debian/0000755000000000000000000000000012125521466007172 5ustar debian/libbam-dev.install0000644000000000000000000000024211702454022012553 0ustar libbam.a usr/lib bam.h usr/include/samtools bgzf.h usr/include/samtools khash.h usr/include/samtools faidx.h usr/include/samtools sam.h usr/include/samtools debian/samtools.bash-completion0000644000000000000000000000110012004336030014014 0ustar # From https://raw.github.com/arq5x/bash_completion/master/samtools revision e931a8b46d9582672cc506e45ad9b4f4d6fbd743 _samtools() { local cur prev opts COMPREPLY=() cur="${COMP_WORDS[COMP_CWORD]}" prev="${COMP_WORDS[COMP_CWORD-1]}" opts="view sort mpileup depth faidx tview index idxstats fixmate flagstat calmd merge rmdup reheader cat targetcut phase pad2unpad" case $prev in samtools) COMPREPLY=( $(compgen -W "${opts}" -- ${cur}) ) ;; esac return 0 } complete -F _samtools -o default samtools debian/reference0000644000000000000000000000112011702454022011036 0ustar @article{HengLi06082009, author = {Li, Heng and Handsaker, Bob and Wysoker, Alec and Fennell, Tim and Ruan, Jue and Homer, Nils and Marth, Gabor and Abecasis, Goncalo and Durbin, Richard and 1000 Genome Project Data Processing Subgroup, }, title = {{The Sequence Alignment/Map (SAM) Format and SAMtools}}, journal = {Bioinformatics}, volume = {}, number = {}, pages = {btp352}, doi = {10.1093/bioinformatics/btp352}, year = {2009}, URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btp352v1}, eprint = {http://bioinformatics.oxfordjournals.org/cgi/reprint/btp352v1.pdf} } debian/compat0000644000000000000000000000000212004336030010353 0ustar 9 debian/README.Debian0000644000000000000000000000200711702454022011223 0ustar SAMtools for Debian. ━━━━━━━━━━━━━━━━━━━━ Extra utilities. ──────────────── The extra utilities found in the ‘misc’ directory of the upstream archive are placed in ‘/usr/share/samtools’ for the Perl and Python scripts, and ‘/usr/lib/samtools’ for the binary executables. The BAM library. ──────────────── Currently, the BAM library only exists in static version. It (actually the whole package) is built with the -fPIC option, to allow the compilation of the Bio::SamTools Perl module on the amd64 platform (Debian package libbio-samtools-perl). Note about how this package is tested. ────────────────────────────────────── At build time, the regression tests of the package are ran. You can consult the results on ‘http://buildd.debian.org/samtools’. -- Charles Plessy Thu, 15 Jul 2010 08:37:41 +0900 debian/gbp.conf0000644000000000000000000000027512125502114010602 0ustar # Configuration file for git-buildpackage and friends [DEFAULT] # use pristine-tar: pristine-tar = True [git-dch] # include 7 digits of the commit id in the changelog enty: id-length = 7 debian/samtools.manpages0000644000000000000000000000003211702454022012534 0ustar samtools.1 debian/razip.1 debian/patches/0000755000000000000000000000000012125513564010621 5ustar debian/patches/fix_segfault_with_small_ref.patch0000644000000000000000000000360612125510732017400 0ustar Description: Fix segfault if position is outside of the reference sequence length Origin: Don Armstrong Index: samtools/bam_plcmd.c =================================================================== --- samtools.orig/bam_plcmd.c +++ samtools/bam_plcmd.c @@ -96,6 +96,7 @@ bam_iter_t iter; bam_header_t *h; int ref_id; + int ref_len; char *ref; const mplp_conf_t *conf; } mplp_aux_t; @@ -139,6 +140,11 @@ qual[i] = qual[i] > 31? qual[i] - 31 : 0; } has_ref = (ma->ref && ma->ref_id == b->core.tid)? 