debian/0000755000000000000000000000000012221664350007167 5ustar debian/rules0000755000000000000000000000015512221663725010255 0ustar #!/usr/bin/make -f %: dh $@ override_dh_auto_configure: SAMTOOLS=/usr/include/samtools dh_auto_configure debian/source/0000755000000000000000000000000012221663725010474 5ustar debian/source/format0000644000000000000000000000001412221663725011702 0ustar 3.0 (quilt) debian/copyright0000644000000000000000000002521112221664057011127 0ustar Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Source: http://cpan.metacpan.org/authors/id/L/LD/LDS/Bio-SamTools-1.39.tar.gz License: GPL-1+ or Artistic-2.0 Disclaimer: This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. See the Artistic License file in the main Perl distribution for specific terms and conditions of use. In addition, the following disclaimers apply: . OICR makes no representations whatsoever as to the SOFTWARE contained herein. It is experimental in nature and is provided WITHOUT WARRANTY OF MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE OR ANY OTHER WARRANTY, EXPRESS OR IMPLIED. OICR MAKES NO REPRESENTATION OR WARRANTY THAT THE USE OF THIS SOFTWARE WILL NOT INFRINGE ANY PATENT OR OTHER PROPRIETARY RIGHT. . By downloading this SOFTWARE, your Institution hereby indemnifies OICR against any loss, claim, damage or liability, of whatsoever kind or nature, which may arise from your Institution's respective use, handling or storage of the SOFTWARE. . If publications result from research using this SOFTWARE, we ask that OICR be acknowledged and/or credit be given to OICR scientists, as scientifically appropriate. Files: * Copyright: © 2009 Ontario Institute for Cancer Research License: GPL-1+ or Artistic-2.0 Files: debian/* Copyright: © 2009-2011 Charles Plessy 2012 Nathan Handler License: GPL-1+ or Artistic-2.0 License: Artistic-2.0 Copyright (c) 2000-2006, The Perl Foundation. . Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed. . . Preamble . This license establishes the terms under which a given free software Package may be copied, modified, distributed, and/or redistributed. The intent is that the Copyright Holder maintains some artistic control over the development of that Package while still keeping the Package available as open source and free software. . You are always permitted to make arrangements wholly outside of this license directly with the Copyright Holder of a given Package. 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On Debian systems, the complete text of the latest version of the GNU General Public License can be found in ‘/usr/share/common-licenses/GPL-1’. debian/watch0000644000000000000000000000016612221663725010230 0ustar version=3 https://metacpan.org/release/Bio-SamTools/ .*/Bio-SamTools-v?(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz|zip)$ debian/changelog0000644000000000000000000001712012221664124011041 0ustar libbio-samtools-perl (1.39-1) unstable; urgency=low cff6561 Imported Upstream version 1.39 -- Charles Plessy Sun, 29 Sep 2013 08:37:36 +0900 libbio-samtools-perl (1.38-1) unstable; urgency=low 715e2d1 Imported Upstream version 1.38 [ Salvatore Bonaccorso ] 6c4f50e Change search.cpan.org based URIs to metacpan.org based URIs [ Charles Plessy ] 9cf0347 Use Debhelper 9. c747b89 Moved README.Debian to README.test as it is all about tests. -- Charles Plessy Fri, 17 May 2013 12:38:01 +0900 libbio-samtools-perl (1.37-1) unstable; urgency=low 183cfbc Imported Upstream version 1.37 [ Nathan Handler ] d734fbe Email change: Nathan Handler -> nhandler@debian.org [ Charles Plessy ] c6aaf4a Conforms with Policy version 3.9.4. 