kemal/SimurgArray
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aee8caa39e5ac2c0141b6145fa93db75645bc8aa
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Author SHA1 Message Date
kemalandClaude Opus 5.5 aee8caa39e PGx: ClinPGx variant-based genes (PGX-008) and --guideline dpwg (PGX-025)
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- fetch_sources.sh downloads ClinPGx clinicalVariants (CC BY-SA 4.0); pgx db build adds genotype-only
  variant-based genes (levels 1A-2B, level 3 for the parity list), rsIDs resolved from the manifest's probes:
  70 genes in the DB.
- pgx phenotype --guideline dpwg: CPIC mappings for CPIC genes (as ClinPGx curates DPWG), no phenotype for
  DPWG-only genes (flags dpwg_via_cpic_mapping / dpwg_mapping_not_available). K-029 updated.

Co-Authored-By: Claude Opus 5.5 <[email protected]>
Claude-Session: https://claude.ai/code/session_01814GKVzZVL3FuF3DeiZXhv
 2026-09-29 17:01:36 +01:00
kemalandClaude Opus 5.5 58dbd8f514 PGx: all CPIC gene kinds — G6PD, variant-based, HLA tags, *0 CN genes (PGX-006/007/021)
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- 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 4dafce3f18 PGx: full call detail (PGX-016..020, 027/028, 031), pgx coverage (PGX-009/035), full HGVS
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- 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.).

Co-Authored-By: Claude Opus 5.5 <[email protected]>
Claude-Session: https://claude.ai/code/session_01814GKVzZVL3FuF3DeiZXhv
 2026-09-29 16:16:39 +01:00
kemalandClaude Opus 5.5 0215af9c9c PGx phenotypes: pgx phenotype|annotate (PGX-024..028, CLI-034)
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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.

Co-Authored-By: Claude Opus 5.5 <[email protected]>
Claude-Session: https://claude.ai/code/session_01814GKVzZVL3FuF3DeiZXhv
 2026-09-29 16:03:27 +01:00