debian/0000755000000000000000000000000012045427204007166 5ustar debian/compat0000644000000000000000000000000212045374424010371 0ustar 9 debian/gbp.conf0000644000000000000000000000027012045374362010612 0ustar # This package is managed with git-buildpackage. [DEFAULT] # use pristine-tar: pristine-tar = True [git-dch] # include 7 digits of the commit id in the changelog enty: id-length = 7 debian/patches/0000755000000000000000000000000012045374362010623 5ustar debian/patches/gzstream.h.patch0000644000000000000000000000102312045374362013722 0ustar Description: To find gzstream.h during Debian package building. Author: Charles Plessy Forwarded: no diff --git a/src/utils/gzstream/gzstream.C b/src/utils/gzstream/gzstream.C index 8cb4590..bbb4ba8 100644 --- a/src/utils/gzstream/gzstream.C +++ b/src/utils/gzstream/gzstream.C @@ -26,7 +26,7 @@ // Standard C++ Library". // ============================================================================ -#include +#include "gzstream.h" #include #include // for memcpy debian/patches/series0000644000000000000000000000002112045374362012031 0ustar gzstream.h.patch debian/bash_completion/0000755000000000000000000000000012045426454012342 5ustar debian/bash_completion/bedtools0000644000000000000000000000117612045426454014105 0ustar _bedtools() { local cur prev opts COMPREPLY=() cur="${COMP_WORDS[COMP_CWORD]}" prev="${COMP_WORDS[COMP_CWORD-1]}" opts="intersect window closest coverage map genomecov merge cluster complement subtract slop flank sort random shuffle annotate multiinter unionbedg pairtobed pairtopair bamtobed bedtobam bamtofastq bedpetobam bed12tobed6 getfasta maskfasta nuc multicov tag jaccard overlap igv links makewindows groupby expand" case $prev in bedtools) COMPREPLY=( $(compgen -f -W "${opts}" -- "$cur") ) ;; esac return 0 } complete -F _bedtools -o default bedtools debian/copyright0000644000000000000000000001242312045374362011131 0ustar Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Source: http://bedtools.googlecode.com/files/BEDTools.v2.17.0.tar.gz License: GPL-2 and MIT and GPL-3+ with runtime exception and zlib BEDTools combines source code under GPL-2, LGPL-2.1 and MIT licenses, and links to libc6, libgcc, libstdc++ and zlib1g. Files: * Copyright: © 2009,2010,2011 Aaron Quinlan © 2010 - Assaf Gordon, CSHL License: GPL-2 Files: src/expand/expand.cpp Copyright: © 2009, 2010, 2011 - Aaron Quinlan License: under-the-MIT-license No further explanation about which MIT license to follow was provided. Files: src/cuffToTrans/Fasta.cpp src/cuffToTrans/Fasta.h src/fastaFromBed/Fasta.cpp src/fastaFromBed/Fasta.h Copyright: © 2010 Erik Garrison License: GPL-2 Source: https://github.com/ekg/fastahack Files: src/utils/BamTools/* Copyright: © 2009-2010 Derek Barnett, Erik Garrison, Gabor Marth, Michael Stromberg 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. Comment: see ‘https://github.com/pezmaster31/bamtools/blob/master/LICENSE’. Source: https://github.com/pezmaster31/bamtools/wiki Files: src/utils/gzstream/gzstream.h Copyright: © 2001 Deepak Bandyopadhyay, Lutz Kettner License: 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 Comment: On Debian systems, you can find a copy of the GNU Lesser General Public License version 2.1 in ‘/usr/share/common-licenses/LGPL-2.1’. Name: gzstream, C++ iostream classes wrapping the zlib compression library. Files: docs/themes/rtd/static/rtd.css_t Homepage: http://sphinx-doc.org Name: Sphinx Copyright: © 2007-2010 by the Sphinx team 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: . * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. . * 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 COPYRIGHT HOLDERS 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 COPYRIGHT OWNER 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. 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 version 2 as published by the Free Software Foundation. . 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’. debian/changelog0000644000000000000000000000531512045427204011044 0ustar bedtools (2.17.0-1) unstable; urgency=low bb9012e Imported Upstream version 2.16.2. 9006b23 Imported Upstream version 2.17.0. 9112569 Documented BEDTools license as a whole. 325689c Removed Pre-Depends: dpkg (>= 1.15.6). a781b14 Conforms with Policy 3.9.4. 84b1167 Use Debhelper 9. 0bf572d Distribute the test suite. 422cd34 Bash completion for BEDTools. -- Charles Plessy Sun, 04 Nov 2012 17:59:41 +0900 bedtools (2.16.1-1) unstable; urgency=low b7f2405 New upstream release. 4add346 Corrected, updated and normalised Debian copyright. 00b426d Conforms to Debian Policy 3.9.3. 