5.7.4

• Fix and update Dockerfile

5.7.3

• Exit with a clearer error message when file does not pass the minimum read threshold
• Update and fix Dockerfile
• Update setup script

5.4.0

• Reduced memory footprint for augment vcf file
• Augmentation can now run per chromosome
• SAM flag filters are now controlled by vafConstantas.pm file
• .bas file now used by default to calculate library size
• added support for cram files

Hotfix - 5.3.9

• Change max reads read when determining read length to 50k
• Modify _get_bam_header_data to get the max read length of ALL bam files encountered and therefore to produce the correct lib_size
• Converted internal SAM flag constants to point to Bio::DB::HTS constants (in the future internal constants could be replaced)
• Added command line options for filter include and exclude of reads when checking read length
• Added very simple test for _get_bam_header_data
• All contribute to fixing #45
• All hard tabs now spaces. Fixes whitespace part of #49

Hotfix-5.3.8

corrected condition in cgpvaf.pl for erroneous PASS flag setting, analysis results were not affected

Hotfix-5.3.6

• Correct query_full to ensure undef return is caught.
• VAF output precision raised from two to four decimal places.

5.3.5 - tabix query hotfix

v5.3.5

• Update samtools and hstlib to v1.7
• Update Bio::DB::HTS to v2.10
• Change tabix->query call to tabix->query_full
• fixed bug in accessing chr prefixed chromosome names for HDR regions

5.3.4

• corrected typo in setup.sh removed safelist branches from .travis
• Added checks for INST_METHOD
• Changed CHANGES.md syntax to markdown linter
• Exonerate install is now skipped if INST_METHOD is 2
• Documentation changes ONLY.

Bugfix 5.3.2

Fixed deletion mismatch bug: Reads in the deletion region were incorrectly assigned to unknown(UNK) read category if a read has mismatch in the 3 prime region* from the deletion position [*region length = deletion length].

Hotfix-5.2.2

• Header line for SAMPLE tag in VCF is now generated from command line parameters
• Fixed bug for missing header data when running with bedonly option