--- /dev/null
+SAMtools for Debian
+-------------------
+
+The extra utilities found in the ‘misc’ directory of the upstream archive are
+placed in ‘/usr/share/samtools’ and ‘/usr/lib/samtools’ for Perl scripts and
+binary executables respectively.
+
+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).
+
+ -- Charles Plessy <plessy@debian.org> Thu, 03 Sep 2009 19:24:02 +0900
--- /dev/null
+The original sources of Samtools were modified by removing the win32 directory.
+This was done using the git-import-orig program from the git-buildpackage
+utilities. This source package is currently migrated from svn-buildpackage to
+git-buildpackage, and a get-orig-source target for debian/rules will be added
+later.
--- /dev/null
+samtools (0.1.7~dfsg-1) UNRELEASED; urgency=low
+
+ * New upstream release: new script sam2vcf.pl, and many other changes.
+ * Package converted to the format ‘3.0 (quilt)’ (debian/source/format).
+
+ -- Charles Plessy <plessy@debian.org> Mon, 16 Nov 2009 14:25:41 +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 <plessy@debian.org> 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 <plessy@debian.org> Thu, 03 Sep 2009 19:29:40 +0900
+
+samtools (0.1.5c-1) unstable; urgency=low
+
+ * Initial release (Closes: #540453)
+
+ -- Charles Plessy <plessy@debian.org> Sun, 16 Aug 2009 14:38:20 +0900
--- /dev/null
+Source: samtools
+Section: science
+Priority: optional
+Maintainer: Debian-Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+DM-Upload-Allowed: yes
+Uploaders: Charles Plessy <plessy@debian.org>
+Build-Depends: debhelper (>= 7), cdbs, libncurses5-dev, zlib1g-dev
+Standards-Version: 3.8.3
+Homepage: http://samtools.sourceforge.net
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/samtools/trunk/?rev=0&sc=0
+Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/samtools/trunk/
+
+Package: samtools
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}
+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.
--- /dev/null
+Machine-readable license summary, see ‘http://dep.debian.net/deps/dep5/’.
+
+
+Name : SAMtools
+Contact : SAMtools mailing list <samtools-help@lists.sourceforge.net>
+Source : http://qa.debian.org/watch/sf.php/samtools/samtools-0.1.7.tar.bz2
+
+
+Copyright : © 2008–2009, Genome Research Ltd.
+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 : bgzf.*, bgzip.c
+Copyright : © 2008 Broad Institute / Massachusetts Institute of Technology
+License : MIT
+
+
+Files : razf.*
+Name : RAZF : Random Access compressed(Z) File
+Copyright : 2008, Jue Ruan <ruanjue@gmail.com>, Heng Li <lh3@sanger.ac.uk>
+License : Similar to NetBSD license.
+
+ 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.*
+License :
+
+ 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/*
+Removed : Missing source.
+
+ The win32 directory is present in the original upstream sources, but
+ was removed from the Debian source package, as it contains binary files for the
+ win32 platform without their corresponding source files.
--- /dev/null
+[DEFAULT]
+pristine-tar = True
+filter-pristine-tar = True
+filter = [
+ "win32"
+ ]
--- /dev/null
+libbam.a usr/lib
+bam.h usr/include
+bgzf.h usr/include
+khash.h usr/include
+faidx.h usr/include
--- /dev/null
+@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}
+}
--- /dev/null
+#!/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
--- /dev/null
+AUTHORS
+debian/reference
+NEWS
--- /dev/null
+examples/ex1.bam
+examples/ex1.fa
+examples/ex1.sam.gz
+examples/00README.txt
--- /dev/null
+#bgzip usr/bin
+razip usr/bin
+samtools usr/bin
+misc/*.pl 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
--- /dev/null
+samtools.1
--- /dev/null
+3.0 (quilt)
--- /dev/null
+DOI: 10.1093/bioinformatics/btp352
+Homepage: http://samtools.sourceforge.net
+PMID: 19505943
+Reference: |
+ @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}
+ }
+Repository: https://samtools.svn.sourceforge.net/svnroot/samtools
--- /dev/null
+version=3
+opts=dversionmangle=s/~dfsg// \
+ http://sf.net/samtools/samtools-([\d\.]*)\.tar\.bz2
projects / samtools.git / commitdiff