++ed by:
Author image Alessandro Vullo
and 1 contributors

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


The Kseq iterator


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


in lib/Bio/DB/HTS.pm
in lib/Bio/DB/HTS/FetchIterator.pm
in lib/Bio/DB/HTS.pm
in lib/Bio/DB/HTS/ReadIterator.pm
in lib/Bio/DB/HTS/Segment.pm
in lib/Bio/DB/HTS/Segment.pm
in lib/Bio/DB/HTS/AlignWrapper.pm
in lib/Bio/DB/HTS/VCF/Header.pm
in lib/Bio/DB/HTS/VCF/HeaderPtr.pm
in lib/Bio/DB/HTS/VCF/Row.pm
in lib/Bio/DB/HTS/VCF/RowPtr.pm
in lib/Bio/DB/HTS/VCF.pm
in lib/Bio/DB/HTS.pm
in lib/Bio/DB/HTS.pm