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).

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

src/simurg/pipeline/pgx_pheno.py

@@ -97,6 +97,12 @@ def run_phenotype(o: PhenoOptions, rep: Reporter) -> int:
                 res = None
             else:
                 res, per = gene_phenotype(t, feas)
+            if g.get("call_type") == "tagging_variant":  # PGX-007: the CPIC result is the tag status itself
+                from simurg.pgx.phenotype import PhenotypeResult
+
+                res, per = PhenotypeResult(g["genotype"], None), []
+            elif g.get("call_type") == "copy_number":
+                res, per = None, []
             flags = list(g.get("flags", [])) + (res.flags if res else [])
             top = g["candidates"][0] if g["candidates"] else {}
             top_alleles = top.get("alleles", [])