kemal
2ca0f44da6
PGx star alleles: pgx star-allele call (PGX-011..021), probe masks vs 1000G, GeT-RM validation (K-029)
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- 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
kemal
82d6153a63
PGx DB: pgx db build from CPIC (PGX-001..005, IN-053, CLI-035)
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- 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.
2026-09-29 13:24:54 +01:00
kemal
cc8c934167
PGx CN: pgx copy-number train|call (CLI-031/032, PCN-001..017, IN-050), region BED v1, demo identities (K-028)
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- 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).
2026-09-29 13:16:19 +01:00
kemal