2 Commits

Include renames

Author	SHA1	Message	Date
kemal	7e9ff28501	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.	2026-09-29 13:24:54 +01:00
kemal	7dc1fbc014	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).	2026-09-29 13:16:19 +01:00