debian/0000755000000000000000000000000012153434137007171 5ustar debian/control0000644000000000000000000000243012153431771010574 0ustar Source: bwa Section: science Priority: optional Maintainer: Debian Med Packaging Team Uploaders: Charles Plessy , Andreas Tille , Carlos Borroto , Ognyan Kulev Build-Depends: debhelper (>= 9), zlib1g-dev Standards-Version: 3.9.4 Homepage: http://bio-bwa.sourceforge.net/ Vcs-Browser: http://anonscm.debian.org/gitweb/?p=debian-med/bwa.git Vcs-Git: git://anonscm.debian.org/debian-med/bwa.git Package: bwa Architecture: amd64 kfreebsd-amd64 Depends: ${shlibs:Depends}, ${misc:Depends} Suggests: samtools Description: Burrows-Wheeler Aligner BWA is a software package for mapping low-divergent sequences against a large reference genome, such as the human genome. It consists of three algorithms: BWA-backtrack, BWA-SW and BWA-MEM. The first algorithm is designed for Illumina sequence reads up to 100bp, while the rest two for longer sequences ranged from 70bp to 1Mbp. BWA-MEM and BWA-SW share similar features such as long-read support and split alignment, but BWA-MEM, which is the latest, is generally recommended for high-quality queries as it is faster and more accurate. BWA-MEM also has better performance than BWA-backtrack for 70-100bp Illumina reads. debian/upstream0000644000000000000000000000127612152370564010764 0ustar Archive: SourceForge FAQ: http://bio-bwa.sourceforge.net/ Homepage: http://bio-bwa.sourceforge.net/ Name: Burrows-Wheeler Aligner Reference: Article: HengLi07152009 Author: Li, Heng and Durbin, Richard Title: Fast and accurate short read alignment with Burrows-Wheeler transform Journal: Bioinformatics Volume: 25 Number: 14 Pages: 1754-1760 Year: 2009 DOI: 10.1093/bioinformatics/btp324 PMID: 19451168 URL: http://bioinformatics.oxfordjournals.org/cgi/content/abstract/25/14/1754 Eprint: http://bioinformatics.oxfordjournals.org/cgi/reprint/25/14/1754.pdf References: http://bio-bwa.sourceforge.net/ Repository: https://github.com/lh3/bwa.git Repository-Browse: https://github.com/lh3/bwa debian/rules0000755000000000000000000000044312152370564010254 0ustar #!/usr/bin/make -f %: dh $@ DEB_BUILD_ARCH := $(shell dpkg-architecture -qDEB_BUILD_ARCH) DFLAGS := -DHAVE_PTHREAD ifneq ($(DEB_BUILD_ARCH), amd64) DFLAGS += -D_NO_SSE2 endif override_dh_auto_build: dh_auto_build -- CFLAGS="-Wall $(CFLAGS) $(CPPFLAGS) $(LDFLAGS)" DFLAGS="$(DFLAGS)" debian/copyright0000644000000000000000000001017412152370564011131 0ustar Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Source: http://sourceforge.net/projects/bio-bwa/files/bwa-0.6.1.tar.bz2 Files: * Copyright: © 2008 Genome Research Ltd (GRL) 2008, by Heng Li © 2003-2006, 2008, 2009, by Heng Li © 2008, 2009 by attractor © 2008 Yuta Mori © 2011 by Attractive Chaos 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: kbtree.h Copyright: © 1997-1999, 2001, John-Mark Gurney. © 2008-2009, Attractive Chaos License: BSD-2-Clause 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: bwt_gen.* Copyright: © 2004, Wong Chi Kwong License: GPL-2+ 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 of the License, or (at your option) any later version. . This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. . You should have received a copy of the GNU General Public License along with this program; if not, write to the Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. Comment: On Debian systems, you can find a copy of the GNU General Public License version 2 in ‘/usr/share/common-licenses/GPL-2’. Files: QSufSort.