Version 0.18.0 alpha 2

• chore(deps): update strkit_rust_ext to 0.16.0
• document wheel build times in README

Full Changelog: v0.18.0-alpha.1...v0.18.0-alpha.2

Version 0.18.0 alpha 1

What's Changed

Features and changes

• Caller:
  • VCFs include variant type (snv or str)
  • 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 calculator for TRGT is now included
  • Excluded regions/calls are now handled via overlap instead of exact match

Bug fixes

• MI:
  • fix(mi): properly subtract sex chromosomes for autosome-only MI calc
  • fix(mi): vcf off-by-one issues for expansionhunter + gangstr

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
• MI:
  • perf(mi): close VCFs earlier when getting contigs

Full Changelog: v0.17.1...v0.18.0-alpha.1

Version 0.17.1

• chore: update Docker image to 3.12-bookworm
• chore(deps): bump strkit_rust_ext to 0.13.1
  • try to fix aarch64 docker build via using prebuilt strkit_rust_ext wheel
• docs: add links to zenodo record

Full Changelog: v0.17.0...v0.17.1

Version 0.17.0

• feat(call): output 95% CIs and supporting read depth in VCFs
• perf(call): don't start a new process for small realign jobs
• refact(call): use time.perf_counter for perf tracking
• chore(call): log adjusted read alignment score too
• chore(viz): update igv.js

Full Changelog: v0.16.0...v0.17.0

Version 0.16.0

• feat(call): parametrize minimum read alignment score
• fix(call): help text for --max-reads
• refact(call): use rust extension for repeat counting + best seq representative
• chore(call): shorter debug logs + log motif
• docs: rm outdated statement on JSON mem usage

Full Changelog: v0.15.0...v0.16.0

Version 0.15.0

What's Changed

Breaking changes

• The Rust component of STRkit is now required. Pre-built wheels of strkit_rust_ext for some platforms are provided, but otherwise you'll need the Rust toolchain to install STRkit 0.15+.
• Fractional TR genotype calling has been removed.
• Support for specifying more than one alignment file at a time has been removed.

Features and changes

• Caller:
  • Optional incorporation of haplotype-tagged reads from phased alignments
  • Phased blocks of SNVs for tandem repeat phasing
  • Progressive output for JSON, VCFs, and TSVs instead of storing all results in memory
  • Tweaked SNV incorporation logic
  • Added a minimum quality threshold for SNV incorporation
  • Better consensus sequence logic
  • More complete VCF output
  • Call reads with > max reads aligned reads (truncate to max reads reads)
  • Log current processing rate: # loci / second
• Visualization
  • chore(viz): disable search items which don't have calls for now
• Log version on startup

Bug fixes

• Caller:
  • Many important fixes for VCF output
    • fix(call): fix VCF output for alts with no common suffix
    • fix(call): handle bad allele list without crashing in VCF output
  • Fix many issues with reference repeat-counting logic
  • fix(call): properly wait for realign process to terminate on timeout
  • fix(call): better contig format detection for snvs
  • fix(call): bug with terminating progress worker (need to reset stuck count)
  • fix(call): mitigate potential divide-by-zero in locus logging
  • fix(call): using mix of process and main logger in SNV helpers
  • fix(call): properly use process worker, log more info about worker ID
  • fix(call): locking logic + SNV flip logic; make SNV calls tuples
  • fix(call): missing lock call for phase set counter
  • fix(call): missing peak k-mer calculation with SNV/HP peaks
  • fix(call): properly normalize peak weights from GMM medians
  • fix(call): fix peak calling from GMM parameters

Performance

• Caller:
  • Reduce reference sequence re-fetching / reference FASTA accesses
  • CIGAR decoding optimization
  • Repeat-counting optimizations
  • Maximum # of iterations for repeat-counting procedures
  • Approximate repeat counting for very large regions
  • Skip regions which take too long to repeat-count
  • Some memory usage improvements
• Misc. micro optimizations (lambdas, partial functions, etc.)

Documentation

• docs: mention installing as a docker container
• docs: clarify that --realign adds time
• docs: specify that BED file should be sorted
• docs: update alliance install instructions
• docs: mention ONT duplex data
• Update output format documentation

Full Changelog: v0.14.0...v0.15.0

Version 0.15.0 alpha 23

• fix(call): vcf output crash

Full Changelog: v0.15.0-alpha.22...v0.15.0-alpha.23

Version 0.15.0 alpha 22

• perf(call): update strkit_rust_ext to 0.12.2 for faster consensus
• feat(call)!: consensus method in JSON output + use best_rep for long TRs
• fix(call): small behaviour glitches in repeat counting
• chore(call): rm unneeded variable assignment
• refact(call): move call_alleles_with_gmm procedure to function

Full Changelog: v0.15.0-alpha.21...v0.15.0-alpha.22

Version 0.15.0 alpha 21

• fix(call): improved SNV peak calling with gaps
• perf(call): faster copy num exploration, esp. of large reference regions
• chore(call): increase queue size stuck limit
• fix(call): bad log message
• fix(call): snv print debugging

Full Changelog: v0.15.0-alpha.20...v0.15.0-alpha.21

Version 0.15.0 alpha 20

• fix(call): missing peak k-mer calculation with SNV/HP peaks
• fix(call): properly adjust ref sequences as a result of offset
• chore(call): debug log for read repeat counting
• perf(call): use offset from guess for successive read copy number det. + fix(call): better system for read guess offset using fraction of length
• perf: set true logger log level

Full Changelog: v0.15.0-alpha.19...v0.15.0-alpha.20