, v). */ static edge_descriptor complement(const edge_descriptor& e) { return std::pair( e.second ^ 1, e.first ^ 1); } public: in_edge_iterator() { } in_edge_iterator(typename graph_traits::out_edge_iterator it) : m_it(it) { } edge_descriptor operator*() const { return complement(*m_it); } bool operator==(const in_edge_iterator& it) const { return m_it == it.m_it; } bool operator!=(const in_edge_iterator& it) const { return m_it != it.m_it; } in_edge_iterator& operator++() { ++m_it; return *this; } in_edge_iterator operator++(int) { in_edge_iterator it = *this; ++*this; return it; } private: out_edge_iterator m_it; }; public: /** Construct an empty contig graph. */ ContigGraph() { } /** Construct a contig graph with n vertices. The underlying * directed graph has two vertices for each contig. */ ContigGraph(vertices_size_type n) : G(2 * n) { } /** Return the in degree of vertex v. */ degree_size_type in_degree(vertex_descriptor v) const { return G::out_degree(get(vertex_complement, *this, v)); } /** Remove all out edges from vertex u. */ void clear_out_edges(vertex_descriptor u) { std::pair adj = G::adjacent_vertices(u); for (adjacency_iterator v = adj.first; v != adj.second; ++v) { vertex_descriptor uc = get(vertex_complement, *this, u); vertex_descriptor vc = get(vertex_complement, *this, *v); if (vc == u) { // When ~v == u, removing (~v,~u), which is (u,~u), // would invalidate our iterator. This edge will be // removed by clear_out_edges. } else G::remove_edge(vc, uc); } G::clear_out_edges(u); } /** Remove all in edges from vertex v. */ void clear_in_edges(vertex_descriptor v) { clear_out_edges(get(vertex_complement, *this, v)); } /** Remove all edges to and from vertex v. */ void clear_vertex(vertex_descriptor v) { clear_out_edges(v); clear_in_edges(v); } /** Add a vertex to this graph. */ vertex_descriptor add_vertex( const vertex_property_type& data = vertex_property_type()) { vertex_descriptor v = G::add_vertex(data); G::add_vertex(data); return v; } /** Remove vertex v from this graph. It is assumed that there * are no edges to or from vertex v. It is best to call * clear_vertex before remove_vertex. */ void remove_vertex(vertex_descriptor v) { G::remove_vertex(v); G::remove_vertex(get(vertex_complement, *this, v)); } /** Add edge (u,v) to this graph. */ std::pair add_edge(vertex_descriptor u, vertex_descriptor v) { vertex_descriptor uc = get(vertex_complement, *this, u); vertex_descriptor vc = get(vertex_complement, *this, v); std::pair e = G::add_edge(u, v); if (u != vc) G::add_edge(vc, uc); return e; } /** Add edge (u,v) to this graph. */ std::pair add_edge(vertex_descriptor u, vertex_descriptor v, const edge_property_type& ep) { vertex_descriptor uc = get(vertex_complement, *this, u); vertex_descriptor vc = get(vertex_complement, *this, v); std::pair e = G::add_edge(u, v, ep); if (u != vc) G::add_edge(vc, uc, ep); return e; } /** Remove the edge (u,v) from this graph. */ void remove_edge(vertex_descriptor u, vertex_descriptor v) { vertex_descriptor uc = get(vertex_complement, *this, u); vertex_descriptor vc = get(vertex_complement, *this, v); G::remove_edge(u, v); if (u != vc) G::remove_edge(vc, uc); } /** Remove the edge e from this graph. */ void remove_edge(edge_descriptor e) { remove_edge(source(e, *this), target(e, *this)); } }; namespace std { template inline void swap(ContigGraph& a, ContigGraph& b) { a.swap(b); } } // IncidenceGraph template std::pair< typename ContigGraph::out_edge_iterator, typename ContigGraph::out_edge_iterator> out_edges( typename ContigGraph::vertex_descriptor u, const ContigGraph& g) { return g.out_edges(u); } template typename ContigGraph::degree_size_type out_degree( typename ContigGraph::vertex_descriptor u, const ContigGraph& g) { return g.out_degree(u); } // BidirectionalGraph template std::pair< typename ContigGraph::in_edge_iterator, typename ContigGraph::in_edge_iterator> in_edges( typename ContigGraph::vertex_descriptor u, const ContigGraph& g) { typedef typename ContigGraph::in_edge_iterator in_edge_iterator; typedef typename ContigGraph::out_edge_iterator out_edge_iterator; std::pair it = out_edges(get(vertex_complement, g, u), g); return std::pair( it.first, it.second); } template typename ContigGraph::degree_size_type in_degree( typename ContigGraph::vertex_descriptor u, const ContigGraph& g) { return g.in_degree(u); } // AdjacencyGraph template std::pair< typename ContigGraph::adjacency_iterator, typename ContigGraph::adjacency_iterator> adjacent_vertices( typename ContigGraph::vertex_descriptor u, const ContigGraph& g) { return g.adjacent_vertices(u); } // VertexListGraph template typename ContigGraph::vertices_size_type num_vertices(const ContigGraph& g) { return g.num_vertices(); } template std::pair::vertex_iterator, typename ContigGraph::vertex_iterator> vertices(const ContigGraph& g) { return g.vertices(); } // EdgeListGraph template typename ContigGraph::edges_size_type num_edges(const ContigGraph& g) { return g.num_edges(); } template std::pair::edge_iterator, typename ContigGraph::edge_iterator> edges(const ContigGraph& g) { return g.edges(); } // AdjacencyMatrix template std::pair::edge_descriptor, bool> edge( typename ContigGraph::vertex_descriptor u, typename ContigGraph::vertex_descriptor v, const ContigGraph& g) { return g.edge(u, v); } // VertexMutableGraph template typename ContigGraph::vertex_descriptor add_vertex(ContigGraph& g) { return g.add_vertex(); } template void remove_vertex( typename ContigGraph::vertex_descriptor u, ContigGraph& g) { g.remove_vertex(u); } // EdgeMutableGraph template void clear_vertex( typename ContigGraph::vertex_descriptor u, ContigGraph& g) { g.clear_vertex(u); } template std::pair::edge_descriptor, bool> add_edge( typename ContigGraph::vertex_descriptor u, typename ContigGraph::vertex_descriptor v, ContigGraph& g) { return g.add_edge(u, v); } template void remove_edge( typename ContigGraph::vertex_descriptor u, typename ContigGraph::vertex_descriptor v, ContigGraph& g) { return g.remove_edge(u, v); } template void remove_edge( typename ContigGraph::edge_descriptor e, ContigGraph& g) { g.remove_edge(e); } // MutableIncidenceGraph template void clear_out_edges( typename ContigGraph::vertex_descriptor u, ContigGraph& g) { g.clear_out_edges(u); } // MutableBidirectionalGraph template void clear_in_edges( typename ContigGraph::vertex_descriptor u, ContigGraph& g) { g.clear_in_edges(u); } // PropertyGraph /** Return true if this vertex has been removed. */ template bool get(vertex_removed_t tag, const ContigGraph& g, typename ContigGraph::vertex_descriptor u) { return get(tag, static_cast(g), u); } template void put(vertex_removed_t tag, ContigGraph& g, typename ContigGraph::vertex_descriptor u, bool flag) { put(tag, static_cast(g), u, flag); put(tag, static_cast(g), get(vertex_complement, g, u), flag); } /** Return the properties of the edge of iterator eit. */ template const typename ContigGraph::edge_property_type& get(edge_bundle_t, const ContigGraph&, typename ContigGraph::out_edge_iterator eit) { return eit.get_property(); } // PropertyGraph template typename vertex_bundle_type::type get(vertex_bundle_t, const ContigGraph& g, typename ContigGraph::vertex_descriptor u) { return g[u]; } template typename edge_bundle_type::type get(edge_bundle_t, const ContigGraph& g, typename ContigGraph::edge_descriptor e) { return g[e]; } // PropertyGraph namespace boost { template struct property_map, vertex_index_t> { typedef typename property_map::type type; typedef type const_type; }; } /** Return the complement of the specified vertex. */ template typename graph_traits::vertex_descriptor get(vertex_complement_t, const ContigGraph&, typename graph_traits::vertex_descriptor u) { return u ^ 1; } /** Return the contig index of the specified vertex. */ template ContigID get(vertex_contig_index_t, const ContigGraph&, typename graph_traits::vertex_descriptor u) { return u.contigIndex(); } /** Return the sense of the specified vertex. */ template bool get(vertex_sense_t, const ContigGraph&, typename graph_traits::vertex_descriptor u) { return u.sense(); } // VertexMutablePropertyGraph template typename ContigGraph::vertex_descriptor add_vertex( const typename vertex_property::type& vp, ContigGraph& g) { return g.add_vertex(vp); } // EdgeMutablePropertyGraph template std::pair::edge_descriptor, bool> add_edge( typename ContigGraph::vertex_descriptor u, typename ContigGraph::vertex_descriptor v, const typename ContigGraph::edge_property_type& ep, ContigGraph& g) { return g.add_edge(u, v, ep); } #endif abyss-1.3.6/Graph/ContigGraphAlgorithms.h000644 002433 001057 00000023716 12153225302 022034 0ustar00traymondassembly000000 000000 #ifndef CONTIGGRAPHALGORITHMS_H #define CONTIGGRAPHALGORITHMS_H 1 #include "Algorithms.h" #include "ContigGraph.h" #include "ContigNode.h" #include "Estimate.h" // for BetterDistanceEst #include "Functional.h" #include "Iterator.h" #include #include #include #include #include #include using boost::graph_traits; /** Return true if the edge e is a palindrome. */ template struct IsPalindrome : std::unary_function< typename graph_traits::edge_descriptor, bool> { IsPalindrome(const Graph& g) : m_g(g) { } bool operator()( typename graph_traits::edge_descriptor e) const { return source(e, m_g) == get(vertex_complement, m_g, target(e, m_g)); } private: const Graph& m_g; }; /** Return whether the outgoing edge of vertex u is contiguous. */ template bool contiguous_out(const Graph& g, typename graph_traits::vertex_descriptor u) { return out_degree(u, g) == 1 && in_degree(*adjacent_vertices(u, g).first, g) == 1; } /** Return whether the incoming edge of vertex u is contiguous. */ template bool contiguous_in(const Graph& g, typename graph_traits::vertex_descriptor u) { return contiguous_out(g, get(vertex_complement, g, u)); } /** Add the outgoing edges of vertex u to vertex uout. */ template void copy_out_edges(Graph &g, typename Graph::vertex_descriptor u, typename Graph::vertex_descriptor uout) { typedef typename graph_traits::vertex_descriptor vertex_descriptor; typedef typename graph_traits::out_edge_iterator out_edge_iterator; typedef typename edge_property::type edge_property_type; assert(u != uout); std::pair edges = g.out_edges(u); bool palindrome = false; edge_property_type palindrome_ep; for (out_edge_iterator e = edges.first; e != edges.second; ++e) { vertex_descriptor v = target(*e, g); vertex_descriptor vc = get(vertex_complement, g, v); if (vc == u) { // When ~v == u, adding the edge (~v,~u), which is (u,~u), // would invalidate our iterator. Add the edge after this // loop completes. palindrome = true; palindrome_ep = g[*e]; } else g.add_edge(uout, v, g[*e]); } if (palindrome) { vertex_descriptor uc = get(vertex_complement, g, u); vertex_descriptor uoutc = get(vertex_complement, g, uout); g.add_edge(uout, uc, palindrome_ep); g.add_edge(uout, uoutc, palindrome_ep); } } /** Add the incoming edges of vertex u to vertex v. */ template void copy_in_edges(Graph& g, typename Graph::vertex_descriptor u, typename Graph::vertex_descriptor v) { copy_out_edges(g, get(vertex_complement, g, u), get(vertex_complement, g, v)); } /** Assemble a path of unambigous out edges starting at vertex u. * u itself is not copied to out. */ template OutIt extend(const Graph& g, typename Graph::vertex_descriptor u, OutIt out) { typedef typename graph_traits::vertex_descriptor vertex_descriptor; std::set seen; while (out_degree(u, g) == 1 && seen.insert(u).second) { u = *adjacent_vertices(u, g).first; *out++ = u; } return out; } /** Assemble an unambiguous path starting at vertex u. * Every edge must satisfy the predicate. */ template OutIt assemble_if(const Graph& g, typename Graph::vertex_descriptor u, OutIt out, Predicate pred) { typedef typename graph_traits::edge_descriptor edge_descriptor; while (contiguous_out(g, u)) { edge_descriptor e = *out_edges(u, g).first; if (!pred(e)) break; *out++ = u; u = target(e, g); } *out++ = u; return out; } /** Remove vertices in the sequence [first, last) from the graph * for which the predicate p is true. Edges incident to those vertices * are removed as well. */ template void remove_vertex_if(Graph& g, It first, It last, Predicate p) { for_each_if(first, last, bind1st(std::mem_fun(&Graph::clear_vertex), &g), p); for_each_if(first, last, bind1st(std::mem_fun(&Graph::remove_vertex), &g), p); } /** Add the vertex and edge propeties of the path [first, last). */ template VP addProp(const Graph& g, It first, It last, const VP*) { typedef typename graph_traits::vertex_descriptor vertex_descriptor; assert(first != last); VP vp = get(vertex_bundle, g, *first); for (It it = first + 1; it != last; ++it) { vertex_descriptor u = *(it - 1); vertex_descriptor v = *it; vp += get(edge_bundle, g, u, v); vp += get(vertex_bundle, g, v); } return vp; } template no_property addProp(const Graph&, It, It, const no_property*) { return no_property(); } template typename vertex_property::type addProp(const Graph& g, It first, It last) { return addProp(g, first, last, (typename vertex_property::type*)NULL); } /** Merge the vertices in the sequence [first, last). * Create a new vertex whose property is the sum of [first, last). * Remove the vertices [first, last). */ template typename graph_traits::vertex_descriptor merge(Graph& g, It first, It last) { typedef typename graph_traits::vertex_descriptor vertex_descriptor; assert(first != last); vertex_descriptor u = add_vertex(addProp(g, first, last), g); copy_in_edges(g, *first, u); copy_out_edges(g, *(last - 1), u); return u; } /** Assemble unambiguous paths. Write the paths to out. * Every edge must satisfy the predicate. */ template OutIt assemble_if(Graph& g, OutIt out, Predicate pred0) { typedef typename Graph::vertex_descriptor vertex_descriptor; typedef typename Graph::vertex_iterator vertex_iterator; // pred(e) = !isPalindrome(e) && pred0(e) binary_compose, std::unary_negate >, Predicate> pred(compose2(std::logical_and(), std::not1(IsPalindrome(g)), pred0)); std::pair uit = g.vertices(); for (vertex_iterator u = uit.first; u != uit.second; ++u) { if (!contiguous_out(g, *u) || contiguous_in(g, *u) || !pred(*out_edges(*u, g).first)) continue; typename output_iterator_traits::value_type path; assemble_if(g, *u, back_inserter(path), pred); assert(path.size() >= 2); assert(path.front() != path.back()); merge(g, path.begin(), path.end()); remove_vertex_if(g, path.begin(), path.end(), not1(std::mem_fun_ref(&ContigNode::ambiguous))); *out++ = path; } return out; } /** Assemble unambiguous paths. Write the paths to out. */ template OutIt assemble(Graph& g, OutIt out) { typedef typename graph_traits::edge_descriptor edge_descriptor; return assemble_if(g, out, True()); } /** Remove tips. * For an edge (u,v), remove the vertex v if deg+(u) > 1, * deg-(v) = 1 and deg+(v) = 0, and p(v) is true. * Stores all removed vertices in result. */ template OutputIt pruneTips_if(Graph& g, OutputIt result, Pred p) { typedef typename graph_traits::adjacency_iterator Vit; typedef typename graph_traits::vertex_iterator Uit; typedef typename graph_traits::vertex_descriptor V; /** Identify the tips. */ std::vector tips; std::pair urange = vertices(g); for (Uit uit = urange.first; uit != urange.second; ++uit) { V u = *uit; if (out_degree(u, g) < 2) continue; std::pair vrange = adjacent_vertices(u, g); for (Vit vit = vrange.first; vit != vrange.second; ++vit) { V v = *vit; //assert(v != u); if (in_degree(v, g) == 1 && out_degree(v, g) == 0 && p(v)) tips.push_back(v); } } /** Remove the tips. */ remove_vertex_if(g, tips.begin(), tips.end(), True()); std::transform(tips.begin(), tips.end(), result, std::mem_fun_ref(&ContigNode::contigIndex)); return result; } /** Remove tips. * For an edge (u,v), remove the vertex v if deg+(u) > 1 * and deg-(v) = 1 and deg+(v) = 0. * Stores all removed vertices in result. */ template OutputIt pruneTips(Graph& g, OutputIt result) { typedef typename graph_traits::vertex_descriptor V; return pruneTips_if(g, result, True()); } /** Remove islands. * For a vertex v, remove v if deg+(v) = 0, deg-(v) = 0 and p(v) is * true. * Stores all removed vertices in result. */ template OutputIt removeIslands_if(Graph& g, OutputIt result, Pred p) { typedef typename graph_traits::vertex_iterator Uit; typedef typename graph_traits::vertex_descriptor V; /** Identify and remove Islands. */ std::pair urange = vertices(g); for (Uit uit = urange.first; uit != urange.second; ++uit) { V u = *uit; if (get(vertex_removed, g, u)) continue; if (p(u) && in_degree(u, g) == 0 && out_degree(u, g) == 0) { *result++ = get(vertex_contig_index, g, u); clear_vertex(u, g); remove_vertex(u, g); } } return result; } /** Add missing complementary edges. */ template size_t addComplementaryEdges(ContigGraph& g) { typedef ContigGraph Graph; typedef graph_traits GTraits; typedef typename GTraits::edge_descriptor E; typedef typename GTraits::edge_iterator Eit; typedef typename GTraits::vertex_descriptor V; std::pair erange = edges(g); size_t numAdded = 0; for (Eit eit = erange.first; eit != erange.second; ++eit) { E e = *eit; V u = source(e, g), v = target(e, g); V uc = get(vertex_complement, g, u); V vc = get(vertex_complement, g, v); E f; bool found; tie(f, found) = edge(vc, uc, g); if (!found) { add_edge(vc, uc, g[e], static_cast(g)); numAdded++; } else if (!(g[e] == g[f])) { // The edge properties do not agree. Select the better. g[e] = g[f] = BetterDistanceEst()(g[e], g[f]); } } return numAdded; } #endif abyss-1.3.6/Graph/DepthFirstSearch.h000644 002433 001057 00000003464 12104026026 020773 0ustar00traymondassembly000000 000000 #ifndef DEPTHFIRSTSEARCH_H #define DEPTHFIRSTSEARCH_H 1 #include "Graph/ContigGraphAlgorithms.h" // for contiguous_in #include using boost::graph_traits; /** * Perform a depth-first search starting first with vertices with * deg-(u) = 0 and then visiting any remaining vertices. */ template void depthFirstSearch(const Graph& g, Visitor vis, ColorMap color) { using boost::color_traits; using boost::property_traits; using boost::tie; typedef graph_traits GTraits; typedef typename GTraits::vertex_descriptor V; typedef typename GTraits::vertex_iterator Vit; typedef typename property_traits::value_type ColorValue; const ColorValue white = color_traits::white(); // Initialize the vertices. Vit uit, ulast; for (tie(uit, ulast) = vertices(g); uit != ulast; ++uit) { V u = *uit; put(color, u, white); vis.initialize_vertex(u, g); } // Visit vertices with deg-(u) = 0. for (tie(uit, ulast) = vertices(g); uit != ulast; ++uit) { V u = *uit; if (get(color, u) == white && in_degree(u, g) == 0) { vis.start_vertex(u, g); boost::detail::depth_first_visit_impl(g, u, vis, color, boost::detail::nontruth2()); } } // Visit vertices where discontiguous-(u). for (tie(uit, ulast) = vertices(g); uit != ulast; ++uit) { V u = *uit; if (get(color, u) == white && !contiguous_in(g, u)) { vis.start_vertex(u, g); boost::detail::depth_first_visit_impl(g, u, vis, color, boost::detail::nontruth2()); } } // Visit the remaining vertices. for (tie(uit, ulast) = vertices(g); uit != ulast; ++uit) { V u = *uit; if (get(color, u) == white) { vis.start_vertex(u, g); boost::detail::depth_first_visit_impl(g, u, vis, color, boost::detail::nontruth2()); } } } #endif abyss-1.3.6/Graph/DirectedGraph.h000644 002433 001057 00000046266 12104026026 020305 0ustar00traymondassembly000000 000000 #ifndef DIRECTEDGRAPH_H #define DIRECTEDGRAPH_H 1 #include "ContigNode.h" #include "Graph/Properties.h" #include #include #include #include /** A directed graph. */ template class DirectedGraph { class Vertex; typedef typename std::vector Vertices; class Edge; typedef typename std::vector Edges; public: // Graph typedef ContigNode vertex_descriptor; // IncidenceGraph typedef std::pair edge_descriptor; typedef unsigned degree_size_type; // BidirectionalGraph typedef void in_edge_iterator; // VertexListGraph typedef unsigned vertices_size_type; // EdgeListGraph typedef unsigned edges_size_type; // PropertyGraph typedef VertexProp vertex_bundled; typedef VertexProp vertex_property_type; typedef EdgeProp edge_bundled; typedef EdgeProp edge_property_type; typedef boost::directed_tag directed_category; typedef boost::allow_parallel_edge_tag edge_parallel_category; struct traversal_category : boost::incidence_graph_tag, boost::adjacency_graph_tag, boost::vertex_list_graph_tag, boost::edge_list_graph_tag { }; /** Iterate through the vertices of this graph. */ class vertex_iterator : public std::iterator { public: vertex_iterator() { } explicit vertex_iterator(vertices_size_type v) : m_v(v) { } const vertex_descriptor& operator *() const { return m_v; } bool operator ==(const vertex_iterator& it) const { return m_v == it.m_v; } bool operator !=(const vertex_iterator& it) const { return m_v != it.m_v; } vertex_iterator& operator ++() { ++m_v; return *this; } vertex_iterator operator ++(int) { vertex_iterator it = *this; ++*this; return it; } private: vertex_descriptor m_v; }; /** Iterate through the out-edges. */ class out_edge_iterator : public std::iterator { typedef typename Edges::const_iterator const_iterator; public: out_edge_iterator() { } out_edge_iterator(const const_iterator& it, vertex_descriptor src) : m_it(it), m_src(src) { } edge_descriptor operator *() const { return edge_descriptor(m_src, m_it->target()); } bool operator ==(const out_edge_iterator& it) const { return m_it == it.m_it; } bool operator !=(const out_edge_iterator& it) const { return m_it != it.m_it; } out_edge_iterator& operator ++() { ++m_it; return *this; } out_edge_iterator operator ++(int) { out_edge_iterator it = *this; ++*this; return it; } const edge_property_type& get_property() const { return m_it->get_property(); } private: const_iterator m_it; vertex_descriptor m_src; }; /** Iterate through adjacent vertices. */ class adjacency_iterator : public Edges::const_iterator { typedef typename Edges::const_iterator It; public: adjacency_iterator() { } adjacency_iterator(const It& it) : It(it) { } vertex_descriptor operator*() const { return It::operator*().target(); } }; /** Iterate through edges. */ class edge_iterator : public std::iterator { void nextVertex() { vertex_iterator vlast = m_g->vertices().second; for (; m_vit != vlast; ++m_vit) { std::pair adj = m_g->adjacent_vertices(*m_vit); if (adj.first != adj.second) { m_eit = adj.first; return; } } // Set m_eit to a known value. static const adjacency_iterator s_eitNULL; m_eit = s_eitNULL; } public: edge_iterator() { } edge_iterator(const DirectedGraph* g, const vertex_iterator& vit) : m_g(g), m_vit(vit) { nextVertex(); } edge_descriptor operator*() const { return edge_descriptor(*m_vit, *m_eit); } bool operator==(const edge_iterator& it) const { return m_vit == it.m_vit && m_eit == it.m_eit; } bool operator!=(const edge_iterator& it) const { return !(*this == it); } edge_iterator& operator++() { if (++m_eit == m_g->adjacent_vertices(*m_vit).second) { ++m_vit; nextVertex(); } return *this; } edge_iterator operator++(int) { edge_iterator it = *this; ++*this; return it; } private: const DirectedGraph* m_g; vertex_iterator m_vit; adjacency_iterator m_eit; }; private: /** A vertex and its properties. */ class Vertex { public: Vertex() { } Vertex(const vertex_property_type& p) : m_prop(p) { } /** Return the properties of this vertex. */ const vertex_property_type& get_property() const { return m_prop; } /** Returns an iterator-range to the out edges of vertex u. */ std::pair out_edges(vertex_descriptor u) const { return make_pair(out_edge_iterator(m_edges.begin(), u), out_edge_iterator(m_edges.end(), u)); } /** Returns an iterator-range to the adjacent vertices. */ std::pair adjacent_vertices() const { return make_pair(m_edges.begin(), m_edges.end()); } /** Return the number of outgoing edges. */ degree_size_type out_degree() const { return m_edges.size(); } /** Add an edge to this vertex. */ bool add_edge(vertex_descriptor v, const edge_property_type& ep) { m_edges.push_back(Edge(v, ep)); return true; } /** Remove the edge to v from this vertex. */ void remove_edge(vertex_descriptor v) { m_edges.erase(remove(m_edges.begin(), m_edges.end(), v), m_edges.end()); } /** Remove all out edges from this vertex. */ void clear_out_edges() { m_edges.clear(); } /** Return the properties of the edge with target v. */ edge_property_type& operator[](vertex_descriptor v) { typename Edges::iterator it = find(m_edges.begin(), m_edges.end(), v); assert(it != m_edges.end()); return it->get_property(); } /** Return the properties of the edge with target v. */ const edge_property_type& operator[](vertex_descriptor v) const { typename Edges::const_iterator it = find(m_edges.begin(), m_edges.end(), v); assert(it != m_edges.end()); return it->get_property(); } /** Return true if edge (u,v) exists. */ bool edge(vertex_descriptor v) const { return count(m_edges.begin(), m_edges.end(), v) > 0; } /** Remove edges that satisfy the predicate. */ template void remove_edge_if(vertex_descriptor u, Predicate predicate) { typename Edges::iterator out = m_edges.begin(); for (typename Edges::iterator it = m_edges.begin(); it != m_edges.end(); ++it) { if (!predicate(edge_descriptor(u, it->target()))) { if (out != it) *out = *it; ++out; } } m_edges.erase(out, m_edges.end()); } private: Edges m_edges; vertex_property_type m_prop; }; /** A directed edge. */ class Edge { public: explicit Edge(vertex_descriptor v, const edge_property_type& ep) : m_target(v), m_ep(ep) { } /** Returns the target vertex of this edge. */ vertex_descriptor target() const { return m_target; } /** Return true if the target of this edge is v. */ bool operator ==(const vertex_descriptor& v) const { return m_target == v; } edge_property_type& get_property() { return m_ep; } const edge_property_type& get_property() const { return m_ep; } private: /** The target vertex of this edge. */ vertex_descriptor m_target; edge_property_type m_ep; }; public: /** Create an empty graph. */ DirectedGraph() { } /** Create a graph with n vertices and zero edges. */ DirectedGraph(vertices_size_type n) : m_vertices(n) { } /** Swap this graph with graph x. */ void swap(DirectedGraph& x) { m_vertices.swap(x.m_vertices); m_removed.swap(x.m_removed); } /** Return properties of vertex u. */ const vertex_property_type& operator[](vertex_descriptor u) const { vertices_size_type ui = get(vertex_index, *this, u); assert(ui < num_vertices()); return m_vertices[ui].get_property(); } /** Returns an iterator-range to the vertices. */ std::pair vertices() const { return make_pair(vertex_iterator(0), vertex_iterator(num_vertices())); } /** Remove all the edges and vertices from this graph. */ void clear() { m_vertices.clear(); m_removed.clear(); } /** Add a vertex to this graph. */ vertex_descriptor add_vertex( const vertex_property_type& vp = vertex_property_type()) { m_vertices.push_back(Vertex(vp)); return vertex_descriptor(num_vertices() - 1); } /** Returns an iterator-range to the out edges of vertex u. */ std::pair out_edges(vertex_descriptor u) const { vertices_size_type ui = get(vertex_index, *this, u); assert(ui < num_vertices()); return m_vertices[ui].out_edges(u); } /** Returns an iterator-range to the adjacent vertices of * vertex u. */ std::pair adjacent_vertices(vertex_descriptor u) const { vertices_size_type ui = get(vertex_index, *this, u); assert(ui < num_vertices()); return m_vertices[ui].adjacent_vertices(); } /** Adds edge (u,v) to this graph. */ std::pair add_edge(vertex_descriptor u, vertex_descriptor v, const edge_property_type& ep = edge_property_type()) { vertices_size_type ui = get(vertex_index, *this, u); assert(ui < num_vertices()); assert(get(vertex_index, *this, v) < num_vertices()); return make_pair(edge_descriptor(u, v), m_vertices[ui].add_edge(v, ep)); } /** Remove the edge (u,v) from this graph. */ void remove_edge(vertex_descriptor u, vertex_descriptor v) { vertices_size_type ui = get(vertex_index, *this, u); assert(ui < num_vertices()); m_vertices[ui].remove_edge(v); } /** Remove the edge e from this graph. */ void remove_edge(edge_descriptor e) { remove_edge(e.first, e.second); } /** Remove all out edges from vertex u. */ void clear_out_edges(vertex_descriptor u) { vertices_size_type ui = get(vertex_index, *this, u); assert(ui < num_vertices()); m_vertices[ui].clear_out_edges(); } /** Remove all edges to and from vertex u from this graph. * O(V+E) */ void clear_vertex(vertex_descriptor u) { clear_out_edges(u); std::pair adj = adjacent_vertices(u); for (adjacency_iterator v = adj.first; v != adj.second; ++v) remove_edge(*v, u); } /** Set the vertex_removed property. */ void put(vertex_removed_t, vertex_descriptor u, bool flag) { vertices_size_type ui = get(vertex_index, *this, u); if (ui >= m_removed.size()) m_removed.resize(ui + 1); m_removed[ui] = flag; } /** Remove vertex u from this graph. It is assumed that there * are no edges to or from vertex u. It is best to call * clear_vertex before remove_vertex. */ void remove_vertex(vertex_descriptor u) { put(vertex_removed, u, true); } /** Return the number of vertices. */ vertices_size_type num_vertices() const { return m_vertices.size(); } /** Return the number of edges. */ edges_size_type num_edges() const { edges_size_type n = 0; std::pair vit = vertices(); for (vertex_iterator v = vit.first; v != vit.second; ++v) n += out_degree(*v); return n; } /** Return the out degree of vertex u. */ degree_size_type out_degree(vertex_descriptor u) const { vertices_size_type ui = get(vertex_index, *this, u); assert(ui < num_vertices()); return m_vertices[ui].out_degree(); } /** Return the nth vertex. */ static vertex_descriptor vertex(vertices_size_type n) { return vertex_descriptor(n); } /** Iterate through the edges of this graph. */ std::pair edges() const { std::pair vit = vertices(); return make_pair(edge_iterator(this, vit.first), edge_iterator(this, vit.second)); } /** Return the edge (u,v) if it exists and a flag indicating * whether the edge exists. */ std::pair edge( vertex_descriptor u, vertex_descriptor v) const { vertices_size_type ui = get(vertex_index, *this, u); assert(ui < num_vertices()); return make_pair(edge_descriptor(u, v), m_vertices[ui].edge(v)); } /** Return properties of edge e. */ edge_property_type& operator[](edge_descriptor e) { vertices_size_type ui = get(vertex_index, *this, e.first); assert(ui < num_vertices()); return m_vertices[ui][e.second]; } /** Return properties of edge e. */ const edge_property_type& operator[](edge_descriptor e) const { vertices_size_type ui = get(vertex_index, *this, e.first); assert(ui < num_vertices()); return m_vertices[ui][e.second]; } /** Remove edges that satisfy the predicate. */ template void remove_edge_if(Predicate predicate) { unsigned i = 0; for (typename Vertices::iterator it = m_vertices.begin(); it != m_vertices.end(); ++it) it->remove_edge_if(vertex(i++), predicate); } /** Return true if this vertex has been removed. */ bool is_removed(vertex_descriptor u) const { vertices_size_type ui = get(vertex_index, *this, u); return ui < m_removed.size() ? m_removed[ui] : false; } private: DirectedGraph& operator =(const DirectedGraph& x); /** The set of vertices. */ Vertices m_vertices; /** Flags indicating vertices that have been removed. */ std::vector m_removed; }; namespace std { template inline void swap(DirectedGraph& a, DirectedGraph& b) { a.swap(b); } } // IncidenceGraph template std::pair< typename DirectedGraph::out_edge_iterator, typename DirectedGraph::out_edge_iterator> out_edges( typename DirectedGraph::vertex_descriptor u, const DirectedGraph& g) { return g.out_edges(u); } template typename DirectedGraph::degree_size_type out_degree( typename DirectedGraph::vertex_descriptor u, const DirectedGraph& g) { return g.out_degree(u); } // AdjacencyGraph template std::pair< typename DirectedGraph::adjacency_iterator, typename DirectedGraph::adjacency_iterator> adjacent_vertices( typename DirectedGraph::vertex_descriptor u, const DirectedGraph& g) { return g.adjacent_vertices(u); } // VertexListGraph template typename DirectedGraph::vertices_size_type num_vertices(const DirectedGraph& g) { return g.num_vertices(); } template std::pair::vertex_iterator, typename DirectedGraph::vertex_iterator> vertices(const DirectedGraph& g) { return g.vertices(); } // EdgeListGraph template typename DirectedGraph::edges_size_type num_edges(const DirectedGraph& g) { return g.num_edges(); } template std::pair::edge_iterator, typename DirectedGraph::edge_iterator> edges(const DirectedGraph& g) { return g.edges(); } // AdjacencyMatrix template std::pair::edge_descriptor, bool> edge( typename DirectedGraph::vertex_descriptor u, typename DirectedGraph::vertex_descriptor v, const DirectedGraph& g) { return g.edge(u, v); } // VertexMutableGraph template typename DirectedGraph::vertex_descriptor add_vertex(DirectedGraph& g) { return g.add_vertex(); } template void remove_vertex( typename DirectedGraph::vertex_descriptor u, DirectedGraph& g) { g.remove_vertex(u); } // EdgeMutableGraph template void clear_vertex( typename DirectedGraph::vertex_descriptor u, DirectedGraph& g) { g.clear_vertex(u); } template std::pair::edge_descriptor, bool> add_edge( typename DirectedGraph::vertex_descriptor u, typename DirectedGraph::vertex_descriptor v, DirectedGraph& g) { return g.add_edge(u, v); } template void remove_edge( typename DirectedGraph::vertex_descriptor u, typename DirectedGraph::vertex_descriptor v, DirectedGraph& g) { g.remove_edge(u, v); } template void remove_edge( typename DirectedGraph::edge_descriptor e, DirectedGraph& g) { g.remove_edge(e); } // MutableIncidenceGraph template void clear_out_edges( typename DirectedGraph::vertex_descriptor u, DirectedGraph& g) { g.clear_out_edges(u); } // MutableEdgeListGraph template void remove_edge_if(Predicate predicate, DirectedGraph& g) { g.remove_edge_if(predicate); } // PropertyGraph /** Return true if this vertex has been removed. */ template bool get(vertex_removed_t, const DirectedGraph& g, typename DirectedGraph::vertex_descriptor u) { return g.is_removed(u); } template void put(vertex_removed_t tag, DirectedGraph& g, typename DirectedGraph::vertex_descriptor u, bool flag) { g.put(tag, u, flag); } /** Return the properties of the edge of iterator eit. */ template const typename DirectedGraph::edge_property_type& get(edge_bundle_t, const DirectedGraph&, typename DirectedGraph::out_edge_iterator eit) { return eit.get_property(); } // PropertyGraph template const VP& get(vertex_bundle_t, const DirectedGraph& g, typename DirectedGraph::vertex_descriptor u) { return g[u]; } template const EP& get(edge_bundle_t, const DirectedGraph& g, typename DirectedGraph::edge_descriptor e) { return g[e]; } // PropertyGraph vertex_index namespace boost { template struct property_map, vertex_index_t> { typedef ContigNodeIndexMap type; typedef type const_type; }; } template ContigNodeIndexMap get(vertex_index_t, const DirectedGraph&) { return ContigNodeIndexMap(); } template ContigNodeIndexMap::reference get(vertex_index_t tag, const DirectedGraph& g, typename DirectedGraph::vertex_descriptor u) { return get(get(tag, g), u); } // VertexMutablePropertyGraph template typename DirectedGraph::vertex_descriptor add_vertex(const VP& vp, DirectedGraph& g) { return g.add_vertex(vp); } // EdgeMutablePropertyGraph template std::pair::edge_descriptor, bool> add_edge( typename DirectedGraph::vertex_descriptor u, typename DirectedGraph::vertex_descriptor v, const typename DirectedGraph::edge_property_type& ep, DirectedGraph& g) { return g.add_edge(u, v, ep); } // NamedGraph template typename DirectedGraph::vertex_descriptor find_vertex(const std::string& name, const DirectedGraph&) { return find_vertex(name, g_contigNames); } template typename DirectedGraph::vertex_descriptor find_vertex(const std::string& name, bool sense, const DirectedGraph&) { return find_vertex(name, sense, g_contigNames); } #endif abyss-1.3.6/Graph/DistIO.h000644 002433 001057 00000002124 12104026026 016714 0ustar00traymondassembly000000 000000 #ifndef DISTIO_H #define DISTIO_H 1 #include #include #include using boost::graph_traits; /** Output a distance estimate graph. */ template std::ostream& write_dist(std::ostream& out, const Graph& g) { typedef typename graph_traits::vertex_descriptor V; typedef typename graph_traits::vertex_iterator Vit; typedef typename graph_traits::out_edge_iterator Eit; std::pair urange = vertices(g); for (Vit uit = urange.first; uit != urange.second; ++uit) { V u = *uit; if (get(vertex_removed, g, u) || out_degree(u, g) + in_degree(u, g) == 0) continue; bool sense = get(vertex_sense, g, u); if (!sense) out << get(vertex_contig_name, g, u); else out << " ;"; std::pair erange = out_edges(u, g); for (Eit eit = erange.first; eit != erange.second; ++eit) { V v = target(*eit, g) ^ sense; assert(!get(vertex_removed, g, v)); out << ' ' << get(vertex_name, g, v) << ',' << get(edge_bundle, g, eit); } if (sense) out << '\n'; } return out; } #endif abyss-1.3.6/Graph/DotIO.h000644 002433 001057 00000016510 12153225276 016557 0ustar00traymondassembly000000 000000 #ifndef DOTIO_H #define DOTIO_H 1 #include "ContigID.h" // for g_contigNames.lock #include "Graph/Options.h" #include "IOUtil.h" #include #include #include // for exit #include #include using boost::graph_traits; template void write_vertex(std::ostream& out, const Graph& g, typename graph_traits::vertex_descriptor u, const VertexProp*) { out << '"' << get(vertex_name, g, u) << "\"" " [" << get(vertex_bundle, g, u) << "]\n"; } template void write_vertex(std::ostream&, const Graph&, typename graph_traits::vertex_descriptor, const no_property*) { } template void write_edges(std::ostream& out, const Graph& g, typename graph_traits::vertex_descriptor u, const EdgeProp*) { typedef typename graph_traits::vertex_descriptor vertex_descriptor; typedef typename graph_traits::out_edge_iterator out_edge_iterator; typedef typename edge_property::type edge_property_type; std::pair adj = out_edges(u, g); for (out_edge_iterator e = adj.first; e != adj.second; ++e) { assert(!get(vertex_removed, g, target(*e, g))); out << get(edge_name, g, *e); const edge_property_type& ep = get(edge_bundle, g, e); if (!(ep == edge_property_type())) out << " [" << ep << ']'; out << '\n'; } } template void write_edges(std::ostream& out, const Graph& g, typename graph_traits::vertex_descriptor u, const no_property*) { typedef typename graph_traits::adjacency_iterator adjacency_iterator; unsigned outdeg = out_degree(u, g); if (outdeg == 0) return; out << '"' << get(vertex_name, g, u) << "\" ->"; if (outdeg > 1) out << " {"; std::pair adj = adjacent_vertices(u, g); for (adjacency_iterator v = adj.first; v != adj.second; ++v) out << " \"" << get(vertex_name, g, *v) << '"'; if (outdeg > 1) out << " }"; out << '\n'; } /** Output a GraphViz dot graph. */ template std::ostream& write_dot(std::ostream& out, const Graph& g) { typedef typename graph_traits::vertex_iterator vertex_iterator; typedef typename vertex_property::type vertex_property_type; typedef typename edge_property::type edge_property_type; out << "digraph adj {\n"; // Graph properties if (opt::k > 0) out << "graph [k=" << opt::k << "]\n" "edge [d=" << -int(opt::k - 1) << "]\n"; // Vertices std::pair vit = vertices(g); for (vertex_iterator u = vit.first; u != vit.second; ++u) { if (get(vertex_removed, g, *u)) continue; write_vertex(out, g, *u, (vertex_property_type*)NULL); } // Edges for (vertex_iterator u = vit.first; u != vit.second; ++u) { if (get(vertex_removed, g, *u)) continue; write_edges(out, g, *u, (edge_property_type*)NULL); } return out << "}\n"; } /** Output a GraphViz dot graph. */ template struct DotWriter { const Graph& g; DotWriter(const Graph& g) : g(g) { } friend std::ostream& operator<<(std::ostream& out, const DotWriter& o) { return write_dot(out, o.g); } }; /** Output a GraphViz dot graph. */ template DotWriter dot_writer(const Graph& g) { return DotWriter(g); } /** Read a string delimited by double quotes. */ static inline std::istream& read_dot_name(std::istream& in, std::string& s) { if (in >> std::ws && in.peek() == '"') { in.get(); getline(in, s, '"'); } else in.clear(std::ios::failbit); return in; } /** Read a vertex descriptor delimited by double quotes. */ template std::istream& read_dot_id(std::istream& in, const Graph& g, typename graph_traits::vertex_descriptor& u) { std::string s; if (read_dot_name(in, s)) u = find_vertex(s, g); return in; } /** Read a GraphViz dot graph. * @param betterEP handle parallel edges */ template std::istream& read_dot(std::istream& in, Graph& g, BetterEP betterEP) { assert(in); typedef typename graph_traits::vertex_descriptor vertex_descriptor; typedef typename vertex_property::type vertex_property_type; typedef typename graph_traits::edge_descriptor edge_descriptor; typedef typename edge_property::type edge_property_type; // Add vertices if this graph is empty. bool addVertices = num_vertices(g) == 0; // Graph properties in >> expect("digraph") >> Ignore('{'); assert(in); edge_property_type defaultEdgeProp; for (bool done = false; !done && in >> std::ws;) { switch (in.peek()) { case 'g': { // Graph Properties in >> expect("graph [ "); if (in.peek() == 'k') { unsigned k; in >> expect("k =") >> k; assert(in); if (opt::k > 0) assert(k == opt::k); opt::k = k; } in >> Ignore(']'); break; } case 'e': // edge // Default edge properties in >> expect("edge [") >> defaultEdgeProp >> Ignore(']'); assert(in); break; default: done = true; break; } if (in >> std::ws && in.peek() == ';') in.get(); } for (std::string uname; read_dot_name(in, uname);) { char c; in >> c; assert(in); if (c == ';') { // Vertex if (addVertices) { vertex_descriptor u = add_vertex(g); put(vertex_name, g, u, uname); } else { vertex_descriptor u = find_vertex(uname, g); assert(get(vertex_index, g, u) < num_vertices(g)); (void)u; } } else if (c == '[') { // Vertex properties vertex_property_type vp; in >> vp >> Ignore(']'); assert(in); if (addVertices) { vertex_descriptor u = add_vertex(vp, g); put(vertex_name, g, u, uname); } else { vertex_descriptor u = find_vertex(uname, g); assert(get(vertex_index, g, u) < num_vertices(g)); if (g[u] != vp) { std::cerr << "error: " "vertex properties do not agree: " "\"" << uname << "\" " "[" << g[u] << "] [" << vp << "]\n"; exit(EXIT_FAILURE); } } } else if (c == '-') { // Edge in >> expect(">"); assert(in); g_contigNames.lock(); vertex_descriptor u = find_vertex(uname, g); if (in >> std::ws && in.peek() == '{') { // Subgraph in >> expect("{"); for (vertex_descriptor v; read_dot_id(in, g, v);) add_edge(u, v, defaultEdgeProp, g); if (in.fail()) in.clear(); in >> expect(" }"); assert(in); } else { vertex_descriptor v; if (!read_dot_id(in, g, v)) { in.clear(); std::cerr << "error: Expected `\"' and saw `" << (char)in.peek() << "'.\n"; exit(EXIT_FAILURE); } assert(in); edge_property_type ep = defaultEdgeProp; if (in >> std::ws && in.peek() == '[') { // Edge properties in >> expect("[") >> ep >> Ignore(']'); assert(in); } edge_descriptor e; bool found; boost::tie(e, found) = edge(u, v, g); if (found) { // Parallel edge edge_property_type& ref = g[e]; ref = betterEP(ref, ep); } else add_edge(u, v, ep, g); } } else { std::cerr << "error: Expected `[' or `->' and saw `" << c << "'.\n"; exit(EXIT_FAILURE); } if (in >> std::ws && in.peek() == ';') in.get(); } if (in.fail()) in.clear(); // Check for the closing brace. in >> expect("}") >> std::ws; assert(in.eof()); assert(num_vertices(g) > 0); return in; } #endif abyss-1.3.6/Graph/FastaIO.h000644 002433 001057 00000001673 12104026026 017057 0ustar00traymondassembly000000 000000 #ifndef FASTAIO_H #define FASTAIO_H 1 #include "Graph/Properties.h" #include #include #include #include #include using boost::graph_traits; /** Read the vertices from a FASTA file. */ template std::istream& read_fasta(std::istream& in, Graph& g) { assert(in); typedef typename graph_traits::vertex_descriptor V; typedef typename vertex_property::type VP; for (std::string uname; in.peek() != EOF && in >> expect(">") >> uname;) { std::string comment; getline(in, comment); assert(in); std::istringstream ss(comment); VP vp; ss >> vp; size_t n = 0; while (in >> std::ws && in.peek() != '>' && in) { in >> Ignore('\n'); assert(in); assert(in.gcount() > 1); n += in.gcount() - 1; } put(vertex_length, vp, n); V u = add_vertex(vp, g); put(vertex_name, g, u, uname); } assert(in.eof()); return in; } #endif abyss-1.3.6/Graph/GraphAlgorithms.h000644 002433 001057 00000006444 12104250114 020662 0ustar00traymondassembly000000 000000 #ifndef GRAPHALGORITHMS_H #define GRAPHALGORITHMS_H 1 #include #include #include using boost::graph_traits; /** * Return the transitive edges. * Find the subset of edges (u,w) in E for which there exists a vertex * v such that the edges (u,v) and (v,w) exist in E. * This algorithm is not a general-purpose transitive reduction * algorithm. It is able to find transitive edges with exactly one * intermediate vertex. */ template void find_transitive_edges(const Graph& g, OutIt out) { typedef graph_traits GTraits; typedef typename GTraits::adjacency_iterator adjacency_iterator; typedef typename GTraits::edge_descriptor edge_descriptor; typedef typename GTraits::out_edge_iterator out_edge_iterator; typedef typename GTraits::vertex_descriptor vertex_descriptor; typedef typename GTraits::vertex_iterator vertex_iterator; std::vector seen(num_vertices(g)); std::pair urange = vertices(g); for (vertex_iterator uit = urange.first; uit != urange.second; ++uit) { vertex_descriptor u = *uit; if (get(vertex_removed, g, u)) continue; // Clear the colour of the adjacent vertices. std::pair vrange = adjacent_vertices(u, g); for (adjacency_iterator vit = vrange.first; vit != vrange.second; ++vit) seen[get(vertex_index, g, *vit)] = false; // Set the colour of all vertices reachable in two hops. for (adjacency_iterator vit = vrange.first; vit != vrange.second; ++vit) { vertex_descriptor v = *vit; if (u == v) // ignore self loops continue; std::pair wrange = adjacent_vertices(v, g); for (adjacency_iterator wit = wrange.first; wit != wrange.second; ++wit) { vertex_descriptor w = *wit; if (v == w) // ignore self loops continue; seen[get(vertex_index, g, w)] = true; } } // Find the transitive edges. std::pair uvrange = out_edges(u, g); for (out_edge_iterator uvit = uvrange.first; uvit != uvrange.second; ++uvit) { edge_descriptor uv = *uvit; vertex_descriptor v = target(uv, g); if (seen[get(vertex_index, g, v)]) { // The edge (u,v) is transitive. Mark it for removal. *out++ = uv; } } } } /** Remove the edges [first,last) from g. * @return the number of removed edges */ template void remove_edges(Graph& g, It first, It last) { for (It it = first; it != last; ++it) remove_edge(*it, g); } /** * Remove transitive edges from the specified graph. * Find and remove the subset of edges (u,w) in E for which there * exists a vertex v such that the edges (u,v) and (v,w) exist in E. * This algorithm is not a general-purpose transitive reduction * algorithm. It is able to find transitive edges with exactly one * intermediate vertex. * @return the number of transitive edges removed from g */ template unsigned remove_transitive_edges(Graph& g) { typedef typename graph_traits::edge_descriptor edge_descriptor; std::vector transitive; find_transitive_edges(g, back_inserter(transitive)); remove_edges(g, transitive.begin(), transitive.end()); return transitive.size(); } #endif abyss-1.3.6/Graph/GraphIO.h000644 002433 001057 00000003425 12104026026 017057 0ustar00traymondassembly000000 000000 #ifndef GRAPHIO_H #define GRAPHIO_H 1 #include "Graph/Options.h" #include "AdjIO.h" #include "AsqgIO.h" #include "DistIO.h" #include "DotIO.h" #include "FastaIO.h" #include "SAMIO.h" #include #include // for abort #include #include #include /** Write the graph g to the specified output stream in the format * specified by opt::format. */ template std::ostream& write_graph(std::ostream& out, const Graph& g, const std::string& program, const std::string& commandLine) { switch (opt::format) { case ADJ: return out << adj_writer(g); case ASQG: return write_asqg(out, g); case DIST: return write_dist(out, g); case DOT: case DOT_MEANCOV: return out << dot_writer(g); case SAM: return write_sam(out, g, program, commandLine); default: assert(false); abort(); } } #include "ContigGraph.h" /** Read a graph. */ template std::istream& read_graph(std::istream& in, ContigGraph& g, BetterEP betterEP) { in >> std::ws; assert(in); switch (in.peek()) { case 'd': // digraph: GraphViz dot format return read_dot(in, g, betterEP); case 'H': // HT: ASQG format return read_asqg(in, g); case '>': // FASTA format for vertices return read_fasta(in, g); default: // adj format return read_adj(in, g, betterEP); } } /** Disallow parallel edges. */ struct DisallowParallelEdges { template EP operator()(const EP& a, const EP& b) const { std::cerr << "error: parallel edges:" " [" << a << "], [" << b << "]\n"; exit(EXIT_FAILURE); } }; /** Read a graph. */ template std::istream& operator>>(std::istream& in, ContigGraph& g) { return read_graph(in, g, DisallowParallelEdges()); } #endif abyss-1.3.6/Graph/GraphUtil.h000644 002433 001057 00000003577 12104026026 017475 0ustar00traymondassembly000000 000000 #ifndef GRAPHUTIL_H #define GRAPHUTIL_H 1 #include "Histogram.h" #include #include #include using boost::graph_traits; /** Return the number of vertices that have been marked as removed. */ template typename graph_traits::vertices_size_type num_vertices_removed(const Graph& g) { typedef graph_traits GTraits; typedef typename GTraits::vertices_size_type vertices_size_type; typedef typename GTraits::vertex_iterator vertex_iterator; vertices_size_type n = 0; std::pair vit = vertices(g); for (vertex_iterator u = vit.first; u != vit.second; ++u) if (get(vertex_removed, g, *u)) n++; return n; } /** Print statistics of the number of vertices and edges. */ template std::ostream& printGraphStats(std::ostream& out, const Graph& g) { using std::setprecision; typedef typename graph_traits::vertex_iterator vertex_iterator; unsigned v = num_vertices(g) - num_vertices_removed(g); unsigned e = num_edges(g); out << "V=" << v << " E=" << e << " E/V=" << setprecision(3) << (float)e / v << std::endl; // Print a histogram of the degree. Histogram h; std::pair vit = vertices(g); for (vertex_iterator u = vit.first; u != vit.second; ++u) { if (get(vertex_removed, g, *u)) continue; h.insert(out_degree(*u, g)); } unsigned n = h.size(); unsigned n0 = h.count(0), n1 = h.count(1), n234 = h.count(2, 4); unsigned n5 = n - (n0 + n1 + n234); return out << "Degree: " << h.barplot(h.maximum() + 1) << "\n" " 01234\n" "0: " << setprecision(2) << (float)100 * n0 / n << "% " "1: " << setprecision(2) << (float)100 * n1 / n << "% " "2-4: " << setprecision(2) << (float)100 * n234 / n << "% " "5+: " << setprecision(2) << (float)100 * n5 / n << "% " "max: " << h.maximum() << std::endl; } #endif abyss-1.3.6/Graph/Options.h000644 002433 001057 00000000435 12104026026 017217 0ustar00traymondassembly000000 000000 #ifndef GRAPH_OPTIONS_H #define GRAPH_OPTIONS_H 1 namespace opt { /** The size of a k-mer. */ extern unsigned k; /** The file format of the graph when writing. */ extern int format; } /** Enumeration of output formats */ enum { ADJ, ASQG, DIST, DOT, DOT_MEANCOV, SAM }; #endif abyss-1.3.6/Graph/PopBubbles.h000644 002433 001057 00000013144 12104026026 017622 0ustar00traymondassembly000000 