3 Commits

Include renames

Author	SHA1	Message	Date
kemal	abea028818	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.).	2026-09-29 16:16:39 +01:00
kemal	9d3242828e	PGx phenotypes: pgx phenotype|annotate (PGX-024..028, CLI-034) ... CPIC lookups by allele function counts or activity values (duplications N x activity, *5/*0 = 0, total-score fallback), Indeterminate when feasible solutions disagree or an allele is not in the guideline; per-sample simurg.pgx/1 JSON and diplotype_annotations.tsv with PGX-026 metadata lines.	2026-09-29 16:03:27 +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