1 : 0; + if (has_ref && (ma->ref_len <= b->core.pos)) { // exclude reads outside of the reference sequence + fprintf(stderr,"[%s] Skipping because %d is outside of %d [ref:%d]\n",__func__,b->core.pos,ma->ref_len,ma->ref_id); + skip = 1; + continue; + } skip = 0; if (has_ref && (ma->conf->flag&MPLP_REALN)) bam_prob_realn_core(b, ma->ref, (ma->conf->flag & MPLP_REDO_BAQ)? 7 : 3); if (has_ref && ma->conf->capQ_thres > 10) { @@ -307,7 +313,11 @@ if (tid0 >= 0 && conf->fai) { // region is set ref = faidx_fetch_seq(conf->fai, h->target_name[tid0], 0, 0x7fffffff, &ref_len); ref_tid = tid0; - for (i = 0; i < n; ++i) data[i]->ref = ref, data[i]->ref_id = tid0; + for (i = 0; i < n; ++i) { + data[i]->ref = ref; + data[i]->ref_id = tid0; + data[i]->ref_len = ref_len; + } } else ref_tid = -1, ref = 0; iter = bam_mplp_init(n, mplp_func, (void**)data); max_depth = conf->max_depth; @@ -325,7 +335,11 @@ if (tid != ref_tid) { free(ref); ref = 0; if (conf->fai) ref = faidx_fetch_seq(conf->fai, h->target_name[tid], 0, 0x7fffffff, &ref_len); - for (i = 0; i < n; ++i) data[i]->ref = ref, data[i]->ref_id = tid; + for (i = 0; i < n; ++i) { + data[i]->ref = ref; + data[i]->ref_id = tid; + data[i]->ref_len = ref_len; + } ref_tid = tid; } if (conf->flag & MPLP_GLF) { debian/patches/series0000644000000000000000000000012412125513404012024 0ustar fix_example_makefile.patch fix_segfault_with_small_ref.patch fix_coverage_cap.patch debian/patches/fix_example_makefile.patch0000644000000000000000000000300512125513470015772 0ustar Description: disable samtools pileup commands in the example tests. ‘samtools pileup’ has been dropped in version 0.1.17. Forwarded: samtools-devel@lists.sourceforge.net Origin: vendor Index: samtools/examples/Makefile =================================================================== --- samtools.orig/examples/Makefile +++ samtools/examples/Makefile @@ -1,5 +1,5 @@ all:../libbam.a ../samtools ../bcftools/bcftools \ - ex1.glf ex1.pileup.gz ex1.bam.bai ex1f-rmduppe.bam ex1f-rmdupse.bam ex1.glfview.gz ex1.bcf calDepth + ex1.bam.bai ex1f-rmduppe.bam ex1f-rmdupse.bam ex1.bcf calDepth @echo; echo \# You can now launch the viewer with: \'samtools tview ex1.bam ex1.fa\'; echo; ex1.fa.fai:ex1.fa @@ -8,12 +8,6 @@ ../samtools import ex1.fa.fai ex1.sam.gz ex1.bam ex1.bam.bai:ex1.bam ../samtools index ex1.bam -ex1.pileup.gz:ex1.bam ex1.fa - ../samtools pileup -cf ex1.fa ex1.bam | gzip > ex1.pileup.gz -ex1.glf:ex1.bam ex1.fa - ../samtools pileup -gf ex1.fa ex1.bam > ex1.glf -ex1.glfview.gz:ex1.glf - ../samtools glfview ex1.glf | gzip > ex1.glfview.gz ex1a.bam:ex1.bam ../samtools view -h ex1.bam | awk 'BEGIN{FS=OFS="\t"}{if(/^@/)print;else{$$1=$$1"a";print}}' | ../samtools view -bS - > $@ ex1b.bam:ex1.bam @@ -40,7 +34,7 @@ (cd ..; make libbam.a) calDepth:../libbam.a calDepth.c - gcc -g -Wall -O2 -I.. calDepth.c -o $@ -L.. -lbam -lm -lz + gcc -g -Wall -O2 -I.. calDepth.c -o $@ -L.. -lbam -lm -lz -lpthread clean: rm -fr *.bam *.bai *.glf* *.fai *.pileup* *~ calDepth *.dSYM ex1*.rg ex1.bcf debian/patches/fix_coverage_cap.patch0000644000000000000000000000126412125510764015130 0ustar Description: increases the coverage cap from 8.000 to 1.000.000 Index: samtools/bam2depth.c =================================================================== --- samtools.orig/bam2depth.c +++ samtools/bam2depth.c @@ -106,6 +106,7 @@ // the core multi-pileup loop mplp = bam_mplp_init(n, read_bam, (void**)data); // initialization + bam_mplp_set_maxcnt(mplp,1000000); // set maxdepth to 1M n_plp = calloc(n, sizeof(int)); // n_plp[i] is the number of covering reads from the i-th BAM plp = calloc(n, sizeof(void*)); // plp[i] points to the array of covering reads (internal in mplp) while (bam_mplp_auto(mplp, &tid, &pos, n_plp, plp) > 0) { // come to the next covered position debian/razip.10000644000000000000000000000135111702454022010372 0ustar .