000000 #ifndef POPBUBBLES_H #define POPBUBBLES_H 1 #include "Common/Options.h" #include "DepthFirstSearch.h" #include #include #include #include #include #include #include #include using boost::graph_traits; /** Record a topological order of the vertices. */ template struct TopoVisitor : public boost::default_dfs_visitor { TopoVisitor(OutIt it) : m_it(it) { } template void finish_vertex(const Vertex& u, Graph&) { *m_it++ = u; } private: OutIt m_it; }; /** Record a topological order of the vertices. */ template void topologicalSort(const Graph& g, It it) { using boost::default_color_type; using boost::property_map; using boost::vector_property_map; typedef typename property_map::type VertexIndexMap; typedef vector_property_map ColorMap; depthFirstSearch(g, TopoVisitor(it), ColorMap(num_vertices(g))); } /** Return true if the specified sequence of vertices is a bubble. */ template bool isBubble(const Graph& g, It first, It last) { typedef typename graph_traits::adjacency_iterator Ait; typedef typename graph_traits::in_edge_iterator Iit; typedef typename graph_traits::vertex_descriptor V; assert(last - first > 1); if (last - first == 2) return false; // unambiguous edge if (*first == get(vertex_complement, g, last[-1])) return false; // palindrome std::set targets(first, first + 1); for (It it = first; it != last - 1; ++it) { std::pair adj = adjacent_vertices(*it, g); targets.insert(adj.first, adj.second); } std::set sources(last - 1, last); for (It it = first + 1; it != last; ++it) { std::pair adj = in_edges(*it, g); for (Iit eit = adj.first; eit != adj.second; ++eit) sources.insert(source(*eit, g)); } std::set bubble(first, last); return sources == bubble && targets == bubble; } typedef std::vector Bubble; typedef std::vector Bubbles; /** Discover bubbles. */ template Bubbles discoverBubbles(const Graph& g) { typedef typename graph_traits::vertex_descriptor V; std::vector topo(num_vertices(g)); topologicalSort(g, topo.rbegin()); Bubbles bubbles; typedef typename std::vector::const_iterator It; for (It first = topo.begin(); first != topo.end(); ++first) { int sum = out_degree(*first, g); if (sum < 2) continue; if (opt::verbose > 3) std::cerr << "* " << get(vertex_name, g, *first) << '\n'; for (It it = first + 1; it != topo.end(); ++it) { unsigned indeg = in_degree(*it, g); unsigned outdeg = out_degree(*it, g); sum -= indeg; if (opt::verbose > 3) std::cerr << get(vertex_name, g, *it) << '\t' << indeg << '\t' << outdeg << '\t' << sum << '\t' << sum + (int)outdeg << '\n'; if (indeg == 0 || sum < 0) break; if (sum == 0) { It last = it + 1; if (isBubble(g, first, last)) { if (opt::verbose > 3) std::cerr << "good\n"; bubbles.push_back(Bubble(first, last)); first = it - 1; } break; } if (outdeg == 0) break; sum += outdeg; } } return bubbles; } /** Return the length of the longest path through the bubble. */ template int longestPath(const Graph& g, const Bubble& topo) { using boost::tie; typedef graph_traits GTraits; typedef typename GTraits::edge_descriptor E; typedef typename GTraits::out_edge_iterator Eit; typedef typename GTraits::vertex_descriptor V; EdgeWeightMap weight(g); /* GCC 4.4.6 has a bug that prevents ContigNode being used as the * key of a std::map. Possibly related to * http://gcc.gnu.org/bugzilla/show_bug.cgi?id=39390 */ boost::unordered_map distance; distance[topo.front()] = 0; for (Bubble::const_iterator it = topo.begin(); it != topo.end(); ++it) { V u = *it; Eit eit, elast; for (tie(eit, elast) = out_edges(u, g); eit != elast; ++eit) { E e = *eit; V v = target(e, g); distance[v] = std::max( distance[v], distance[u] + weight[e]); } } V v = topo.back(); return distance[v] - g[v].length; } /** Scaffold over the bubble between vertices u and w. * Add an edge (u,w) with the distance property set to the length of * the largest branch of the bubble. */ template void scaffoldBubble(Graph& g, const Bubble& bubble) { typedef graph_traits GTraits; typedef typename GTraits::adjacency_iterator Ait; typedef typename GTraits::vertex_descriptor V; assert(bubble.size() > 2); V u = bubble.front(), w = bubble.back(); if (edge(u, w, g).second) { // Already scaffolded. return; } assert(isBubble(g, bubble.begin(), bubble.end())); add_edge(u, w, std::max(longestPath(g, bubble), 1), g); } /** Replace each bubble in the graph with a single edge. * Remove the vertices in the bubbles from the graph. * @return the vertices that were removed from the graph */ template std::vector::vertex_descriptor> popBubbles(Graph& g) { typedef typename graph_traits::vertex_descriptor V; typedef std::vector Vertices; Vertices popped; Bubbles bubbles = discoverBubbles(g); for (Bubbles::const_iterator it = bubbles.begin(); it != bubbles.end(); ++it) { scaffoldBubble(g, *it); popped.insert(popped.end(), it->begin() + 1, it->end() - 1); } for (typename Vertices::const_iterator it = popped.begin(); it != popped.end(); ++it) { V u = *it; clear_vertex(u, g); remove_vertex(u, g); } return popped; } #endif abyss-1.3.6/Graph/Properties.h000644 002433 001057 00000004013 12104026026 017714 0ustar00traymondassembly000000 000000 #ifndef GRAPH_PROPERTIES_H #define GRAPH_PROPERTIES_H 1 #include #include #include /** The distance between two vertices. */ enum edge_distance_t { edge_distance }; /** The complementary vertex of a skew-symmetric graph. */ enum vertex_complement_t { vertex_complement }; /** The index of a contig. */ enum vertex_contig_index_t { vertex_contig_index }; /** The name of a contig without an orientation. */ enum vertex_contig_name_t { vertex_contig_name }; /** The coverage of a vertex. */ enum vertex_coverage_t { vertex_coverage }; /** The length of a vertex. */ enum vertex_length_t { vertex_length }; /** A property indicating that this vertex has been removed. */ enum vertex_removed_t { vertex_removed }; /** The orientation of a vertex. */ enum vertex_sense_t { vertex_sense }; using boost::edge_bundle; using boost::edge_bundle_t; using boost::edge_name; using boost::edge_name_t; using boost::edge_weight; using boost::edge_weight_t; using boost::no_property; using boost::vertex_bundle; using boost::vertex_bundle_t; using boost::vertex_index; using boost::vertex_index_t; using boost::vertex_name; using boost::vertex_name_t; using boost::edge_bundle_type; using boost::edge_property; using boost::vertex_bundle_type; using boost::vertex_property; namespace boost { BOOST_INSTALL_PROPERTY(edge, distance); BOOST_INSTALL_PROPERTY(vertex, complement); BOOST_INSTALL_PROPERTY(vertex, contig_index); BOOST_INSTALL_PROPERTY(vertex, contig_name); BOOST_INSTALL_PROPERTY(vertex, coverage); BOOST_INSTALL_PROPERTY(vertex, length); BOOST_INSTALL_PROPERTY(vertex, removed); BOOST_INSTALL_PROPERTY(vertex, sense); } /** No property. */ struct NoProperty { NoProperty(...) { } bool operator==(const NoProperty&) const { return true; } friend std::ostream& operator<<(std::ostream& out, const NoProperty&) { return out; } friend std::istream& operator>>(std::istream& in, NoProperty&) { return in; } }; template void put(Tag, NoProperty&, unsigned) { } #endif abyss-1.3.6/Graph/SAMIO.h000644 002433 001057 00000004214 12153225271 016442 0ustar00traymondassembly000000 000000 #ifndef SAMIO_H #define SAMIO_H 1 #include "ContigNode.h" #include "Graph/Properties.h" #include #include using boost::graph_traits; /** Output a graph in SAM alignment format. * vertex_descriptor must be convertible to a ContigNode * vertex_property_type must have members length and coverage * edge_property_type must have a member distance */ template std::ostream& write_sam(std::ostream& out, const Graph& g, const std::string& program, const std::string& commandLine) { typedef typename graph_traits::vertex_iterator vertex_iterator; typedef typename vertex_property::type vertex_property_type; typedef typename graph_traits::edge_iterator edge_iterator; typedef typename edge_property::type edge_property_type; out << "@HD\tVN:1.0\n" "@PG\tID:" << program << "\tVN:" VERSION "\t" "CL:" << commandLine << '\n'; std::pair vit = vertices(g); for (vertex_iterator u = vit.first; u != vit.second; ++u, ++u) { if (get(vertex_removed, g, *u)) continue; const vertex_property_type& vp = g[*u]; out << "@SQ\tSN:" << get(vertex_contig_name, g, *u) << "\tLN:" << vp.length; if (vp.coverage > 0) out << "\tXC:" << vp.coverage; out << '\n'; } std::pair eit = edges(g); for (edge_iterator e = eit.first; e != eit.second; ++e) { ContigNode u = source(*e, g), v = target(*e, g); assert(!get(vertex_removed, g, v)); int distance = get(edge_distance, g, *e); if (get(vertex_removed, g, u) || distance >= 0) continue; unsigned flag = u.sense() == v.sense() ? 0 : 0x10; //FREVERSE unsigned alen = -distance; unsigned pos = 1 + (u.sense() ? 0 : g[u].length - alen); out << get(vertex_contig_name, g, v) // QNAME << '\t' << flag // FLAG << '\t' << get(vertex_contig_name, g, u) // RNAME << '\t' << pos // POS << "\t255\t"; // MAPQ // CIGAR unsigned clip = g[v].length - alen; if (u.sense()) out << clip << 'H' << alen << "M\t"; else out << alen << 'M' << clip << "H\t"; // MRNM MPOS ISIZE SEQ QUAL out << "*\t0\t0\t*\t*\n"; } return out; } #endif abyss-1.3.6/Graph/gc.cc000644 002433 001057 00000005336 12116214002 016314 0ustar00traymondassembly000000 000000 /** Convert a graph to dot format. * Written by Shaun Jackman . */ #include "ContigGraph.h" #include "DirectedGraph.h" #include "GraphIO.h" #include "GraphUtil.h" #include "IOUtil.h" #include "Uncompress.h" #include #include #include using namespace std; #define PROGRAM "abyss-gc" static const char VERSION_MESSAGE[] = PROGRAM " (" PACKAGE_NAME ") " VERSION "\n" "Written by Shaun Jackman.\n" "\n" "Copyright 2013 Canada's Michael Smith Genome Science Centre\n"; static const char USAGE_MESSAGE[] = "Usage: " PROGRAM " [FILE]...\n" "Count the number of vertices and edges in a graph.\n" "\n" " Options:\n" "\n" " -v, --verbose display verbose output\n" " --help display this help and exit\n" " --version output version information and exit\n" "\n" "Report bugs to <" PACKAGE_BUGREPORT ">.\n"; namespace opt { unsigned k; // used by DotIO static int verbose; } static const char shortopts[] = "v"; enum { OPT_HELP = 1, OPT_VERSION }; static const struct option longopts[] = { { "verbose", no_argument, NULL, 'v' }, { "help", no_argument, NULL, OPT_HELP }, { "version", no_argument, NULL, OPT_VERSION }, { NULL, 0, NULL, 0 } }; /** Read a graph from the specified file. */ template static void readGraph(const string& path, Graph& g, BetterEP betterEP) { if (opt::verbose > 0) cout << "Reading `" << path << "'...\n"; ifstream fin(path.c_str()); istream& in = path == "-" ? cin : fin; assert_good(in, path); read_graph(in, g, betterEP); assert(in.eof()); printGraphStats(cout, g); g_contigNames.lock(); } /** Read a graph from the specified files. */ template void readGraphs(Graph& g, It first, It last, BetterEP betterEP) { if (first != last) { for (It it = first; it < last; ++it) readGraph(*it, g, betterEP); } else readGraph("-", g, betterEP); } int main(int argc, char** argv) { bool die = false; for (int c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;) { istringstream arg(optarg != NULL ? optarg : ""); switch (c) { case '?': die = true; break; case 'v': opt::verbose++; break; case OPT_HELP: cout << USAGE_MESSAGE; exit(EXIT_SUCCESS); case OPT_VERSION: cout << VERSION_MESSAGE; exit(EXIT_SUCCESS); } if (optarg != NULL && !arg.eof()) { cerr << PROGRAM ": invalid option: `-" << (char)c << optarg << "'\n"; exit(EXIT_FAILURE); } } if (die) { cerr << "Try `" << PROGRAM << " --help' for more information.\n"; exit(EXIT_FAILURE); } ContigGraph > g; readGraphs(g, argv + optind, argv + argc, DisallowParallelEdges()); assert_good(cout, "-"); return 0; } abyss-1.3.6/Graph/todot.cc000644 002433 001057 00000011106 12116214002 017044 0ustar00traymondassembly000000 000000 /** Convert a graph to dot format. * Written by Shaun Jackman . */ #include "ContigGraph.h" #include "ContigProperties.h" #include "DirectedGraph.h" #include "Estimate.h" #include "GraphIO.h" #include "GraphUtil.h" #include "IOUtil.h" #include "Uncompress.h" #include #include #include #include // for ostream_iterator #include using namespace std; using namespace std::rel_ops; #define PROGRAM "abyss-todot" static const char VERSION_MESSAGE[] = PROGRAM " (" PACKAGE_NAME ") " VERSION "\n" "Written by Shaun Jackman.\n" "\n" "Copyright 2013 Canada's Michael Smith Genome Science Centre\n"; static const char USAGE_MESSAGE[] = "Usage: " PROGRAM " [FILE]...\n" "Convert the specified graph to dot format.\n" "\n" " Options:\n" "\n" " -k, --kmer=N report the mean k-mer coverage, otherwise\n" " the sum k-mer coverage is reported\n" " --adj output the graph in adj format\n" " --asqg output the graph in asqg format\n" " --dist output the graph in dist format\n" " --dot output the graph in dot format [default]\n" " --dot-meancov same as above but give the mean coverage\n" " --sam output the graph in SAM format\n" " -e, --estimate output distance estimates\n" " -v, --verbose display verbose output\n" " --help display this help and exit\n" " --version output version information and exit\n" "\n" "Report bugs to <" PACKAGE_BUGREPORT ">.\n"; namespace opt { unsigned k; // used by Distance static int verbose; /** Output distance estimates. */ bool estimate; /** Output format */ int format = DOT; // used by ContigProperties } static const char shortopts[] = "ek:v"; enum { OPT_HELP = 1, OPT_VERSION }; static const struct option longopts[] = { { "adj", no_argument, &opt::format, ADJ }, { "asqg", no_argument, &opt::format, ASQG }, { "dist", no_argument, &opt::format, DIST }, { "dot", no_argument, &opt::format, DOT }, { "dot-meancov", no_argument, &opt::format, DOT_MEANCOV }, { "sam", no_argument, &opt::format, SAM }, { "estimate", no_argument, NULL, 'e' }, { "kmer", required_argument, NULL, 'k' }, { "verbose", no_argument, NULL, 'v' }, { "help", no_argument, NULL, OPT_HELP }, { "version", no_argument, NULL, OPT_VERSION }, { NULL, 0, NULL, 0 } }; /** Read a graph from the specified file. */ template static void readGraph(const string& path, Graph& g, BetterEP betterEP) { if (opt::verbose > 0) cerr << "Reading `" << path << "'...\n"; ifstream fin(path.c_str()); istream& in = path == "-" ? cin : fin; assert_good(in, path); read_graph(in, g, betterEP); assert(in.eof()); if (opt::verbose > 0) printGraphStats(cerr, g); g_contigNames.lock(); } /** Read a graph from the specified files. */ template void readGraphs(Graph& g, It first, It last, BetterEP betterEP) { if (first != last) { for (It it = first; it < last; ++it) readGraph(*it, g, betterEP); } else readGraph("-", g, betterEP); } int main(int argc, char** argv) { string commandLine; { ostringstream ss; char** last = argv + argc - 1; copy(argv, last, ostream_iterator(ss, " ")); ss << *last; commandLine = ss.str(); } bool die = false; for (int c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;) { istringstream arg(optarg != NULL ? optarg : ""); switch (c) { case '?': die = true; break; case 'e': opt::estimate = true; break; case 'k': arg >> opt::k; break; case 'v': opt::verbose++; break; case OPT_HELP: cout << USAGE_MESSAGE; exit(EXIT_SUCCESS); case OPT_VERSION: cout << VERSION_MESSAGE; 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/** The sentinel symbol. */ static T SENTINEL() { return std::numeric_limits::max(); } public: /** Count the occurrences of the symbols of [first, last). */ template void assign(It first, It last) { assert(first < last); m_data.clear(); // Determine the size of the alphabet ignoring the sentinel. T n = 0; for (It it = first; it != last; ++it) if (*it != SENTINEL()) n = std::max(n, *it); n++; assert(n < std::numeric_limits::max()); m_data.resize(n, wat_array::BitArray(last - first)); size_t i = 0; for (It it = first; it != last; ++it, ++i) { T c = *it; if (c == SENTINEL()) continue; assert(c < m_data.size()); m_data[c].SetBit(1, i); } std::for_each(m_data.begin(), m_data.end(), std::mem_fun_ref(&wat_array::BitArray::Build)); } /** Return the size of the string. */ size_t size() const { assert(!m_data.empty()); return m_data.front().length(); } /** Return the number of occurrences of the specified symbol. */ size_t count(T c) const { return m_data[c].one_num(); } /** Return the count of symbol c in s[0, i). */ size_t rank(T c, size_t i) const { return m_data[c].Rank(1, i); } /** Return the symbol at the specified position. */ T at(size_t i) const { assert(!m_data.empty()); assert(i < m_data.front().length()); for (Data::const_iterator it = m_data.begin(); it != m_data.end(); ++it) if (it->Lookup(i)) return it - m_data.begin(); return std::numeric_limits::max(); } /** Store this data structure. */ friend std::ostream& operator<<(std::ostream& out, const BitArrays& o) { uint32_t n = o.m_data.size(); out.write(reinterpret_cast(&n), sizeof n); for (Data::const_iterator it = o.m_data.begin(); it != o.m_data.end(); ++it) it->Save(out); return out; } /** Load this data structure. */ friend std::istream& operator>>(std::istream& in, BitArrays& o) { o.m_data.clear(); uint32_t n = 0; if (!in.read(reinterpret_cast(&n), sizeof n)) return in; assert(n > 0); assert(n < std::numeric_limits::max()); o.m_data.resize(n); for (Data::iterator it = o.m_data.begin(); it != o.m_data.end(); ++it) it->Load(in); return in; } private: typedef std::vector Data; Data m_data; }; #endif abyss-1.3.6/FMIndex/bit_array.cc000644 002433 001057 00000013072 12015543262 020137 0ustar00traymondassembly000000 000000 /* * Copyright (c) 2010 Daisuke Okanohara * * Redistribution and use in source and binary forms, with or without * modification, are permitted provided that the following conditions * are met: * * 1. Redistributions of source code must retain the above Copyright * notice, this list of conditions and the following disclaimer. * * 2. Redistributions in binary form must reproduce the above Copyright * notice, this list of conditions and the following disclaimer in the * documentation and/or other materials provided with the distribution. * * 3. Neither the name of the authors nor the names of its contributors * may be used to endorse or promote products derived from this * software without specific prior written permission. */ #include "bit_array.h" #include "BitUtil.h" // for popcount #include namespace wat_array { BitArray::BitArray() : length_(0), one_num_(0){ } BitArray::BitArray(uint64_t length){ Init(length); } BitArray::~BitArray(){ } uint64_t BitArray::length() const { return length_; } uint64_t BitArray::one_num() const{ return one_num_; } void BitArray::Init(uint64_t length){ length_ = length; one_num_ = 0; uint64_t block_num = (length + BLOCK_BITNUM - 1) / BLOCK_BITNUM; bit_blocks_.resize(block_num); } void BitArray::Clear(){ std::vector().swap(bit_blocks_); std::vector().swap(rank_tables_); length_ = 0; one_num_ = 0; } void BitArray::Build() { one_num_ = 0; uint64_t table_num = ((bit_blocks_.size() + TABLE_INTERVAL - 1) / TABLE_INTERVAL) + 1; rank_tables_.resize(table_num); for (size_t i = 0; i < bit_blocks_.size(); ++i){ if ((i % TABLE_INTERVAL) == 0){ rank_tables_[i/TABLE_INTERVAL] = one_num_; } one_num_ += PopCount(bit_blocks_[i]); } rank_tables_.back() = one_num_; } void BitArray::SetBit(uint64_t bit, uint64_t pos) { if (!bit) return; bit_blocks_[pos / BLOCK_BITNUM] |= (1LLU << (pos % BLOCK_BITNUM)); } uint64_t BitArray::Rank(uint64_t bit, uint64_t pos) const { if (pos > length_) return NOTFOUND; if (bit) return RankOne(pos); else return pos - RankOne(pos); } uint64_t BitArray::Select(uint64_t bit, uint64_t rank) const { if (bit){ if (rank > one_num_) return NOTFOUND; } else { if (rank > length_ - one_num_) return NOTFOUND; } uint64_t block_pos = SelectOutBlock(bit, rank); uint64_t block = (bit) ? bit_blocks_[block_pos] : ~bit_blocks_[block_pos]; return block_pos * BLOCK_BITNUM + SelectInBlock(block, rank); } uint64_t BitArray::SelectOutBlock(uint64_t bit, uint64_t& rank) const { // binary search over tables uint64_t left = 0; uint64_t right = rank_tables_.size(); while (left < right){ uint64_t mid = (left + right) / 2; uint64_t length = BLOCK_BITNUM * TABLE_INTERVAL * mid; if (GetBitNum(rank_tables_[mid], length, bit) < rank) { left = mid+1; } else { right = mid; } } uint64_t table_ind = (left != 0) ? left - 1: 0; uint64_t block_pos = table_ind * TABLE_INTERVAL; rank -= GetBitNum(rank_tables_[table_ind], block_pos * BLOCK_BITNUM, bit); // sequential search over blocks for ( ; block_pos < bit_blocks_.size(); ++block_pos){ uint64_t rank_next= GetBitNum(PopCount(bit_blocks_[block_pos]), BLOCK_BITNUM, bit); if (rank <= rank_next){ break; } rank -= rank_next; } return block_pos; } uint64_t BitArray::SelectInBlock(uint64_t x, uint64_t rank) { uint64_t x1 = x - ((x & 0xAAAAAAAAAAAAAAAALLU) >> 1); uint64_t x2 = (x1 & 0x3333333333333333LLU) + ((x1 >> 2) & 0x3333333333333333LLU); uint64_t x3 = (x2 + (x2 >> 4)) & 0x0F0F0F0F0F0F0F0FLLU; uint64_t pos = 0; for (;; pos += 8){ uint64_t rank_next = (x3 >> pos) & 0xFFLLU; if (rank <= rank_next) break; rank -= rank_next; } uint64_t v2 = (x2 >> pos) & 0xFLLU; if (rank > v2) { rank -= v2; pos += 4; } uint64_t v1 = (x1 >> pos) & 0x3LLU; if (rank > v1){ rank -= v1; pos += 2; } uint64_t v0 = (x >> pos) & 0x1LLU; if (v0 < rank){ rank -= v0; pos += 1; } return pos; } uint64_t BitArray::Lookup(uint64_t pos) const { return (bit_blocks_[pos / BLOCK_BITNUM] >> (pos % BLOCK_BITNUM)) & 1LLU; } uint64_t BitArray::RankOne(uint64_t pos) const { uint64_t block_ind = pos / BLOCK_BITNUM; uint64_t table_ind = block_ind / TABLE_INTERVAL; assert(table_ind < rank_tables_.size()); uint64_t rank = rank_tables_[table_ind]; for (uint64_t i = table_ind * TABLE_INTERVAL; i < block_ind; ++i){ rank += PopCount(bit_blocks_[i]); } rank += PopCountMask(bit_blocks_[block_ind], pos % BLOCK_BITNUM); return rank; } /** Return the Hamming weight of x. */ uint64_t BitArray::PopCount(uint64_t x) { return popcount(x); } uint64_t BitArray::PopCountMask(uint64_t x, uint64_t offset) { if (offset == 0) return 0; return PopCount(x & ((1LLU << offset) - 1)); } uint64_t BitArray::GetBitNum(uint64_t one_num, uint64_t num, uint64_t bit) { if (bit) return one_num; else return num - one_num; } void BitArray::PrintForDebug(std::ostream& os) const { for (uint64_t i = 0; i < length_; ++i){ if (Lookup(i)) os << "1"; else os << "0"; if (((i+1) % 8) == 0) { os << " "; } } } void BitArray::Save(std::ostream& os) const{ os.write((const char*)(&length_), sizeof(length_)); os.write((const char*)(&bit_blocks_[0]), sizeof(bit_blocks_[0]) * bit_blocks_.size()); } void BitArray::Load(std::istream& is){ Clear(); is.read((char*)(&length_), sizeof(length_)); Init(length_); is.read((char*)(&bit_blocks_[0]), sizeof(bit_blocks_[0]) * bit_blocks_.size()); Build(); } } abyss-1.3.6/FMIndex/bit_array.h000644 002433 001057 00000004021 12015543262 017773 0ustar00traymondassembly000000 000000 /* * Copyright (c) 2010 Daisuke Okanohara * * Redistribution and use in source and binary forms, with or without * modification, are permitted provided that the following conditions * are met: * * 1. Redistributions of source code must retain the above Copyright * notice, this list of conditions and the following disclaimer. * * 2. Redistributions in binary form must reproduce the above Copyright * notice, this list of conditions and the following disclaimer in the * documentation and/or other materials provided with the distribution. * * 3. Neither the name of the authors nor the names of its contributors * may be used to endorse or promote products derived from this * software without specific prior written permission. */ #ifndef WAT_ARRAY_BIT_ARRAY_HPP_ #define WAT_ARRAY_BIT_ARRAY_HPP_ #include #include #include namespace wat_array { enum { NOTFOUND = 0xFFFFFFFFFFFFFFFFLLU }; class BitArray { private: enum { BLOCK_BITNUM = 64, TABLE_INTERVAL = 4 }; public: BitArray(); ~BitArray(); BitArray(uint64_t size); uint64_t length() const; uint64_t one_num() const; void Init(uint64_t size); void Clear(); void SetBit(uint64_t bit, uint64_t pos); void Build(); uint64_t Rank(uint64_t bit, uint64_t pos) const; uint64_t Select(uint64_t bit, uint64_t rank) const; uint64_t Lookup(uint64_t pos) const; static uint64_t PopCount(uint64_t x); static uint64_t PopCountMask(uint64_t x, uint64_t offset); static uint64_t SelectInBlock(uint64_t x, uint64_t rank); static uint64_t GetBitNum(uint64_t one_num, uint64_t num, uint64_t bit); void PrintForDebug(std::ostream& os) const; void Save(std::ostream& os) const; void Load(std::istream& is); private: uint64_t RankOne(uint64_t pos) const; uint64_t SelectOutBlock(uint64_t bit, uint64_t& rank) const; private: std::vector bit_blocks_; std::vector rank_tables_; uint64_t length_; uint64_t one_num_; }; } #endif // WAT_ARRAY_BIT_ARRAY_HPP_ abyss-1.3.6/FMIndex/DAWG.h000644 002433 001057 00000007135 12104026026 016543 0ustar00traymondassembly000000 000000 /* Directed acyclic word graph. */ #ifndef DAWG_H #define DAWG_H 1 #include "FMIndex.h" #include #include #include // for distance #include #include using boost::graph_traits; /** An FM-index is a representation of a DAWG. */ typedef FMIndex DAWG; // Graph namespace boost { template <> struct graph_traits { typedef DAWG::size_type size_type; // Graph typedef std::pair vertex_descriptor; typedef boost::directed_tag directed_category; struct traversal_category : boost::incidence_graph_tag { }; typedef boost::disallow_parallel_edge_tag edge_parallel_category; // IncidenceGraph typedef std::pair edge_descriptor; typedef unsigned degree_size_type; // VertexListGraph /** Vertex iterator. */ struct vertex_iterator : public vertex_descriptor { vertex_iterator() : vertex_descriptor(0, 0) { } vertex_iterator(size_type l, size_type u) : vertex_descriptor(l, u) { } vertex_descriptor operator*() const { return *this; }; }; // IncidenceGraph /** Out edge iterator. */ class out_edge_iterator : public std::iterator { public: out_edge_iterator() : m_g(NULL), m_u(), m_v(), m_i(0) { } out_edge_iterator(const DAWG& g, vertex_descriptor u, degree_size_type i) : m_g(&g), m_u(u), m_v(), m_i(i) { next(); } edge_descriptor operator*() const { return edge_descriptor(m_u, m_v); } bool operator==(const out_edge_iterator& it) const { return m_g == it.m_g && m_u == it.m_u && m_i == it.m_i; } bool operator!=(const out_edge_iterator& it) const { return !(*this == it); } out_edge_iterator& operator++() { assert(m_i < m_g->alphabetSize()); ++m_i; next(); return *this; } out_edge_iterator operator++(int) { out_edge_iterator it = *this; ++*this; return it; } private: /** Skip to the next edge that is present. */ void next() { for (; m_i < m_g->alphabetSize(); m_i++) { m_v = vertex_descriptor( m_g->update(m_u.first, m_i), m_g->update(m_u.second, m_i)); if (m_v.first < m_v.second) break; } } const DAWG* m_g; vertex_descriptor m_u; vertex_descriptor m_v; degree_size_type m_i; }; // out_edge_iterator }; // graph_traits } // namespace boost // IncidenceGraph static inline std::pair< graph_traits::out_edge_iterator, graph_traits::out_edge_iterator> out_edges( graph_traits::vertex_descriptor u, const DAWG& g) { typedef graph_traits::out_edge_iterator Eit; return std::pair( Eit(g, u, 0), Eit(g, u, g.alphabetSize())); } static inline graph_traits::degree_size_type out_degree( graph_traits::vertex_descriptor u, const DAWG& g) { typedef graph_traits::out_edge_iterator Eit; std::pair it = out_edges(u, g); return std::distance(it.first, it.second); } // VertexListGraph static inline std::pair::vertex_iterator, graph_traits::vertex_iterator> vertices(const DAWG& g) { typedef graph_traits::vertex_iterator Vit; return std::pair(Vit(0, g.size() + 1), Vit()); } // PropertyGraph static inline DAWG::value_type get(boost::vertex_name_t, const DAWG& g, graph_traits::vertex_descriptor u) { assert(u.first < u.second); return u.first == 0 ? '$' : g.symbolAt(u.first); } static inline DAWG::value_type get(boost::edge_name_t, const DAWG& g, graph_traits::edge_descriptor e) { graph_traits::vertex_descriptor v = target(e, g); assert(v.first < v.second); return g.symbolAt(v.first); } #endif abyss-1.3.6/FMIndex/FMIndex.h000644 002433 001057 00000033525 12176307445 017335 0ustar00traymondassembly000000 000000 #ifndef FMINDEX_H #define FMINDEX_H 1 #include "config.h" #include "BitArrays.h" #include "IOUtil.h" #include "sais.hxx" #include #include #include #include // for exit #include #include #include // for numeric_limits #include #include #include /** An FM index. */ class FMIndex { /** A symbol. */ typedef uint8_t T; /** The sentinel symbol. */ static T SENTINEL() { return std::numeric_limits::max(); } public: /** An index. */ typedef boost::uint_t::least size_type; /** An index for SAIS, which must be signed. */ typedef boost::int_t::least sais_size_type; /** The type of a symbol. */ typedef T value_type; /** A suffix array interval. */ struct SAInterval { size_type l, u; SAInterval(size_type l, size_type u) : l(l), u(u) { } SAInterval(const FMIndex& fm) : l(1), u(fm.m_occ.size()) { } bool empty() const { return l >= u; } bool operator==(const SAInterval& x) const { return x.l == l && x.u == u; } size_type size() const { assert(l <= u); return u - l; } }; /** A match of a substring of a query sequence to an FM index. */ struct Match : public SAInterval { unsigned qstart, qend; Match(size_type l, size_type u, unsigned qstart, unsigned qend) : SAInterval(l, u), qstart(qstart), qend(qend) { } unsigned qspan() const { assert(qstart <= qend); return qend - qstart; } }; FMIndex() : m_sampleSA(1) { } /** Return the size of the string not counting the sentinel. */ size_t size() const { return m_occ.size() - 1; } /** The size of the alphabet. */ unsigned alphabetSize() const { return m_alphabet.size(); } /** Encode the alphabet of [first, last). */ template void encode(It first, It last) const { assert(first < last); assert(!m_alphabet.empty()); std::transform(first, last, first, Translate(*this)); } /** Decode the alphabet of [first, last). */ template void decode(It first, It last) const { assert(first < last); assert(!m_alphabet.empty()); for (It it = first; it < last; ++it) *it = m_alphabet[*it]; } /** Build the BWT of [first, last). * The BWT including the sentinel is stored in [first, last]. * @return the position of the sentinel */ template size_type buildBWT(It first, It last) const { assert(first < last); assert(size_t(last - first) < std::numeric_limits::max()); encode(first, last); std::replace(first, last, SENTINEL(), T(0)); std::cerr << "Building the Burrows-Wheeler transform...\n"; size_t n = last - first; std::vector sa(n); assert(sizeof (size_type) == sizeof (sais_size_type)); sais_size_type sentinel = saisxx_bwt(first, first, &sa[0], (sais_size_type)n, (sais_size_type)m_alphabet.size()); assert(sentinel >= 0); if (sentinel < 0) abort(); // Insert the sentinel. std::copy_backward(first + sentinel, last, last + 1); first[sentinel] = SENTINEL(); return sentinel; } /** Set the specified element of the sampled suffix array. */ void setSA(size_t sai, size_t pos) { if (sai % m_sampleSA == 0) { size_t i = sai / m_sampleSA; assert(i < m_sa.size()); m_sa[i] = pos; } } /** Construct the suffix array from the FM index. */ void constructSuffixArray() { // The length of the original string. size_t n = m_occ.size() - 1; assert(n > 0); assert(m_sampleSA > 0); m_sa.resize(n / m_sampleSA + 1); size_t sai = 0; for (size_t i = n; i > 0; i--) { setSA(sai, i); T c = m_occ.at(sai); assert(c != SENTINEL()); sai = m_cf[c] + m_occ.rank(c, sai); assert(sai > 0); } setSA(sai, 0); } /** Build an FM-index of the specified BWT. */ template void assignBWT(It first, It last) { assert(last - first > 1); assert(size_t(last - first) < std::numeric_limits::max()); std::cerr << "Building the character occurrence table...\n"; m_occ.assign(first, last); countOccurrences(); // Construct the suffix array from the FM index. std::cerr << "Building the suffix array...\n"; constructSuffixArray(); } /** Build an FM-index of the specified data. */ template void assign(It first, It last) { assert(first < last); assert(size_t(last - first) < std::numeric_limits::max()); encode(first, last); std::replace(first, last, SENTINEL(), T(0)); // Construct the suffix array. std::cerr << "Building the suffix array...\n"; size_t n = last - first; m_sampleSA = 1; m_sa.resize(n + 1); m_sa[0] = n; assert(sizeof (size_type) == sizeof (sais_size_type)); int status = saisxx(first, reinterpret_cast(&m_sa[1]), (sais_size_type)n, (sais_size_type)m_alphabet.size()); assert(status == 0); if (status != 0) abort(); // Construct the Burrows-Wheeler transform. std::vector bwt; std::cerr << "Building the Burrows-Wheeler transform...\n"; bwt.resize(m_sa.size()); for (size_t i = 0; i < m_sa.size(); i++) bwt[i] = m_sa[i] == 0 ? SENTINEL() : first[m_sa[i] - 1]; std::cerr << "Building the character occurrence table...\n"; m_occ.assign(bwt.begin(), bwt.end()); countOccurrences(); } /** Sample the suffix array. */ void sampleSA(unsigned period) { assert(period > 0); if (period == m_sampleSA) return; assert(m_sampleSA == 1); m_sampleSA = period; if (m_sampleSA == 1 || m_sa.empty()) return; std::vector::iterator out = m_sa.begin(); for (size_t i = 0; i < m_sa.size(); i += m_sampleSA) *out++ = m_sa[i]; m_sa.erase(out, m_sa.end()); assert(!m_sa.empty()); } /** Return the specified element of the suffix array. */ size_t at(size_t i) const { assert(i < m_occ.size()); size_t n = 0; while (i % m_sampleSA != 0) { T c = m_occ.at(i); i = c == SENTINEL() ? 0 : m_cf[c] + m_occ.rank(c, i); n++; } assert(i / m_sampleSA < m_sa.size()); size_t pos = m_sa[i / m_sampleSA] + n; return pos < m_occ.size() ? pos : pos - m_occ.size(); } /** Return the specified element of the suffix array. */ size_t operator[](size_t i) const { return at(i); } /** Return the symbol at the specifed position of the BWT. */ T bwtAt(size_t i) const { assert(i < m_occ.size()); T c = m_occ.at(i); assert(c != SENTINEL()); assert(c < m_alphabet.size()); return m_alphabet[c]; } /** Return the first symbol of the specified suffix. */ T symbolAt(size_t i) const { assert(i < m_occ.size()); std::vector::const_iterator it = std::upper_bound(m_cf.begin(), m_cf.end(), i); assert(it != m_cf.begin()); T c = it - m_cf.begin() - 1; assert(c < m_alphabet.size()); return m_alphabet[c]; } /** Decompress the index. */ template void decompress(It out) { // Construct the original string. std::vector s; for (size_t i = 0;;) { assert(i < m_occ.size()); T c = m_occ.at(i); if (c == SENTINEL()) break; s.push_back(c); i = m_cf[c] + m_occ.rank(c, i); assert(i > 0); } // Translate the character set and output the result. for (std::vector::reverse_iterator it = s.rbegin(); it != s.rend(); ++it) { T c = *it; assert(c < m_alphabet.size()); *out++ = m_alphabet[c]; } } /** Extend a suffix array coordinate by one character to the left. */ size_type update(size_type i, T c) const { assert(c < m_cf.size()); return m_cf[c] + m_occ.rank(c, i); } /** Extend a suffix array interval by one character to the left. */ SAInterval update(SAInterval sai, T c) const { return SAInterval(update(sai.l, c), update(sai.u, c)); } /** Search for an exact match. */ template SAInterval findExact(It first, It last, SAInterval sai) const { assert(first < last); for (It it = last - 1; it >= first && !sai.empty(); --it) { T c = *it; if (c == SENTINEL()) return SAInterval(0, 0); sai = update(sai, c); } return sai; } /** Search for an exact match. */ template SAInterval findExact(const String& q) const { String s(q.size()); std::transform(q.begin(), q.end(), s.begin(), Translate(*this)); return findExact(s.begin(), s.end()); } /** Search for a suffix of the query that matches a prefix of the * target. */ template OutIt findOverlapSuffix(It first, It last, OutIt out, unsigned minOverlap) const { assert(first < last); SAInterval sai(*this); for (It it = last - 1; it >= first && !sai.empty(); --it) { T c = *it; if (c == SENTINEL()) break; sai = update(sai, c); if (sai.empty()) break; if (unsigned(last - it) < minOverlap) continue; SAInterval sai1 = update(sai, 0); if (!sai1.empty()) *out++ = Match(sai1.l, sai1.u, it - first, last - first); } return out; } /** Search for a suffix of the query that matches a prefix of the * target. */ template OutIt findOverlapSuffix(const std::string& q, OutIt out, unsigned minOverlap) const { std::string s = q; std::transform(s.begin(), s.end(), s.begin(), Translate(*this)); return findOverlapSuffix(s.begin(), s.end(), out, minOverlap); } /** Search for a prefix of the query that matches a suffix of the * target. */ template OutIt findOverlapPrefix(const std::string& q, OutIt out, unsigned minOverlap) const { std::string s = q; std::transform(s.begin(), s.end(), s.begin(), Translate(*this)); typedef std::string::const_iterator It; It first = s.begin(); for (It it = first + minOverlap; it <= s.end(); ++it) { SAInterval sai = findExact(first, it, update(SAInterval(*this), 0)); if (!sai.empty()) *out++ = Match(sai.l, sai.u, 0, it - first); } return out; } /** Search for a matching suffix of the query. */ template Match findSuffix(It first, It last, MemoIt memoIt) const { assert(first < last); SAInterval sai(*this); It it; for (it = last - 1; it >= first && !sai.empty(); --it) { T c = *it; if (c == SENTINEL()) break; SAInterval sai1 = update(sai, c); if (sai1.empty()) break; sai = sai1; if (*memoIt == sai) { // This vertex of the prefix DAWG has been visited. break; } *memoIt++ = sai; } return Match(sai.l, sai.u, it - first + 1, last - first); } /** Search for a matching substring of the query at least k long. * @return the longest match */ template Match findSubstring(It first, It last, unsigned k) const { assert(first < last); Match best(0, 0, 0, k > 0 ? k - 1 : 0); // Record which vertices of the prefix DAWG have been visited. std::vector memo(last - first, SAInterval(0, 0)); SAInterval* memoIt = &memo[0]; for (It it = last; it > first; --it) { if (unsigned(it - first) < best.qspan()) return best; Match interval = findSuffix(first, it, memoIt++); if (interval.qspan() > best.qspan()) best = interval; } return best; } /** Translate from ASCII to the indexed alphabet. */ struct Translate { Translate(const FMIndex& fmIndex) : m_fmIndex(fmIndex) { } T operator()(unsigned char c) const { return c < m_fmIndex.m_mapping.size() ? m_fmIndex.m_mapping[c] : SENTINEL(); } private: const FMIndex& m_fmIndex; }; /** Search for a matching substring of the query at least k long. * @return the longest match and the number of matches */ Match find(const std::string& q, unsigned k) const { std::string s = q; std::transform(s.begin(), s.end(), s.begin(), Translate(*this)); return findSubstring(s.begin(), s.end(), k); } /** Set the alphabet to [first, last). * The character '\0' is treated specially and not included in the * alphabet. */ template void setAlphabet(It first, It last) { assert(first < last); std::vector mask(std::numeric_limits::max()); for (It it = first; it < last; ++it) { assert((size_t)*it < mask.size()); mask[*it] = true; } // Remove the character '\0' from the alphabet. mask[0] = false; m_alphabet.clear(); m_mapping.clear(); for (unsigned c = 0; c < mask.size(); ++c) { if (!mask[c]) continue; m_mapping.resize(c + 1, std::numeric_limits::max()); m_mapping[c] = m_alphabet.size(); m_alphabet.push_back(c); } assert(!m_alphabet.empty()); } /** Set the alphabet to the characters of s. */ void setAlphabet(const std::string& s) { assert(!s.empty()); setAlphabet(s.begin(), s.end()); } #define STRINGIFY(X) #X #define FM_VERSION_BITS(BITS) "FM " STRINGIFY(BITS) " 1" #define FM_VERSION FM_VERSION_BITS(FMBITS) /** Store an index. */ friend std::ostream& operator<<(std::ostream& out, const FMIndex& o) { out << FM_VERSION << '\n' << o.m_sampleSA << '\n'; out << o.m_alphabet.size() << '\n'; out.write(reinterpret_cast(&o.m_alphabet[0]), o.m_alphabet.size() * sizeof o.m_alphabet[0]); out << o.m_sa.size() << '\n'; out.write(reinterpret_cast(&o.m_sa[0]), o.m_sa.size() * sizeof o.m_sa[0]); return out << o.m_occ; } /** Load an index. */ friend std::istream& operator>>(std::istream& in, FMIndex& o) { std::string version; std::getline(in, version); assert(in); if (version != FM_VERSION) { std::cerr << "error: the version of this FM-index, `" << version << "', does not match the version required " "by this program, `" FM_VERSION "'.\n"; exit(EXIT_FAILURE); } in >> o.m_sampleSA; assert(in); size_t n; in >> n >> expect("\n"); assert(in); assert(n < std::numeric_limits::max()); o.m_alphabet.resize(n); in.read(reinterpret_cast(&o.m_alphabet[0]), n * sizeof o.m_alphabet[0]); o.setAlphabet(o.m_alphabet.begin(), o.m_alphabet.end()); in >> n >> expect("\n"); assert(in); assert(n < std::numeric_limits::max()); o.m_sa.resize(n); in.read(reinterpret_cast(&o.m_sa[0]), n * sizeof o.m_sa[0]); in >> o.m_occ; assert(in); o.countOccurrences(); return in; } private: /** Build the cumulative frequency table m_cf from m_occ. */ void countOccurrences() { assert(!m_alphabet.empty()); m_cf.resize(m_alphabet.size()); // The sentinel character occurs once. m_cf[0] = 1; for (unsigned i = 0; i < m_cf.size() - 1; ++i) m_cf[i + 1] = m_cf[i] + m_occ.count(i); } unsigned m_sampleSA; std::vector m_alphabet; std::vector m_mapping; std::vector m_cf; std::vector m_sa; BitArrays m_occ; }; #endif abyss-1.3.6/FMIndex/sais.hxx000644 002433 001057 00000046177 12153215204 017353 0ustar00traymondassembly000000 000000 /* * sais.hxx for sais * Copyright (c) 2008-2010 Yuta Mori All Rights Reserved. * * 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. */ #ifndef _SAIS_HXX #define _SAIS_HXX 1 #ifdef __cplusplus #include #include #include #ifdef __INTEL_COMPILER #pragma warning(disable : 383 981 1418) #endif #ifdef _MSC_VER #pragma warning(push) #pragma warning(disable : 4365) #endif namespace saisxx_private { /* find the start or end of each bucket */ template void getCounts(const string_type T, bucket_type C, index_type n, index_type k) { index_type i; for(i = 0; i < k; ++i) { C[i] = 0; } for(i = 0; i < n; ++i) { ++C[T[i]]; } } template void getBuckets(const bucketC_type C, bucketB_type B, index_type k, bool end) { index_type i, sum = 0; if(end != false) { for(i = 0; i < k; ++i) { sum += C[i]; B[i] = sum; } } else { for(i = 0; i < k; ++i) { sum += C[i]; B[i] = sum - C[i]; } } } template void LMSsort1(string_type T, sarray_type SA, bucketC_type C, bucketB_type B, index_type n, index_type k, bool recount) { typedef typename std::iterator_traits::value_type char_type; sarray_type b; index_type i, j; char_type c0, c1; /* compute SAl */ if(recount != false) { getCounts(T, C, n, k); } getBuckets(C, B, k, false); /* find starts of buckets */ j = n - 1; b = SA + B[c1 = T[j]]; --j; *b++ = (T[j] < c1) ? ~j : j; for(i = 0; i < n; ++i) { if(0 < (j = SA[i])) { assert(T[j] >= T[j + 1]); if((c0 = T[j]) != c1) { B[c1] = b - SA; b = SA + B[c1 = c0]; } assert(i < (b - SA)); --j; *b++ = (T[j] < c1) ? ~j : j; SA[i] = 0; } else if(j < 0) { SA[i] = ~j; } } /* compute SAs */ if(recount != false) { getCounts(T, C, n, k); } getBuckets(C, B, k, true); /* find ends of buckets */ for(i = n - 1, b = SA + B[c1 = 0]; 0 <= i; --i) { if(0 < (j = SA[i])) { assert(T[j] <= T[j + 1]); if((c0 = T[j]) != c1) { B[c1] = b - SA; b = SA + B[c1 = c0]; } assert((b - SA) <= i); --j; *--b = (T[j] > c1) ? ~(j + 1) : j; SA[i] = 0; } } } template index_type LMSpostproc1(string_type T, sarray_type SA, index_type n, index_type m) { typedef typename std::iterator_traits::value_type char_type; index_type i, j, p, q, plen, qlen, name; char_type c0, c1; bool diff; /* compact all the sorted substrings into the first m items of SA 2*m must be not larger than n (proveable) */ assert(0 < n); for(i = 0; (p = SA[i]) < 0; ++i) { SA[i] = ~p; assert((i + 1) < n); } if(i < m) { for(j = i, ++i;; ++i) { assert(i < n); if((p = SA[i]) < 0) { SA[j++] = ~p; SA[i] = 0; if(j == m) { break; } } } } /* store the length of all substrings */ i = n - 1; j = n - 1; c0 = T[n - 1]; do { c1 = c0; } while((0 <= --i) && ((c0 = T[i]) >= c1)); for(; 0 <= i;) { do { c1 = c0; } while((0 <= --i) && ((c0 = T[i]) <= c1)); if(0 <= i) { SA[m + ((i + 1) >> 1)] = j - i; j = i + 1; do { c1 = c0; } while((0 <= --i) && ((c0 = T[i]) >= c1)); } } /* find the lexicographic names of all substrings */ for(i = 0, name = 0, q = n, qlen = 0; i < m; ++i) { p = SA[i], plen = SA[m + (p >> 1)], diff = true; if((plen == qlen) && ((q + plen) < n)) { for(j = 0; (j < plen) && (T[p + j] == T[q + j]); ++j) { } if(j == plen) { diff = false; } } if(diff != false) { ++name, q = p, qlen = plen; } SA[m + (p >> 1)] = name; } return name; } template void LMSsort2(string_type T, sarray_type SA, bucketC_type C, bucketB_type B, bucketD_type D, index_type n, index_type k) { typedef typename std::iterator_traits::value_type char_type; sarray_type b; index_type i, j, t, d; char_type c0, c1; /* compute SAl */ getBuckets(C, B, k, false); /* find starts of buckets */ j = n - 1; b = SA + B[c1 = T[j]]; --j; t = (T[j] < c1); j += n; *b++ = (t & 1) ? ~j : j; for(i = 0, d = 0; i < n; ++i) { if(0 < (j = SA[i])) { if(n <= j) { d += 1; j -= n; } assert(T[j] >= T[j + 1]); if((c0 = T[j]) != c1) { B[c1] = b - SA; b = SA + B[c1 = c0]; } assert(i < (b - SA)); --j; t = c0; t = (t << 1) | (T[j] < c1); if(D[t] != d) { j += n; D[t] = d; } *b++ = (t & 1) ? ~j : j; SA[i] = 0; } else if(j < 0) { SA[i] = ~j; } } for(i = n - 1; 0 <= i; --i) { if(0 < SA[i]) { if(SA[i] < n) { SA[i] += n; for(j = i - 1; SA[j] < n; --j) { } SA[j] -= n; i = j; } } } /* compute SAs */ getBuckets(C, B, k, true); /* find ends of buckets */ for(i = n - 1, d += 1, b = SA + B[c1 = 0]; 0 <= i; --i) { if(0 < (j = SA[i])) { if(n <= j) { d += 1; j -= n; } assert(T[j] <= T[j + 1]); if((c0 = T[j]) != c1) { B[c1] = b - SA; b = SA + B[c1 = c0]; } assert((b - SA) <= i); --j; t = c0; t = (t << 1) | (T[j] > c1); if(D[t] != d) { j += n; D[t] = d; } *--b = (t & 1) ? ~(j + 1) : j; SA[i] = 0; } } } template index_type LMSpostproc2(sarray_type SA, index_type n, index_type m) { index_type i, j, d, name; /* compact all the sorted LMS substrings into the first m items of SA */ assert(0 < n); for(i = 0, name = 0; (j = SA[i]) < 0; ++i) { j = ~j; if(n <= j) { name += 1; } SA[i] = j; assert((i + 1) < n); } if(i < m) { for(d = i, ++i;; ++i) { assert(i < n); if((j = SA[i]) < 0) { j = ~j; if(n <= j) { name += 1; } SA[d++] = j; SA[i] = 0; if(d == m) { break; } } } } if(name < m) { /* store the lexicographic names */ for(i = m - 1, d = name + 1; 0 <= i; --i) { if(n <= (j = SA[i])) { j -= n; --d; } SA[m + (j >> 1)] = d; } } else { /* unset flags */ for(i = 0; i < m; ++i) { if(n <= (j = SA[i])) { j -= n; SA[i] = j; } } } return name; } /* compute SA and BWT */ template void induceSA(string_type T, sarray_type SA, bucketC_type C, bucketB_type B, index_type n, index_type k, bool recount) { typedef typename std::iterator_traits::value_type char_type; sarray_type b; index_type i, j; char_type c0, c1; /* compute SAl */ if(recount != false) { getCounts(T, C, n, k); } getBuckets(C, B, k, false); /* find starts of buckets */ b = SA + B[c1 = T[j = n - 1]]; *b++ = ((0 < j) && (T[j - 1] < c1)) ? ~j : j; for(i = 0; i < n; ++i) { j = SA[i], SA[i] = ~j; if(0 < j) { if((c0 = T[--j]) != c1) { B[c1] = b - SA; b = SA + B[c1 = c0]; } *b++ = ((0 < j) && (T[j - 1] < c1)) ? ~j : j; } } /* compute SAs */ if(recount != false) { getCounts(T, C, n, k); } getBuckets(C, B, k, true); /* find ends of buckets */ for(i = n - 1, b = SA + B[c1 = 0]; 0 <= i; --i) { if(0 < (j = SA[i])) { if((c0 = T[--j]) != c1) { B[c1] = b - SA; b = SA + B[c1 = c0]; } *--b = ((j == 0) || (T[j - 1] > c1)) ? ~j : j; } else { SA[i] = ~j; } } } template int computeBWT(string_type T, sarray_type SA, bucketC_type C, bucketB_type B, index_type n, index_type k, bool recount) { typedef typename std::iterator_traits::value_type char_type; sarray_type b; index_type i, j, pidx = -1; char_type c0, c1; /* compute SAl */ if(recount != false) { getCounts(T, C, n, k); } getBuckets(C, B, k, false); /* find starts of buckets */ b = SA + B[c1 = T[j = n - 1]]; *b++ = ((0 < j) && (T[j - 1] < c1)) ? ~j : j; for(i = 0; i < n; ++i) { if(0 < (j = SA[i])) { SA[i] = ~((index_type)(c0 = T[--j])); if(c0 != c1) { B[c1] = b - SA; b = SA + B[c1 = c0]; } *b++ = ((0 < j) && (T[j - 1] < c1)) ? ~j : j; } else if(j != 0) { SA[i] = ~j; } } /* compute SAs */ if(recount != false) { getCounts(T, C, n, k); } getBuckets(C, B, k, true); /* find ends of buckets */ for(i = n - 1, b = SA + B[c1 = 0]; 0 <= i; --i) { if(0 < (j = SA[i])) { SA[i] = (c0 = T[--j]); if(c0 != c1) { B[c1] = b - SA; b = SA + B[c1 = c0]; } *--b = ((0 < j) && (T[j - 1] > c1)) ? ~((index_type)T[j - 1]) : j; } else if(j != 0) { SA[i] = ~j; } else { pidx = i; } } return pidx; } template std::pair stage1sort(string_type T, sarray_type SA, bucketC_type C, bucketB_type B, index_type n, index_type k, unsigned flags) { typedef typename std::iterator_traits::value_type char_type; sarray_type b; index_type i, j, name, m; char_type c0, c1; getCounts(T, C, n, k); getBuckets(C, B, k, true); /* find ends of buckets */ for(i = 0; i < n; ++i) { SA[i] = 0; } b = SA + n - 1; i = n - 1; j = n; m = 0; c0 = T[n - 1]; do { c1 = c0; } while((0 <= --i) && ((c0 = T[i]) >= c1)); for(; 0 <= i;) { do { c1 = c0; } while((0 <= --i) && ((c0 = T[i]) <= c1)); if(0 <= i) { *b = j; b = SA + --B[c1]; j = i; ++m; assert(B[c1] != (n - 1)); do { c1 = c0; } while((0 <= --i) && ((c0 = T[i]) >= c1)); } } SA[n - 1] = 0; if(1 < m) { if(flags & (16 | 32)) { assert((j + 1) < n); ++B[T[j + 1]]; if(flags & 16) { index_type *D; try { D = new index_type[k * 2]; } catch(...) { D = 0; } if(D == 0) { return std::make_pair(-2, -2); } for(i = 0, j = 0; i < k; ++i) { j += C[i]; if(B[i] != j) { assert(SA[B[i]] != 0); SA[B[i]] += n; } D[i] = D[i + k] = 0; } LMSsort2(T, SA, C, B, D, n, k); delete[] D; } else { bucketB_type D = B - k * 2; for(i = 0, j = 0; i < k; ++i) { j += C[i]; if(B[i] != j) { assert(SA[B[i]] != 0); SA[B[i]] += n; } D[i] = D[i + k] = 0; } LMSsort2(T, SA, C, B, D, n, k); } name = LMSpostproc2(SA, n, m); } else { LMSsort1(T, SA, C, B, n, k, (flags & (4 | 64)) != 0); name = LMSpostproc1(T, SA, n, m); } } else if(m == 1) { *b = j + 1; name = 1; } else { name = 0; } return std::make_pair(m, name); } template index_type stage3sort(string_type T, sarray_type SA, bucketC_type C, bucketB_type B, index_type n, index_type m, index_type k, unsigned flags, bool isbwt) { typedef typename std::iterator_traits::value_type char_type; index_type i, j, p, q, pidx = 0; char_type c0, c1; if((flags & 8) != 0) { getCounts(T, C, n, k); } /* put all left-most S characters into their buckets */ if(1 < m) { getBuckets(C, B, k, 1); /* find ends of buckets */ i = m - 1, j = n, p = SA[m - 1], c1 = T[p]; do { q = B[c0 = c1]; while(q < j) { SA[--j] = 0; } do { SA[--j] = p; if(--i < 0) { break; } p = SA[i]; } while((c1 = T[p]) == c0); } while(0 <= i); while(0 < j) { SA[--j] = 0; } } if(isbwt == false) { induceSA(T, SA, C, B, n, k, (flags & (4 | 64)) != 0); } else { pidx = computeBWT(T, SA, C, B, n, k, (flags & (4 | 64)) != 0); } return pidx; } /* find the suffix array SA of T[0..n-1] in {0..k}^n use a working space (excluding s and SA) of at most 2n+O(1) for a constant alphabet */ template int suffixsort(string_type T, sarray_type SA, index_type fs, index_type n, index_type k, bool isbwt) { typedef typename std::iterator_traits::value_type char_type; sarray_type RA, C, B; index_type *Cp, *Bp; index_type i, j, m, name, pidx, newfs; unsigned flags = 0; char_type c0, c1; /* stage 1: reduce the problem by at least 1/2 sort all the S-substrings */ C = B = SA; /* for warnings */ Cp = 0, Bp = 0; if(k <= 256) { try { Cp = new index_type[k]; } catch(...) { Cp = 0; } if(Cp == 0) { return -2; } if(k <= fs) { B = SA + (n + fs - k); flags = 1; } else { try { Bp = new index_type[k]; } catch(...) { Bp = 0; } if(Bp == 0) { return -2; } flags = 3; } } else if(k <= fs) { C = SA + (n + fs - k); if(k <= (fs - k)) { B = C - k; flags = 0; } else if(k <= 1024) { try { Bp = new index_type[k]; } catch(...) { Bp = 0; } if(Bp == 0) { return -2; } flags = 2; } else { B = C; flags = 64 | 8; } } else { try { Cp = new index_type[k]; } catch(...) { Cp = 0; } if(Cp == 0) { return -2; } Bp = Cp; flags = 4 | 8; } if((n <= ((std::numeric_limits::max)() / 2)) && (2 <= (n / k))) { if(flags & 1) { flags |= ((k * 2) <= (fs - k)) ? 