Version 0.18.0

What's Changed

Features and changes

• Caller:
  • VCFs include variant type (snv or str) and, for STRs, include read-level data and SNV support count
  • VCF alts now properly set the anchor (5') base if different from the reference, or are * if completely deleted
  • VCF no longer includes an unused header line
• MI:
  • A STRkit VCF calculator is now included
  • A length-based LongTR VCF calculator is now included
  • A calculator for TRGT is now included
  • Excluded regions/calls are now handled via overlap instead of exact match
  • More in-progress data is now logged
  • Renamed --trf-bed option to --motif-bed

Bug fixes

• Caller:
  • fix(call): update strkit_rust_ext to 0.17.0 to fix --use-hp
  • fix(call): errors from offsetting the entire flank seq
• MI:
  • fix(mi): properly subtract sex chromosomes for autosome-only MI calc
  • fix(mi): vcf off-by-one issues for expansionhunter + gangstr
  • fix(mi): an issue with the Straglr calculator

Performance

• Caller:
  • More code has been moved to Rust
  • libdeflate is now used for reading BGZF files, which should be significantly quicker
  • Decoding CIGARs and finding alignment pairs are marginally quicker via better Numpy use
  • A few other minor performance changes in terms of memory and runtime
• MI:
  • perf(mi): close VCFs earlier when getting contigs

Full Changelog: v0.17.1...v0.18.0