\" Generated by help2man 1.36 and edited later with vi. .\" This manual page was forwarded upstream on November 17th, 2009. .TH RAZIP "1" "November 2009" "razip " "Bioinformatics tools" .SH NAME razip \- Compress and decompress files in RAZip format .SH SYNOPSIS .B razip [\fIoptions\fR] [\fIfile\fR] ... .SH DESCRIPTION razip is a program to compress and decopmress files in RAZip format. The corresponding file suffix is `.rz'. .SH OPTIONS \fB\-c\fR write on standard output, keep original files unchanged .TP \fB\-d\fR decompress .TP \fB\-l\fR list compressed file contents .TP \fB\-b\fR INT decompress at INT position in the uncompressed file .TP \fB\-s\fR INT decompress INT bytes in the uncompressed file .TP \fB\-h\fR give this help debian/samtools.examples0000644000000000000000000000015411702454022012564 0ustar examples/ex1.bam examples/ex1.fa examples/ex1.sam.gz examples/00README.txt examples/toy.fa examples/toy.sam debian/copyright0000644000000000000000000001162412125507077011133 0ustar Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Source: https://github.com/samtools/samtools/archive/0.1.19.tar.gz Files: * Copyright: © 2008–2010, Genome Research Ltd. (GRL) © 2003–2006, 2008–2011, by Heng Li © 2010 Broad Institute © 2008 Broad Institute / Massachusetts Institute of Technology © 2008, 2009, 2011, 2012 Attractive Chaos License: MIT Files: misc/export2sam.pl bam_cat.c Copyright: © 2010 Illumina, Inc. License: MIT Files: razf.* Copyright: 2008, Jue Ruan , Heng Li License: NetBSD-similar 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. . THIS SOFTWARE IS PROVIDED BY THE AUTHOR AND CONTRIBUTORS ``AS IS'' AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE AUTHOR OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. Name: RAZF : Random Access compressed(Z) File Files: misc/md5.* Copyright: no copyright is claimed License: MD5-fourmilab This code implements the MD5 message-digest algorithm. The algorithm is due to Ron Rivest. This code was written by Colin Plumb in 1993, no copyright is claimed. This code is in the public domain; do with it what you wish. . Equivalent code is available from RSA Data Security, Inc. This code has been tested against that, and is equivalent, except that you don't need to include two pages of legalese with every copy. . To compute the message digest of a chunk of bytes, declare an MD5Context structure, pass it to MD5Init, call MD5Update as needed on buffers full of bytes, and then call MD5Final, which will fill a supplied 16-byte array with the digest. Files: win32/xcurses.h win32/libcurses.a Copyright: Public Domain License: public-domain This file is part of PDCurses (http://pdcurses.sourceforge.net/), which is in the public domain. Files: win32/z*.h win32/libz.a Copyright: © 1995-2005 Jean-loup Gailly and Mark Adler License: zlib This software is provided 'as-is', without any express or implied warranty. In no event will the authors be held liable for any damages arising from the use of this software. . Permission is granted to anyone to use this software for any purpose, including commercial applications, and to alter it and redistribute it freely, subject to the following restrictions: . 1. The origin of this software must not be misrepresented; you must not claim that you wrote the original software. If you use this software in a product, an acknowledgment in the product documentation would be appreciated but is not required. 2. Altered source versions must be plainly marked as such, and must not be misrepresented as being the original software. 