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

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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.

Co-Authored-By: Claude Opus 5.5 <[email protected]>
Claude-Session: https://claude.ai/code/session_01814GKVzZVL3FuF3DeiZXhv
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kemalandClaude Opus 5.5 committed 2026-09-27 16:13:40 +01:00
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README.md
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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** (full specification and roadmap).
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
bash scripts/bootstrap_refs.sh # clone reference open-source repos into refs/