Version 0.25.0 alpha 2

What's Changed

Features and changes

• Caller:
  • Add catalog loci count + hash to VCF and JSON output
  • Add annotation feature to report GFF3-STR overlaps (#18); specifiable via --annotation-file
  • Add SPOA as a POA implementation + parameterize POA implementation (--poa) for STR consensus sequences
  • Add an option to require only one full flank sequence (--allow-only-one-full-flank)
  • Parameterize --significant-clip-threshold for read trimming during SNV finding
  • Deprecate --hq – this functionality is now enabled by default; --force-gm-filter can disable it again.
  • Expose --gm-filter-expansion-ratio parameter for controlling allele call filtering when one peak looks like a possible expansion.
• Converter:
  • Add TRF .dat -> .bed converter (#19)
  • Add sort flag for position-sorted output (#20)
  • Improve TRGT converter
• Web visualization:
  • Add argument to specify a port other than the default (--port, default is 5011)

Performance

• Caller:
  • Rewrite some locus-calling process functions in Rust
  • Small improvements with Python-Rust data round-tripping
  • Various import optimizations to slightly reduce memory usage
  • Small logging performance improvements

Bug Fixes

• Caller:
  • Prevent --min-allele-reads from being above --min-reads
  • Fix an incorrect IUPAC code
  • Validate locus BED files have at least 4 columns

Styling

• Web visualization:
  • Italicize the k in k-mer

Known Issues

• Locus catalog hashes appear to be unstable

Full Changelog: v0.25.0-alpha.1...v0.25.0-alpha.2

Version 0.25.0 alpha 1

What's Changed

Features and changes

• Caller:
  • Add catalog loci count + hash to VCF and JSON output
  • Parameterize --significant-clip-threshold for read trimming during SNV finding
• Web visualization:
  • Add argument to specify a port other than the default (--port, default is 5011)

Performance

• Caller:
  • Rewrite some locus-calling process functions in Rust
  • Various import optimizations to slightly reduce memory usage
  • Small logging performance improvements

Styling

• Web visualization:
  • Italicize the k in k-mer

Full Changelog: v0.24.2...v0.25.0-alpha.1

Version 0.24.2

What's Changed

Fixes

• Caller:
  • fix pickling error with STRkitAlignedCoords – addresses error mentioned in #14 (comment)

Full Changelog: v0.24.1...v0.24.2

Version 0.24.1

What's Changed

Fixes

• Caller:
  • fix(call): locus_def access issues in realign (fixes #14)
• JSON:
  • fix(json): fix numpy c contiguous errors with indented json output

Misc.

• chore: add python 3.13 classifier

Full Changelog: v0.24.0...v0.24.1

Version 0.24.0

What's Changed

Features and changes

• Caller:
  • Address #13 via new locus IDs and VCF features:
    • Add a new catalog format (backwards compatibility is maintained) for specifying a locus ID
    • Specify a default ID format of locus# where # is the 1-based index of the locus in the catalog file
    • Add BED_START and BED_END INFO fields to VCF output
    • Further document coordinate extension and --respect-ref flag behaviour
• Pathogenic locus catalog
  • Update catalog to include locus IDs
  • Fix web rendering

Full Changelog: v0.23.0...v0.24.0

Version 0.23.0

What's Changed

BREAKING

• New minimum required Rust version for compilation: 1.85.0

Features and changes

• Caller:
  • feat(call): new ploidy representation by @davidlougheed in #11
  • more VCF information in header - source=strkit, phasing=partial, strkitVersion
  • better locus validation
  • various performance improvements, especially with BAM file loading and data passing
  • new user-tuneable parameters (see documentation)
  • JSON and log output now contains average read coverage
• Convert:
  • feat(convert): revive converter with revised/more options by @davidlougheed in #10
• Visualization:
  • feat(viz): add toggle kmer collapse checkbox
  • feat(viz): add aliases for visualize command
  • style(viz): increase visualizer font sizes

Fixes

• Caller:
  • Fix an issue with using the wrong normalized contig name in one place
  • Fix a sporadic issue with non-contiguous numpy arrays
• Mendelian inheritance calculators:
  • fix(mi): update straglr MI calculator columns
• Visualization:
  • fix(viz): misc issues with old visualize fn

Dependencies

• Allow newer versions of some dependencies
• Updates the strkit_rust_ext version

Documentation

• Miscellaneous documentation improvements

Full Changelog: v0.22.0...v0.23.0

Version 0.23.0 alpha 6

• feat(viz): add toggle kmer collapse checkbox
• fix(viz): misc issues with old visualize fn
• style(viz): increase visualizer font sizes
• chore(call): another revert to diagnose genotyping regression

Full Changelog: v0.23.0-alpha.5...v0.23.0-alpha.6

Version 0.23.0 alpha 5

• chore(call): try to fix genotyping quality regression
• docs: mention caveat of SNV mode

Full Changelog: v0.23.0-alpha.4...v0.23.0-alpha.5

Version 0.23.0 alpha 4

• chore(call): disable some possibly suspicious perf optimizations
• chore(call): more debug haplotag logging
• refact: consistent main logger get behaviour with log level

Full Changelog: v0.23.0-alpha.3...v0.23.0-alpha.4

Version 0.23.0 alpha 3

• feat(call): output average read depths overall and per-contig in JSON report
• chore(call): log when profiling is enabled
• fix(mi): update straglr MI calculator columns
• chore(mi): log execution of caller

Full Changelog: v0.23.0-alpha.2...v0.23.0-alpha.3