7dd10a2 Normalised VCS URLs according to lintian. -- Charles Plessy Sun, 06 Jan 2013 09:04:28 +0900 libbio-samtools-perl (1.36-1) unstable; urgency=low [ Charles Plessy ] * [abf3eaa] Imported Upstream version 1.36 * [d30ef61] Normalised Debian copyright file with 'cme fix dpkg-copyright'. * [6f6c6f3] Summarised License of the whole package in the copyright file. * [d5182f1] Conforms to Debian Policy version 3.9.3. [ gregor herrmann ] * [c3db6d4] Update {versioned,alternative} (build) dependencies. -- Charles Plessy Sun, 09 Sep 2012 10:02:55 +0900 libbio-samtools-perl (1.33-1) unstable; urgency=low * [5fd8406] New upstream release 1.33 [ Nathan Handler ] * [4058f51] Add myself to Uploaders and debian/copyright * [01985a1] Remove version from perl Build-Depend. oldstable has 5.10 * [5b63fda] Don't Build-Depend on libmodule-build-perl (included in core since 5.10) * [af3530d] Remove version from libbio-perl-perl Build-Depend. Nothing older in archive * [d6d6dca] Don't Depend on perl, ${perl:Depends} will pull it in * [64ad8db] Turn short description into noun phrase based on abstract in upstream META.json [ Charles Plessy ] * [bb4b659] Renamed debian/upstream-metadata.yaml to debian/upstream. -- Charles Plessy Sun, 29 Jan 2012 14:38:27 +0900 libbio-samtools-perl (1.32-1) unstable; urgency=low [36ac64b] New upstream release. [dfb9312] Depend on BioPerl 1.6.901, following Upstream. -- Charles Plessy Wed, 23 Nov 2011 16:26:32 +0900 libbio-samtools-perl (1.31-1) unstable; urgency=low [abb8487] New upstream release 1.31 [e222e9f] New upstream release 1.30 [5d83169] Normalised debian/copyright by loading and saving it with config-edit. [de38fdb] Include 7 digits of the commit id in the changelog enty. -- Charles Plessy Tue, 01 Nov 2011 19:22:49 +0900 libbio-samtools-perl (1.29-1) unstable; urgency=low [ Charles Plessy ] * (Build)-Depend on libbio-perl-perl instead of bioperl (debian/control). [ Maximilian Gass ] * New upstream release * Switch to source format 3.0 (quilt) * Format Depends in debian/control * Remove debian/libbio-samtools-perl.docs to fix duplicate changelog * Update debian/copyright * Add copyright assignment to Charles Plessy for debian/* * Replace inline Artistic-2.0 with properly wrapped version from upstream's LICENSE file * Merge Comment into body of GPL-1+ * Remove unused Artistic License section -- Charles Plessy Tue, 28 Jun 2011 13:26:10 +0900 libbio-samtools-perl (1.28-2) unstable; urgency=low * libbam-dev’s bam.h file moved to ‘/usr/include/samtools’. - Build-depend on libbam-dev >= 0.1.16-1~ (debian/control). - Override dh_auto_configure to indicate path (debian/rules). - Use Debhelper 8 (debian/control, debian/compat). * Incremented Standards-Version to reflect conformance with Policy 3.9.2 (debian/control, no changes needed). * Validated debian/copyright with ‘config-edit -application dpkg-copyright’. -- Charles Plessy Fri, 20 May 2011 15:02:02 +0900 libbio-samtools-perl (1.28-1) unstable; urgency=low * New upstream release. -- Charles Plessy Mon, 04 Apr 2011 20:45:31 +0900 libbio-samtools-perl (1.27-1) unstable; urgency=low * Requires libbam 0.1.9 or superior (debian/control). * Conformance with Policy 3.9.1: - Point to GPL-1 instead of GPL in debian/copyright. - Incremented Standards-Version in debian/control. * Reformatted to debian/copyright DEP-5 format. -- Charles Plessy Tue, 08 Mar 2011 20:09:10 +0900 libbio-samtools-perl (1.20-1) unstable; urgency=low * New upstream release. * Incremented Standards-Version to reflect conformance with Policy 3.9.0 (debian/control, no changes needed). -- Charles Plessy Sat, 17 Jul 2010 10:44:34 +0900 libbio-samtools-perl (1.19-1) unstable; urgency=low * New upstream release. -- Charles Plessy Mon, 24 May 2010 16:25:08 +0900 libbio-samtools-perl (1.14-1) unstable; urgency=low * New upstream release with a new script, bamToGBrowse.pl. * Depend and Build-Depend on bioperl >= 1.6 (debian/control). * t/data/ex1.bam.bai and t/data/ex1.fa.fai are now part of the upstream source, so we do not delete them any more in the clean target of debian/rules. -- Charles Plessy Tue, 06 Apr 2010 13:41:17 +0900 libbio-samtools-perl (1.12-1) unstable; urgency=low * New upstream release. -- Charles Plessy Fri, 19 Mar 2010 22:46:54 +0900 libbio-samtools-perl (1.11-1) unstable; urgency=low * New upstream release. -- Charles Plessy Sat, 06 Mar 2010 20:29:02 +0900 libbio-samtools-perl (1.10-1) unstable; urgency=low * New Upstream version. * Incremented Standards-Version to reflect conformance with Policy 