Truvari v3.1.2

[ACEnglish]

• 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

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This discussion was created from the release Truvari v3.1.2.