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

Property Value
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.

Alternatives

Package Version Architecture Repository
libbio-samtools-perl_1.39-1+b1_i386.deb 1.39 i386 Debian Main
libbio-samtools-perl - - -

Requires

Name Value
libbio-perl-perl -
libc6 >= 2.14
perl >= 5.20.0-4
perlapi-5.20.0 -
zlib1g >= 1:1.2.3.3

Download

Type URL
Binary Package libbio-samtools-perl_1.39-1+b1_amd64.deb
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

Path
/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.

See Also

Package Description
libbio-scf-perl_1.03-2+b1_amd64.deb Perl extension for reading and writing SCF sequence files
libbio2jack0-dev_0.9-2.1_amd64.deb oss/alsa to jack porting lib - development files
libbio2jack0_0.9-2.1_amd64.deb oss/alsa to jack porting lib - runtime files
libbiococoa-dev_2.2.2-2+b1_amd64.deb Bioinformatics framework for GNUstep and Cocoa (development files)
libbiococoa2_2.2.2-2+b1_amd64.deb Bioinformatics framework for GNUstep and Cocoa (library files)
libbiojava-java-demos_1.7.1-5_all.deb Example programs for BioJava
libbiojava-java-doc_1.7.1-5_all.deb [Biology] Documentation for BioJava
libbiojava-java_1.7.1-5_all.deb Java API to biological data and applications (default version)
libbiojava1.7-java_1.7.1-5_all.deb Java API to biological data and applications (version 1.7)
libbiojava3-java-doc_3.1.0+dfsg-2_all.deb [Biology] Documentation for BioJava
libbiojava3-java_3.1.0+dfsg-2_all.deb Java API to biological data and applications (default version)
libbiojava3.0-java_3.1.0+dfsg-2_all.deb Java API to biological data and applications (version 3)
libbiosig-dev_1.3.0-2+b2_amd64.deb I/O library for biomedical data - development files
libbiosig1_1.3.0-2+b2_amd64.deb I/O library for biomedical data - dynamic library
libbisho-common-dev_0.27.2+git20111122.9e68ef3d-2_amd64.deb Meego web services settings library (development files)
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