Version 0.5.0 alpha 3

• feat[mi]: add optional multiple testing correction
• chore[viz]: switch to proper release of igv.js
• lint[mi]: missing __all__ declaration for strkit JSON MI calc

Version 0.5.0 alpha 2

• fix[call]: fix error preventing TSV output

Version 0.5.0 alpha 1

• feat!: more compact JSON representation
• chore!: bump min. Python version to 3.8
• feat[mi]: chi-squared test for de novo mutation based on read counts
• feat[mi]: support for MI reports from STRkit JSON files; required for chi-squared testing

Version 0.4.0

• feat[call]!: new JSON report format for calling output, with parameters/runtime/indentation
• feat[call]: tweaked calling approach
  • use flanking data from both sides at once
  • filter out low-confidence reads for better ONT calling; threshold controlled by --min-avg-phred
  • optional fractional repeat calling mode (at beginning or end of repeat)
  • replace low-confidence bases with wildcards
  • extend boundaries of TR region slightly to detect more indels
• fix[call]: some off-by-one errors
• perf[call]: use numpy methods in more places

Version 0.4.0-rc.3

• feat[call]!: new JSON report format
• feat[call]: extended boundaries from ref to detect mapped inserts/deletes in more places
• feat[call]: replace low-confidence bases with wildcard in TR candidates
• revert[call]: (from 0.4.0-rc.2) turn off fractional calling by default and restore old int functionality
• feat[viz]: support for fractional repeats in browser
• fix[call]: an off-by-one error when getting flanking sequences
• perf[call]: a few performance improvements with numpy
• chore: update minimum required dependencies

Version 0.4.0-rc.2

• fix: PyPI release

Version 0.4.0-rc.1

• feat![call]: tweaked calling approach
  • features:
    • fractional copy number calling
    • (hopefully) improved high-error read support
    • (hopefully) better small mis-alignment handling
• adds --min-avg-phred and --integer options to strkit call
• feat[call]: indent JSON output for caller reports by default
• fix[call]: off-by-one error when fetching reference TR sequence
• perf[call]: wrong variable used to limit search direction when calling read copy number

Version 0.3.0

• feat[mi]: JSON report generator for + --no-tsv suppression flag for stdout
• feat[call]: allow pooling reads from multiple read files
• chore[mi]: use --trf-bed to filter loci if specified for all callers
• fix[mi]: fix handling of missing calls in VCF for gangSTR

Version 0.3.0-rc.4

• fix[mi]: fix handling of missing calls in VCF for gangSTR

Version 0.3.0-rc.3

• chore[mi]: use --trf-bed to filter loci if specified for all callers