kemal
f7d883826d
Normalization 1.1.2 reproduces all 109,191 bins of the 1000 Genomes Omni2.5 GTCs (AutoCall 1.6.2.2) with 0 ULP difference, reserved fields included; 1.2.0 and 1.1.2 are bit-identical to the no-FMA gtc2vcf oracle on 36 GSA samples. AWS run: 33 min, ~$0.15, no resources left.
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), P2 (canonical model, raw X/Y) and P3 (normalization) are
complete — see docs/validation/. Each is validated on 2141 vendor GTCs of the 1000 Genomes Omni2.5 set
(normalization transforms bit-identical).
Available commands: simurg version, simurg inspect <files…> [--json], simurg ingest, simurg normalize.
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.