Version 0.15.0 alpha 9

• perf(call): don't search candidates if we're at perfect score
• perf(call): search fewer candidates if close to best possible copy num
• chore(call): skip loci where ref flank has too many N
• chore(call): consistent logging with early locus skips

Full Changelog: v0.15.0-alpha.8...v0.15.0-alpha.9

Version 0.15.0 alpha 8

• fix(call): skip results which have None in peaks
• feat(call): quality checks on SNVs
• perf(call): don't search candidates if we're at perfect score

Full Changelog: v0.15.0-alpha.7...v0.15.0-alpha.8

Version 0.15.0 alpha 7

• feat!: only allow one BAM file + port more code to Rust
• feat(call)!: max reads param
• perf(call): early-skip loci with >3 reads with extremely poor (slow) alignment
• fix(call): bad logic for pure SNV peak assignment read threshold
• chore(call): eliminate abs min read threshold for SNV incorporation
• perf(call): small optimizations for lambdas
• Logging:
  • chore(call): log how many workers we start if >1
  • chore(call): log allele determining time for slow loci
  • chore(call): log # loaded loci

Full Changelog: v0.15.0-alpha.6...v0.15.0-alpha.7

Version 0.15.0 alpha 6

• fix(call): issues with SNV selection and phasing
• fix: don't attach multiple streams to process loggers
• chore(call): log assign time with long-running call message

Full Changelog: v0.15.0-alpha.5...v0.15.0-alpha.6

Version 0.15.0 alpha 5

• feat(call): output motif and ref copy num in VCF
• feat(call): output peak assign method in VCF
• feat(call): join/remap synonymous phase sets
• fix(call): vcf output with missed calls
• fix(call): don't output duplicate SNV alleles
• fix(call): handle empty allele with a warning
• fix(call): better contig format detection for snvs
• fix(call): use best representative sequence as a pseudo-consensus
• chore(call): set timeout on locks as a failsafe
• perf(call): use Rust component for cigar pair decoding
• perf(call): switch to strkit_rust_ext/numpy arrays for coords/consensus

Full Changelog: v0.15.0-alpha.4...v0.15.0-alpha.5

Version 0.15.0 alpha 4

• fix(call): handle bad allele list without crashing in VCF output
• chore(call): more robust logic for multiprocess queue handling
• chore: update dependencies

Full Changelog: v0.15.0-alpha.3...v0.15.0-alpha.4

Version 0.15.0 alpha 3

• feat(call): progressive output for TSVs/VCFs
• perf(call): faster performance using custom CIGAR decoder
• chore(call): log loci/second
• fix: docker image building

Full Changelog: v0.15.0-alpha.2...v0.15.0-alpha.3

Version 0.15.0 alpha 2

• chore: log version on command exec startup
• chore(call): only log warning if we don't have a set sample ID
• fix(call): properly wait for realign process to terminate on timeout

Full Changelog: v0.15.0a1...v0.15.0-alpha.2

Version 0.15.0a1

• refact(call)!: use params object for calling methods
• feat(call): optional incorporation of HP tags from haplotagged alignment
  • feat(call): if in haplotag mode, output phased VCFs
• feat(call): initial implementation of snv haplotype-block phasing
• perf(call): decode cigar optimization
• perf(call): upgrade strkit_rust_ext to 0.6.0
• fix(call): properly terminate realign process if it times out
• chore(call): tell user how to pass sample id manually
• chore: enable rustdeps in Dockerfile
• misc. documentation updates

Full Changelog: v0.14.0...v0.15.0a1

Version 0.14.0

• feat(call): add copy num and allele depth fields to VCF
• feat(call): output VCF to stdout if stdout is passed as filename
• feat: ci-built docker image
• docs: update info about writing output files

Full Changelog: v0.13.1...v0.14.0