fetch_sources.sh downloads PharmVar per-gene zips; pgx db build adds core alleles for genes CPIC does not
define (normalised against the FASTA, *1 = reference). Masks re-derived with the new variants. GeT-RM:
CYP3A4 15/15, CYP2A6 7/9; all comparable genes 154/168 (CYP1A2/CYP2C8 definitions differ from GeT-RM's).
- 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.
kemal