- WIT-18 Added support for using a config file for per sv type settings in place of command line arguments for bin sizes, basepair distance, percent distance, included filters, excluded filters, and variant types.
- WIT-38 Added command line argument 'variantTypes' to allow for selection of variant types to include in analysis.
- WIT-43 Output INFO field deterministically.
- WIT-57 Added per-type sizes settings through config file.
- WIT-74 CN=. should be Not Assessed
- WIT-75 Update the stratification for CopyNumberVariant to split into CopyNumberGain and CopyNumberLoss
- WIT-89 Chromosomes in annotated vcf will be output in same order as query or truth, whichever is the superset. If neither is a superset, it will be output in alpha-numeric order.
- WIT-93 Unify names in WIN tag.
- WIT-95 Sample fields that consist of all MissingValue (.) will now be compacted to a single MissingValue (i.e. .:.:.:. becomes .)
- WIT-98 Support taking in a bed and only evaluating using that bed file.
- WIT-102 Insertions' default BPD changed to be 100bp instead of 500bp.
- WIT-105 Add API method to allow users to print out a single sample vcf of the result.
- WIT-108 Update PD default to be 0.25 instead of 0.05
- WIT-86 Fix bug with how complex indel END positions are calculated
- WIT-94 witty.er never outputs second breakend of pair in annotated vcf
- WIT-101 Evaluation of overlaps doesn't take into account PD and BPD of target
- WIT-103 Witty.er threw exception on ref sites.
- WIT-107 PD and BPD could be inconsistent between CIPOS and CIEND in some cases