5 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	ef1a608ee8	derive_masks: keep pysam's downloaded tabix indexes in data/pgx/cache, not the working directory ... Co-Authored-By: Claude Opus 5.5 <[email protected]> Claude-Session: https://claude.ai/code/session_01814GKVzZVL3FuF3DeiZXhv	2026-09-29 16:00:25 +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
kemalandClaude Opus 5.5	bf9fdaa2f3	PGx DB: pgx db build from CPIC (PGX-001..005, IN-053, CLI-035) ... - scripts/pgx/fetch_sources.sh: CPIC API tables (CC0) into a dated folder with version and hashes. - simurg/pgx/db.py: CPIC HGVS locations and values -> left-normalised VCF variants (SNV, del, ins, dup, repeats, delins, chrM); IUPAC values are core-allele wildcards; alleles without definitions are flagged. - pipeline/pgx_db.py: deterministic SQLite (content-hash name), probe_map via the SNV VCF site mapper; GSA v4 PGx: 22 genes, 1354 alleles, 5002 probe links; two builds byte-identical. Co-Authored-By: Claude Opus 5.5 <[email protected]> Claude-Session: https://claude.ai/code/session_01814GKVzZVL3FuF3DeiZXhv	2026-09-29 13:24:54 +01:00
kemalandClaude Opus 5.5	58e70bc894	PGx CN: pgx copy-number train|call (CLI-031/032, PCN-001..017, IN-050), region BED v1, demo identities (K-028) ... - simurg/pgx/cn.py: per-region CN mixture, mu_c = delta + gamma*log2((c+1)/3), free lower CN-0 component, Hardy-Weinberg-constrained weights over haplotype copy numbers, EM from a grid of label starts. - pipeline/pgx_cn.py: model file (.simurg-pgxcn), batch rules (PCN-004), per-sample CN VCF + tbi, batch and sample summaries. - The GSA v4 PGx demo arrays are 30 CEPH/1000G individuals (scripts/pgx/demo36_identity.tsv); against NYGC 30x SV RD_CN 224/240 region calls agree (GSTM1, UGT2B17 30/30), in-sample (docs/validation/V2_pgx_cn.md). Co-Authored-By: Claude Opus 5.5 <[email protected]> Claude-Session: https://claude.ai/code/session_01814GKVzZVL3FuF3DeiZXhv	2026-09-29 13:16:19 +01:00