VCF support for RLE and fix to same-as-reference allele normalization to RLE#589

Merged

theferrit32 merged 42 commits intomainfrom

issue-577-VCF-RLE

Dec 15, 2025

Commits on Oct 15, 2025

Initial revision of ReferenceLengthExpression in VCF annotator
theferrit32
committed
No longer need FieldName.default_value since we can rely on pysam
theferrit32
committed

Commits on Oct 16, 2025

Commits on Oct 22, 2025

Adding some tests
theferrit32
committed

Commits on Nov 11, 2025

Commits on Nov 12, 2025

Commits on Nov 17, 2025

Merge remote-tracking branch 'origin/main' into issue-577-VCF-RLE
theferrit32
committed

Commits on Nov 18, 2025

Reset casettes for RLE tests after merge from main
theferrit32
committed

Commits on Nov 20, 2025

Commits on Nov 26, 2025

Do not normalize same-as-ref. Further refactoring and documentation in _normalize_allele. More tests
theferrit32
committed

Commits on Dec 3, 2025