openvax / varcode / 24684481501
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Unify Outcome contract + SV annotator MutantTranscript (closes #339 #335 #338 #340 #337 #336) (#342)

* Unify Outcome.effect contract across SV + splice (#339)

Every MultiOutcomeEffect now yields Outcome(effect=<MutationEffect>, ...)
so downstream consumers can iterate outcome.effect.short_description
and outcome.effect.mutant_protein_sequence uniformly without branching
on whether the underlying producer is a StructuralVariantEffect, a
SpliceOutcomeSet, or an ExonicSpliceSite.

- Add PredictedIntronRetention and PredictedCrypticSpliceSite effect
  classes so SpliceOutcomeSet stubs (previously coding_effect=None)
  still satisfy the MutationEffect interface.
- Add description: Optional[str] field to Outcome for human narratives
  distinct from effect.short_description (the HGVS-style label).
- Override SpliceOutcomeSet.outcomes and StructuralVariantEffect.outcomes
  to attach splice_outcome / sv_type evidence and description.
- Simplify candidate_proteins and mutant_protein_sequences on
  SpliceOutcomeSet via a shared _protein_str helper.
- SpliceCandidate stays as the public back-compat surface; its shape
  and serialization are unchanged.

* SV annotator emits MutantTranscript with reference_segments (#335)

Every StructuralVariantEffect subclass now carries a MutantTranscript
describing the rearranged allele. Before this change, SV effects
exposed no cdna_sequence or ReferenceSegment shape, so downstream
tools that wanted to read the fused/deleted/duplicated cDNA had to
recompute it themselves.

- Add mutant_transcript= kwarg to StructuralVariantEffect +
  LargeDeletion + LargeDuplication; wire through the annotator.
- Add _build_{deletion,duplication,inversion,fusion,translocation}_
  mutant_transcript helpers that construct the segment layout and
  populate cdna_sequence where derivable from cached cDNA (DEL / DUP).
- INV, BND→fusion, and BND→translocation get the segment shape but
  cdna_sequence stays None; sequence assembly for these lands in... (continued)
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