3. This notice may not be removed or altered from any source distribution. . Jean-loup Gailly Mark Adler jloup@gzip.org madler@alumni.caltech.edu License: MIT 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. debian/changelog0000644000000000000000000001555212125521456011053 0ustar samtools (0.1.19-1) unstable; urgency=low cb9bd50 Imported https://github.com/samtools/samtools/archive/0.1.19.tar.gz 1e6d442 new tools ace2sam, bamcheck, plot-bamcheck, r2plot.lua, vcfutils.lua. 2f2d5c5 debian/copyright: collapsed copyright notices from main holders. e194f9e Removed fix_float_tag.patch, corrected upstream. 9c0e543 Refreshed patches. 3e7e0ec Renamed no-pileup-tests.patch fix_example_makefile.patch. 8d8550e example/Makefile: pass -lpthread when compiling calDepth. fc32243 harden by concatenating Debian's LDFLAGS and CPPFLAGS in CFLAGS. 6f75b48 debian/control: normalised with cme. e13bb5e debian/control: normalised VCS URLs. a1b1b00 debian/control: deleted DM-Upload-Allowed field. ddcd54e Use NEWS as upstream changelog. 81ad760 Conforms to Policy version 3.9.4. -- Charles Plessy Sat, 30 Mar 2013 17:31:47 +0900 samtools (0.1.18-4) unstable; urgency=low [Charles Plessy] * debian/copyright: Normalised with config-model * added bash completion * Build-depend on Debhelper 9 * Pass build flaggs set by dpkg-buildflags via Debhelper * Moved DOI and PubMed to the Reference namespace * Do not compress the example binary alignment file * Mention ‘SAMtools’ in libbam-dev's description [Andreas Tille] * debian/upstream: replaced BibTeX entry [Dominique Belhachemi] * added patch to fix float tag bug (upstream bug 71) -- Dominique Belhachemi Fri, 21 Dec 2012 12:09:18 -0500 samtools (0.1.18-3) unstable; urgency=low * upload 0.1.18-2 closed the wrong bug, correction: * added patch to fix segfault in mpileup (Closes: #653042) * added patch to fix coverage cap (Closes: #671524) -- Dominique Belhachemi Fri, 27 Jul 2012 11:11:41 -0400 samtools (0.1.18-2) unstable; urgency=low * added patch to fix segfault in mpileup (Closes: #544976) * added patch to fix coverage cap (Closes: #671524) -- Dominique Belhachemi Thu, 26 Jul 2012 18:30:48 -0400 samtools (0.1.18-1) unstable; urgency=low [b990d9d3] New upstream release. [d59366b9] Updated copyright statements. [aa08abe5] Compress binary packages with xz. [9a36c994] Added a DEP 3 header to debian/patches/no-pileup-tests.patch. -- Charles Plessy Tue, 06 Sep 2011 16:52:04 +0900 samtools (0.1.17-1) unstable; urgency=low * New upstream release 0.1.17 (6 July, 2011). * bcftools.1 and samtools.1 merged (debian/rules, debian/samtools.manpages). * Patched the example makefile to not use samtools pileup, deprecated. (debian/control, debian/rules, debian/patches/series, debian/patches/no-pileup-tests.patch) -- Charles Plessy Mon, 11 Jul 2011 21:04:30 +0900 samtools (0.1.16-1) unstable; urgency=low * New upstream release, implementing SAM Spec v1.4. * Distribute sam.h and the other headers in /usr/include/samtools. Closes: #625622, #626044, LP: #690997. -- Charles Plessy Thu, 19 May 2011 13:24:25 +0900 samtools (0.1.15-1) unstable; urgency=low * New upstream release. * Incremented Standards-Version to reflect conformance with Policy 3.9.2 (debian/control, no changes needed). * debian/watch directly interrogates and downloads froms SourceForge. -- Charles Plessy Tue, 12 Apr 2011 19:44:41 +0900 samtools (0.1.14-1) unstable; urgency=low * New upstream release. -- Charles Plessy Tue, 29 Mar 2011 13:13:54 +0900 samtools (0.1.13-1) unstable; urgency=low * New upstream release: - backward incompatible with VCF/BCF generated by samtools older than r921 inclusive (0.1.12a is r862); - buildable with with ld --as-needed (Closes: #606004); - the helper tool bcf-fix.pl was removed. * Install the manual page