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libbio-samtools-perl

read SAM/BAM nucleotide sequence aligment database files

Variants:
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.
Homepage:
Package version:1.20-1
Architecture:amd64
Distribution:Debian
Filename:libbio-samtools-perl_1.20-1_amd64.deb

/usr/share/doc/libbio-samtools-perl/README.Debian

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

/usr/share/man/man3/Bio::DB::Bam::AlignWrapper.3pm.gz

Bio::DB::Bam::AliUseraContributed PerBio::DB::Bam::AlignWrapper(3pm)



NAME
       Bio::DB::Bam::AlignWrapper -- Add high-level methods to
       Bio::DB::Bam::Alignment

SYNOPSIS
       See Bio::DB::Bam::Alignment.

DESCRIPTION
       This is a wrapper around Bio::DB::Bam::Alignment that adds
       the following high-level methods. These are described in
       detail in "High-level Bio::DB::Ba
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/usr/share/man/man3/Bio::DB::Bam::Alignment.3pm.gz

Bio::DB::Bam::AliUsernContributed Perl DBio::DB::Bam::Alignment(3pm)



NAME
       Bio::DB::Bam::Alignment -- The SAM/BAM alignment object

SYNOPSIS
        use Bio::DB::Sam;

        my $sam = Bio::DB::Sam->new(-fasta=>"data/ex1.fa",
                                    -bam  =>"data/ex1.bam");

        my @alignments = $sam->get_features_by_location(-seq_id => 'seq2',
                           
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/usr/share/man/man3/Bio::DB::Bam::Pileup.3pm.gz

Bio::DB::Bam::PilUser3Contributed Perl DocuBio::DB::Bam::Pileup(3pm)



NAME
       Bio::DB::Bam::Pi
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/usr/share/man/man3/Bio::DB::Bam::PileupWrapper.3pm.gz

Bio::DB::Bam::PilUserrContributed PeBio::DB::Bam::PileupWrapper(3pm)



NAME
       Bio::DB::Bam::Pi
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/usr/share/man/man3/Bio::DB::Bam::Query.3pm.gz

Bio::DB::Bam::QueUserpContributed Perl DocumBio::DB::Bam::Query(3pm)



NAME
       Bio::DB::Bam::Qu
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/usr/share/man/man3/Bio::DB::Bam::Target.3pm.gz

Bio::DB::Bam::TarUser3Contributed Perl DocuBio::DB::Bam::Target(3pm)



NAME
       Bio::DB::Bam::Ta
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/usr/share/man/man3/Bio::DB::Sam.3pm.gz

Bio::DB::Sam(3pm)User Contributed Perl DocumentatioBio::DB::Sam(3pm)



NAME
       Bio::DB::Sam -- 
more»

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