Search results for "dist:Bio-SamTools Bio::SamTools"
Bio::DB::Sam - Read SAM/BAM database files
This module 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...
LDS/Bio-SamTools-1.43 - 12 Feb 2016 19:33:32 UTC
Bio::DB::Bam::Query - Object representing the query portion of a BAM/SAM alignment
This is a simple Bio::SeqFeatureI object that represents the query part of a SAM alignment. Methods POD ERRORS Hey! The above document had some coding errors, which are explained below: Around line 8: =over is the last thing in the document?!...
LDS/Bio-SamTools-1.43 - 12 Feb 2016 19:33:32 UTC
Bio::DB::Bam::Pileup - Object passed to pileup() callback
A Bio::DB::Bam::Pileup object (or a Bio::DB::Bam::PileupWrapper object) is passed to the callback passed to the Bio::DB::Sam->pileup() method for each column in a sequence alignment. The only difference between the two is that the latter returns the ...
LDS/Bio-SamTools-1.43 - 12 Feb 2016 19:33:32 UTC
Bio::DB::Bam::Target - Object representing the query portion of a BAM/SAM alignment in NATIVE alignment
LDS/Bio-SamTools-1.43
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12 Feb 2016 19:33:32 UTC
Bio::DB::Bam::Alignment - The SAM/BAM alignment object
The Bio::DB::Bam::Alignment and Bio::DB::Bam::AlignWrapper classes together represent an alignment between a sequence read (the "query") and a reference sequence (the "target"). Bio::DB::Bam::Alignment adheres strictly to the C-level BAM library's de...
LDS/Bio-SamTools-1.43 - 12 Feb 2016 19:33:32 UTC
Bio::DB::Sam::Constants - Constants for use with SAM/BAM
This module exports several constants for use with the SAM/BAM module. See the SAM documentation for their interpretation. Cigar operations BAM_CIGAR_SHIFT BAM_CIGAR_MASK BAM_CMATCH BAM_CINS BAM_CDEL BAM_CREF_SKIP BAM_CSOFT_CLIP BAM_CHARD_CLIP BAM_CP...
LDS/Bio-SamTools-1.43 - 12 Feb 2016 19:33:32 UTC
Bio::DB::Bam::AlignWrapper - Add high-level methods to Bio::DB::Bam::Alignment
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::Bam::Alignment methods" in Bio::DB::Bam::Alignment. add_segment() add a new subfeature to split alignme...
LDS/Bio-SamTools-1.43 - 12 Feb 2016 19:33:32 UTC
Bio::DB::Bam::PileupWrapper - Add high-level methods to Bio::DB::Bam::Pileup
See Bio::DB::Bam::Pileup for documentation of this object's methods. This class is used by the high-level API to return Bio::DB::Bam::AlignWrapper objects from the call to alignment() rather than Bio::DB::Bam::Alignment....
LDS/Bio-SamTools-1.43 - 12 Feb 2016 19:33:32 UTC