of bcftools (debian/rules, debian/samtools.manpages). Closes: #616025. -- Charles Plessy Wed, 02 Mar 2011 13:54:34 +0900 samtools (0.1.12a-1) unstable; urgency=low * New upstream release. * Use bzip2 compression for the binary packages (debian/rules). * Incremented debhelper compatibility level to 8, in case ‘--‘ is not available in earlier versions (debian/compat, debian/control). -- Charles Plessy Fri, 03 Dec 2010 13:32:21 +0900 samtools (0.1.10-1) unstable; urgency=low * New upstream release. -- Charles Plessy Wed, 17 Nov 2010 20:32:40 +0900 samtools (0.1.9-1) unstable; urgency=low * New upstream release, and new program: bcftools. * debian/rules, debian/samtools.install: install bcftools, its manpage, and bcf-fix.pl and vcfutils.pl. * debian/samtools.examples, debian/rules: install and clean new examples. * Incremented Standards-Version to reflect conformance with Policy 3.9.1 (debian/control, no changes needed). * Updated and reformatted debian/copyright according to latest DEP-5 draft. -- Charles Plessy Mon, 01 Nov 2010 20:06:32 +0900 samtools (0.1.8-1) unstable; urgency=low * New upstream release. * Updated the VCS fields to the current Git repository (debian/control). * Install python scripts in usr/share/samtools, and suggest python (debian/samtools.install, debian/rules, debian/control). * Incremented Standards-Version to reflect conformance with Policy 3.9.0 (debian/control, no changes needed). * Added notes on how the package is tested (debian/README.Debian). -- Charles Plessy Wed, 14 Jul 2010 14:08:59 +0900 samtools (0.1.7a~dfsg-1) unstable; urgency=low * New upstream release: new script sam2vcf.pl, and many other changes. * Package converted to the format ‘3.0 (quilt)’ (debian/source/format). * Wrote a manual page for razip (debian/razip.1). * Better clean the example directory to make the source package buildable twice in a row (debian/rules). -- Charles Plessy Tue, 17 Nov 2009 21:38:24 +0900 samtools (0.1.6~dfsg-1) unstable; urgency=low * New upstream release. * Upstream sources repackaged to remove the win32 directory: - The removal was done with git-import-orig in a parallel Git repository, and the corresponding debian/gbp.conf file was added to this package. - Mangled the ~dfsg string of the Debian version in debian/watch. - Added a debian/README.source file and explanations in debian/copyright. -- Charles Plessy Mon, 14 Sep 2009 21:58:36 +0900 samtools (0.1.5c-2) unstable; urgency=low * Rebuilt with -fPIC (debian/rules, README.Debian). * Small corrections to the description from upstream (debian/changelog). * Incremented Standards-Version to reflect conformance with Policy 3.8.3 (no changes needed). -- Charles Plessy Thu, 03 Sep 2009 19:29:40 +0900 samtools (0.1.5c-1) unstable; urgency=low * Initial release (Closes: #540453) -- Charles Plessy Sun, 16 Aug 2009 14:38:20 +0900 debian/samtools.docs0000644000000000000000000000003112125521106011666 0ustar AUTHORS debian/reference debian/samtools.install0000644000000000000000000000071512125516606012426 0ustar #bgzip usr/bin bcftools/bcftools usr/bin razip usr/bin samtools usr/bin bcftools/vcfutils.pl usr/share/samtools misc/*.pl usr/share/samtools misc/*.py usr/share/samtools misc/*.lua usr/share/samtools misc/plot-bamcheck usr/share/samtools misc/wgsim usr/lib/samtools misc/ace2sam usr/lib/samtools misc/bamcheck usr/lib/samtools misc/maq2sam-long usr/lib/samtools misc/maq2sam-short usr/lib/samtools misc/md5fa usr/lib/samtools misc/md5sum-lite usr/lib/samtools debian/source/0000755000000000000000000000000011702454022010463 5ustar debian/source/format0000644000000000000000000000001411702454022011671 0ustar 3.0 (quilt) debian/rules0000755000000000000000000000202012125521070010233 0ustar #!