Truvari v3.2.0

• Removed truvari.copy_entry for pysam.VariantRecord.translate a 10x faster operation
• Faster truvari collapse (@c8b319b)
• When building MatchResult between variants with shared start/end positions, we save processing work by skipping haplotype creation and just compare REFs/ALTs directly.
• Updated documentation to reference the paper https://doi.org/10.1101/2022.02.21.481353
• New truvari anno density for identifying regions with 'sparse' and 'dense' overlapping SVs (details)
• Better bench genotype reporting with summary.txt having a gt_matrix of Base GT x Comp GT for all Base calls' best, TP match.
• New truvari anno bpovl for intersecting against tab-delimited files (details)
• New truvari divide command to split VCFs into independent parts (details)
• Replaced --buffer parameter with --minhaplen for slightly better matching specificity
• Bugfix - truvari anno trf no longer duplicates entries spanning multple parallelization regions
• Bugfix - collapse MatchId/CollapseId annotation wasn't working
• Bugfixes - from wwliao (@4dd9968 @ef2cfb3)
• Bugfixes - Issues #107, #108

Truvari v3.1.0

Expanded bench annotation and code re-usability

• Bench annotations are more informative and now placed on false positives/negatives as well.
• A new vcf iteration technique is faster and uses less memory.
• Improvements to the code's readability and expanded developer docs allows Truvari
  to be used not only as a tool, but as a library.

Full Updates

• https://github.com/spiralgenetics/truvari/wiki/Updates#truvari-31

What's Changed

• python-levenshtein: 0.12.1 -> 0.12.2 by @scalavision in #69
• Create CODE_OF_CONDUCT.md by @ACEnglish in #73
• Fix if condition by @wwliao in #79
• Remove redundant code by @wwliao in #81
• See wiki for full details

New Contributors

• @scalavision made their first contribution in #69
• @wwliao made their first contribution in #79

Full Changelog: v3.0.1...v3.1.0