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).

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

SIMURGARRAY_FUNCTIONAL_SPEC.md

@@ -2759,7 +2759,10 @@ about **algorithms or numerics**, the plan wins. Each such conflict found during
 
   In a region whose CN is n ≠ 2, the variant copy number `k ∈ {0..n}` is the maximum-likelihood value under the
   observed BAF ~ N(k/n, σ²), with σ estimated per batch from AB clusters. It is reported as `variant_copy_number`.
-  GS enters as a per-call error rate: ε(GS) = 0.5·(1 − GS)², clipped to [1e-4, 0.25] [OURS]. (src: B-30, E-41)
+  GS enters as a per-call error rate: ε = 1e-3 for GS ≥ 0.15 and 0.05 below [OURS, calibrated: after probe masking
+  (PGX-010), 0 of 9 740 GSA v4 PGx calls at DB variants disagreed with 1000G 30x in any GS bin, so errors are
+  probe-specific and belong in the mask; the earlier ε(GS) = 0.5·(1 − GS)² made correct low-GS calls such as
+  CYP2C9 rs1799853 at GS 0.16 lose to the prior; K-029]. (src: B-30, E-41)
 
 - **PGX-013** `§11 · v2` **Candidate enumeration [DIFF: solver-free].**
   - For each gene, SimurgArray enumerates diplotypes from the gene's haplotypes: star alleles, `*0`, duplications