v2.5.0

Major Changes

• New definition of "sync groups" (complex variants) when attributing credit to variants. The new definition will break dependencies if the selected (rather than all possible) backtracking path(s) pass(es) through the reference diagonal. As a result, there should be more smaller sync groups, and fewer partial credit calls.
• Precision-recall backtracking algorithm now maximizes TP calls
• Removed the -s, --smallest-variant option. It offers no runtime benefits and will negatively impact performance (since small variants are prematurely filtered, they cannot be found equivalent to remaining variants). Instead, stratify variants after benchmarking or adjust the --sv-threshold and -l --largest-variant parameters to evaluate the desired variants.

Minor bugfixes

• Fixed an erroneous return instead of break statement that caused segfaults in v2.4.0 when using --cluster gap or --cluster size.
• Fixed a logical error that caused left_reach and right_reach to not be calculated for the first and last clusters on a contig, resulting in incorrect superclustering.