P7: differential-testing harness (simurg compare) and nightly run on the Pi

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- compare/core: EXACT/NEAR/DISCREPANCY/UNKNOWN with the plan §16.3 tolerances (abs, float32 ULP), NaN = NaN,
  locus classes (assay, variant type, chromosome group, intensity-only); fields absent on both sides are
  not applicable
- compare/records: GTC vs GTC (per-locus arrays, transforms per bin, controls, sample statistics; metadata
  listed, not counted) and VCF vs VCF (records keyed incl. ID; SNV/MNV/indel, merged, multi-allelic classes)
- simurg compare A B (files or folders paired by name): summary.json, discrepancies.tsv.gz (never truncated),
  self-contained dashboard.html; --tolerance, --fail-on-discrepancy (exit 3)
- scripts/nightly.py + install_nightly.sh (crontab 02:30): unit tests, GSA vs gtc2vcf (GTC + VCF), VCF
  regression vs golden, Omni2.5 subset vs vendor GTCs; first run PASS on every step
- tests/unit/test_compare.py; docs/validation/P7.md, README

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kemal committed 2026-09-28 17:00:37 +01:00

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src/simurg/compare/__init__.py

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