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

Version 0.15.0 alpha 19

• fix(call): get_repeat_count logic and performance
• fix(call): impose max iters on ref cn getter + fix ref cn logic
• fix(call): missing lock call for phase set counter
• fix(call): locking logic + SNV flip logic; make SNV calls tuples
• fix: use Union type hint for py3.9 compat
• chore(call): reduce a lock acquire timeout
• perf(call): fetch from ref FASTA 1-2 times per locus instead of 3-4
• perf(call): cache ref total seq for use in realign; log slow ref cn counting

Full Changelog: v0.15.0-alpha.18...v0.15.0-alpha.19

Version 0.15.0 alpha 18

• fix(call): using mix of process and main logger in SNV helpers
• fix(call): properly use process worker, log more info about worker ID
• chore(mi): adapt MI code to new main logger system + fix(mi): issues with logger from last refact
• perf(call): del jobs when finished with var

Full Changelog: v0.15.0-alpha.17...v0.15.0-alpha.18

Version 0.15.0 alpha 17

• fix(call): mitigate potential divide-by-zero in locus logging
• chore(call): handle otherwise-unhandled exceptions during locus calling
• chore(call): reduce locus counter lock timeout
• Logging:
  • chore(call): log more paths in locus worker fn
  • chore(call): log wording
  • chore(call): more locus call process logging

Full Changelog: v0.15.0-alpha.16...v0.15.0-alpha.17

Version 0.15.0 alpha 16

• perf(call): add get_repeat_count max iters
• perf(call): clean up some file objects in worker fn a bit earlier

Full Changelog: v0.15.0-alpha.15...v0.15.0-alpha.16

Version 0.15.0 alpha 15

• chore(call): resolve VCF reference path
• fix(call): issue with consensus fallback
• fix(call): bug with terminating progress worker
• chore(call): log # get_repeat_count iters
• chore(call): more specific debug log when outputting VCF

Full Changelog: v0.15.0-alpha.14...v0.15.0-alpha.15

Version 0.15.0 alpha 14

• fix(call): better multi-stage strategy for determining TR consensus seqs
• fix(call): null out call data on empty allele properly
• fix(call): better handle missing call data in VCF output
• chore(call): rm overly verbose log
• chore(call): log get_repeat_count time for pathological reads
• chore(call): more logging of pathological sequence information
• docs: update install info

Full Changelog: v0.15.0-alpha.13...v0.15.0-alpha.14

Version 0.15.0 alpha 13

• perf(call): skip loci with pathologically-poorly-aligning reads

Full Changelog: v0.15.0-alpha.12...v0.15.0-alpha.13