v4.2.1: htslib 1.11+libdeflate

• Correct htslib install for container
• add libdeflate via base container
• standardise install methods

v4.0.0 - fragment based counting

• alleleCounter now counts per-fragment rather than per-read when overlaps occur.
  1. When members of a pair overlap and calls match the depth and allele seen are only counted once.
  2. When mate reads disagree on the call, the depth is counted as 2 and both allele counts incremented.
• Reworked perl to wrap C alleleCounter and just handle the extra format changes.
• Removed dependency on Bio::DB::HTS.
• Update to HTSlib 1.7
• Merged #43, providing 10X processing mode.

v3.3.1

• Fixed samtools installation tests

v3.2.2

Update htslib version to bring CGP stack in line

v3.1.1 - Dependancy correction

Fixes a missing dependancy only seen for those installing alleleCount without other elements of the cancerit stack.

v3.1.0 - Release gender integration

Minor release adding some functionality migrated from other projects into this more appropriate package.

v3.0.1 - htslib upgrade / legacy removal

• Removes dependancy on legacy versions of samtools in perl code.
• Upgrades to more recent version of htslib not requiring patch.

v2.2.0 - Added command line argument to filter on contig

• Added a contig filter commandline argument

V2.1.1 - bugfix release

Corrects failure to capture -q option in alleleCounter.pl - please note the C version (alleleCounter) is equivalent but much more efficient.

v2.1.0 Added htslib cram support with patch to htslib-1.2

Corrected bug in bam_access.c malloc where region wasn't allocated properly
Added patch to htslib-1.2 for full cram support (Resolves #9 )
Added version option to allelCounter c code commandline args