5 Commits

Include renames

Author	SHA1	Message	Date
kemalandClaude Opus 5.5	83654ddaef	PGx validation on GSE165845: WGS-derived star truth, 2-fold masks, array-resolvable concordance ... - scripts/pgx/wgs_star_truth.py: star alleles from the 1000G 30x phased panel with the DB definitions (wildcard-aware haplotype assignment; checked against GeT-RM on the demo CEPH individuals). - validate_star_getrm.py: --all-genes, --individuals, --coverage (projection onto what the array can see); replicate_concordance.py. - 120 individuals x 3 GSA v1 arrays: array-resolvable 1637/1710 (95.7 %), top 1223/1800 (chip lacks many defining variants), GeT-RM subset 28/35, replicates 99.2 % without the failed array (V2_pgx_star.md, K-029). Co-Authored-By: Claude Opus 5.5 <[email protected]> Claude-Session: https://claude.ai/code/session_01814GKVzZVL3FuF3DeiZXhv	2026-09-29 19:00:34 +01:00
kemalandClaude Opus 5.5	4176ef33de	PGx: PharmVar genes (CYP1A2, CYP2A6, CYP2A13, CYP2C8, CYP3A4), CYP2A6 *4 from CN (PGX-001/006) ... fetch_sources.sh downloads PharmVar per-gene zips; pgx db build adds core alleles for genes CPIC does not define (normalised against the FASTA, *1 = reference). Masks re-derived with the new variants. GeT-RM: CYP3A4 15/15, CYP2A6 7/9; all comparable genes 154/168 (CYP1A2/CYP2C8 definitions differ from GeT-RM's). Co-Authored-By: Claude Opus 5.5 <[email protected]> Claude-Session: https://claude.ai/code/session_01814GKVzZVL3FuF3DeiZXhv	2026-09-29 16:50:27 +01:00
kemalandClaude Opus 5.5	1428535e91	PGx: CYP2D6 structures from sub-region CN — *68+*4, *36+*10, *13 (PGX-013/018) ... Sub-region CNs (p5, intron 2, exon 9) resolve full copies and *36/*68/*13 units; candidates carry the tandem names, background alleles, and CPIC activity sums. GeT-RM: CYP2D6 13/15 top (NA12878 *3/*68+*4 and NA11832 *1/*68+*4 exact), 15/15 within feasible; all genes 132/144. Co-Authored-By: Claude Opus 5.5 <[email protected]> Claude-Session: https://claude.ai/code/session_01814GKVzZVL3FuF3DeiZXhv	2026-09-29 16:29:54 +01:00
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