PGx: full call detail (PGX-016..020, 027/028, 031), pgx coverage (PGX-009/035), full HGVS

- supporting_variants.tsv, unresolved_variants.tsv, variants_not_covered.tsv with PGX-026 metadata; per-allele
  supporting/unresolved sites for both alleles of every candidate; variant_change vs top, distant_alternative,
  unexplained_variants, alleles_impacted_by_no_call, alleles_tested.
- simurg pgx coverage: callable / not_covered / masked / equivalent_to per allele and manifest.
- HGVS on GRCh38 RefSeq accessions (NC_...:g.).

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

docs/messages.md

@@ -106,6 +106,7 @@ Generated from `src/simurg/core/errors.py` — do not edit by hand.
 | `W_PGX_BATCH_BELOW_RECOMMENDED` | warning | Fewer passing samples than recommended | PCN-004 |
 | `W_PGX_BATCH_COMPOSITION` | warning | Batch spans several lots/batches or > 14 days of scans | PCN-006 |
 | `W_PGX_NO_ALT_CONTIG` | warning | FASTA lacks a contig carrying a PGx region; REF written as N | IN-062 |
+| `W_PGX_NO_PROBE_MAP` | warning | The PGx DB has no probe map for this manifest | PGX-035 |
 | `W_PGX_REGION_FEW_PROBES` | warning | PGx CN region has fewer than 10 unmasked probes | PCN-008 |
 | `W_QC_LABEL_SANITIZED` | warning | Dataset label was sanitized | QC-042 |
 | `W_QC_NO_BAF` | warning | GTC has no B-allele frequencies; contamination not estimated | QC-064 |

docs/validation/V2_pgx_star.md

@@ -61,6 +61,14 @@ so the per-call error is 1e-3 (GS ≥ 0.15) and errors are handled by the probe
 * CPIC now defines the GRCh38 reference as its own allele where it differs from *1 (CYP2C19 *38): a sample
   heterozygous at the *1-defining rs3758581 fits *1/*38 best (raw score 0.98), but *38 has no CPIC frequency, so the
   prior keeps *1/*1 on top — which is what legacy GeT-RM reports.
+* `simurg pgx coverage` (PGX-009/035) on GSA v4 PGx with the mask: 438 alleles callable, 68 array-equivalent to
+  another allele, 88 not covered, 4 masked. Against the reference's known limitations: CYP4F2 *2 not covered (reported
+  as *1) and *4 ≡ *3 — as the reference; UGT1A1 *28 callable (its C>CAT probe matches 1000G) and *37 masked (the
+  C>CATAT probe fails); CYP2D6 *40/*58 and NUDT15 *6/*9 are separable here (CPIC core definitions differ from the
+  reference's).
+* Detail outputs (PGX-016 … PGX-020, PGX-027/028, PGX-031): `supporting_variants.tsv`, `unresolved_variants.tsv`,
+  `variants_not_covered.tsv`, per-allele supporting/unresolved sites for **both** alleles of every candidate,
+  `variant_change` vs the top solution (`distant_alternative` above 3 changes), `unexplained_variants`, full HGVS on
+  GRCh38 RefSeq accessions.
 * Not yet: named-haplotype (G6PD), variant-based and tagging genes; CYP2D6 hybrids (*13, *36, *68); PharmVar-only
-  genes (CYP2A6, CYP3A4, CYP1A2, …); DPWG tables; the full per-allele supporting/unresolved-variant detail of
-  PGX-027/028 (`supporting_variants.tsv`, `unresolved_variants.tsv`, `variants_not_covered.tsv`).
+  genes (CYP2A6, CYP3A4, CYP1A2, …); DPWG tables.