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P0: project setup (packaging, CI, licences, data/oracle scripts)

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- 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
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kemal committed 2026-09-27 16:56:39 +01:00
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SIMURGARRAY_MASTER_PLAN.md
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@@ -814,17 +814,17 @@ precision/recall vs 1000G WGS CNV/SV callsets; PGx diplotype concordance vs WGS-
Vendor files are for personal research use only and are **never committed**. `scripts/fetch_data.sh <tier>` downloads,
records SHA-256 in `data/CHECKSUMS.sha256`, and unpacks.
### Tier P0 — small, start here (~3 GB)
### Tier P0 — small, start here (~1.4 GB; verified 2026-09-27)
| Dataset | URL | Notes |
|---|---|---|
| Bioconductor IlluminaDataTestFiles | https://bioconductor.org/packages/IlluminaDataTestFiles | Artistic-2.0 → **may be committed** as IDAT parser fixtures |
| Bioconductor hapmap370k | https://bioconductor.org/packages/hapmap370k | Artistic-2.0; 40 HapMap IDATs |
| GDA v1 Demo 36 (IDATs) | https://webdata.illumina.com/downloads/productfiles/global-diversity-array/infinium-global-diversity-array-8-v1-0-D1-demo-data-36.zip | 465 MB; 3 CEU trios incl. NA12878 + replicates |
| GDA v1 sample sheet | https://support.illumina.com/content/dam/illumina-support/documents/downloads/productfiles/global-diversity-array/infinium-global-diversity-array-8-v1-0_D1_SampleSheet_Demo_36.csv | has Parent1/Parent2/Replicate |
| GDA v1 BPM / CSV / EGT | https://webdata.illumina.com/downloads/productfiles/global-diversity-array/infinium-global-diversity-array-8-v1-0-D1-manifest-file-bpm.zip (and `…-csv.zip`, `…-D1-cluster-file.zip`; page: https://support.illumina.com/array/array_kits/infinium-global-diversity-array/product-files.html) | |
| GSA v4 PGx demo (36 samples) | https://support.illumina.com/downloads/infinium-gsa-v4-pgx-demo-data-set-iscan.html | 872 MB; product files at https://support.illumina.com/array/array_kits/infinium-global-screening-array-v4-pgx/product-files.html |
| **GSA v4 PGx demo IDATs (36 samples, 72 IDATs)** | https://support.illumina.com/content/dam/illumina-support/documents/documentation/chemistry_documentation/infinium_assays/infinium-gsa-pgx/idats_Demo_36.zip | 872 MB; primary small fixture. BPM/CSV/EGT from the same folder (`GSA-PGx-48v4-0_20079540_E2_{bpm,csv,ClusterFile}.zip`) |
| Bioconductor IlluminaDataTestFiles | https://bioconductor.org/packages/IlluminaDataTestFiles | Artistic-2.0 → **may be committed** as IDAT parser fixtures; includes 2 encrypted IDATs (negative tests) |
| GDA v1 BPM / CSV / EGT + demo sample sheet | https://support.illumina.com/array/array_kits/infinium-global-diversity-array/product-files.html | second design (1.9 M loci). Note: the "GDA Demo 36" bundle is a **GenomeStudio project, not IDATs** |
| GRCh37 & GRCh38 FASTA | e.g. GRCh38 no-alt analysis set (NCBI) | contigs named per manifest |
(Bioconductor `hapmap370k` is no longer in the current release.) Oracle GTCs for P1–P4 are generated locally with
gtc2vcf `idat2gtc` (MIT) from the GSA demo IDATs — see `docs/validation/P1.md`.
### Tier P1 — validation core (~170 GB)
| Dataset | URL | Notes |
|---|---|---|