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Wire load_vcf's SV path end-to-end (#264) (#357)

* Wire load_vcf's SV path end-to-end (#264)

Most of #264 was already shipped (StructuralVariant class, parse_symbolic_alt,
parse_structural_variants=True flag, StructuralVariantAnnotator). This PR
closes the remaining gaps that stopped the path from being usable end-to-end.

- vcf.py: SV rows now parse FORMAT/sample columns. Previously the symbolic
  branch put `sample_info: None` in metadata, dropping per-sample data that
  somatic SV callers (Manta, DELLY, GRIDSS) routinely ship.

- vcf.py: split the skip warning so users hear a different message when SVs
  are dropped because parse_structural_variants=False (now points at the
  flag) vs when the parser couldn't recognize the ALT shape with the flag
  on (still tracked as #264 follow-up). Spanning `*` is silent — every
  consumer drops it and a warning every time would be noise.

- sv_allele_parser.py: extract INSSEQ / SVINSSEQ from INFO into the
  StructuralVariant.alt_assembly slot so long-read assembly callers can
  feed inserted sequences through to the SV annotator (which already
  prefers alt_assembly over inferring from breakpoints).

- sv_allele_parser.py: parse the integer out of <CN0> / <CN3> etc. into
  info["copy_number"]. Both still collapse to sv_type="CNV", but downstream
  code can now distinguish a zero-copy deletion from a higher-copy
  duplication without re-parsing the ALT.

- effect_prediction.py: SV variants now dispatch to StructuralVariantAnnotator
  by default. predict_variant_effects has no kind-based dispatch — every
  variant goes to the registry default (protein_diff today). When a user
  loads a VCF with parse_structural_variants=True and calls vc.effects(),
  the loaded StructuralVariant flows to protein_diff which annotates the
  placeholder ref="N"/alt="A" and emits ExonLoss/NoncodingTranscript instead
  of LargeDeletion. Adding `if annotator is None and variant.is_structural:`
  routes SVs to the right annotator wit... (continued)
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