25587312529
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Ran 09 May 2026 01:14AM UTC

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Build # 25587312529

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push

github

Committed by

iskandr

Commit Message

Bump version to 4.19.0

Adds germline-aware effect prediction (#268, via #360):

- New public API: GermlineContext (#359, in 4.18.0); apply_germline_to_transcript,
  predict_germline_aware_effect, enumerate_phase_hypotheses, detect_loh,
  default_germline_window, PhaseHypothesis (this release).
- New effect class: PhaseAmbiguousEffect (MultiOutcomeEffect subclass)
  for the unknown-phase-codon-overlap case. Per-haplotype outcomes carry
  haplotype / phase_state / germline_variants in evidence so RNA evidence
  (#259) and other axes align by haplotype tag.
- New kwargs: Variant.effects(germline=...), VariantCollection.effects(
  germline=..., validate_reference=...).
- LOH detection: effect.is_loh = True when a 'somatic' call shares
  position+alt with a germline het.
- Sparseness propagation: SPARSE / HOTSPOTS_ONLY contexts mark effects
  with germline_unknown=True when the somatic's window has no germline
  calls (absence-as-unknown rather than absence-as-ref/ref).
- Cross-VCF build mismatch: GenomeBuildMismatchError raised at
  VariantCollection.effects(germline=ctx) before annotation begins;
  opt out via validate_reference=False.

Back-compat: germline=None (default) is byte-identical to today's
reference-relative behaviour. Full suite: 1114 passed, 2 skipped.

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