Version 0.21.0

What's Changed

Features and changes

• Caller:
  • feat(call): output read- and locus-level mean align scores
• MI calculators:
  • feat(mi): add --mismatch-out-mi for controlling MI locus output

Fixes

• Caller:
  • fix(call): bad log message for really bad align time

Dependencies

• Allow PySAM 0.23 and SciPy 1.15

Full Changelog: v0.20.0...v0.21.0

Version 0.21.0 alpha 2

• feat(call): output read- and locus-level mean align scores
• fix(call): bad log message for really bad align time

Full Changelog: v0.21.0-alpha.1...v0.21.0-alpha.2

Version 0.21.0 alpha 1

• feat(mi): add --mismatch-out-mi for controlling MI locus output

Full Changelog: v0.20.0...v0.21.0-alpha.1

Version 0.20.0

What's Changed

Features and changes

• chore!: remove Python 3.9 support
• Caller:
  • feat(call): don't skip supplemental reads by default
  • feat(call): output alt consensus method with VCF
  • chore(call): parametrize --max-rcn-iters
  • chore(call): better read repeat count log msg
  • chore(call): tweak logic for starting count offsets
• MI calculators:
  • feat(mi): add generic VCF length-based calculator
  • feat(mi): add STRdust alias for generic VCF calculator
  • feat(mi): sequence-wise MI calculations
  • chore(mi): log all MI values progressively
  • chore(mi): use copy n. for TRGT vs. allele lengths

Fixes

• Caller:
  • fix(call): properly handle n_alleles=0

Performance

• Caller:
  • feat(call): subset reads with long tracts for consensus
• MI:
  • perf(mi): (maybe) slight perf increase for overlaps

Full Changelog: v0.19.0...v0.20.0

Version 0.19.0

What's Changed

Features and changes

• Caller:
  • VCFs now include a larger section of upstream sequence, which can capture some misaligned indels
  • Log strkit_rust_ext version

Fixes

• Caller:
  • fix(call): logic error with flank seq trimming
  • fix(call): consistent VCF allele sorting
  • fix(call): correct logic for ref extension

Performance

• Caller:
  • perf(call): move duplicate function def to Rust
  • Update strkit_rust_ext - gives newer, faster libdeflate

Full Changelog: v0.18.0...v0.19.0

Version 0.19.0 alpha 1

• feat(call): include larger VCF anchors - capture 5' variation
• fix(call): logic error with flank seq trimming
• fix(call): consistent VCF allele sorting
• fix(call): correct logic for ref extension
• perf(call): move duplicate function def to Rust
• perf(call): update strkit_rust_ext to 0.18.1 - gives newer libdeflate
• chore(call): log strkit_rust_ext version

Full Changelog: v0.18.0...v0.19.0-alpha.1

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

Version 0.18.0 alpha 5

• feat(call): output read-level copy number histograms in VCF
• perf(call): reduce more import memory usage
• minor refactors

Full Changelog: v0.18.0-alpha.4...v0.18.0-alpha.5

Version 0.18.0 alpha 4

• fix(call): missed refactored import

Full Changelog: v0.18.0-alpha.3...v0.18.0-alpha.4

Version 0.18.0 alpha 3

• perf(call): lower mem with specific importing + early deleting

Full Changelog: v0.18.0-alpha.2...v0.18.0-alpha.3