v2.6.4

Minor fix in output file header

• Fix ERRTYPE vs ERR_TYPE inconsistency by @JosephLalli in #42

v2.6.3

Bug fixes related to CHM13

• VCF and FASTA sequences are now converted to uppercase, closes #40
• no error raised when end of sequence is reached (caused by deletion near end of FASTA), closes #38

v2.6.2

Fix segfault when splitting superclusters on haploid genome

• Fixes #39

v2.6.1

Fix WFA error when variant is at end of contig

• fixes #38

v2.6.0

Add --max-supercluster-size option

• Previously, supercluster size can blow up in regions with high-density variations, with no upper restrictions on size.
• This caused an explosion in required RAM and runtime, causing vcfdist to crash. There was no way to evaluate these regions.
• This release limits maximum supercluster size by providing a --max-supercluster-size parameter

v2.5.3

Fix variant clustering near contig edge

• Fixed #28, an out-of-range error when the clustering alignment algorithm goes off the end of a contig

v2.5.2

Bugfix in alignment distance

• fixed indexing error (#27) in --distance option causing large RAM usage

v2.5.1

Minor bugfixes

• realignment options -rq and -rt no longer cause timer crashes
• fixed off-by-one error in --distance causing additional edits

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.

v2.4.0

Major changes

• changed handling of BED regions (see wiki) to exclude variants on border, necessary to be consistent with Truvari and how ground truth BEDs were generated

Minor updates

• added -lm and -lstdc++ during linking, which should allow clang++ compilation (working towards bioconda release)
• removed libstdc++fs dependency (further increasing compatibility)