32 : 16; } else if((flags == 0) && ((k * 2) <= (fs - k * 2))) { flags |= 32; } } { std::pair r; if(Cp != 0) { if(Bp != 0) { r = stage1sort(T, SA, Cp, Bp, n, k, flags); } else { r = stage1sort(T, SA, Cp, B, n, k, flags); } } else { if(Bp != 0) { r = stage1sort(T, SA, C, Bp, n, k, flags); } else { r = stage1sort(T, SA, C, B, n, k, flags); } } m = r.first, name = r.second; } if(m < 0) { if(flags & (1 | 4)) { delete[] Cp; } if(flags & 2) { delete[] Bp; } return -2; } /* stage 2: solve the reduced problem recurse if names are not yet unique */ if(name < m) { if(flags & 4) { delete[] Cp; } if(flags & 2) { delete[] Bp; } newfs = (n + fs) - (m * 2); if((flags & (1 | 4 | 64)) == 0) { if((k + name) <= newfs) { newfs -= k; } else { flags |= 8; } } assert((n >> 1) <= (newfs + m)); RA = SA + m + newfs; for(i = m + (n >> 1) - 1, j = m - 1; m <= i; --i) { if(SA[i] != 0) { RA[j--] = SA[i] - 1; } } if(suffixsort(RA, SA, newfs, m, name, false) != 0) { if(flags & 1) { delete[] Cp; } return -2; } i = n - 1; j = m - 1; c0 = T[n - 1]; do { c1 = c0; } while((0 <= --i) && ((c0 = T[i]) >= c1)); for(; 0 <= i;) { do { c1 = c0; } while((0 <= --i) && ((c0 = T[i]) <= c1)); if(0 <= i) { RA[j--] = i + 1; do { c1 = c0; } while((0 <= --i) && ((c0 = T[i]) >= c1)); } } for(i = 0; i < m; ++i) { SA[i] = RA[SA[i]]; } if(flags & 4) { try { Cp = new index_type[k]; } catch(...) { Cp = 0; } if(Cp == 0) { return -2; } Bp = Cp; } if(flags & 2) { try { Bp = new index_type[k]; } catch(...) { Bp = 0; } if(Bp == 0) { if(flags & 1) { delete[] Cp; } return -2; } } } /* stage 3: induce the result for the original problem */ if(Cp != 0) { if(Bp != 0) { pidx = stage3sort(T, SA, Cp, Bp, n, m, k, flags, isbwt); } else { pidx = stage3sort(T, SA, Cp, B, n, m, k, flags, isbwt); } } else { if(Bp != 0) { pidx = stage3sort(T, SA, C, Bp, n, m, k, flags, isbwt); } else { pidx = stage3sort(T, SA, C, B, n, m, k, flags, isbwt); } } if(flags & (1 | 4)) { delete[] Cp; } if(flags & 2) { delete[] Bp; } return pidx; } } /* namespace saisxx_private */ /** * @brief Constructs the suffix array of a given string in linear time. * @param T[0..n-1] The input string. (random access iterator) * @param SA[0..n-1] The output array of suffixes. (random access iterator) * @param n The length of the given string. * @param k The alphabet size. * @return 0 if no error occurred, -1 or -2 otherwise. */ template int saisxx(string_type T, sarray_type SA, index_type n, index_type k = 256) { typedef typename std::iterator_traits::value_type savalue_type; assert((std::numeric_limits::min)() < 0); assert((std::numeric_limits::min)() < 0); assert((std::numeric_limits::max)() == (std::numeric_limits::max)()); assert((std::numeric_limits::min)() == (std::numeric_limits::min)()); if((n < 0) || (k <= 0)) { return -1; } if(n <= 1) { if(n == 1) { SA[0] = 0; } return 0; } return saisxx_private::suffixsort(T, SA, (index_type)0, n, k, false); } /** * @brief Constructs the burrows-wheeler transformed string of a given string in linear time. * @param T[0..n-1] The input string. (random access iterator) * @param U[0..n-1] The output string. (random access iterator) * @param A[0..n-1] The temporary array. (random access iterator) * @param n The length of the given string. * @param k The alphabet size. * @return The primary index if no error occurred, -1 or -2 otherwise. */ template index_type saisxx_bwt(string_type T, string_type U, sarray_type A, index_type n, index_type k = 256) { typedef typename std::iterator_traits::value_type savalue_type; typedef typename std::iterator_traits::value_type char_type; index_type i, pidx; assert((std::numeric_limits::min)() < 0); assert((std::numeric_limits::min)() < 0); assert((std::numeric_limits::max)() == (std::numeric_limits::max)()); assert((std::numeric_limits::min)() == (std::numeric_limits::min)()); if((n < 0) || (k <= 0)) { return -1; } if(n <= 1) { if(n == 1) { U[0] = T[0]; } return n; } pidx = saisxx_private::suffixsort(T, A, (index_type)0, n, k, true); if(0 <= pidx) { U[0] = T[n - 1]; for(i = 0; i < pidx; ++i) { U[i + 1] = (char_type)A[i]; } for(i += 1; i < n; ++i) { U[i] = (char_type)A[i]; } pidx += 1; } return pidx; } #ifdef _MSC_VER #pragma warning(pop) #endif #endif /* __cplusplus */ #endif /* _SAIS_HXX */ abyss-1.3.6/FMIndex/count.cc000644 002433 001057 00000011336 12176305753 017325 0ustar00traymondassembly000000 000000 #include "BitUtil.h" #include "DAWG.h" #include "Uncompress.h" #include #include #include #include #include #include #include #include #include #include using namespace std; using boost::default_color_type; #define PROGRAM "abyss-count" static const char VERSION_MESSAGE[] = PROGRAM " (" PACKAGE_NAME ") " VERSION "\n" "Written by Shaun Jackman.\n" "\n" "Copyright 2013 Canada's Michael Smith Genome Science Centre\n"; static const char USAGE_MESSAGE[] = "Usage: " PROGRAM " [OPTION]... [FASTA]\n" "Count k-mer of the specified file.\n" "The index file TARGET.fm will be used if present.\n" "\n" " Options:\n" "\n" " -k, --kmer the size of a k-mer\n" " -v, --verbose display verbose output\n" " --help display this help and exit\n" " --version output version information and exit\n" "\n" "Report bugs to <" PACKAGE_BUGREPORT ">.\n"; namespace opt { /** The size of a k-mer. */ static unsigned k; /** Verbose output. */ static int verbose; }; static const char shortopts[] = "k:v"; enum { OPT_HELP = 1, OPT_VERSION }; static const struct option longopts[] = { { "kmer", no_argument, NULL, 'k' }, { "verbose", no_argument, NULL, 'v' }, { "help", no_argument, NULL, OPT_HELP }, { "version", no_argument, NULL, OPT_VERSION }, { NULL, 0, NULL, 0 } }; /** A directed acyclic word graph. */ typedef DAWG Graph; /** A color map that always returns white. */ struct WhiteMap { typedef graph_traits::vertex_descriptor key_type; typedef default_color_type value_type; typedef value_type& reference; typedef boost::lvalue_property_map_tag category; }; default_color_type get(const WhiteMap&, graph_traits::vertex_descriptor) { return boost::white_color; } void put(WhiteMap&, graph_traits::vertex_descriptor, default_color_type) { } /** Count k-mer. */ class CountKmerVisitor : public boost::default_dfs_visitor { typedef graph_traits::edge_descriptor E; typedef graph_traits::vertex_descriptor V; public: CountKmerVisitor(vector& s) : m_s(s) { assert(m_s.empty()); m_s.reserve(opt::k); } bool operator()(V u, const Graph& g) const { assert(m_s.size() < opt::k); if (u.first == 0) return false; char c = get(boost::vertex_name, g, u); m_s.push_back(c); if (c == '-') return true; if (m_s.size() < opt::k) return false; assert(m_s.size() == opt::k); unsigned count = u.second - u.first; copy(m_s.rbegin(), m_s.rend(), ostream_iterator(cout)); cout << '\t' << count << '\n'; return true; } void finish_vertex(V u, const Graph&) { if (m_s.empty()) { assert(u.first == 0); (void)u; } else m_s.pop_back(); } private: vector& m_s; }; // CountKmerVisitor /** Read an FM index. */ static void readFMIndex(FMIndex& g, const string& faPath) { string fmPath = faPath + ".fm"; ifstream in(fmPath.c_str()); if (in) { if (opt::verbose > 0) cerr << "Reading `" << fmPath << "'...\n"; assert_good(in, fmPath); in >> g; assert_good(in, fmPath); in.close(); return; } // Build the FM index. std::vector s; if (string(faPath) == "-") { if (opt::verbose > 0) std::cerr << "Reading stdin...\n"; copy(istreambuf_iterator(cin), istreambuf_iterator(), back_inserter(s)); assert_good(cin, "stdin"); } else { if (opt::verbose > 0) std::cerr << "Reading `" << faPath << "'...\n"; readFile(faPath.c_str(), s); } g.assign(s.begin(), s.end()); } int main(int argc, char** argv) { bool die = false; for (int c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;) { istringstream arg(optarg != NULL ? optarg : ""); switch (c) { case 'k': arg >> opt::k; break; case 'v': opt::verbose++; break; case OPT_HELP: cout << USAGE_MESSAGE; exit(EXIT_SUCCESS); case OPT_VERSION: cout << VERSION_MESSAGE; exit(EXIT_SUCCESS); } if (optarg != NULL && !arg.eof()) { cerr << PROGRAM ": invalid option: `-" << (char)c << optarg << "'\n"; exit(EXIT_FAILURE); } } if (opt::k <= 0) { cerr << PROGRAM ": " << "missing -k,--kmer option\n"; die = true; } if (argc - optind > 1) { cerr << PROGRAM ": too many arguments\n"; die = true; } if (die) { cerr << "Try `" << PROGRAM << " --help' for more information.\n"; exit(EXIT_FAILURE); } string faPath(optind < argc ? argv[optind] : "-"); // Read the FM index. Graph g; readFMIndex(g, faPath); // Count k-mer. vector s; boost::depth_first_visit(g, *vertices(g).first, CountKmerVisitor(s), WhiteMap(), CountKmerVisitor(s)); assert_good(cout, "stdout"); return 0; } abyss-1.3.6/FMIndex/abyss-dawg.cc000644 002433 001057 00000007646 12176305753 020247 0ustar00traymondassembly000000 000000 #include "BitUtil.h" #include "DAWG.h" #include "Uncompress.h" #include #include #include #include #include #include #include #include #include #include #include #include using namespace std; using boost::default_dfs_visitor; #define PROGRAM "abyss-dawg" static const char VERSION_MESSAGE[] = PROGRAM " (" PACKAGE_NAME ") " VERSION "\n" "Written by Shaun Jackman.\n" "\n" "Copyright 2013 Canada's Michael Smith Genome Science Centre\n"; static const char USAGE_MESSAGE[] = "Usage: " PROGRAM " [OPTION]... [FASTA]\n" "Output a directed acyclic word graph (DAWG) of the specified file.\n" "The index file TARGET.fm will be used if present.\n" "\n" " Options:\n" "\n" " -v, --verbose display verbose output\n" " --help display this help and exit\n" " --version output version information and exit\n" "\n" "Report bugs to <" PACKAGE_BUGREPORT ">.\n"; namespace opt { /** Verbose output. */ static int verbose; }; static const char shortopts[] = "v"; enum { OPT_HELP = 1, OPT_VERSION }; static const struct option longopts[] = { { "verbose", no_argument, NULL, 'v' }, { "help", no_argument, NULL, OPT_HELP }, { "version", no_argument, NULL, OPT_VERSION }, { NULL, 0, NULL, 0 } }; /** A directed acyclic word graph. */ typedef DAWG Graph; /** DAWG visitor. */ struct DAWGVisitor : public default_dfs_visitor { typedef graph_traits::edge_descriptor E; typedef graph_traits::vertex_descriptor V; void examine_edge(E e, const Graph& g) { using boost::edge_name; V u = source(e, g); V v = target(e, g); char c = get(edge_name, g, e); cout << '"' << u.first << ',' << u.second << "\" -> \"" << v.first << ',' << v.second << "\"" " [label=\""; if (isprint(c)) cout << c; else cout << "0x" << hex << (unsigned)c << dec; cout << "\"]\n"; } }; /** Read an FM index. */ static void readFMIndex(FMIndex& g, const string& faPath) { string fmPath = faPath + ".fm"; ifstream in(fmPath.c_str()); if (in) { if (opt::verbose > 0) cerr << "Reading `" << fmPath << "'...\n"; assert_good(in, fmPath); in >> g; assert_good(in, fmPath); in.close(); return; } // Build the FM index. std::vector s; if (string(faPath) == "-") { if (opt::verbose > 0) std::cerr << "Reading stdin...\n"; copy(istreambuf_iterator(cin), istreambuf_iterator(), back_inserter(s)); assert_good(cin, "stdin"); } else { if (opt::verbose > 0) std::cerr << "Reading `" << faPath << "'...\n"; readFile(faPath.c_str(), s); } g.assign(s.begin(), s.end()); } int main(int argc, char** argv) { bool die = false; for (int c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;) { istringstream arg(optarg != NULL ? optarg : ""); switch (c) { case 'v': opt::verbose++; break; case OPT_HELP: cout << USAGE_MESSAGE; exit(EXIT_SUCCESS); case OPT_VERSION: cout << VERSION_MESSAGE; exit(EXIT_SUCCESS); } if (optarg != NULL && !arg.eof()) { cerr << PROGRAM ": invalid option: `-" << (char)c << optarg << "'\n"; exit(EXIT_FAILURE); } } if (argc - optind > 1) { cerr << PROGRAM ": too many arguments\n"; die = true; } if (die) { cerr << "Try `" << PROGRAM << " --help' for more information.\n"; exit(EXIT_FAILURE); } string faPath(optind < argc ? argv[optind] : "-"); using boost::default_color_type; using boost::depth_first_visit; using boost::make_assoc_property_map; typedef graph_traits::vertex_descriptor V; // Read the FM index. 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size_t size; std::string id; FAIRecord() : offset(0), size(0) { } FAIRecord(size_t offset, size_t size, const std::string& id) : offset(offset), size(size), id(id) { } friend std::ostream& operator<<(std::ostream& out, const FAIRecord& o) { return out << o.id << '\t' << o.size << '\t' << o.offset << '\t' << o.size << '\t' << o.size + 1; } friend std::istream& operator>>(std::istream& in, FAIRecord& o) { size_t lineLen, lineBinLen; in >> o.id >> o.size >> o.offset >> lineLen >> lineBinLen; if (!in) return in; assert(o.size == lineLen || lineLen == lineBinLen); return in >> Ignore('\n'); } }; /** An indexed FASTA (fai) file. */ class FastaIndex { typedef std::vector Data; struct CompareOffset { /** Used with upper_bound. */ bool operator()(size_t a, const FAIRecord& b) const { return a < b.offset; } }; public: typedef boost::tuple SeqPos; /** Return the number of contigs. */ size_t size() { return m_data.size(); } /** Return the size of the FASTA file. */ size_t fileSize() const { assert(!m_data.empty()); return m_data.back().offset + m_data.back().size + 1; } typedef Data::const_iterator const_iterator; const_iterator begin() const { return m_data.begin(); } const_iterator end() const { return m_data.end(); } /** Index the specified FASTA file. */ void index(const std::string& path) { m_data.clear(); std::ifstream in(path.c_str()); assert_good(in, path); char c; for (std::string id; in >> c && in >> id && in >> Ignore('\n');) { assert(c == '>'); assert(!id.empty()); std::streampos offset = in.tellg(); assert(offset > 0); in >> Ignore('\n'); size_t n = in.gcount(); assert(n > 0); m_data.push_back(FAIRecord(offset, n - 1, id)); } assert(in.eof()); } /** Translate a file offset to a sequence:position coordinate. */ SeqPos operator[](size_t offset) const { Data::const_iterator it = std::upper_bound( m_data.begin(), m_data.end(), offset, CompareOffset()); assert(it != m_data.begin()); --it; assert(it != m_data.end()); assert(it->offset <= offset); assert(offset < it->offset + it->size); return SeqPos(*it, offset - it->offset); } /** Write FASTA headers to the specified seekable stream. */ void writeFASTAHeaders(std::ostream& out) const { assert(out); if (!out.seekp(0)) return; for (Data::const_iterator it = m_data.begin(); it != m_data.end(); ++it) { out << '>' << it->id << ' '; assert(it->offset > 0); if (!out.seekp(it->offset - 1)) break; out << '\n'; if (!out.seekp(it->offset + it->size)) break; out << '\n'; } } /** Write this index to a stream in SAM format. */ void writeSAMHeader(std::ostream& out) const { for (Data::const_iterator it = m_data.begin(); it != m_data.end(); ++it) out << "@SQ\tSN:" << it->id << "\tLN:" << it->size << '\n'; } /** Write this index to a stream. */ friend std::ostream& operator<<(std::ostream& out, const FastaIndex& o) { std::copy(o.m_data.begin(), o.m_data.end(), std::ostream_iterator(out, "\n")); return out; } /** Read a FASTA index from a stream. */ friend std::istream& operator>>(std::istream& in, FastaIndex& o) { assert(in.good()); o.m_data.clear(); // Count the number of records. if (in.seekg(0, std::ios::beg)) { size_t n = 0; while (in) if (in.get() == '\n') n++; o.m_data.reserve(n); in.clear(); in.seekg(0, std::ios::beg); assert(in.good()); } else in.clear(); // Read the records. for (FAIRecord rec; in >> rec;) { if (!o.m_data.empty()) assert(rec.offset > o.m_data.back().offset); o.m_data.push_back(rec); } assert(in.eof()); assert(!o.m_data.empty()); return in; } private: Data m_data; }; #endif abyss-1.3.6/DataLayer/FastaInterleave.h000644 002433 001057 00000003137 12015543262 021457 0ustar00traymondassembly000000 000000 #ifndef FASTAINTERLEAVE_H #define FASTAINTERLEAVE_H 1 #include "FastaReader.h" #include #include class FastaInterleave { typedef FastaReader Stream; typedef std::vector Streams; public: FastaInterleave(char** first, char** last, int flags) : m_it(m_streams.begin()), m_fail(false) { assert(first != last); m_streams.reserve(last - first); for (char** p = first; p < last; ++p) m_streams.push_back(new Stream(*p, flags)); m_it = m_streams.begin(); } ~FastaInterleave() { for (Streams::iterator it = m_streams.begin(); it != m_streams.end(); ++it) delete *it; } /** Return true if all the streams are eof. */ bool eof() const { for (Streams::const_iterator it = m_streams.begin(); it != m_streams.end(); ++it) if (!(*it)->eof()) return false; return true; } /** Return true if any of the streams are good. */ operator void*() const { return m_fail ? NULL : const_cast(this); } /** Extract one record from the next stream. */ template friend FastaInterleave& operator>>( FastaInterleave& in, Record& o) { for (unsigned i = 0; i < in.m_streams.size(); ++i) { assert(in.m_it != in.m_streams.end()); bool good = **in.m_it >> o; if (++in.m_it == in.m_streams.end()) in.m_it = in.m_streams.begin(); if (good) { in.m_fail = false; return in; } } in.m_fail = true; return in; } private: /** The streams. */ Streams m_streams; /** The next stream from which to read. */ Streams::iterator m_it; /** True when all streams have failed. */ bool m_fail; }; #endif abyss-1.3.6/DataLayer/FastaReader.cpp000644 002433 001057 00000022713 12176307177 021132 0ustar00traymondassembly000000 000000 #include "FastaReader.h" #include "DataLayer/Options.h" #include "IOUtil.h" #include #include #include #include #include #include #include using namespace std; namespace opt { /** Discard reads that failed the chastity filter. */ int chastityFilter = 1; /** Trim masked (lower case) characters from the ends of * sequences. */ int trimMasked = 1; /** minimum quality threshold */ int qualityThreshold; /** quality offset, usually 33 or 64 */ int qualityOffset; } /** Output an error message. */ ostream& FastaReader::die() { return cerr << m_path << ':' << m_line << ": error: "; } FastaReader::FastaReader(const char* path, int flags, int len) : m_path(path), m_fin(path), m_in(strcmp(path, "-") == 0 ? cin : m_fin), m_flags(flags), m_line(0), m_unchaste(0), m_end(numeric_limits::max()), m_maxLength(len) { if (strcmp(path, "-") != 0) assert_good(m_fin, path); if (m_in.peek() == EOF) cerr << m_path << ':' << m_line << ": warning: " "file is empty\n"; } /** Split the fasta file into nsections and seek to the start * of section. */ void FastaReader::split(unsigned section, unsigned nsections) { assert(nsections >= section); assert(section > 0); assert(strcmp(m_path, "-") != 0); if (nsections == 1) return; // Move the get pointer to the first entry in this section and // update the m_end if there is more than one section. m_in.seekg(0, ios::end); streampos length = m_in.tellg(); assert(length > 0); streampos start = length * (section - 1) / nsections; streampos end = length * section / nsections; assert(end > 0); if (end < length) { m_in.seekg(end); if (m_in.peek() == '>') end += 1; } m_end = end; m_in.seekg(start); if (start > 0) { m_in.ignore(numeric_limits::max(), '\n'); m_in.ignore(numeric_limits::max(), '>'); if (m_in.peek() == EOF) cerr << m_path << ':' << section << ": warning: " "there are no contigs in this section\n"; m_in.putback('>'); } assert(m_end > 0); assert(m_in.good()); } /** Return whether this read passed the chastity filter. */ bool FastaReader::isChaste(const string& s, const string& line) { if (s == "1" || s == "Y") { return true; } else if (s == "0" || s == "N") { return false; } else { die() << "chastity filter should be one of 0, 1, N or Y\n" "and saw `" << s << "' near\n" << line << endl; exit(EXIT_FAILURE); } } /** Check that the seqeuence and quality agree in length. */ void FastaReader::checkSeqQual(const string& s, const string& q) { if (s.length() != q.length()) { die() << "sequence and quality must be the same length near\n" << s << '\n' << q << endl; exit(EXIT_FAILURE); } } /** Return whether the read seq is in colour space. */ static bool isColourSpace(const string& seq) { assert(!seq.empty()); size_t i = seq.find_first_of("ACGTacgt0123", 1); return i != string::npos && isdigit(seq[i]); } /** Read a single record. */ Sequence FastaReader::read(string& id, string& comment, char& anchor, string& q) { next_record: id.clear(); comment.clear(); anchor = 0; q.clear(); // Discard comments. while (m_in.peek() == '#') ignoreLines(1); signed char recordType = m_in.peek(); Sequence s; unsigned qualityOffset = 0; if (recordType == EOF || m_in.tellg() >= m_end) { m_in.seekg(0, ios::end); m_in.clear(std::ios::eofbit | std::ios::failbit); return s; } else if (recordType == '>' || recordType == '@') { // Read the header. string header; getline(header); istringstream headerStream(header); headerStream >> recordType >> id >> ws; std::getline(headerStream, comment); // Ignore SAM headers. if (id.length() == 2 && isupper(id[0]) && isupper(id[1]) && comment.length() > 2 && comment[2] == ':') goto next_record; // Casava FASTQ format if (comment.size() > 3 && comment[1] == ':' && comment[3] == ':') { // read, chastity, flags, index: 1:Y:0:AAAAAA if (opt::chastityFilter && comment[2] == 'Y') { m_unchaste++; if (recordType == '@') { ignoreLines(3); } else { while (m_in.peek() != '>' && m_in.peek() != '#' && ignoreLines(1)) ; } goto next_record; } if (id.size() > 2 && id.rbegin()[1] != '/') { // Add the read number to the ID. id += '/'; id += comment[0]; } } getline(s); if (recordType == '>') { // Read a multi-line FASTA record. string line; while (m_in.peek() != '>' && m_in.peek() != '#' && getline(line)) s += line; if (m_in.eof()) m_in.clear(); } if (recordType == '@') { char c = m_in.get(); if (c != '+') { string line; getline(line); die() << "expected `+' and saw "; if (m_in.eof()) cerr << "end-of-file\n"; else cerr << "`" << c << "' near\n" << c << line << "\n"; exit(EXIT_FAILURE); } ignoreLines(1); getline(q); } else q.clear(); if (s.empty()) { die() << "sequence with ID `" << id << "' is empty\n"; exit(EXIT_FAILURE); } bool colourSpace = isColourSpace(s); if (colourSpace && !isdigit(s[0])) { // The first character is the primer base. The second // character is the dibase read of the primer and the // first base of the sample, which is not part of the // assembly. assert(s.length() > 2); anchor = colourToNucleotideSpace(s[0], s[1]); s.erase(0, 2); q.erase(0, 1); } if (!q.empty()) checkSeqQual(s, q); if (opt::trimMasked && !colourSpace) { // Removed masked (lower case) sequence at the beginning // and end of the read. size_t trimFront = 0; while (trimFront <= s.length() && islower(s[trimFront])) trimFront++; size_t trimBack = s.length(); while (trimBack > 0 && islower(s[trimBack - 1])) trimBack--; s.erase(trimBack); s.erase(0, trimFront); if (!q.empty()) { q.erase(trimBack); q.erase(0, trimFront); } } if (flagFoldCase()) transform(s.begin(), s.end(), s.begin(), ::toupper); qualityOffset = 33; } else { string line; vector fields; fields.reserve(22); getline(line); istringstream in(line); string field; while (std::getline(in, field, '\t')) fields.push_back(field); if (fields.size() >= 11 && (fields[9].length() == fields[10].length() || fields[10] == "*")) { // SAM unsigned flags = strtoul(fields[1].c_str(), NULL, 0); if (flags & 0x100) // FSECONDARY goto next_record; if (opt::chastityFilter && (flags & 0x200)) { // FQCFAIL m_unchaste++; goto next_record; } id = fields[0]; switch (flags & 0xc1) { // FPAIRED|FREAD1|FREAD2 case 0: case 1: // FPAIRED comment = "0:"; break; case 0x41: // FPAIRED|FREAD1 id += "/1"; comment = "1:"; break; case 0x81: // FPAIRED|FREAD2 id += "/2"; comment = "2:"; break; default: die() << "invalid flags: `" << id << "' near" << line << endl; exit(EXIT_FAILURE); } comment += flags & 0x200 ? "Y:0:" : "N:0:"; // FQCFAIL s = fields[9]; q = fields[10]; if (s == "*") s.clear(); if (q == "*") q.clear(); if (flags & 0x10) { // FREVERSE s = reverseComplement(s); reverse(q.begin(), q.end()); } qualityOffset = 33; if (!q.empty()) checkSeqQual(s, q); } else if (fields.size() == 11 || fields.size() == 22) { // qseq or export if (opt::chastityFilter && !isChaste(fields.back(), line)) { m_unchaste++; goto next_record; } ostringstream o; o << fields[0]; for (int i = 1; i < 6; i++) if (!fields[i].empty()) o << ':' << fields[i]; if (!fields[6].empty() && fields[6] != "0") o << '#' << fields[6]; // The reverse read is typically the second read, but is // the third read of an indexed run. o << '/' << (fields[7] == "3" ? "2" : fields[7]); id = o.str(); comment = fields[7]; comment += isChaste(fields.back(), line) ? ":N:0:" : ":Y:0:"; s = fields[8]; q = fields[9]; qualityOffset = 64; checkSeqQual(s, q); } else { die() << "Expected either `>' or `@' or 11 fields\n" "and saw `" << recordType << "' and " << fields.size() << " fields near\n" << line << endl; exit(EXIT_FAILURE); } } if (opt::qualityOffset > 0) qualityOffset = opt::qualityOffset; // Trim from the 3' end to the maximum length. Then, trim based on // quality. if (m_maxLength > 0) { s.erase(m_maxLength); q.erase(m_maxLength); } if (opt::qualityThreshold > 0 && !q.empty()) { assert(s.length() == q.length()); static const char ASCII[] = " !\"#$%&'()*+,-./0123456789:;<=>?" "@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\\]^_" "`abcdefghijklmnopqrstuvwxyz{|}~"; assert(qualityOffset > (unsigned)ASCII[0]); const char* goodQual = ASCII + (qualityOffset - ASCII[0]) + opt::qualityThreshold; size_t trimFront = q.find_first_of(goodQual); size_t trimBack = q.find_last_of(goodQual) + 1; if (trimFront >= trimBack) { // The entire read is poor quality. s.erase(1); q.erase(1); } else if (trimFront > 0 || trimBack < q.length()) { s.erase(trimBack); s.erase(0, trimFront); q.erase(trimBack); q.erase(0, trimFront); } } assert(qualityOffset >= 33); if (flagConvertQual() && qualityOffset != 33) { // Convert to standard quality (ASCII 33). for (string::iterator it = q.begin(); it != q.end(); ++it) { int x = *it - qualityOffset; if (x < -5 || x > 41) { die() << "quality " << x << " is out of range -5 <= q <= 41 near\n" << q << '\n' << string(it - q.begin(), ' ') << "^\n"; exit(EXIT_FAILURE); } *it = 33 + max(0, x); } } return s; } abyss-1.3.6/DataLayer/FastaReader.h000644 002433 001057 00000010373 12104250113 020550 0ustar00traymondassembly000000 000000 #ifndef FASTAREADER_H #define FASTAREADER_H 1 #include "Sequence.h" #include "StringUtil.h" // for chomp #include #include // for exit #include #include #include // for numeric_limits #include /** Read a FASTA, FASTQ, export, qseq or SAM file. */ class FastaReader { public: enum { /** Fold lower-case characters to upper-case. */ FOLD_CASE = 0, NO_FOLD_CASE = 1, /** Convert to standard quality. */ NO_CONVERT_QUALITY = 0, CONVERT_QUALITY = 2, }; bool flagFoldCase() { return ~m_flags & NO_FOLD_CASE; } bool flagConvertQual() { return m_flags & CONVERT_QUALITY; } FastaReader(const char* path, int flags, int len = 0); ~FastaReader() { if (!m_in.eof()) { std::string line; getline(line); die() << "expected end-of-file near\n" << line << '\n'; exit(EXIT_FAILURE); } } Sequence read(std::string& id, std::string& comment, char& anchor, std::string& qual); /** Split the fasta file into nsections and seek to the start * of section. */ void split(unsigned section, unsigned nsections); /** Return whether this stream is at end-of-file. */ bool eof() const { return m_in.eof(); }; /** Return whether this stream is good. */ operator void*() const { return m_in; } /** Return the next character of this stream. */ int peek() { return m_in.peek(); } /** Interface for manipulators. */ FastaReader& operator>>(std::istream& (*f)(std::istream&)) { f(m_in); return *this; } /** Returns the number of unchaste reads. */ unsigned unchaste() const { return m_unchaste; } FastaReader& operator >>(Sequence& seq) { std::string id, comment, qual; char anchor; seq = this->read(id, comment, anchor, qual); return *this; } private: /** Read a single line. */ std::istream& getline(std::string& s) { if (std::getline(m_in, s)) { chomp(s, '\r'); m_line++; } return m_in; } /** Ignore the specified number of lines. */ std::istream& ignoreLines(unsigned n) { for (unsigned i = 0; i < n; ++i) { if (m_in.ignore( std::numeric_limits::max(), '\n')) m_line++; } return m_in; } std::ostream& die(); bool isChaste(const std::string& s, const std::string& line); void checkSeqQual(const std::string& s, const std::string& q); const char* m_path; std::ifstream m_fin; std::istream& m_in; /** Flags indicating parsing options. */ int m_flags; /** Number of lines read. */ unsigned m_line; /** Count of unchaste reads. */ unsigned m_unchaste; /** Position of the end of the current section. */ std::streampos m_end; /** Trim sequences to this length. 0 is unlimited. */ const int m_maxLength; }; /** A FASTA record. */ struct FastaRecord { /** Identifier */ std::string id; /** Comment following the first white-space of the header */ std::string comment; /** Anchor base for a colour-space sequence */ char anchor; /** The sequence */ Sequence seq; FastaRecord() { } FastaRecord(const std::string& id, const std::string& comment, const Sequence& seq) : id(id), comment(comment), anchor(0), seq(seq) { } friend FastaReader& operator >>(FastaReader& in, FastaRecord& o) { std::string q; o.seq = in.read(o.id, o.comment, o.anchor, q); return in; } friend std::ostream& operator <<(std::ostream& out, const FastaRecord& o) { out << '>' << o.id; if (!o.comment.empty()) out << ' ' << o.comment; return out << '\n' << o.seq << '\n'; } }; /** A FASTQ record. */ struct FastqRecord : FastaRecord { /** Quality */ std::string qual; FastqRecord() { } FastqRecord(const std::string& id, const std::string& comment, const Sequence& seq, const std::string& qual) : FastaRecord(id, comment, seq), qual(qual) { assert(seq.length() == qual.length()); } friend FastaReader& operator >>(FastaReader& in, FastqRecord& o) { o.seq = in.read(o.id, o.comment, o.anchor, o.qual); return in; } friend std::ostream& operator <<(std::ostream& out, const FastqRecord& o) { if (o.qual.empty()) return out << static_cast(o); out << '@' << o.id; if (!o.comment.empty()) out << ' ' << o.comment; return out << '\n' << o.seq << "\n" "+\n" << o.qual << '\n'; } }; #endif //FASTAREADER_H abyss-1.3.6/DataLayer/FastaWriter.cpp000644 002433 001057 00000002416 12015543262 021167 0ustar00traymondassembly000000 000000 #include "FastaWriter.h" #include "Common/Options.h" #include #include #include #include #include // for strerror #include #include // for fsync using namespace std; static inline void die(const string& s) { cerr << "error: writing to `" << s << "': " << strerror(errno) << endl; exit(EXIT_FAILURE); } FastaWriter::FastaWriter(const char* path, bool append) : m_path(path), m_fileHandle(fopen(path, append ? "a" : "w")) { if (m_fileHandle == NULL) die(m_path); } FastaWriter::~FastaWriter() { int n = fsync(fileno(m_fileHandle)); if (n < 0) die(m_path); n = fclose(m_fileHandle); if (n < 0) die(m_path); m_fileHandle = NULL; } void FastaWriter::WriteSequence(const Sequence& seq, unsigned id, unsigned multiplicity, const string& comment) { assert(m_fileHandle != NULL); const char *sep = comment.empty() ? "" : " "; int n = opt::rank < 0 ? fprintf(m_fileHandle, ">%llu %zu %u%s%s\n%s\n", (long long unsigned)id, seq.length(), multiplicity, sep, comment.c_str(), seq.c_str()) : fprintf(m_fileHandle, ">%u:%llu %zu %u%s%s\n%s\n", opt::rank, (long long unsigned)id, seq.length(), multiplicity, sep, comment.c_str(), seq.c_str()); if (n < 0) die(m_path); } abyss-1.3.6/DataLayer/FastaWriter.h000644 002433 001057 00000001217 11746352100 020631 0ustar00traymondassembly000000 000000 #ifndef FASTAWRITER_H #define FASTAWRITER_H 1 #include "Sequence.h" #include /** Output a FASTA file. */ class FastaWriter { public: // Constructor opens file FastaWriter(const char* path, bool append = false); // Destructor closes it ~FastaWriter(); /** Write a sequence with a comment. */ void WriteSequence(const Sequence& seq, unsigned id, unsigned multiplicity, const std::string& comment); /** Write a sequence. */ void WriteSequence(const Sequence& seq, unsigned id, unsigned multiplicity) { WriteSequence(seq, id, multiplicity, ""); } private: const char *m_path; FILE* m_fileHandle; }; #endif abyss-1.3.6/DataLayer/Options.h000644 002433 001057 00000000276 12100625253 020032 0ustar00traymondassembly000000 000000 #ifndef DATALAYER_OPTIONS #define DATALAYER_OPTIONS 1 namespace opt { extern int chastityFilter; extern int trimMasked; extern int qualityOffset; extern int qualityThreshold; } #endif abyss-1.3.6/DataLayer/fac.cc000644 002433 001057 00000013623 12176305753 017303 0ustar00traymondassembly000000 000000 /** Calculate assembly contiguity statistics. * Written by Shaun Jackman . */ #include "config.h" #include "Common/Histogram.h" #include "Common/IOUtil.h" #include "Common/Sequence.h" // for isACGT #include "DataLayer/FastaReader.h" #include "DataLayer/Options.h" #include "Uncompress.h" #include #include #include #include using namespace std; #define PROGRAM "abyss-fac" static const char VERSION_MESSAGE[] = PROGRAM " (" PACKAGE_NAME ") " VERSION "\n" "Written by Shaun Jackman.\n" "\n" "Copyright 2013 Canada's Michael Smith Genome Science Centre\n"; static const char USAGE_MESSAGE[] = "Usage: " PROGRAM " [OPTION]... [FILE]...\n" "Calculate assembly contiguity statistics.\n" "\n" " Options:\n" "\n" " -e, --exp-size=N expected genome size. Will calculate NG50\n" " and associated stats\n" " -s, -t, --min-length=N ignore sequences shorter than N bp [500]\n" " -d, --delimiter=S use S for the field delimiter [\\t]\n" " -j, --jira output JIRA format\n" " -m, --mmd output MultiMarkdown format\n" " --chastity discard unchaste sequences [default]\n" " --no-chastity do not discard unchaste sequences\n" " --trim-masked trim masked bases from the end\n" " --no-trim-masked do not trim masked bases from the ends\n" " of sequences [default]\n" " --count-ambig count ambiguity codes in sequences\n" " --no-count-ambig do not count ambiguity codes in sequences [default]\n" " -v, --verbose display verbose output\n" " --help display this help and exit\n" " --version output version information and exit\n" "\n" "Report bugs to <" PACKAGE_BUGREPORT ">.\n"; namespace opt { static unsigned minLength = 500; static long long unsigned expSize = 0; static string delimiter = "\t"; static int format; static int verbose; static int countAmbig; } enum { TAB, JIRA, MMD }; static const char shortopts[] = "d:jms:t:e:v"; enum { OPT_HELP = 1, OPT_VERSION }; static const struct option longopts[] = { { "exp-size", no_argument, NULL, 'e' }, { "min-length", no_argument, NULL, 's' }, { "delimiter", required_argument, NULL, 'd' }, { "jira", no_argument, NULL, 'j' }, { "mmd", no_argument, NULL, 'm' }, { "chastity", no_argument, &opt::chastityFilter, 1 }, { "no-chastity", no_argument, &opt::chastityFilter, 0 }, { "trim-masked", no_argument, &opt::trimMasked, 1 }, { "no-trim-masked", no_argument, &opt::trimMasked, 0 }, { "count-ambig", no_argument, &opt::countAmbig, 1 }, { "no-count-ambig", no_argument, &opt::countAmbig, 0 }, { "help", no_argument, NULL, OPT_HELP }, { "version", no_argument, NULL, OPT_VERSION }, { NULL, 0, NULL, 0 } }; /** FastaReader flags. */ static const int FASTAREADER_FLAGS = FastaReader::NO_FOLD_CASE; /** Print contiguity statistics. */ static void printContiguityStatistics(const char* path) { static bool printHeader = true; if (string(path) == "---") { if (printHeader == false) cout << '\n'; printHeader = true; return; } // Read the sequences and count the lengths. Histogram h; FastaReader in(path, FASTAREADER_FLAGS); for (string s; in >> s;) h.insert(opt::countAmbig ? s.length() : count_if(s.begin(), s.end(), isACGT)); assert(in.eof()); // Print the table header. if (opt::format == JIRA && printHeader) { printHeader = false; const char* sep = "\t||"; cout << "||" << "n" << sep << "n:" << opt::minLength << sep << "n:N50" << sep; if (opt::expSize > 0) cout << "n:NG50" << sep << "NG50" << sep; cout << "min" << sep << "N80" << sep << "N50" << sep << "N20" << sep << "max" << sep << "sum" << sep << "name" << sep << '\n'; } else if (opt::format == MMD && printHeader) { printHeader = false; const char* sep = "\t|"; cout << "n" << sep << "n:" << opt::minLength << sep << "n:N50" << sep; if (opt::expSize > 0) cout << "n:NG50" << sep << "NG50" << sep; cout << "min" << sep << "N80" << sep << "N50" << sep << "N20" << sep << "max" << sep << "sum" << sep << "name" << '\n'; if (opt::expSize > 0) cout << "------" << sep << "------" << sep; cout << "------" << sep << "------" << sep << "------" << sep << "------" << sep << "------" << sep << "------" << sep << "------" << sep << "------" << sep << "------" << sep << "------" << '\n'; } // Print the table. if (opt::format == JIRA) cout << '|'; printContiguityStats(cout, h, opt::minLength, printHeader, opt::delimiter, opt::expSize) << opt::delimiter << path; if (opt::format == JIRA) cout << opt::delimiter; cout << endl; printHeader = false; } int main(int argc, char** argv) { opt::trimMasked = false; bool die = false; for (int c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;) { istringstream arg(optarg != NULL ? optarg : ""); switch (c) { case '?': die = true; break; case 'd': opt::delimiter = arg.str(); arg.clear(ios::eofbit); break; case 'j': opt::delimiter = "\t|"; opt::format = JIRA; break; case 'm': opt::delimiter = "\t|"; opt::format = MMD; break; case 'e': arg >> opt::expSize; break; case 's': case 't': arg >> opt::minLength; break; case 'v': opt::verbose++; break; case OPT_HELP: cout << USAGE_MESSAGE; exit(EXIT_SUCCESS); case OPT_VERSION: cout << VERSION_MESSAGE; exit(EXIT_SUCCESS); } if (optarg != NULL && !arg.eof()) { cerr << PROGRAM ": invalid option: `-" << (char)c << optarg << "'\n"; exit(EXIT_FAILURE); } } if (die) { cerr << "Try `" << PROGRAM << " --help' for more information.\n"; exit(EXIT_FAILURE); } if (optind == argc) printContiguityStatistics("-"); else for_each(argv + optind, argv + argc, printContiguityStatistics); cout.flush(); assert_good(cout, "stdout"); return 0; } abyss-1.3.6/DataLayer/abyss-tofastq.cc000644 002433 001057 00000013134 12116214002 021323 0ustar00traymondassembly000000 000000 /** Convert various file formats to FASTQ format. * Written by Shaun Jackman . */ #include "config.h" #include "DataLayer/Options.h" #include "FastaInterleave.h" #include "FastaReader.h" #include "IOUtil.h" #include "Uncompress.h" #include #include #include #include #include #include using namespace std; #define PROGRAM "abyss-tofastq" static const char VERSION_MESSAGE[] = PROGRAM " (" PACKAGE_NAME ") " VERSION "\n" "Written by Shaun Jackman.\n" "\n" "Copyright 2013 Canada's Michael Smith Genome Science Centre\n"; static const char USAGE_MESSAGE[] = "Usage: " PROGRAM " [OPTION]... [FILE]...\n" "Convert to FASTQ format. The input format may be FASTA, FASTQ,\n" "qseq, export, SAM or BAM format and compressed with gz, bz2 or xz\n" "and may be tarred.\n" "\n" " Options:\n" "\n" " --cat concatenate the records [default]\n" " -i, --interleave interleave the records\n" " --fastq ouput FASTQ format [default]\n" " --fasta ouput FASTA format\n" " --chastity discard unchaste reads [default]\n" " --no-chastity do not discard unchaste reads\n" " --trim-masked trim masked bases from the ends of reads\n" " --no-trim-masked do not trim masked bases from the ends\n" " of reads [default]\n" " -q, --trim-quality=N trim bases from the ends of reads whose\n" " quality is less than the threshold\n" " --standard-quality zero quality is `!' (33)\n" " default for FASTQ and SAM files\n" " --illumina-quality zero quality is `@' (64)\n" " default for qseq and export files\n" " -v, --verbose display verbose output\n" " --help display this help and exit\n" " --version output version information and exit\n" "\n" "Report bugs to <" PACKAGE_BUGREPORT ">.\n"; namespace opt { /** Interleave the lines of each file. */ static int interleave; static int toFASTQ = 1; static int verbose; } static const char shortopts[] = "iq:v"; enum { OPT_HELP = 1, OPT_VERSION }; static const struct option longopts[] = { { "cat", no_argument, &opt::interleave, 0 }, { "interleave", no_argument, &opt::interleave, 1 }, { "fasta", no_argument, &opt::toFASTQ, 0 }, { "fastq", no_argument, &opt::toFASTQ, 1 }, { "chastity", no_argument, &opt::chastityFilter, 1 }, { "no-chastity", no_argument, &opt::chastityFilter, 0 }, { "trim-masked", no_argument, &opt::trimMasked, 1 }, { "no-trim-masked", no_argument, &opt::trimMasked, 0 }, { "trim-quality", required_argument, NULL, 'q' }, { "standard-quality", no_argument, &opt::qualityOffset, 33 }, { "illumina-quality", no_argument, &opt::qualityOffset, 64 }, { "help", no_argument, NULL, OPT_HELP }, { "version", no_argument, NULL, OPT_VERSION }, { NULL, 0, NULL, 0 } }; /** FastaReader flags. */ static const int FASTAREADER_FLAGS = FastaReader::NO_FOLD_CASE | FastaReader::CONVERT_QUALITY; /** Total count. */ static struct { unsigned records; unsigned characters; } g_total; template static void convert(const char* path) { FastaReader in(path, FASTAREADER_FLAGS); unsigned records = 0, characters = 0; for (Record record; in >> record;) { cout << record; assert_good(cout, "stdout"); records++; characters += record.seq.size(); } assert(in.eof()); g_total.records += records; g_total.characters += characters; if (opt::verbose) cerr << records << '\t' << characters << '\t' << path << '\n'; } /** Interleave the records. */ template static void interleave(char** first, char** last) { FastaInterleave in(first, last, FASTAREADER_FLAGS); unsigned records = 0, characters = 0; for (Record record; in >> record;) { cout << record; assert_good(cout, "stdout"); records++; characters += record.seq.size(); } assert(in.eof()); g_total.records += records; g_total.characters += characters; } int main(int argc, char** argv) { opt::trimMasked = false; if (string(argv[0]).find("tofasta") != string::npos) opt::toFASTQ = false; bool die = false; for (int c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;) { istringstream arg(optarg != NULL ? optarg : ""); switch (c) { case '?': die = true; break; case 'i': opt::interleave = true; break; case 'q': arg >> opt::qualityThreshold; break; case 'v': opt::verbose++; break; case OPT_HELP: cout << USAGE_MESSAGE; exit(EXIT_SUCCESS); case OPT_VERSION: cout << VERSION_MESSAGE; exit(EXIT_SUCCESS); } if (optarg != NULL && !arg.eof()) { cerr << PROGRAM ": invalid option: `-" << (char)c << optarg << "'\n"; exit(EXIT_FAILURE); } } if (die) { cerr << "Try `" << PROGRAM << " --help' for more information.\n"; exit(EXIT_FAILURE); } typedef void (*F)(const char*); F convertFasta = convert; F convertFastq = convert; F f = opt::toFASTQ ? convertFastq : convertFasta; if (optind == argc) { f("-"); } else if (!opt::interleave || argc - optind == 1) { // Concatenate. for_each(argv + optind, argv + argc, f); 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first != last; ++first) if (p(*first)) f(*first); return f; } #if __GXX_EXPERIMENTAL_CXX0X__ using std::copy_if; #else /** Copies each element in the range [first, last) into the range * starting at result for which the predicate p is true. */ template OutputIt copy_if(InputIt first, InputIt last, OutputIt result, Pred pred) { for (; first != last; ++first) { if (pred(*first)) { *result = *first; ++result; } } return result; } #endif /** Sorts the elements in the range [first,last) ordered by the value * returned by the unary function op, which is called once for each * element in the range [first,last). The copy constructor of the * value_type of It is not used. */ template void sort_by_transform(It first, It last, Op op) { typedef typename std::iterator_traits::difference_type size_type; typedef typename Op::result_type key_type; size_type n = last - first; std::vector< std::pair > keys; keys.reserve(n); for (It it = first; it != last; ++it) keys.push_back(std::make_pair(op(*it), it - first)); sort(keys.begin(), keys.end()); for (size_type i = 0; i < n; i++) { size_type j = keys[i].second; while (j < i) j = keys[j].second; if (i != j) std::swap(first[i], first[j]); keys[i].second = j; } } #endif abyss-1.3.6/Common/Alignment.h000644 002433 001057 00000004121 12104026026 017665 0ustar00traymondassembly000000 000000 #ifndef ALIGNMENT_H #define ALIGNMENT_H 1 #include #include #include #include /** An ungapped alignment of a query to a target. */ struct Alignment { std::string contig; int contig_start_pos; int read_start_pos; int align_length; int read_length; bool isRC; Alignment() { } Alignment(const Alignment& o, std::string /*qid*/, std::string /*seq*/) { *this = o; } Alignment(std::string contig, int contig_start, int read_start, int align_length, int read_length, bool isRC) : contig(contig), contig_start_pos(contig_start), read_start_pos(read_start), align_length(align_length), read_length(read_length), isRC(isRC) { } /** * Return the taret position at the query start. * Note: not alignment start, and may be negative */ int targetAtQueryStart() const { unsigned tend = contig_start_pos + align_length; return !isRC ? contig_start_pos - read_start_pos : int(tend + read_start_pos); } /** Return the distance between the specified alignments. * May be used to calculate fragment size when the alignments are * mate pairs. */ int operator-(const Alignment& o) const { return targetAtQueryStart() - o.targetAtQueryStart(); } /** Return an alignment of the reverse complement of the query to * the same target. */ Alignment flipQuery() const { Alignment rc(*this); unsigned qend = read_start_pos + align_length; assert(qend <= (unsigned)read_length); rc.read_start_pos = read_length - qend; rc.isRC = !isRC; return rc; } static int calculateReverseReadStart(int read_start_pos, int read_length, int align_length) { unsigned qend = read_start_pos + align_length; return read_length - qend; } friend std::istream& operator >>(std::istream& in, Alignment& a) { return in >> a.contig >> a.contig_start_pos >> a.read_start_pos >> a.align_length >> a.read_length >> a.isRC; } friend std::ostream& operator <<(std::ostream& out, const Alignment& a) { return out << a.contig << ' ' << a.contig_start_pos << ' ' << a.read_start_pos << ' ' << a.align_length << ' ' << a.read_length << ' ' << a.isRC; } }; // struct Alignment #endif abyss-1.3.6/Common/BitUtil.h000644 002433 001057 00000002307 12176307177 017351 0ustar00traymondassembly000000 000000 #ifndef BITUTILS_H #define BITUTILS_H 1 #include "config.h" #include // for exit #include /** The return value of the CPUID instruction. */ struct CPUID { unsigned a, b, c, d; }; /** Return the result of the CPUID instruction * or -1 if it is not supported. */ static inline CPUID cpuid(unsigned op) { CPUID x; #if __GNUC__ && __x86_64__ __asm__("cpuid" : "=a" (x.a), "=b" (x.b), "=c" (x.c), "=d" (x.d) : "a" (op)); return x; #else (void)op; x.a = x.b = x.c = x.d = static_cast(-1); return x; #endif } /** Return whether this processor has the POPCNT instruction. */ static inline bool havePopcnt() { return cpuid(1).c & (1 << 23); } static const bool hasPopcnt = havePopcnt(); /** Return the Hamming weight of x. */ static inline uint64_t popcount(uint64_t x) { #if HAVE_POPCNT && __GNUC__ && __x86_64__ if (hasPopcnt) { __asm__("popcnt %1,%0" : "=r" (x) : "r" (x)); return x; } #endif x = (x & 0x5555555555555555ULL) + ((x >> 1) & 0x5555555555555555ULL); x = (x & 0x3333333333333333ULL) + ((x >> 2) & 0x3333333333333333ULL); x = (x + (x >> 4)) & 0x0f0f0f0f0f0f0f0fULL; x = x + (x >> 8); x = x + (x >> 16); x = x + (x >> 32); return x & 0x7FLLU; } #endif abyss-1.3.6/Common/ConstString.h000644 002433 001057 00000006206 12104026026 020232 0ustar00traymondassembly000000 000000 #ifndef CONSTSTRING_H #define CONSTSTRING_H 1 #include #include #include #include /** An immutable string that does not allocate resources. */ class cstring { public: cstring(const char* p) : m_p(p) { } cstring(const std::string& s) : m_p(s.c_str()) { } /** Return the size of this string. */ size_t size() const { return strlen(m_p); } /** Return a null-terminated sequence of characters. */ const char* c_str() const { return m_p; } operator const char*() const { return m_p; } bool operator==(const cstring& o) const { return m_p == o.m_p || strcmp(m_p, o.m_p) == 0; } bool operator<(const cstring& o) const { return m_p != o.m_p && strcmp(m_p, o.m_p) < 0; } friend std::ostream& operator<<(std::ostream& out, const cstring& o) { return out << o.m_p; } protected: const char* m_p; }; /** An immutable string. */ class const_string : public cstring { public: const_string(const std::string& s) : cstring(strcpy(new char[s.size() + 1], s.c_str())) { } #if __GXX_EXPERIMENTAL_CXX0X__ const_string(const_string&& s) : cstring(s.m_p) { s.m_p = NULL; } #endif #if 0 /* Should be like this, but... */ const_string(const const_string& s) : cstring(strcpy(new char[s.size() + 1], s.c_str())) { } #else /** Copy constructor. * When a vector grows, libstdc++ calls the copy constructor for * each element of the vector, which would invalidate any cstring * that point to this const_string. To work around this issue, the * new const_string gets the original data, and the old * const_string gets the copy, which will probably be destructed * soon. Making the copy is wasteful, but the C++ standard does * not help us out here. */ const_string(const const_string& s) : cstring(s.c_str()) { const_cast(s).m_p = strcpy(new char[s.size() + 1], s.c_str()); } #endif ~const_string() { delete[] m_p; } const_string& operator=(const const_string& s) { assert(false); if (this == &s) return *this; assert(m_p != s.m_p); delete[] m_p; m_p = strcpy(new char[s.size() + 1], s.c_str()); return *this; } void swap(const_string& s) { std::swap(m_p, s.m_p); } private: const_string(); const_string(const char* s); const_string(const cstring&); bool operator==(const const_string& s); }; namespace std { template <> inline void swap(const_string& a, const_string& b) { a.swap(b); } } #include "HashFunction.h" /** Return the hash of the null-terminated string s. */ static inline size_t hash(const char* s) { return hashmem(s, strlen(s)); } namespace std { template struct hash; template <> struct hash { size_t operator()(const cstring& s) const { return ::hash(s); } }; } // namespace std namespace std { namespace tr1 { template struct hash; template <> struct hash { size_t operator()(const cstring& s) const { return ::hash(s); } }; } // namespace tr1 } // namespace std namespace __gnu_cxx { template struct hash; template <> struct hash { size_t operator()(const cstring& s) const { return ::hash(s); } }; } // namespace __gnu_cxx #endif abyss-1.3.6/Common/ContigID.h000644 002433 001057 00000002374 12104026026 017417 0ustar00traymondassembly000000 000000 #ifndef CONTIGID_H #define CONTIGID_H 1 #include "ConstString.h" #include "Dictionary.h" #include #include #include #include /** The dictionary of contig names. */ extern Dictionary g_contigNames; /** The next unique contig name. */ extern unsigned g_nextContigName; /** Set the next contig name returned by createContigName. */ static inline void setNextContigName(cstring s) { std::istringstream iss((std::string)s); if (iss >> g_nextContigName && iss.eof()) ++g_nextContigName; else g_nextContigName = 0; } /** Return the next unique contig name. */ static inline std::string createContigName() { if (g_nextContigName == 0) { assert(!g_contigNames.empty()); setNextContigName(g_contigNames.back()); } std::ostringstream ss; ss << g_nextContigName++; return ss.str(); } /** A contig index. */ class ContigID { public: ContigID() { } explicit ContigID(unsigned index) : m_index(index) { }; /** Return the index. */ operator unsigned() const { return m_index; } /** The insertion operator is not implemented to prevent * unintentional use of the cast operator (unsigned). */ friend std::ostream& operator<<(std::ostream&, const ContigID&); private: /** The index. */ unsigned m_index; }; #endif abyss-1.3.6/Common/ContigID.cpp000644 002433 001057 00000000115 12104026026 017741 0ustar00traymondassembly000000 000000 #include "ContigID.h" Dictionary g_contigNames; unsigned g_nextContigName; abyss-1.3.6/Common/ContigNode.h000644 002433 001057 00000014660 12104026026 020011 0ustar00traymondassembly000000 000000 #ifndef CONTIGNODE_H #define CONTIGNODE_H 1 #include "config.h" // for WORDS_BIGENDIAN #include "ContigID.h" #include "Graph/Properties.h" #include "StringUtil.h" #include #include #include // for strtoul #include #include // for intptr_t #include #include /** A vertex of a contig graph, which is a pair of a contig index and * an orientation. */ class ContigNode { public: ContigNode() { } ContigNode(const ContigNode& o) : m_index(o.m_index) { } /** Construct from a vertex index. */ explicit ContigNode(unsigned index) : m_index(index) { } /** Construct from a contig index and an orientation. */ ContigNode(unsigned index, bool sense) : m_index(2 * index + sense) { } /** Construct from a contig index and an orientation. */ ContigNode(unsigned index, int sense) : m_index(2 * index + sense) { assert(sense == 0 || sense == 1); } /** Construct an ambiguous ContigNode. */ ContigNode(unsigned n, char c) : m_index(-(int)n) { assert(n > 0); assert(c == 'N'); (void)c; } bool operator==(const ContigNode& o) const { return m_index == o.m_index; } bool operator!