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

Version 0.13.1

• fix(call): VCF output with --respect-ref

Full Changelog: v0.13.0...v0.13.1

Version 0.13.0

• feat(call)!: don't include needless suffix sequences in VCF output
• feat(call): write unphased SNVs to VCF
• fix(call): fix pyFAMSA crash when generating consensus sequences
• fix(call): handling of selecting median-peak standard deviation and weights (impacted peak assignment)
• fix(call): auto-kill zombie progress processes
• docs: beginnings of output documentation

Full Changelog: v0.12.0...v0.13.0

Version 0.12.0

What's Changed

• refact(mi)!: remove re-call MI calculators
• feat: basic VCF output using --vcf
• feat: optional allele consensus calculation using --vcf or --consensus
• fix(mi): tandem-genotypes MI calculation crash
• chore(mi): remove unimpl. hipstr from list of MI callers available

Full Changelog: v0.11.8...v0.12.0

Version 0.12.0 alpha 1

• fix(mi): tandem-genotypes MI calculation crash for real this time
• refact(mi)!: remove re-call MI calculators
• chore(mi): remove unimpl. hipstr from list of MI callers available

Full Changelog: v0.11.8...v0.12.0-alpha.1

Version 0.11.8

• fix(mi): handle null genotypes from Tandem-genotypes correctly (pt. 2)

Full Changelog: v0.11.7...v0.11.8

Version 0.11.7

• fix(mi): handle null genotypes from Tandem-genotypes correctly
• chore: update dev dependencies

Full Changelog: v0.11.6...v0.11.7

Version 0.11.6

• fix(mi): incorrect MI% plus/minus 1 copy value in MI report histogram

Full Changelog: v0.11.5...v0.11.6