72c3c94 Verbose Debhelper. -- Charles Plessy Fri, 16 Mar 2012 19:06:49 +0900 bedtools (2.15.0-1) unstable; urgency=low 3f8e754 Upstream version 2.15.0. f27b295 Build-depend on python because of scripts/makeBashScripts.py. 2e3e8e8 Removed the /usr/bin/groupBy wrapper, as groupBy is also distributed by the filo package. -- Charles Plessy Wed, 11 Jan 2012 15:07:45 +0900 bedtools (2.14.3-1) unstable; urgency=low 04f6aa3 Bugfix release. -- Charles Plessy Fri, 04 Nov 2011 09:25:38 +0900 bedtools (2.14.2-1) unstable; urgency=low 356313d Bugfix release. -- Charles Plessy Thu, 03 Nov 2011 12:15:32 +0900 bedtools (2.14.1-1) unstable; urgency=low bce732c New upstream release and new tool, multiBedIntersect. -- Charles Plessy Thu, 03 Nov 2011 11:14:35 +0900 bedtools (2.13.4-1) unstable; urgency=low e553c37 New upstream release. -- Charles Plessy Sat, 29 Oct 2011 11:08:02 +0900 bedtools (2.13.3-1ubuntu1) precise; urgency=low * Pre-Depends: dpkg (>= 1.15.6) for xz compression support. Needed until after Ubuntu 12.04 LTS. -- Colin Watson Mon, 17 Oct 2011 21:30:47 +0100 bedtools (2.13.3-1) unstable; urgency=low ea1c596 New upstream release. -- Charles Plessy Wed, 05 Oct 2011 17:18:15 +0900 bedtools (2.13.2-1) unstable; urgency=low 1930a26 New upstream release. -- Charles Plessy Sat, 24 Sep 2011 09:34:29 +0900 bedtools (2.13.1-1) unstable; urgency=low 2e3fe5e New upstream release. ff5450e Compress source and binary packages with xz. ef58a33 Suggest filo for the groupBy command. df206c0 Mangle debian/watch download URL. 2fe7cff Simplified repacking as upstream tarballs do not contain ‘*/*DS_Store’ files anymore. -- Charles Plessy Sat, 10 Sep 2011 23:32:43 +0900 bedtools (2.12.0-1) unstable; urgency=low * Initial release (Closes: #629597) -- Charles Plessy Wed, 08 Jun 2011 17:01:19 +0900 debian/README.source0000644000000000000000000000027312045374362011355 0ustar This package uses a patch system, please refer to the following documentation: /usr/share/doc/quilt/README.source -- Charles Plessy Thu, 03 Feb 2011 22:32:18 +0900 debian/source/0000755000000000000000000000000012045374362010474 5ustar debian/source/format0000644000000000000000000000001412045374362011702 0ustar 3.0 (quilt) debian/rules0000755000000000000000000000075512045413613010254 0ustar #!/usr/bin/make -f export DH_VERBOSE=1 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 DEB_DH_BUILDDEB_ARGS = -- -Z xz DEB_INSTALL_CHANGELOGS_ALL := RELEASE_HISTORY DEB_COMPRESS_EXCLUDE = test get-orig-source: uscan --no-symlink --force-download --download-version $(DEB_UPSTREAM_VERSION) binary-fixup/bedtools:: rm $(CURDIR)/debian/bedtools/usr/bin/groupBy # distributed in the filo package. debian/docs0000644000000000000000000000001312045413652010035 0ustar README.rst debian/watch0000644000000000000000000000031512045374362010224 0ustar # Compulsory line, this is a version 3 file version=3 opts=downloadurlmangle=s|//code.google.com|| \ http://code.google.com/p/bedtools/downloads/list //bedtools.googlecode.com/files/BEDTools.v(.*).tar.gz debian/install0000644000000000000000000000016712045426626010572 0ustar bin/* usr/bin genomes usr/share/bedtools test/* usr/share/bedtools/test debian/bash_completion/* etc/bash_completion.d debian/control0000644000000000000000000000177212045422746010606 0ustar Source: bedtools Section: science Priority: optional Maintainer: Debian Med Packaging Team Uploaders: Charles Plessy Build-Depends: cdbs, debhelper (>= 9), quilt, python, zlib1g-dev Standards-Version: 3.9.4 Homepage: http://code.google.com/p/bedtools/ Vcs-Browser: http://git.debian.org/?p=debian-med/bedtools.git Vcs-Git: git://git.debian.org/debian-med/bedtools.git Package: bedtools Architecture: any Depends: ${shlibs:Depends}, ${misc:Depends} Suggests: filo Description: suite of utilities for comparing genomic features The BEDTools utilities allow one to address common genomics tasks such as finding feature overlaps and computing coverage. The utilities are largely based on four widely-used file formats: BED, GFF/GTF, VCF, and SAM/BAM. Using BEDTools, one can develop sophisticated pipelines that answer complicated research questions by streaming several BEDTools together. . The groupBy utility is distribued in the filo package. debian/upstream0000644000000000000000000000157012045374362010762 0ustar Archive: Google Code Bug-Database: http://code.google.com/p/bedtools/issues Contact: http://groups.google.com/group/bedtools-discuss Name: BEDTools Homepage: http://code.google.com/p/bedtools/ Reference: author: Quinlan, Aaron R. and Hall, Ira M. title: | BEDTools: a flexible suite of utilities for comparing genomic features volume: 26 number: 6 pages: 841-842 year: 2010 doi: 10.1093/bioinformatics/btq033 URL: http://bioinformatics.oxfordjournals.org/content/26/6/841.abstract eprint: http://bioinformatics.oxfordjournals.org/content/26/6/841.full.pdf+html journal: Bioinformatics pmid: 20110278 Repository: https://github.com/arq5x/bedtools.git Repository-Browse: https://github.com/arq5x/bedtools Watch: | version=3 opts=downloadurlmangle=s|//code.google.com|| \ http://code.google.com/p/bedtools/downloads/list //bedtools.googlecode.com/files/BEDTools.v(.*).tar.gz