3 Commits

Include renames

Author	SHA1	Message	Date
kemal	cea710f7b7	P5: cloud task for cohort QC validation; configurable gp3 throughput; batched contamination map ... - scripts/cloud/tasks/p5.sh: P4 preset re-check, genotype (v5) with QC, validate_p5_large.py - scripts/validate_p5_large.py: identify samples via het pattern vs 1000G VCF; sex, parent-offspring, Mendel, contamination/control distributions - trial.sh: DISK_MBPS / DISK_IOPS - qc/contamination: bounded map batches (executor.map submits eagerly)	2026-09-28 09:10:02 +01:00
kemal	e6cf273ab4	P4: unit tests for calling/BAF/LRR/sex/CLI; vendor validation script ... - tests/unit/test_genotype.py: fuzzy memberships incl. NaN rules, calls at cluster centres, intensity threshold, BAF/LRR interpolation and NaN pattern, LogR-dev locus set, sex rules v1/v2, TOP-strand base calls, invariant dates, end-to-end `simurg genotype` (summary schema, pass-through columns, thread/layout determinism, overwrite refusal) - tests/oracle/test_p4_genotype.py: 36 GSA samples x 2 versions byte-identical to the oracle - scripts/validate_p4_large.py + cloud task p4: compare every vendor GTC field by field and as whole files; reports which sex rule matches	2026-09-28 00:10:47 +01:00
kemal	bf00b0e453	P3: vectorised nearest-neighbour search; task-driven cloud trials ... - fit.py: exact and binned nearest-neighbour searches use one distance matrix per searched bin (first-minimum rule kept); fit 2.6 s -> 1.4 s per GSA sample, still bit-identical to the oracle - scripts/validate_p3_large.py: refits 1.2.0 and 1.1.2 transforms for every vendor GTC and reports ULP distances per field - cloud trial runs scripts/cloud/tasks/<TASK>.sh (TASK=p3 default; p1p2 = previous validation + ingest)	2026-09-27 22:57:03 +01:00