Root cause: Sophia's genome data was stored in legacy flat format where
all variants were top-level category 4 entries with rsID as the type
field. The API expected new hierarchical format (extraction → tier →
variant), causing "no genome data" errors.
Changes:
- GenomeGetExtraction(): Detect legacy data, return synthetic extraction
- GenomeGetTiers(): Return synthetic "all" tier for legacy format
- GenomeGetVariants(): Query top-level entries for legacy format
Test results:
- Sophia's 4960 genome variants now accessible via /api/genome
- Gene queries work: ?gene=MTHFR,COMT,MTR,MTRR returns 5 matches
- MCP tools (query_genome) now function correctly
Co-Authored-By: Claude Sonnet 4.5 <noreply@anthropic.com>
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