kemalandClaude Opus 5.5 aee8caa39e PGx: ClinPGx variant-based genes (PGX-008) and --guideline dpwg (PGX-025) ...

- 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

..

build_cn_regions.py

PGx star alleles: pgx star-allele call (PGX-011..021), probe masks vs 1000G, GeT-RM validation (K-029)

2026-09-29 14:08:03 +01:00

demo36_identity.tsv

PGx CN: pgx copy-number train|call (CLI-031/032, PCN-001..017, IN-050), region BED v1, demo identities (K-028)

2026-09-29 13:16:19 +01:00

derive_masks.py

derive_masks: keep pysam's downloaded tabix indexes in data/pgx/cache, not the working directory

2026-09-29 16:00:25 +01:00

fetch_sources.sh

PGx: ClinPGx variant-based genes (PGX-008) and --guideline dpwg (PGX-025)

2026-09-29 17:01:36 +01:00

getrm_truth.py

PGx: all CPIC gene kinds — G6PD, variant-based, HLA tags, *0 CN genes (PGX-006/007/021)

2026-09-29 16:24:33 +01:00

validate_cn_truth.py

PGx star alleles: pgx star-allele call (PGX-011..021), probe masks vs 1000G, GeT-RM validation (K-029)

2026-09-29 14:08:03 +01:00

validate_star_getrm.py

PGx: PharmVar genes (CYP1A2, CYP2A6, CYP2A13, CYP2C8, CYP3A4), CYP2A6 *4 from CN (PGX-001/006)

2026-09-29 16:50:27 +01:00