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Bio-SamTools-1.28
River stage zero No dependents

Changes for version 1.28

  • *Fixed coverage calculations so that sections of reads that cover the reference genome which are marked in the CIGAR string as 'N' (skip) or 'D' (delete) do not contribute to coverage. *The bamToGBrowse.pl script now takes advantage of genomeCoveragetoBed from the BedTools package. If this executable is installed, BigWig generation will speed up noticeably.

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::Bam::Target
Object representing the query portion of a BAM/SAM alignment in NATIVE 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::Sam::Fai
in lib/Bio/DB/Sam.pm
Bio::DB::Sam::SamToGBrowse
in lib/Bio/DB/Sam/SamToGBrowse.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