# 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)**, **P3 (normalization)** and **P4 (genotype
calling, GTC output)** are complete — see `docs/validation/`. Each is validated on 2141 vendor GTCs of the 1000 Genomes Omni2.5 set
(normalization bit-identical; genotypes/scores identical in 2138/2141 samples).
Available commands: `simurg version`, `simurg inspect <files…> [--json]`, `simurg ingest`, `simurg normalize`, `simurg genotype`.

## Quick start

```bash
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`.