=(const ContigNode& o) const { return m_index != o.m_index; } bool operator<(const ContigNode& o) const { return m_index < o.m_index; } /** Return the complement of this vertex if sense is true. */ ContigNode operator^(bool sense) const { assert(!ambiguous()); return ContigNode(m_index ^ sense); } /** Return whether this ContigNode is ambiguous. */ bool ambiguous() const { return m_index < 0; } /** Return the vertex index. */ unsigned index() const { assert(!ambiguous()); return m_index; } /** Return the contig index. */ unsigned id() const { return ambiguous() ? m_index : m_index / 2; } /** Return the contig index as a ContigID. */ ContigID contigIndex() const { assert(!ambiguous()); return ContigID(id()); } /** Return the orientation of this vertex. */ bool sense() const { assert(!ambiguous()); return m_index & 1; } /** Return the length in k-mer of this ambiguous contig. */ unsigned length() const { assert(ambiguous()); return -m_index; } /** Return the string of Ns. */ std::string ambiguousSequence() const { assert(ambiguous()); unsigned n = length(); if (n > 100000) { std::cerr << "warning: scaffold gap is longer than 100 kbp: " << n << '\n'; } else if (n > 1000000) { std::cerr << "error: scaffold gap is longer than 1 Mbp: " << n << '\n'; exit(EXIT_FAILURE); } return std::string(n, 'N'); } /** Toggle the orientation of this vertex if sense is true. */ ContigNode& operator^=(bool sense) { assert(!ambiguous()); m_index ^= sense; return *this; } /** Increment this vertex index. */ ContigNode& operator++() { assert(!ambiguous()); ++m_index; return *this; } private: int m_index; }; /** Return the hash value of this ContigNode. */ static inline unsigned hash_value(const ContigNode& o) { return o.index(); } /** Vertex index property map of a ContigNode. */ struct ContigNodeIndexMap : boost::put_get_helper { typedef ContigNode key_type; typedef unsigned value_type; typedef value_type reference; typedef boost::readable_property_map_tag category; reference operator[](const key_type& u) const { return u.index(); } }; /** Contig index property map of a ContigNode. */ struct ContigIndexMap : boost::put_get_helper { typedef ContigNode key_type; typedef ContigID value_type; typedef value_type reference; typedef boost::readable_property_map_tag category; reference operator[](const key_type& u) const { return u.contigIndex(); } }; /** Return the contig name of the specified vertex. */ template Dictionary::name_reference get(vertex_contig_name_t, const Graph&, ContigNode u) { assert(!u.ambiguous()); return get(g_contigNames, u.id()); } /** The string representation of a vertex name. */ struct VertexName : std::pair { typedef std::pair Base; VertexName(const char* s, char c) : Base(reinterpret_cast(s), c) { assert(c == '+' || c == '-'); } VertexName(unsigned n, char c) : Base(n, c) { assert(c == 'N'); } friend std::ostream& operator<<( std::ostream& out, const VertexName& o) { if (o.second == 'N') out << o.first; else out << reinterpret_cast(o.first); return out << o.second; } }; /** Return the name of the specified vertex. */ static inline VertexName get(const Dictionary& pmap, ContigNode u) { return u.ambiguous() ? VertexName(u.length(), 'N') : VertexName(get(pmap, u.id()), u.sense() ? '-' : '+'); } /** Return the name of the specified vertex. */ template VertexName get(vertex_name_t, const Graph&, ContigNode u) { return get(g_contigNames, u); } /** Set the name of the specified vertex. */ template void put(vertex_name_t, const Graph&, ContigNode u, const std::string& name) { assert(!name.empty()); char c = name[name.size() - 1]; if (c == '+' || c == '-') put(g_contigNames, u.id(), name.substr(0, name.size() - 1)); else put(g_contigNames, u.id(), name); } /** The string representation of an edge name. */ struct EdgeName : std::pair { typedef std::pair Base; EdgeName(Base::first_type a, Base::second_type b) : Base(a, b) { } friend std::ostream& operator<<( std::ostream& out, const EdgeName& o) { return out << '"' << o.first << "\" -> \"" << o.second << '"'; } }; /** Return the name of the specified edge. */ static inline EdgeName get(const Dictionary& pmap, std::pair e) { return EdgeName(get(pmap, e.first), get(pmap, e.second)); } /** Return the name of the specified edge. */ template EdgeName get(edge_name_t, const Graph& g, std::pair e) { return EdgeName( get(vertex_name, g, source(e, g)), get(vertex_name, g, target(e, g))); } /** Find the vertex with the specified name. */ static inline ContigNode find_vertex( std::string name, bool sense, const Dictionary& pmap) { assert(!name.empty()); return ContigNode(get(pmap, name), sense); } /** Find the vertex with the specified name. */ static inline ContigNode find_vertex( std::string name, const Dictionary& pmap) { assert(!name.empty()); char c = chop(name); assert(c == '+' || c == '-' || c == 'N'); return c == 'N' ? ContigNode(strtoul(name.c_str(), NULL, 0), 'N') : find_vertex(name, c == '-', pmap); } #endif abyss-1.3.6/Common/ContigPath.h000644 002433 001057 00000003527 12104026026 020020 0ustar00traymondassembly000000 000000 #ifndef CONTIGPATH_H #define CONTIGPATH_H 1 #include "ContigNode.h" #include #include #include #include #include #include #include #include /** A sequence of ContigNode. */ typedef std::vector ContigPath; /** Reverse and complement the specified path. */ template void reverseComplement(T first, T last) { std::reverse(first, last); for (T it = first; it < last; ++it) if (!it->ambiguous()) *it ^= 1; } /** Return the reverse complement of the specified path. */ static inline ContigPath reverseComplement(const ContigPath& path) { ContigPath rc(path.rbegin(), path.rend()); for (ContigPath::iterator it = rc.begin(); it < rc.end(); ++it) if (!it->ambiguous()) *it ^= 1; return rc; } static inline std::ostream& operator<<(std::ostream& out, const ContigPath& o) { assert(!o.empty()); ContigPath::const_iterator it = o.begin(); out << get(g_contigNames, *it); for (++it; it != o.end(); ++it) out << ' ' << get(g_contigNames, *it); return out; } static inline std::istream& operator>>(std::istream& in, ContigPath& o) { o.clear(); std::string s; if (getline(in, s)) { std::istringstream ss(s); for (std::string name; ss >> name;) o.push_back(find_vertex(name, g_contigNames)); assert(ss.eof()); } return in; } static inline void markSeenInPath(std::istream& in, std::vector& marked) { assert(in.good()); std::string s; ContigPath path; while (in >> s >> path) { if (path.empty()) { size_t i = get(g_contigNames, s); assert(i < marked.size()); marked[i] = true; } for (ContigPath::const_iterator it = path.begin(); it != path.end(); ++it) { if (!it->ambiguous()) { size_t i = it->contigIndex(); assert(i < marked.size()); marked[i] = true; } } } assert(in.eof()); } #endif abyss-1.3.6/Common/ContigProperties.h000644 002433 001057 00000012617 12104250113 021254 0ustar00traymondassembly000000 000000 #ifndef CONTIGPROPERTIES_H #define CONTIGPROPERTIES_H 1 #include "ContigNode.h" #include "Graph/Options.h" #include "Graph/Properties.h" #include "IOUtil.h" #include #include #include #include using boost::graph_traits; /** Contig length property. */ struct Length { unsigned length; bool operator==(const Length& o) const { return length == o.length; } Length& operator+=(const Length& o) { length += o.length; return *this; } template Length& operator+=(const T& o) { assert((int)length + (int)o.distance > 0); length += o.distance; return *this; } friend std::ostream& operator<<(std::ostream& out, const Length& o) { return out << "l=" << o.length; } friend std::istream& operator>>(std::istream& in, Length& o) { if (in >> std::ws && in.peek() == 'l') return in >> expect("l =") >> o.length; else return in >> o.length; } }; static inline void put(vertex_length_t, Length& vp, unsigned length) { vp.length = length; } static inline void put(vertex_coverage_t, Length&, unsigned) { } /** The length and coverage of a contig. */ struct ContigProperties { unsigned length; unsigned coverage; ContigProperties() : length(0), coverage(0) { } ContigProperties(unsigned length, unsigned coverage) : length(length), coverage(coverage) { } bool operator==(const ContigProperties& o) const { return length == o.length && coverage == o.coverage; } ContigProperties& operator +=(const ContigProperties& o) { length += o.length; coverage += o.coverage; return *this; } friend std::ostream& operator <<(std::ostream& out, const ContigProperties& o) { float coverage = opt::k <= 0 ? 0 : (float)o.coverage / (o.length - opt::k + 1); switch (opt::format) { case ADJ: return out << ' ' << o.length << ' ' << o.coverage; case DOT: return out << "l=" << o.length << " C=" << o.coverage; case DOT_MEANCOV: assert(opt::k > 0); return out << "l=" << o.length << " c=" << coverage; case SAM: out << "\tLN:" << o.length; return opt::k > 0 ? (out << "\tXc:" << coverage) : (out << "\tXC:" << o.coverage); } return out; } friend std::istream& operator >>(std::istream& in, ContigProperties& o) { if (in >> std::ws && in.peek() == 'l') { in >> expect("l =") >> o.length; if (in >> std::ws && in.peek() == 'C') in >> expect("C =") >> o.coverage; return in; } else if (in.peek() == 'C') { return in >> expect("C=") >> o.coverage >> expect(", l=") >> o.length; } else return in >> o.length >> o.coverage; } }; static inline void put(vertex_length_t, ContigProperties& vp, unsigned length) { vp.length = length; } static inline void put(vertex_coverage_t, ContigProperties& vp, unsigned coverage) { vp.coverage = coverage; } /** The distance between two contigs. */ struct Distance { int distance; Distance() : distance(-opt::k + 1) { } Distance(int d) : distance(d) { } bool operator==(const Distance& o) const { return distance == o.distance; } bool operator!=(const Distance& o) const { return distance != o.distance; } friend std::ostream& operator<<(std::ostream& out, const Distance& o) { return out << "d=" << o.distance; } friend std::istream& operator>>(std::istream& in, Distance& o) { in >> expect(" d = "); if (in.peek() == '"') return in >> expect("\"") >> o.distance >> expect("\""); else return in >> o.distance; } }; /** Add the specified distance (overlap) to the specified contig * length. */ template ContigProperties& operator+=(ContigProperties& a, const T& b) { assert((int)a.length + (int)b.distance > 0); a.length += b.distance; return a; } /** Return the distance between two vertices. */ template int get(edge_distance_t, const Graph& g, typename graph_traits::edge_descriptor e) { return g[e].distance; } /** Return the edge properties of (u,v) unless either u or v is * ambiguous, in which case return a default-constructed instance of * the edge properties. */ template typename edge_bundle_type::type get(edge_bundle_t, const Graph& g, ContigNode u, ContigNode v) { typedef typename graph_traits::edge_descriptor edge_descriptor; if (u.ambiguous() || v.ambiguous()) { return typename edge_bundle_type::type(); } else { std::pair e = edge(u, v, g); if (!e.second) std::cerr << "error: no edge " << get(vertex_name, g, u) << " -> " << get(vertex_name, g, v) << '\n'; assert(e.second); return g[e.first]; } } /** Edge weight property map. */ template struct EdgeWeightMap { typedef typename Graph::edge_descriptor key_type; typedef int value_type; typedef value_type reference; typedef boost::readable_property_map_tag category; EdgeWeightMap(const Graph& g) : m_g(g) { } reference operator[](const key_type& e) const { int weight = m_g[e].distance + m_g[target(e, m_g)].length; if (weight <= 0) std::cerr << "error: invalid edge: " << get(edge_name, m_g, e) << " [" << get(edge_bundle, m_g, e) << "]\n"; assert(weight > 0); return weight; } private: const Graph& m_g; }; /** Return the edge weight. */ template typename EdgeWeightMap::value_type get(edge_weight_t, const Graph& g, typename graph_traits::edge_descriptor e) { return EdgeWeightMap(g)[e]; } #endif abyss-1.3.6/Common/Dictionary.h000644 002433 001057 00000005635 12104026026 020067 0ustar00traymondassembly000000 000000 #ifndef DICTIONARY_H #define DICTIONARY_H 1 #include "ConstString.h" #include "UnorderedMap.h" #include #include #include #include #include /** A bidirectional map of indices and names. */ class Dictionary { public: typedef unsigned index_type; typedef unsigned index_reference; typedef std::string name_type; typedef cstring name_reference; typedef std::vector Vector; typedef unordered_map Map; Dictionary() : m_locked(false) { } /** Insert the specified name. */ index_reference insert(const name_type& name) { m_vec.push_back(name); std::pair inserted = m_map.insert(Map::value_type( m_vec.back(), m_map.size())); if (!inserted.second) { std::cerr << "error: duplicate ID: `" << name << "'\n"; exit(EXIT_FAILURE); } return inserted.first->second; } /** If the specified index is within this dictionary, ensure * that the name is identical, otherwise append the name to * this dictionary. */ void put(index_type index, const name_type& name) { if (index < m_vec.size()) { assert(getName(index) == name); } else { assert(!m_locked); assert(index == m_vec.size()); index_type i = insert(name); assert(i == index); (void)i; } } /** Return the index of the specified name. */ index_reference getIndex(const name_type& name) const { Map::const_iterator it = m_map.find(name); if (it == m_map.end()) { std::cerr << "error: unexpected ID: `" << name << "'\n"; exit(EXIT_FAILURE); } return it->second; } /** Return the name of the specified index. */ name_reference getName(index_type index) const { assert(index < m_vec.size()); return m_vec[index]; } /** Lock this dictionary. No further elements may be added. */ void lock() { m_locked = true; } /** Unlock this dictionary. */ void unlock() { m_locked = false; } /** Return true if this dictionary is empty. */ bool empty() const { return m_vec.empty(); } /** Return the number of elements in this dictionary. */ size_t size() const { return m_vec.size(); } /** Return the number of elements with the specified name. */ size_t count(const name_type& name) const { return m_map.count(name); } /** Return the last name in this dictionary. */ name_reference back() const { assert(!m_vec.empty()); return m_vec.back(); } private: Map m_map; Vector m_vec; bool m_locked; }; static inline Dictionary::name_reference get( const Dictionary& pmap, Dictionary::index_type index) { return pmap.getName(index); } static inline void put(Dictionary& pmap, Dictionary::index_type index, const Dictionary::name_type& name) { pmap.put(index, name); } static inline Dictionary::index_reference get( const Dictionary& pmap, Dictionary::name_type name) { return pmap.getIndex(name); } #endif abyss-1.3.6/Common/Estimate.h000644 002433 001057 00000010136 12104026026 017525 0ustar00traymondassembly000000 000000 #ifndef ESTIMATE_H #define ESTIMATE_H 1 #include "ContigID.h" #include "ContigNode.h" #include "Graph/Options.h" // for opt::k #include "IOUtil.h" #include #include // for ceilf #include #include #include #include #include #include #include namespace opt { /** The acceptable error of a distance estimate. */ extern unsigned distanceError; } /** An estimate of the distance between two contigs. */ struct DistanceEst { int distance; unsigned numPairs; float stdDev; DistanceEst() : distance(-opt::k + 1), numPairs(0), stdDev(0) { } DistanceEst(int distance) : distance(distance), numPairs(0), stdDev(distance) { } DistanceEst(int distance, unsigned numPairs, float stdDev) : distance(distance), numPairs(numPairs), stdDev(stdDev) { } bool operator==(const DistanceEst& o) const { return distance == o.distance && numPairs == o.numPairs && stdDev == o.stdDev; } friend std::ostream& operator<<(std::ostream& out, const DistanceEst& o) { if (opt::format != DIST) { out << "d=" << o.distance; if (o.stdDev > 0 || o.numPairs > 0) out << " e=" << std::fixed << std::setprecision(1) << o.stdDev << " n=" << o.numPairs; return out; } else return out << o.distance << ',' << o.numPairs << ',' << std::fixed << std::setprecision(1) << o.stdDev; } friend std::istream& operator>>(std::istream& in, DistanceEst& o) { if (in >> std::ws && in.peek() == 'd') { if (!(in >> expect("d =") >> o.distance >> std::ws)) return in; if (in.peek() == ']') { o.stdDev = o.numPairs = 0; return in; } else if (in.peek() == ',') return in >> expect(", e =") >> o.stdDev >> expect(", n =") >> o.numPairs; else return in >> expect(" e =") >> o.stdDev >> expect(" n =") >> o.numPairs; } else return in >> o.distance >> expect(",") >> o.numPairs >> expect(",") >> o.stdDev; } }; /** Return the better of two distance estimates. * Return the estimate whose error is least, or when the errors are * equal, return the larger distance estimate. * Add the number of pairs. */ struct BetterDistanceEst { NoProperty operator()( const NoProperty& a, const NoProperty&) const { return a; } DistanceEst operator()( const DistanceEst& a, const DistanceEst& b) const { bool which = a.stdDev != b.stdDev ? a.stdDev < b.stdDev : a.distance > b.distance; DistanceEst x = which ? a : b; x.numPairs = a.numPairs + b.numPairs; return x; } }; /** Merge two distance estimates. */ struct MergeDistanceEst { DistanceEst operator()( const DistanceEst& a, const DistanceEst& b) const { int x1 = a.distance, x2 = b.distance; double v1 = a.stdDev * a.stdDev, v2 = b.stdDev * b.stdDev; DistanceEst x; x.distance = (int)round((x1 * v2 + x2 * v1) / (v1 + v2)); x.stdDev = sqrt(v1 * v2 / (v1 + v2)); x.numPairs = a.numPairs + b.numPairs; return x; } }; /** Return the allowed error for the given estimate. */ static inline unsigned allowedError(float stddev) { /** The number of standard deviations. */ const int NUM_SIGMA = 3; return (unsigned)ceilf(NUM_SIGMA * stddev + opt::distanceError); } /** Distance estimates to and from a particular contig. */ struct EstimateRecord { typedef std::pair Estimate; typedef std::vector Estimates; ContigID refID; Estimates estimates[2]; /** Read the distance estimates for one contig. */ friend std::istream& operator >>(std::istream& in, EstimateRecord& o) { o.estimates[false].clear(); o.estimates[true].clear(); std::string name; in >> name; if (!in) return in; o.refID = ContigID(get(g_contigNames, name)); for (int rc = false; rc <= true; ++rc) { std::string s; std::getline(in, s, !rc ? ';' : '\n'); std::istringstream ss(s); for (Estimate ep; getline(ss >> std::ws, s, ',');) { ep.first = find_vertex(s, g_contigNames); if (ss >> ep.second) o.estimates[rc].push_back(ep); } assert(ss.eof()); } return in; } }; namespace std { template<> inline void swap(EstimateRecord&, EstimateRecord&) { assert(false); } } #endif abyss-1.3.6/Common/Fcontrol.cpp000644 002433 001057 00000000401 11746352077 020110 0ustar00traymondassembly000000 000000 #include "Fcontrol.h" #include /* Set the FD_CLOEXEC flag of the specified file descriptor. */ int setCloexec(int fd) { int flags = fcntl(fd, F_GETFD, 0); if (flags == -1) return -1; flags |= FD_CLOEXEC; return fcntl(fd, F_SETFD, flags); } abyss-1.3.6/Common/Fcontrol.h000644 002433 001057 00000000111 11746352077 017553 0ustar00traymondassembly000000 000000 #ifndef FCONTROL_H #define FCONTROL_H 1 int setCloexec(int fd); #endif abyss-1.3.6/Common/Functional.h000644 002433 001057 00000003565 11746352077 020107 0ustar00traymondassembly000000 000000 #ifndef FUNCTIONAL_H #define FUNCTIONAL_H 1 #include /** A functor that always returns true. */ template struct True : std::unary_function { bool operator()(const Arg&) const { return true; } }; /** A functor to adapt a pointer to a member variable. */ template struct MemVar : std::unary_function { MemVar(Result Arg::* p) : m_p(p) { } Result operator()(const Arg& arg) const { return arg.*m_p; } private: Result Arg::* m_p; }; /** Return a functor to adapt a pointer to a member variable. */ template MemVar mem_var(Result Arg::* p) { return MemVar(p); } /** A functor, f1(f2(x)). */ template struct unary_compose : std::unary_function < typename F2::argument_type, typename F1::result_type> { unary_compose(const F1& f1, const F2& f2) : f1(f1), f2(f2) { } typename F1::result_type operator()( const typename F2::argument_type& x) const { return f1(f2(x)); } private: F1 f1; F2 f2; }; /** Return a functor, f1(f2(x)). */ template unary_compose compose1(const F1& f1, const F2& f2) { return unary_compose(f1, f2); } /** A functor, f(g1(x), g2(x)). */ template struct binary_compose : std::unary_function < typename G1::argument_type, typename F::result_type> { binary_compose(const F& f, const G1& g1, const G2& g2) : f(f), g1(g1), g2(g2) { } typename G1::result_type operator()( const typename G1::argument_type& x) const { return f(g1(x), g2(x)); } private: F f; G1 g1; G2 g2; }; /** Return a functor, f(g1(x), g2(x)). */ template binary_compose compose2( const F& f, const G1& g1, const G2& g2) { return binary_compose(f, g1, g2); } #endif abyss-1.3.6/Common/HashFunction.h000644 002433 001057 00000000344 12104026026 020343 0ustar00traymondassembly000000 000000 #ifndef HASHFUNCTION_H #define HASHFUNCTION_H 1 #include "city.h" #include #include static inline uint64_t hashmem(const void *p, size_t n) { return CityHash64(static_cast(p), n); } #endif abyss-1.3.6/Common/Histogram.cpp000644 002433 001057 00000005002 12015543262 020245 0ustar00traymondassembly000000 000000 #include "Histogram.h" #include #include #include #include using namespace std; /** Remove samples less than the specified threshold. */ Histogram Histogram::trimLow(T threshold) const { Histogram h; for (Histogram::Map::const_iterator it = m_map.begin(); it != m_map.end(); it++) if (it->first >= threshold) h.insert(it->first, it->second); return h; } /** Trim off the bottom fraction/2 and top fraction/2 data points. * At least (1 - fraction) of the data will remain. */ Histogram Histogram::trimFraction(double fraction) const { double low_cutoff = fraction/2; double high_cutoff = 1.0f - fraction/2; size_type n = size(); double cumulative = 0; Histogram newHist; for (Histogram::Map::const_iterator it = m_map.begin(); it != m_map.end(); it++) { double temp_total = cumulative + (double)it->second / n; if (temp_total > low_cutoff && cumulative < high_cutoff) newHist.insert(it->first, it->second); cumulative = temp_total; } return newHist; } /** Bin these elements into n buckets. The number of buckets returned * may be smaller than n. */ Histogram::Bins Histogram::bin(unsigned n) const { Histogram::Bins bins; bins.reserve(n); T nperbucket = (T)ceilf((float)(maximum() - minimum()) / n); T next = minimum() + nperbucket; Histogram::Bins::value_type count = 0; for (Histogram::Map::const_iterator it = m_map.begin(); it != m_map.end(); it++) { if (it->first >= next) { bins.push_back(count); count = 0; next += nperbucket; } count += it->second; } if (count > 0) bins.push_back(count); return bins; } /** Return a unicode bar plot. * @param n number of buckets */ string Histogram::barplot(unsigned nbins) const { /** Unicode bar characters. */ static const char* bars[10] = { " ", "_", "\342\226\201", // 9601 "\342\226\202", // 9602 "\342\226\203", // 9603 "\342\226\204", // 9604 "\342\226\205", // 9605 "\342\226\206", // 9606 "\342\226\207", // 9607 "\342\226\210", // 9608 }; Histogram::Bins bins = bin(nbins); ostringstream ss; Histogram::Bins::value_type max = 1 + *max_element(bins.begin(), bins.end()); for (Histogram::Bins::const_iterator it = bins.begin(); it != bins.end(); ++it) ss << bars[10 * *it / max]; string s(ss.str()); while (!s.empty() && *s.rbegin() == ' ') s.erase(s.size() - 1); return s; } /** Return a unicode bar plot. */ string Histogram::barplot() const { const char *columns = getenv("COLUMNS"); return barplot(columns == NULL ? 80 : strtoul(columns, NULL, 0)); } abyss-1.3.6/Common/Histogram.h000644 002433 001057 00000017536 12176305753 017742 0ustar00traymondassembly000000 000000 #ifndef HISTOGRAM_H #define HISTOGRAM_H 1 #include "StringUtil.h" // for toEng #include #include // for INT_MAX #include #include #include #include #include #include /** A histogram of type T, which is int be default. * A histogram may be implemented as a multiset. This class aims * to provide a similar interface to a multiset. */ class Histogram { typedef int T; typedef size_t size_type; typedef std::map Map; typedef long long unsigned accumulator; public: typedef Map::const_iterator const_iterator; Histogram() { } /** Construct a histogram of the specified elements. */ template Histogram(InputIterator first, InputIterator last) { for (InputIterator it = first; it != last; ++it) insert(*it); } /** Construct a histogram from a vector, where the index into the * vector is the sample, and the value at that index is the number * of times that sample was observed. */ explicit Histogram(std::vector v) { for (T i = 0; i < (T)v.size(); i++) if (v[i] > 0) m_map.insert(std::make_pair(i, v[i])); } void insert(T value) { m_map[value]++; } void insert(T value, size_type count) { m_map[value] += count; } size_type count(T value) const { Map::const_iterator iter = m_map.find(value); return iter == m_map.end() ? 0 : iter->second; } /** Return the number of elements in the range [lo,hi]. */ size_type count(T lo, T hi) const { assert(lo <= hi); size_type n = 0; Map::const_iterator last = m_map.upper_bound(hi); for (Map::const_iterator it = m_map.lower_bound(lo); it != last; ++it) n += it->second; return n; } T minimum() const { return empty() ? 0 : m_map.begin()->first; } T maximum() const { return empty() ? 0 : m_map.rbegin()->first; } bool empty() const { return m_map.empty(); } size_type size() const { size_type n = 0; for (Map::const_iterator it = m_map.begin(); it != m_map.end(); ++it) n += it->second; return n; } /** Return the sum. */ accumulator sum() const { accumulator total = 0; for (Map::const_iterator it = m_map.begin(); it != m_map.end(); ++it) total += (accumulator)it->first * it->second; return total; } /** Return the mean. */ double mean() const { accumulator n = 0, total = 0; for (Map::const_iterator it = m_map.begin(); it != m_map.end(); ++it) { n += it->second; total += (accumulator)it->first * it->second; } return (double)total / n; } double variance() const { accumulator n = 0, total = 0, squares = 0; for (Map::const_iterator it = m_map.begin(); it != m_map.end(); ++it) { n += it->second; total += (accumulator)it->first * it->second; squares += (accumulator)it->first * it->first * it->second; } return (squares - (double)total * total / n) / n; } double sd() const { return sqrt(variance()); } /** Return the specified percentile. */ T percentile(float p) const { size_type x = (size_type)ceil(p * size()); size_type n = 0; for (Map::const_iterator it = m_map.begin(); it != m_map.end(); ++it) { n += it->second; if (n >= x) return it->first; } return maximum(); } /** Return the median. */ T median() const { return percentile(0.5); } /** Return the largest weight in the arg min of partial sum of * weights. */ T argMin(accumulator x) const { accumulator total = 0; for (Map::const_iterator it = m_map.begin(); it != m_map.end(); ++it) { total += (accumulator)it->first * it->second; if (total >= x) return it->first; } return maximum(); } /** Return the specified weighted percentile. */ T weightedPercentile(float p) const { return argMin((accumulator)ceil(p * sum())); } /** Return the N50. */ T n50() const { return weightedPercentile(0.5); } /** Return the first local minimum or zero if a minimum is not * found. */ T firstLocalMinimum() const { const unsigned SMOOTHING = 4; assert(!empty()); Map::const_iterator minimum = m_map.begin(); size_type count = 0; for (Map::const_iterator it = m_map.begin(); it != m_map.end(); ++it) { if (it->second <= minimum->second) { minimum = it; count = 0; } else if (++count >= SMOOTHING) break; } if (minimum->first == maximum()) return 0; return minimum->first; } void eraseNegative() { for (Map::iterator it = m_map.begin(); it != m_map.end();) if (it->first < 0) m_map.erase(it++); else ++it; } /** Remove noise from the histogram. Noise is defined as a * sample x where h[x-1] == 0 && h[x+1] == 0. */ void removeNoise() { for (Map::iterator it = m_map.begin(); it != m_map.end();) { if (m_map.count(it->first - 1) == 0 && m_map.count(it->first + 1) == 0) m_map.erase(it++); else ++it; } } /** Remove outliers from the histogram. A sample is an outlier * if it is outside the range [Q1 - k*(Q3-Q1), Q3 + k*(Q3-Q1)] * where k = 20. */ void removeOutliers() { T q1 = percentile(0.25); T q3 = percentile(0.75); T l = q1 - 20 * (q3 - q1); T u = q3 + 20 * (q3 - q1); for (Map::iterator it = m_map.begin(); it != m_map.end();) { if (it->first < l || it->first > u) m_map.erase(it++); else ++it; } } /** Negate each element of this histogram. */ Histogram negate() const { Histogram h; for (Map::const_iterator it = m_map.begin(); it != m_map.end(); ++it) h.m_map.insert(std::make_pair(-it->first, it->second)); return h; } Histogram trimFraction(double fraction) const; Histogram trimLow(T threshold) const; typedef std::vector Bins; Bins bin(unsigned n) const; std::string barplot() const; std::string barplot(unsigned nbins) const; const_iterator begin() const { return m_map.begin(); } const_iterator end() const { return m_map.end(); } /** Return a vector representing this histogram. */ std::vector toVector() const { assert(minimum() >= 0); #if 0 std::vector v(maximum()+1); #else // CommLayer::reduce requires the arrays have the same size. std::vector v(65536); assert(maximum() < (T)v.size()); #endif for (Map::const_iterator it = m_map.begin(); it != m_map.end(); ++it) v[it->first] = it->second; return v; } friend std::ostream& operator<<(std::ostream& o, const Histogram& h) { for (Map::const_iterator it = h.m_map.begin(); it != h.m_map.end(); ++it) o << it->first << '\t' << it->second << '\n'; return o; } friend std::istream& operator>>(std::istream& in, Histogram& h) { Histogram::T value; size_type count; while (in >> value >> count) h.insert(value, count); assert(in.eof()); return in; } private: Map m_map; }; namespace std { template<> inline void swap(Histogram&, Histogram&) { assert(false); } } /** Print assembly contiguity statistics. */ static inline std::ostream& printContiguityStats( std::ostream& out, const Histogram& h0, unsigned minSize, bool printHeader = true, const std::string& sep = "\t", const long long unsigned expSize = 0) { Histogram h = h0.trimLow(minSize); if (printHeader) { out << "n" << sep << "n:" << minSize << sep << "n:N50" << sep; if (expSize > 0) out << "n:NG50" << sep << "NG50" << sep; out << "min" << sep << "N80" << sep << "N50" << sep << "N20" << sep << "max" << sep << "sum\n"; } unsigned n50 = h.n50(); out << toEng(h0.size()) << sep << toEng(h.size()) << sep << toEng(h.count(n50, INT_MAX)) << sep; long long unsigned sum = h.sum(); if (expSize > 0) { unsigned ng50; if (sum < expSize/2) ng50 = h.minimum(); else ng50 = h.argMin(sum - expSize/2); out << toEng(h.count(ng50, INT_MAX)) << sep << toEng(ng50) << sep; } return out << toEng(h.minimum()) << sep << toEng(h.weightedPercentile(1 - 0.8)) << sep << toEng(n50) << sep << toEng(h.weightedPercentile(1 - 0.2)) << sep << toEng(h.maximum()) << sep << toEng(sum); } #endif abyss-1.3.6/Common/IOUtil.h000644 002433 001057 00000004643 12156674223 017144 0ustar00traymondassembly000000 000000 #ifndef IOUTIL_H #define IOUTIL_H 1 #include #include #include #include // for strerror #include #include #include // for numeric_limits #include /** Print an error message and exit if stream is not good. */ static inline void assert_good(const std::ios& stream, const std::string& path) { if (!stream.good()) { std::cerr << "error: `" << path << "': " << strerror(errno) << std::endl; exit(EXIT_FAILURE); } } /** Print an error message and exit if stream is not eof. */ static inline void assert_eof(std::istream& in, const std::string& path) { if (!in.eof()) { in.clear(); std::string s; std::getline(in, s); std::cerr << "error: `" << path << "': " "Expected end-of-file and saw `" << s << "'\n"; exit(EXIT_FAILURE); } } /** This input stream manipulator skips the specified string. */ struct expect { const char* s; expect(const char* s) : s(s) { } }; static inline std::istream& operator>>(std::istream& in, expect o) { for (const char* p = o.s; *p != '\0'; ++p) { if (*p == ' ') { in >> std::ws; } else { char c = in.get(); if (!in || c != *p) { std::cerr << "error: Expected `" << p << "' and saw "; if (in) std::cerr << '`' << c << "'\n"; else if (in.eof()) std::cerr << "end-of-file\n"; else std::cerr << "I/O error\n"; exit(EXIT_FAILURE); } } } return in; } /** This input stream manipulator discards characters until reaching * the delimeter. */ struct Ignore { const char delim; size_t n; Ignore(const char delim, size_t n = std::numeric_limits::max()) : delim(delim), n(n) { } }; static inline std::istream& operator>>(std::istream& in, Ignore o) { return in.ignore(o.n, o.delim); } /** Read a file and store it in the specified vector. */ template static inline void readFile(const char* path, Vector& s) { std::ifstream in(path); assert_good(in, path); in.seekg(0, std::ios::end); ssize_t n = in.tellg(); assert(n > 0); s.resize(n); in.seekg(0, std::ios::beg); assert_good(in, path); char *p = reinterpret_cast(&s[0]); #if __MACH__ // Read 1 GB at a time. Reads of 2 GB or more fail. const ssize_t N = 1024 * 1024 * 1024; for (; n > N; n -= N, p += N) { in.read(p, N); assert_good(in, path); assert(in.gcount() == N); } #endif in.read(p, n); assert_good(in, path); assert(in.gcount() == n); } #endif abyss-1.3.6/Common/Iterator.h000644 002433 001057 00000004462 12104026026 017550 0ustar00traymondassembly000000 000000 #ifndef ITERATOR_H #define ITERATOR_H 1 #include /** A counting output iterator. */ class CountingOutputIterator { public: explicit CountingOutputIterator(size_t& count) : m_count(count) { m_count = 0; } CountingOutputIterator& operator++() { ++m_count; return *this; } CountingOutputIterator& operator*() { return *this; } template CountingOutputIterator& operator=(const T&) { return *this; } private: size_t& m_count; }; /** An output stream iterator, like ostream_iterator, that outputs the * a delimiter before and after the item. */ template > class affix_ostream_iterator : public std::iterator { public: typedef charT char_type; typedef traits traits_type; typedef std::basic_ostream ostream_type; typedef void value_type; affix_ostream_iterator(ostream_type& s, charT const *prefix, charT const *suffix = NULL) : os(&s), prefix(prefix), suffix(suffix) {} affix_ostream_iterator& operator =(T const &item) { if (prefix != NULL) *os << prefix; *os << item; if (suffix != NULL) *os << suffix; return *this; } affix_ostream_iterator &operator*() { return *this; } affix_ostream_iterator &operator++() { return *this; } affix_ostream_iterator &operator++(int) { return *this; } private: std::basic_ostream *os; charT const* prefix; charT const* suffix; }; /** Traits of an output iterator. */ template struct output_iterator_traits { typedef typename OutputIterator::value_type value_type; }; /** Traits of a back_insert_iterator. */ template struct output_iterator_traits< std::back_insert_iterator > { typedef typename Container::value_type value_type; }; /** Traits of an ostream_iterator. */ template struct output_iterator_traits< std::ostream_iterator > { typedef T value_type; }; /** Traits of an affix_ostream_iterator. */ template struct output_iterator_traits< affix_ostream_iterator > { typedef T value_type; }; #endif abyss-1.3.6/Common/Kmer.cpp000644 002433 001057 00000027145 12114244673 017226 0ustar00traymondassembly000000 000000 #include "config.h" #include "Kmer.h" #include "Common/Options.h" #include "HashFunction.h" #include #include using namespace std; /** The size of a k-mer. This variable is static and is shared by all * instances. */ unsigned Kmer::s_length; /** The size of a k-mer in bytes. */ unsigned Kmer::s_bytes; static unsigned seqIndexToByteNumber(unsigned seqIndex); static unsigned seqIndexToBaseIndex(unsigned seqIndex); static uint8_t getBaseCode(const char* pSeq, unsigned byteNum, unsigned index); static void setBaseCode(char* pSeq, unsigned byteNum, unsigned index, uint8_t base); /** Construct a k-mer from a string. */ Kmer::Kmer(const Sequence& seq) { assert(seq.length() == s_length); memset(m_seq, 0, NUM_BYTES); const char* p = seq.data(); for (unsigned i = 0; i < s_length; i++) set(i, baseToCode(*p++)); } /** Compare two k-mer. */ int Kmer::compare(const Kmer& other) const { return memcmp(m_seq, other.m_seq, bytes()); } /** Compute a hash-like value of the packed sequence over the first 16 * bases and the reverse complement of the last 16 bases * The reverse complement of the last 16 bases is used so that a * sequence and its reverse complement will hash to the same value. * @todo make this faster */ unsigned Kmer::getCode() const { /* At k=19, this hash function always returns an even number due * to the sequence and its reverse complement overlapping when the * xor is calculated. A more general solution is needed. */ const unsigned NUM_BYTES = s_length < 20 ? s_length/8 : 4; Kmer rc = *this; rc.reverseComplement(); const unsigned prime = 101; unsigned sum = 0; for (unsigned i = 0; i < NUM_BYTES; i++) sum = prime * sum + (m_seq[i] ^ rc.m_seq[i]); return sum; } size_t Kmer::getHashCode() const { // Hash numbytes - 1 to avoid getting different hash values for // the same sequence for n % 4 != 0 sequences. return hashmem(m_seq, bytes() - 1); } /** Return the string representation of this sequence. */ Sequence Kmer::str() const { Sequence s; s.reserve(s_length); for (unsigned i = 0; i < s_length; i++) s.push_back(codeToBase(at(i))); return s; } /** Swap the positions of four bases. */ static const uint8_t swapBases[256] = { 0x00, 0x40, 0x80, 0xc0, 0x10, 0x50, 0x90, 0xd0, 0x20, 0x60, 0xa0, 0xe0, 0x30, 0x70, 0xb0, 0xf0, 0x04, 0x44, 0x84, 0xc4, 0x14, 0x54, 0x94, 0xd4, 0x24, 0x64, 0xa4, 0xe4, 0x34, 0x74, 0xb4, 0xf4, 0x08, 0x48, 0x88, 0xc8, 0x18, 0x58, 0x98, 0xd8, 0x28, 0x68, 0xa8, 0xe8, 0x38, 0x78, 0xb8, 0xf8, 0x0c, 0x4c, 0x8c, 0xcc, 0x1c, 0x5c, 0x9c, 0xdc, 0x2c, 0x6c, 0xac, 0xec, 0x3c, 0x7c, 0xbc, 0xfc, 0x01, 0x41, 0x81, 0xc1, 0x11, 0x51, 0x91, 0xd1, 0x21, 0x61, 0xa1, 0xe1, 0x31, 0x71, 0xb1, 0xf1, 0x05, 0x45, 0x85, 0xc5, 0x15, 0x55, 0x95, 0xd5, 0x25, 0x65, 0xa5, 0xe5, 0x35, 0x75, 0xb5, 0xf5, 0x09, 0x49, 0x89, 0xc9, 0x19, 0x59, 0x99, 0xd9, 0x29, 0x69, 0xa9, 0xe9, 0x39, 0x79, 0xb9, 0xf9, 0x0d, 0x4d, 0x8d, 0xcd, 0x1d, 0x5d, 0x9d, 0xdd, 0x2d, 0x6d, 0xad, 0xed, 0x3d, 0x7d, 0xbd, 0xfd, 0x02, 0x42, 0x82, 0xc2, 0x12, 0x52, 0x92, 0xd2, 0x22, 0x62, 0xa2, 0xe2, 0x32, 0x72, 0xb2, 0xf2, 0x06, 0x46, 0x86, 0xc6, 0x16, 0x56, 0x96, 0xd6, 0x26, 0x66, 0xa6, 0xe6, 0x36, 0x76, 0xb6, 0xf6, 0x0a, 0x4a, 0x8a, 0xca, 0x1a, 0x5a, 0x9a, 0xda, 0x2a, 0x6a, 0xaa, 0xea, 0x3a, 0x7a, 0xba, 0xfa, 0x0e, 0x4e, 0x8e, 0xce, 0x1e, 0x5e, 0x9e, 0xde, 0x2e, 0x6e, 0xae, 0xee, 0x3e, 0x7e, 0xbe, 0xfe, 0x03, 0x43, 0x83, 0xc3, 0x13, 0x53, 0x93, 0xd3, 0x23, 0x63, 0xa3, 0xe3, 0x33, 0x73, 0xb3, 0xf3, 0x07, 0x47, 0x87, 0xc7, 0x17, 0x57, 0x97, 0xd7, 0x27, 0x67, 0xa7, 0xe7, 0x37, 0x77, 0xb7, 0xf7, 0x0b, 0x4b, 0x8b, 0xcb, 0x1b, 0x5b, 0x9b, 0xdb, 0x2b, 0x6b, 0xab, 0xeb, 0x3b, 0x7b, 0xbb, 0xfb, 0x0f, 0x4f, 0x8f, 0xcf, 0x1f, 0x5f, 0x9f, 0xdf, 0x2f, 0x6f, 0xaf, 0xef, 0x3f, 0x7f, 0xbf, 0xff }; #if MAX_KMER > 96 # include typedef bitset<2 * MAX_KMER> Seq; #else # define SEQ_WORDS ((Kmer::NUM_BYTES + 7)/8) # define SEQ_BITS (64 * SEQ_WORDS) # define SEQ_FULL_WORDS ((int)Kmer::NUM_BYTES/8) # define SEQ_ODD_BYTES (Kmer::NUM_BYTES - 8*SEQ_FULL_WORDS) /** A sequence of bits of length SEQ_BITS. */ struct Seq { uint64_t x[SEQ_WORDS]; /** Return the number of bits in this sequence. */ static unsigned size() { return SEQ_BITS; } /** Flip all the bits. */ void flip() { for (unsigned i = 0; i < SEQ_WORDS; i++) x[i] = ~x[i]; } /** Shift right by the specified number of bits. */ void operator>>=(uint8_t n) { if (n == 0) return; #if MAX_KMER <= 32 x[0] >>= n; #elif MAX_KMER <= 64 uint64_t x0 = x[0], x1 = x[1]; if (n < 64) { x[0] = x0 >> n; x[1] = x1 >> n | x0 << (64 - n); } else { x[0] = 0; x[1] = x0 >> (n - 64); } #elif MAX_KMER <= 96 uint64_t x0 = x[0], x1 = x[1], x2 = x[2]; if (n < 64) { x[0] = x0 >> n; x[1] = x1 >> n | x0 << (64 - n); x[2] = x2 >> n | x1 << (64 - n); } else if (n == 64) { x[0] = 0; x[1] = x0; x[2] = x1; } else if (n < 128) { n -= 64; x[0] = 0; x[1] = x0 >> n; x[2] = x1 >> n | x0 << (64 - n); } else { n -= 128; x[0] = 0; x[1] = 0; x[2] = x0 >> n; } #else # error #endif } }; #endif /** Load with appropriate endianness for shifting. */ static Seq load(const uint8_t *src) { Seq seq; #if MAX_KMER > 96 # if WORDS_BIGENDIAN const uint64_t *s = reinterpret_cast(src); uint64_t *d = reinterpret_cast(&seq + 1); copy(s, s + SEQ_WORDS, reverse_iterator(d)); # else uint8_t *d = reinterpret_cast(&seq); memcpy(d, src, sizeof seq); reverse(d, d + sizeof seq); # endif #else uint64_t *px = seq.x; const uint8_t *p = src; for (int i = 0; i < SEQ_FULL_WORDS; i++) { *px++ = (uint64_t)p[0] << 56 | (uint64_t)p[1] << 48 | (uint64_t)p[2] << 40 | (uint64_t)p[3] << 32 | (uint64_t)p[4] << 24 | (uint64_t)p[5] << 16 | (uint64_t)p[6] << 8 | (uint64_t)p[7] << 0; p += 8; } if (SEQ_ODD_BYTES > 0) { uint64_t x = 0; if (SEQ_ODD_BYTES > 0) x |= (uint64_t)p[0] << 56; if (SEQ_ODD_BYTES > 1) x |= (uint64_t)p[1] << 48; if (SEQ_ODD_BYTES > 2) x |= (uint64_t)p[2] << 40; if (SEQ_ODD_BYTES > 3) x |= (uint64_t)p[3] << 32; if (SEQ_ODD_BYTES > 4) x |= (uint64_t)p[4] << 24; if (SEQ_ODD_BYTES > 5) x |= (uint64_t)p[5] << 16; if (SEQ_ODD_BYTES > 6) x |= (uint64_t)p[6] << 8; if (SEQ_ODD_BYTES > 7) x |= (uint64_t)p[7] << 0; *px = x; } #endif return seq; } /** * Reverse the bytes by storing them in the reverse order of * loading, and reverse the words in the same fashion. */ static void storeReverse(uint8_t *dest, const Seq seq) { #if MAX_KMER > 96 # if WORDS_BIGENDIAN const uint64_t *s = reinterpret_cast(&seq); uint64_t *d = reinterpret_cast(dest); copy(s, s + SEQ_WORDS, reverse_iterator(d + SEQ_WORDS)); reverse(dest, dest + Kmer::NUM_BYTES); # else memcpy(dest, &seq, Kmer::NUM_BYTES); # endif #else const uint64_t *px = &seq.x[SEQ_WORDS-1]; # if WORDS_BIGENDIAN for (int i = 0; i < SEQ_FULL_WORDS; i++) { dest[0] = *px >> 0; dest[1] = *px >> 8; dest[2] = *px >> 16; dest[3] = *px >> 24; dest[4] = *px >> 32; dest[5] = *px >> 40; dest[6] = *px >> 48; dest[7] = *px >> 56; dest += 8; px--; } # else uint64_t *d = (uint64_t*)dest; for (int i = 0; i < SEQ_FULL_WORDS; i++) *d++ = *px--; dest = (uint8_t*)d; # endif if (SEQ_ODD_BYTES > 0) dest[0] = *px >> 0; if (SEQ_ODD_BYTES > 1) dest[1] = *px >> 8; if (SEQ_ODD_BYTES > 2) dest[2] = *px >> 16; if (SEQ_ODD_BYTES > 3) dest[3] = *px >> 24; if (SEQ_ODD_BYTES > 4) dest[4] = *px >> 32; if (SEQ_ODD_BYTES > 5) dest[5] = *px >> 40; if (SEQ_ODD_BYTES > 6) dest[6] = *px >> 48; if (SEQ_ODD_BYTES > 7) dest[7] = *px >> 56; #endif } /** Reverse-complement this sequence. */ void Kmer::reverseComplement() { Seq seq = load((uint8_t*)m_seq); // Complement the bits. if (!opt::colourSpace) seq.flip(); // Shift the bits flush to the right of the double word. seq >>= seq.size() - 2*s_length; storeReverse((uint8_t*)m_seq, seq); // Reverse the pairs of bits withing a byte. unsigned numBytes = bytes(); for (unsigned i = 0; i < numBytes; i++) m_seq[i] = swapBases[(uint8_t)m_seq[i]]; } void Kmer::setLastBase(extDirection dir, uint8_t base) { set(dir == SENSE ? s_length - 1 : 0, base); } /** Shift the sequence left and append a new base to the end. * @return the base shifted out */ uint8_t Kmer::shiftAppend(uint8_t base) { unsigned numBytes = bytes(); uint8_t shiftIn = base; for(int i = numBytes - 1; i >= 0; i--) { unsigned index = (unsigned)i == numBytes - 1 ? seqIndexToBaseIndex(s_length - 1) : 3; shiftIn = leftShiftByte(m_seq, i, index, shiftIn); } return shiftIn; } /** Shift the sequence right and prepend a new base at the front. * @return the base shifted out */ uint8_t Kmer::shiftPrepend(uint8_t base) { unsigned numBytes = bytes(); unsigned lastBaseByte = seqIndexToByteNumber(s_length - 1); unsigned lastBaseIndex = seqIndexToBaseIndex(s_length - 1); // save the last base (which gets shifted out) uint8_t lastBase = getBaseCode(m_seq, lastBaseByte, lastBaseIndex); // Zero the last base, which is required by compare. setBaseCode(m_seq, lastBaseByte, lastBaseIndex, 0); uint8_t shiftIn = base; for(unsigned i = 0; i <= numBytes - 1; i++) { // index is always zero unsigned index = 0; shiftIn = rightShiftByte(m_seq, i, index, shiftIn); } return lastBase; } uint8_t Kmer::leftShiftByte(char* pSeq, unsigned byteNum, unsigned index, uint8_t base) { // save the first base uint8_t outBase = (pSeq[byteNum] >> 6) & 0x3; // shift left one position pSeq[byteNum] <<= 2; // Set the new base setBaseCode(pSeq, byteNum, index, base); return outBase; } uint8_t Kmer::rightShiftByte(char* pSeq, unsigned byteNum, unsigned index, uint8_t base) { // save the last base uint8_t outBase = pSeq[byteNum] & 0x3; // shift right one position pSeq[byteNum] >>= 2; // add the new base setBaseCode(pSeq, byteNum, index, base); return outBase; } //Set a base by byte number/ sub index // beware, this does not check for out of bounds access static void setBaseCode(char* pSeq, unsigned byteNum, unsigned index, uint8_t base) { // shift the value into position unsigned shiftValue = 2*(3 - index); base <<= shiftValue; // clear the value uint8_t mask = 0x3; mask <<= shiftValue; mask = ~mask; pSeq[byteNum] &= mask; // set the appropriate value with an OR pSeq[byteNum] |= base; } /** Return the base at the specified index. */ uint8_t Kmer::at(unsigned i) const { assert(i < s_length); return getBaseCode(m_seq, seqIndexToByteNumber(i), seqIndexToBaseIndex(i)); } /** Set the base at the specified index. */ void Kmer::set(unsigned i, uint8_t base) { assert(i < s_length); setBaseCode(m_seq, seqIndexToByteNumber(i), seqIndexToBaseIndex(i), base); } uint8_t Kmer::getLastBaseChar() const { return codeToBase(at(s_length - 1)); } // get a base code by the byte number and sub index static uint8_t getBaseCode(const char* pSeq, unsigned byteNum, unsigned index) { unsigned shiftLen = 2 * (3 - index); return (pSeq[byteNum] >> shiftLen) & 0x3; } static unsigned seqIndexToByteNumber(unsigned seqIndex) { return seqIndex / 4; } static unsigned seqIndexToBaseIndex(unsigned seqIndex) { return seqIndex % 4; } /** Return true if this sequence is a palindrome. */ bool Kmer::isPalindrome() const { return s_length % 2 == 1 && !opt::colourSpace ? false : *this == ::reverseComplement(*this); } /** Return true if the length k-1 subsequence is a palindrome. */ bool Kmer::isPalindrome(extDirection dir) const { if (s_length % 2 == 0 && !opt::colourSpace) return false; Kmer seq(*this); if (dir == SENSE) seq.shiftAppend(0); else seq.setLastBase(SENSE, 0); Kmer rc(*this); rc.reverseComplement(); if (dir == SENSE) rc.setLastBase(SENSE, 0); else rc.shiftAppend(0); return seq == rc; } abyss-1.3.6/Common/Kmer.h000644 002433 001057 00000005036 12104026026 016653 0ustar00traymondassembly000000 000000 #ifndef Kmer_H #define Kmer_H 1 #include "config.h" #include "Sense.h" #include "Sequence.h" #include #include // for memcpy #include #include /** A k-mer. */ class Kmer { public: Kmer() { } explicit Kmer(const Sequence& seq); int compare(const Kmer& other) const; bool operator==(const Kmer& other) const { return compare(other) == 0; } bool operator!