From: Charles Plessy Date: Mon, 11 Jul 2011 11:18:59 +0000 (+0900) Subject: Merge commit 'upstream/0.1.17' X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=samtools.git;a=commitdiff_plain;h=e2bd290b8643f0a728c282a8b825392307750210;hp=b301e959d73eee0955c57004f344f17af00703f4 Merge commit 'upstream/0.1.17' --- diff --git a/debian/README.Debian b/debian/README.Debian new file mode 100644 index 0000000..6a6b574 --- /dev/null +++ b/debian/README.Debian @@ -0,0 +1,29 @@ +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 diff --git a/debian/changelog b/debian/changelog new file mode 100644 index 0000000..a2d32ce --- /dev/null +++ b/debian/changelog @@ -0,0 +1,109 @@ +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 diff --git a/debian/compat b/debian/compat new file mode 100644 index 0000000..45a4fb7 --- /dev/null +++ b/debian/compat @@ -0,0 +1 @@ +8 diff --git a/debian/control b/debian/control new file mode 100644 index 0000000..26ba80e --- /dev/null +++ b/debian/control @@ -0,0 +1,33 @@ +Source: samtools +Section: science +Priority: optional +Maintainer: Debian Med Packaging Team +DM-Upload-Allowed: yes +Uploaders: Charles Plessy +Build-Depends: debhelper (>= 8), cdbs, libncurses5-dev, zlib1g-dev +Standards-Version: 3.9.2 +Homepage: http://samtools.sourceforge.net +Vcs-Browser: http://git.debian.org/?p=debian-med/samtools.git +Vcs-Git: git://git.debian.org/debian-med/samtools.git + +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. diff --git a/debian/copyright b/debian/copyright new file mode 100644 index 0000000..4fc8462 --- /dev/null +++ b/debian/copyright @@ -0,0 +1,126 @@ +Format: http://dep.debian.net/deps/dep5/ +Source: http://qa.debian.org/watch/sf.php/samtools/samtools-0.1.16.tar.bz2 + +Files: * +Copyright: © 2008–2010, Genome Research Ltd. (GRL) +License: MIT + +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. + +Files: kprobaln.h, kprobaln.c +Copyright: © 2003-2006, 2008-2010, by Heng Li +License: MIT + +Files: bcftools/bcf.h +Copyright: © 2010 Broad Institute +License: MIT + +Files: misc/export2sam.pl, bam_cat.c +Copyright: © 2008–2009, Genome Research Ltd. +Copyright: © 2010 Illumina, Inc. +License: MIT + +Files: bgzf.*, bgzip.c +Copyright: © 2008 Broad Institute / Massachusetts Institute of Technology +License: MIT + +Files: khash.h +Copyright: © 2008, 2009, 2011 by Attractive Chaos +License: MIT + +Files: bcftools/kmin.? +Copyright: © 2008, 2010 by Attractive Chaos +License: MIT + +Files: knetfile.c +Copyright: © 2008 by Genome Research Ltd (GRL). + 2010 by Attractive Chaos +License: MIT + +Files: razf.* +Name: RAZF : Random Access compressed(Z) File +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. + +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 +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 +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 diff --git a/debian/gbp.conf b/debian/gbp.conf new file mode 100644 index 0000000..728355b --- /dev/null +++ b/debian/gbp.conf @@ -0,0 +1,5 @@ +# Configuration file for git-buildpackage and friends + +[DEFAULT] +# use pristine-tar: +pristine-tar = True diff --git a/debian/libbam-dev.install b/debian/libbam-dev.install new file mode 100644 index 0000000..4ffff63 --- /dev/null +++ b/debian/libbam-dev.install @@ -0,0 +1,6 @@ +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 diff --git a/debian/razip.1 b/debian/razip.1 new file mode 100644 index 0000000..aa06283 --- /dev/null +++ b/debian/razip.1 @@ -0,0 +1,28 @@ +.\" 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 diff --git a/debian/reference b/debian/reference new file mode 100644 index 0000000..a6bf486 --- /dev/null +++ b/debian/reference @@ -0,0 +1,12 @@ +@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} +} diff --git a/debian/rules b/debian/rules new file mode 100755 index 0000000..3605b20 --- /dev/null +++ b/debian/rules @@ -0,0 +1,20 @@ +#!/usr/bin/make -f + +include /usr/share/cdbs/1/rules/debhelper.mk +include /usr/share/cdbs/1/class/makefile.mk + +CFLAGS += -fPIC + +DEB_MAKE_BUILD_TARGET = all all-recur razip lib +DEB_MAKE_CHECK_TARGET = -C examples all + +DEB_DH_BUILDDEB_ARGS = -- -Z=bzip2 + +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 + +binary-fixup/samtools:: + sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' $(CURDIR)/debian/samtools/usr/share/samtools/varfilter.py diff --git a/debian/samtools.docs b/debian/samtools.docs new file mode 100644 index 0000000..14d5ce6 --- /dev/null +++ b/debian/samtools.docs @@ -0,0 +1,3 @@ +AUTHORS +debian/reference +NEWS diff --git a/debian/samtools.examples b/debian/samtools.examples new file mode 100644 index 0000000..5a25472 --- /dev/null +++ b/debian/samtools.examples @@ -0,0 +1,6 @@ +examples/ex1.bam +examples/ex1.fa +examples/ex1.sam.gz +examples/00README.txt +examples/toy.fa +examples/toy.sam diff --git a/debian/samtools.install b/debian/samtools.install new file mode 100644 index 0000000..7976c52 --- /dev/null +++ b/debian/samtools.install @@ -0,0 +1,12 @@ +#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/wgsim 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 diff --git a/debian/samtools.manpages b/debian/samtools.manpages new file mode 100644 index 0000000..e28faa0 --- /dev/null +++ b/debian/samtools.manpages @@ -0,0 +1,3 @@ +samtools.1 +debian/razip.1 +bcftools/bcftools.1 diff --git a/debian/source/format b/debian/source/format new file mode 100644 index 0000000..163aaf8 --- /dev/null +++ b/debian/source/format @@ -0,0 +1 @@ +3.0 (quilt) diff --git a/debian/upstream-metadata.yaml b/debian/upstream-metadata.yaml new file mode 100644 index 0000000..572f854 --- /dev/null +++ b/debian/upstream-metadata.yaml @@ -0,0 +1,19 @@ +Archive: SourceForge +DOI: 10.1093/bioinformatics/btp352 +Homepage: http://samtools.sourceforge.net +mr: + checkout: debcheckout -a git://git.debian.org/debian-med/samtools.git +Name: SAM tools +PMID: 19505943 +Reference: + 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: 25 + number: 16 + pages: 2078-2079 + 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 +Repository: https://samtools.svn.sourceforge.net/svnroot/samtools diff --git a/debian/watch b/debian/watch new file mode 100644 index 0000000..e95bcd4 --- /dev/null +++ b/debian/watch @@ -0,0 +1,4 @@ +version=3 +opts=downloadurlmangle=s|/download||,filenamemangle=s|http://sourceforge.net/projects/samtools/files/samtools/.+?/||;s|.download|| \ + http://sourceforge.net/projects/samtools/files/samtools/ \ + http://sourceforge.net/projects/samtools/files/samtools/.+?/samtools-(.*).tar.bz2/download