3.8.4 (debian/control, no changes needed). -- Charles Plessy Thu, 11 Feb 2010 23:21:58 +0900 libbio-samtools-perl (1.09-1) unstable; urgency=low * New Upstream Versions adding support for remote access to BAM databases on http/ftp servers. -- Charles Plessy Fri, 11 Dec 2009 22:53:34 +0900 libbio-samtools-perl (1.07-1) unstable; urgency=low * New upstream release. - IMPORTANT API CHANGE 1: The feature strand now returns +1 or -1 to indicate whether the query was reverse complemented in the SAM file. - IMPORTANT API CHANGE 2: The $feature->query object's dna() and seq() methods now return the sequence as it was read, rather than the reverse complemented version as represented in the SAM file. $feature->qseq() returns the reverse complemented version as before. * Removed mention that libbio-samtools-perl is built against a static library since it was agree with the release team that the package can enter in Testing. -- Charles Plessy Mon, 23 Nov 2009 17:20:21 +0900 libbio-samtools-perl (1.06-1) unstable; urgency=low * New Upstream Version (Bio::DB::Sam modified to work with GBrowse 1). * Added a few informations about upstream in debian/upstream-metadata.yaml. * Documented how I test the package in README.Debian. -- Charles Plessy Sun, 08 Nov 2009 11:43:43 +0900 libbio-samtools-perl (1.05-1) unstable; urgency=low * New upstream release. - Bio::DB::Sam->seq_id() method no longer lower-cases reference names. - Quashed enormous memory leak in the pileup() function. -- Charles Plessy Mon, 28 Sep 2009 12:58:26 +0900 libbio-samtools-perl (1.04-1) unstable; urgency=low * Initial Release (Closes: #543487). -- Charles Plessy Tue, 15 Sep 2009 18:55:53 +0900 debian/upstream0000644000000000000000000000054412221663725010762 0ustar # Experimental gatherer of metadata about Upstream. # See http://upstream-metadata.debian.net Archive: CPAN Contact: Lincoln Stein Homepage: http://search.cpan.org/dist/Bio-SamTools/ Name: Bio-SamTools Watch: | version=3 http://search.cpan.org/dist/Bio-SamTools/ .*/Bio-SamTools-v?(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz|zip)$ debian/README.test0000644000000000000000000000036212221663725011033 0ustar Note about how this package is tested: At build time, the regression tests of the CPAN package are ran. You can consult the results on ‘http://buildd.debian.org/libbio-samtools-perl’. -- Charles Plessy, Mon, 23 Nov 2009 17:16:56 +0900 debian/control0000644000000000000000000000266512221664350010603 0ustar Source: libbio-samtools-perl Maintainer: Debian Perl Group Uploaders: Charles Plessy , Nathan Handler Section: perl Priority: optional Build-Depends: debhelper (>= 9), perl, zlib1g-dev, libbam-dev (>= 0.1.16-1~), # needed for the tests: libbio-perl-perl Standards-Version: 3.9.4 Vcs-Browser: http://anonscm.debian.org/gitweb/?p=pkg-perl/packages/libbio-samtools-perl.git Vcs-Git: git://anonscm.debian.org/pkg-perl/packages/libbio-samtools-perl.git Homepage: https://metacpan.org/release/Bio-SamTools/ Package: libbio-samtools-perl Architecture: any Depends: ${perl:Depends}, ${shlibs:Depends}, ${misc:Depends}, libbio-perl-perl Enhances: gbrowse, samtools Description: Perl interface to SamTools library for DNA sequencing Bio::SamTools provides a Perl interface to the libbam library for indexed and unindexed SAM/BAM sequence alignment databases. It provides support for retrieving information on individual alignments, read pairs, and alignment coverage information across large regions. It also provides callback functionality for calling SNPs and performing other base-by-base functions. Most operations are compatible with the BioPerl Bio::SeqFeatureI interface, allowing BAM files to be used as a backend to the GBrowse genome browser application. debian/gbp.conf0000644000000000000000000000032512221663725010613 0ustar # This source package is managed with git-buildpackage and uses pristine-tar. [DEFAULT] # use pristine-tar: pristine-tar = True [git-dch] # include 7 digits of the commit id in the changelog enty: id-length = 7 debian/compat0000644000000000000000000000000212221663725010372 0ustar 9