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v4.3.0

  • Add script to convert allelecount output to JSON

v4.2.1

  • Update so docker and native install use same install scripts behind the scenes
  • Docker now actually has htslib 1.11
  • htslib compiled with libdeflate for improved performance

v4.2.0

  • Updated to hstlib 1.11

v4.1.0

  • Created Docker file and build scripts to generate a containeraized code

v4.0.2

  • Added checking of iterator error codes when calling sam_itr_next

v4.0.1

Behaviour change

When the proper pair filter flag is used, this code now checks that the paired-end orientation is also used. This will mean that mate-pair orientation (F/F or R/R) will be rejected

  • Where a proper pair filter is used, now check for the correct paired-end orientation of F/R.
  • If this is not met the read is ignored.

v4.0.0

  • alleleCounter now counts per-fragment rather than per-read when overlaps occur.
  • Reworked perl to wrap C alleleCounter and just handle the extra format changes.
  • No dep on Bio::DB::HTS now.
  • Update to HTSlib 1.7
  • Merged #43, providing 10X processing mode.

v3.3.1

  • Fix setup.sh bug skipping samtools install

v3.3.0

  • Added -d commandline option. It triggers 'dense' mode. Best used where there
  • are many SNPs for example AscatNGS and Battenberg allelecount steps
  • Added -f commandline option. Flag value of reads to retain in allele counting
  • Added -F commandline option. Flag value of reads to exclude in allele counting

v3.1.0

  • Adds filter and keep flags commandline options for read filtering
  • Adds dense SNP option
  • Change install of Bio::DB::HTS to use fixed version of htslib and Bio::DB::HTS

v3.0.0

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

v2.2.0

  • Added contig filter commandline option

v2.1.0

  • Added version info to makefile and option to display to alleleCount C code.
  • Fixed bug in c code where region wasn't malloc-ing enough for the contig name.