* Copyright: 1999, N. Jesper Larsson License: other This software may be used freely for any purpose. However, when distributed, the original source must be clearly stated, and, when the source code is distributed, the copyright notice must be retained and any alterations in the code must be clearly marked. No warranty is given regarding the quality of this software. debian/source/0000755000000000000000000000000012152370564010473 5ustar debian/source/format0000644000000000000000000000001412152370564011701 0ustar 3.0 (quilt) debian/watch0000644000000000000000000000032712152370564010226 0ustar version=3 opts=downloadurlmangle=s|/download||,filenamemangle=s|http://sourceforge.net/projects/bio-bwa/files/||;s|.download|| \ http://sf.net/bio-bwa/bwa-([\d\.]+[\da-f]*)\.(?:tgz|tbz|txz|(?:tar\.(?:gz|bz2|xz))) debian/compat0000644000000000000000000000000212152370564010371 0ustar 9 debian/docs0000644000000000000000000000004212152372431010035 0ustar NEWS README.md debian/NEWS.Debian debian/changelog0000644000000000000000000001155512153433717011055 0ustar bwa (0.7.5a-2) unstable; urgency=low * Fixed FTBFS: SSE2 is required so require amd64-based architecture for now. (9284b99) * Updated Vcs-* fields. (521828c) * New package description taken from homepage. (0ad135b) * Standards-Version: 3.9.4 (3ce8e1a) -- Ognyan Kulev Tue, 04 Jun 2013 21:51:41 +0300 bwa (0.7.5a-1) unstable; urgency=low [ Charles Plessy ] - Imported Upstream version 0.7.0 (947c814) - solid2fastq.pl was removed upstream. (4d08b81) - Bash completion. (ad07300) - Updated list of BWA's commands. (c330e89) [ Ognyan Kulev ] - Imported upstream version 0.7.5a (ec16902, Closes: #710682) - README is renamed to README.md by upstream. (f42f5c0) - Standards-Version: 3.9.4 (no changes needed) - Removed DM-Upload-Allowed field. (78af085) - Added myself as uploader. (86455dc) -- Ognyan Kulev Tue, 04 Jun 2013 08:51:31 +0300 bwa (0.6.2-1) unstable; urgency=low [ Carlos Borroto ] * New upstream release [ Andreas Tille ] * debian/control: - versioned Build-Depends debhelper >= 9 - Standards-Version: 3.9.3 (no changes needed) - Add Carlos Borroto as uploader to make sure a package with his changes is not considered as NMU * debian/docs: Add NEWS.Debian * debian/watch: Use SF redirector as suggested by lintian -- Andreas Tille Tue, 26 Jun 2012 09:20:46 +0200 bwa (0.6.1-1) unstable; urgency=low [b794564] New upstream release. [fc9894b] Pass -D_NO_SSE2 everywhere except on amd64 (Closes: #648803). [52312b6] Corrected changelog: 0.6.0-1 was actually uploaded to unstable. -- Charles Plessy Wed, 30 Nov 2011 19:36:04 +0900 bwa (0.6.0-1) unstable; urgency=low [9ce640c] New upstream release (not to use in a production pipeline). [e641dd6] Corrected the name of the file downloaded by uscan. [4ada685] Pass Dpkg build flags to the compiler through Debhelper 9. Thanks, Niels Thykier! -- Charles Plessy Mon, 14 Nov 2011 19:28:44 +0900 bwa (0.5.10-1) unstable; urgency=low [a01f6ca] New upstream release. [6d7bc7f] Conforms with Debian Policy version 3.9.2. [125c73d] Corrected Vcs-Git URL. [37f43c9] Normalised machine-readable copyright file with config-edit. [4e2e0d0] Distribute xa2multi.pl in ‘usr/share/bwa’. [b106d64] Removed redundant ChangeLog file, already installed by Debhelper. -- Charles Plessy Mon, 14 Nov 2011 13:12:50 +0900 bwa (0.5.9-2) unstable; urgency=low * Watchfile should not regard rc releases. * Drop cdbs in favour of dh -- Andreas Tille Fri, 11 Mar 2011 22:49:07 +0100 bwa (0.5.9-1) unstable; urgency=low * New usptream release - Upstream moved to GitHub (debian/upstream-metadata.yaml). - Checked copyright; one file was removed (debian/copyright). * Migrated the Debian source package to Git (debian/control). * Use Debhelper 8 (debian/control, debian/compat). -- Charles Plessy Tue, 08 Feb 2011 16:11:12 +0900 bwa (0.5.8c-1) unstable; urgency=low * Bug fix release, reverting the scoring system back to the one used in 0.5.7. 