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kemalandClaude Opus 5.5 ee4ebaaa1e 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.

Co-Authored-By: Claude Opus 5.5 <[email protected]>
Claude-Session: https://claude.ai/code/session_01814GKVzZVL3FuF3DeiZXhv

2026-09-27 15:20:06 +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

CLAUDE.md

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

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

README.md

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

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

SIMURGARRAY_MASTER_PLAN.md

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

2026-09-27 15:20:06 +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 (full specification and roadmap).

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