openvax / varcode / 24735595406
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Cryptic donor/acceptor materialization under genomic_sequence (#296) (#350)

Completes the cryptic-splice portion of #296. The
enumerate_splice_outcomes genomic_sequence provider now scans ±50
bp (configurable) around the canonical splice boundary on BOTH the
exon and intron sides for the highest-scoring cryptic motif and
materializes a MutantTranscript that uses the cryptic site in
place of the disrupted canonical one.

Behavior:

- For a disrupted canonical donor, scan the exon's 3' tail AND the
  intron's 5' head for weak GT consensus (9-bp MAG|GTRAGT window).
  Exonic cryptic → truncates the exon. Intronic cryptic → extends
  the exon through part of the intron.
- Mirror pattern for acceptor: scan intron tail + exon 5' head
  (4-bp YAG|G window).
- Highest-scoring non-canonical site wins.
- cDNA edit is a deletion (truncation) or insertion (extension) at
  the exon boundary; translate from CDS start for
  mutant_protein_sequence.
- Description includes the cryptic genomic position and motif score
  so consumers can filter / audit.

Reverse-strand support: scan region is fetched in forward-strand
coords from the provider, then reverse-complemented for
transcript-order processing.

No provider → pre-#296 stub behavior preserved.

Tests cover: implanted donor motif picked up at expected offset;
implanted acceptor motif likewise; no-motif scan falls back to
stub; provider absent keeps pre-#296 behavior.
Source Files on build 24735595406
Detailed source file information is not available for this build.