kemal
bf00b0e453
- 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)
SimurgArray
Personal research toolkit for Illumina Infinium genotyping BeadChip data (IDAT → normalization → genotype calling → BAF/LRR → QC → VCF/PLINK; later CN/LOH, PGx, cluster training).
- SIMURGARRAY_MASTER_PLAN.md — architecture, algorithms, roadmap
- SIMURGARRAY_FUNCTIONAL_SPEC.md — 416 itemised requirements (CLI, inputs, outputs, QC, CN, PGx, methylation, edge cases)
docs/validation/— per-phase validation reports ·docs/known_unknowns.md— findings log ·docs/research/— background
Status
Phases P0 (setup), P1 (file parsers) and P2 (canonical model, raw X/Y) are complete — see
docs/validation/. Validated on 2141 vendor GTCs of the 1000 Genomes Omni2.5 set.
Available commands: simurg version, simurg inspect <files…> [--json], simurg ingest.
Quick start
uv venv && uv pip install -e ".[dev]"
uv run pytest tests/unit # no downloads needed
bash scripts/bootstrap_refs.sh # reference open-source repos → refs/ (oracles)
bash scripts/fetch_data.sh p0 # ~1.4 GB of public test data → data/
bash scripts/make_oracle_gtcs.sh # builds gtc2vcf, writes oracle GTCs
uv run pytest tests/oracle # real-data acceptance tests (add -m "not slow" to skip the long ones)
uv run simurg inspect data/p0/gsa_v4_pgx/idats_Demo_36/idats_Demo_36/207895980019/207895980019_R03C01_Grn.idat
Vendor data files are downloaded for personal research use only and are never committed. See THIRD_PARTY_NOTICES.md.