PGx star alleles: pgx star-allele call (PGX-011..021), probe masks vs 1000G, GeT-RM validation (K-029)

- simurg/pgx/star.py: solver-free diplotype enumeration incl. CN forms (deletion, xN), wildcards, array-equivalence
  classes, raw_score/score with CPIC frequency priors; calibrated error model (spec PGX-012 amended).
- pipeline/pgx_star.py: DB gene models, SNV + PGx CN VCF evidence, masks, diplotype_summary.tsv + pgx_calls.json.
- scripts/pgx: derive_masks.py (array vs 1000G 30x over HTTPS, GS calibration), getrm_truth.py,
  validate_star_getrm.py.
- GSA v4 PGx demo vs GeT-RM (16 CEPH): 100/109 gene calls; CYP2D6/2C19/2C9 41/45 (docs/validation/V2_pgx_star.md).

scripts/pgx/validate_cn_truth.py

@@ -59,10 +59,12 @@ def main() -> int:
         tot[1] += len(pairs)
         res[region] = {"record": rid, "concordant": ok, "n": len(pairs),
                        "rate": round(ok / len(pairs), 4) if pairs else None,
-                       "truth_to_call_mismatches": dict(collections.Counter(f"{t}->{c}" for t, c in pairs if t != c))}  # fmt: skip
+                       "truth_to_call_mismatches": dict(collections.Counter(
+                           f"{t}->{c}" for t, c in pairs if t != c))}  # fmt: skip
     summary = {"individuals": len(calls), "regions": res, "overall": {"concordant": tot[0], "n": tot[1],
                "rate": round(tot[0] / tot[1], 4) if tot[1] else None},
-               "gstt1_cn_distribution": dict(sorted(collections.Counter(c.get("GSTT1", ".") for c in calls.values()).items()))}  # fmt: skip
+               "gstt1_cn_distribution": dict(sorted(collections.Counter(
+                   c.get("GSTT1", ".") for c in calls.values()).items()))}  # fmt: skip
     a.out.write_text(json.dumps(summary, indent=1))
     print(json.dumps(summary, indent=1))
     return 0