As Truvari's adoption and functionality grows, we decided to spend time working on sustainability and performance of the tool. Multiple Actions for CI/CD have been added. Many components have been refactored for speed, and other 'cruft' code has been removed. Some of these changes (particularly the switch to using edlib for sequence similarity) affects the results. Therefore, we've bumped to a new major release version.

- Working on speed improvements
- Added edlib as the default when calculating pctseq_sim, keeping Levenstein as an option (--use-lev).
- truvari bench summary's gt_precision/gt_recall are replaced by gt_concordance, which is just the percent of TP-comp calls with a concordant genotype. --no-ref has better functionality. --giabreport is different.
- Added —keep common to truvari collapse, which allows one to choose to keep the allele with the highest MAC.
- truvari collapse --hap wasn't working correctly. The assumptions about the calls being phased wasn't being properly used (e.g. don't collapse 1|1) and the NumCollapsed was being populated before the single-best match was chosen. The latter is a reporting problem, but the former had an effect on the results with ~3% of collapsed calls being mis-collapsed.
- truvari anno trf is now faster and simpler in its approach and whats reported.. and hopefully more useful.
- truvari anno grm has min_size and regions arguments added.
- truv2df has become truvari vcf2df where the default is vcf conversion with options to run on a truvari bench output directory. It also allows a specific sample to be parsed with --format and better Number=A handling.
- NeighId added to truvari anno numneigh, which works like bedtools cluster.
- The method af_calc now makes MAC/AC.
- Added 'partial' to truvari anno remap.
- Added truvari anno svinfo.
- Removed truvari stats as truvari vcf2df is better and began building community-driven summaries.
- Ubiquitous single version.
- - Added a Dockerfile and instructions for making a Truvari docker container.
- Code and repository cleaning.
- Github actions for automated pylint, testing, and releases to pypi.
- Preserving per-version documentation from the wiki in docs/.