0.5.8a/b may produce a CIGAR like 10M2I10M4D2M which should not happen in principle. Such wrong cigars also incur errors in indel calling when samtools is in use (Closes: #601568). * Incremented Standards-Version to reflect conformance with Policy 3.9.1 (debian/control, no changes needed). * debian/copyright updated and reformatted. -- Charles Plessy Wed, 27 Oct 2010 21:14:34 +0900 bwa (0.5.8a-1) unstable; urgency=low * New upstream release. * Use the more convenient viewsvn as VCS-Broswer (debian/control). * Incremented Standards-Version to reflect conformance with Policy 3.9.0 (debian/control, no changes needed). -- Charles Plessy Wed, 30 Jun 2010 10:44:30 +0900 bwa (0.5.7-1) unstable; urgency=low * New upstream release. -- Charles Plessy Tue, 02 Mar 2010 23:33:06 +0900 bwa (0.5.6-1) unstable; urgency=low * New upstream release. * Incremented Standards-Version to reflect conformance with Policy 3.8.4 (debian/control). -- Charles Plessy Wed, 17 Feb 2010 12:48:57 +0900 bwa (0.5.5-1) unstable; urgency=low * New upstream release. * Using Dpkg source format version ‘3.0 (quilt)’ (debian/source/format). -- Charles Plessy Wed, 11 Nov 2009 23:05:19 +0900 bwa (0.5.4-1) unstable; urgency=low * New upstream release, see ‘/usr/share/doc/bwa/NEWS.gz’. * Refreshed debian/copyright. * Reflected the rename of dBWT-Sw to BWA-SW in the package's description (debian/control). -- Charles Plessy Mon, 19 Oct 2009 13:59:42 +0900 bwa (0.5.3-1) unstable; urgency=low * Initial release (Closes: #548719) -- Charles Plessy Thu, 08 Oct 2009 19:20:41 +0900 debian/bash_completion/0000755000000000000000000000000012152370564012341 5ustar debian/bash_completion/bwa0000644000000000000000000000060012152370564013031 0ustar _bwa() { local cur prev opts COMPREPLY=() cur="${COMP_WORDS[COMP_CWORD]}" prev="${COMP_WORDS[COMP_CWORD-1]}" opts="index aln samse sampe bwasw fastmap mem fa2pac pac2bwt pac2bwtgen bwtupdate bwt2sa" case $prev in bwa) COMPREPLY=( $(compgen -W "${opts}" -- ${cur}) ) ;; esac return 0 } complete -F _bwa -o default bwa debian/manpages0000644000000000000000000000000612152370564010705 0ustar bwa.1 debian/gbp.conf0000644000000000000000000000032112152370564010606 0ustar # This source package is managed with git-buildpackage and pristine-tar. [DEFAULT] # use pristine-tar: pristine-tar = True [git-dch] # include 7 digits of the commit id in the changelog entry: id-length = 7 debian/NEWS.Debian0000644000000000000000000000044512152370564011056 0ustar bwa (0.6.0-1) unstable; urgency=low Branch 0.6.x index data structure changed and is incompatible with index data structure previously used by branch 0.5.x. You will need to rebuild all your indexes. -- Carlos Borroto Thu, 22 Jun 2012 15:53:58 -0400 debian/install0000644000000000000000000000026312152370564010565 0ustar bwa usr/bin # A different solid2fastq.pl script is present in the maq package. qualfa2fq.pl usr/share/bwa xa2multi.pl usr/share/bwa debian/bash_completion/* etc/bash_completion.d