PGx: PharmVar genes (CYP1A2, CYP2A6, CYP2A13, CYP2C8, CYP3A4), CYP2A6 *4 from CN (PGX-001/006)

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).

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

scripts/pgx/validate_star_getrm.py

@@ -57,7 +57,9 @@ def _ugt2b17(t: str) -> int:  # *2 = whole-gene deletion
 
 
 CN_TRUTH = {"GSTM1": _gstm1, "GSTT1": _gstt1, "UGT2B17": _ugt2b17}  # capped: GSTM1 at 1, the others at 2
-LEGACY_NOMENCLATURE = {"UGT1A1", "SLCO1B1"}  # GeT-RM uses pre-2023 names (*60, SLCO1B1 *1B/*17/*21) not in CPIC
+# GeT-RM uses older names or definitions than the current CPIC/PharmVar ones: UGT1A1 *60 and SLCO1B1 *1B/*17/*21
+# (pre-2023), CYP1A2 lettered alleles (*1F …), CYP2C8 *19 (PharmVar now defines rs2071426 alone as *19; GeT-RM *1)
+LEGACY_NOMENCLATURE = {"UGT1A1", "SLCO1B1", "CYP1A2", "CYP2C8"}
 
 
 def truth_alternatives(text: str) -> list[list[set[str]]]: