kemal
368c97b9aa
- pyproject (uv/hatch, ruff, mypy strict, pytest markers), MIT LICENSE, THIRD_PARTY_NOTICES with verbatim BSD-2 (BeadArrayFiles) and MIT (gtc2vcf) - CI workflow for Gitea/GitHub Actions: lint, type check, unit tests - fetch_data.sh p0 now fetches the GSA v4 PGx demo IDATs (the GDA "Demo 36" bundle is a GenomeStudio project), unpacks archives, fixes pipefail bug - make_oracle_gtcs.sh builds bcftools + gtc2vcf and writes oracle GTCs - plan §17: corrected P0 dataset table
28 lines
1.4 KiB
Markdown
28 lines
1.4 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)** and **P1 (file parsers)** are complete — see `docs/validation/P1.md`.
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Available commands: `simurg version`, `simurg inspect <files…> [--json]`.
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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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