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Bio-DB-HTS-2.10
River stage one • 1 direct dependent • 1 total dependent
2 ++

Changes for version 2.1

  • add missing test file to manifest

Changes for version 2.10

  • Tabix changes: header represented as empty string when none is available; querying over an unrecognised seq region returns undefined, not an iterator
  • Bugfix: read SAM header when iterating over alignments, see issue #54
  • Bugfix: could not handle sorting when building index for CRAM files PR#64 - https://github.com/Ensembl/Bio-DB-HTS/pull/64, courtesy of John Marshall
  • Implement filter for features of type coverage
  • Minor warning, memory leak and typo fixes PR#58 - https://github.com/Ensembl/Bio-DB-HTS/pull/58, courtesy of Keiran Raine
  • Minimal support for BAM with csi index (no index generation)

Documentation

Bio::DB::HTS::Kseq::Iterator
The Kseq iterator

Modules

Bio::DB::HTS
Read files using HTSlib including BAM/CRAM, Tabix and BCF database files
Bio::DB::HTS::AlignWrapper
Add high-level methods to Bio::DB::HTS::Alignment
Bio::DB::HTS::Alignment
The HTS alignment object
Bio::DB::HTS::Constants
Constants for use with SAM/BAM
Bio::DB::HTS::Faidx
Perl extension for accessing bgzip compressed and indexed FASTA using htslib
Bio::DB::HTS::Kseq
Bindings to Kseq
Bio::DB::HTS::Kseq::Record
Entry from a Kseq iterator
Bio::DB::HTS::Pileup
Object passed to pileup() callback
Bio::DB::HTS::PileupWrapper
Add high-level methods to Bio::DB::HTS::Pileup
Bio::DB::HTS::Query
Object representing the query portion of a BAM/SAM alignment
Bio::DB::HTS::Tabix
Object oriented access to the underlying tbx C methods
Bio::DB::HTS::Tabix::Iterator
XS module wrapping around a tabix hts_itr_t
Bio::DB::HTS::Target
Object representing the query portion of a BAM/SAM alignment in NATIVE alignment
Bio::DB::HTS::VCF
Read VCF/BCF data files

Provides

Bio::DB::HTS::Fai
in lib/Bio/DB/HTS.pm
Bio::DB::HTS::FetchIterator
in lib/Bio/DB/HTS/FetchIterator.pm
Bio::DB::HTS::ReadIterator
in lib/Bio/DB/HTS/ReadIterator.pm
Bio::DB::HTS::Segment
in lib/Bio/DB/HTS/Segment.pm
Bio::DB::HTS::Segment::Iterator
in lib/Bio/DB/HTS/Segment.pm
Bio::DB::HTS::SplitAlignmentPart
in lib/Bio/DB/HTS/AlignWrapper.pm
Bio::DB::HTS::VCF::Header
in lib/Bio/DB/HTS/VCF/Header.pm
Bio::DB::HTS::VCF::HeaderPtr
in lib/Bio/DB/HTS/VCF/HeaderPtr.pm
Bio::DB::HTS::VCF::Row
in lib/Bio/DB/HTS/VCF/Row.pm
Bio::DB::HTS::VCF::RowPtr
in lib/Bio/DB/HTS/VCF/RowPtr.pm
Bio::DB::HTS::VCF::Sweep
in lib/Bio/DB/HTS/VCF.pm
Bio::DB::HTSfile
in lib/Bio/DB/HTS.pm
Bio::SeqFeature::HTSCoverage
in lib/Bio/DB/HTS.pm

Other files