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

..

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

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

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 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_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 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