libbio-samtools-perl_1.39-1+b1_amd64.deb


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Description

libbio-samtools-perl - Perl interface to SamTools library for DNA sequencing

Distribution: Debian 8 (Jessie)
Repository: Debian Main amd64
Package name: libbio-samtools-perl
Package version: 1.39
Package release: 1+b1
Package architecture: amd64
Package type: deb
Installed size: 588 B
Download size: 190.48 KB
Official Mirror: ftp.br.debian.org
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.

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    Download

    Source package: libbio-samtools-perl

    Install Howto

    1. Update the package index:
      # sudo apt-get update
    2. Install libbio-samtools-perl deb package:
      # sudo apt-get install libbio-samtools-perl

    Files

    • /usr/bin/bam2bedgraph
    • /usr/bin/bamToGBrowse.pl
    • /usr/bin/chrom_sizes.pl
    • /usr/bin/genomeCoverageBed.pl
    • /usr/lib/x86_64-linux-gnu/perl5/5.20/Bio/DB/Sam.pm
    • /usr/lib/x86_64-linux-gnu/perl5/5.20/Bio/DB/Bam/AlignWrapper.pm
    • /usr/lib/x86_64-linux-gnu/perl5/5.20/Bio/DB/Bam/Alignment.pm
    • /usr/lib/x86_64-linux-gnu/perl5/5.20/Bio/DB/Bam/FetchIterator.pm
    • /usr/lib/x86_64-linux-gnu/perl5/5.20/Bio/DB/Bam/Pileup.pm
    • /usr/lib/x86_64-linux-gnu/perl5/5.20/Bio/DB/Bam/PileupWrapper.pm
    • /usr/lib/x86_64-linux-gnu/perl5/5.20/Bio/DB/Bam/Query.pm
    • /usr/lib/x86_64-linux-gnu/perl5/5.20/Bio/DB/Bam/ReadIterator.pm
    • /usr/lib/x86_64-linux-gnu/perl5/5.20/Bio/DB/Bam/Target.pm
    • /usr/lib/x86_64-linux-gnu/perl5/5.20/Bio/DB/Sam/Constants.pm
    • /usr/lib/x86_64-linux-gnu/perl5/5.20/Bio/DB/Sam/SamToGBrowse.pm
    • /usr/lib/x86_64-linux-gnu/perl5/5.20/Bio/DB/Sam/Segment.pm
    • /usr/lib/x86_64-linux-gnu/perl5/5.20/auto/Bio/DB/Sam/Sam.bs
    • /usr/lib/x86_64-linux-gnu/perl5/5.20/auto/Bio/DB/Sam/Sam.so
    • /usr/share/doc/libbio-samtools-perl/changelog.Debian.amd64.gz
    • /usr/share/doc/libbio-samtools-perl/changelog.Debian.gz
    • /usr/share/doc/libbio-samtools-perl/changelog.gz
    • /usr/share/doc/libbio-samtools-perl/copyright
    • /usr/share/man/man3/Bio::DB::Bam::AlignWrapper.3pm.gz
    • /usr/share/man/man3/Bio::DB::Bam::Alignment.3pm.gz
    • /usr/share/man/man3/Bio::DB::Bam::Pileup.3pm.gz
    • /usr/share/man/man3/Bio::DB::Bam::PileupWrapper.3pm.gz
    • /usr/share/man/man3/Bio::DB::Bam::Query.3pm.gz
    • /usr/share/man/man3/Bio::DB::Bam::Target.3pm.gz
    • /usr/share/man/man3/Bio::DB::Sam.3pm.gz
    • /usr/share/man/man3/Bio::DB::Sam::Constants.3pm.gz

    Changelog

    2013-09-29 - Charles Plessy <plessy@debian.org> libbio-samtools-perl (1.39-1) unstable; urgency=low cff6561 Imported Upstream version 1.39

    2013-05-17 - Charles Plessy <plessy@debian.org> 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.

    2013-01-06 - Charles Plessy <plessy@debian.org> 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.

    2012-09-09 - Charles Plessy <plessy@debian.org> 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.

    2012-01-29 - Charles Plessy <plessy@debian.org> 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.

    2011-11-23 - Charles Plessy <plessy@debian.org> libbio-samtools-perl (1.32-1) unstable; urgency=low [36ac64b] New upstream release. [dfb9312] Depend on BioPerl 1.6.901, following Upstream.

    2011-11-01 - Charles Plessy <plessy@debian.org> 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.

    2011-06-28 - Charles Plessy <plessy@debian.org> 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

    2011-05-20 - Charles Plessy <plessy@debian.org> 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’.

    2011-04-04 - Charles Plessy <plessy@debian.org> libbio-samtools-perl (1.28-1) unstable; urgency=low * New upstream release.

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