Skip to content

Releases: cancerit/alleleCount

v4.2.1: htslib 1.11+libdeflate

17 Nov 18:25
Compare
Choose a tag to compare
  • Correct htslib install for container
  • add libdeflate via base container
  • standardise install methods

v4.0.0 - fragment based counting

06 Mar 11:23
77ee1f1
Compare
Choose a tag to compare
  • 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

24 Jul 14:03
Compare
Choose a tag to compare
  • Fixed samtools installation tests

v3.2.2

01 Feb 10:04
Compare
Choose a tag to compare

Update htslib version to bring CGP stack in line

v3.1.1 - Dependancy correction

01 Jul 10:43
Compare
Choose a tag to compare

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

v3.1.0 - Release gender integration

01 Jul 10:44
Compare
Choose a tag to compare

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

v3.0.1 - htslib upgrade / legacy removal

30 Mar 13:52
Compare
Choose a tag to compare
  • 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

23 Mar 11:30
Compare
Choose a tag to compare
  • Added a contig filter commandline argument

V2.1.1 - bugfix release

20 Jul 08:37
Compare
Choose a tag to compare

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

14 Apr 09:26
Compare
Choose a tag to compare

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