kemal
fca3f5f72f
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.
30 lines
1.6 KiB
Markdown
30 lines
1.6 KiB
Markdown
# SimurgArray
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Personal research toolkit for Illumina Infinium genotyping BeadChip data
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(IDAT → normalization → genotype calling → BAF/LRR → QC → VCF/PLINK; later CN/LOH, PGx, cluster training).
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- **SIMURGARRAY_MASTER_PLAN.md** — architecture, algorithms, roadmap
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- **SIMURGARRAY_FUNCTIONAL_SPEC.md** — 416 itemised requirements (CLI, inputs, outputs, QC, CN, PGx, methylation, edge cases)
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- `docs/validation/` — per-phase validation reports · `docs/known_unknowns.md` — findings log · `docs/research/` — background
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## Status
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Phases **P0 (setup)**, **P1 (file parsers)**, **P2 (canonical model, raw X/Y)** and **P3 (normalization)** are
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complete — see `docs/validation/`. Each is validated on 2141 vendor GTCs of the 1000 Genomes Omni2.5 set
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(normalization transforms bit-identical).
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Available commands: `simurg version`, `simurg inspect <files…> [--json]`, `simurg ingest`, `simurg normalize`.
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## Quick start
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```bash
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uv venv && uv pip install -e ".[dev]"
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uv run pytest tests/unit # no downloads needed
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bash scripts/bootstrap_refs.sh # reference open-source repos → refs/ (oracles)
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bash scripts/fetch_data.sh p0 # ~1.4 GB of public test data → data/
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bash scripts/make_oracle_gtcs.sh # builds gtc2vcf, writes oracle GTCs
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uv run pytest tests/oracle # real-data acceptance tests (add -m "not slow" to skip the long ones)
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uv run simurg inspect data/p0/gsa_v4_pgx/idats_Demo_36/idats_Demo_36/207895980019/207895980019_R03C01_Grn.idat
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```
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Vendor data files are downloaded for personal research use only and are never committed. See `THIRD_PARTY_NOTICES.md`.
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