# CHANGES

## NEXT

* 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

## 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.

# CHANGES

## NEXT

* 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

## 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.

Document change to alleleCounter behaviour
Document change to alleleCounter behaviour
