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Bio-SamTools-1.07
River stage zero No dependents

Changes for version 1.07

  • 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.

Modules

Bio::DB::Bam::AlignWrapper
Add high-level methods to Bio::DB::Bam::Alignment
Bio::DB::Bam::Alignment
The SAM/BAM alignment object
Bio::DB::Bam::Pileup
Object passed to pileup() callback
Bio::DB::Bam::PileupWrapper
Add high-level methods to Bio::DB::Bam::Pileup
Bio::DB::Bam::Query
Object representing the query portion of a BAM/SAM alignment
Bio::DB::Sam
Read SAM/BAM database files
Bio::DB::Sam::Constants
Constants for use with SAM/BAM

Provides

Bio::DB::Bam
in lib/Bio/DB/Sam.pm
Bio::DB::Bam::FetchIterator
in lib/Bio/DB/Bam/FetchIterator.pm
Bio::DB::Bam::ReadIterator
in lib/Bio/DB/Bam/ReadIterator.pm
Bio::DB::Bam::SplitAlignmentPart
in lib/Bio/DB/Bam/AlignWrapper.pm
Bio::DB::Bam::Target
in lib/Bio/DB/Bam/Target.pm
Bio::DB::Sam::Fai
in lib/Bio/DB/Sam.pm
Bio::DB::Sam::Segment
in lib/Bio/DB/Sam/Segment.pm
Bio::DB::Sam::Segment::Iterator
in lib/Bio/DB/Sam/Segment.pm
Bio::SeqFeature::Coverage
in lib/Bio/DB/Sam.pm

Other files