PGx: all CPIC gene kinds — G6PD, variant-based, HLA tags, *0 CN genes (PGX-006/007/021)

- DB build resolves the PGX-007 tag variants from the manifest's probes; coverage over all gene kinds.
- Variant-based genes reported per variant (rs.. REF/ALT | Reference) with the CPIC lowest-activity diplotype;
  tagging genes as positive/negative with the population caveat; GSTM1/GSTT1/UGT2B17 *0 from targeted CN.
- Case-insensitive phenotype keys (MT-RNR1). GeT-RM check extended to VKORC1 and the CN genes:
  131/144 gene calls (docs/validation/V2_pgx_star.md).

scripts/pgx/getrm_truth.py

@@ -31,6 +31,10 @@ def main() -> int:
     rows = list(wb[wb.sheetnames[0]].iter_rows(values_only=True))
     head = [str(h or "").split("\n")[0].strip() for h in rows[1]]
     col = {g: head.index(g) for g in GENES if g in head}
+    vk = next((i for i, h in enumerate(rows[1]) if str(h or "").startswith("VKORC1") and "rs9923231" in str(h)
+               and "Reference" not in str(h)), None)  # fmt: skip
+    if vk is not None:
+        col["VKORC1"] = vk  # c.-1639G>A genotype, e.g. "GA"
     out = []
     for r in rows[2:]:
         if not r or not r[1] or str(r[1]).strip() not in inds: