kemal/SimurgArray
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Author SHA1 Message Date
kemal be05793d20 Tidy the repository: remove docs/research and bench, fix references
ci / test (3.13) (push) Failing after 10s
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ci / test (3.12) (push) Failing after 9s
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2026-09-30 08:07:35 +01:00
kemal 368c97b9aa P0: project setup (packaging, CI, licences, data/oracle scripts) 
- 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
 2026-09-27 16:56:39 +01:00
kemal 180b6f160a Add functional specification (416 items) and link it from plan/docs 
SIMURGARRAY_FUNCTIONAL_SPEC.md defines externally visible behaviour:
CLI, inputs, genotyping outputs, QC and report, cytogenetics CNV/LOH,
targeted PGx copy number, star alleles, methylation control QC, edge-case
catalogue, performance targets, open questions and a traceability table.
 2026-09-27 16:13:40 +01:00
kemal b63852e775 SimurgArray: master plan, repo scaffolding and data/ref fetch scripts 
Phase 0 deliverables: full technical specification and roadmap
(SIMURGARRAY_MASTER_PLAN.md), bootstrap script for reference
open-source repos and tiered dataset fetch script with checksums.
 2026-09-27 15:20:06 +01:00