Version 0.6.0 alpha 1

• fix[call]: error when running without counting k-mers
• change[call]: explicitly skip supplemental reads
• feat[call]: add optional local realignment step
• feat[call]: indicate in-region chimeral reads in JSON report
• chore[call]: improve some debug messages
• chore[viz]: finer increments for plotting Gaussians

Version 0.5.0

• feat![call]: more compact JSON representation
• chore!: bump minimum Python version to 3.8
• chore: update various dependency requirements
• feat: semi-'complete' catalog of pathogenic loci in HG38
• perf: optionally faster JSON (de)serialization via orjson; install with strkit[rustdeps] extra
• perf: improve startup performance especially on clusters
• feat[call]: hardcode OMP_NUM_THREADS setting before numpy import to ensure proper performance
• feat[call]: motif-length k-mer counting for alleles/reads to detect motif heterogeneity
• feat[call]: changed peak calling: tries to avoid assigning all reads to one peak
• feat[call]: add --seed command line argument to specify a random seed for replication
• feat[call]: add flag to turn off reference coordinate extension, which remains on by default
• feat[cli]: short flag aliases for various commands
• feat[cli]: version flag
• feat[mi]: chi-squared and Mann-Whitney U test for de novo mutation in trios based on read copy numbers
  • optional multiple testing correction flag
• feat[mi]: support for MI reports from STRkit JSON files; required for above testing
• feat[viz]: better rendering of Gaussian curves to fit to histogram bars
• feat[viz]: support multiple alignment files
• perf[mi]: try to reduce memory usage a bit
• chore[viz]: switch to proper new release of igv.js (v2.13.1)
• docs: improved documentation

Version 0.5.0 beta 4

• perf: move more importing into respective entry point functions for faster startup times
• fix[viz]: fix insertion popup styling in IGV.js

Version 0.5.0 beta 3

• feat[call]: add flag to turn off reference coordinate extension, which remains on by default
• feat[viz]: support multiple alignment files
• chore[catalog]: add more loci to pathogenic loci catalog
• chore: bump orjson and dev dependencies
• perf: move entry point imports into exec functions improve startup performance

Version 0.5.0 beta 2

• fix[call]: TypeError when encountering an uncalled locus
• chore: make orjson optional with a rustdeps extra
• refact: use more modern Python type hints

Version 0.5.0 beta 1

• docs: additions about possible analyses and usage
• feat: semi-'complete' catalog of pathogenic loci in HG38
• feat[call]: motif-length k-mer counting for alleles/reads to detect motif heterogeneity
• feat[mi]: add Wilcoxon-Mann-Whitney test option
• feat[call]: handle comments in locus files
• fix[call]: missing seed for re-caller

Version 0.5.0 alpha 7

• perf: switch to orjson for JSON (de)serialization
• feat[viz]: better rendering of Gaussian curves to fit to histogram bars
• fix[viz]: issue when loading igv browser
• chore[mi]: add help text for CLI --mt-corr flag (vs. earlier alpha)
• fix[call]: serialization error (vs. earlier alpha)
• chore: update Flask, scipy

Version 0.5.0 alpha 6

• fix[mi]: statistically suspicious resampling prior to x2 test
• fix[mi]: x2 test: don't use pseudocounts and properly remove bins instead
• perf[mi]: try to reduce memory usage a bit
• feat[call]: short flag aliases for CLI
• feat: add version command line flag

Version 0.5.0 alpha 5

• feat[call]: add --seed command line argument to specify a random seed for replicability

Version 0.5.0 alpha 4

• feat[call]: hardcode OMP_NUM_THREADS setting before numpy import to ensure proper performance
• feat[call]: better(?) peak calling by hand: tries to avoid assigning all reads to one peak
• chore[viz]: bump igv.js to 2.13.1
• docs: fix copyright, update OMP note, and add note on generating a compressed reference genome