openvax / varcode / 24755346503
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HaplotypeEffect + apply_variants_to_transcript (#269) (#353)

Third and biggest slice of #269. When a phase resolver (VCF PS tag,
Isovar assembly, long-read haplotype caller) groups two or more cis
variants on the same transcript, varcode now builds a single joint
MutantTranscript instead of computing per-variant effects
independently. The two representations coexist on the returned
EffectCollection — consumers pick the granularity they need.

New:

- apply_variants_to_transcript(variants, transcript) in
  mutant_transcript.py. Generalizes the single-variant builder to
  apply multiple edits at once. Sorts by cDNA offset, validates no
  overlap (returns None on conflict so callers fall back), applies
  high-to-low so earlier offsets aren't shifted. Factors the
  per-variant resolution out into _resolve_variant_edit so the
  single-variant and multi-variant paths share the same validated
  logic.
- HaplotypeEffect class in effect_classes.py. Subclasses
  TranscriptMutationEffect + MultiOutcomeEffect. Carries variants
  (tuple), transcript, mutant_transcript, phase_source. Short
  description emits HGVS cis notation: [v1;v2].
- build_haplotype_effects() in phasing.py. Groups variants by
  transcript, partitions each transcript's variants into cis sets
  using phase_resolver.in_cis(), and builds one HaplotypeEffect per
  cis group of size ≥ 2. Prefers a resolver-provided
  MutantTranscript (Isovar assembly) over DNA inference when
  available — the observed molecule beats the inferred one.
- VariantCollection.effects(phase_resolver=...) now threads through
  to build_haplotype_effects and appends HaplotypeEffects onto the
  returned collection alongside per-variant effects.
- HaplotypeEffect registered in effect_priority ordering at the top
  (novel joint product has highest transcript-level impact).

Tests (10):

- apply_variants_to_transcript joint cDNA correctness, conflict
  rejection, order independence.
- IsovarPhaseResolver driving HaplotypeEffect... (continued)
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