=(const Kmer& other) const { return compare(other) != 0; } bool operator<(const Kmer& other) const { return compare(other) < 0; } Sequence str() const; unsigned getCode() const; size_t getHashCode() const; static unsigned length() { return s_length; } /** Set the length of a k-mer. * This value is shared by all instances. */ static void setLength(unsigned length) { assert(length <= MAX_KMER); s_length = length; s_bytes = (length + 3) / 4; } void reverseComplement(); bool isPalindrome() const; bool isPalindrome(extDirection dir) const; void setLastBase(extDirection dir, uint8_t base); uint8_t getLastBaseChar() const; uint8_t shift(extDirection dir, uint8_t base = 0) { return dir == SENSE ? shiftAppend(base) : shiftPrepend(base); } /** Return the number of bytes needed. */ static unsigned bytes() { return s_bytes; } static unsigned serialSize() { return NUM_BYTES; } size_t serialize(void* dest) const { memcpy(dest, m_seq, sizeof m_seq); return sizeof m_seq; } size_t unserialize(const void* src) { memcpy(m_seq, src, sizeof m_seq); return sizeof m_seq; } friend std::ostream& operator<<(std::ostream& out, const Kmer& o) { return out << o.str(); } private: uint8_t shiftAppend(uint8_t base); uint8_t shiftPrepend(uint8_t base); uint8_t at(unsigned i) const; void set(unsigned i, uint8_t base); static uint8_t leftShiftByte(char* pSeq, unsigned byteNum, unsigned index, uint8_t base); static uint8_t rightShiftByte(char* pSeq, unsigned byteNum, unsigned index, uint8_t base); public: #if MAX_KMER > 96 # if MAX_KMER % 32 != 0 # error MAX_KMER must be a multiple of 32. # endif #else # if MAX_KMER % 4 != 0 # error MAX_KMER must be a multiple of 4. # endif #endif static const unsigned NUM_BYTES = MAX_KMER / 4; protected: static unsigned s_length; static unsigned s_bytes; char m_seq[NUM_BYTES]; }; /** Return the reverse complement of the specified k-mer. */ static inline Kmer reverseComplement(const Kmer& seq) { Kmer rc(seq); rc.reverseComplement(); return rc; } struct hashKmer { size_t operator()(const Kmer& o) const { return o.getHashCode(); } }; #endif abyss-1.3.6/Common/Log.cpp000644 002433 001057 00000000544 12015543262 017037 0ustar00traymondassembly000000 000000 #include "Log.h" #include "Common/Options.h" #include using namespace std; /** Print a log message if the verbosity level is at least the * specified level. */ ostream& logger(int level) { if (opt::verbose < level) { static ostream bitBucket(NULL); return bitBucket; } if (opt::rank >= 0) cout << opt::rank << ": "; return cout; } abyss-1.3.6/Common/Log.h000644 002433 001057 00000000134 12015543262 016477 0ustar00traymondassembly000000 000000 #ifndef LOG_H #define LOG_H 1 #include std::ostream& logger(int level); #endif abyss-1.3.6/Common/MemoryUtil.h000644 002433 001057 00000002070 12104026026 020056 0ustar00traymondassembly000000 000000 #ifndef MEMORYUTIL_H #define MEMORYUTIL_H 1 #include "config.h" #include #include #include // for sbrk #if __MACH__ # include // for mach_task_self # include // for task_info #endif /** Return the number of bytes used by the data and stack segments. * @return -1 on error */ static inline ssize_t getMemoryUsage() { #if __MACH__ struct task_basic_info t_info; mach_msg_type_number_t t_info_count = TASK_BASIC_INFO_COUNT; int status = task_info(mach_task_self(), TASK_BASIC_INFO, (task_info_t)&t_info, &t_info_count); assert(status == KERN_SUCCESS); return status == KERN_SUCCESS ? (ssize_t)t_info.virtual_size : -1; #elif HAVE_GETPAGESIZE std::ifstream in("/proc/self/statm"); size_t size, resident, share, text, lib, data; return in >> size >> resident >> share >> text >> lib >> data ? ssize_t(data * getpagesize()) : -1; #else /** Start of the data segment. */ static intptr_t sbrk0 = reinterpret_cast(sbrk(0)); return reinterpret_cast(sbrk(0)) - sbrk0; #endif } #endif abyss-1.3.6/Common/Options.cpp000644 002433 001057 00000000334 12104026026 017737 0ustar00traymondassembly000000 000000 #include "Common/Options.h" namespace opt { /** Colour space sequences */ bool colourSpace; /** MPI rank */ int rank = -1; /** Number of MPI processes */ int numProc = 1; /** Verbose output */ int verbose; } abyss-1.3.6/Common/Options.h000644 002433 001057 00000000417 11746352077 017431 0ustar00traymondassembly000000 000000 #ifndef COMMON_OPTIONS_H #define COMMON_OPTIONS_H 1 /** * Global variables that are mostly constant for the duration of the * execution of the program. */ namespace opt { extern bool colourSpace; extern int numProc; extern int rank; extern int verbose; } #endif abyss-1.3.6/Common/PMF.h000644 002433 001057 00000002510 12104026026 016371 0ustar00traymondassembly000000 000000 #ifndef PMF_H #define PMF_H 1 #include "Histogram.h" #include #include #include class Histogram; /** Probability mass function */ class PMF { public: /** Construct a PMF from a histogram. */ PMF(const Histogram& h) : m_dist(h.maximum() + 1), m_mean(h.mean()), m_stdDev(h.sd()) { unsigned count = h.size(); m_minp = (double)1 / count; for (size_t i = 0; i < m_dist.size(); i++) { unsigned n = h.count(i); m_dist[i] = n > 0 ? (double)n / count : m_minp; } } /** Return the probability of x. */ double operator[](size_t x) const { return x < m_dist.size() ? m_dist[x] : m_minp; } /** Return the minimum probability. */ double minProbability() const { return m_minp; } /** Return the minimum value. */ size_t minValue() const { return 0; } /** Return the maximum value. */ size_t maxValue() const { assert(!m_dist.empty()); return m_dist.size() - 1; } /** Return the mean of this distribution. */ double mean() const { return m_mean; } /** Return the standard deviation of the sampled mean * of n observations. */ double getSampleStdDev(unsigned n) const { return m_stdDev / sqrt(n); } private: std::vector m_dist; double m_mean; double m_stdDev; double m_minp; }; namespace std { template<> inline void swap(PMF&, PMF&) { assert(false); } } #endif abyss-1.3.6/Common/SAM.h000644 002433 001057 00000020325 12176307445 016413 0ustar00traymondassembly000000 000000 #ifndef SAM_H #define SAM_H 1 #include "config.h" // for SAM_SEQ_QUAL #include "Alignment.h" #include // for swap #include // for exit #include #include // for numeric_limits #include #include namespace opt { /** The minimal alignment size. */ static unsigned minAlign = 1; } /** A SAM alignment of a single query. */ struct SAMAlignment { std::string rname; int pos; unsigned short flag; unsigned short mapq; std::string cigar; /** Flag */ enum { /** the read is paired in sequencing, no matter whether it is * mapped in a pair */ FPAIRED = 1, /** the read is mapped in a proper pair */ FPROPER_PAIR = 2, /** the read itself is unmapped; conflictive with FPROPER_PAIR */ FUNMAP = 4, /** the mate is unmapped */ FMUNMAP = 8, /** the read is mapped to the reverse strand */ FREVERSE = 16, /** the mate is mapped to the reverse strand */ FMREVERSE = 32, /** this is read1 */ FREAD1 = 64, /** this is read2 */ FREAD2 = 128, /** not primary alignment */ FSECONDARY = 256, /** QC failure */ FQCFAIL = 512, /** optical or PCR duplicate */ FDUP = 1024, }; SAMAlignment() { } /** Consturct a single-end alignment. */ SAMAlignment(const Alignment& a) : rname(a.contig), pos(a.contig_start_pos), flag(a.isRC ? FREVERSE : 0), mapq(255) { unsigned qend = a.read_start_pos + a.align_length; int clip0 = a.read_start_pos; int clip1 = a.read_length - qend; assert(clip1 >= 0); if (a.isRC) std::swap(clip0, clip1); std::ostringstream s; if (clip0 > 0) s << clip0 << 'S'; s << a.align_length << 'M'; if (clip1 > 0) s << clip1 << 'S'; cigar = s.str(); } bool isPaired() const { return flag & FPAIRED; } bool isUnmapped() const { return flag & FUNMAP; } bool isMateUnmapped() const { return flag & FMUNMAP; } bool isReverse() const { return flag & FREVERSE; } bool isMateReverse() const { return flag & FMREVERSE; } bool isRead1() const { return flag & FREAD1; } bool isRead2() const { return flag & FREAD2; } /** The alignment coordinates of a gapped alignment. */ struct CigarCoord { /** The length of the query sequence. */ unsigned qlen; /** The start of the alignment on the query. */ unsigned qstart; /** The length of the alignment on the query. */ unsigned qspan; /** The length of the alignment on the target. */ unsigned tspan; /** Parse the specified CIGAR string. */ CigarCoord(const std::string& cigar) : qlen(0), qstart(0), qspan(0), tspan(0) { if (cigar == "*") return; std::istringstream in(cigar); bool first = true; unsigned len; char type; while (in >> len >> type) { switch (type) { case 'H': case 'S': if (first) qstart = len; qlen += len; break; case 'M': case 'X': case '=': qlen += len; qspan += len; tspan += len; break; case 'I': qlen += len; qspan += len; break; case 'D': case 'N': case 'P': tspan += len; break; default: std::cerr << "error: invalid CIGAR: `" << cigar << "'\n"; exit(EXIT_FAILURE); } first = false; } assert(in.eof()); } }; /** * Return the position of the first base of the query on the * target extrapolated from the start of the alignment. */ int targetAtQueryStart() const { CigarCoord a(cigar); assert(a.qstart + a.qspan <= a.qlen); return isReverse() ? pos + a.tspan + (a.qlen - a.qspan - a.qstart) : pos - a.qstart; } /** Parse the specified CIGAR string. * @return an alignment setting the fields read_start_pos, * align_length, and read_length. The other fields will be * uninitialized. */ static Alignment parseCigar(const std::string& cigar, bool isRC) { Alignment a; std::istringstream in(cigar); unsigned len; char type; in >> len >> type; assert(in.good()); unsigned clip0 = 0; switch (type) { case 'H': case 'S': clip0 = len; in >> len >> type; assert(in.good()); if (type != 'M') { // Ignore a malformatted CIGAR string whose first // non-clipping operation is not M. std::cerr << "warning: malformatted CIGAR: " << cigar << std::endl; in >> len >> type; assert(in.good()); } assert(type == 'M'); a.align_length = len; break; case 'M': a.align_length = len; break; default: std::cerr << "error: invalid CIGAR: `" << cigar << "'\n"; exit(EXIT_FAILURE); } unsigned qlen = clip0 + a.align_length; unsigned clip1 = 0; while (in >> len >> type) { switch (type) { case 'H': case 'S': case 'I': case 'M': case 'X': case '=': qlen += len; clip1 += len; break; case 'D': case 'N': case 'P': break; default: std::cerr << "error: invalid CIGAR: `" << cigar << "'\n"; exit(EXIT_FAILURE); } } a.read_start_pos = isRC ? clip1 : clip0; a.read_length = qlen; assert(in.eof()); return a; } operator Alignment() const { assert(~flag & FUNMAP); bool isRC = flag & FREVERSE; // strand of the query Alignment a = parseCigar(cigar, isRC); a.contig = rname; a.contig_start_pos = pos; a.isRC = isRC; return a; } }; /** A SAM alignment of a query and its mate. */ struct SAMRecord : SAMAlignment { std::string qname; std::string mrnm; int mpos; int isize; #if SAM_SEQ_QUAL std::string seq; std::string qual; #endif SAMRecord() { } /** Consturct a single-end alignment. */ explicit SAMRecord(const SAMAlignment& a, const std::string& qname = "*", #if SAM_SEQ_QUAL const std::string& seq = "*", const std::string& qual = "*" #else const std::string& /*seq*/ = "*", const std::string& /*qual*/ = "*" #endif ) : SAMAlignment(a), qname(qname), mrnm("*"), mpos(-1), isize(0) #if SAM_SEQ_QUAL , seq(seq), qual(qual) #endif { } /** Construct a paired-end alignment. */ SAMRecord(const Alignment& a0, const Alignment& a1) { *this = SAMRecord(a0); flag |= FPAIRED; if (a1.isRC) flag |= FMREVERSE; mrnm = a1.contig; mpos = a1.contig_start_pos; isize = a1.targetAtQueryStart() - a0.targetAtQueryStart(); } /** Set the mate mapping fields. */ void fixMate(const SAMAlignment& o) { flag &= ~(FPROPER_PAIR | FMUNMAP | FMREVERSE); flag |= FPAIRED; if (o.isUnmapped()) flag |= FMUNMAP; if (o.isReverse()) flag |= FMREVERSE; mrnm = o.rname; mpos = o.pos; isize = isMateUnmapped() ? 0 : o.targetAtQueryStart() - targetAtQueryStart(); // Fix unaligned mates if (!o.isUnmapped() && isUnmapped()) { rname = o.rname; pos = o.pos; } else if (o.isUnmapped() && !isUnmapped()) { mrnm = "="; mpos = pos; } } /** * Return the position of the first base of the mate query on the * target extrapolated from the start of the alignment. */ int mateTargetAtQueryStart() const { return targetAtQueryStart() + isize; } friend std::ostream& operator <<(std::ostream& out, const SAMRecord& o) { return out << o.qname << '\t' << o.flag << '\t' << o.rname << '\t' << (1 + o.pos) << '\t' << o.mapq << '\t' << o.cigar << '\t' << (o.mrnm == o.rname ? "=" : o.mrnm) << '\t' << (1 + o.mpos) << '\t' << o.isize #if SAM_SEQ_QUAL << '\t' << o.seq << '\t' << o.qual; #else << "\t*\t*"; #endif } friend std::istream& operator >>(std::istream& in, SAMRecord& o) { in >> o.qname >> o.flag >> o.rname >> o.pos >> o.mapq >> o.cigar >> o.mrnm >> o.mpos >> o.isize; #if SAM_SEQ_QUAL in >> o.seq >> o.qual; #endif in.ignore(std::numeric_limits::max(), '\n'); if (!in) return in; o.pos--; o.mpos--; if (o.mrnm == "=") o.mrnm = o.rname; // Set the paired flags if qname ends in /1 or /2. unsigned l = o.qname.length(); if (l >= 2 && o.qname[l-2] == '/') { switch (o.qname[l-1]) { case '1': o.flag |= FPAIRED | FREAD1; break; case '2': case '3': o.flag |= FPAIRED | FREAD2; break; default: return in; } o.qname.resize(l - 2); assert(!o.qname.empty()); } // Set the unmapped flag if the alignment is not long enough. CigarCoord a(o.cigar); if (a.qspan < opt::minAlign || a.tspan < opt::minAlign) o.flag |= FUNMAP; return in; } }; /** Set the mate mapping fields of a0 and a1. */ static inline void fixMate(SAMRecord& a0, SAMRecord& a1) { a0.fixMate(a1); a1.fixMate(a0); } #endif abyss-1.3.6/Common/Sense.h000644 002433 001057 00000000571 11746352077 017054 0ustar00traymondassembly000000 000000 #ifndef SENSE_H #define SENSE_H 1 #include enum extDirection { SENSE = 0, ANTISENSE = 1, NUM_DIRECTIONS }; static inline extDirection operator !(extDirection dir) { return dir == SENSE ? ANTISENSE : SENSE; } static inline extDirection& operator ++(extDirection& dir) { assert(dir == SENSE || dir == ANTISENSE); return dir = extDirection(dir + 1); } #endif abyss-1.3.6/Common/SeqExt.cpp000644 002433 001057 00000000661 11746352077 017543 0ustar00traymondassembly000000 000000 #include "SeqExt.h" #include "Common/Options.h" #include /** Return the complementary adjacency. * If the assembly is in colour space, this is a no-op. */ SeqExt SeqExt::complement() const { static const uint8_t complements[16] = { 0x0, 0x8, 0x4, 0xc, 0x2, 0xa, 0x6, 0xe, 0x1, 0x9, 0x5, 0xd, 0x3, 0xb, 0x7, 0xf }; assert(m_record < 1< #include #include static const unsigned NUM_BASES = 4; /** The adjacent vertices of a Kmer. */ class SeqExt { public: SeqExt() : m_record(0) { }; explicit SeqExt(uint8_t base) : m_record(1< 0; } /** Return whether this kmer has more than one adjacent kmer. */ bool isAmbiguous() const { bool powerOfTwo = (m_record & (m_record - 1)) > 0; return m_record > 0 && powerOfTwo; } /** Return the complementary adjacency. */ SeqExt complement() const; SeqExt operator ~() const { return complement(); } friend std::ostream& operator <<(std::ostream& out, const SeqExt& o) { assert(o.m_record < 1< #include #include #include // for abort #include #include using namespace std; enum { A, C, G, T }; static const int cstont[4][4] = { { A, C, G, T }, { C, A, T, G }, { G, T, A, C }, { T, G, C, A } }; /** Return the complement of the specified nucleotide. */ char complementBaseChar(char c) { char rc; switch (toupper(c)) { case 'A': rc = 'T'; break; case 'C': rc = 'G'; break; case 'G': rc = 'C'; break; case 'T': rc = 'A'; break; case 'N': rc = 'N'; break; case '.': rc = '.'; break; case 'M': rc = 'K'; break; // A or C case 'R': rc = 'Y'; break; // A or G case 'W': rc = 'W'; break; // A or T case 'S': rc = 'S'; break; // C or G case 'Y': rc = 'R'; break; // C or T case 'K': rc = 'M'; break; // G or T case 'V': rc = 'B'; break; // A or C or G case 'H': rc = 'D'; break; // A or C or T case 'D': rc = 'H'; break; // A or G or T case 'B': rc = 'V'; break; // C or G or T default: cerr << "error: unexpected character: `" << c << "'\n"; assert(false); abort(); } return islower(c) ? tolower(rc) : rc; } /** Return the reverse complement of the specified sequence. */ Sequence reverseComplement(const Sequence& s) { Sequence rc(s); reverse(rc.begin(), rc.end()); if (!opt::colourSpace) transform(rc.begin(), rc.end(), rc.begin(), complementBaseChar); return rc; } static const uint8_t b2C[256] = { 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, //0 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, //1 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, //2 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0x00, 0x01, 0x02, 0x03, 0xFF, 0xFF, 0xFF, 0xFF, //3 0 1 2 3 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0x00, 0xFF, 0x01, 0xFF, 0xFF, 0xFF, 0x02, //4 A C G 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0x03, 0xFF, 0xFF, 0xFF, //5 T 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, //6 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, //7 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, //8 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, //9 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, //A 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, //B 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, //C 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, //D 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, //E 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, //F 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF }; /** Return the base enumeration for the specified character. */ uint8_t baseToCode(char base) { uint8_t r = b2C[unsigned(base)]; if (r != 0xFF) return r; cerr << "error: unexpected character: '" << base << "'\n"; assert(false); abort(); } char codeToBase(uint8_t code) { assert(code < 4); return (opt::colourSpace ? "0123" : "ACGT")[code]; } char colourToNucleotideSpace(char anchor, char cs) { return cs == '.' ? 'N' : "ACGT"[cstont[baseToCode(anchor)][baseToCode(cs)]]; } Sequence colourToNucleotideSpace(char anchor, const Sequence& seq) { int seed = baseToCode(anchor); ostringstream s; s << anchor; for (string::const_iterator it = seq.begin(); it != seq.end(); ++it) { seed = cstont[seed][baseToCode(*it)]; s << codeToBase(seed); } return s.str(); } char nucleotideToColourSpace(char a, char b) { if (toupper(a) == 'N' || toupper(b) == 'N') return islower(a) || islower(b) ? 'n' : 'N'; return "0123"[cstont[baseToCode(a)][baseToCode(b)]]; } /** Convert the specified ambiguity code to a bitmask. */ unsigned ambiguityToBitmask(char c) { if (isdigit(c)) // colour space return 1 << baseToCode(c); static const unsigned ambiguityToBitmaskTable[26] = { 0x1, // 'A' ---A 0xe, // 'B' TGC- 0x2, // 'C' --C- 0xd, // 'D' TG-A 0x0, // 'E' 0x0, // 'F' 0x4, // 'G' -G-- 0xb, // 'H' T-CA 0x0, // 'I' 0x0, // 'J' 0xc, // 'K' TG-- 0x0, // 'L' 0x3, // 'M' --CA 0xf, // 'N' ACGT 0x0, // 'O' 0x0, // 'P' 0x0, // 'Q' 0x5, // 'R' -G-A 0x6, // 'S' -GC- 0x8, // 'T' T--- 0x0, // 'U' 0x7, // 'V' -GCA 0x9, // 'W' T--A 0x0, // 'X' 0xa, // 'Y' T-C- 0x0, // 'Z' }; unsigned i = toupper(c) - 'A'; assert(i < 26); unsigned x = ambiguityToBitmaskTable[i]; assert(x > 0); return x; } /** Convert the specified bitmask to an ambiguity code. */ unsigned bitmaskToAmbiguity(unsigned x) { static const char bitmaskToAmbiguityTable[16] = { 'N', //---- 'A', //---A 'C', //--C- 'M', //--CA 'G', //-G-- 'R', //-G-A 'S', //-GC- 'V', //-GCA 'T', //T--- 'W', //T--A 'Y', //T-C- 'H', //T-CA 'K', //TG-- 'D', //TG-A 'B', //TGC- 'N', //TGCA }; assert(x < 16); return bitmaskToAmbiguityTable[x]; } abyss-1.3.6/Common/Sequence.h000644 002433 001057 00000002552 12104026026 017525 0ustar00traymondassembly000000 000000 #ifndef SEQUENCE_H #define SEQUENCE_H 1 #include #include typedef std::string Sequence; Sequence reverseComplement(const Sequence& s); Sequence colourToNucleotideSpace(char anchor, const Sequence& seq); char colourToNucleotideSpace(char anchor, char cs); char nucleotideToColourSpace(char a, char b); uint8_t baseToCode(char base); char codeToBase(uint8_t code); /** Return true if c is one of [ACGTacgt]. */ static inline bool isACGT(char c) { return c == 'A' || c == 'C' || c == 'G' || c == 'T' || c == 'a' || c == 'c' || c == 'g' || c == 't'; } unsigned ambiguityToBitmask(char c); unsigned bitmaskToAmbiguity(unsigned x); /** Return the bitwise-and of the specified ambiguity codes. */ static inline char ambiguityAnd(char ca, char cb) { char c = bitmaskToAmbiguity( ambiguityToBitmask(ca) & ambiguityToBitmask(cb)); return islower(ca) && islower(cb) ? tolower(c) : c; } /** Return the bitwise-or of the specified ambiguity codes. */ static inline char ambiguityOr(char ca, char cb) { char c = bitmaskToAmbiguity( ambiguityToBitmask(ca) | ambiguityToBitmask(cb)); return islower(ca) || islower(cb) ? tolower(c) : c; } /** Return whether one ambiguity code is a subset of the other. */ static inline bool ambiguityIsSubset(char a, char b) { char intersection = ambiguityAnd(a, b); return intersection == a || intersection == b; } #endif abyss-1.3.6/Common/SignalHandler.cpp000644 002433 001057 00000002573 12016774060 021040 0ustar00traymondassembly000000 000000 /** * Signal handling code, particularly SIGCHLD. */ #include "SignalHandler.h" #include #include #include // for perror #include #include #include #include using namespace std; /** Print the specified exit status. */ static void printStatus(pid_t pid, int status) { if (WIFEXITED(status)) cerr << "PID " << pid << " exited with status " << WEXITSTATUS(status) << endl; else if (WIFSIGNALED(status)) cerr << "PID " << pid << " killed by signal " << WTERMSIG(status) << endl; else cerr << "PID " << pid << " exited with code " << status << endl; } /** SIGCHLD handler. Reap child processes and report an error if any * fail. */ static void sigchldHandler(int sig) { assert(sig == SIGCHLD); (void)sig; pid_t pid; int status; while ((pid = waitpid(-1, &status, WNOHANG)) > 0) { // Writing to cerr in a signal handler is not allowed, but // we're about to exit and an error message would be really // helpful. if (status != 0) { printStatus(pid, status); exit(EXIT_FAILURE); } } if (pid == -1 && errno != ECHILD) { perror("waitpid"); exit(EXIT_FAILURE); } } /** Install a handler for SIGCHLD. */ void signalInit() { struct sigaction action; action.sa_handler = sigchldHandler; sigemptyset(&action.sa_mask); action.sa_flags = SA_RESTART; sigaction(SIGCHLD, &action, NULL); } abyss-1.3.6/Common/SignalHandler.h000644 002433 001057 00000000116 11746352077 020505 0ustar00traymondassembly000000 000000 #ifndef SIGNALHANDLER_H #define SIGNALHANDLER_H 1 void signalInit(); #endif abyss-1.3.6/Common/StringUtil.h000644 002433 001057 00000003674 12104026026 020067 0ustar00traymondassembly000000 000000 #ifndef STRINGUTIL_H #define STRINGUTIL_H 1 #include #include #include #include /** Return the last character of s and remove it. */ static inline char chop(std::string& s) { assert(s.length() > 1); unsigned back = s.length() - 1; char c = s[back]; s.erase(back); return c; } /** If the last character of s is c, remove it and return true. */ static inline bool chomp(std::string& s, char c = '\n') { unsigned back = s.length() - 1; if (!s.empty() && s[back] == c) { s.erase(back); return true; } else return false; } /** Return the SI representation of n. */ static inline std::string toSI(double n) { std::ostringstream s; s << std::setprecision(3); if (n < 1e3) s << n << ' '; else if (n < 1e6) s << n/1e3 << " k"; else if (n < 1e9) s << n/1e6 << " M"; else if (n < 1e12) s << n/1e9 << " G"; else s << n/1e12 << " T"; return s.str(); } /** Return the engineering string representation of n. */ template static inline std::string toEng(T n) { std::ostringstream s; s << std::setprecision(4); if (n < 10000000) s << n; else if (n < 1e9) s << n/1e6 << "e6"; else if (n < 1e12) s << n/1e9 << "e9"; else s << n/1e12 << "e12"; return s.str(); } /** Return true if the second string is a prefix of the string s. */ template bool startsWith(const std::string& s, const char (&prefix)[N]) { size_t n = N - 1; return s.size() > n && equal(s.begin(), s.begin() + n, prefix); } /** Return true if the second string is a suffix of the string s. */ template bool endsWith(const std::string& s, const char (&suffix)[N]) { size_t n = N - 1; return s.size() > n && equal(s.end() - n, s.end(), suffix); } /** Return true if the second string is a suffix of the string s. */ static inline bool endsWith(const std::string& s, const std::string& suffix) { size_t n = suffix.size(); return s.size() > n && equal(s.end() - n, s.end(), suffix.begin()); } #endif abyss-1.3.6/Common/SuffixArray.h000644 002433 001057 00000004035 11746352100 020224 0ustar00traymondassembly000000 000000 #ifndef SUFFIXARRAY_H #define SUFFIXARRAY_H 1 #include "ConstString.h" #include "ContigNode.h" #include #include #include #include /** A suffix array augmented with a mapped value type. */ class SuffixArray { public: typedef cstring key_type; typedef ContigNode mapped_type; typedef std::pair value_type; typedef std::vector::const_iterator const_iterator; /** Construct an empty suffix array. */ SuffixArray(unsigned minOverlap) : m_minOverlap(minOverlap), m_dirty(false) { } /** Insert the specified sequence into this suffix array. */ template void insert(const T& seq, const mapped_type& data) { m_dirty = true; typedef typename T::const_pointer It; It last = &seq[seq.size() - m_minOverlap + 1]; for (It it = &seq[1]; it < last; ++it) m_data.push_back(value_type(it, data)); } /** Insert the specified sequence into this suffix array. */ template void insert(const std::pair& x) { insert(x.first, x.second); } /** Construct the suffix array. */ void construct() { if (m_dirty) sort(m_data.begin(), m_data.end()); m_dirty = false; } /** Find all the elements whose suffix matches the prefix of the * specified query sequence. * @return the range of matches as a pair of iterators */ template std::pair equal_range( const T& seq) const { assert(!m_dirty); return std::equal_range(m_data.begin(), m_data.end(), key_type(&seq[0]), Compare()); } size_t size() const { return m_data.size(); } const_iterator begin() const { return m_data.begin(); } const_iterator end() const { return m_data.end(); } private: /** Comparison functor. */ struct Compare { bool operator()(const value_type& a, const key_type& b) const { return a.first < b; } bool operator()(const key_type& a, const value_type& b) const { return a < b.first; } }; unsigned m_minOverlap; bool m_dirty; std::vector m_data; }; #endif abyss-1.3.6/Common/Timer.cpp000644 002433 001057 00000000544 11746352100 017375 0ustar00traymondassembly000000 000000 #include "Timer.h" #include "Log.h" #include using namespace std; // Constructor starts the timer Timer::Timer(string funcString) : m_funcStr(funcString), m_start(clock()) { } // Destructor stops it and prints Timer::~Timer() { logger(2) << m_funcStr << ": " << setprecision(3) << (double)(clock() - m_start) / CLOCKS_PER_SEC << " s\n"; } abyss-1.3.6/Common/Timer.h000644 002433 001057 00000000460 12104026026 017031 0ustar00traymondassembly000000 000000 #ifndef TIMER_H #define TIMER_H 1 #include /** * Time the duration between the construction and destruction of this * timer object and log that duration. */ class Timer { public: Timer(std::string funcString); ~Timer(); private: std::string m_funcStr; clock_t m_start; }; #endif abyss-1.3.6/Common/Uncompress.cpp000644 002433 001057 00000012500 12114244743 020451 0ustar00traymondassembly000000 000000 /** Uncompress input files using pipes. * Hook the standard file opening functions, open, fopen and fopen64. * If the extension of the file being opened indicates the file is * compressed (.gz, .bz2, .xz), open a pipe to a program that * decompresses that file (gunzip, bunzip2 or xzdec) and return a * handle to the open pipe. * @author Shaun Jackman */ #include "config.h" #if HAVE_LIBDL #include "Fcontrol.h" #include "SignalHandler.h" #include "StringUtil.h" #include #include // for perror #include #include #include #include using namespace std; static const char* wgetExec(const string& path) { return startsWith(path, "http://") ? "wget -O-" : startsWith(path, "https://") ? "wget -O-" : startsWith(path, "ftp://") ? "wget -O-" : NULL; } static const char* zcatExec(const string& path) { return endsWith(path, ".ar") ? "ar -p" : endsWith(path, ".tar") ? "tar -xOf" : endsWith(path, ".tar.Z") ? "tar -zxOf" : endsWith(path, ".tar.gz") ? "tar -zxOf" : endsWith(path, ".tar.bz2") ? "tar -jxOf" : endsWith(path, ".tar.xz") ? "tar --use-compress-program=xzdec -xOf" : endsWith(path, ".Z") ? "gunzip -c" : endsWith(path, ".gz") ? "gunzip -c" : endsWith(path, ".bz2") ? "bunzip2 -c" : endsWith(path, ".xz") ? "xzdec -c" : endsWith(path, ".zip") ? "unzip -p" : endsWith(path, ".bam") ? "samtools view -h" : endsWith(path, ".jf") ? "jellyfish dump" : endsWith(path, ".jfq") ? "jellyfish qdump" : endsWith(path, ".sra") ? "fastq-dump -Z --split-spot" : endsWith(path, ".url") ? "wget -O- -i" : NULL; } extern "C" { /** Open a pipe to uncompress the specified file. * Not thread safe. * @return a file descriptor */ static int uncompress(const char *path) { const char *wget = wgetExec(path); const char *zcat = wget != NULL ? wget : zcatExec(path); assert(zcat != NULL); int fd[2]; if (pipe(fd) == -1) return -1; int err = setCloexec(fd[0]); assert(err == 0); (void)err; char arg0[16], arg1[16], arg2[16]; int n = sscanf(zcat, "%s %s %s", arg0, arg1, arg2); assert(n == 2 || n == 3); /* It would be more portable to use fork than vfork, but fork can * fail with ENOMEM when the process calling fork is using a lot * of memory. A workaround for this problem is to set * sysctl vm.overcommit_memory=1 */ #if HAVE_WORKING_VFORK pid_t pid = vfork(); #else pid_t pid = fork(); #endif if (pid == -1) return -1; if (pid == 0) { dup2(fd[1], STDOUT_FILENO); close(fd[1]); if (n == 2) execlp(arg0, arg0, arg1, path, NULL); else execlp(arg0, arg0, arg1, arg2, path, NULL); // Calling perror after vfork is not allowed, but we're about // to exit and an error message would be really helpful. perror(arg0); _exit(EXIT_FAILURE); } else { close(fd[1]); return fd[0]; } } /** Open a pipe to uncompress the specified file. * @return a FILE pointer */ static FILE* funcompress(const char* path) { int fd = uncompress(path); if (fd == -1) { perror(path); exit(EXIT_FAILURE); } return fdopen(fd, "r"); } typedef FILE* (*fopen_t)(const char *path, const char *mode); /** If the specified file is compressed, return a pipe that * uncompresses it. */ FILE *fopen(const char *path, const char *mode) { static fopen_t real_fopen; if (real_fopen == NULL) real_fopen = (fopen_t)dlsym(RTLD_NEXT, "fopen"); if (real_fopen == NULL) { fprintf(stderr, "error: dlsym fopen: %s\n", dlerror()); exit(EXIT_FAILURE); } // open a web address if (wgetExec(path) != NULL) return funcompress(path); // to check if the file exists, we need to attempt to open it FILE* stream = real_fopen(path, mode); if (string(mode) != "r" || !stream || zcatExec(path) == NULL) return stream; else { fclose(stream); return funcompress(path); } } /** If the specified file is compressed, return a pipe that * uncompresses it. */ FILE *fopen64(const char *path, const char *mode) { static fopen_t real_fopen64; if (real_fopen64 == NULL) real_fopen64 = (fopen_t)dlsym(RTLD_NEXT, "fopen64"); if (real_fopen64 == NULL) { fprintf(stderr, "error: dlsym fopen64: %s\n", dlerror()); exit(EXIT_FAILURE); } // open a web address if (wgetExec(path) != NULL) return funcompress(path); // to check if the file exists, we need to attempt to open it FILE* stream = real_fopen64(path, mode); if (string(mode) != "r" || !stream || zcatExec(path) == NULL) return stream; else { fclose(stream); return funcompress(path); } } typedef int (*open_t)(const char *path, int flags, mode_t mode); /** If the specified file is compressed, return a pipe that * uncompresses it. */ int open(const char *path, int flags, mode_t mode) { static open_t real_open; if (real_open == NULL) real_open = (open_t)dlsym(RTLD_NEXT, "open"); if (real_open == NULL) { fprintf(stderr, "error: dlsym open: %s\n", dlerror()); exit(EXIT_FAILURE); } // open a web address if (wgetExec(path) != NULL) return uncompress(path); // to check if the file exists, we need to attempt to open it int filedesc = real_open(path, flags, mode); if (mode != ios_base::in || filedesc < 0 || zcatExec(path) == NULL) return filedesc; else { close(filedesc); return uncompress(path); } } } // extern "C" #endif // HAVE_LIBDL /** Initialize the uncompress module. */ bool uncompress_init() { #if HAVE_LIBDL signalInit(); #endif return HAVE_LIBDL; } abyss-1.3.6/Common/Uncompress.h000644 002433 001057 00000000415 12104026026 020107 0ustar00traymondassembly000000 000000 #ifndef UNCOMPRESS_H #define UNCOMPRESS_H 1 bool uncompress_init(); namespace { const bool uncompressInitialized = uncompress_init(); bool getUncompressInitialized() __attribute__((unused)); bool getUncompressInitialized() { return uncompressInitialized; } } #endif abyss-1.3.6/Common/UnorderedMap.h000644 002433 001057 00000000644 12104026026 020342 0ustar00traymondassembly000000 000000 #ifndef UNORDEREDMAP_H #define UNORDEREDMAP_H 1 #include "config.h" #if HAVE_UNORDERED_MAP # include using std::unordered_map; using std::unordered_multimap; #elif HAVE_TR1_UNORDERED_MAP # include using std::tr1::unordered_map; using std::tr1::unordered_multimap; #else # include using boost::unordered_map; using boost::unordered_multimap; #endif #endif abyss-1.3.6/Common/cholesky.hpp000644 002433 001057 00000015402 12104026026 020134 0ustar00traymondassembly000000 000000 /** -*- c++ -*- \file cholesky.hpp \brief cholesky decomposition */ /* - begin : 2005-08-24 - copyright : (C) 2005 by Gunter Winkler, Konstantin Kutzkow - email : guwi17@gmx.de This library is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version. This library 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 Lesser General Public License for more details. You should have received a copy of the GNU Lesser General Public License along with this library; if not, write to the Free Software Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA */ #ifndef _H_CHOLESKY_HPP_ #define _H_CHOLESKY_HPP_ #include #include #include #include #include #include #include #include namespace ublas = boost::numeric::ublas; /** \brief decompose the symmetric positive definit matrix A into product L L^T. * * \param MATRIX type of input matrix * \param TRIA type of lower triangular output matrix * \param A square symmetric positive definite input matrix (only the lower triangle is accessed) * \param L lower triangular output matrix * \return nonzero if decompositon fails (the value ist 1 + the numer of the failing row) */ template < class MATRIX, class TRIA > size_t cholesky_decompose(const MATRIX& A, TRIA& L) { using namespace ublas; typedef typename MATRIX::value_type T; assert( A.size1() == A.size2() ); assert( A.size1() == L.size1() ); assert( A.size2() == L.size2() ); const size_t n = A.size1(); for (size_t k=0 ; k < n; k++) { double qL_kk = A(k,k) - inner_prod( project( row(L, k), range(0, k) ), project( row(L, k), range(0, k) ) ); if (qL_kk <= 0) { return 1 + k; } else { double L_kk = sqrt( qL_kk ); L(k,k) = L_kk; matrix_column cLk(L, k); project( cLk, range(k+1, n) ) = ( project( column(A, k), range(k+1, n) ) - prod( project(L, range(k+1, n), range(0, k)), project(row(L, k), range(0, k) ) ) ) / L_kk; } } return 0; } /** \brief decompose the symmetric positive definit matrix A into product L L^T. * * \param MATRIX type of matrix A * \param A input: square symmetric positive definite matrix (only the lower triangle is accessed) * \param A output: the lower triangle of A is replaced by the cholesky factor * \return nonzero if decompositon fails (the value ist 1 + the numer of the failing row) */ template < class MATRIX > size_t cholesky_decompose(MATRIX& A) { using namespace ublas; typedef typename MATRIX::value_type T; const MATRIX& A_c(A); const size_t n = A.size1(); for (size_t k=0 ; k < n; k++) { double qL_kk = A_c(k,k) - inner_prod( project( row(A_c, k), range(0, k) ), project( row(A_c, k), range(0, k) ) ); if (qL_kk <= 0) { return 1 + k; } else { double L_kk = sqrt( qL_kk ); matrix_column cLk(A, k); project( cLk, range(k+1, n) ) = ( project( column(A_c, k), range(k+1, n) ) - prod( project(A_c, range(k+1, n), range(0, k)), project(row(A_c, k), range(0, k) ) ) ) / L_kk; A(k,k) = L_kk; } } return 0; } #if 0 using namespace ublas; // Operations: // n * (n - 1) / 2 + n = n * (n + 1) / 2 multiplications, // n * (n - 1) / 2 additions // Dense (proxy) case template void inplace_solve (const matrix_expression &e1, vector_expression &e2, lower_tag, column_major_tag) { std::cout << " is_lc "; typedef typename E2::size_type size_type; typedef typename E2::difference_type difference_type; typedef typename E2::value_type value_type; BOOST_UBLAS_CHECK (e1 ().size1 () == e1 ().size2 (), bad_size ()); BOOST_UBLAS_CHECK (e1 ().size2 () == e2 ().size (), bad_size ()); size_type size = e2 ().size (); for (size_type n = 0; n < size; ++ n) { #ifndef BOOST_UBLAS_SINGULAR_CHECK BOOST_UBLAS_CHECK (e1 () (n, n) != value_type/*zero*/(), singular ()); #else if (e1 () (n, n) == value_type/*zero*/()) singular ().raise (); #endif value_type t = e2 () (n) / e1 () (n, n); e2 () (n) = t; if (t != value_type/*zero*/()) { project( e2 (), range(n+1, size) ) .minus_assign( t * project( column( e1 (), n), range(n+1, size) ) ); } } } #endif /** \brief decompose the symmetric positive definit matrix A into product L L^T. * * \param MATRIX type of matrix A * \param A input: square symmetric positive definite matrix (only the lower triangle is accessed) * \param A output: the lower triangle of A is replaced by the cholesky factor * \return nonzero if decompositon fails (the value ist 1 + the numer of the failing row) */ template < class MATRIX > size_t incomplete_cholesky_decompose(MATRIX& A) { using namespace ublas; typedef typename MATRIX::value_type T; // read access to a const matrix is faster const MATRIX& A_c(A); const size_t n = A.size1(); for (size_t k=0 ; k < n; k++) { double qL_kk = A_c(k,k) - inner_prod( project( row( A_c, k ), range(0, k) ), project( row( A_c, k ), range(0, k) ) ); if (qL_kk <= 0) { return 1 + k; } else { double L_kk = sqrt( qL_kk ); // aktualisieren for (size_t i = k+1; i < A.size1(); ++i) { T* Aik = A.find_element(i, k); if (Aik != 0) { *Aik = ( *Aik - inner_prod( project( row( A_c, k ), range(0, k) ), project( row( A_c, i ), range(0, k) ) ) ) / L_kk; } } A(k,k) = L_kk; } } return 0; } /** \brief solve system L L^T x = b inplace * * \param L a triangular matrix * \param x input: right hand side b; output: solution x */ template < class TRIA, class VEC > void cholesky_solve(const TRIA& L, VEC& x, ublas::lower) { using namespace ublas; // ::inplace_solve(L, x, lower_tag(), typename TRIA::orientation_category () ); inplace_solve(L, x, lower_tag() ); inplace_solve(trans(L), x, upper_tag()); } #endif abyss-1.3.6/Common/city.cc000644 002433 001057 00000035542 12104250113 017064 0ustar00traymondassembly000000 000000 // Copyright (c) 2011 Google, Inc. // // 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. // // CityHash, by Geoff Pike and Jyrki Alakuijala // // This file provides CityHash64() and related functions. // // It's probably possible to create even faster hash functions by // writing a program that systematically explores some of the space of // possible hash functions, by using SIMD instructions, or by // compromising on hash quality. #include "config.h" #include #include #include // for memcpy and memset using namespace std; static uint64 UNALIGNED_LOAD64(const char *p) { uint64 result; memcpy(&result, p, sizeof(result)); return result; } static uint32 UNALIGNED_LOAD32(const char *p) { uint32 result; memcpy(&result, p, sizeof(result)); return result; } #if !defined(WORDS_BIGENDIAN) #define uint32_in_expected_order(x) (x) #define uint64_in_expected_order(x) (x) #else #ifdef _MSC_VER #include #define bswap_32(x) _byteswap_ulong(x) #define bswap_64(x) _byteswap_uint64(x) #elif defined(__APPLE__) // Mac OS X / Darwin features #include #define bswap_32(x) OSSwapInt32(x) #define bswap_64(x) OSSwapInt64(x) #else #include #endif #define uint32_in_expected_order(x) (bswap_32(x)) #define uint64_in_expected_order(x) (bswap_64(x)) #endif // WORDS_BIGENDIAN #if !defined(LIKELY) #if HAVE_BUILTIN_EXPECT #define LIKELY(x) (__builtin_expect(!!(x), 1)) #else #define LIKELY(x) (x) #endif #endif static uint64 Fetch64(const char *p) { return uint64_in_expected_order(UNALIGNED_LOAD64(p)); } static uint32 Fetch32(const char *p) { return uint32_in_expected_order(UNALIGNED_LOAD32(p)); } // Some primes between 2^63 and 2^64 for various uses. static const uint64 k0 = 0xc3a5c85c97cb3127ULL; static const uint64 k1 = 0xb492b66fbe98f273ULL; static const uint64 k2 = 0x9ae16a3b2f90404fULL; static const uint64 k3 = 0xc949d7c7509e6557ULL; // Bitwise right rotate. Normally this will compile to a single // instruction, especially if the shift is a manifest constant. static uint64 Rotate(uint64 val, int shift) { // Avoid shifting by 64: doing so yields an undefined result. return shift == 0 ? val : ((val >> shift) | (val << (64 - shift))); } // Equivalent to Rotate(), but requires the second arg to be non-zero. // On x86-64, and probably others, it's possible for this to compile // to a single instruction if both args are already in registers. static uint64 RotateByAtLeast1(uint64 val, int shift) { return (val >> shift) | (val << (64 - shift)); } static uint64 ShiftMix(uint64 val) { return val ^ (val >> 47); } static uint64 HashLen16(uint64 u, uint64 v) { return Hash128to64(uint128(u, v)); } static uint64 HashLen0to16(const char *s, size_t len) { if (len > 8) { uint64 a = Fetch64(s); uint64 b = Fetch64(s + len - 8); return HashLen16(a, RotateByAtLeast1(b + len, len)) ^ b; } if (len >= 4) { uint64 a = Fetch32(s); return HashLen16(len + (a << 3), Fetch32(s + len - 4)); } if (len > 0) { uint8 a = s[0]; uint8 b = s[len >> 1]; uint8 c = s[len - 1]; uint32 y = static_cast(a) + (static_cast(b) << 8); uint32 z = len + (static_cast(c) << 2); return ShiftMix(y * k2 ^ z * k3) * k2; } return k2; } // This probably works well for 16-byte strings as well, but it may be overkill // in that case. static uint64 HashLen17to32(const char *s, size_t len) { uint64 a = Fetch64(s) * k1; uint64 b = Fetch64(s + 8); uint64 c = Fetch64(s + len - 8) * k2; uint64 d = Fetch64(s + len - 16) * k0; return HashLen16(Rotate(a - b, 43) + Rotate(c, 30) + d, a + Rotate(b ^ k3, 20) - c + len); } // Return a 16-byte hash for 48 bytes. Quick and dirty. // Callers do best to use "random-looking" values for a and b. static pair WeakHashLen32WithSeeds( uint64 w, uint64 x, uint64 y, uint64 z, uint64 a, uint64 b) { a += w; b = Rotate(b + a + z, 21); uint64 c = a; a += x; a += y; b += Rotate(a, 44); return make_pair(a + z, b + c); } // Return a 16-byte hash for s[0] ... s[31], a, and b. Quick and dirty. static pair WeakHashLen32WithSeeds( const char* s, uint64 a, uint64 b) { return WeakHashLen32WithSeeds(Fetch64(s), Fetch64(s + 8), Fetch64(s + 16), Fetch64(s + 24), a, b); } // Return an 8-byte hash for 33 to 64 bytes. static uint64 HashLen33to64(const char *s, size_t len) { uint64 z = Fetch64(s + 24); uint64 a = Fetch64(s) + (len + Fetch64(s + len - 16)) * k0; uint64 b = Rotate(a + z, 52); uint64 c = Rotate(a, 37); a += Fetch64(s + 8); c += Rotate(a, 7); a += Fetch64(s + 16); uint64 vf = a + z; uint64 vs = b + Rotate(a, 31) + c; a = Fetch64(s + 16) + Fetch64(s + len - 32); z = Fetch64(s + len - 8); b = Rotate(a + z, 52); c = Rotate(a, 37); a += Fetch64(s + len - 24); c += Rotate(a, 7); a += Fetch64(s + len - 16); uint64 wf = a + z; uint64 ws = b + Rotate(a, 31) + c; uint64 r = ShiftMix((vf + ws) * k2 + (wf + vs) * k0); return ShiftMix(r * k0 + vs) * k2; } uint64 CityHash64(const char *s, size_t len) { if (len <= 32) { if (len <= 16) { return HashLen0to16(s, len); } else { return HashLen17to32(s, len); } } else if (len <= 64) { return HashLen33to64(s, len); } // For strings over 64 bytes we hash the end first, and then as we // loop we keep 56 bytes of state: v, w, x, y, and z. uint64 x = Fetch64(s + len - 40); uint64 y = Fetch64(s + len - 16) + Fetch64(s + len - 56); uint64 z = HashLen16(Fetch64(s + len - 48) + len, Fetch64(s + len - 24)); pair v = WeakHashLen32WithSeeds(s + len - 64, len, z); pair w = WeakHashLen32WithSeeds(s + len - 32, y + k1, x); x = x * k1 + Fetch64(s); // Decrease len to the nearest multiple of 64, and operate on 64-byte chunks. len = (len - 1) & ~static_cast(63); do { x = Rotate(x + y + v.first + Fetch64(s + 8), 37) * k1; y = Rotate(y + v.second + Fetch64(s + 48), 42) * k1; x ^= w.second; y += v.first + Fetch64(s + 40); z = Rotate(z + w.first, 33) * k1; v = WeakHashLen32WithSeeds(s, v.second * k1, x + w.first); w = WeakHashLen32WithSeeds(s + 32, z + w.second, y + Fetch64(s + 16)); std::swap(z, x); s += 64; len -= 64; } while (len != 0); return HashLen16(HashLen16(v.first, w.first) + ShiftMix(y) * k1 + z, HashLen16(v.second, w.second) + x); } uint64 CityHash64WithSeed(const char *s, size_t len, uint64 seed) { return CityHash64WithSeeds(s, len, k2, seed); } uint64 CityHash64WithSeeds(const char *s, size_t len, uint64 seed0, uint64 seed1) { return HashLen16(CityHash64(s, len) - seed0, seed1); } // A subroutine for CityHash128(). Returns a decent 128-bit hash for strings // of any length representable in signed long. Based on City and Murmur. static uint128 CityMurmur(const char *s, size_t len, uint128 seed) { uint64 a = Uint128Low64(seed); uint64 b = Uint128High64(seed); uint64 c = 0; uint64 d = 0; signed long l = len - 16; if (l <= 0) { // len <= 16 a = ShiftMix(a * k1) * k1; c = b * k1 + HashLen0to16(s, len); d = ShiftMix(a + (len >= 8 ? Fetch64(s) : c)); } else { // len > 16 c = HashLen16(Fetch64(s + len - 8) + k1, a); d = HashLen16(b + len, c + Fetch64(s + len - 16)); a += d; do { a ^= ShiftMix(Fetch64(s) * k1) * k1; a *= k1; b ^= a; c ^= ShiftMix(Fetch64(s + 8) * k1) * k1; c *= k1; d ^= c; s += 16; l -= 16; } while (l > 0); } a = HashLen16(a, c); b = HashLen16(d, b); return uint128(a ^ b, HashLen16(b, a)); } uint128 CityHash128WithSeed(const char *s, size_t len, uint128 seed) { if (len < 128) { return CityMurmur(s, len, seed); } // We expect len >= 128 to be the common case. Keep 56 bytes of state: // v, w, x, y, and z. pair v, w; uint64 x = Uint128Low64(seed); uint64 y = Uint128High64(seed); uint64 z = len * k1; v.first = Rotate(y ^ k1, 49) * k1 + Fetch64(s); v.second = Rotate(v.first, 42) * k1 + Fetch64(s + 8); w.first = Rotate(y + z, 35) * k1 + x; w.second = Rotate(x + Fetch64(s + 88), 53) * k1; // This is the same inner loop as CityHash64(), manually unrolled. do { x = Rotate(x + y + v.first + Fetch64(s + 8), 37) * k1; y = Rotate(y + v.second + Fetch64(s + 48), 42) * k1; x ^= w.second; y += v.first + Fetch64(s + 40); z = Rotate(z + w.first, 33) * k1; v = WeakHashLen32WithSeeds(s, v.second * k1, x + w.first); w = WeakHashLen32WithSeeds(s + 32, z + w.second, y + Fetch64(s + 16)); std::swap(z, x); s += 64; x = Rotate(x + y + v.first + Fetch64(s + 8), 37) * k1; y = Rotate(y + v.second + Fetch64(s + 48), 42) * k1; x ^= w.second; y += v.first + Fetch64(s + 40); z = Rotate(z + w.first, 33) * k1; v = WeakHashLen32WithSeeds(s, v.second * k1, x + w.first); w = WeakHashLen32WithSeeds(s + 32, z + w.second, y + Fetch64(s + 16)); std::swap(z, x); s += 64; len -= 128; } while (LIKELY(len >= 128)); x += Rotate(v.first + z, 49) * k0; z += Rotate(w.first, 37) * k0; // If 0 < len < 128, hash up to 4 chunks of 32 bytes each from the end of s. for (size_t tail_done = 0; tail_done < len; ) { tail_done += 32; y = Rotate(x + y, 42) * k0 + v.second; w.first += Fetch64(s + len - tail_done + 16); x = x * k0 + w.first; z += w.second + Fetch64(s + len - tail_done); w.second += v.first; v = WeakHashLen32WithSeeds(s + len - tail_done, v.first + z, v.second); } // At this point our 56 bytes of state should contain more than // enough information for a strong 128-bit hash. We use two // different 56-byte-to-8-byte hashes to get a 16-byte final result. x = HashLen16(x, v.first); y = HashLen16(y + z, w.first); return uint128(HashLen16(x + v.second, w.second) + y, HashLen16(x + w.second, y + v.second)); } uint128 CityHash128(const char *s, size_t len) { if (len >= 16) { return CityHash128WithSeed(s + 16, len - 16, uint128(Fetch64(s) ^ k3, Fetch64(s + 8))); } else if (len >= 8) { return CityHash128WithSeed(NULL, 0, uint128(Fetch64(s) ^ (len * k0), Fetch64(s + len - 8) ^ k1)); } else { return CityHash128WithSeed(s, len, uint128(k0, k1)); } } #if 0 // #ifdef __SSE4_2__ #include #include // Requires len >= 240. static void CityHashCrc256Long(const char *s, size_t len, uint32 seed, uint64 *result) { uint64 a = Fetch64(s + 56) + k0; uint64 b = Fetch64(s + 96) + k0; uint64 c = result[0] = HashLen16(b, len); uint64 d = result[1] = Fetch64(s + 120) * k0 + len; uint64 e = Fetch64(s + 184) + seed; uint64 f = seed; uint64 g = 0; uint64 h = 0; uint64 i = 0; uint64 j = 0; uint64 t = c + d; // 240 bytes of input per iter. size_t iters = len / 240; len -= iters * 240; do { #define CHUNK(multiplier, z) \ { \ uint64 old_a = a; \ a = Rotate(b, 41 ^ z) * multiplier + Fetch64(s); \ b = Rotate(c, 27 ^ z) * multiplier + Fetch64(s + 8); \ c = Rotate(d, 41 ^ z) * multiplier + Fetch64(s + 16); \ d = Rotate(e, 33 ^ z) * multiplier + Fetch64(s + 24); \ e = Rotate(t, 25 ^ z) * multiplier + Fetch64(s + 32); \ t = old_a; \ } \ f = _mm_crc32_u64(f, a); \ g = _mm_crc32_u64(g, b); \ h = _mm_crc32_u64(h, c); \ i = _mm_crc32_u64(i, d); \ j = _mm_crc32_u64(j, e); \ s += 40 CHUNK(1, 1); CHUNK(k0, 0); CHUNK(1, 1); CHUNK(k0, 0); CHUNK(1, 1); CHUNK(k0, 0); } while (--iters > 0); while (len >= 40) { CHUNK(k0, 0); len -= 40; } if (len > 0) { s = s + len - 40; CHUNK(k0, 0); } j += i << 32; a = HashLen16(a, j); h += g << 32; b += h; c = HashLen16(c, f) + i; d = HashLen16(d, e + result[0]); j += e; i += HashLen16(h, t); e = HashLen16(a, d) + j; f = HashLen16(b, c) + a; g = HashLen16(j, i) + c; result[0] = e + f + g + h; a = ShiftMix((a + g) * k0) * k0 + b; result[1] += a + result[0]; a = ShiftMix(a * k0) * k0 + c; result[2] = a + result[1]; a = ShiftMix((a + e) * k0) * k0; result[3] = a + result[2]; } // Requires len < 240. static void CityHashCrc256Short(const char *s, size_t len, uint64 *result) { char buf[240]; memcpy(buf, s, len); memset(buf + len, 0, 240 - len); CityHashCrc256Long(buf, 240, ~static_cast(len), result); } void CityHashCrc256(const char *s, size_t len, uint64 *result) { if (LIKELY(len >= 240)) { CityHashCrc256Long(s, len, 0, result); } else { CityHashCrc256Short(s, len, result); } } uint128 CityHashCrc128WithSeed(const char *s, size_t len, uint128 seed) { if (len <= 900) { return CityHash128WithSeed(s, len, seed); } else { uint64 result[4]; CityHashCrc256(s, len, result); uint64 u = Uint128High64(seed) + result[0]; uint64 v = Uint128Low64(seed) + result[1]; return uint128(HashLen16(u, v + result[2]), HashLen16(Rotate(v, 32), u * k0 + result[3])); } } uint128 CityHashCrc128(const char *s, size_t len) { if (len <= 900) { return CityHash128(s, len); } else { uint64 result[4]; CityHashCrc256(s, len, result); return uint128(result[2], result[3]); } } #endif abyss-1.3.6/Common/city.h000644 002433 001057 00000007125 12104026026 016726 0ustar00traymondassembly000000 000000 // Copyright (c) 2011 Google, Inc. // // 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. // // CityHash, by Geoff Pike and Jyrki Alakuijala // // This file provides a few functions for hashing strings. On x86-64 // hardware in 2011, CityHash64() is faster than other high-quality // hash functions, such as Murmur. This is largely due to higher // instruction-level parallelism. CityHash64() and CityHash128() also perform // well on hash-quality tests. // // CityHash128() is optimized for relatively long strings and returns // a 128-bit hash. For strings more than about 2000 bytes it can be // faster than CityHash64(). // // Functions in the CityHash family are not suitable for cryptography. // // WARNING: This code has not been tested on big-endian platforms! // It is known to work well on little-endian platforms that have a small penalty // for unaligned reads, such as current Intel and AMD moderate-to-high-end CPUs. // // By the way, for some hash functions, given strings a and b, the hash // of a+b is easily derived from the hashes of a and b. This property // doesn't hold for any hash functions in this file. #ifndef CITY_HASH_H_ #define CITY_HASH_H_ #include // for size_t. #include #include typedef uint8_t uint8; typedef uint32_t uint32; typedef uint64_t uint64; typedef std::pair uint128; inline uint64 Uint128Low64(const uint128& x) { return x.first; } inline uint64 Uint128High64(const uint128& x) { return x.second; } // Hash function for a byte array. uint64 CityHash64(const char *buf, size_t len); // Hash function for a byte array. For convenience, a 64-bit seed is also // hashed into the result. uint64 CityHash64WithSeed(const char *buf, size_t len, uint64 seed); // Hash function for a byte array. For convenience, two seeds are also // hashed into the result. uint64 CityHash64WithSeeds(const char *buf, size_t len, uint64 seed0, uint64 seed1); // Hash function for a byte array. uint128 CityHash128(const char *s, size_t len); // Hash function for a byte array. For convenience, a 128-bit seed is also // hashed into the result. uint128 CityHash128WithSeed(const char *s, size_t len, uint128 seed); // Hash 128 input bits down to 64 bits of output. // This is intended to be a reasonably good hash function. inline uint64 Hash128to64(const uint128& x) { // Murmur-inspired hashing. const uint64 kMul = 0x9ddfea08eb382d69ULL; uint64 a = (Uint128Low64(x) ^ Uint128High64(x)) * kMul; a ^= (a >> 47); uint64 b = (Uint128High64(x) ^ a) * kMul; b ^= (b >> 47); b *= kMul; return b; } #endif // CITY_HASH_H_ abyss-1.3.6/Assembly/Makefile.in000644 002433 001057 00000072565 12176317670 020234 0ustar00traymondassembly000000 000000 # Makefile.in generated by automake 1.14 from Makefile.am. # @configure_input@ # Copyright (C) 1994-2013 Free Software Foundation, Inc. # This Makefile.in is free software; the Free Software Foundation # gives unlimited permission to copy and/or distribute it, # with or without modifications, as long as this notice is preserved. # This program is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY, to the extent permitted by law; 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namespace AssemblyAlgorithms { /** Return the kmer which are adjacent to this kmer. */ void generateSequencesFromExtension(const Kmer& currSeq, extDirection dir, SeqExt extension, vector& outseqs) { vector extensions; Kmer extSeq(currSeq); extSeq.shift(dir); // Check for the existance of the 4 possible extensions for (unsigned i = 0; i < NUM_BASES; i++) { // Does this sequence have an extension? if(extension.checkBase(i)) { extSeq.setLastBase(dir, i); outseqs.push_back(extSeq); } } } /** Load k-mer with coverage data. * @return the number of k-mer loaded */ static size_t loadKmer(ISequenceCollection& g, FastaReader& in) { assert(opt::rank == -1); size_t count = 0; for (FastaRecord rec; in >> rec;) { assert(rec.seq.size() == opt::kmerSize); istringstream iss(rec.id); float coverage = 1; iss >> coverage; assert(iss); assert(iss.eof()); g.add(Kmer(rec.seq), max(1, (int)ceilf(coverage))); if (++count % 1000000 == 0) { logger(1) << "Read " << count << " k-mer. "; g.printLoad(); } g.pumpNetwork(); } assert(in.eof()); return count; } /** Load sequence data into the collection. */ void loadSequences(ISequenceCollection* seqCollection, string inFile) { Timer timer("LoadSequences " + inFile); logger(0) << "Reading `" << inFile << "'...