/usr/bin/make -f include /usr/share/cdbs/1/rules/debhelper.mk include /usr/share/cdbs/1/class/makefile.mk include /usr/share/cdbs/1/rules/patchsys-quilt.mk CFLAGS += -fPIC $(LDFLAGS) $(CPPFLAGS) DEB_MAKE_BUILD_TARGET = all all-recur razip lib DEB_MAKE_CHECK_TARGET = -C examples all DEB_COMPRESS_EXCLUDE = .bam DEB_DH_BUILDDEB_ARGS = -- -Z=xz DEB_INSTALL_CHANGELOGS_ALL = NEWS clean:: $(RM) examples/calDepth examples/ex1.bam examples/ex1.bam.bai examples/ex1.fa.fai examples/ex1.glf examples/ex1.glfview.gz examples/ex1.pileup.gz examples/ex1a.bam examples/ex1b.bam examples/ex1f-rmduppe.bam examples/ex1f-rmdupse.bam examples/ex1f.bam examples/ex1f.rg examples/ex1.bcf binary-install/samtools:: install -m 644 bcftools/README $(CURDIR)/debian/samtools/usr/share/doc/samtools/README.bcftools ln -s samtools.1.gz $(CURDIR)/debian/samtools/usr/share/man/man1/bcftools.1.gz dh_bash-completion binary-fixup/samtools:: sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' $(CURDIR)/debian/samtools/usr/share/samtools/varfilter.py debian/watch0000644000000000000000000000011612125515221010211 0ustar version=3 https://github.com/samtools/samtools/tags .*/v?(\d[\d\.]+)\.tar\.gz debian/control0000644000000000000000000000327612125520646010604 0ustar Source: samtools Maintainer: Debian Med Packaging Team Uploaders: Charles Plessy , Dominique Belhachemi Section: science Priority: optional Build-Depends: debhelper (>= 9), bash-completion, cdbs, quilt, libncurses5-dev, zlib1g-dev Standards-Version: 3.9.4 Vcs-Browser: http://anonscm.debian.org/gitweb/?p=debian-med/samtools.git Vcs-Git: git://anonscm.debian.org/debian-med/samtools.git Homepage: http://samtools.sourceforge.net Package: samtools Architecture: any Depends: ${shlibs:Depends}, ${misc:Depends} Suggests: python Description: processing sequence alignments in SAM and BAM formats Samtools is a set of utilities that manipulate nucleotide sequence alignments in the binary BAM format. It imports from and exports to the ascii SAM (Sequence Alignment/Map) format, does sorting, merging and indexing, and allows to retrieve reads in any regions swiftly. It is designed to work on a stream, and is able to open a BAM (not SAM) file on a remote FTP or HTTP server. Package: libbam-dev Architecture: any Section: libdevel Depends: ${shlibs:Depends}, ${misc:Depends} Description: manipulates nucleotide sequence alignments in BAM or SAM format The BAM library provides I/O and various operations on manipulating nucleotide sequence alignments in the BAM (Binary Alignment/Mapping) or SAM (Sequence Alignment/Map) format. It now supports importing from or exporting to SAM, sorting, merging, generating pileup, and quickly retrieval of reads overlapped with a specified region. . This library is part of SAMtools. debian/upstream0000644000000000000000000000146712125517676010775 0ustar Archive: SourceForge Changelog: https://raw.github.com/samtools/samtools/HEAD/NEWS Homepage: http://samtools.sourceforge.net mr: checkout: debcheckout -a git://git.debian.org/debian-med/samtools.git Name: SAM tools Reference: author: Heng Li and Bob Handsaker and Alec Wysoker and Tim Fennell and Jue Ruan and Nils Homer and Gabor Marth and Goncalo Abecasis and Richard Durbin and 1000 Genome Project Data Processing Subgroup title: The Sequence Alignment/Map (SAM) Format and SAMtools journal: Bioinformatics volume: 25 number: 16 pages: 2078-2079 doi: 10.1093/bioinformatics/btp352 PMID: 19505943 year: 2009 URL: http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btp352v1 eprint: http://bioinformatics.oxfordjournals.org/cgi/reprint/btp352v1.pdf Repository: https://github.com/samtools/samtools