1.6.1

Bug Fixes

• Percent-encode INFO string values per VCF 4.3 spec (#15) (636026f)

1.6.0

Features

• Use reference FASTA sequence dictionary for VCF header contigs (#14) (8501d30)

Miscellaneous Tasks

• Bump the github-actions group with 3 updates (#8) (e058d70)
• Bump rapidfuzz in the python-runtime group (#9) (6783e2e)
• Bump the python-dev group with 2 updates (#10) (5cf7fe2)
• Bump the python-dev group with 2 updates (#13) (3a728ff)
• Bump astral-sh/setup-uv in the github-actions group (#12) (3113077)
• Bump pysam in the python-runtime group (#11) (451c10d)
• Regenerate lockfile for 1.6.0 (3cd1916)

1.5.0

Bug Fixes

• Resolve the mitochondrion in a UCSC reference FASTA (#7) (357de6c)

Features

• Emit UCSC chr-prefixed contigs by default (#6) (e49b304)

1.4.0

Bug Fixes

• Honor chain strand and default liftover-fail to lenient (#5) (d3c56c5)

1.3.0

Documentation

• Use the extensionless PyPI badge URL to refresh camo cache (da4ed5d)

Features

• Default-strict liftover and reference validation (#4) (da1a3d0)

Miscellaneous Tasks

• Remove template CLAUDE.md scaffold (f2e0adf)

1.2.0

Miscellaneous Tasks

• Bump astral-sh/setup-uv (#1) (3f5cf68)
• Bump the python-dev group across 1 directory with 4 updates (#3) (78b9214)
• Bump defopt in the python-runtime group across 1 directory (#2) (9417c58)

1.1.0

Documentation

• Simplify README/CONTRIBUTING (2dba8e4)
• Drop the redundant note about bgzip output (b3d7f1c)

Features

• Use hg38/hg19 as the primary --build keys with GRCh aliases (5cad265)
• Emit bgzipped, tabix-indexed VCF for .gz output paths (6504b47)

Miscellaneous Tasks

• Update uv.lock for 1.1.0 (8fd2ba1)

1.0.0

Bug Fixes

• Map CCLE numeric sex chromosomes and drop off-contig records (2b12e7c)

Documentation

• Document usage with a MOLT-4 example (b45a04c)
• Use --reference in the example and drop the redundant human-only note (1a5a3b1)
• Simplify README (b37d5b5)
• Lead installation with the PyPI release (a1fce27)

Features

• Generate truth-track VCFs for CCLE cell lines (c5db5fc)
• Suggest close cell-line names when a query does not resolve (7e00c6f)
• Record the pre-liftover locus in an ORIGINAL_LOCUS INFO field (c394f26)

Miscellaneous Tasks

• Scaffold cellme from fulcrumgenomics/python-template (6887c93)

Testing

• Cover builds, cell-line resolution, and VCF construction (4ad8b14)

Ci

• Harden code-checks workflow permissions and checkout (2e9a163)
• Add tag-triggered PyPI trusted-publishing workflow (e42381b)
• Bump pypi-publish to v1.14.2 for Metadata-Version 2.5 support (45c2e19)
• Pin pypi-publish to the v1.14.2 commit sha, not the tag object (38c3c54)
• Give git-cliff a token and pull-requests read scope (7129f66)