\n"; if (inFile.find(".kmer") != string::npos) { if (opt::rank <= 0) seqCollection->setColourSpace(false); seqCollection->load(inFile.c_str()); return; } size_t count = 0, count_good = 0, count_small = 0, count_nonACGT = 0; FastaReader reader(inFile.c_str(), FastaReader::FOLD_CASE); if (endsWith(inFile, ".jf") || endsWith(inFile, ".jfq")) { // Load k-mer with coverage data. count = loadKmer(*seqCollection, reader); count_good = count; } else for (Sequence seq; reader >> seq;) { size_t len = seq.length(); if (opt::kmerSize > len) { count_small++; continue; } if (opt::rank <= 0 && count == 0 && seqCollection->empty()) { // Detect colour-space reads. bool colourSpace = seq.find_first_of("0123") != string::npos; seqCollection->setColourSpace(colourSpace); if (colourSpace) cout << "Colour-space assembly\n"; } if (isalnum(seq[0])) { if (opt::colourSpace) assert(isdigit(seq[0])); else assert(isalpha(seq[0])); } bool good = seq.find_first_not_of("ACGT0123") == string::npos; bool discarded = true; for (unsigned i = 0; i < len - opt::kmerSize + 1; i++) { Sequence kmer(seq, i, opt::kmerSize); if (good || kmer.find_first_not_of("ACGT0123") == string::npos) { seqCollection->add(Kmer(kmer)); discarded = false; } } if (discarded) count_nonACGT++; else count_good++; if (++count % 100000 == 0) { logger(1) << "Read " << count << " reads. "; seqCollection->printLoad(); } seqCollection->pumpNetwork(); } assert(reader.eof()); logger(1) << "Read " << count << " reads. "; seqCollection->printLoad(); if (count_small > 0) cerr << "`" << inFile << "': " "discarded " << count_small << " reads " "shorter than " << opt::kmerSize << " bases\n"; if (reader.unchaste() > 0) cerr << "`" << inFile << "': " "discarded " << reader.unchaste() << " unchaste reads\n"; if (count_nonACGT > 0) cerr << "`" << inFile << "': " "discarded " << count_nonACGT << " reads " "containing non-ACGT characters\n"; if (count_good == 0) cerr << "warning: `" << inFile << "': " "contains no usable sequence\n"; if (opt::rank <= 0 && count == 0 && seqCollection->empty()) { /* The master process did not load any data, which means that * it hasn't told the slave processes whether this assembly is * in colour-space. Rather than fail right now, assume that * the assembly is not colour space. If the assumption is * incorrect, the assembly will fail pretty quickly as soon as * one of the slave processes sees a colour-space read. */ assert(!opt::colourSpace); seqCollection->setColourSpace(false); } } /** Generate the adjacency information for each sequence in the * collection. */ void generateAdjacency(ISequenceCollection* seqCollection) { Timer timer("GenerateAdjacency"); size_t count = 0; size_t numBasesSet = 0; for (ISequenceCollection::iterator iter = seqCollection->begin(); iter != seqCollection->end(); ++iter) { if (iter->second.deleted()) continue; if (++count % 1000000 == 0) logger(1) << "Finding adjacent k-mer: " << count << '\n'; for (extDirection dir = SENSE; dir <= ANTISENSE; ++dir) { Kmer testSeq(iter->first); uint8_t adjBase = testSeq.shift(dir); for (unsigned i = 0; i < NUM_BASES; i++) { testSeq.setLastBase(dir, i); if (seqCollection->setBaseExtension( testSeq, !dir, adjBase)) numBasesSet++; } } seqCollection->pumpNetwork(); } if (numBasesSet > 0) logger(0) << "Added " << numBasesSet << " edges.\n"; } /** Mark the specified vertex and its neighbours. * @return the number of marked edges */ static size_t markNeighbours(ISequenceCollection* g, const ISequenceCollection::value_type& u, extDirection sense) { vector adj; generateSequencesFromExtension(u.first, sense, u.second.getExtension(sense), adj); for (vector::iterator v = adj.begin(); v != adj.end(); ++v) g->mark(*v, !sense); return adj.size(); } /** Mark ambiguous branches and branches from palindromes for removal. * @return the number of branches marked */ size_t markAmbiguous(ISequenceCollection* g) { Timer timer(__func__); size_t progress = 0; size_t countv = 0, counte = 0; for (ISequenceCollection::iterator it = g->begin(); it != g->end(); ++it) { if (it->second.deleted()) continue; if (++progress % 1000000 == 0) logger(1) << "Splitting: " << progress << '\n'; if (it->first.isPalindrome()) { countv += 2; g->mark(it->first); counte += markNeighbours(g, *it, SENSE); } else { for (extDirection sense = SENSE; sense <= ANTISENSE; ++sense) { if (it->second.getExtension(sense).isAmbiguous() || it->first.isPalindrome(sense)) { countv++; g->mark(it->first, sense); counte += markNeighbours(g, *it, sense); } } } g->pumpNetwork(); } logger(0) << "Marked " << counte << " edges of " << countv << " ambiguous vertices." << endl; return countv; } /** Remove the edges of marked and deleted vertices. * @return the number of branches removed */ size_t splitAmbiguous(ISequenceCollection* pSC) { Timer timer(__func__); size_t count = 0; for (ISequenceCollection::iterator it = pSC->begin(); it != pSC->end(); ++it) { if (!it->second.deleted()) continue; for (extDirection sense = SENSE; sense <= ANTISENSE; ++sense) { if (it->second.marked(sense)) { removeExtensionsToSequence(pSC, *it, sense); count++; } } pSC->pumpNetwork(); } logger(0) << "Split " << count << " ambigiuous branches.\n"; return count; } /** Open the bubble file. */ void openBubbleFile(ofstream& out) { if (opt::snpPath.empty()) return; string path; if (opt::rank < 0) { path = opt::snpPath; } else { ostringstream s; s << "snp-" << opt::rank << ".fa"; path = s.str(); } out.open(path.c_str()); assert_good(out, path); } /** Pop bubbles. */ size_t popBubbles(SequenceCollectionHash* seqCollection, ostream& out) { Timer timer("PopBubbles"); size_t numPopped = 0; // Set the cutoffs const unsigned maxNumBranches = 3; const unsigned maxLength = opt::bubbleLen - opt::kmerSize + 1; for (ISequenceCollection::iterator iter = seqCollection->begin(); iter != seqCollection->end(); ++iter) { if (iter->second.deleted()) continue; ExtensionRecord extRec = iter->second.extension(); for (extDirection dir = SENSE; dir <= ANTISENSE; ++dir) { if (extRec.dir[dir].isAmbiguous()) { // Found a potential bubble, examine each branch bool stop = false; // Create the branch group BranchGroup branchGroup(dir, maxNumBranches, iter->first); initiateBranchGroup(branchGroup, iter->first, extRec.dir[dir]); // Iterate over the branches while(!stop) { size_t numBranches = branchGroup.size(); for (unsigned j = 0; j < numBranches; ++j) { // Get the extensions of this branch ExtensionRecord extRec; int multiplicity = -1; const Kmer& lastKmer = branchGroup[j].back().first; bool success = seqCollection->getSeqData( lastKmer, extRec, multiplicity); assert(success); (void)success; processBranchGroupExtension(branchGroup, j, lastKmer, extRec, multiplicity, maxLength); } // At this point all branches should have the same // length or one will be a noext. branchGroup.updateStatus(maxLength); BranchGroupStatus status = branchGroup.getStatus(); if (status == BGS_TOOLONG || status == BGS_TOOMANYBRANCHES || status == BGS_NOEXT) { stop = true; } else if(status == BGS_JOINED) { static unsigned snpID; writeBubble(out, branchGroup, ++snpID); assert(branchGroup.isAmbiguous( *seqCollection)); collapseJoinedBranches(seqCollection, branchGroup); assert(!branchGroup.isAmbiguous( *seqCollection)); numPopped++; stop = true; } else assert(status == BGS_ACTIVE); } } } seqCollection->pumpNetwork(); } if (numPopped > 0) cout << "Removed " << numPopped << " bubbles.\n"; return numPopped; } // Populate a branch group with the inital branches from a sequence void initiateBranchGroup(BranchGroup& group, const Kmer& seq, const SeqExt& extension) { vector extSeqs; generateSequencesFromExtension(seq, group.getDirection(), extension, extSeqs); assert(extSeqs.size() > 1); for (vector::iterator seqIter = extSeqs.begin(); seqIter != extSeqs.end(); ++seqIter) group.addBranch(BranchRecord(group.getDirection()), *seqIter); } /** Process an a branch group extension. */ bool processBranchGroupExtension(BranchGroup& group, size_t branchIndex, const Kmer& seq, ExtensionRecord ext, int multiplicity, unsigned maxLength) { BranchRecord& branch = group[branchIndex]; branch.setData(make_pair(seq, KmerData(multiplicity, ext))); extDirection dir = group.getDirection(); if (ext.dir[!dir].isAmbiguous()) { // Check that this fork is due to branches of our bubble // merging back together. If not, stop this bubble. if (branch.size() < 2) { group.setNoExtension(); return false; } vector extKmer; generateSequencesFromExtension(seq, !dir, ext.dir[!dir], extKmer); assert(extKmer.size() > 1); for (vector::iterator it = extKmer.begin(); it != extKmer.end(); ++it) { assert(branch.size() > 1); if (!group.exists(branch.size() - 2, *it)) { group.setNoExtension(); return false; } } // Ignore the ambiguity. ext.dir[!dir].clear(); } if (ext.dir[dir].isAmbiguous()) { // Create a new branch to follow the fork. vector extKmer; generateSequencesFromExtension(seq, dir, ext.dir[dir], extKmer); assert(extKmer.size() > 1); BranchRecord original = branch; vector::iterator it = extKmer.begin(); branch.push_back(make_pair(*it++, KmerData())); for (; it != extKmer.end(); ++it) group.addBranch(original, *it); return group.isExtendable(); } Kmer nextKmer = seq; if (processLinearExtensionForBranch(branch, nextKmer, ext, multiplicity, maxLength, false)) branch.push_back(make_pair(nextKmer, KmerData())); else group.setNoExtension(); return group.isExtendable(); } /** Write a bubble to the specified file. */ void writeBubble(ostream& out, const BranchGroup& group, unsigned id) { if (opt::snpPath.empty()) return; char allele = 'A'; for (BranchGroup::const_iterator it = group.begin(); it != group.end(); ++it) { const BranchRecord& currBranch = *it; Sequence contig(currBranch); out << '>' << id << allele++ << ' ' << contig.length() << ' ' << currBranch.calculateBranchMultiplicity() << '\n' << contig.c_str() << '\n'; } assert(out.good()); } /** Collapse a bubble to a single path. */ void collapseJoinedBranches(ISequenceCollection* collection, BranchGroup& group) { const BranchRecord& best = group[0]; logger(5) << "Popping " << best.size() << ' ' << best.front().first << '\n'; // Add the k-mer from the dead branches. map doomed; for (BranchGroup::const_iterator branchIt = group.begin() + 1; branchIt != group.end(); ++branchIt) { const BranchRecord& branch = *branchIt; for (BranchRecord::const_iterator it = branch.begin(); it != branch.end(); ++it) doomed.insert(*it); } // Remove the k-mer that are in the good branch. for (BranchRecord::const_iterator it = best.begin(); it != best.end(); ++it) doomed.erase(it->first); // Remove the dead k-mer from the assembly. for (map::const_iterator it = doomed.begin(); it != doomed.end(); ++it) removeSequenceAndExtensions(collection, *it); } /** * Remove a k-mer and update the extension records of the k-mer that * extend to it. */ void removeSequenceAndExtensions(ISequenceCollection* seqCollection, const ISequenceCollection::value_type& seq) { // This removes the reverse complement as well seqCollection->remove(seq.first); removeExtensionsToSequence(seqCollection, seq, SENSE); removeExtensionsToSequence(seqCollection, seq, ANTISENSE); } /** Remove all the extensions to this sequence. */ void removeExtensionsToSequence(ISequenceCollection* seqCollection, const ISequenceCollection::value_type& seq, extDirection dir) { SeqExt extension(seq.second.getExtension(dir)); Kmer testSeq(seq.first); uint8_t extBase = testSeq.shift(dir); for (unsigned i = 0; i < NUM_BASES; i++) { if (extension.checkBase(i)) { testSeq.setLastBase(dir, i); seqCollection->removeExtension(testSeq, !dir, extBase); } } } /** The number of k-mer that have been eroded. */ static size_t g_numEroded; /** Return the number of k-mer that have been eroded. */ size_t getNumEroded() { size_t numEroded = g_numEroded; g_numEroded = 0; logger(0) << "Eroded " << numEroded << " tips.\n"; return numEroded; } /** Consider the specified k-mer for erosion. * @return the number of k-mer eroded, zero or one */ size_t erode(ISequenceCollection* c, const ISequenceCollection::value_type& seq) { if (seq.second.deleted()) return 0; extDirection dir; SeqContiguity contiguity = checkSeqContiguity(seq, dir); if (contiguity == SC_CONTIGUOUS) return 0; const KmerData& data = seq.second; if (data.getMultiplicity() < opt::erode || data.getMultiplicity(SENSE) < opt::erodeStrand || data.getMultiplicity(ANTISENSE) < opt::erodeStrand) { removeSequenceAndExtensions(c, seq); g_numEroded++; return 1; } else return 0; } /** The given sequence has changed. */ static void erosionObserver(ISequenceCollection* c, const ISequenceCollection::value_type& seq) { erode(c, seq); } // // Erode data off the ends of the graph, one by one // size_t erodeEnds(ISequenceCollection* seqCollection) { Timer erodeEndsTimer("Erode"); assert(g_numEroded == 0); seqCollection->attach(erosionObserver); for (ISequenceCollection::iterator iter = seqCollection->begin(); iter != seqCollection->end(); ++iter) { erode(seqCollection, *iter); seqCollection->pumpNetwork(); } seqCollection->detach(erosionObserver); return getNumEroded(); } static size_t trimSequences(SequenceCollectionHash* seqCollection, unsigned maxBranchCull); /** Trimming driver function */ void performTrim(SequenceCollectionHash* seqCollection) { if (opt::trimLen == 0) return; unsigned rounds = 0; size_t total = 0; for (unsigned trim = 1; trim < opt::trimLen; trim *= 2) { rounds++; total += trimSequences(seqCollection, trim); } size_t count; while ((count = trimSequences(seqCollection, opt::trimLen)) > 0) { rounds++; total += count; } cout << "Pruned " << total << " tips in " << rounds << " rounds.\n"; } /** Return the adjacency of this sequence. * @param considerMarks when true, treat a marked vertex as having * no edges */ SeqContiguity checkSeqContiguity( const ISequenceCollection::value_type& seq, extDirection& outDir, bool considerMarks) { assert(!seq.second.deleted()); bool child = seq.second.hasExtension(SENSE) && !(considerMarks && seq.second.marked(SENSE)); bool parent = seq.second.hasExtension(ANTISENSE) && !(considerMarks && seq.second.marked(ANTISENSE)); if(!child && !parent) { //this sequence is completely isolated return SC_ISLAND; } else if(!child) { outDir = ANTISENSE; return SC_ENDPOINT; } else if(!parent) { outDir = SENSE; return SC_ENDPOINT; } else { // sequence is contiguous return SC_CONTIGUOUS; } } /** Prune tips shorter than maxBranchCull. */ static size_t trimSequences(SequenceCollectionHash* seqCollection, unsigned maxBranchCull) { Timer timer("TrimSequences"); cout << "Pruning tips shorter than " << maxBranchCull << " bp...\n"; size_t numBranchesRemoved = 0; for (ISequenceCollection::iterator iter = seqCollection->begin(); iter != seqCollection->end(); ++iter) { if (iter->second.deleted()) continue; extDirection dir; // dir will be set to the trimming direction if the sequence // can be trimmed. SeqContiguity status = checkSeqContiguity(*iter, dir); if (status == SC_CONTIGUOUS) continue; else if(status == SC_ISLAND) { // remove this sequence, it has no extensions seqCollection->mark(iter->first); numBranchesRemoved++; continue; } BranchRecord currBranch(dir); Kmer currSeq = iter->first; while(currBranch.isActive()) { ExtensionRecord extRec; int multiplicity = -1; bool success = seqCollection->getSeqData( currSeq, extRec, multiplicity); assert(success); (void)success; processLinearExtensionForBranch(currBranch, currSeq, extRec, multiplicity, maxBranchCull); } // The branch has ended check it for removal, returns true if // it was removed. if(processTerminatedBranchTrim(seqCollection, currBranch)) { numBranchesRemoved++; } seqCollection->pumpNetwork(); } size_t numSweeped = removeMarked(seqCollection); if (numBranchesRemoved > 0) logger(0) << "Pruned " << numSweeped << " k-mer in " << numBranchesRemoved << " tips.\n"; return numBranchesRemoved; } /** Extend this branch. */ bool extendBranch(BranchRecord& branch, Kmer& kmer, SeqExt ext) { if (!ext.hasExtension()) { branch.terminate(BS_NOEXT); return false; } else if (ext.isAmbiguous()) { branch.terminate(BS_AMBI_SAME); return false; } else { vector adj; generateSequencesFromExtension(kmer, branch.getDirection(), ext, adj); assert(adj.size() == 1); kmer = adj.front(); return true; } } /** * Process the extension for this branch for the trimming algorithm * CurrSeq is the current sequence being inspected (the next member to * be added to the branch). The extension record is the extensions of * that sequence and multiplicity is the number of times that kmer * appears in the data set. After processing currSeq is unchanged if * the branch is no longer active or else it is the generated * extension. If the parameter addKmer is true, add the k-mer to the * branch. */ bool processLinearExtensionForBranch(BranchRecord& branch, Kmer& currSeq, ExtensionRecord extensions, int multiplicity, unsigned maxLength, bool addKmer) { /** Stop contig assembly at palindromes. */ const bool stopAtPalindromes = maxLength == UINT_MAX; extDirection dir = branch.getDirection(); if (branch.isTooLong(maxLength)) { // Too long. branch.terminate(BS_TOO_LONG); return false; } else if (extensions.dir[!dir].isAmbiguous()) { // Ambiguous. branch.terminate(BS_AMBI_OPP); return false; } else if (stopAtPalindromes && currSeq.isPalindrome()) { // Palindrome. branch.terminate(BS_AMBI_SAME); return false; } if (addKmer) branch.push_back(make_pair(currSeq, KmerData(multiplicity, extensions))); if (branch.isTooLong(maxLength)) { // Too long. branch.terminate(BS_TOO_LONG); return false; } else if (stopAtPalindromes && currSeq.isPalindrome(dir)) { // Palindrome. branch.terminate(BS_AMBI_SAME); return false; } return extendBranch(branch, currSeq, extensions.dir[dir]); } /** Trim the specified branch if it meets trimming criteria. * @return true if the specified branch was trimmed */ bool processTerminatedBranchTrim(ISequenceCollection* seqCollection, BranchRecord& branch) { assert(!branch.isActive()); assert(!branch.empty()); if (branch.getState() == BS_NOEXT || branch.getState() == BS_AMBI_OPP) { logger(5) << "Pruning " << branch.size() << ' ' << branch.front().first << '\n'; for (BranchRecord::iterator it = branch.begin(); it != branch.end(); ++it) seqCollection->mark(it->first); return true; } else return false; } /** Remove all marked k-mer. * @return the number of removed k-mer */ size_t removeMarked(ISequenceCollection* pSC) { Timer timer(__func__); size_t count = 0; for (ISequenceCollection::iterator it = pSC->begin(); it != pSC->end(); ++it) { if (it->second.deleted()) continue; if (it->second.marked()) { removeSequenceAndExtensions(pSC, *it); count++; } pSC->pumpNetwork(); } if (count > 0) logger(1) << "Removed " << count << " marked k-mer.\n"; return count; } /** Assemble a contig. * @return the number of k-mer below the coverage threshold */ size_t assembleContig( ISequenceCollection* seqCollection, FastaWriter* writer, BranchRecord& branch, unsigned id) { assert(!branch.isActive()); assert(branch.getState() == BS_NOEXT || branch.getState() == BS_AMBI_SAME || branch.getState() == BS_AMBI_OPP); // Assemble the contig. Sequence contig(branch); size_t kmerCount = branch.calculateBranchMultiplicity(); if (writer != NULL) writer->WriteSequence(contig, id, kmerCount); // Remove low-coverage contigs. float coverage = (float)kmerCount / branch.size(); if (opt::coverage > 0 && coverage < opt::coverage) { for (BranchRecord::iterator it = branch.begin(); it != branch.end(); ++it) seqCollection->remove(it->first); return branch.size(); } return 0; } /** Assemble contigs. * @return the number of contigs assembled */ size_t assemble(SequenceCollectionHash* seqCollection, FastaWriter* fileWriter) { Timer timer("Assemble"); size_t kmerCount = 0; unsigned contigID = 0; size_t assembledKmer = 0; size_t lowCoverageKmer = 0; size_t lowCoverageContigs = 0; for (ISequenceCollection::iterator iter = seqCollection->begin(); iter != seqCollection->end(); ++iter) { if (iter->second.deleted()) continue; kmerCount++; extDirection dir; SeqContiguity status = checkSeqContiguity(*iter, dir, true); if (status == SC_CONTIGUOUS) continue; else if(status == SC_ISLAND) { BranchRecord currBranch(SENSE); currBranch.push_back(*iter); currBranch.terminate(BS_NOEXT); size_t removed = assembleContig(seqCollection, fileWriter, currBranch, contigID++); assembledKmer += currBranch.size(); if (removed > 0) { lowCoverageContigs++; lowCoverageKmer += removed; } continue; } assert(status == SC_ENDPOINT); BranchRecord currBranch(dir); currBranch.push_back(*iter); Kmer currSeq = iter->first; extendBranch(currBranch, currSeq, iter->second.getExtension(dir)); assert(currBranch.isActive()); while(currBranch.isActive()) { ExtensionRecord extRec; int multiplicity = -1; bool success = seqCollection->getSeqData( currSeq, extRec, multiplicity); assert(success); (void)success; processLinearExtensionForBranch(currBranch, currSeq, extRec, multiplicity, UINT_MAX); } if (currBranch.isCanonical()) { size_t removed = assembleContig(seqCollection, fileWriter, currBranch, contigID++); assembledKmer += currBranch.size(); if (removed > 0) { lowCoverageContigs++; lowCoverageKmer += removed; } } seqCollection->pumpNetwork(); } if (opt::coverage > 0) { cout << "Found " << assembledKmer << " k-mer in " << contigID << " contigs before removing low-coverage contigs.\n" "Removed " << lowCoverageKmer << " k-mer in " << lowCoverageContigs << " low-coverage contigs.\n"; } else { assert(assembledKmer <= kmerCount); size_t circularKmer = kmerCount - assembledKmer; if (circularKmer > 0) cout << "Left " << circularKmer << " unassembled k-mer in circular contigs.\n"; cout << "Assembled " << assembledKmer << " k-mer in " << contigID << " contigs.\n"; } return contigID; } /** Return the k-mer coverage histogram. */ Histogram coverageHistogram(const ISequenceCollection& c) { Histogram h; for (ISequenceCollection::const_iterator it = c.begin(); it != c.end(); ++it) { if (it->second.deleted()) continue; h.insert(it->second.getMultiplicity()); } return h; } /** Calculate a k-mer coverage threshold from the given k-mer coverage * histogram. */ static float calculateCoverageThreshold(const Histogram& h) { float cov = h.firstLocalMinimum(); if (opt::rank <= 0) { if (cov == 0) cout << "Unable to determine minimum k-mer coverage\n"; else cout << "Minimum k-mer coverage is " << cov << endl; } for (unsigned iteration = 0; iteration < 100; iteration++) { Histogram trimmed = h.trimLow((unsigned)roundf(cov)); if (opt::rank <= 0) logger(1) << "Coverage: " << cov << "\t" "Reconstruction: " << trimmed.size() << endl; unsigned median = trimmed.median(); float cov1 = sqrt(median); if (cov1 == cov) { // The coverage threshold has converged. if (opt::rank <= 0) cout << "Using a coverage threshold of " << (unsigned)roundf(cov) << "...\n" "The median k-mer coverage is " << median << "\n" "The reconstruction is " << trimmed.size() << endl; return cov; } cov = cov1; } if (opt::rank <= 0) cerr << "warning: coverage threshold did not converge" << endl; return 0; } /** Set the coverage-related parameters e and c from the given k-mer * coverage histogram. */ void setCoverageParameters(const Histogram& h) { if (!opt::coverageHistPath.empty() && opt::rank <= 0) { ofstream histFile(opt::coverageHistPath.c_str()); assert_good(histFile, opt::coverageHistPath); histFile << h; assert(histFile.good()); } float minCov = calculateCoverageThreshold(h); if (opt::rank <= 0) { if (minCov == 0) cout << "Unable to determine the " "k-mer coverage threshold" << endl; else cout << "The k-mer coverage threshold is " << minCov << endl; } if (minCov < 2) minCov = 2; if ((int)opt::erode < 0) { opt::erode = (unsigned)roundf(minCov); if (opt::rank <= 0) cout << "Setting parameter e (erode) to " << opt::erode << endl; } if ((int)opt::erodeStrand < 0) { opt::erodeStrand = minCov <= 2 ? 0 : 1; if (opt::rank <= 0) cout << "Setting parameter E (erodeStrand) to " << opt::erodeStrand << endl; } if (opt::coverage < 0) { opt::coverage = minCov; if (opt::rank <= 0) cout << "Setting parameter c (coverage) to " << opt::coverage << endl; } } }; abyss-1.3.6/Assembly/AssemblyAlgorithms.h000644 002433 001057 00000006660 12104026026 022121 0ustar00traymondassembly000000 000000 #ifndef ASSEMBLYALGORITHMS_H #define ASSEMBLYALGORITHMS_H 1 #include "BranchGroup.h" #include "BranchRecord.h" #include "FastaWriter.h" #include "SequenceCollection.h" #include #include class Histogram; /** A summary of the in- and out-degree of a vertex. */ enum SeqContiguity { SC_ISLAND, // sequence is completely isolated SC_ENDPOINT, // one end of the sequence is open SC_CONTIGUOUS // the sequence is closed on both ends }; /** De Bruijn graph assembly algorithms. */ namespace AssemblyAlgorithms { // Read a sequence file and load them into the collection void loadSequences(ISequenceCollection* seqCollection, std::string inFile); /** Generate the adjacency information for all the sequences in the * collection. This is required before any other algorithm can run. */ void generateAdjacency(ISequenceCollection* seqCollection); Histogram coverageHistogram(const ISequenceCollection& c); void setCoverageParameters(const Histogram& h); /* Erosion. Remove k-mer from the ends of blunt contigs. */ size_t erodeEnds(ISequenceCollection* seqCollection); size_t erode(ISequenceCollection* c, const ISequenceCollection::value_type& seq); size_t getNumEroded(); size_t removeMarked(ISequenceCollection* pSC); // Check whether a sequence can be trimmed SeqContiguity checkSeqContiguity( const ISequenceCollection::value_type& seq, extDirection& outDir, bool considerMarks = false); // process a terminated branch for trimming bool processTerminatedBranchTrim( ISequenceCollection* seqCollection, BranchRecord& branch); bool extendBranch(BranchRecord& branch, Kmer& kmer, SeqExt ext); // Process the extensions of the current sequence for trimming bool processLinearExtensionForBranch(BranchRecord& branch, Kmer& currSeq, ExtensionRecord extensions, int multiplicity, unsigned maxLength, bool addKmer = true); /** Populate the branch group with the initial extensions to this * sequence. */ void initiateBranchGroup(BranchGroup& group, const Kmer& seq, const SeqExt& extension); // process an a branch group extension bool processBranchGroupExtension(BranchGroup& group, size_t branchIndex, const Kmer& seq, ExtensionRecord extensions, int multiplicity, unsigned maxLength); void openBubbleFile(std::ofstream& out); void writeBubble(std::ostream& out, const BranchGroup& group, unsigned id); void collapseJoinedBranches( ISequenceCollection* seqCollection, BranchGroup& group); /* Split the remaining ambiguous nodes to allow for a non-redundant * assembly. Remove extensions to/from ambiguous sequences to avoid * generating redundant/wrong contigs. */ size_t markAmbiguous(ISequenceCollection* seqCollection); size_t splitAmbiguous(ISequenceCollection* seqCollection); size_t assembleContig(ISequenceCollection* seqCollection, FastaWriter* writer, BranchRecord& branch, unsigned id); void removeSequenceAndExtensions(ISequenceCollection* seqCollection, const ISequenceCollection::value_type& seq); void removeExtensionsToSequence(ISequenceCollection* seqCollection, const ISequenceCollection::value_type& seq, extDirection dir); void generateSequencesFromExtension(const Kmer& currSeq, extDirection dir, SeqExt extension, std::vector& outseqs); /* Non-distributed graph algorithms. */ void performTrim(SequenceCollectionHash* seqCollection); size_t popBubbles(SequenceCollectionHash* pSC, std::ostream& out); size_t assemble(SequenceCollectionHash* seqCollection, FastaWriter* fileWriter = NULL); }; #endif abyss-1.3.6/Assembly/BranchGroup.cpp000644 002433 001057 00000004571 12104026026 021054 0ustar00traymondassembly000000 000000 #include "BranchGroup.h" #include "Algorithms.h" #include #include using namespace std; // Check the stop conditions for the bubble growth BranchGroupStatus BranchGroup::updateStatus(unsigned maxLength) { assert(m_branches.size() <= m_maxNumBranches); if (m_status != BGS_ACTIVE) return m_status; // Check if the no extension flag is set if(m_noExt) { m_status = BGS_NOEXT; return m_status; } // Check if any branches are too long or any sequence has a loop for (BranchGroupData::const_iterator iter = m_branches.begin(); iter != m_branches.end(); ++iter) { if (iter->isTooLong(maxLength)) { m_status = BGS_TOOLONG; return m_status; } } BranchGroupData::const_iterator it = m_branches.begin(); const Kmer& lastSeq = it->back().first; while (++it != m_branches.end()) if (it->back().first != lastSeq) return m_status = BGS_ACTIVE; // All the branches of the bubble have joined. // Remove the last base, which is identical for every branch. for_each(m_branches.begin(), m_branches.end(), mem_fun_ref(&BranchRecord::pop_back)); // Sort the branches by coverage. sort_by_transform(m_branches.begin(), m_branches.end(), mem_fun_ref(&BranchRecord::calculateBranchMultiplicity)); reverse(m_branches.begin(), m_branches.end()); return m_status = BGS_JOINED; } /** Return whether any branches of this group are active. */ bool BranchGroup::isActive() const { for (BranchGroupData::const_iterator it = m_branches.begin(); it != m_branches.end(); ++it) if (it->isActive()) return true; return false; } /** Return whether this branch is extendable. */ bool BranchGroup::isExtendable() { if (m_noExt) return false; // A group is extendable when all the branches are the same // length. All the branches are lockstepped for growth. BranchGroupData::iterator it = m_branches.begin(); unsigned length = it++->size(); for (; it != m_branches.end(); ++it) if (it->size() != length) return false; return true; } /** Return whether this branch is ambiguous at its origin. Also * returns false if the origin of the branch has since been deleted. */ bool BranchGroup::isAmbiguous(const SequenceCollectionHash& g) const { // Get fresh data from the collection to check that this bubble // does in fact still exist. const KmerData& data = g.getSeqAndData(m_origin).second; return data.deleted() ? false : data.isAmbiguous(m_dir); } abyss-1.3.6/Assembly/BranchGroup.h000644 002433 001057 00000006657 11746352077 020553 0ustar00traymondassembly000000 000000 #ifndef BRANCHGROUP_H #define BRANCHGROUP_H 1 #include "BranchRecord.h" #include "SequenceCollection.h" #include // for swap #include #include enum BranchGroupStatus { BGS_ACTIVE, BGS_NOEXT, BGS_JOINED, BGS_TOOLONG, BGS_TOOMANYBRANCHES }; /** A container of BranchRecord. */ class BranchGroup { public: typedef std::vector BranchGroupData; typedef BranchGroupData::iterator iterator; typedef BranchGroupData::const_iterator const_iterator; BranchGroup() : m_dir(SENSE), m_maxNumBranches(0), m_noExt(false), m_status(BGS_ACTIVE) { } BranchGroup(extDirection dir, size_t maxNumBranches, const Kmer &origin) : m_dir(dir), m_origin(origin), m_maxNumBranches(maxNumBranches), m_noExt(false), m_status(BGS_ACTIVE) { m_branches.reserve(m_maxNumBranches); } BranchGroup(extDirection dir, size_t maxNumBranches, const Kmer &origin, const BranchRecord& branch) : m_dir(dir), m_origin(origin), m_maxNumBranches(maxNumBranches), m_noExt(false), m_status(BGS_ACTIVE) { m_branches.reserve(m_maxNumBranches); m_branches.push_back(branch); } BranchGroup(const BranchGroup& o) : m_branches(o.m_branches), m_dir(o.m_dir), m_origin(o.m_origin), m_maxNumBranches(o.m_maxNumBranches), m_noExt(o.m_noExt), m_status(o.m_status) { m_branches.reserve(m_maxNumBranches); } /** Add a branch to this group. */ BranchRecord& addBranch(const BranchRecord& branch) { assert(m_branches.size() < m_maxNumBranches); m_branches.push_back(branch); return m_branches.back(); } /** Add a branch to this group and extend the new branch with * the given k-mer. */ void addBranch(const BranchRecord& branch, const Kmer& kmer) { if (m_branches.size() < m_maxNumBranches) addBranch(branch).push_back( std::make_pair(kmer, KmerData())); else m_status = BGS_TOOMANYBRANCHES; } /** Return the specified branch. */ BranchRecord& operator [](unsigned id) { return m_branches[id]; } /** Return the number of branches in this group. */ size_t size() const { return m_branches.size(); } /** Return whether a branch contains the specified k-mer at * the index i. */ bool exists(unsigned i, const Kmer& kmer) const { for (BranchGroupData::const_iterator it = m_branches.begin(); it != m_branches.end(); ++it) if (it->exists(i, kmer)) return true; return false; } BranchGroupStatus updateStatus(unsigned maxLength); // return the current status of the branch BranchGroupStatus getStatus() const { return m_status; } // set the no extension flag void setNoExtension() { m_noExt = true; } bool isActive() const; // is the no extension flag set? bool isNoExt() const { return m_noExt; } bool isExtendable(); // return the direction of growth extDirection getDirection() const { return m_dir; } iterator begin() { return m_branches.begin(); } iterator end() { return m_branches.end(); } const_iterator begin() const { return m_branches.begin(); } const_iterator end() const { return m_branches.end(); } bool isAmbiguous(const SequenceCollectionHash& c) const; private: BranchGroup& operator =(const BranchGroup& o); BranchGroupData m_branches; extDirection m_dir; Kmer m_origin; size_t m_maxNumBranches; bool m_noExt; BranchGroupStatus m_status; }; namespace std { template <> inline void swap(BranchGroup&, BranchGroup&) { assert(false); } } #endif abyss-1.3.6/Assembly/BranchRecord.cpp000644 002433 001057 00000002721 11746352077 021214 0ustar00traymondassembly000000 000000 #include "BranchRecord.h" using namespace std; /** Calculate the total multiplicity of this branch. */ int BranchRecord::calculateBranchMultiplicity() const { assert(!m_data.empty()); int total = 0; for (BranchData::const_iterator it = m_data.begin(); it != m_data.end(); ++it) { int m = it->second.getMultiplicity(); assert(m > 0); total += m; } assert(total > 0); return total; } /** Build a contig from a branch. */ BranchRecord::operator Sequence() const { assert(!m_data.empty()); Sequence outseq; outseq.reserve(m_data.front().first.length() + m_data.size() - 1); if (m_dir == SENSE) { BranchData::const_iterator iter = m_data.begin(); outseq = iter->first.str(); ++iter; for (; iter != m_data.end(); ++iter) outseq.append(1, iter->first.getLastBaseChar()); } else { BranchData::const_reverse_iterator iter = m_data.rbegin(); outseq = iter->first.str(); ++iter; for (; iter != m_data.rend(); ++iter) outseq.append(1, iter->first.getLastBaseChar()); } return outseq; } /** * Return whether this branch is the canonical representation of the * contig that it represents. A contig has two ends, and the contig * is output starting from the lexicographically smaller end. */ bool BranchRecord::isCanonical() const { assert(size() > 1); Kmer first = front().first; Kmer last = back().first; if (getDirection() == SENSE) last.reverseComplement(); else first.reverseComplement(); assert(first != last); return first < last; } abyss-1.3.6/Assembly/BranchRecord.h000644 002433 001057 00000006216 12104026026 020641 0ustar00traymondassembly000000 000000 #ifndef BRANCHRECORD_H #define BRANCHRECORD_H 1 #include "Kmer.h" #include "KmerData.h" #include // for swap #include #include #include enum BranchState { // The branch can be extended. BS_ACTIVE, // The branch has ended because of a lack of sequence to extend to BS_NOEXT, // The branch has ended because the extension from this branch is // ambigious. BS_AMBI_SAME, // The branch has ended because the extension to this branch is // ambigiuous. BS_AMBI_OPP, // The branch is too long. BS_TOO_LONG, }; /** A sequence of Kmer. */ class BranchRecord { public: typedef std::pair value_type; typedef std::vector BranchData; typedef BranchData::iterator iterator; typedef BranchData::const_iterator const_iterator; BranchRecord() : m_dir(SENSE), m_state(BS_ACTIVE) { } explicit BranchRecord(extDirection dir) : m_dir(dir), m_state(BS_ACTIVE) { } void swap(BranchRecord& o) { std::swap(m_data, o.m_data); std::swap(m_dir, o.m_dir); std::swap(m_state, o.m_state); } operator Sequence() const; /** Return true if this sequence has no elements. */ bool empty() const { return m_data.empty(); } /** Return the number of elements. */ size_t size() const { return m_data.size(); } /** Add the element x at the end. */ void push_back(const value_type& x) { m_data.push_back(x); } /** Remove the last k-mer. */ void pop_back() { assert(!m_data.empty()); m_data.pop_back(); } /** Return the first element. */ const value_type& front() const { assert(!m_data.empty()); return m_data.front(); } /** Return the last element. */ const value_type& back() const { assert(!m_data.empty()); return m_data.back(); } /** Terminate this branch with the specified reason. */ void terminate(BranchState reason) { assert(reason != BS_ACTIVE); m_state = reason; } /** Return whether this branch is active. */ bool isActive() const { return m_state == BS_ACTIVE; } /** Return the state of this branch. */ BranchState getState() const { return m_state; } /** Return the direction of this branch. */ extDirection getDirection() const { return m_dir; } /** Set the properties of the last element. */ void setData(const value_type& o) { assert(m_data.back().first == o.first); m_data.back().second = o.second; } iterator begin() { return m_data.begin(); } iterator end() { return m_data.end(); } const_iterator begin() const { return m_data.begin(); } const_iterator end() const { return m_data.end(); } /** Return true if the k-mer at position i is the specified * k-mer. */ bool exists(unsigned i, const Kmer& kmer) const { assert(i < m_data.size()); return m_data[i].first == kmer; } /** Return true if this branch is longer than maxLength. */ bool isTooLong(unsigned maxLength) const { return size() > maxLength; } int calculateBranchMultiplicity() const; bool isCanonical() const; private: BranchData m_data; extDirection m_dir; BranchState m_state; }; namespace std { template <> inline void swap(BranchRecord& a, BranchRecord& b) { a.swap(b); } } #endif abyss-1.3.6/Assembly/DotWriter.cpp000644 002433 001057 00000003360 12104026026 020560 0ustar00traymondassembly000000 000000 /** Written by Shaun Jackman . */ #include "DotWriter.h" #include "SequenceCollection.h" #include "Graph/ContigGraphAlgorithms.h" #include #include using namespace std; typedef SequenceCollectionHash Graph; typedef graph_traits::vertex_iterator vertex_iterator; typedef graph_traits::adjacency_iterator adjacency_iterator; /** Write out the specified contig. */ static void writeContig(ostream& out, const Graph& g, const Kmer& u) { if (contiguous_in(g, u)) return; unsigned n = 1; Kmer v = u; while (contiguous_out(g, v)) { n++; v = *adjacent_vertices(v, g).first; } out << u << " -> " << v; if (n > 2) out << " [label=" << n << ']'; out << '\n'; } /** Write out the contigs that split at the specified sequence. */ static void writeEdges(ostream& out, const Graph& g, const Kmer& u) { unsigned outdeg = out_degree(u, g); if (outdeg == 0) return; out << u << " ->"; if (outdeg > 1) out << " {"; std::pair adj = adjacent_vertices(u, g); for (adjacency_iterator v = adj.first; v != adj.second; ++v) out << ' ' << *v; if (outdeg > 1) out << " }"; out << '\n'; } /** Write out a dot graph around the specified sequence. */ static void write_vertex(ostream& out, const Graph& g, const Kmer& u) { if (contiguous_out(g, u)) writeContig(out, g, u); else writeEdges(out, g, u); } /** Write out a dot graph for the specified collection. */ void DotWriter::write(ostream& out, const Graph& g) { out << "digraph g {\n"; std::pair vit = vertices(g); for (vertex_iterator u = vit.first; u != vit.second; ++u) { if (get(vertex_removed, g, *u)) continue; write_vertex(out, g, *u); } out << "}" << endl; } abyss-1.3.6/Assembly/DotWriter.h000644 002433 001057 00000000321 11746352077 020242 0ustar00traymondassembly000000 000000 #ifndef DOTWRITER_H #define DOTWRITER_H 1 #include "SequenceCollection.h" #include class DotWriter { public: static void write(std::ostream& out, const SequenceCollectionHash& c); }; #endif abyss-1.3.6/Assembly/ISequenceCollection.h000644 002433 001057 00000004340 12156175015 022210 0ustar00traymondassembly000000 000000 #ifndef ISEQUENCECOLLECTION_H #define ISEQUENCECOLLECTION_H 1 #include "config.h" #include "Kmer.h" #include "KmerData.h" #if HAVE_GOOGLE_SPARSE_HASH_MAP # include typedef google::sparse_hash_map SequenceDataHash; #else # include "UnorderedMap.h" typedef unordered_map SequenceDataHash; #endif /** The interface of a map of Kmer to KmerData. */ class ISequenceCollection { public: typedef SequenceDataHash::value_type value_type; typedef SequenceDataHash::iterator iterator; typedef SequenceDataHash::const_iterator const_iterator; virtual ~ISequenceCollection() { } virtual void add(const Kmer& seq, unsigned coverage = 1) = 0; virtual void remove(const Kmer& seq) = 0; virtual void setFlag(const Kmer& seq, SeqFlag flag) = 0; /** Mark the specified sequence in both directions. */ void mark(const Kmer& seq) { setFlag(seq, SeqFlag(SF_MARK_SENSE | SF_MARK_ANTISENSE)); } /** Mark the specified sequence. */ void mark(const Kmer& seq, extDirection sense) { setFlag(seq, sense == SENSE ? SF_MARK_SENSE : SF_MARK_ANTISENSE); } virtual bool empty() const = 0; virtual void printLoad() const = 0; virtual void removeExtension(const Kmer& seq, extDirection dir, SeqExt ext) = 0; /** Remove the specified edge of this k-mer. */ void removeExtension(const Kmer& seq, extDirection dir, uint8_t base) { removeExtension(seq, dir, SeqExt(base)); } /** Remove all the edges of this k-mer. */ void clearExtensions(const Kmer& seq, extDirection dir) { removeExtension(seq, dir, SeqExt::mask(0xf)); } virtual bool setBaseExtension(const Kmer& seq, extDirection dir, uint8_t base) = 0; // Receive and dispatch packets if necessary. virtual size_t pumpNetwork() = 0; virtual iterator begin() = 0; virtual const_iterator begin() const = 0; virtual iterator end() = 0; virtual const_iterator end() const = 0; // Observer pattern typedef void (*SeqObserver)(ISequenceCollection* c, const value_type& seq); virtual void attach(SeqObserver f) = 0; virtual void detach(SeqObserver f) = 0; virtual void load(const char *path) = 0; virtual void setColourSpace(bool flag) = 0; }; #endif abyss-1.3.6/Assembly/KmerData.h000644 002433 001057 00000007054 12104026026 017776 0ustar00traymondassembly000000 000000 #ifndef KMERDATA_H #define KMERDATA_H 1 #include "Sense.h" #include "SeqExt.h" #include #include #include enum SeqFlag { SF_MARK_SENSE = 0x1, SF_MARK_ANTISENSE = 0x2, SF_DELETE = 0x4, }; static inline SeqFlag complement(SeqFlag flag) { unsigned out = 0; if (flag & SF_MARK_SENSE) out |= SF_MARK_ANTISENSE; if (flag & SF_MARK_ANTISENSE) out |= SF_MARK_SENSE; if (flag & SF_DELETE) out |= SF_DELETE; return SeqFlag(out); } /** A pair of SeqExt; one for out edges and one for in edges. */ struct ExtensionRecord { SeqExt dir[2]; ExtensionRecord operator ~() const { ExtensionRecord o; o.dir[SENSE] = dir[ANTISENSE].complement(); o.dir[ANTISENSE] = dir[SENSE].complement(); return o; } }; /** * The data associated with a Kmer, including its coverage, flags * and adjacent Kmer. */ class KmerData { /** Maximum value of k-mer coverage. */ #define COVERAGE_MAX 32767U public: KmerData() : m_flags(0) { m_multiplicity[SENSE] = 1; m_multiplicity[ANTISENSE] = 0; } KmerData(extDirection dir, unsigned multiplicity) : m_flags(0) { assert(multiplicity <= COVERAGE_MAX); m_multiplicity[dir] = multiplicity; m_multiplicity[!dir] = 0; } KmerData(unsigned multiplicity, ExtensionRecord ext) : m_flags(0), m_ext(ext) { setMultiplicity(multiplicity); } unsigned getMultiplicity(extDirection dir) const { return m_multiplicity[dir]; } unsigned getMultiplicity() const { return m_multiplicity[SENSE] + m_multiplicity[ANTISENSE]; } void addMultiplicity(extDirection dir, unsigned n = 1) { m_multiplicity[dir] = std::min(m_multiplicity[dir] + n, COVERAGE_MAX); assert(m_multiplicity[dir] > 0); } /** Set the multiplicity (not strand specific). */ void setMultiplicity(unsigned multiplicity) { assert(multiplicity <= 2*COVERAGE_MAX); // Split the multiplicity over both senses. m_multiplicity[SENSE] = (multiplicity + 1) / 2; m_multiplicity[ANTISENSE] = multiplicity / 2; assert(getMultiplicity() == multiplicity); } void setFlag(SeqFlag flag) { m_flags |= flag; } bool isFlagSet(SeqFlag flag) const { return m_flags & flag; } void clearFlag(SeqFlag flag) { m_flags &= ~flag; } /** Return true if the specified sequence is deleted. */ bool deleted() const { return isFlagSet(SF_DELETE); } /** Return true if the specified sequence is marked. */ bool marked(extDirection sense) const { return isFlagSet(sense == SENSE ? SF_MARK_SENSE : SF_MARK_ANTISENSE); } /** Return true if the specified sequence is marked. */ bool marked() const { return isFlagSet(SeqFlag(SF_MARK_SENSE | SF_MARK_ANTISENSE)); } ExtensionRecord extension() const { return m_ext; } SeqExt getExtension(extDirection dir) const { return m_ext.dir[dir]; } void setBaseExtension(extDirection dir, uint8_t base) { m_ext.dir[dir].setBase(base); } void removeExtension(extDirection dir, SeqExt ext) { m_ext.dir[dir].clear(ext); } bool hasExtension(extDirection dir) const { return m_ext.dir[dir].hasExtension(); } bool isAmbiguous(extDirection dir) const { return m_ext.dir[dir].isAmbiguous(); } /** Return the complement of this data. */ KmerData operator~() const { KmerData o; o.m_flags = complement(SeqFlag(m_flags)); o.m_multiplicity[0] = m_multiplicity[1]; o.m_multiplicity[1] = m_multiplicity[0]; o.m_ext = ~m_ext; return o; } friend std::ostream& operator<<( std::ostream& out, const KmerData& o) { return out << "C=" << o.m_multiplicity[0] + o.m_multiplicity[1]; } protected: uint8_t m_flags; uint16_t m_multiplicity[2]; ExtensionRecord m_ext; }; #endif abyss-1.3.6/Assembly/Options.cpp000644 002433 001057 00000016636 12116214001 020275 0ustar00traymondassembly000000 000000 /** Written by Shaun Jackman . */ #include "config.h" #include "Common/Options.h" #include "DataLayer/Options.h" #include "Kmer.h" #include #include // for INT_MAX #include #include #include #include #include using namespace std; #define PROGRAM "ABYSS" namespace opt { static const char VERSION_MESSAGE[] = PROGRAM " (" PACKAGE_NAME ") " VERSION "\n" "Written by Jared Simpson and Shaun Jackman.\n" "\n" "Copyright 2013 Canada's Michael Smith Genome Science Centre\n"; static const char USAGE_MESSAGE[] = "Usage: " PROGRAM " [OPTION]... FILE...\n" "Assemble the input files, FILE, which may be in FASTA, FASTQ,\n" "qseq, export, SAM or BAM format and compressed with gz, bz2 or xz.\n" "\n" " Options:\n" "\n" " --chastity discard unchaste reads [default]\n" " --no-chastity do not discard unchaste reads\n" " --trim-masked trim masked bases from the ends of reads\n" " [default]\n" " --no-trim-masked do not trim masked bases from the ends of\n" " reads\n" " -q, --trim-quality=N trim bases from the ends of reads whose\n" " quality is less than the threshold\n" " --standard-quality zero quality is `!' (33)\n" " default for FASTQ and SAM files\n" " --illumina-quality zero quality is `@' (64)\n" " default for qseq and export files\n" " -o, --out=FILE write the contigs to FILE\n" " -k, --kmer=N k-mer size\n" " -t, --trim-length=N maximum length of dangling edges to trim\n" " -c, --coverage=FLOAT remove contigs with mean k-mer coverage\n" " less than this threshold\n" " -b, --bubbles=N pop bubbles shorter than N bp [3*k]\n" " -b0, --no-bubbles do not pop bubbles\n" " -e, --erode=N erode bases at the ends of blunt contigs\n" " with coverage less than this threshold\n" " -E, --erode-strand=N erode bases at the ends of blunt contigs\n" " with coverage less than this threshold on\n" " either strand\n" " --coverage-hist=FILE write the k-mer coverage histogram to FILE\n" " -g, --graph=FILE generate a graph in dot format\n" " -s, --snp=FILE record popped bubbles in FILE\n" " -v, --verbose display verbose output\n" " --help display this help and exit\n" " --version output version information and exit\n" "\n" "Report bugs to <" PACKAGE_BUGREPORT ">.