5.2.1

added condition to test vcf extension when bed file is absent

5.2.0

• added functionality to process bed file per chromosome
• progress file check during concatenation step ignores already processed chromosomes
• vcf file extension is optional if --bedOnly option is selected

Hotfix-5.1.3

• Fixed broken INFO tags in vcf and tsv
• tags -t option is now only applicable to tsv file

Hotfix-5.1.2

forced default shell to bash for system command

5.1.1

updated sort command to custom sort -k1,1 -k2,2n -k4,5

5.1.0

User can now run per chromosome analysis [useful to run in parallel ] and concatenate the resulting files

Works with mixed read length and amplicon

• Removed exonerate parameter to filter alignments based on score
• Removed condition to discard alignment length smaller than read length
• Added user defined option to specify exonerat percent value
• Increased padding to extended reference sequence -- this will allow to map longer reads in amplicon data.

4.5.6

• added HDR parameter to cgpvaf
• Updated version of vafCorrect to install correctly
• Fixed version of Bio::DB::HTS to 2.3
• Fixed version of htslib to 1.3.2

Hotfix release - updated version tag

4.5.5

updated version tag

Optional HDR region bed file

removed default files used by -hdr option and it is now optional to provide this file