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openvax / varcode / 24674031352
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Add StructuralVariantAnnotator with multi-outcome SV effects (#252) (#333)

Third annotator in the registry. Classifies structural-variant
consequences per transcript and returns
:class:`MultiOutcomeEffect` subclasses whose ``outcomes`` tuple is
the harmonized interchange shape from #299.

**New effect classes** in ``varcode/effects/effect_classes.py``:

* ``StructuralVariantEffect`` — base, inherits
  ``TranscriptMutationEffect + MultiOutcomeEffect``
* ``LargeDeletion`` — SV deletes one or more exons
* ``LargeDuplication`` — SV duplicates exons (also used for
  ``<CNV>`` gains and symbolic ``<INS>``)
* ``Inversion`` — SV inverts a region that crosses exons
* ``GeneFusion`` — breakend mate lands on another protein-coding
  transcript; carries ``partner_transcript``
* ``TranslocationToIntergenic`` — breakend mate lands off-gene
* ``CrypticExonCandidate`` — placeholder class for PR 11's motif
  scorer to attach as extra ``Outcome`` entries

**New annotator** at ``varcode/annotators/structural_variant.py``:

* ``name = "structural_variant"``
* ``supports = {"DEL", "DUP", "INV", "INS", "CNV", "BND"}``
* Dispatches on ``StructuralVariant.sv_type``, classifies exon
  overlap via the transcript's exons, routes breakends to fusion /
  translocation based on mate location

Integration hooks (documented in module docstring, not wired here):

* ``alt_assembly`` on :class:`StructuralVariant` (long-read
  resolution) — annotator accepts but doesn't consume yet; fused-
  protein computation from assembled alleles is a future refinement
* Short-read RNA evidence (Isovar-style) — attaches additional
  :class:`Outcome` entries with ``source="isovar"``, no subclassing
* External splice predictors — same pattern, ``source="spliceai"``
  and scores in ``evidence``

Registry: both ``varcode.annotators`` and the top-level package
export ``StructuralVariantAnnotator`` and ``ProteinDiffEffectAnnotator``.
Registered at import time alongside ``fast`` and ``protein_diff``.

Tes... (continued)
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