\n"; /** k-mer length */ int kmerSize = -1; int k; // used by Graph /** k-mer range */ int kMin = -1; int kMax = -1; int kStep = 1; /** erosion coverage */ unsigned erode = (unsigned)-1; /** erosion strand coverage */ unsigned erodeStrand = (unsigned)-1; /** trim length */ int trimLen = -1; /** Coverage cutoff. */ float coverage = -1; /** Pop bubbles shorter than N bp. */ int bubbleLen = -1; /** coverage histogram path */ string coverageHistPath; /** output contigs path */ string contigsPath; /** temporary output contigs path * Each node stores its contigs in its own file temporarily. */ string contigsTempPath; /** graph output */ string graphPath; /** output bubble path */ string snpPath; /** input FASTA files */ vector inFiles; static const char shortopts[] = "b:c:e:E:g:k:o:q:s:t:v"; enum { OPT_HELP = 1, OPT_VERSION, COVERAGE_HIST }; static const struct option longopts[] = { { "out", required_argument, NULL, 'o' }, { "kmer", required_argument, NULL, 'k' }, { "trim-length", required_argument, NULL, 't' }, { "chastity", no_argument, &opt::chastityFilter, 1 }, { "no-chastity", no_argument, &opt::chastityFilter, 0 }, { "trim-masked", no_argument, &opt::trimMasked, 1 }, { "no-trim-masked", no_argument, &opt::trimMasked, 0 }, { "trim-quality", required_argument, NULL, 'q' }, { "standard-quality", no_argument, &opt::qualityOffset, 33 }, { "illumina-quality", no_argument, &opt::qualityOffset, 64 }, { "coverage", required_argument, NULL, 'c' }, { "coverage-hist", required_argument, NULL, COVERAGE_HIST }, { "bubble-length", required_argument, NULL, 'b' }, { "no-bubbles", no_argument, &opt::bubbleLen, 0 }, { "erode", required_argument, NULL, 'e' }, { "erode-strand", required_argument, NULL, 'E' }, { "no-erode", no_argument, (int*)&erode, 0 }, { "graph", required_argument, NULL, 'g' }, { "snp", required_argument, NULL, 's' }, { "verbose", no_argument, NULL, 'v' }, { "help", no_argument, NULL, OPT_HELP }, { "version", no_argument, NULL, OPT_VERSION }, { NULL, 0, NULL, 0 } }; /** Parse the specified command line. */ void parse(int argc, char* const* argv) { ostringstream sargv; if (opt::rank <= 0) { char* const* last = argv + argc - 1; copy(argv, last, ostream_iterator(sargv, " ")); sargv << *last; } bool die = false; for (int c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;) { istringstream arg(optarg != NULL ? optarg : ""); switch (c) { case '?': die = true; break; case 'b': arg >> bubbleLen; break; case 'c': arg >> coverage; break; case 'k': arg >> kmerSize; k = kmerSize; kMin = kmerSize; switch (arg.get()) { case ',': arg >> kMax; kStep = kMax - kMin; break; case '-': arg >> kMax; if (arg.get() == ':') arg >> kStep; break; default: kMax = kmerSize; } assert(kMin <= kMax); break; case COVERAGE_HIST: getline(arg, coverageHistPath); break; case 'o': getline(arg, contigsPath); break; case 'e': arg >> erode; break; case 'E': arg >> erodeStrand; break; case 't': arg >> trimLen; break; case 'g': getline(arg, graphPath); break; case 'q': arg >> opt::qualityThreshold; break; case 's': getline(arg, snpPath); break; case 'v': verbose++; break; case OPT_HELP: cout << USAGE_MESSAGE; exit(EXIT_SUCCESS); case OPT_VERSION: cout << VERSION_MESSAGE; exit(EXIT_SUCCESS); } if (optarg != NULL && !arg.eof()) { cerr << PROGRAM ": invalid option: `-" << (char)c << optarg << "'\n"; exit(EXIT_FAILURE); } } if (kmerSize <= 0) { cerr << PROGRAM ": missing -k,--kmer option\n"; die = true; } if (contigsPath.empty()) { cerr << PROGRAM ": missing -o,--out option\n"; die = true; } if (argv[optind] == NULL) { cerr << PROGRAM ": missing input sequence file argument\n"; die = true; } if (die) { cerr << "Try `" PROGRAM " --help' for more information.\n"; exit(EXIT_FAILURE); } assert(opt::qualityThreshold <= 40); if (opt::rank <= 0 && opt::coverage >= 0 && opt::erode == (unsigned)-1) cerr << "warning: -c,--coverage was specified, " "but -e,--erode was not specified\n" "Previously, the default was -e2 (or --erode=2)." << endl; if (trimLen < 0) trimLen = kmerSize; if (bubbleLen < 0) bubbleLen = 3*kmerSize; assert(bubbleLen == 0 || bubbleLen > kmerSize); if (bubbleLen == 0) snpPath.clear(); Kmer::setLength(kmerSize); inFiles.resize(argc - optind); copy(&argv[optind], &argv[argc], inFiles.begin()); if (rank >= 0) { ostringstream s; s << "contigs-" << opt::rank << ".fa"; contigsTempPath = s.str(); } if (opt::rank <= 0) cout << PACKAGE_STRING "\n" << sargv.str() << endl; } } // namespace opt abyss-1.3.6/Assembly/Options.h000644 002433 001057 00000001132 12114244673 017743 0ustar00traymondassembly000000 000000 #ifndef ASSEMBLY_OPTIONS_H #define ASSEMBLY_OPTIONS_H 1 #include #include namespace opt { extern unsigned kmerSize; extern unsigned kMin; extern unsigned kMax; extern unsigned kStep; extern unsigned erode; extern unsigned erodeStrand; extern unsigned trimLen; extern float coverage; extern unsigned bubbleLen; extern std::string coverageHistPath; extern std::string contigsPath; extern std::string contigsTempPath; extern std::string graphPath; extern std::string snpPath; extern std::vector inFiles; void parse(int argc, char* const* argv); } #endif abyss-1.3.6/Assembly/SequenceCollection.cpp000644 002433 001057 00000015114 12104026026 022421 0ustar00traymondassembly000000 000000 #include "config.h" #include "SequenceCollection.h" #include "Log.h" #include "Common/Options.h" #include "MemoryUtil.h" #include "StringUtil.h" // for toSI #include "Timer.h" #include #include #include #include #include using namespace std; SequenceCollectionHash::SequenceCollectionHash() : m_seqObserver(NULL), m_adjacencyLoaded(false) { #if HAVE_GOOGLE_SPARSE_HASH_MAP // sparse_hash_set uses 2.67 bits per element on a 64-bit // architecture and 2 bits per element on a 32-bit architecture. // The number of elements is rounded up to a power of two. if (opt::rank >= 0) { // Make room for 200 million k-mers. Approximately 58 million // 96-mers fit into 2 GB of ram, which results in a hash load // of 0.216, and approximately 116 million 32-mers, which // results in a hash load of 0.432. m_data.rehash(200000000); m_data.min_load_factor(0.2); } else { // Allocate a big hash for a single processor. m_data.rehash(1<<29); m_data.max_load_factor(0.4); } #endif } /** Add the specified k-mer to this collection. */ void SequenceCollectionHash::add(const Kmer& seq, unsigned coverage) { bool rc; SequenceCollectionHash::iterator it = find(seq, rc); if (it == m_data.end()) { #if HAVE_GOOGLE_SPARSE_HASH_MAP if (m_data.empty()) { /* sparse_hash_set requires that set_deleted_key() * is called before calling erase(). */ Kmer rc(reverseComplement(seq)); assert(rc != seq); m_data.set_deleted_key(rc); } #endif m_data.insert(make_pair(seq, KmerData(SENSE, coverage))); } else it->second.addMultiplicity(rc ? ANTISENSE : SENSE, coverage); } /** Clean up by erasing sequences flagged as deleted. * @return the number of sequences erased */ size_t SequenceCollectionHash::cleanup() { Timer(__func__); size_t count = 0; for (iterator it = m_data.begin(); it != m_data.end();) { if (it->second.deleted()) { m_data.erase(it++); count++; } else ++it; } shrink(); return count; } /** Return the complement of the specified base. * If the assembly is in colour space, this is a no-op. */ static inline uint8_t complementBaseCode(uint8_t base) { return opt::colourSpace ? base : ~base & 0x3; } /** Add an edge to this k-mer. */ bool SequenceCollectionHash::setBaseExtension( const Kmer& kmer, extDirection dir, uint8_t base) { bool rc; SequenceCollectionHash::iterator it = find(kmer, rc); if (it == m_data.end()) return false; bool palindrome = kmer.isPalindrome(); if (!rc || palindrome) it->second.setBaseExtension(dir, base); if (rc || palindrome) it->second.setBaseExtension(!dir, complementBaseCode(base)); return true; } /** Remove the specified extensions from this k-mer. */ void SequenceCollectionHash::removeExtension(const Kmer& kmer, extDirection dir, SeqExt ext) { bool rc; SequenceCollectionHash::iterator it = find(kmer, rc); assert(it != m_data.end()); bool palindrome = kmer.isPalindrome(); if (!rc || palindrome) it->second.removeExtension(dir, ext); if (rc || palindrome) it->second.removeExtension(!dir, ~ext); notify(*it); } void SequenceCollectionHash::setFlag(const Kmer& key, SeqFlag flag) { bool rc; SequenceCollectionHash::iterator it = find(key, rc); assert(it != m_data.end()); it->second.setFlag(rc ? complement(flag) : flag); } void SequenceCollectionHash::wipeFlag(SeqFlag flag) { for (SequenceCollectionHash::iterator it = m_data.begin(); it != m_data.end(); ++it) it->second.clearFlag(flag); } /** Print the load of the hash table. */ void SequenceCollectionHash::printLoad() const { size_t size = m_data.size(); size_t buckets = m_data.bucket_count(); logger(1) << "Hash load: " << size << " / " << buckets << " = " << setprecision(3) << (float)size / buckets << " using " << toSI(getMemoryUsage()) << "B" << endl; } /** Return an iterator pointing to the specified k-mer or its * reverse complement. Return in rc whether the sequence is reversed. */ SequenceCollectionHash::iterator SequenceCollectionHash::find( const Kmer& key, bool& rc) { SequenceCollectionHash::iterator it = find(key); if (it != m_data.end()) { rc = false; return it; } else { rc = true; return find(reverseComplement(key)); } } /** Return an iterator pointing to the specified k-mer or its * reverse complement. Return in rc whether the sequence is reversed. */ SequenceCollectionHash::const_iterator SequenceCollectionHash::find( const Kmer& key, bool& rc) const { SequenceCollectionHash::const_iterator it = find(key); if (it != m_data.end()) { rc = false; return it; } else { rc = true; return find(reverseComplement(key)); } } /** Return the sequence and data of the specified key. * The key sequence may not contain data. The returned sequence will * contain data. */ const SequenceCollectionHash::value_type& SequenceCollectionHash:: getSeqAndData(const Kmer& key) const { bool rc; SequenceCollectionHash::const_iterator it = find(key, rc); // rc should not be ignored. This seems quite dubious. // The edges of this k-mer should be complemented. assert(it != m_data.end()); return *it; } /** Return the data of the specified key. */ bool SequenceCollectionHash::getSeqData(const Kmer& key, ExtensionRecord& extRecord, int& multiplicity) const { bool rc; SequenceCollectionHash::const_iterator it = find(key, rc); if (it == m_data.end()) return false; const KmerData data = it->second; extRecord = rc ? ~data.extension() : data.extension(); multiplicity = data.getMultiplicity(); return true; } #include /** Write this collection to disk. * @param path does not include the extension */ void SequenceCollectionHash::store(const char* path) { assert(path != NULL); #if HAVE_GOOGLE_SPARSE_HASH_MAP ostringstream s; s << path; if (opt::rank >= 0) s << '-' << setfill('0') << setw(3) << opt::rank; s << ".kmer"; FILE* f = fopen(s.str().c_str(), "w"); if (f == NULL) { perror(s.str().c_str()); exit(EXIT_FAILURE); } shrink(); m_data.write_metadata(f); m_data.write_nopointer_data(f); fclose(f); #else // Not supported. assert(false); exit(EXIT_FAILURE); #endif } /** Load this collection from disk. */ void SequenceCollectionHash::load(const char* path) { #if HAVE_GOOGLE_SPARSE_HASH_MAP FILE* f = fopen(path, "r"); if (f == NULL) { perror(path); exit(EXIT_FAILURE); } m_data.read_metadata(f); m_data.read_nopointer_data(f); fclose(f); m_adjacencyLoaded = true; #else (void)path; // Not supported. assert(false); exit(EXIT_FAILURE); #endif } /** Indicate that this is a colour-space collection. */ void SequenceCollectionHash::setColourSpace(bool flag) { if (!m_data.empty()) assert(opt::colourSpace == flag); opt::colourSpace = flag; } abyss-1.3.6/Assembly/SequenceCollection.h000644 002433 001057 00000017275 12104026026 022100 0ustar00traymondassembly000000 000000 #ifndef SEQUENCECOLLECTION_H #define SEQUENCECOLLECTION_H 1 #include "Graph/Properties.h" #include "ISequenceCollection.h" #include #include #include using boost::graph_traits; /** A map of Kmer to KmerData. */ class SequenceCollectionHash : public ISequenceCollection { public: typedef SequenceDataHash::key_type key_type; typedef SequenceDataHash::mapped_type mapped_type; typedef SequenceDataHash::value_type value_type; typedef mapped_type vertex_property_type; typedef no_property edge_property_type; SequenceCollectionHash(); void add(const Kmer& seq, unsigned coverage = 1); /** Remove the specified sequence if it exists. */ void remove(const Kmer& seq) { setFlag(seq, SF_DELETE); } // Clean up by erasing sequences flagged as deleted. size_t cleanup(); /** Shrink the hash table. */ void shrink() { m_data.rehash(0); printLoad(); } // Print the load of the hash table. void printLoad() const; // Set flag for sequence seq void setFlag(const Kmer& seq, SeqFlag flag); // Clear the specified flag from every sequence in the // collection. void wipeFlag(SeqFlag flag); bool setBaseExtension(const Kmer& seq, extDirection dir, uint8_t base); void removeExtension(const Kmer& seq, extDirection dir, SeqExt ext); // get the extensions of a sequence bool getSeqData(const Kmer& seq, ExtensionRecord& extRecord, int& multiplicity) const; const value_type& getSeqAndData(const Kmer& key) const; /** Return the data associated with the specified key. */ const mapped_type operator[](const key_type& key) const { bool rc; SequenceCollectionHash::const_iterator it = find(key, rc); assert(it != m_data.end()); return rc ? ~it->second : it->second; } iterator begin() { return m_data.begin(); } const_iterator begin() const { return m_data.begin(); } iterator end() { return m_data.end(); } const_iterator end() const { return m_data.end(); } /** Return true if this collection is empty. */ bool empty() const { return m_data.empty(); } /** Return the number of sequences in this collection. */ size_t size() const { return m_data.size(); } // Not a network sequence collection. Nothing to do. size_t pumpNetwork() { return 0; } /** Attach the specified observer. */ void attach(SeqObserver f) { assert(m_seqObserver == NULL); m_seqObserver = f; } /** Detach the specified observer. */ void detach(SeqObserver f) { assert(m_seqObserver == f); (void)f; m_seqObserver = NULL; } void load(const char *path); void store(const char* path); bool isAdjacencyLoaded() const { return m_adjacencyLoaded; } void setColourSpace(bool flag); private: iterator find(const Kmer& key) { return m_data.find(key); } const_iterator find(const Kmer& key) const { return m_data.find(key); } iterator find(const Kmer& key, bool& rc); const_iterator find(const Kmer& key, bool& rc) const; /** Call the observers of the specified sequence. */ void notify(const value_type& seq) { if (m_seqObserver != NULL) m_seqObserver(this, seq); } /** The underlying collection. */ SequenceDataHash m_data; /** The observers. Only a single observer is implemented.*/ SeqObserver m_seqObserver; /** Whether adjacency information has been loaded. */ bool m_adjacencyLoaded; }; // Graph namespace boost { template <> struct graph_traits { // Graph typedef SequenceCollectionHash::key_type vertex_descriptor; typedef boost::directed_tag directed_category; struct traversal_category : boost::adjacency_graph_tag, boost::vertex_list_graph_tag { }; typedef boost::disallow_parallel_edge_tag edge_parallel_category; // IncidenceGraph typedef std::pair edge_descriptor; typedef unsigned degree_size_type; typedef void out_edge_iterator; // BidirectionalGraph typedef void in_edge_iterator; // VertexListGraph typedef size_t vertices_size_type; // EdgeListGraph typedef void edge_iterator; typedef void edges_size_type; // AdjacencyGraph /** Iterate through the adjacent vertices of a vertex. */ struct adjacency_iterator : public std::iterator { /** Skip to the next edge that is present. */ void next() { for (; m_i < NUM_BASES && !m_adj.checkBase(m_i); m_i++) { } if (m_i < NUM_BASES) m_v.setLastBase(SENSE, m_i); } public: adjacency_iterator() : m_i(NUM_BASES) { } adjacency_iterator( vertex_descriptor u, SeqExt adj) : m_v(u), m_adj(adj), m_i(0) { m_v.shift(SENSE); next(); } const vertex_descriptor& operator*() const { assert(m_i < NUM_BASES); return m_v; } bool operator==(const adjacency_iterator& it) const { return m_i == it.m_i; } bool operator!=(const adjacency_iterator& it) const { return !(*this == it); } adjacency_iterator& operator++() { assert(m_i < NUM_BASES); ++m_i; next(); return *this; } private: vertex_descriptor m_v; SeqExt m_adj; short unsigned m_i; }; // adjacency_iterator // VertexListGraph /** Iterate through the vertices of this graph. */ struct vertex_iterator : public std::iterator { typedef SequenceCollectionHash::const_iterator It; public: vertex_iterator(const It& it) : m_it(it), m_sense(false) { } const vertex_descriptor operator*() const { return m_sense ? reverseComplement(m_it->first) : m_it->first; } bool operator==(const vertex_iterator& it) const { return m_it == it.m_it && m_sense == it.m_sense; } bool operator!=(const vertex_iterator& it) const { return !(*this == it); } vertex_iterator& operator++() { if (m_sense) { ++m_it; m_sense = false; } else m_sense = true; return *this; } private: It m_it; bool m_sense; }; // vertex_iterator }; // graph_traits } // namespace boost // IncidenceGraph static inline graph_traits::degree_size_type out_degree( graph_traits::vertex_descriptor u, const SequenceCollectionHash& g) { return g[u].getExtension(SENSE).outDegree(); } // BidirectionalGraph static inline graph_traits::degree_size_type in_degree(graph_traits::vertex_descriptor u, const SequenceCollectionHash& g) { return g[u].getExtension(ANTISENSE).outDegree(); } // AdjacencyGraph static inline std::pair::adjacency_iterator, graph_traits::adjacency_iterator> adjacent_vertices( graph_traits::vertex_descriptor u, const SequenceCollectionHash& g) { typedef graph_traits::adjacency_iterator adjacency_iterator; SeqExt adj = g[u].getExtension(SENSE); return std::make_pair(adjacency_iterator(u, adj), adjacency_iterator()); } // VertexListGraph static inline std::pair::vertex_iterator, graph_traits::vertex_iterator> vertices(const SequenceCollectionHash& g) { return std::make_pair(g.begin(), g.end()); } // PropertyGraph /** Return the reverse complement of the specified k-mer. */ static inline graph_traits::vertex_descriptor get(vertex_complement_t, const SequenceCollectionHash&, graph_traits::vertex_descriptor u) { return reverseComplement(u); } static inline bool get(vertex_removed_t, const SequenceCollectionHash& g, graph_traits::vertex_descriptor u) { return g.getSeqAndData(u).second.deleted(); } static inline no_property get(edge_bundle_t, const SequenceCollectionHash&, graph_traits::edge_descriptor) { return no_property(); } #endif abyss-1.3.6/doc/Makefile.in000644 002433 001057 00000035467 12176317672 017224 0ustar00traymondassembly000000 000000 # Makefile.in generated by automake 1.14 from Makefile.am. # @configure_input@ # Copyright (C) 1994-2013 Free Software Foundation, Inc. # This Makefile.in is free software; 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Users wishing to run a full assembly with ABySS are recommended to use abyss-pe as their entry point rather than the ABYSS program. abyss-pe is a Makefile that coordinates many of the ABySS tools (including ABYSS) in order to run the full ABySS assembly pipeline. abyss-pe is capable of doing many things that ABYSS is not, such as leveraging the distance information provided by paired end reads and mate pair reads. .TP \fB--chastity\fR discard unchaste reads [default] .TP \fB--no-chastity\fR do not discard unchaste reads .TP \fB--trim-masked\fR trim masked bases from the ends of reads [default] .TP \fB--no-trim-masked\fR do not trim masked bases from the ends of reads .TP \fB-q\fR, \fB--trim-quality\fR=\fITHRESHOLD\fR trim bases from the ends of reads whose quality is less than the threshold .TP \fB--standard-quality\fR zero quality is `!' (33) .br default for FASTQ and SAM files .TP \fB--illumina-quality\fR zero quality is `@' (64) .br default for qseq and export files .TP \fB\-o\fR, \fB\-\-out\fR=\fIFILE\fR write the contigs to FILE .TP \fB\-k\fR, \fB\-\-kmer\fR=\fIKMER_SIZE\fR k\-mer size .TP \fB\-t\fR, \fB\-\-trim\-length\fR=\fITRIM_LENGTH\fR maximum length of dangling edges to trim .TP \fB\-c\fR, \fB\-\-coverage\fR=\fICOVERAGE\fR remove contigs with mean k-mer coverage less than this threshold .TP \fB\-b\fR, \fB\-\-bubbles\fR=\fIN\fR pop bubbles shorter than N bp (default: 3*k). .TP \fB\-b\fR0, \fB\-\-no\-bubbles\fR do not pop bubbles .TP \fB\-e\fR, \fB\-\-erode\fR=\fICOVERAGE\fR erode bases at the ends of blunt contigs with coverage less than this threshold .TP \fB\-E\fR, \fB\-\-erode-strand\fR=\fICOVERAGE\fR erode bases at the ends of blunt contigs with coverage less than this threshold on either strand .TP \fB\-\-coverage-hist\fR=\fIFILE\fR record the k-mer coverage histogram in FILE .TP \fB\-g\fR, \fB\-\-graph\fR=\fIFILE\fR generate a graph in dot format .TP \fB\-s\fR, \fB\-\-snp\fR=\fIFILE\fR record popped bubbles in FILE .TP \fB\-v\fR, \fB\-\-verbose\fR display verbose output .TP \fB\-\-help\fR display this help and exit .TP \fB\-\-version\fR output version information and exit .SH AUTHOR Written by Jared Simpson and Shaun Jackman. .SH "REPORTING BUGS" Report bugs to . .SH COPYRIGHT Copyright 2013 Canada's Michael Smith Genome Science Centre abyss-1.3.6/doc/abyss-pe.1000644 002433 001057 00000012735 12176307177 016754 0ustar00traymondassembly000000 000000 .TH abyss-pe "1" "2013-Jul" "abyss-pe (ABySS) 1.3.6" "User Commands" .SH NAME abyss-pe - assemble reads into contigs .SH SYNOPSIS .B abyss-pe [\fIOPTION\fR]... [\fIPARAMETER\fR=\fIVALUE\fR]... [\fIMAKE_TARGET\fR]... .SH DESCRIPTION Assemble the reads of the input files into contigs. The reads may be in FASTA, FASTQ, qseq, export, SRA, SAM or BAM format and may be compressed with gz, bz2 or xz and may be tarred. abyss-pe is a Makefile script. Any options of make may also be used with abyss-pe. .SS "Parameters of abyss-pe" .TP \fBname\fR, \fBJOB_NAME\fR The name of this assembly. The resulting scaffolds will be stored in ${name}-scaffolds.fa. .TP .B in input files. Use this variable when assembling data from a single library. .TP .B lib a quoted list of whitespace-separated paired-end library names. Use this varible when assembling data from multiple paired-end libraries. For each library name in lib, the user must define a variable on the command line with the same name, which indicates the read files for that library. See \fBEXAMPLES\fR below for a concrete example of usage. .TP .B pe list of paired-end libraries that will be used only for merging unitigs into contigs and will not contribute toward the consensus sequence. .TP .B mp list of mate-pair libraries that will be used for scaffolding. Mate-pair libraries do not contribute toward the consensus sequence. .TP .B se files containing single-end reads .TP .B a maximum number of branches of a bubble [2] .TP .B b maximum length of a bubble (bp) [10000] .TP .B c minimum mean k-mer coverage of a unitig [sqrt(median)] .TP .B d allowable error of a distance estimate (bp) [6] .TP .B e minimum erosion k-mer coverage [sqrt(median)] .TP .B E minimum erosion k-mer coverage per strand [1] .TP .B j number of threads [2] .TP .B k size of k-mer (bp) .TP .B l minimum alignment length of a read (bp) [k] .TP .B m minimum overlap of two unitigs (bp) [30] .TP .B n minimum number of pairs required for building contigs [10] .TP .B N minimum number of pairs required for building scaffolds [n] .TP .B p minimum sequence identity of a bubble [0.9] .TP .B q minimum base quality [3] .br Trim bases from the ends of reads whose quality is less q. .TP .B s minimum unitig size required for building contigs (bp) [200] .br The seed length should be at least twice the value of k. If more sequence is assembled than the expected genome size, try increasing s. .TP .B S minimum contig size required for building scaffolds (bp) [s] .TP .B t minimum tip size (bp) [2k] .TP .B v v=-v to enable verbose logging .TP \fBnp\fR, \fBNSLOTS\fR the number of processes of an MPI assembly .TP .B mpirun the path to mpirun .TP .B aligner the program to use to align the reads to the contigs [map] .br map, kaligner, bwa, bwasw, bowtie or bowtie2 .TP .B cs convert colour-space contigs to nucleotide contigs following assembly .SS "Options of make" .TP \fB-n\fR, \fB--dry-run\fR Print the commands that would be executed, but do not execute them. .SS "Make targets for abyss-pe" .TP .B default Equivalent to `scaffolds scaffolds-dot stats'. .TP .B unitigs Assemble unitigs. .TP .B unitigs-dot Output the unitig overlap graph. .TP .B pe-sam Map paired-end reads to the unitigs and output a SAM file. .TP .B pe-bam Map paired-end reads to the unitigs and output a BAM file. .TP .B pe-index Generate an index of the unitigs used by abyss-map. .TP .B contigs Assemble contigs. .TP .B contigs-dot Output the contig overlap graph. .TP .B mp-sam Map mate-pair reads to the contigs and output a SAM file. .TP .B mp-bam Map mate-pair reads to the contigs and output a BAM file. .TP .B mp-index Generate an index of the contigs used by abyss-map. .TP .B scaffolds Assemble scaffolds. .TP .B scaffolds-dot Output the scaffold overlap graph. .TP .B stats Display assembly contiguity statistics. .TP .B clean Remove intermediate files. .TP .B version Display the version of abyss-pe. .TP .B versions Display the versions of all programs used by abyss-pe. .TP .B help Display a helpful message. .SH "ENVIRONMENT VARIABLES" Any parameter that may be specified on the command line may also be specified in an environment variable. .TP .B PATH must contain the directory where the ABySS executables are installed. Use `abyss-pe versions` to check that PATH is configured correctly. .TP .B TMPDIR specifies a directory to use for temporary files .SS "Scheduler integration" ABySS integrates well with cluster job schedulers, such as: * SGE (Sun Grid Engine) * Portable Batch System (PBS) * Load Sharing Facility (LSF) * IBM LoadLeveler The SGE environment variables JOB_NAME, SGE_TASK_ID and NSLOTS may be used to specify the parameters name, k and np, respectively, and similarly for other schedulers. .SH EXAMPLES .SS "One paired-end library" abyss-pe k=64 name=ecoli in='reads1.fa reads2.fa' .SS "Multiple paired-end libraries" abyss-pe k=64 name=ecoli lib='lib1 lib2' \\ .br lib1='lib1_1.fa lib1_2.fa' lib2='lib2_1.fa lib2_2.fa' \\ .br se='se1.fa se2.fa' .SS "Paired-end and mate-pair libraries abyss-pe k=64 name=ecoli lib='pe1 pe2' mp='mp1 mp2' \\ .br pe1='pe1_1.fa pe1_2.fa' pe2='pe2_1.fa pe2_2.fa' \\ .br mp1='mp1_1.fa mp1_2.fa' mp2='mp2_1.fa mp2_2.fa' \\ .br se='se1.fa se2.fa' .SS MPI abyss-pe np=8 k=64 name=ecoli in='reads1.fa reads2.fa' .SS SGE qsub -N ecoli -t 64 -pe openmpi 8 \\ .br abyss-pe n=10 in='reads1.fa reads2.fa' .SH "SEE ALSO" make(1), ABYSS(1) .SH AUTHOR Written by Shaun Jackman. .SH "REPORTING BUGS" Report bugs to . .SH COPYRIGHT Copyright 2013 Canada's Michael Smith Genome Science Centre abyss-1.3.6/doc/abyss-tofastq.1000644 002433 001057 00000001223 12176307177 020017 0ustar00traymondassembly000000 000000 .TH abyss-tofastq "1" "2013-Jul" "ABySS 1.3.6" "User Commands" .SH NAME abyss-tofastq \- convert various file formats to FASTQ format .br abyss-tofasta \- convert various file formats to FASTA format .SH SYNOPSIS \fBabyss-tofastq\fR [\fIFILE\fR]... .br or .br \fBabyss-tofasta\fR [\fIFILE\fR]... .SH DESCRIPTION Convert the input files to FASTA or FASTQ format. 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endobj 89 0 obj 117 endobj 108 0 obj << /Length 109 0 R /Type /XObject /Subtype /Image /Width 131 /Height 60 /Interpolate true /ColorSpace 191 0 R /SMask 266 0 R /BitsPerComponent 8 /Filter /FlateDecode >> stream x1 Om /@a 0` 0` 0` 0` 0` 0` 0` 0` 0` 0` 0`c`\ endstream endobj 109 0 obj 126 endobj 96 0 obj << /Length 97 0 R /Type /XObject /Subtype /Image /Width 112 /Height 40 /Interpolate true /ColorSpace 191 0 R /SMask 268 0 R /BitsPerComponent 8 /Filter /FlateDecode >> stream xЁàS_Pa 0` 0` 0` 0` 0` 0`?04 endstream endobj 97 0 obj 82 endobj 144 0 obj << /Length 145 0 R /Type /XObject /Subtype /Image /Width 112 /Height 40 /Interpolate true /ColorSpace 191 0 R /SMask 270 0 R /BitsPerComponent 8 /Filter /FlateDecode >> stream xЁàS_Pa 0` 0` 0` 0` 0` 0`?04 endstream endobj 145 0 obj 82 endobj 160 0 obj << /Length 161 0 R /Type /XObject /Subtype /Image /Width 75 /Height 60 /Interpolate true /ColorSpace 191 0 R /SMask 272 0 R /BitsPerComponent 8 /Filter /FlateDecode >> stream x1 Om O@a 0` 0` 0` 0` 0` 0`4 endstream endobj 161 0 obj 83 endobj 154 0 obj << /Length 155 0 R /Type /XObject /Subtype /Image /Width 119 /Height 60 /Interpolate true /ColorSpace 191 0 R /SMask 274 0 R /BitsPerComponent 8 /Filter /FlateDecode >> stream x  O( 0` 0` 0` 0` 0` 0` 0` 0` 0` 0` S endstream endobj 155 0 obj 117 endobj 182 0 obj << /Length 183 0 R /Type /XObject /Subtype /Image /Width 75 /Height 60 /Interpolate true /ColorSpace 191 0 R /SMask 276 0 R /BitsPerComponent 8 /Filter /FlateDecode >> stream x1 Om O@a 0` 0` 0` 0` 0` 0`4 endstream endobj 183 0 obj 83 endobj 84 0 obj << /Length 85 0 R /Type /XObject /Subtype /Image /Width 119 /Height 60 /Interpolate true /ColorSpace 191 0 R /SMask 278 0 R /BitsPerComponent 8 /Filter /FlateDecode >> stream x  O( 0` 0` 0` 0` 0` 0` 0` 0` 0` 0` S endstream endobj 85 0 obj 117 endobj 104 0 obj << /Length 105 0 R /Type /XObject /Subtype /Image /Width 140 /Height 40 /Interpolate true /ColorSpace 191 0 R /SMask 280 0 R /BitsPerComponent 8 /Filter /FlateDecode >> stream xЁàSPa 0` 0` 0` 0` 0` 0` 0` 0A endstream endobj 105 0 obj 97 endobj 10 0 obj << /Length 11 0 R /Type /XObject /Subtype /Image /Width 112 /Height 40 /Interpolate true /ColorSpace 191 0 R /SMask 282 0 R /BitsPerComponent 8 /Filter /FlateDecode >> stream xЁàS_Pa 0` 0` 0` 0` 0` 0`?04 endstream endobj 11 0 obj 82 endobj 82 0 obj << /Length 83 0 R /Type /XObject /Subtype /Image /Width 112 /Height 40 /Interpolate true /ColorSpace 191 0 R /SMask 284 0 R /BitsPerComponent 8 /Filter /FlateDecode >> stream xЁàS_Pa 0` 0` 0` 0` 0` 0`?04 endstream endobj 83 0 obj 82 endobj 70 0 obj << /Length 71 0 R /Type /XObject /Subtype /Image /Width 119 /Height 60 /Interpolate true /ColorSpace 191 0 R /SMask 286 0 R /BitsPerComponent 8 /Filter /FlateDecode >> stream x  O( 0` 0` 0` 0` 0` 0` 0` 0` 0` 0` S endstream endobj 71 0 obj 117 endobj 176 0 obj << /Length 177 0 R /Type /XObject /Subtype /Image /Width 75 /Height 60 /Interpolate true /ColorSpace 191 0 R /SMask 288 0 R /BitsPerComponent 8 /Filter /FlateDecode >> stream x1 Om O@a 0` 0` 0` 0` 0` 0`4 endstream endobj 177 0 obj 83 endobj 150 0 obj << /Length 151 0 R /Type /XObject /Subtype /Image /Width 130 /Height 60 /Interpolate true /ColorSpace 191 0 R /SMask 290 0 R /BitsPerComponent 8 /Filter /FlateDecode >> stream x  Om7@a 0` 0` 0` 0` 0` 0` 0` 0` 0` 0` 0`o`[h endstream endobj 151 0 obj 125 endobj 162 0 obj << /Length 163 0 R /Type /XObject /Subtype /Image /Width 114 /Height 60 /Interpolate true /ColorSpace 191 0 R /SMask 292 0 R /BitsPerComponent 8 /Filter /FlateDecode >> stream x1 Om @a 0` 0` 0` 0` 0` 0` 0` 0` 0` P( endstream endobj 163 0 obj 113 endobj 8 0 obj << /Length 9 0 R /Type /XObject /Subtype /Image /Width 114 /Height 60 /Interpolate true /ColorSpace 191 0 R /SMask 294 0 R /BitsPerComponent 8 /Filter /FlateDecode >> stream x1 Om @a 0` 0` 0` 0` 0` 0` 0` 0` 0` P( endstream endobj 9 0 obj 113 endobj 110 0 obj << /Length 111 0 R /Type /XObject /Subtype /Image /Width 113 /Height 40 /Interpolate true /ColorSpace 191 0 R /SMask 296 0 R /BitsPerComponent 8 /Filter /FlateDecode >> stream x1 Om @a 0` 0` 0` 0` 0` 0`4 endstream endobj 111 0 obj 83 endobj 90 0 obj << /Length 91 0 R /Type /XObject /Subtype /Image /Width 140 /Height 40 /Interpolate true /ColorSpace 191 0 R /SMask 298 0 R /BitsPerComponent 8 /Filter /FlateDecode >> stream xЁàSPa 0` 0` 0` 0` 0` 0` 0` 0A endstream endobj 91 0 obj 97 endobj 134 0 obj << /Length 135 0 R /Type /XObject /Subtype /Image /Width 119 /Height 60 /Interpolate true /ColorSpace 191 0 R /SMask 300 0 R /BitsPerComponent 8 /Filter /FlateDecode >> stream x  O( 0` 0` 0` 0` 0` 0` 0` 0` 0` 0` S endstream endobj 135 0 obj 117 endobj 136 0 obj << /Length 137 0 R /Type /XObject /Subtype /Image /Width 112 /Height 40 /Interpolate true /ColorSpace 191 0 R /SMask 302 0 R /BitsPerComponent 8 /Filter /FlateDecode >> stream xЁàS_Pa 0` 0` 0` 0` 0` 0`?04 endstream endobj 137 0 obj 82 endobj 132 0 obj << /Length 133 0 R /Type /XObject /Subtype /Image /Width 75 /Height 60 /Interpolate true /ColorSpace 191 0 R /SMask 304 0 R /BitsPerComponent 8 /Filter /FlateDecode >> stream x1 Om O@a 0` 0` 0` 0` 0` 0`4 endstream endobj 133 0 obj 83 endobj 72 0 obj << /Length 73 0 R /Type /XObject /Subtype /Image /Width 112 /Height 40 /Interpolate true /ColorSpace 191 0 R /SMask 306 0 R /BitsPerComponent 8 /Filter /FlateDecode >> stream xЁàS_Pa 0` 0` 0` 0` 0` 0`?04 endstream endobj 73 0 obj 82 endobj 142 0 obj << /Length 143 0 R /Type /XObject /Subtype /Image /Width 112 /Height 40 /Interpolate true /ColorSpace 191 0 R /SMask 308 0 R /BitsPerComponent 8 /Filter /FlateDecode >> stream xЁàS_Pa 0` 0` 0` 0` 0` 0`?04 endstream endobj 143 0 obj 82 endobj 122 0 obj << /Length 123 0 R /Type /XObject /Subtype /Image /Width 112 /Height 40 /Interpolate true /ColorSpace 191 0 R /SMask 310 0 R /BitsPerComponent 8 /Filter /FlateDecode >> stream xЁàS_Pa 0` 0` 0` 0` 0` 0`?04 endstream endobj 123 0 obj 82 endobj 54 0 obj << /Length 55 0 R /Type /XObject /Subtype /Image /Width 119 /Height 60 /Interpolate true /ColorSpace 191 0 R /SMask 312 0 R /BitsPerComponent 8 /Filter /FlateDecode >> stream x  O( 0` 0` 0` 0` 0` 0` 0` 0` 0` 0` S endstream endobj 55 0 obj 117 endobj 168 0 obj << /Length 169 0 R /Type /XObject /Subtype /Image /Width 75 /Height 60 /Interpolate true /ColorSpace 191 0 R /SMask 314 0 R /BitsPerComponent 8 /Filter /FlateDecode >> stream x1 Om O@a 0` 0` 0` 0` 0` 0`4 endstream endobj 169 0 obj 83 endobj 64 0 obj << /Length 65 0 R /Type /XObject /Subtype /Image /Width 112 /Height 40 /Interpolate true /ColorSpace 191 0 R /SMask 316 0 R /BitsPerComponent 8 /Filter /FlateDecode >> stream xЁàS_Pa 0` 0` 0` 0` 0` 0`?04 endstream endobj 65 0 obj 82 endobj 86 0 obj << /Length 87 0 R /Type /XObject /Subtype /Image /Width 112 /Height 40 /Interpolate true /ColorSpace 191 0 R /SMask 318 0 R /BitsPerComponent 8 /Filter /FlateDecode >> stream xЁàS_Pa 0` 0` 0` 0` 0` 0`?04 endstream endobj 87 0 obj 82 endobj 164 0 obj << /Length 165 0 R /Type /XObject /Subtype /Image /Width 112 /Height 40 /Interpolate true /ColorSpace 191 0 R /SMask 320 0 R /BitsPerComponent 8 /Filter /FlateDecode >> stream xЁàS_Pa 0` 0` 0` 0` 0` 0`?04 endstream endobj 165 0 obj 82 endobj 92 0 obj << /Length 93 0 R /Type /XObject /Subtype /Image /Width 114 /Height 60 /Interpolate true /ColorSpace 191 0 R /SMask 322 0 R /BitsPerComponent 8 /Filter /FlateDecode >> stream x1 Om @a 0` 0` 0` 0` 0` 0` 0` 0` 0` P( endstream endobj 93 0 obj 113 endobj 74 0 obj << /Length 75 0 R /Type /XObject /Subtype /Image /Width 119 /Height 60 /Interpolate true /ColorSpace 191 0 R /SMask 324 0 R /BitsPerComponent 8 /Filter /FlateDecode >> stream x  O( 0` 0` 0` 0` 0` 0` 0` 0` 0` 0` S endstream endobj 75 0 obj 117 endobj 94 0 obj << /Length 95 0 R /Type /XObject /Subtype /Image /Width 75 /Height 60 /Interpolate true /ColorSpace 191 0 R /SMask 326 0 R /BitsPerComponent 8 /Filter /FlateDecode >> stream x1 Om O@a 0` 0` 0` 0` 0` 0`4 endstream endobj 95 0 obj 83 endobj 16 0 obj << /Length 17 0 R /Type /XObject /Subtype /Image /Width 112 /Height 40 /Interpolate true /ColorSpace 191 0 R /SMask 328 0 R /BitsPerComponent 8 /Filter /FlateDecode >> stream xЁàS_Pa 0` 0` 0` 0` 0` 0`?04 endstream endobj 17 0 obj 82 endobj 24 0 obj << /Length 25 0 R /Type /XObject /Subtype /Image /Width 114 /Height 60 /Interpolate true /ColorSpace 191 0 R /SMask 330 0 R /BitsPerComponent 8 /Filter /FlateDecode >> stream x1 Om @a 0` 0` 0` 0` 0` 0` 0` 0` 0` P( endstream endobj 25 0 obj 113 endobj 184 0 obj << /Length 185 0 R /Type /XObject /Subtype /Image /Width 140 /Height 40 /Interpolate true /ColorSpace 191 0 R /SMask 332 0 R /BitsPerComponent 8 /Filter /FlateDecode >> stream xЁàSPa 0` 0` 0` 0` 0` 0` 0` 0A endstream endobj 185 0 obj 97 endobj 138 0 obj << /Length 139 0 R /Type /XObject /Subtype /Image /Width 119 /Height 60 /Interpolate true /ColorSpace 191 0 R /SMask 334 0 R /BitsPerComponent 8 /Filter /FlateDecode >> stream x  O( 0` 0` 0` 0` 0` 0` 0` 0` 0` 0` S endstream endobj 139 0 obj 117 endobj 102 0 obj << /Length 103 0 R /Type /XObject /Subtype /Image /Width 75 /Height 60 /Interpolate true /ColorSpace 191 0 R /SMask 336 0 R /BitsPerComponent 8 /Filter /FlateDecode >> stream x1 Om O@a 0` 0` 0` 0` 0` 0`4 endstream endobj 103 0 obj 83 endobj 66 0 obj << /Length 67 0 R /Type /XObject /Subtype /Image /Width 112 /Height 40 /Interpolate true /ColorSpace 191 0 R /SMask 338 0 R /BitsPerComponent 8 /Filter /FlateDecode >> stream xЁàS_Pa 0` 0` 0` 0` 0` 0`?04 endstream endobj 67 0 obj 82 endobj 22 0 obj << /Length 23 0 R /Type /XObject /Subtype /Image /Width 112 /Height 40 /Interpolate true /ColorSpace 191 0 R /SMask 340 0 R /BitsPerComponent 8 /Filter /FlateDecode >> stream xЁàS_Pa 0` 0` 0` 0` 0` 0`?04 endstream endobj 23 0 obj 82 endobj 166 0 obj << /Length 167 0 R /Type /XObject /Subtype /Image /Width 119 /Height 60 /Interpolate true /ColorSpace 191 0 R /SMask 342 0 R /BitsPerComponent 8 /Filter /FlateDecode >> stream x  O( 0` 0` 0` 0` 0` 0` 0` 0` 0` 0` S endstream endobj 167 0 obj 117 endobj 46 0 obj << /Length 47 0 R /Type /XObject /Subtype /Image /Width 119 /Height 60 /Interpolate true /ColorSpace 191 0 R /SMask 344 0 R /BitsPerComponent 8 /Filter /FlateDecode >> stream x  O( 0` 0` 0` 0` 0` 0` 0` 0` 0` 0` S endstream endobj 47 0 obj 117 endobj 156 0 obj << /Length 157 0 R /Type /XObject /Subtype /Image /Width 131 /Height 40 /Interpolate true /ColorSpace 191 0 R /SMask 346 0 R /BitsPerComponent 8 /Filter /FlateDecode >> stream xЁàSPa 0` 0` 0` 0` 0` 0` 0`=h endstream endobj 157 0 obj 91 endobj 126 0 obj << /Length 127 0 R /Type /XObject /Subtype /Image /Width 119 /Height 60 /Interpolate true /ColorSpace 191 0 R /SMask 348 0 R /BitsPerComponent 8 /Filter /FlateDecode >> stream x  O( 0` 0` 0` 0` 0` 0` 0` 0` 0` 0` S endstream endobj 127 0 obj 117 endobj 28 0 obj << /Length 29 0 R /Type /XObject /Subtype /Image /Width 112 /Height 40 /Interpolate true /ColorSpace 191 0 R /SMask 350 0 R /BitsPerComponent 8 /Filter /FlateDecode >> stream xЁàS_Pa 0` 0` 0` 0` 0` 0`?04 endstream endobj 29 0 obj 82 endobj 40 0 obj << /Length 41 0 R /Type /XObject /Subtype /Image /Width 119 /Height 60 /Interpolate true /ColorSpace 191 0 R /SMask 352 0 R /BitsPerComponent 8 /Filter /FlateDecode >> stream x  O( 0` 0` 0` 0` 0` 0` 0` 0` 0` 0` S endstream endobj 41 0 obj 117 endobj 68 0 obj << /Length 69 0 R /Type /XObject /Subtype /Image /Width 112 /Height 40 /Interpolate true /ColorSpace 191 0 R /SMask 354 0 R /BitsPerComponent 8 /Filter /FlateDecode >> stream xЁàS_Pa 0` 0` 0` 0` 0` 0`?04 endstream endobj 69 0 obj 82 endobj 38 0 obj << /Length 39 0 R /Type /XObject /Subtype /Image /Width 119 /Height 60 /Interpolate true /ColorSpace 191 0 R /SMask 356 0 R /BitsPerComponent 8 /Filter /FlateDecode >> stream x  O( 0` 0` 0` 0` 0` 0` 0` 0` 0` 0` S endstream endobj 39 0 obj 117 endobj 18 0 obj << /Length 19 0 R /Type /XObject /Subtype /Image /Width 130 /Height 40 /Interpolate true /ColorSpace 191 0 R /SMask 358 0 R /BitsPerComponent 8 /Filter /FlateDecode >> stream x1 Om @a 0` 0` 0` 0` 0` 0` 0`< endstream endobj 19 0 obj 92 endobj 12 0 obj << /Length 13 0 R /Type /XObject /Subtype /Image /Width 112 /Height 40 /Interpolate true /ColorSpace 191 0 R /SMask 360 0 R /BitsPerComponent 8 /Filter /FlateDecode >> stream xЁàS_Pa 0` 0` 0` 0` 0` 0`?04 endstream endobj 13 0 obj 82 endobj 44 0 obj << /Length 45 0 R /Type /XObject /Subtype /Image /Width 75 /Height 60 /Interpolate true /ColorSpace 191 0 R /SMask 362 0 R /BitsPerComponent 8 /Filter /FlateDecode >> stream x1 Om O@a 0` 0` 0` 0` 0` 0`4 endstream endobj 45 0 obj 83 endobj 60 0 obj << /Length 61 0 R /Type /XObject /Subtype /Image /Width 75 /Height 60 /Interpolate true /ColorSpace 191 0 R /SMask 364 0 R /BitsPerComponent 8 /Filter /FlateDecode >> stream x1 Om O@a 0` 0` 0` 0` 0` 0`4 endstream endobj 61 0 obj 83 endobj 14 0 obj << /Length 15 0 R /Type /XObject /Subtype /Image /Width 112 /Height 40 /Interpolate true /ColorSpace 191 0 R /SMask 366 0 R /BitsPerComponent 8 /Filter /FlateDecode >> stream xЁàS_Pa 0` 0` 0` 0` 0` 0`?04 endstream endobj 15 0 obj 82 endobj 98 0 obj << /Length 99 0 R /Type /XObject /Subtype /Image /Width 130 /Height 40 /Interpolate true /ColorSpace 191 0 R /SMask 368 0 R /BitsPerComponent 8 /Filter /FlateDecode >> stream x1 Om @a 0` 0` 0` 0` 0` 0` 0`< endstream endobj 99 0 obj 92 endobj 112 0 obj << /Length 113 0 R /Type /XObject /Subtype /Image /Width 112 /Height 40 /Interpolate true /ColorSpace 191 0 R /SMask 370 0 R /BitsPerComponent 8 /Filter /FlateDecode >> stream xЁàS_Pa 0` 0` 0` 0` 0` 0`?04 endstream endobj 113 0 obj 82 endobj 340 0 obj << /Length 341 0 R /Type /XObject /Subtype /Image /Width 112 /Height 40 /ColorSpace /DeviceGray /Interpolate true /BitsPerComponent 8 /Filter /FlateDecode >> stream x헿kP͏[cnbD-V%CCM$픡IE(8(NA _{A׷<~dsll0K1 !I1weWAaX0 4+ F" 0.;!rƑ)1Y{ e%q:HS' E!jR3ƵEymdt-szCOF.oZGN]o.#ꃂzqU|w !ӏѠS*^]'i*7x9GtteLh<-UZd6l2*l:erzIB <;>gGw񣻯~[2B][@o>O^;/yP\ypiy5ϻz)œ/? endstream endobj 341 0 obj 588 endobj 258 0 obj << /Length 259 0 R /Type /XObject /Subtype /Image /Width 119 /Height 60 /ColorSpace /DeviceGray /Interpolate true /BitsPerComponent 8 /Filter /FlateDecode >> stream xc` FF&FFFLmdfeec`gcceafBO@&@bFfVn>!Qq)iYZ) 1^N6$32r((ijhki*Iq0cGHRA]Ɩ@KEV ZVnAIE[gO߀ Z7K5Y>xbSбpK̢>LK3Tf{KPZ%(>47%VOQf-#+|nESg߄=muEin&jRkyŕ#2+Zϝ`ެ] VڲBФ'fW?{kVZ6ojgUF Zv~)M+Woܲ`uNh̋p6TFX+ e^7gv2صk疵Ÿ+![+mY7a-Oewh/s7ACZ*[ 2ZVh2qeO\fnغώ ftyBQkԣ0F!0F3$5& W+#;jt:0D`! bNe`al tfI&g4 endstream endobj 259 0 obj 627 endobj 326 0 obj << /Length 327 0 R /Type /XObject /Subtype /Image /Width 75 /Height 60 /ColorSpace /DeviceGray /Interpolate true /BitsPerComponent 8 /Filter /FlateDecode >> stream xc`y7TYXXI,,LLL21sprs 89X cbf' qs#(*)+B$PVRfgaB#+ P_G]IFT^J[i?;QF͓ڴmQ`fT[iJ %l[>}mvn^5.3V[(K7l߳(wז'e%,FVqҎ6 ҨY0>+VGVc(?V @FhbቁXRE*=՚kQF$klS @ K 10Pk P % 1lElW endstream endobj 327 0 obj 581 endobj 298 0 obj << /Length 299 0 R /Type /XObject /Subtype /Image /Width 140 /Height 40 /ColorSpace /DeviceGray /Interpolate true /BitsPerComponent 8 /Filter /FlateDecode >> stream xc`C/p ##3 +] 3#aae`geAs 3+78݀ ?/;+3R01q I*() (+Hp2#+' ݀ 1adR1svspwu57TfcG+wPDt@lTX8?' ҂HnQ4p ϩ띵d tkW,Y`#Qe#肖 Vmڶ>` e8 s"[L=}vعe͂I9aHnaW1+혱lÎ=޶v䦼p'}.xa7.,(p<=Pe]FYnjT,oP^ L8kk3$ @oKRtjJRQm)VA#7O"9($ WSոQj@ DVDKot @h}{3B2FCo2~z endstream endobj 299 0 obj 619 endobj 296 0 obj << /Length 297 0 R /Type /XObject /Subtype /Image /Width 113 /Height 40 /ColorSpace /DeviceGray /Interpolate true /BitsPerComponent 8 /Filter /FlateDecode >> stream x헿kP͏[cnbD-V%CCM$픡IE(8(NA _{A1{xϔLߜ{{Co6 !X q$rHq $ L2 €t5?H`tg7&qBlw' )@|PĉˉrB9PHQ,rld}% e%u9ղHN3G)E+#)մK3ZZy"Ԍn RłgT`S< JZ7K{񩆐GR2"a -4tkv!fnߖ -%mSwj8 {ֳmG I{ǹ]2|uq^/]1wC ퟜ_ٍЙLgNaa_ XW&oBoQP8S/(YӪtD|U̪O0d6_ub!l<*l2oh) >4dc6BF_7˞n6cO7ٓgkU[l}a|Ġ}#ZDis1QZDClwk\_fx_CW_>O ? endstream endobj 297 0 obj 589 endobj 230 0 obj << /Length 231 0 R /Type /XObject /Subtype /Image /Width 112 /Height 40 /ColorSpace /DeviceGray /Interpolate true /BitsPerComponent 8 /Filter /FlateDecode >> stream x헿kP͏[cnbD-V%CCM$픡IE(8(NA _{A׷<~dsll0K1 !I1weWAaX0 4+ F" 0.;!rƑ)1Y{ e%q:HS' E!jR3ƵEymdt-szCOF.oZGN]o.#ꃂzqU|w !ӏѠS*^]'i*7x9GtteLh<-UZd6l2*l:erzIB <;>gGw񣻯~[2B][@o>O^;/yP\ypiy5ϻz)œ/? endstream endobj 231 0 obj 588 endobj 212 0 obj << /Length 213 0 R /Type /XObject /Subtype /Image /Width 112 /Height 40 /ColorSpace /DeviceGray /Interpolate true /BitsPerComponent 8 /Filter /FlateDecode >> stream x헿kP͏[cnbD-V%CCM$픡IE(8(NA _{A׷<~dsll0K1 !I1weWAaX0 4+ F" 0.;!rƑ)1Y{ e%q:HS' E!jR3ƵEymdt-szCOF.oZGN]o.#ꃂzqU|w !ӏѠS*^]'i*7x9GtteLh<-UZd6l2*l:erzIB <;>gGw񣻯~[2B][@o>O^;/yP\ypiy5ϻz)œ/? endstream endobj 213 0 obj 588 endobj 284 0 obj << /Length 285 0 R /Type /XObject /Subtype /Image /Width 112 /Height 40 /ColorSpace /DeviceGray /Interpolate true /BitsPerComponent 8 /Filter /FlateDecode >> stream x헿kP͏[cnbD-V%CCM$픡IE(8(NA _{A׷<~dsll0K1 !I1weWAaX0 4+ F" 0.;!rƑ)1Y{ e%q:HS' E!jR3ƵEymdt-szCOF.oZGN]o.#ꃂzqU|w !ӏѠS*^]'i*7x9GtteLh<-UZd6l2*l:erzIB <;>gGw񣻯~[2B][@o>O^;/yP\ypiy5ϻz)œ/? endstream endobj 285 0 obj 588 endobj 256 0 obj << /Length 257 0 R /Type /XObject /Subtype /Image /Width 112 /Height 40 /ColorSpace /DeviceGray /Interpolate true /BitsPerComponent 8 /Filter /FlateDecode >> stream x헿kP͏[cnbD-V%CCM$픡IE(8(NA _{A׷<~dsll0K1 !I1weWAaX0 4+ F" 0.;!rƑ)1Y{ e%q:HS' E!jR3ƵEymdt-szCOF.oZGN]o.#ꃂzqU|w !ӏѠS*^]'i*7x9GtteLh<-UZd6l2*l:erzIB <;>gGw񣻯~[2B][@o>O^;/yP\ypiy5ϻz)œ/? endstream endobj 257 0 obj 588 endobj 320 0 obj << /Length 321 0 R /Type /XObject /Subtype /Image /Width 112 /Height 40 /ColorSpace /DeviceGray /Interpolate true /BitsPerComponent 8 /Filter /FlateDecode >> stream x헿kP͏[cnbD-V%CCM$픡IE(8(NA _{A׷<~dsll0K1 !I1weWAaX0 4+ F" 0.;!rƑ)1Y{ e%q:HS' E!jR3ƵEymdt-szCOF.oZGN]o.#ꃂzqU|w !ӏѠS*^]'i*7x9GtteLh<-UZd6l2*l:erzIB <;>gGw񣻯~[2B][@o>O^;/yP\ypiy5ϻz)œ/? endstream endobj 321 0 obj 588 endobj 192 0 obj << /Length 193 0 R /Type /XObject /Subtype /Image /Width 119 /Height 60 /ColorSpace /DeviceGray /Interpolate true /BitsPerComponent 8 /Filter /FlateDecode >> stream xc` FF&FFFLmdfeec`gcceafBO@&@bFfVn>!Qq)iYZ) 1^N6$32r((ijhki*Iq0cGHRA]Ɩ@KEV ZVnAIE[gO߀ Z7K5Y>xbSбpK̢>LK3Tf{KPZ%(>47%VOQf-#+|nESg߄=muEin&jRkyŕ#2+Zϝ`ެ] VڲBФ'fW?{kVZ6ojgUF Zv~)M+Woܲ`uNh̋p6TFX+ e^7gv2صk疵Ÿ+![+mY7a-Oewh/s7ACZ*[ 2ZVh2qeO\fnغώ ftyBQkԣ0F!0F3$5& W+#;jt:0D`! bNe`al tfI&g4 endstream endobj 193 0 obj 627 endobj 236 0 obj << /Length 237 0 R /Type /XObject /Subtype /Image /Width 75 /Height 60 /ColorSpace /DeviceGray /Interpolate true /BitsPerComponent 8 /Filter /FlateDecode >> stream xc`y7TYXXI,,LLL21sprs 89X cbf' qs#(*)+B$PVRfgaB#+ P_G]IFT^J[i?;QF͓ڴmQ`fT[iJ %l[>}mvn^5.3V[(K7l߳(wז'e%,FVqҎ6 ҨY0>+VGVc(?V @FhbቁXRE*=՚kQF$klS @ K 10Pk P % 1lElW endstream endobj 237 0 obj 581 endobj 350 0 obj << /Length 351 0 R /Type /XObject /Subtype /Image /Width 112 /Height 40 /ColorSpace /DeviceGray /Interpolate true /BitsPerComponent 8 /Filter /FlateDecode >> stream x헿kP͏[cnbD-V%CCM$픡IE(8(NA _{A׷<~dsll0K1 !I1weWAaX0 4+ F" 0.;!rƑ)1Y{ e%q:HS' E!jR3ƵEymdt-szCOF.oZGN]o.#ꃂzqU|w !ӏѠS*^]'i*7x9GtteLh<-UZd6l2*l:erzIB <;>gGw񣻯~[2B][@o>O^;/yP\ypiy5ϻz)œ/? endstream endobj 351 0 obj 588 endobj 338 0 obj << /Length 339 0 R /Type /XObject /Subtype /Image /Width 112 /Height 40 /ColorSpace /DeviceGray /Interpolate true /BitsPerComponent 8 /Filter /FlateDecode >> stream x헿kP͏[cnbD-V%CCM$픡IE(8(NA _{A׷<~dsll0K1 !I1weWAaX0 4+ F" 0.;!rƑ)1Y{ e%q:HS' E!jR3ƵEymdt-szCOF.oZGN]o.#ꃂzqU|w !ӏѠS*^]'i*7x9GtteLh<-UZd6l2*l:erzIB <;>gGw񣻯~[2B][@o>O^;/yP\ypiy5ϻz)œ/? endstream endobj 339 0 obj 588 endobj 300 0 obj << /Length 301 0 R /Type /XObject /Subtype /Image /Width 119 /Height 60 /ColorSpace /DeviceGray /Interpolate true /BitsPerComponent 8 /Filter /FlateDecode >> stream xc` FF&FFFLmdfeec`gcceafBO@&@bFfVn>!Qq)iYZ) 1^N6$32r((ijhki*Iq0cGHRA]Ɩ@KEV ZVnAIE[gO߀ Z7K5Y>xbSбpK̢>LK3Tf{KPZ%(>47%VOQf-#+|nESg߄=muEin&jRkyŕ#2+Zϝ`ެ] VڲBФ'fW?{kVZ6ojgUF Zv~)M+Woܲ`uNh̋p6TFX+ e^7gv2صk疵Ÿ+![+mY7a-Oewh/s7ACZ*[ 2ZVh2qeO\fnغώ ftyBQkԣ0F!0F3$5& W+#;jt:0D`! bNe`al tfI&g4 endstream endobj 301 0 obj 627 endobj 234 0 obj << /Length 235 0 R /Type /XObject /Subtype /Image /Width 119 /Height 60 /ColorSpace /DeviceGray /Interpolate true /BitsPerComponent 8 /Filter /FlateDecode >> stream xc` FF&FFFLmdfeec`gcceafBO@&@bFfVn>!Qq)iYZ) 1^N6$32r((ijhki*Iq0cGHRA]Ɩ@KEV ZVnAIE[gO߀ Z7K5Y>xbSбpK̢>LK3Tf{KPZ%(>47%VOQf-#+|nESg߄=muEin&jRkyŕ#2+Zϝ`ެ] VڲBФ'fW?{kVZ6ojgUF Zv~)M+Woܲ`uNh̋p6TFX+ e^7gv2صk疵Ÿ+![+mY7a-Oewh/s7ACZ*[ 2ZVh2qeO\fnغώ ftyBQkԣ0F!0F3$5& W+#;jt:0D`! bNe`al tfI&g4 endstream endobj 235 0 obj 627 endobj 264 0 obj << /Length 265 0 R /Type /XObject /Subtype /Image /Width 119 /Height 60 /ColorSpace /DeviceGray /Interpolate true /BitsPerComponent 8 /Filter /FlateDecode >> stream xc` FF&FFFLmdfeec`gcceafBO@&@bFfVn>!Qq)iYZ) 1^N6$32r((ijhki*Iq0cGHRA]Ɩ@KEV ZVnAIE[gO߀ Z7K5Y>xbSбpK̢>LK3Tf{KPZ%(>47%VOQf-#+|nESg߄=muEin&jRkyŕ#2+Zϝ`ެ] VڲBФ'fW?{kVZ6ojgUF Zv~)M+Woܲ`uNh̋p6TFX+ e^7gv2صk疵Ÿ+![+mY7a-Oewh/s7ACZ*[ 2ZVh2qeO\fnغώ ftyBQkԣ0F!0F3$5& W+#;jt:0D`! bNe`al tfI&g4 endstream endobj 265 0 obj 627 endobj 198 0 obj << /Length 199 0 R /Type /XObject /Subtype /Image /Width 112 /Height 40 /ColorSpace /DeviceGray /Interpolate true /BitsPerComponent 8 /Filter /FlateDecode >> stream x헿kP͏[cnbD-V%CCM$픡IE(8(NA _{A׷<~dsll0K1 !I1weWAaX0 4+ F" 0.;!rƑ)1Y{ e%q:HS' E!jR3ƵEymdt-szCOF.oZGN]o.#ꃂzqU|w !ӏѠS*^]'i*7x9GtteLh<-UZd6l2*l:erzIB <;>gGw񣻯~[2B][@o>O^;/yP\ypiy5ϻz)œ/? endstream endobj 199 0 obj 588 endobj 274 0 obj << /Length 275 0 R /Type /XObject /Subtype /Image /Width 119 /Height 60 /ColorSpace /DeviceGray /Interpolate true /BitsPerComponent 8 /Filter /FlateDecode >> stream xc` FF&FFFLmdfeec`gcceafBO@&@bFfVn>!Qq)iYZ) 1^N6$32r((ijhki*Iq0cGHRA]Ɩ@KEV ZVnAIE[gO߀ Z7K5Y>xbSбpK̢>LK3Tf{KPZ%(>47%VOQf-#+|nESg߄=muEin&jRkyŕ#2+Zϝ`ެ] VڲBФ'fW?{kVZ6ojgUF Zv~)M+Woܲ`uNh̋p6TFX+ e^7gv2صk疵Ÿ+![+mY7a-Oewh/s7ACZ*[ 2ZVh2qeO\fnغώ ftyBQkԣ0F!0F3$5& W+#;jt:0D`! bNe`al tfI&g4 endstream endobj 275 0 obj 627 endobj 308 0 obj << /Length 309 0 R /Type /XObject /Subtype /Image /Width 112 /Height 40 /ColorSpace /DeviceGray /Interpolate true /BitsPerComponent 8 /Filter /FlateDecode >> stream x헿kP͏[cnbD-V%CCM$픡IE(8(NA _{A׷<~dsll0K1 !I1weWAaX0 4+ F" 0.;!rƑ)1Y{ e%q:HS' E!jR3ƵEymdt-szCOF.oZGN]o.#ꃂzqU|w !ӏѠS*^]'i*7x9GtteLh<-UZd6l2*l:erzIB <;>gGw񣻯~[2B][@o>O^;/yP\ypiy5ϻz)œ/? endstream endobj 309 0 obj 588 endobj 250 0 obj << /Length 251 0 R /Type /XObject /Subtype /Image /Width 140 /Height 40 /ColorSpace /DeviceGray /Interpolate true /BitsPerComponent 8 /Filter /FlateDecode >> stream xc`C/p ##3 +] 3#aae`geAs 3+78݀ ?/;+3R01q I*() (+Hp2#+' ݀ 1adR1svspwu57TfcG+wPDt@lTX8?' ҂HnQ4p ϩ띵d tkW,Y`#Qe#肖 Vmڶ>` e8 s"[L=}vعe͂I9aHnaW1+혱lÎ=޶v䦼p'}.xa7.,(p<=Pe]FYnjT,oP^ L8kk3$ @oKRtjJRQm)VA#7O"9($ WSոQj@ DVDKot @h}{3B2FCo2~z endstream endobj 251 0 obj 619 endobj 278 0 obj << /Length 279 0 R /Type /XObject /Subtype /Image /Width 119 /Height 60 /ColorSpace /DeviceGray /Interpolate true /BitsPerComponent 8 /Filter /FlateDecode >> stream xc` FF&FFFLmdfeec`gcceafBO@&@bFfVn>!Qq)iYZ) 1^N6$32r((ijhki*Iq0cGHRA]Ɩ@KEV ZVnAIE[gO߀ Z7K5Y>xbSбpK̢>LK3Tf{KPZ%(>47%VOQf-#+|nESg߄=muEin&jRkyŕ#2+Zϝ`ެ] VڲBФ'fW?{kVZ6ojgUF Zv~)M+Woܲ`uNh̋p6TFX+ e^7gv2صk疵Ÿ+![+mY7a-Oewh/s7ACZ*[ 2ZVh2qeO\fnغώ ftyBQkԣ0F!0F3$5& W+#;jt:0D`! bNe`al tfI&g4 endstream endobj 279 0 obj 627 endobj 336 0 obj << /Length 337 0 R /Type /XObject /Subtype /Image /Width 75 /Height 60 /ColorSpace /DeviceGray /Interpolate true /BitsPerComponent 8 /Filter /FlateDecode >> stream xc`y7TYXXI,,LLL21sprs 89X cbf' qs#(*)+B$PVRfgaB#+ P_G]IFT^J[i?;QF͓ڴmQ`fT[iJ %l[>}mvn^5.3V[(K7l߳(wז'e%,FVqҎ6 ҨY0>+VGVc(?V @FhbቁXRE*=՚kQF$klS @ K 10Pk P % 1lElW endstream endobj 337 0 obj 581 endobj 272 0 obj << /Length 273 0 R /Type /XObject /Subtype /Image /Width 75 /Height 60 /ColorSpace /DeviceGray /Interpolate true /BitsPerComponent 8 /Filter /FlateDecode >> stream xc`y7TYXXI,,LLL21sprs 89X cbf' qs#(*)+B$PVRfgaB#+ P_G]IFT^J[i?;QF͓ڴmQ`fT[iJ %l[>}mvn^5.3V[(K7l߳(wז'e%,FVqҎ6 ҨY0>+VGVc(?V @FhbቁXRE*=՚kQF$klS @ K 10Pk P % 1lElW endstream endobj 273 0 obj 581 endobj 362 0 obj << /Length 363 0 R /Type /XObject /Subtype /Image /Width 75 /Height 60 /ColorSpace /DeviceGray /Interpolate true /BitsPerComponent 8 /Filter /FlateDecode >> stream xc`y7TYXXI,,LLL21sprs 89X cbf' qs#(*)+B$PVRfgaB#+ P_G]IFT^J[i?;QF͓ڴmQ`fT[iJ %l[>}mvn^5.3V[(K7l߳(wז'e%,FVqҎ6 ҨY0>+VGVc(?V @FhbቁXRE*=՚kQF$klS @ K 10Pk P % 1lElW endstream endobj 363 0 obj 581 endobj 348 0 obj << /Length 349 0 R /Type /XObject /Subtype /Image /Width 119 /Height 60 /ColorSpace /DeviceGray /Interpolate true /BitsPerComponent 8 /Filter /FlateDecode >> stream xc` FF&FFFLmdfeec`gcceafBO@&@bFfVn>!Qq)iYZ) 1^N6$32r((ijhki*Iq0cGHRA]Ɩ@KEV ZVnAIE[gO߀ Z7K5Y>xbSбpK̢>LK3Tf{KPZ%(>47%VOQf-#+|nESg߄=muEin&jRkyŕ#2+Zϝ`ެ] VڲBФ'fW?