3 Commits

Include renames

Author	SHA1	Message	Date
kemal	46422b8de4	PGx: CYP2D6 structures from sub-region CN — *68+*4, *36+*10, *13 (PGX-013/018) ... Sub-region CNs (p5, intron 2, exon 9) resolve full copies and *36/*68/*13 units; candidates carry the tandem names, background alleles, and CPIC activity sums. GeT-RM: CYP2D6 13/15 top (NA12878 *3/*68+*4 and NA11832 *1/*68+*4 exact), 15/15 within feasible; all genes 132/144.	2026-09-29 16:29:54 +01:00
kemal	e567d12684	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).	2026-09-29 16:24:33 +01:00
kemal	194c087b24	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).	2026-09-29 14:08:03 +01:00