Support for phased genotypes

[0.10.0]

Added

• Support for phased genotypes

Changed

• Update GitHub actions automation workflows

Fixed

• IndexError when FORMAT fields contain only a single value

What's Changed

• Fix IndexError when FORMAT fields contain only a single value and support for phased GTs by @fellen31 in #106
• Update workflows by @dnil in #107
• Version 0.10.0 by @dnil in #108

Full Changelog: v0.9.5...v0.10.0

TRGT MotifCount, PathologicStruc and TRID parsing fixes

[0.9.5]

Added

• More tests for trgt repeats parsing

Changed

• Updated build actions, set Docker build provenance, use two-stage build and a non-root user for Docker image

Fixed

• Set STR_STATUS to most severe consequence for given repeat strings (TRGT decompose)
• More TRGT PathologicStruc locus annotations to demo resources
• Always check and export TRGT repeat keys as well
• Motif counts for TRGT alleles erroneously summed
• TRID for a couple of STRchive style entries with "_" need exact matching since the gene id alone is not unique

Fix bug with no ref on multi-allele TRGT FORMAT decompose

[0.9.4]

Fixed

• Bug with no ref on multi-allele FORMAT decompose

What's Changed

• Decompose missing ref by @dnil in #85
• bump to v0.9.4 by @dnil in #87

Full Changelog: v0.9.3...v0.9.4

`setuptools` import issue and switch build system to `uv`

[0.9.3]

Fixed

• Switch build system to uv-hatchling
• Version from importlib metadata

Fix output of multi individual format and unannotated loci

[0.9.2]

Fixed

• Use codecov badge and fix scout link on README page
• Added a test for TRGT MCs set to .
• Added CLI test for TRGT file
• Codecov upload hidden artifact issue
• Incorrect multisample, multiallele FORMAT output
• Write unannotated entries (not in definition file) to output (reverted to pre-0.9 behaviour)

v0.9.1

[0.9.1]

Added

• Added github action test and release workflows

Fixed

• Docs for TRGT annotation
• Fallback setting allele size to 0 if MC is only set to "." and TRGT annotation requested

Support for TRGT VCFs

[0.9.0]

• Add Docker image
• Parse TRGT VCFs - in particular, decompose and parse FORMAT.MC
• Bring in updated loci references from raredisese reference-files
• Fix processing TRGT VCFs with missing MC and TRIDs without underscore [#59(https://github.com//pull/59)
• Updates to pathogenic motifs for two loci: RFC1, RAPGEF2

Catalog patch DAB1, POLG

• Fix DAB1 pathologic repeat unit name Update POLG coords, quite a bit on hg38

Ob1 corrections, with a little help from my friends

[0.8.0]

Off by one error on PathogenticMin output. All affected have at least been cautioned pre_mutation with proper size.
Added script to check HGNCId-symbol correspondence against genenames.org.
Added script to compare two variant_catalogs and warn on disagreeing field items.
Sync min/max between hg19, hg38 for ATN1, DMPK, FMR1 and TBP.Update BEAN1 documentation reference.
Update PABPN1 source tag.
Update GLS and RFC1 hg19 coordinates (zero based off by one).
Update NIPA1 locus definition updating hg19 to the current ExHu one.
Update ARX and SOX3 0-based off by one. Usually unproblematic, but gives ugly gap on REViewer alignments.
Update HTT PathogenicMin and NormalMax so already reduced penetrance are pathogenic - and mark intermediate pre_mutation.
Update pathologic region annotation on (mostly hg38 liftOver) loci affecting alternate region naming for ATXN7, ATXN8OS, FXN, HTT, CNBP, NOP56.
Update DAB1 repeat unit (revcomp) and off by one coordinates.

Merge pull request #30 from moonso/release_v0.7.1

Increase rank score to get above CG default loading threshold.