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).

docs/validation/V2_pgx_star.md

@@ -41,7 +41,9 @@ Status: **implemented for CPIC star-allele genes, interim validation** (2026-09-
 | GSTM1 (CN: DEL/DEL vs present) | 9/9 | 9/9 |
 | GSTT1 (CN 0/1/2) | 7/9 | 7/9 |
 | UGT2B17 (CN) | 2/2 | 2/2 |
-| **total** | **132/144 (91.7 %)** | **135/144 (93.8 %)** |
+| CYP3A4 (PharmVar) | **15/15** | 15/15 |
+| CYP2A6 (PharmVar; *4 deletion from CN) | 7/9 | 8/9 |
+| **total** | **154/168 (91.7 %)** | **158/168 (94.0 %)** |
 
 PGX-032 target (≥ 90 % for CYP2D6/CYP2C19/CYP2C9 against truth): **42/45 = 93 %** (top solution), 45/45 within
 the array-equivalent feasible solutions.
@@ -52,8 +54,10 @@ CYP2D6 structures (PGX-013) come from the three sub-region CNs (`simurg.pgx.star
 array cannot separate (both within the feasible set).
 Details and every discordant call: `V2_pgx_star_getrm16.json`.
 
-Not in the total (GeT-RM uses pre-2023 names the CPIC definitions no longer carry): UGT1A1 (GeT-RM `*60`;
-0/9 top) and SLCO1B1 (`*1B/*17/*21` vs CPIC `*37/*15/*20`; 9/15 top).
+Not in the total (GeT-RM uses older names or definitions than CPIC/PharmVar today): UGT1A1 (GeT-RM `*60`;
+0/9 top), SLCO1B1 (`*1B/*17/*21` vs CPIC `*37/*15/*20`; 9/15), CYP1A2 (lettered `*1F`; 0/9) and CYP2C8 (PharmVar now
+defines rs2071426 alone as `*19`; the array calls it concordantly with 1000G, GeT-RM reports those carriers as
+`*1`; 8/15).
 
 Remaining discordances: CYP2D6 *2 vs *1 where the array cannot separate them (prior picks *1), CYP2C19 *8, TPMT *21, CYP2B6 *27, CYP4F2 *2 — rare
 alleles whose defining variants are absent or masked on this array.
@@ -84,5 +88,8 @@ so the per-call error is 1e-3 (GS ≥ 0.15) and errors are handled by the probe
   `Reference`, phenotype diplotype from the two lowest-activity carried variants), HLA-A/B tag variants (PGX-007,
   positions resolved from the manifest's probes, flag `tag_caveat`), and GSTM1/GSTT1/UGT2B17 `*0` genotypes from
   the targeted CN (PGX-006).
-* Not yet: PharmVar-only
-  genes (CYP2A6, CYP3A4, CYP1A2, …); DPWG tables.
+* PharmVar genes without CPIC definitions (CYP1A2, CYP2A6, CYP2A13, CYP2C8, CYP3A4; PharmVar 6.2.29): core alleles
+  from the GRCh38 haplotype VCFs, `*1` = reference, prior reference 0.8 (no population frequencies); genotype only
+  (no CPIC phenotype). The probe mask was re-derived with these variants (one more record: CYP2A6 19:40843845 C>A,
+  concordance 0.47, which had produced false *5 calls).
+* Not yet: DPWG tables.