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Bio-DB-HTS-3.01
River stage one • 1 direct dependent • 1 total dependent
2 ++

Changes for version 3.01

  • HTSlib 1.9 compatibility
  • CentOS 7 compatible installation, courtesy of John Marshall
  • BioPerl version agnostic installation process
  • bugfix #75: reset versioning to avoid confusing perl runtime
  • bugfix #81: install in sudo-less environments, e.g. docker containers PR#83 - https://github.com/Ensembl/Bio-DB-HTS/pull/83, courtesy of John Marshall
  • bugfix #76, #82 - memory leaks due to improper use of bcf_get_format_float/_char/_int32() buffers PR#84 - https://github.com/Ensembl/Bio-DB-HTS/pull/84, courtesy of John Marshall
  • Ignore .gzi index files and clean test output files PR#87 - https://github.com/Ensembl/Bio-DB-HTS/pull/87, courtesy of John Marshall
  • Documentation fixes

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
Bio::DB::HTS::VCF::Iterator
XS module wrapping around a hts_itr_t

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::HTSfile
in lib/Bio/DB/HTS.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