Bugfix release 4.1.1

Fixed bug introduced during object oriented conversion, it was never in the original production release 3.2.x

4.1.0

Object oriented codebase
Contains pre-calculated VAF values in FORMAT field for both augmented and consolidated output
Easy to submit farm jobs since per sample commands were now written into separate file.
Unmatched normal is now automatically linked if it resides in another project
Progress is tracked per chromosome which means failed jobs can be resumed from last unsuccessful chromosome.

4.0.0

Object oriented codebase
Contains pre-calculated VAF values in FORMAT field
Easy to submit to farm as per sample commands were now written into separate file.
Unmatched normal is now automatically linked across the projects
Progress is tracked per chromosome which means failed jobs can be resumed from last unsuccessful chromosome.

3.2.4

Added condition to check variant that fall at the end of a chromosome

3.2.3

Added option to create config file for user defined list of samples

3.2.2

Added .BAS file symlink generation

3.2.0

Added per nucleotide count, mutant base is counted only if it matches with original caveman call.

3.1.0

Added x10 specific result type for BAM, added additional reference genome constant for x10

3.0.0

Updated ref pos calculation for inserted bases where tandem duplication causing lot of ambiguous reads

2.7.0

1. Released new bug fix for vcfCommons — BUG: When both the reads from a pair are mapped on different strand at same variant location those reads were counted twice towards total count for either REF or ALT allele.
   This bug has now fixed and only read with best alignment [ based on distance of variant position in a read] on one of the strand is counted towards total count.
2. Log is now written in a log file created in the user’s working directory.