PGx: ClinPGx variant-based genes (PGX-008) and --guideline dpwg (PGX-025)

- fetch_sources.sh downloads ClinPGx clinicalVariants (CC BY-SA 4.0); pgx db build adds genotype-only
  variant-based genes (levels 1A-2B, level 3 for the parity list), rsIDs resolved from the manifest's probes:
  70 genes in the DB.
- pgx phenotype --guideline dpwg: CPIC mappings for CPIC genes (as ClinPGx curates DPWG), no phenotype for
  DPWG-only genes (flags dpwg_via_cpic_mapping / dpwg_mapping_not_available). K-029 updated.
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kemal committed 2026-09-29 17:01:36 +01:00
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@@ -92,4 +92,12 @@ so the per-call error is 1e-3 (GS ≥ 0.15) and errors are handled by the probe
from the GRCh38 haplotype VCFs, `*1` = reference, prior reference 0.8 (no population frequencies); genotype only
(no CPIC phenotype). The probe mask was re-derived with these variants (one more record: CYP2A6 19:40843845 C>A,
concordance 0.47, which had produced false *5 calls).
* Not yet: DPWG tables.
* ClinPGx clinical-annotation variants (CC BY-SA 4.0; levels 1A–2B, and level 3 for the PGX-008 parity genes) add
genotype-only variant-based genes — OPRM1, COMT, DRD2, ANKK1, MTHFR, F5, … (43 genes, 171 of 187 rsIDs resolved on
GSA v4 PGx from the manifest's probes). The DB now holds 70 genes (16 star-allele, G6PD, 2 HLA tag, 51
variant-based; spec parity list: 58). `pgx coverage`: 1225 alleles callable, 93 array-equivalent, 437 not
covered, 5 masked.
* `--guideline dpwg` (PGX-025): ClinPGx curates DPWG guidelines with the CPIC allele-function and phenotype mappings
for genes CPIC covers, so those genes reuse the CPIC tables (flag `dpwg_via_cpic_mapping`); DPWG-only genes
(CYP1A2, CYP3A4, F5) have no public machine-readable mapping and get phenotype `null` with the flag
`dpwg_mapping_not_available` (K-029).