SimurgArray

54 Commits

Author	SHA1	Message	Date
kemal	705138d70b	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	854cf95029	Add sanitized Phase-0 research archive under docs/research Research notes R1-R4, documentation-study files A-E (source of the functional spec's `src:` tags) and PGx coverage CSVs, rewritten to use neutral naming and current project decisions (plan §2).	2026-09-27 16:27:34 +01:00
kemal	336a6b8226	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	631c1d030d	SimurgArray: master plan, repo scaffolding and data/ref fetch scripts Phase 0 deliverables: full technical specification and roadmap (SIMURGARRAY_MASTER_PLAN.md), CLAUDE.md, bootstrap script for reference open-source repos and tiered dataset fetch script with checksums.	2026-09-27 15:20:06 +01:00