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.
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.
kemal