2 Commits

Include renames

Author	SHA1	Message	Date
kemalandClaude Opus 5.5	58dbd8f514	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	2026-09-29 16:24:33 +01:00
kemalandClaude Opus 5.5	d91c8ea576	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	2026-09-29 14:08:03 +01:00