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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

scripts

SimurgArray: master plan, repo scaffolding and data/ref fetch scripts

2026-09-27 15:20:06 +01:00

.gitignore

SimurgArray: master plan, repo scaffolding and data/ref fetch scripts

2026-09-27 15:20:06 +01:00

README.md

Add functional specification (416 items) and link it from plan/docs

2026-09-27 16:13:40 +01:00

SIMURGARRAY_FUNCTIONAL_SPEC.md

Add functional specification (416 items) and link it from plan/docs

2026-09-27 16:13:40 +01:00

SIMURGARRAY_MASTER_PLAN.md

Add functional specification (416 items) and link it from plan/docs

2026-09-27 16:13:40 +01:00

README.md

SimurgArray

Personal research toolkit for Illumina Infinium genotyping BeadChip data (IDAT → normalization → genotype calling → BAF/LRR → QC → VCF/PLINK; later CN/LOH, PGx, cluster training).

Start with SIMURGARRAY_MASTER_PLAN.md (architecture, algorithms, roadmap) and SIMURGARRAY_FUNCTIONAL_SPEC.md (416 itemised requirements: CLI, inputs, outputs, QC, CN, PGx, methylation, edge cases).

bash scripts/bootstrap_refs.sh     # clone reference open-source repos into refs/
bash scripts/fetch_data.sh p0      # download small test datasets into data/