- WIT-67 Added per-sample overall Base level stats
- WIT-77 Added binning for Insertions based on insertion size. Binning is done only for stats generation. Evaluation is still similar to BreakEnds where there is no size consideration, only the insertion point.
- WIT-81 Output tags, even if they're missing a value
- WIT-85 In the stats.json, output an OverallStats section for each VariantType that adds stats across all bins to help address WIT-84
- WIT-63 ref call (0/0) is counted as FP instead of NotAssessed
- WIT-64 For CNV/DUP/DEL variants with a CN field but given a missing value (dot) should be ignored and annotated as NotAssessed instead of crash, other variants should ignore CN information.
- WIT-66 When CN with a valid number is specified in the entry, it should be treated as CNVs even when SVTYPE is DEL/DUP etc
- WIT-69 Wow tag was a flag in INFO field when no overlapping (should be a missing value string, aka dot).
- WIT-73 Variant length calculation is off-by-one
- WIT-82 Base-level FP stats count some coordinate regions multiple times
- WIT-83 base-level stats are incorrect because coordinate merging did not consider whether regions were on different contigs
- WIT-84 Base-level stats summaries will have some regions counted more than once