Changes for version 2.4

  • github repo move to https://github.com/Ensembl/Bio-DB-HTS
  • -Wformat=no removed from build options
  • check results of archive fetches

Documentation

The Kseq iterator

Modules

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

Provides

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.pm
in lib/Bio/DB/HTS.pm
in lib/Bio/DB/HTS.pm