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

..

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 DB: pgx db build from CPIC (PGX-001..005, IN-053, CLI-035)

2026-09-29 13:24:54 +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: all CPIC gene kinds — G6PD, variant-based, HLA tags, *0 CN genes (PGX-006/007/021)

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