Strkit

* [fix(call): issues with SNV selection and phasing](https://github.com/davidlougheed/strkit/commit/2454cca9612920c00dfcf79ceeb5bf05b128e653)
* [fix: don't attach multiple streams to process loggers](https://github.com/davidlougheed/strkit/commit/6752876670083a000623159cdec6c26c4bb458f6)
* [chore(call): log assign time with long-running call message](https://github.com/davidlougheed/strkit/commit/837d69ad9cf74105b38c38510f25906adfe46ed4)

**Full Changelog**: https://github.com/davidlougheed/strkit/compare/v0.15.0-alpha.5...v0.15.0-alpha.6

* [feat(call): output motif and ref copy num in VCF](https://github.com/davidlougheed/strkit/commit/ffb9fc440bcd431bdd4ebc8a8cc4693772a80ae1)
* [feat(call): output peak assign method in VCF](https://github.com/davidlougheed/strkit/commit/f767b2ddb725b24091135632117f758e0d8c5201)
* [feat(call): join/remap synonymous phase sets](https://github.com/davidlougheed/strkit/commit/111bb7df14f1df718c9d526173fedd33822ebfa9)
* [fix(call): vcf output with missed calls](https://github.com/davidlougheed/strkit/commit/345e387edd5d1004d714514c817701f6fb2787c9)
* [fix(call): don't output duplicate SNV alleles](https://github.com/davidlougheed/strkit/commit/b76a83412568206154e888c1b9f53eeaf0287146)
* [fix(call): handle empty allele with a warning](https://github.com/davidlougheed/strkit/commit/6d494fcc27690aa7fac7a8c4c7f2a0fb309aa115)
* [fix(call): better contig format detection for snvs](https://github.com/davidlougheed/strkit/commit/a12dfc22641c25e1101a69532b81b6c2bf654e7a)
* [fix(call): use best representative sequence as a pseudo-consensus](https://github.com/davidlougheed/strkit/commit/2c63662dcf5bbbb3f13732894603630272a806fd)
* [chore(call): set timeout on locks as a failsafe](https://github.com/davidlougheed/strkit/commit/c6a7ff83009db4b6a8ebb37d2bbaab53b5b94822)
* [perf(call): use Rust component for cigar pair decoding](https://github.com/davidlougheed/strkit/commit/2e5eff53e4b9dcd2de9758d7ed64dd621401fb9e)
* [perf(call): switch to strkit_rust_ext/numpy arrays for coords/consensus](https://github.com/davidlougheed/strkit/commit/3ed408023f042c51e0ea09449c6fbf0b65187b00)

**Full Changelog**: https://github.com/davidlougheed/strkit/compare/v0.15.0-alpha.4...v0.15.0-alpha.5

* [fix(call): handle bad allele list without crashing in VCF output](https://github.com/davidlougheed/strkit/commit/e936745bfa3e0d6ff7e45bbd5e973d8d7a4c883e)
* [chore(call): more robust logic for multiprocess queue handling](https://github.com/davidlougheed/strkit/commit/92ef2d996eb5ed7693df78625d82f700bb7fb73e)
* [chore: update dependencies](https://github.com/davidlougheed/strkit/commit/5f70c6ef1c1565504b98ab3cd74edb2c5998ae6a)

**Full Changelog**: https://github.com/davidlougheed/strkit/compare/v0.15.0-alpha.3...v0.15.0-alpha.4

* [feat(call): progressive output for TSVs/VCFs](https://github.com/davidlougheed/strkit/commit/4339ed07e540791f46271d5c4546f26df8fc113f)
* [perf(call): faster performance using custom CIGAR decoder](https://github.com/davidlougheed/strkit/commit/bfaf99eed9558541ef35229aa608e492fdb80889)
* [chore(call): log loci/second](https://github.com/davidlougheed/strkit/commit/8f02ec595affb3e662431d7cb4d152f6d3811ec1)
* [fix: docker image building](https://github.com/davidlougheed/strkit/commit/eeda0b5c36460ff6573313ce6840f71640b0c13f)

**Full Changelog**: https://github.com/davidlougheed/strkit/compare/v0.15.0-alpha.2...v0.15.0-alpha.3

* [chore: log version on command exec startup](https://github.com/davidlougheed/strkit/commit/399a4b015111538580aaeb8a940e380942354c96)
* [chore(call): only log warning if we don't have a set sample ID](https://github.com/davidlougheed/strkit/commit/e7a545fb5b654bf34a609ad29c8bb68f59e6db0b)
* [fix(call): properly wait for realign process to terminate on timeout](https://github.com/davidlougheed/strkit/commit/63e1cff1fc8dca9e3c266088c88540b6c8871b30)

**Full Changelog**: https://github.com/davidlougheed/strkit/compare/v0.15.0a1...v0.15.0-alpha.2

* [refact(call)!: use params object for calling methods](https://github.com/davidlougheed/strkit/commit/d9999a0742e88758fe9c17f2b9d8d9905d294089)
* [feat(call): optional incorporation of HP tags from haplotagged alignment](https://github.com/davidlougheed/strkit/commit/71c2d7f7002f0cf9534520034729c9b079cc450a)
* [feat(call): if in haplotag mode, output phased VCFs](https://github.com/davidlougheed/strkit/commit/deaae645a68ab487316e58c99e5843d40b4cf802)
* [feat(call): initial implementation of snv haplotype-block phasing](https://github.com/davidlougheed/strkit/commit/a6770fb75ea376e8b7be50daac7f676ae4f31fbc)
* [perf(call): decode cigar optimization](https://github.com/davidlougheed/strkit/commit/efd538523fd194d5cf5900f93d531222abffe14c)
* [perf(call): upgrade strkit_rust_ext to 0.6.0](https://github.com/davidlougheed/strkit/commit/ee089b6e662f08528092ed4d7a69b5e9e69dd465)
* [fix(call): properly terminate realign process if it times out](https://github.com/davidlougheed/strkit/commit/6b267e14062218052780f06a94e0c51f9fe37f22)
* [chore(call): tell user how to pass sample id manually](https://github.com/davidlougheed/strkit/commit/4a8bd426d78b53decb2e664a5abfd66cb9402850)
* [chore: enable rustdeps in Dockerfile](https://github.com/davidlougheed/strkit/commit/4c6ef74a81e60f4a12f20d7a8de95adee90334a0)
* misc. documentation updates

**Full Changelog**: https://github.com/davidlougheed/strkit/compare/v0.14.0...v0.15.0a1