kemalandClaude Opus 5.5 bf9fdaa2f3 PGx DB: pgx db build from CPIC (PGX-001..005, IN-053, CLI-035) ...

- scripts/pgx/fetch_sources.sh: CPIC API tables (CC0) into a dated folder with version and hashes.
- simurg/pgx/db.py: CPIC HGVS locations and values -> left-normalised VCF variants (SNV, del, ins, dup,
  repeats, delins, chrM); IUPAC values are core-allele wildcards; alleles without definitions are flagged.
- pipeline/pgx_db.py: deterministic SQLite (content-hash name), probe_map via the SNV VCF site mapper;
  GSA v4 PGx: 22 genes, 1354 alleles, 5002 probe links; two builds byte-identical.

Co-Authored-By: Claude Opus 5.5 <[email protected]>
Claude-Session: https://claude.ai/code/session_01814GKVzZVL3FuF3DeiZXhv

2026-09-29 13:24:54 +01:00

..

research

Add sanitized Phase-0 research archive under docs/research

2026-09-27 16:27:34 +01:00

validation

PGx CN: pgx copy-number train|call (CLI-031/032, PCN-001..017, IN-050), region BED v1, demo identities (K-028)

2026-09-29 13:16:19 +01:00

known_unknowns.md

PGx CN: pgx copy-number train|call (CLI-031/032, PCN-001..017, IN-050), region BED v1, demo identities (K-028)

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messages.md

PGx DB: pgx db build from CPIC (PGX-001..005, IN-053, CLI-035)

2026-09-29 13:24:54 +01:00

user_guide.md

sesame oracle: explicit platform, cache fallback

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