{kVZ6ojgUF Zv~)M+Woܲ`uNh̋p6TFX+ e^7gv2صk疵Ÿ+![+mY7a-Oewh/s7ACZ*[ 2ZVh2qeO\fnغώ ftyBQkԣ0F!0F3$5& W+#;jt:0D`! bNe`al tfI&g4 endstream endobj 349 0 obj 627 endobj 238 0 obj << /Length 239 0 R /Type /XObject /Subtype /Image /Width 75 /Height 60 /ColorSpace /DeviceGray /Interpolate true /BitsPerComponent 8 /Filter /FlateDecode >> stream xc`y7TYXXI,,LLL21sprs 89X cbf' qs#(*)+B$PVRfgaB#+ P_G]IFT^J[i?;QF͓ڴmQ`fT[iJ %l[>}mvn^5.3V[(K7l߳(wז'e%,FVqҎ6 ҨY0>+VGVc(?V @FhbቁXRE*=՚kQF$klS @ K 10Pk P % 1lElW endstream endobj 239 0 obj 581 endobj 224 0 obj << /Length 225 0 R /Type /XObject /Subtype /Image /Width 112 /Height 40 /ColorSpace /DeviceGray /Interpolate true /BitsPerComponent 8 /Filter /FlateDecode >> stream x헿kP͏[cnbD-V%CCM$픡IE(8(NA _{A׷<~dsll0K1 !I1weWAaX0 4+ F" 0.;!rƑ)1Y{ e%q:HS' E!jR3ƵEymdt-szCOF.oZGN]o.#ꃂzqU|w !ӏѠS*^]'i*7x9GtteLh<-UZd6l2*l:erzIB <;>gGw񣻯~[2B][@o>O^;/yP\ypiy5ϻz)œ/? endstream endobj 225 0 obj 588 endobj 246 0 obj << /Length 247 0 R /Type /XObject /Subtype /Image /Width 112 /Height 40 /ColorSpace /DeviceGray /Interpolate true /BitsPerComponent 8 /Filter /FlateDecode >> stream x헿kP͏[cnbD-V%CCM$픡IE(8(NA _{A׷<~dsll0K1 !I1weWAaX0 4+ F" 0.;!rƑ)1Y{ e%q:HS' E!jR3ƵEymdt-szCOF.oZGN]o.#ꃂzqU|w !ӏѠS*^]'i*7x9GtteLh<-UZd6l2*l:erzIB <;>gGw񣻯~[2B][@o>O^;/yP\ypiy5ϻz)œ/? endstream endobj 247 0 obj 588 endobj 268 0 obj << /Length 269 0 R /Type /XObject /Subtype /Image /Width 112 /Height 40 /ColorSpace /DeviceGray /Interpolate true /BitsPerComponent 8 /Filter /FlateDecode >> stream x헿kP͏[cnbD-V%CCM$픡IE(8(NA _{A׷<~dsll0K1 !I1weWAaX0 4+ F" 0.;!rƑ)1Y{ e%q:HS' E!jR3ƵEymdt-szCOF.oZGN]o.#ꃂzqU|w !ӏѠS*^]'i*7x9GtteLh<-UZd6l2*l:erzIB <;>gGw񣻯~[2B][@o>O^;/yP\ypiy5ϻz)œ/? endstream endobj 269 0 obj 588 endobj 270 0 obj << /Length 271 0 R /Type /XObject /Subtype /Image /Width 112 /Height 40 /ColorSpace /DeviceGray /Interpolate true /BitsPerComponent 8 /Filter /FlateDecode >> stream x헿kP͏[cnbD-V%CCM$픡IE(8(NA _{A׷<~dsll0K1 !I1weWAaX0 4+ F" 0.;!rƑ)1Y{ e%q:HS' E!jR3ƵEymdt-szCOF.oZGN]o.#ꃂzqU|w !ӏѠS*^]'i*7x9GtteLh<-UZd6l2*l:erzIB <;>gGw񣻯~[2B][@o>O^;/yP\ypiy5ϻz)œ/? endstream endobj 271 0 obj 588 endobj 294 0 obj << /Length 295 0 R /Type /XObject /Subtype /Image /Width 114 /Height 60 /ColorSpace /DeviceGray /Interpolate true /BitsPerComponent 8 /Filter /FlateDecode >> stream x혽kPu`H!EPqiIQ29BB tpcrhA)DEr.,B<9/HAt$I72xy?s>a($ .ŠA2ߧ$)9ATp$Eª" ߃$5Hޥ3:b2d"J2Rk-g󅒁R!Sڵ$`o!jbl |~{M!h*gT͚Uo4Ҩ[5jRQY1[# 5V[k' lJ31̖M;2t,MųK|꾏')dm*ۈ{vgcƒ|C! {F|)=;ٗ,8_GT sgZ#dr0 =6:2_/hXto\#SuoYr&MOp)$#=2bBo7VN`o  K $%o3!_$! endstream endobj 295 0 obj 594 endobj 280 0 obj << /Length 281 0 R /Type /XObject /Subtype /Image /Width 140 /Height 40 /ColorSpace /DeviceGray /Interpolate true /BitsPerComponent 8 /Filter /FlateDecode >> stream xc`C/p ##3 +] 3#aae`geAs 3+78݀ ?/;+3R01q I*() (+Hp2#+' ݀ 1adR1svspwu57TfcG+wPDt@lTX8?' ҂HnQ4p ϩ띵d tkW,Y`#Qe#肖 Vmڶ>` e8 s"[L=}vعe͂I9aHnaW1+혱lÎ=޶v䦼p'}.xa7.,(p<=Pe]FYnjT,oP^ L8kk3$ @oKRtjJRQm)VA#7O"9($ WSոQj@ DVDKot @h}{3B2FCo2~z endstream endobj 281 0 obj 619 endobj 304 0 obj << /Length 305 0 R /Type /XObject /Subtype /Image /Width 75 /Height 60 /ColorSpace /DeviceGray /Interpolate true /BitsPerComponent 8 /Filter /FlateDecode >> stream xc`y7TYXXI,,LLL21sprs 89X cbf' qs#(*)+B$PVRfgaB#+ P_G]IFT^J[i?;QF͓ڴmQ`fT[iJ %l[>}mvn^5.3V[(K7l߳(wז'e%,FVqҎ6 ҨY0>+VGVc(?V @FhbቁXRE*=՚kQF$klS @ K 10Pk P % 1lElW endstream endobj 305 0 obj 581 endobj 332 0 obj << /Length 333 0 R /Type /XObject /Subtype /Image /Width 140 /Height 40 /ColorSpace /DeviceGray /Interpolate true /BitsPerComponent 8 /Filter /FlateDecode >> stream xc`C/p ##3 +] 3#aae`geAs 3+78݀ ?/;+3R01q I*() (+Hp2#+' ݀ 1adR1svspwu57TfcG+wPDt@lTX8?' ҂HnQ4p ϩ띵d tkW,Y`#Qe#肖 Vmڶ>` e8 s"[L=}vعe͂I9aHnaW1+혱lÎ=޶v䦼p'}.xa7.,(p<=Pe]FYnjT,oP^ L8kk3$ @oKRtjJRQm)VA#7O"9($ WSոQj@ DVDKot @h}{3B2FCo2~z endstream endobj 333 0 obj 619 endobj 216 0 obj << /Length 217 0 R /Type /XObject /Subtype /Image /Width 141 /Height 40 /ColorSpace /DeviceGray /Interpolate true /BitsPerComponent 8 /Filter /FlateDecode >> stream xc`C2p##3 +} 3#.aae`geAs3+78 ?/+3R01q I*()(+H]UL|R Zz&F*rBadR1svspwu0TfG +wPDt@lTX'+VZ̰[D)> stream xc` FF&FFFLmdfeec`gcceafBO@&@bFfVn>!Qq)iYZ) 1^N6$32r((ijhki*Iq0cGHRA]Ɩ@KEV ZVnAIE[gO߀ Z7K5Y>xbSбpK̢>LK3Tf{KPZ%(>47%VOQf-#+|nESg߄=muEin&jRkyŕ#2+Zϝ`ެ] VڲBФ'fW?{kVZ6ojgUF Zv~)M+Woܲ`uNh̋p6TFX+ e^7gv2صk疵Ÿ+![+mY7a-Oewh/s7ACZ*[ 2ZVh2qeO\fnغώ ftyBQkԣ0F!0F3$5& W+#;jt:0D`! bNe`al tfI&g4 endstream endobj 219 0 obj 627 endobj 260 0 obj << /Length 261 0 R /Type /XObject /Subtype /Image /Width 75 /Height 60 /ColorSpace /DeviceGray /Interpolate true /BitsPerComponent 8 /Filter /FlateDecode >> stream xc`y7TYXXI,,LLL21sprs 89X cbf' qs#(*)+B$PVRfgaB#+ P_G]IFT^J[i?;QF͓ڴmQ`fT[iJ %l[>}mvn^5.3V[(K7l߳(wז'e%,FVqҎ6 ҨY0>+VGVc(?V @FhbቁXRE*=՚kQF$klS @ K 10Pk P % 1lElW endstream endobj 261 0 obj 581 endobj 200 0 obj << /Length 201 0 R /Type /XObject /Subtype /Image /Width 119 /Height 60 /ColorSpace /DeviceGray /Interpolate true /BitsPerComponent 8 /Filter /FlateDecode >> stream xc` FF&FFFLmdfeec`gcceafBO@&@bFfVn>!Qq)iYZ) 1^N6$32r((ijhki*Iq0cGHRA]Ɩ@KEV ZVnAIE[gO߀ Z7K5Y>xbSбpK̢>LK3Tf{KPZ%(>47%VOQf-#+|nESg߄=muEin&jRkyŕ#2+Zϝ`ެ] VڲBФ'fW?{kVZ6ojgUF Zv~)M+Woܲ`uNh̋p6TFX+ e^7gv2صk疵Ÿ+![+mY7a-Oewh/s7ACZ*[ 2ZVh2qeO\fnغώ ftyBQkԣ0F!0F3$5& W+#;jt:0D`! bNe`al tfI&g4 endstream endobj 201 0 obj 627 endobj 356 0 obj << /Length 357 0 R /Type /XObject /Subtype /Image /Width 119 /Height 60 /ColorSpace /DeviceGray /Interpolate true /BitsPerComponent 8 /Filter /FlateDecode >> stream xc` FF&FFFLmdfeec`gcceafBO@&@bFfVn>!Qq)iYZ) 1^N6$32r((ijhki*Iq0cGHRA]Ɩ@KEV ZVnAIE[gO߀ Z7K5Y>xbSбpK̢>LK3Tf{KPZ%(>47%VOQf-#+|nESg߄=muEin&jRkyŕ#2+Zϝ`ެ] VڲBФ'fW?{kVZ6ojgUF Zv~)M+Woܲ`uNh̋p6TFX+ e^7gv2صk疵Ÿ+![+mY7a-Oewh/s7ACZ*[ 2ZVh2qeO\fnغώ ftyBQkԣ0F!0F3$5& W+#;jt:0D`! bNe`al tfI&g4 endstream endobj 357 0 obj 627 endobj 360 0 obj << /Length 361 0 R /Type /XObject /Subtype /Image /Width 112 /Height 40 /ColorSpace /DeviceGray /Interpolate true /BitsPerComponent 8 /Filter /FlateDecode >> stream x헿kP͏[cnbD-V%CCM$픡IE(8(NA _{A׷<~dsll0K1 !I1weWAaX0 4+ F" 0.;!rƑ)1Y{ e%q:HS' E!jR3ƵEymdt-szCOF.oZGN]o.#ꃂzqU|w !ӏѠS*^]'i*7x9GtteLh<-UZd6l2*l:erzIB <;>gGw񣻯~[2B][@o>O^;/yP\ypiy5ϻz)œ/? endstream endobj 361 0 obj 588 endobj 328 0 obj << /Length 329 0 R /Type /XObject /Subtype /Image /Width 112 /Height 40 /ColorSpace /DeviceGray /Interpolate true /BitsPerComponent 8 /Filter /FlateDecode >> stream x헿kP͏[cnbD-V%CCM$픡IE(8(NA _{A׷<~dsll0K1 !I1weWAaX0 4+ F" 0.;!rƑ)1Y{ e%q:HS' E!jR3ƵEymdt-szCOF.oZGN]o.#ꃂzqU|w !ӏѠS*^]'i*7x9GtteLh<-UZd6l2*l:erzIB <;>gGw񣻯~[2B][@o>O^;/yP\ypiy5ϻz)œ/? endstream endobj 329 0 obj 588 endobj 292 0 obj << /Length 293 0 R /Type /XObject /Subtype /Image /Width 114 /Height 60 /ColorSpace /DeviceGray /Interpolate true /BitsPerComponent 8 /Filter /FlateDecode >> stream x혽kPu`H!EPqiIQ29BB tpcrhA)DEr.,B<9/HAt$I72xy?s>a($ .ŠA2ߧ$)9ATp$Eª" ߃$5Hޥ3:b2d"J2Rk-g󅒁R!Sڵ$`o!jbl |~{M!h*gT͚Uo4Ҩ[5jRQY1[# 5V[k' lJ31̖M;2t,MųK|꾏')dm*ۈ{vgcƒ|C! {F|)=;ٗ,8_GT sgZ#dr0 =6:2_/hXto\#SuoYr&MOp)$#=2bBo7VN`o  K $%o3!_$! endstream endobj 293 0 obj 594 endobj 214 0 obj << /Length 215 0 R /Type /XObject /Subtype /Image /Width 75 /Height 60 /ColorSpace /DeviceGray /Interpolate true /BitsPerComponent 8 /Filter /FlateDecode >> stream xc`y7TYXXI,,LLL21sprs 89X cbf' qs#(*)+B$PVRfgaB#+ P_G]IFT^J[i?;QF͓ڴmQ`fT[iJ %l[>}mvn^5.3V[(K7l߳(wז'e%,FVqҎ6 ҨY0>+VGVc(?V @FhbቁXRE*=՚kQF$klS @ K 10Pk P % 1lElW endstream endobj 215 0 obj 581 endobj 228 0 obj << /Length 229 0 R /Type /XObject /Subtype /Image /Width 112 /Height 40 /ColorSpace /DeviceGray /Interpolate true /BitsPerComponent 8 /Filter /FlateDecode >> stream x헿kP͏[cnbD-V%CCM$픡IE(8(NA _{A׷<~dsll0K1 !I1weWAaX0 4+ F" 0.;!rƑ)1Y{ e%q:HS' E!jR3ƵEymdt-szCOF.oZGN]o.#ꃂzqU|w !ӏѠS*^]'i*7x9GtteLh<-UZd6l2*l:erzIB <;>gGw񣻯~[2B][@o>O^;/yP\ypiy5ϻz)œ/? endstream endobj 229 0 obj 588 endobj 232 0 obj << /Length 233 0 R /Type /XObject /Subtype /Image /Width 112 /Height 40 /ColorSpace /DeviceGray /Interpolate true /BitsPerComponent 8 /Filter /FlateDecode >> stream x헿kP͏[cnbD-V%CCM$픡IE(8(NA _{A׷<~dsll0K1 !I1weWAaX0 4+ F" 0.;!rƑ)1Y{ e%q:HS' E!jR3ƵEymdt-szCOF.oZGN]o.#ꃂzqU|w !ӏѠS*^]'i*7x9GtteLh<-UZd6l2*l:erzIB <;>gGw񣻯~[2B][@o>O^;/yP\ypiy5ϻz)œ/? endstream endobj 233 0 obj 588 endobj 244 0 obj << /Length 245 0 R /Type /XObject /Subtype /Image /Width 112 /Height 40 /ColorSpace /DeviceGray /Interpolate true /BitsPerComponent 8 /Filter /FlateDecode >> stream x헿kP͏[cnbD-V%CCM$픡IE(8(NA _{A׷<~dsll0K1 !I1weWAaX0 4+ F" 0.;!rƑ)1Y{ e%q:HS' E!jR3ƵEymdt-szCOF.oZGN]o.#ꃂzqU|w !ӏѠS*^]'i*7x9GtteLh<-UZd6l2*l:erzIB <;>gGw񣻯~[2B][@o>O^;/yP\ypiy5ϻz)œ/? endstream endobj 245 0 obj 588 endobj 342 0 obj << /Length 343 0 R /Type /XObject /Subtype /Image /Width 119 /Height 60 /ColorSpace /DeviceGray /Interpolate true /BitsPerComponent 8 /Filter /FlateDecode >> stream xc` FF&FFFLmdfeec`gcceafBO@&@bFfVn>!Qq)iYZ) 1^N6$32r((ijhki*Iq0cGHRA]Ɩ@KEV ZVnAIE[gO߀ Z7K5Y>xbSбpK̢>LK3Tf{KPZ%(>47%VOQf-#+|nESg߄=muEin&jRkyŕ#2+Zϝ`ެ] VڲBФ'fW?{kVZ6ojgUF Zv~)M+Woܲ`uNh̋p6TFX+ e^7gv2صk疵Ÿ+![+mY7a-Oewh/s7ACZ*[ 2ZVh2qeO\fnغώ ftyBQkԣ0F!0F3$5& W+#;jt:0D`! bNe`al tfI&g4 endstream endobj 343 0 obj 627 endobj 364 0 obj << /Length 365 0 R /Type /XObject /Subtype /Image /Width 75 /Height 60 /ColorSpace /DeviceGray /Interpolate true /BitsPerComponent 8 /Filter /FlateDecode >> stream xc`y7TYXXI,,LLL21sprs 89X cbf' qs#(*)+B$PVRfgaB#+ P_G]IFT^J[i?;QF͓ڴmQ`fT[iJ %l[>}mvn^5.3V[(K7l߳(wז'e%,FVqҎ6 ҨY0>+VGVc(?V @FhbቁXRE*=՚kQF$klS @ K 10Pk P % 1lElW endstream endobj 365 0 obj 581 endobj 346 0 obj << /Length 347 0 R /Type /XObject /Subtype /Image /Width 131 /Height 40 /ColorSpace /DeviceGray /Interpolate true /BitsPerComponent 8 /Filter /FlateDecode >> stream x헿OP+EkiIAD-K-  :u LXHL L4 ,B"#7^hLtsQ01 $ ǰ8O2 tT @~Hè^RXՀ;rFQ)Y6 e%v8ג'1Eڀj\SƵFymt-[ 뻵 zY Nd)M,Y F@o$np@|C/C".|Xe ^ܵArua endstream endobj 347 0 obj 591 endobj 266 0 obj << /Length 267 0 R /Type /XObject /Subtype /Image /Width 131 /Height 60 /ColorSpace /DeviceGray /Interpolate true /BitsPerComponent 8 /Filter /FlateDecode >> stream x홽kPu!&BX"1.drҡ6B tpcrhA)D rdoɖ/x'~ ϻN@/ A0r\GN )8'd(bd)"\9Yœ)1d<Bpٰ$ҙ\^CL>wI'1B`xZjR#Z.z- 8J !wJl4b> stream xc` FF&FFFLmdfeec`gcceafBO@&@bFfVn>!Qq)iYZ) 1^N6$32r((ijhki*Iq0cGHRA]Ɩ@KEV ZVnAIE[gO߀ Z7K5Y>xbSбpK̢>LK3Tf{KPZ%(>47%VOQf-#+|nESg߄=muEin&jRkyŕ#2+Zϝ`ެ] VڲBФ'fW?{kVZ6ojgUF Zv~)M+Woܲ`uNh̋p6TFX+ e^7gv2صk疵Ÿ+![+mY7a-Oewh/s7ACZ*[ 2ZVh2qeO\fnغώ ftyBQkԣ0F!0F3$5& W+#;jt:0D`! bNe`al tfI&g4 endstream endobj 325 0 obj 627 endobj 370 0 obj << /Length 371 0 R /Type /XObject /Subtype /Image /Width 112 /Height 40 /ColorSpace /DeviceGray /Interpolate true /BitsPerComponent 8 /Filter /FlateDecode >> stream x헿kP͏[cnbD-V%CCM$픡IE(8(NA _{A׷<~dsll0K1 !I1weWAaX0 4+ F" 0.;!rƑ)1Y{ e%q:HS' E!jR3ƵEymdt-szCOF.oZGN]o.#ꃂzqU|w !ӏѠS*^]'i*7x9GtteLh<-UZd6l2*l:erzIB <;>gGw񣻯~[2B][@o>O^;/yP\ypiy5ϻz)œ/? endstream endobj 371 0 obj 588 endobj 316 0 obj << /Length 317 0 R /Type /XObject /Subtype /Image /Width 112 /Height 40 /ColorSpace /DeviceGray /Interpolate true /BitsPerComponent 8 /Filter /FlateDecode >> stream x헿kP͏[cnbD-V%CCM$픡IE(8(NA _{A׷<~dsll0K1 !I1weWAaX0 4+ F" 0.;!rƑ)1Y{ e%q:HS' E!jR3ƵEymdt-szCOF.oZGN]o.#ꃂzqU|w !ӏѠS*^]'i*7x9GtteLh<-UZd6l2*l:erzIB <;>gGw񣻯~[2B][@o>O^;/yP\ypiy5ϻz)œ/? endstream endobj 317 0 obj 588 endobj 318 0 obj << /Length 319 0 R /Type /XObject /Subtype /Image /Width 112 /Height 40 /ColorSpace /DeviceGray /Interpolate true /BitsPerComponent 8 /Filter /FlateDecode >> stream x헿kP͏[cnbD-V%CCM$픡IE(8(NA _{A׷<~dsll0K1 !I1weWAaX0 4+ F" 0.;!rƑ)1Y{ e%q:HS' E!jR3ƵEymdt-szCOF.oZGN]o.#ꃂzqU|w !ӏѠS*^]'i*7x9GtteLh<-UZd6l2*l:erzIB <;>gGw񣻯~[2B][@o>O^;/yP\ypiy5ϻz)œ/? endstream endobj 319 0 obj 588 endobj 254 0 obj << /Length 255 0 R /Type /XObject /Subtype /Image /Width 117 /Height 40 /ColorSpace /DeviceGray /Interpolate true /BitsPerComponent 8 /Filter /FlateDecode >> stream xc`t F*> stream x헿kP֘ئ1iCdqhh#ЂDڡ2X:8)BppQ:Pk/)> stream xc`y7TYXXI,,LLL21sprs 89X cbf' qs#(*)+B$PVRfgaB#+ P_G]IFT^J[i?;QF͓ڴmQ`fT[iJ %l[>}mvn^5.3V[(K7l߳(wז'e%,FVqҎ6 ҨY0>+VGVc(?V @FhbቁXRE*=՚kQF$klS @ K 10Pk P % 1lElW endstream endobj 289 0 obj 581 endobj 344 0 obj << /Length 345 0 R /Type /XObject /Subtype /Image /Width 119 /Height 60 /ColorSpace /DeviceGray /Interpolate true /BitsPerComponent 8 /Filter /FlateDecode >> stream xc` FF&FFFLmdfeec`gcceafBO@&@bFfVn>!Qq)iYZ) 1^N6$32r((ijhki*Iq0cGHRA]Ɩ@KEV ZVnAIE[gO߀ Z7K5Y>xbSбpK̢>LK3Tf{KPZ%(>47%VOQf-#+|nESg߄=muEin&jRkyŕ#2+Zϝ`ެ] VڲBФ'fW?{kVZ6ojgUF Zv~)M+Woܲ`uNh̋p6TFX+ e^7gv2صk疵Ÿ+![+mY7a-Oewh/s7ACZ*[ 2ZVh2qeO\fnغώ ftyBQkԣ0F!0F3$5& W+#;jt:0D`! bNe`al tfI&g4 endstream endobj 345 0 obj 627 endobj 202 0 obj << /Length 203 0 R /Type /XObject /Subtype /Image /Width 112 /Height 40 /ColorSpace /DeviceGray /Interpolate true /BitsPerComponent 8 /Filter /FlateDecode >> stream x헿kP͏[cnbD-V%CCM$픡IE(8(NA _{A׷<~dsll0K1 !I1weWAaX0 4+ F" 0.;!rƑ)1Y{ e%q:HS' E!jR3ƵEymdt-szCOF.oZGN]o.#ꃂzqU|w !ӏѠS*^]'i*7x9GtteLh<-UZd6l2*l:erzIB <;>gGw񣻯~[2B][@o>O^;/yP\ypiy5ϻz)œ/? endstream endobj 203 0 obj 588 endobj 352 0 obj << /Length 353 0 R /Type /XObject /Subtype /Image /Width 119 /Height 60 /ColorSpace /DeviceGray /Interpolate true /BitsPerComponent 8 /Filter /FlateDecode >> stream xc` FF&FFFLmdfeec`gcceafBO@&@bFfVn>!Qq)iYZ) 1^N6$32r((ijhki*Iq0cGHRA]Ɩ@KEV ZVnAIE[gO߀ Z7K5Y>xbSбpK̢>LK3Tf{KPZ%(>47%VOQf-#+|nESg߄=muEin&jRkyŕ#2+Zϝ`ެ] VڲBФ'fW?{kVZ6ojgUF Zv~)M+Woܲ`uNh̋p6TFX+ e^7gv2صk疵Ÿ+![+mY7a-Oewh/s7ACZ*[ 2ZVh2qeO\fnغώ ftyBQkԣ0F!0F3$5& W+#;jt:0D`! bNe`al tfI&g4 endstream endobj 353 0 obj 627 endobj 282 0 obj << /Length 283 0 R /Type /XObject /Subtype /Image /Width 112 /Height 40 /ColorSpace /DeviceGray /Interpolate true /BitsPerComponent 8 /Filter /FlateDecode >> stream x헿kP͏[cnbD-V%CCM$픡IE(8(NA _{A׷<~dsll0K1 !I1weWAaX0 4+ F" 0.;!rƑ)1Y{ e%q:HS' E!jR3ƵEymdt-szCOF.oZGN]o.#ꃂzqU|w !ӏѠS*^]'i*7x9GtteLh<-UZd6l2*l:erzIB <;>gGw񣻯~[2B][@o>O^;/yP\ypiy5ϻz)œ/? endstream endobj 283 0 obj 588 endobj 366 0 obj << /Length 367 0 R /Type /XObject /Subtype /Image /Width 112 /Height 40 /ColorSpace /DeviceGray /Interpolate true /BitsPerComponent 8 /Filter /FlateDecode >> stream x헿kP͏[cnbD-V%CCM$픡IE(8(NA _{A׷<~dsll0K1 !I1weWAaX0 4+ F" 0.;!rƑ)1Y{ e%q:HS' E!jR3ƵEymdt-szCOF.oZGN]o.#ꃂzqU|w !ӏѠS*^]'i*7x9GtteLh<-UZd6l2*l:erzIB <;>gGw񣻯~[2B][@o>O^;/yP\ypiy5ϻz)œ/? endstream endobj 367 0 obj 588 endobj 196 0 obj << /Length 197 0 R /Type /XObject /Subtype /Image /Width 112 /Height 40 /ColorSpace /DeviceGray /Interpolate true /BitsPerComponent 8 /Filter /FlateDecode >> stream x헿kP͏[cnbD-V%CCM$픡IE(8(NA _{A׷<~dsll0K1 !I1weWAaX0 4+ F" 0.;!rƑ)1Y{ e%q:HS' E!jR3ƵEymdt-szCOF.oZGN]o.#ꃂzqU|w !ӏѠS*^]'i*7x9GtteLh<-UZd6l2*l:erzIB <;>gGw񣻯~[2B][@o>O^;/yP\ypiy5ϻz)œ/? endstream endobj 197 0 obj 588 endobj 252 0 obj << /Length 253 0 R /Type /XObject /Subtype /Image /Width 112 /Height 40 /ColorSpace /DeviceGray /Interpolate true /BitsPerComponent 8 /Filter /FlateDecode >> stream x헿kP͏[cnbD-V%CCM$픡IE(8(NA _{A׷<~dsll0K1 !I1weWAaX0 4+ F" 0.;!rƑ)1Y{ e%q:HS' E!jR3ƵEymdt-szCOF.oZGN]o.#ꃂzqU|w !ӏѠS*^]'i*7x9GtteLh<-UZd6l2*l:erzIB <;>gGw񣻯~[2B][@o>O^;/yP\ypiy5ϻz)œ/? endstream endobj 253 0 obj 588 endobj 322 0 obj << /Length 323 0 R /Type /XObject /Subtype /Image /Width 114 /Height 60 /ColorSpace /DeviceGray /Interpolate true /BitsPerComponent 8 /Filter /FlateDecode >> stream x혽kPu`H!EPqiIQ29BB tpcrhA)DEr.,B<9/HAt$I72xy?s>a($ .ŠA2ߧ$)9ATp$Eª" ߃$5Hޥ3:b2d"J2Rk-g󅒁R!Sڵ$`o!jbl |~{M!h*gT͚Uo4Ҩ[5jRQY1[# 5V[k' lJ31̖M;2t,MųK|꾏')dm*ۈ{vgcƒ|C! {F|)=;ٗ,8_GT sgZ#dr0 =6:2_/hXto\#SuoYr&MOp)$#=2bBo7VN`o  K $%o3!_$! endstream endobj 323 0 obj 594 endobj 204 0 obj << /Length 205 0 R /Type /XObject /Subtype /Image /Width 112 /Height 40 /ColorSpace /DeviceGray /Interpolate true /BitsPerComponent 8 /Filter /FlateDecode >> stream x헿kP͏[cnbD-V%CCM$픡IE(8(NA _{A׷<~dsll0K1 !I1weWAaX0 4+ F" 0.;!rƑ)1Y{ e%q:HS' E!jR3ƵEymdt-szCOF.oZGN]o.#ꃂzqU|w !ӏѠS*^]'i*7x9GtteLh<-UZd6l2*l:erzIB <;>gGw񣻯~[2B][@o>O^;/yP\ypiy5ϻz)œ/? endstream endobj 205 0 obj 588 endobj 306 0 obj << /Length 307 0 R /Type /XObject /Subtype /Image /Width 112 /Height 40 /ColorSpace /DeviceGray /Interpolate true /BitsPerComponent 8 /Filter /FlateDecode >> stream x헿kP͏[cnbD-V%CCM$픡IE(8(NA _{A׷<~dsll0K1 !I1weWAaX0 4+ F" 0.;!rƑ)1Y{ e%q:HS' E!jR3ƵEymdt-szCOF.oZGN]o.#ꃂzqU|w !ӏѠS*^]'i*7x9GtteLh<-UZd6l2*l:erzIB <;>gGw񣻯~[2B][@o>O^;/yP\ypiy5ϻz)œ/? endstream endobj 307 0 obj 588 endobj 334 0 obj << /Length 335 0 R /Type /XObject /Subtype /Image /Width 119 /Height 60 /ColorSpace /DeviceGray /Interpolate true /BitsPerComponent 8 /Filter /FlateDecode >> stream xc` FF&FFFLmdfeec`gcceafBO@&@bFfVn>!Qq)iYZ) 1^N6$32r((ijhki*Iq0cGHRA]Ɩ@KEV ZVnAIE[gO߀ Z7K5Y>xbSбpK̢>LK3Tf{KPZ%(>47%VOQf-#+|nESg߄=muEin&jRkyŕ#2+Zϝ`ެ] VڲBФ'fW?{kVZ6ojgUF Zv~)M+Woܲ`uNh̋p6TFX+ e^7gv2صk疵Ÿ+![+mY7a-Oewh/s7ACZ*[ 2ZVh2qeO\fnغώ ftyBQkԣ0F!0F3$5& W+#;jt:0D`! bNe`al tfI&g4 endstream endobj 335 0 obj 627 endobj 208 0 obj << /Length 209 0 R /Type /XObject /Subtype /Image /Width 114 /Height 60 /ColorSpace /DeviceGray /Interpolate true /BitsPerComponent 8 /Filter /FlateDecode >> stream x혽kPu`H!EPqiIQ29BB tpcrhA)DEr.,B<9/HAt$I72xy?s>a($ .ŠA2ߧ$)9ATp$Eª" ߃$5Hޥ3:b2d"J2Rk-g󅒁R!Sڵ$`o!jbl |~{M!h*gT͚Uo4Ҩ[5jRQY1[# 5V[k' lJ31̖M;2t,MųK|꾏')dm*ۈ{vgcƒ|C! {F|)=;ٗ,8_GT sgZ#dr0 =6:2_/hXto\#SuoYr&MOp)$#=2bBo7VN`o  K $%o3!_$! endstream endobj 209 0 obj 594 endobj 226 0 obj << /Length 227 0 R /Type /XObject /Subtype /Image /Width 112 /Height 40 /ColorSpace /DeviceGray /Interpolate true /BitsPerComponent 8 /Filter /FlateDecode >> stream x헿kP͏[cnbD-V%CCM$픡IE(8(NA _{A׷<~dsll0K1 !I1weWAaX0 4+ F" 0.;!rƑ)1Y{ e%q:HS' E!jR3ƵEymdt-szCOF.oZGN]o.#ꃂzqU|w !ӏѠS*^]'i*7x9GtteLh<-UZd6l2*l:erzIB <;>gGw񣻯~[2B][@o>O^;/yP\ypiy5ϻz)œ/? endstream endobj 227 0 obj 588 endobj 310 0 obj << /Length 311 0 R /Type /XObject /Subtype /Image /Width 112 /Height 40 /ColorSpace /DeviceGray /Interpolate true /BitsPerComponent 8 /Filter /FlateDecode >> stream x헿kP͏[cnbD-V%CCM$픡IE(8(NA _{A׷<~dsll0K1 !I1weWAaX0 4+ F" 0.;!rƑ)1Y{ e%q:HS' E!jR3ƵEymdt-szCOF.oZGN]o.#ꃂzqU|w !ӏѠS*^]'i*7x9GtteLh<-UZd6l2*l:erzIB <;>gGw񣻯~[2B][@o>O^;/yP\ypiy5ϻz)œ/? endstream endobj 311 0 obj 588 endobj 220 0 obj << /Length 221 0 R /Type /XObject /Subtype /Image /Width 112 /Height 40 /ColorSpace /DeviceGray /Interpolate true /BitsPerComponent 8 /Filter /FlateDecode >> stream x헿kP͏[cnbD-V%CCM$픡IE(8(NA _{A׷<~dsll0K1 !I1weWAaX0 4+ F" 0.;!rƑ)1Y{ e%q:HS' E!jR3ƵEymdt-szCOF.oZGN]o.#ꃂzqU|w !ӏѠS*^]'i*7x9GtteLh<-UZd6l2*l:erzIB <;>gGw񣻯~[2B][@o>O^;/yP\ypiy5ϻz)œ/? endstream endobj 221 0 obj 588 endobj 330 0 obj << /Length 331 0 R /Type /XObject /Subtype /Image /Width 114 /Height 60 /ColorSpace /DeviceGray /Interpolate true /BitsPerComponent 8 /Filter /FlateDecode >> stream x혽kPu`H!EPqiIQ29BB tpcrhA)DEr.,B<9/HAt$I72xy?s>a($ .ŠA2ߧ$)9ATp$Eª" ߃$5Hޥ3:b2d"J2Rk-g󅒁R!Sڵ$`o!jbl |~{M!h*gT͚Uo4Ҩ[5jRQY1[# 5V[k' lJ31̖M;2t,MųK|꾏')dm*ۈ{vgcƒ|C! {F|)=;ٗ,8_GT sgZ#dr0 =6:2_/hXto\#SuoYr&MOp)$#=2bBo7VN`o  K $%o3!_$! endstream endobj 331 0 obj 594 endobj 248 0 obj << /Length 249 0 R /Type /XObject /Subtype /Image /Width 112 /Height 40 /ColorSpace /DeviceGray /Interpolate true /BitsPerComponent 8 /Filter /FlateDecode >> stream x헿kP͏[cnbD-V%CCM$픡IE(8(NA _{A׷<~dsll0K1 !I1weWAaX0 4+ F" 0.;!rƑ)1Y{ e%q:HS' E!jR3ƵEymdt-szCOF.oZGN]o.#ꃂzqU|w !ӏѠS*^]'i*7x9GtteLh<-UZd6l2*l:erzIB <;>gGw񣻯~[2B][@o>O^;/yP\ypiy5ϻz)œ/? endstream endobj 249 0 obj 588 endobj 314 0 obj << /Length 315 0 R /Type /XObject /Subtype /Image /Width 75 /Height 60 /ColorSpace /DeviceGray /Interpolate true /BitsPerComponent 8 /Filter /FlateDecode >> stream xc`y7TYXXI,,LLL21sprs 89X cbf' qs#(*)+B$PVRfgaB#+ P_G]IFT^J[i?;QF͓ڴmQ`fT[iJ %l[>}mvn^5.3V[(K7l߳(wז'e%,FVqҎ6 ҨY0>+VGVc(?V @FhbቁXRE*=՚kQF$klS @ K 10Pk P % 1lElW endstream endobj 315 0 obj 581 endobj 194 0 obj << /Length 195 0 R /Type /XObject /Subtype /Image /Width 112 /Height 40 /ColorSpace /DeviceGray /Interpolate true /BitsPerComponent 8 /Filter /FlateDecode >> stream x헿kP͏[cnbD-V%CCM$픡IE(8(NA _{A׷<~dsll0K1 !I1weWAaX0 4+ F" 0.;!rƑ)1Y{ e%q:HS' E!jR3ƵEymdt-szCOF.oZGN]o.#ꃂzqU|w !ӏѠS*^]'i*7x9GtteLh<-UZd6l2*l:erzIB <;>gGw񣻯~[2B][@o>O^;/yP\ypiy5ϻz)œ/? endstream endobj 195 0 obj 588 endobj 354 0 obj << /Length 355 0 R /Type /XObject /Subtype /Image /Width 112 /Height 40 /ColorSpace /DeviceGray /Interpolate true /BitsPerComponent 8 /Filter /FlateDecode >> stream x헿kP͏[cnbD-V%CCM$픡IE(8(NA _{A׷<~dsll0K1 !I1weWAaX0 4+ F" 0.;!rƑ)1Y{ e%q:HS' E!jR3ƵEymdt-szCOF.oZGN]o.#ꃂzqU|w !ӏѠS*^]'i*7x9GtteLh<-UZd6l2*l:erzIB <;>gGw񣻯~[2B][@o>O^;/yP\ypiy5ϻz)œ/? endstream endobj 355 0 obj 588 endobj 242 0 obj << /Length 243 0 R /Type /XObject /Subtype /Image /Width 119 /Height 60 /ColorSpace /DeviceGray /Interpolate true /BitsPerComponent 8 /Filter /FlateDecode >> stream xc` FF&FFFLmdfeec`gcceafBO@&@bFfVn>!Qq)iYZ) 1^N6$32r((ijhki*Iq0cGHRA]Ɩ@KEV ZVnAIE[gO߀ Z7K5Y>xbSбpK̢>LK3Tf{KPZ%(>47%VOQf-#+|nESg߄=muEin&jRkyŕ#2+Zϝ`ެ] VڲBФ'fW?{kVZ6ojgUF Zv~)M+Woܲ`uNh̋p6TFX+ e^7gv2صk疵Ÿ+![+mY7a-Oewh/s7ACZ*[ 2ZVh2qeO\fnغώ ftyBQkԣ0F!0F3$5& W+#;jt:0D`! bNe`al tfI&g4 endstream endobj 243 0 obj 627 endobj 276 0 obj << /Length 277 0 R /Type /XObject /Subtype /Image /Width 75 /Height 60 /ColorSpace /DeviceGray /Interpolate true /BitsPerComponent 8 /Filter /FlateDecode >> stream xc`y7TYXXI,,LLL21sprs 89X cbf' qs#(*)+B$PVRfgaB#+ P_G]IFT^J[i?;QF͓ڴmQ`fT[iJ %l[>}mvn^5.3V[(K7l߳(wז'e%,FVqҎ6 ҨY0>+VGVc(?V @FhbቁXRE*=՚kQF$klS @ K 10Pk P % 1lElW endstream endobj 277 0 obj 581 endobj 262 0 obj << /Length 263 0 R /Type /XObject /Subtype /Image /Width 112 /Height 40 /ColorSpace /DeviceGray /Interpolate true /BitsPerComponent 8 /Filter /FlateDecode >> stream x헿kP͏[cnbD-V%CCM$픡IE(8(NA _{A׷<~dsll0K1 !I1weWAaX0 4+ F" 0.;!rƑ)1Y{ e%q:HS' E!jR3ƵEymdt-szCOF.oZGN]o.#ꃂzqU|w !ӏѠS*^]'i*7x9GtteLh<-UZd6l2*l:erzIB <;>gGw񣻯~[2B][@o>O^;/yP\ypiy5ϻz)œ/? endstream endobj 263 0 obj 588 endobj 302 0 obj << /Length 303 0 R /Type /XObject /Subtype /Image /Width 112 /Height 40 /ColorSpace /DeviceGray /Interpolate true /BitsPerComponent 8 /Filter /FlateDecode >> stream x헿kP͏[cnbD-V%CCM$픡IE(8(NA _{A׷<~dsll0K1 !I1weWAaX0 4+ F" 0.;!rƑ)1Y{ e%q:HS' E!jR3ƵEymdt-szCOF.oZGN]o.#ꃂzqU|w !ӏѠS*^]'i*7x9GtteLh<-UZd6l2*l:erzIB <;>gGw񣻯~[2B][@o>O^;/yP\ypiy5ϻz)œ/? endstream endobj 303 0 obj 588 endobj 312 0 obj << /Length 313 0 R /Type /XObject /Subtype /Image /Width 119 /Height 60 /ColorSpace /DeviceGray /Interpolate true /BitsPerComponent 8 /Filter /FlateDecode >> stream xc` FF&FFFLmdfeec`gcceafBO@&@bFfVn>!Qq)iYZ) 1^N6$32r((ijhki*Iq0cGHRA]Ɩ@KEV ZVnAIE[gO߀ Z7K5Y>xbSбpK̢>LK3Tf{KPZ%(>47%VOQf-#+|nESg߄=muEin&jRkyŕ#2+Zϝ`ެ] VڲBФ'fW?{kVZ6ojgUF Zv~)M+Woܲ`uNh̋p6TFX+ e^7gv2صk疵Ÿ+![+mY7a-Oewh/s7ACZ*[ 2ZVh2qeO\fnغώ ftyBQkԣ0F!0F3$5& W+#;jt:0D`! bNe`al tfI&g4 endstream endobj 313 0 obj 627 endobj 222 0 obj << /Length 223 0 R /Type /XObject /Subtype /Image /Width 112 /Height 40 /ColorSpace /DeviceGray /Interpolate true /BitsPerComponent 8 /Filter /FlateDecode >> stream x헿kP͏[cnbD-V%CCM$픡IE(8(NA _{A׷<~dsll0K1 !I1weWAaX0 4+ F" 0.;!rƑ)1Y{ e%q:HS' E!jR3ƵEymdt-szCOF.oZGN]o.#ꃂzqU|w !ӏѠS*^]'i*7x9GtteLh<-UZd6l2*l:erzIB <;>gGw񣻯~[2B][@o>O^;/yP\ypiy5ϻz)œ/? endstream endobj 223 0 obj 588 endobj 210 0 obj << /Length 211 0 R /Type /XObject /Subtype /Image /Width 119 /Height 60 /ColorSpace /DeviceGray /Interpolate true /BitsPerComponent 8 /Filter /FlateDecode >> stream xc` FF&FFFLmdfeec`gcceafBO@&@bFfVn>!Qq)iYZ) 1^N6$32r((ijhki*Iq0cGHRA]Ɩ@KEV ZVnAIE[gO߀ Z7K5Y>xbSбpK̢>LK3Tf{KPZ%(>47%VOQf-#+|nESg߄=muEin&jRkyŕ#2+Zϝ`ެ] VڲBФ'fW?{kVZ6ojgUF Zv~)M+Woܲ`uNh̋p6TFX+ e^7gv2صk疵Ÿ+![+mY7a-Oewh/s7ACZ*[ 2ZVh2qeO\fnغώ ftyBQkԣ0F!0F3$5& W+#;jt:0D`! bNe`al tfI&g4 endstream endobj 211 0 obj 627 endobj 290 0 obj << /Length 291 0 R /Type /XObject /Subtype /Image /Width 130 /Height 60 /ColorSpace /DeviceGray /Interpolate true /BitsPerComponent 8 /Filter /FlateDecode >> stream x홿k@aH!EPqiIQ29BB tp!.RVyugɖ{} <~$I$o`}uyA ,CQGF4BFˠA@@Rjh<#&F4Uy'b X2ufRɘ&y(_i#W(MĔ֯e44>_TXϏJ)kWE%Λ5n7-4vݪtLN -ijvvkd$ V ΤH*Ws4Fs{J. 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"abyss-bowtie: invalid option: $OPTARG"; exit 1;; esac done shift $((OPTIND-1)) query=("$@") target=${query[${#query[@]}-1]} unset query[${#query[@]}-1] index=$target.1.ebwt # Build the index. if [ ! -r $index ]; then echo >&2 "Building the index $index..." echo >&2 bowtie-build $target $target bowtie-build $target $target 1>&2 elif [ $index -ot $target ]; then echo >&2 "The index $index is stale. Rebuilding the index..." echo >&2 bowtie-build $target $target bowtie-build $target $target 1>&2 else echo >&2 "The index $index is up to date." fi # Map the reads. echo >&2 $bowtie $target "${query[@]}" exec abyss-tofastq -i "${query[@]}" |$bowtie $target - abyss-1.3.6/bin/abyss-bowtie2000755 002433 001057 00000002250 12104026027 017540 0ustar00traymondassembly000000 000000 #!/bin/bash set -eu case $1 in --help) cat <&2 "abyss-bowtie2: invalid option: $OPTARG" exit 1;; esac done shift $((OPTIND-1)) query=("$@") target=${query[${#query[@]}-1]} unset query[${#query[@]}-1] index=$target.1.bt2 # Build the index. if [ ! -r $index ]; then echo >&2 "Building the index $index..." echo >&2 bowtie2-build $target $target bowtie2-build $target $target 1>&2 elif [ $index -ot $target ]; then echo >&2 "The index $index is stale. Rebuilding the index..." echo >&2 bowtie2-build $target $target bowtie2-build $target $target 1>&2 else echo >&2 "The index $index is up to date." fi # Map the reads. echo >&2 $bowtie2_align $target "${query[@]}" exec abyss-tofastq -i "${query[@]}" |$bowtie2_align $target - abyss-1.3.6/bin/abyss-bwa000755 002433 001057 00000002270 12104026027 016740 0ustar00traymondassembly000000 000000 #!/bin/bash set -eu case $1 in --help) cat <&1 |head -n4 exit ;; esac # Parse the command line. bwa_aln='bwa aln' bwa_index='bwa index -a bwtsw' while getopts :j:l:v opt; do case $opt in j) bwa_aln="$bwa_aln -t$OPTARG";; l) ;; v) ;; \?) echo >&2 "abyss-bwa: invalid option: $OPTARG"; exit 1;; esac done shift $((OPTIND-1)) query=("$@") target=${query[${#query[@]}-1]} unset query[${#query[@]}-1] index=$target.bwt # Build the index. if [ ! -r $index ]; then echo >&2 "Building the index $index..." echo >&2 $bwa_index $target $target $bwa_index $target $target 1>&2 elif [ $index -ot $target ]; then echo >&2 "The index $index is stale. Rebuilding the index..." echo >&2 $bwa_index $target $target $bwa_index $target $target 1>&2 else echo >&2 "The index $index is up to date." fi # Map the reads. echo >&2 $bwa_aln $target "${query[@]}" exec abyss-tofastq -i "${query[@]}" \ |$bwa_aln $target - \ |bwa samse $target - <(abyss-tofastq -i "${query[@]}") abyss-1.3.6/bin/abyss-bwasw000755 002433 001057 00000002522 12104026027 017312 0ustar00traymondassembly000000 000000 #!/bin/bash set -eu case $1 in --help) cat <&1 |head -n4 exit ;; esac # Parse the command line. bwasw='bwa bwasw' bwa_index='bwa index -a bwtsw' while getopts :j:l:v opt; do case $opt in j) bwasw="$bwasw -t$OPTARG";; l) ;; v) ;; \?) echo >&2 "abyss-bwasw: invalid option: $OPTARG"; exit 1;; esac done shift $((OPTIND-1)) query=("$@") target=${query[${#query[@]}-1]} unset query[${#query[@]}-1] index=$target.bwt # Build the index. if [ ! -r $index ]; then echo >&2 "Building the index $index..." echo >&2 $bwa_index $target $target $bwa_index $target $target 1>&2 elif [ $index -ot $target ]; then echo >&2 "The index $index is stale. Rebuilding the index..." echo >&2 $bwa_index $target $target $bwa_index $target $target 1>&2 else echo >&2 "The index $index is up to date." fi # Map the reads. echo >&2 $bwasw $target "${query[@]}" exec abyss-tofastq -i "${query[@]}" \ |$bwasw $target - \ |awk ' BEGIN { OFS = "\t" } /^@/ { print; next } $1 == x { next } { x = $1 } sub("/1$", "", $1) > 0 { $2 = or($2, 0x41) print; next } sub("/[23]$", "", $1) > 0 { $2 = or($2, 0x81) print; next } { print } ' abyss-1.3.6/bin/abyss-fatoagp000755 002433 001057 00000002400 12104026027 017603 0ustar00traymondassembly000000 000000 #!/usr/bin/perl # Convert a FASTA file of scaffolds to a FASTA file of contigs and an # AGP file. # Written by Shaun Jackman . use strict; use Getopt::Std qw'getopts'; my %opt; getopts 'f:s:', \%opt; my $opt_fasta = $opt{'f'}; my $opt_min_len = defined $opt{'s'} ? $opt{'s'} : 200; open FASTA, ">$opt_fasta" or die "error: `$opt_fasta': $!\n" if $opt_fasta; while (<>) { die unless /^>/; chomp; my ($scafid, undef) = split ' ', $_, 2; substr $scafid, 0, 1, ''; my $scafseq = <>; chomp $scafseq; my $scaflen = $scafseq =~ tr/ACGTacgt//; next if $scaflen < $opt_min_len; my @ctgseqs = split /([Nn]+)/, $scafseq; my $i = 0; my $x = 0; for my $ctgseq (@ctgseqs) { my $len = length $ctgseq; # object object_beg object_end part_number print 'scaffold', $scafid, "\t", $x + 1, "\t", $x + $len, "\t", $i + 1, "\t"; if ($ctgseq =~ /^[nN]/) { # component_type gap_length gap_type linkage print "N\t", $len, "\tscaffold\tyes\tpaired-ends\n"; } else { my $ctgid = 'contig' . $scafid . '_' . ($i / 2); # component_type component_id # component_beg component_end orientation print "W\t", $ctgid, "\t1\t", $len, "\t+\n"; print FASTA '>', $ctgid, "\n", $ctgseq, "\n" if $opt_fasta; } $i++; $x += $len; } } abyss-1.3.6/bin/abyss-kaligner000755 002433 001057 00000000047 12015543263 017772 0ustar00traymondassembly000000 000000 #!/bin/bash set -eu exec KAligner "$@" abyss-1.3.6/bin/abyss-pe000755 002433 001057 00000026676 12176317327 016632 0ustar00traymondassembly000000 000000 #!/usr/bin/make -rRf # Run the ABySS assembler. # Written by Shaun Jackman . # Set pipefail to require that all commands of a pipe must succeed. SHELL=/bin/bash -o pipefail # Define this environment variable on Mac OS X to read # compressed files. export DYLD_FORCE_FLAT_NAMESPACE=1 # Integrate with Sun Grid Engine (SGE) ifdef JOB_NAME name?=$(JOB_NAME) endif ifdef SGE_TASK_ID k?=$(SGE_TASK_ID) endif ifdef NSLOTS ifneq ($(NSLOTS), 1) np?=$(NSLOTS) endif endif # Integrate with Portable Batch System (PBS) ifdef PBS_JOBNAME name?=$(PBS_JOBNAME) endif ifdef PBS_ARRAYID k?=$(PBS_ARRAYID) endif ifdef PBS_NODEFILE NSLOTS=$(shell wc -l <$(PBS_NODEFILE)) ifneq ($(NSLOTS), 1) np?=$(NSLOTS) endif endif # Integrate with Load Sharing Facility (LSF) ifdef LSB_JOBNAME name?=$(LSB_JOBNAME) endif ifdef LSB_JOBINDEX k?=$(LSB_JOBINDEX) endif ifdef LSB_DJOB_NUMPROC ifneq ($(LSB_DJOB_NUMPROC), 1) np?=$(LSB_DJOB_NUMPROC) endif endif ifdef LSF_BINDIR mpirun?=$(LSF_BINDIR)/mpirun.lsf endif # Integrate with IBM LoadLeveler ifdef LOADL_JOB_NAME name?=$(LOADL_JOB_NAME) endif ifdef LOADL_STEP_ID k?=$(LOADL_STEP_ID) endif ifdef LOADL_HOSTFILE NSLOTS=$(shell wc -l <$(LOADL_HOSTFILE)) ifneq ($(NSLOTS), 1) np?=$(NSLOTS) endif endif # Integrate with SLURM ifdef SLURM_JOB_NAME name?=$(SLURM_JOB_NAME) endif ifdef SLURM_JOBID k?=$(SLURM_JOBID) endif ifdef SLURM_NTASKS np?=$(SLURM_NTASKS) endif # Determine the path to mpirun mpirun?=$(shell which mpirun) ifeq ($(mpirun),) mpirun=mpirun endif # Determine the path to the ABySS executables path?=$(shell if ! which ABYSS >/dev/null 2>/dev/null; then \ dirname $(MAKEFILE_LIST); fi) ifdef path PATH:=$(path):$(PATH) endif ifdef lib map=$(foreach a,$(2),$(call $(1),$(a))) deref=$($1) in?=$(call map, deref, $(lib)) else ifdef in lib?=$(name) $(lib)?=$(in) endif endif pe?=$(lib) mp?=$(pe) # Strip spaces from the file paths ifdef in override in:=$(strip $(in)) endif ifdef se override se:=$(strip $(se)) endif # ABYSS parameters q ?= 3 abyssopt += -k$k -q$q ifdef e abyssopt += -e$e endif ifdef E abyssopt += -E$E endif ifdef t abyssopt += -t$t endif ifdef c abyssopt += -c$c endif ifdef b abyssopt += -b$b pbopt += -b$b endif abyssopt += $v --coverage-hist=coverage.hist -s $*-bubbles.fa # Number of threads ifdef PE_HOSTFILE hostname?=$(shell hostname -f) j?=$(shell awk '$$1 == "$(hostname)" {print $$2}' $(PE_HOSTFILE)) endif ifeq ($j,) j:=$(np) endif ifeq ($j,) j:=2 endif # AdjList parameters m?=50 # PopBubbles parameters p?=0.9 pbopt += -p$p # Aligner parameters aligner?=map align?=abyss-$(aligner) mapopt=$v -j$j -l$($*_l) $(ALIGNER_OPTIONS) $(MAP_OPTIONS) # fixmate parameters ifeq ($(align),abyss-kaligner) fixmate?=ParseAligns else fixmate?=abyss-fixmate endif fmopt=$v -l$($*_l) $(FIXMATE_OPTIONS) # DistanceEst parameters l?=$k s?=200 n?=10 libs=$(pe) $(mp) $(foreach i,$(libs),$(eval $i_l?=$l)) $(foreach i,$(libs),$(eval $i_s?=$s)) $(foreach i,$(libs),$(eval $i_n?=$n)) deopt=$v -j$j -k$k -l$($*_l) -s$($*_s) -n$($*_n) $($*_de) \ $(DISTANCEEST_OPTIONS) # SimpleGraph parameters ifdef d sgopt += -d$d endif # PathConsensus parameters ifdef a pcopt += -a$a endif pcopt += -p$p # Scaffold parameters S?=$s N?=$n # BWA-SW parameters bwaswopt=-t$j BWASW_OPTIONS='-b9 -q16 -r1 -w500' # Remove environment variables unexport in se $(lib) $(pe) $(mp) # Check the mandatory parameters ifndef name error:: @>&2 echo 'abyss-pe: missing parameter `name`' endif ifndef k error:: @>&2 echo 'abyss-pe: missing parameter `k`' endif ifeq ($(lib)$(in)$(se),) error:: @>&2 echo 'abyss-pe: missing parameter `lib`, `in` or `se`' endif default: error:: @>&2 echo 'Try `abyss-pe help` for more information.' @false # Help and version messages help: @printf '\ Usage: abyss-pe [OPTION]... [PARAMETER=VALUE]... [COMMAND]...\n\ Assemble reads into contigs and scaffolds. ABySS is a de novo\n\ sequence assembler intended for short paired-end reads and large\n\ genomes. See the abyss-pe man page for documentation of assembly\n\ parameters and commands. abyss-pe is a Makefile script, and so\n\ options of `make` may also be used with abyss-pe. See the `make`\n\ man page for documentation.\n\ \n\ Report bugs to .\n' version: @printf '\ abyss-pe (ABySS) 1.3.6\n\ Written by Shaun Jackman.\n\ \n\ Copyright 2012 Canada'\''s Michael Smith Genome Science Centre\n' versions: version @ABYSS --version; echo @-ABYSS-P --version; echo @AdjList --version; echo @DistanceEst --version; echo @MergeContigs --version; echo @MergePaths --version; echo @Overlap --version; echo @PathConsensus --version; echo @PathOverlap --version; echo @PopBubbles --version; echo @SimpleGraph --version; echo @abyss-fac --version; echo @abyss-filtergraph --version; echo @abyss-fixmate --version; echo @abyss-map --version; echo @abyss-scaffold --version; echo @abyss-todot --version; echo @$(align) --version; echo @awk --version; echo @sort --version; echo @-mpirun --version # Determine the default target default: unitigs ifneq ($(in),) default: contigs contigs-dot endif ifneq ($(mp),) default: scaffolds scaffolds-dot endif default: stats # Define the commands (phony targets) unitigs: $(name)-unitigs.fa unitigs-dot: $(name)-unitigs.dot pe-index: $(name)-3.fa.fm pe-sam: $(addsuffix -3.sam.gz, $(pe)) pe-bam: $(addsuffix -3.bam.bai, $(pe)) contigs: $(name)-contigs.fa contigs-dot: $(name)-contigs.dot mp-index: $(name)-6.fa.fm mp-sam: $(addsuffix -6.sam.gz, $(mp)) mp-bam: $(addsuffix -6.bam.bai, $(mp)) scaffolds: $(name)-scaffolds.fa scaffolds-dot: $(name)-scaffolds.dot all: default bam stats clean: rm -f *.adj *.dot *.sam.gz *.hist *.dist *.path *.path[123] .PHONY: bam default stats \ unitigs unitigs-dot \ pe-index pe-sam pe-bam contigs contigs-dot \ mp-index mp-sam mp-bam scaffolds scaffolds-dot \ all clean help version versions .DELETE_ON_ERROR: .SECONDARY: # Utilities %.fa.fm: %.fa abyss-index $v $< %.bam: %.sam.gz samtools view -Sb $< -o $@ %.bam.bai: %.bam samtools index $< # Assemble unitigs %-1.fa: ifdef np $(mpirun) -np $(np) ABYSS-P $(abyssopt) $(ABYSS_OPTIONS) -o $@ $(in) $(se) else ABYSS $(abyssopt) $(ABYSS_OPTIONS) -o $@ $(in) $(se) endif # Find overlapping contigs %-1.adj: %-1.fa AdjList $v -k$k -m$m $< >$@ # Remove shim contigs %-2.adj: %-1.adj abyss-filtergraph $v -k$k -g $@ $^ >$*-1.path # Pop bubbles %-2.path %-3.adj: %-1.fa %-2.adj PopBubbles $v -j$j -k$k $(pbopt) $(POPBUBBLES_OPTIONS) -g $*-3.adj $^ >$*-2.path %-3.fa: %-1.fa %-2.adj %-2.path MergeContigs $v -k$k -o $@ $^ awk '!/^>/ {x[">" $$1]=1; next} {getline s} $$1 in x {print $$0 "\n" s}' \ $*-2.path $*-1.fa >$*-indel.fa %-3.dot: %-3.adj abyss-todot $v -k$k $< >$@ %-unitigs.fa: %-3.fa ln -sf $< $@ %-unitigs.dot: %-3.dot ln -sf $< $@ # Estimate distances between unitigs %-3.sam.gz %-3.hist: $(name)-3.fa $(align) $(mapopt) $(strip $($*)) $< \ |$(fixmate) $(fmopt) -h $*-3.hist \ |sort -snk3 -k4 \ |gzip >$*-3.sam.gz %-3.bam %-3.hist: $(name)-3.fa $(align) $(mapopt) $(strip $($*)) $< \ |$(fixmate) $(fmopt) -h $*-3.hist \ |sort -snk3 -k4 \ |samtools view -Sb - -o $*-3.bam %-3.dist: %-3.sam.gz %-3.hist gunzip -c $< \ |DistanceEst $(deopt) -o $@ $*-3.hist %-3.dist: %-3.bam %-3.hist samtools view -h $< \ |DistanceEst $(deopt) -o $@ $*-3.hist %-3.dist: $(name)-3.fa $(align) $(mapopt) $(strip $($*)) $< \ |$(fixmate) $(fmopt) -h $*-3.hist \ |sort -snk3 -k4 \ |DistanceEst $(deopt) -o $@ $*-3.hist dist=$(addsuffix -3.dist, $(pe)) ifneq ($(name)-3.dist, $(dist)) $(name)-3.dist: $(name)-3.fa $(dist) abyss-todot $v --dist -e $^ >$@ $(name)-3.bam: $(addsuffix -3.bam, $(pe)) samtools merge -r $@ $^ endif # Find overlaps between contigs %-4.fa %-4.adj: %-3.fa %-3.adj %-3.dist Overlap $v $(OVERLAP_OPTIONS) -k$k -g $*-4.adj -o $*-4.fa $^ # Assemble contigs %-4.path1: %-4.adj %-3.dist SimpleGraph $v $(sgopt) $(SIMPLEGRAPH_OPTIONS) -j$j -k$k -o $@ $^ %-4.path2: %-4.adj %-4.path1 MergePaths $v $(MERGEPATHS_OPTIONS) -j$j -k$k -o $@ $^ %-4.path3: %-4.adj %-4.path2 PathOverlap --assemble $v -k$k $^ >$@ ifndef cs %-5.path %-5.fa %-5.adj: %-3.fa %-4.fa %-4.adj %-4.path3 cat $(wordlist 1, 2, $^) \ |PathConsensus $v -k$k $(pcopt) -o $*-5.path -s $*-5.fa -g $*-5.adj - $(wordlist 3, 4, $^) %-6.fa: %-3.fa %-4.fa %-5.fa %-5.adj %-5.path cat $(wordlist 1, 3, $^) |MergeContigs $v -k$k -o $@ - $(wordlist 4, 5, $^) else %-5.adj %-5.path: %-4.adj %-4.path3 ln -sf $*-4.adj $*-5.adj ln -sf $*-4.path3 $*-5.path %-cs.fa: %-3.fa %-4.fa %-4.adj %-4.path3 cat $(wordlist 1, 2, $^) |MergeContigs $v -k$k -o $@ - $(wordlist 3, 4, $^) # Convert colour-space sequence to nucleotides %-6.fa: %-cs.fa KAligner $v --seq -m -j$j -l$l $(in) $(se) $< \ |Consensus $v -o $@ $< endif %-6.dot: %-5.adj %-5.path PathOverlap --overlap $v --dot -k$k $^ >$@ %-contigs.fa: %-6.fa ln -sf $< $@ %-contigs.dot: %-6.dot ln -sf $< $@ # Estimate distances between contigs %-6.sam.gz %-6.hist: $(name)-6.fa $(align) $(mapopt) $(strip $($*)) $< \ |$(fixmate) $(fmopt) -h $*-6.hist \ |sort -snk3 -k4 \ |gzip >$*-6.sam.gz %-6.bam %-6.hist: $(name)-6.fa $(align) $(mapopt) $(strip $($*)) $< \ |$(fixmate) $(fmopt) -h $*-6.hist \ |sort -snk3 -k4 \ |samtools view -Sb - -o $*-6.bam %-6.dist.dot: %-6.sam.gz %-6.hist gunzip -c $< \ |DistanceEst --dot $(deopt) -o $@ $*-6.hist %-6.dist.dot: %-6.bam %-6.hist samtools view -h $< \ |DistanceEst --dot $(deopt) -o $@ $*-6.hist %-6.dist.dot: $(name)-6.fa $(align) $(mapopt) $(strip $($*)) $< \ |$(fixmate) $(fmopt) -h $*-6.hist \ |sort -snk3 -k4 \ |DistanceEst --dot $(deopt) -o $@ $*-6.hist # Scaffold %-6.path: $(name)-6.dot $(addsuffix -6.dist.dot, $(mp)) abyss-scaffold $v -k$k -s$S -n$N -g $@.dot $(SCAFFOLD_OPTIONS) $^ >$@ %-7.path %-7.adj %-7.fa: %-6.fa %-6.dot %-6.path PathConsensus $v -k$k $(pcopt) -s $*-7.fa -g $*-7.adj -o $*-7.path $^ %-8.fa: %-6.fa %-7.fa %-7.adj %-7.path cat $(wordlist 1, 2, $^) \ |MergeContigs $v -k$k -o $*-8.fa - $(wordlist 3, 4, $^) %-8.dot: %-7.adj %-7.path PathOverlap --overlap $v --dot -k$k $^ >$@ %-scaffolds.fa: %-8.fa ln -sf $< $@ %-scaffolds.dot: %-8.dot ln -sf $< $@ # Create the final BAM file ifneq ($(mp),) bam: $(name)-scaffolds.bam.bai else ifneq ($(in),) bam: $(name)-contigs.bam.bai else bam: $(name)-unitigs.bam.bai endif endif $(name)-unitigs.bam: %.bam: %.fa $(align) $v -j$j -l$l $(ALIGNER_OPTIONS) $(se) $< \ |samtools view -Su - |samtools sort -o - - >$@ $(name)-contigs.bam $(name)-scaffolds.bam: %.bam: %.fa $(align) $v -j$j -l$l $(ALIGNER_OPTIONS) \ $(call map, deref, $(sort $(lib) $(pe) $(mp))) $< \ |$(fixmate) $(fmopt) \ |sort -snk3 -k4 \ |samtools view -Sb - >$@ # Align the variants to the assembly %.fa.bwt: %.fa bwa index $< %-variants.bam: %.fa.bwt bwa bwasw -t$j $*.fa <(cat $(name)-bubbles.fa $(name)-indel.fa) \ |samtools view -Su - |samtools sort -o - - >$@ %-variants.vcf.gz: %.fa %-variants.bam samtools mpileup -Buf $^ |bcftools view -vp1 - |bgzip >$@ %.gz.tbi: %.gz tabix -pvcf $< # Calculate assembly contiguity statistics stats: $(name)-stats $(name)-stats: %-stats: %-unitigs.fa ifneq ($(in),) $(name)-stats: %-stats: %-contigs.fa endif ifneq ($(mp),) $(name)-stats: %-stats: %-scaffolds.fa endif $(name)-stats: abyss-fac $(FAC_OPTIONS) $^ |tee $@ # Create an AGP file and FASTA file of scaftigs from scaffolds %.agp %-agp.fa: %.fa abyss-fatoagp $(FATOAGP_OPTIONS) -f $*-agp.fa $< >$*.agp # Align the contigs to the reference %-$(ref).sam.gz: %.fa bwa bwasw $(bwaswopt) $(BWASW_OPTIONS) $($(ref)) $< |gzip >$@ # Find breakpoints in the alignments %.break: %.sam.gz abyss-samtobreak $(SAMTOBREAK_OPTIONS) $< >$@ abyss-1.3.6/bin/abyss-samtoafg000755 002433 001057 00000010547 12104026027 017776 0ustar00traymondassembly000000 000000 #!/usr/bin/perl use strict; use Getopt::Long; use Pod::Usage; sub version { print < \$opt_eid, 'iid|i=s' => \$opt_iid, 'mean|m=i' => \$opt_mean, 'sd|s=i' => \$opt_sd, 'help' => sub { pod2usage(-verbose => 1) }, 'man' => sub { pod2usage(-verbose => 2) }, 'version' => \&version); for (@ARGV) { die "cannot read `$_'" unless $_ eq '-' || -r } # Output the library record (LIB). print "{LIB\neid:$opt_eid\niid:$opt_iid\n"; print "{DST\nmea:$opt_mean\nstd:$opt_sd\n}\n" if defined $opt_mean && defined $opt_sd; print "}\n"; sub getMateID($) { my $id = shift; return $id =~ s%/1$%/2% || $id =~ s%/2$%/1% ? $id : undef; } my ($g_red_iid, $g_frg_iid, @ctg_eids, @ctg_seqs, %reds, %frgs, %tles); # Output a read (RED) and possibly a fragment (FRG). sub createRead($$$) { my ($eid, $seq, $qlt) = @_; die "error: duplicate sequence ID `$eid'" if exists $reds{$eid}; my $red_iid = ++$g_red_iid; (my $frg_eid = $eid) =~ s/\/[12]$//; my ($my_frg_iid, $mate_iid); if (exists $frgs{$frg_eid}) { $my_frg_iid = delete $frgs{$frg_eid}; my $mate_eid = getMateID($eid); die unless defined $mate_eid; $mate_iid = delete $reds{$mate_eid}; die unless defined $mate_iid; } else { $my_frg_iid = $frgs{$frg_eid} = ++$g_frg_iid; $reds{$eid} = $red_iid; } # Output a read (RED) record. my $qlength = length $seq; print "{RED\nclr:0,$qlength\niid:$red_iid\neid:$eid\n", "frg:$my_frg_iid\n", "seq:\n$seq\n.\nqlt:\n$qlt\n.\n}\n"; # Output a fragment (FRG) record. if (defined $mate_iid) { print "{FRG\nrds:$mate_iid,$red_iid\nlib:$opt_iid\n", "eid:$frg_eid\niid:$my_frg_iid\ntyp:I\n}\n"; } return $red_iid; } # Return the left and right soft clipping of this CIGAR string. sub parseCigar($) { my $cigar = shift; my $clipLeft = $cigar =~ /^([0-9]+)S/ ? $1 : 0; my $clipRight = $cigar =~ /([0-9]+)S$/ ? $1 : 0; return ($clipLeft, $clipRight); } # Record the alignment (TLE) records. while (<>) { chomp; next if /^#/ || /^@/; if (/^>([^ ]+)/) { my $eid = $1; chomp (my $seq = <>); push @ctg_eids, $eid; push @ctg_seqs, $seq; next; } my ($qid, $flag, $tid, $tstart, $mapq, $cigar, $rnext, $pnext, $tlen, $qseq, $qqual) = split '\t'; die unless defined $qqual; $tstart--; # convert to zero-based coordinate $qid .= "/1" if $flag & 0x40; #FREAD1 $qid .= "/2" if $flag & 0x80; #FREAD2 my $rc = $flag & 0x10; #FREVERSE if ($rc) { # Reverse and complement the sequence. $qseq =~ tr/ACGTacgt/TGCAtgca/; $qseq = reverse $qseq; $qqual = reverse $qqual; } my $riid = createRead($qid, $qseq, $qqual); next if $flag & 0x4; #FUNMAP my $qlength = length $qseq; die if length $qqual != $qlength; my ($qstart, $clipRight) = parseCigar($cigar); my $qend = $qlength - $clipRight; die unless $qstart < $qend; my $clr = $rc ? "$qend,$qstart" : "$qstart,$qend"; $tles{$tid} .= "{TLE\nclr:$clr\noff:$tstart\nsrc:$riid\n}\n"; } # Output the contig (CTG) and alignment (TLE) records. my $ctg_iid = 0; for my $ctg_eid (@ctg_eids) { my $seq = shift @ctg_seqs; next if length $tles{$ctg_eid} == 0; # Split long lines. my $qlt = 'I' x (length $seq); $seq =~ s/.{60}/$&\n/sg; $qlt =~ s/.{60}/$&\n/sg; # Contig sequence. $ctg_iid++; print "{CTG\niid:$ctg_iid\n", "eid:$ctg_eid\n", "seq:\n", $seq, "\n.\n", "qlt:\n", $qlt, "\n.\n"; print $tles{$ctg_eid}; print "}\n"; } =pod =head1 NAME abyss-samtoafg - create an AMOS AFG file from a SAM file =head1 SYNOPSIS B F F >F B B<-cb> F B<-m> F B F =head1 DESCRIPTION Create an AMOS AFG file from a FASTA file and a SAM file. =head1 OPTIONS =over =item B<-e>,B<--eid> the EID of the library =item B<-i>,B<--iid> the IID of the library =item B<-m>,B<--mean> the mean of the fragment-size =item B<-s>,B<--sd> the standard deviation of the fragment-size =back =head1 AUTHOR Written by Shaun Jackman. =head1 REPORTING BUGS Report bugs to . =head1 COPYRIGHT Copyright 2012 Canada's Michael Smith Genome Science Centre =head1 SEE ALSO http://www.bcgsc.ca/platform/bioinfo/software/abyss http://amos.sourceforge.net/hawkeye abyss-1.3.6/bin/abyss-adjtodot.pl000755 002433 001057 00000001717 11746352100 020423 0ustar00traymondassembly000000 000000 #!/usr/bin/perl # Convert an ABySS adjacency file to GraphViz dot format. # Written by Shaun Jackman . use strict; print "digraph adj {\n"; while (<>) { chomp; my ($id, $length, $coverage, $a, $b); if (/;.*;/) { ($id, $length, $coverage, $a, $b) = /^([^ ]+)\s+([^ ]+)\s+([^ ]+)\s;\s*(.*)\s;\s*(.*)$/; } elsif (/;/) { ($id, $length, $a, $b) = /^([^ ]+)\s+([^ ]+)\s*(.*)\s;\s*(.*)$/; } else { s/,0/+/g; s/,1/-/g; ($id, $length, $a, $b) = /(.*) (.*) \[(.*)\] \[(.*)\]/; } my @a = split ' ', $a; my @b = split ' ', $b; my $attr = "l=$length"; $attr .= " C=$coverage" if defined $coverage; print qq{"$id+" \[$attr];\n}; print qq{"$id+"}; if (@a > 0) { print ' -> {'; print qq{ "$_"} for @a; print ' }'; } print ";\n"; print qq{"$id-" \[$attr];\n}; print qq{"$id-"}; if (@b > 0) { print ' -> {'; for (@b) { my $x = $_; $x =~ y/+-/-+/; print qq{ "$x"}; } print ' }'; } print ";\n"; } print "}\n"; abyss-1.3.6/bin/abyss-cstont000755 002433 001057 00000003715 11746352100 017513 0ustar00traymondassembly000000 000000 #!/usr/bin/perl # Convert colour-space FASTA sequences to nucleotide FASTA sequences. # Written by Shaun Jackman . # Usage: cstofasta data.csfa >data.fa use strict; use Getopt::Long; use Pod::Usage; my %opt; GetOptions(\%opt, qw'help man'); pod2usage(-verbose => 1) if $opt{help}; pod2usage(-verbose => 2) if $opt{man}; my %table = ( 'A' => ['A', 'C', 'G', 'T'], 'C' => ['C', 'A', 'T', 'G'], 'G' => ['G', 'T', 'A', 'C'], 'T' => ['T', 'G', 'C', 'A'] ); sub cs_to_nt($$) { my $seed = shift; my $cs = shift; for (my $i = 0; $i < length $cs; $i++) { my $p = \substr($cs, $i, 1); $$p = $seed = $table{$seed}[$$p]; } return $cs; } my ($id, $comment); while (<>) { chomp; if (/^[ACGT]/) { my $seed = substr $_, 0, 1, ''; print "$id$comment\n", substr(cs_to_nt($seed, $_), 1), "\n"; } elsif (/^[0123]/) { for my $seed (qw'A C G T') { print "${id}_$seed$comment\n$seed", cs_to_nt($seed, $_), "\n"; } } elsif (/^>/) { ($id, $comment) = split ' ', $_, 2; $comment = ' ' . $comment if $comment; } elsif (/^#/) { print "$_\n"; } else { die "error: what is `$_'"; } } =pod =head1 NAME abyss-cstont - convert colour-space FASTA sequences to nucleotide FASTA sequences =head1 SYNOPSIS B F >F =head1 DESCRIPTION Either reads or contigs may be converted from colour-space sequences to nucleotide sequences. If the first character of the input sequence is not a nucleotide, each colour-space contig will be converted to four nucleotide contigs, one for each possible starting nucleotide. =head1 EXAMPLE $ printf '>1\nA0000' |abyss-cstont >1 AAA $ printf '>1\n0000' |abyss-cstont >1_A AAAAA >1_C CCCCC >1_G GGGGG >1_T TTTTT =head1 AUTHOR Written by Shaun Jackman. =head1 REPORTING BUGS Report bugs to . =head1 COPYRIGHT Copyright 2009 Canada's Michael Smith Genome Science Centre =head1 SEE ALSO L http://www.bcgsc.ca/platform/bioinfo/software/abyss abyss-1.3.6/bin/abyss-fac.pl000755 002433 001057 00000004750 12104026027 017337 0ustar00traymondassembly000000 000000 #!/usr/bin/perl # abyss-fac (FASTA count) # Calculate assembly contiguity statistics, such as N50. # Written by Shaun Jackman . use strict; use Getopt::Std qw'getopts'; $| = 1; my %opt; getopts 'g:hHjt:', \%opt; my $opt_threshold = defined $opt{'t'} ? $opt{'t'} : 200; my $opt_filename = $opt{'H'} || (@ARGV > 1 && !$opt{'h'}); my $opt_jira = $opt{'j'}; my $opt_genome_size = $opt{'g'}; sub eng($) { my $x = shift; return $x if $x < 10000000; return substr($x / 1000000, 0, 5) . 'e6' if $x < 1000000000; return substr($x / 1000000000, 0, 5) . 'e9'; } my ($short, $sum); my @x; sub count($$) { my $id = shift; my $seq = uc shift; my $x = $seq =~ tr/ACGT//; my $colourspace = $seq =~ tr/0123//; die unless $x == 0 || $colourspace == 0; $x = $colourspace if $x == 0; if ($x < $opt_threshold) { $short++; return; } $sum += $x; push @x, $x; } sub fac($) { my $path = shift; $short = $sum = 0; @x = (); my $id; my $seq; open IN, "<$path" or die "$path: $!\n"; while () { chomp; if (/^>/) { count $id, $seq if defined $id; $id = $_; $seq = ''; } else { $seq .= $_; } } count $id, $seq if defined $id; close IN; my $n = @x; if ($n > 0) { @x = sort { $a <=> $b } @x; my $min = $x[0]; my $max = $x[-1]; my $n50_target = defined $opt_genome_size ? $opt_genome_size : $sum; my ($n20, $n20sum, $nn50, $n50, $n50sum, $n80, $n80sum); while (@x > 0 && $n80sum < 0.8 * $n50_target) { my $x = pop @x; if ($n20sum < 0.2 * $n50_target) { $n20 = $x; $n20sum += $x; } if ($n50sum < 0.5 * $n50_target) { $nn50++; $n50 = $x; $n50sum += $x; } if ($n80sum < 0.8 * $n50_target) { $n80 = $x; $n80sum += $x; } } my $ntotal = $short + $n; format Spaces = @<<<<<<<@<<<<<<<@<<<<<<<@<<<<<<<@<<<<<<<@<<<<<<<@<<<<<<<@<<<<<<<@<<<<<<<@* eng($ntotal), eng($n), $nn50, $min, $n80, $n50, $n20, $max, eng($sum), $path . format Pipes = |@<<<<<<|@<<<<<<|@<<<<<<|@<<<<<<|@<<<<<<|@<<<<<<|@<<<<<<|@<<<<<<|@<<<<<<|@*| eng($ntotal), eng($n), $nn50, $min, $n80, $n50, $n20, $max, eng($sum), $path . $~ = $opt_jira ? 'Pipes' : 'Spaces'; $^ = $opt_jira ? 'Pipes_TOP' : 'Spaces_TOP'; write; } else { print STDERR "warning: `$path' is empty\n"; } } format Spaces_TOP = n n:@<<<< n:N50 min N80 N50 N20 max sum $opt_threshold . format Pipes_TOP = ||n ||n:@<<<||n:N50 ||min ||N80 ||N50 ||N20 ||max ||sum || $opt_threshold . @ARGV = ('-') if @ARGV == 0; fac $_ foreach @ARGV; abyss-1.3.6/bin/abyss-joindist000755 002433 001057 00000002674 12104026027 020022 0ustar00traymondassembly000000 000000 #!/usr/bin/perl # Join multiple ABySS distance estimate files. # Written by Shaun Jackman . use strict; use Getopt::Long; use Pod::Usage; my %opt; GetOptions(\%opt, qw'help man'); pod2usage(-verbose => 1) if $opt{help}; pod2usage(-verbose => 2) if $opt{man}; my (%id, %a, %b); while (<>) { chomp; my ($id, $rest) = split ' ', $_, 2; my ($a, $b) = split ';', $rest, 2; my @a = split ' ', $a; my @b = split ' ', $b; $id{$id} = 1; for (@a) { my ($to, $d, $n, $sd) = split ','; if (!exists $a{$id}{$to} || $sd < $a{$id}{$to}) { $a{$id}{$to} = "$sd $d $n"; } } for (@b) { my ($to, $d, $n, $sd) = split ','; if (!exists $b{$id}{$to} || $sd < $b{$id}{$to}) { $b{$id}{$to} = "$sd $d $n"; } } } for my $id (sort {$a<=>$b} keys %id) { print $id; for my $to (sort {$a<=>$b} keys %{$a{$id}}) { my ($sd, $d, $n) = split ' ', $a{$id}{$to}; print " $to,$d,$n,$sd"; } print ' ;'; for my $to (sort {$a<=>$b} keys %{$b{$id}}) { my ($sd, $d, $n) = split ' ', $b{$id}{$to}; print " $to,$d,$n,$sd"; } print "\n"; } =pod =head1 NAME abyss-joindist - Join multiple ABySS distance estimate files. =head1 SYNOPSIS B F... >F =head1 AUTHOR Written by Shaun Jackman. =head1 REPORTING BUGS Report bugs to . =head1 COPYRIGHT Copyright 2009 Canada's Michael Smith Genome Science Centre =head1 SEE ALSO L http://www.bcgsc.ca/platform/bioinfo/software/abyss