kemal
d163b34eca
- signal/normalization/numerics.py: vendor percentile, trimmean, MAD sigma (old/new), bisquare robust fits, float32/float64 typing and sequential sums reproduced exactly (ported from gtc2vcf, MIT) - signal/normalization/fit.py: outlier removal, offset, rotation, shear, scale, nn12/rr12, single-channel model for small Infinium I bins, exact and binned nearest-neighbour sweeps; vendor quirks marked QUIRK - signal/normalization/apply.py: affine transform and theta/R - pipeline/normalize.py + CLI `simurg normalize` - oracle GTCs rebuilt with -ffp-contract=off (aarch64 gcc fuses a*b+c by default, shifting the last bits); the old FMA oracle differed by <=4 ULP Result: transforms bit-identical to the oracle for all 36 GSA samples x 48 bins, for both normalization versions (3456/3456 bins, 0 ULP).
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).
- SIMURGARRAY_MASTER_PLAN.md — architecture, algorithms, roadmap
- SIMURGARRAY_FUNCTIONAL_SPEC.md — 416 itemised requirements (CLI, inputs, outputs, QC, CN, PGx, methylation, edge cases)
docs/validation/— per-phase validation reports ·docs/known_unknowns.md— findings log ·docs/research/— background
Status
Phases P0 (setup), P1 (file parsers) and P2 (canonical model, raw X/Y) are complete — see
docs/validation/. Validated on 2141 vendor GTCs of the 1000 Genomes Omni2.5 set.
Available commands: simurg version, simurg inspect <files…> [--json], simurg ingest.
Quick start
uv venv && uv pip install -e ".[dev]"
uv run pytest tests/unit # no downloads needed
bash scripts/bootstrap_refs.sh # reference open-source repos → refs/ (oracles)
bash scripts/fetch_data.sh p0 # ~1.4 GB of public test data → data/
bash scripts/make_oracle_gtcs.sh # builds gtc2vcf, writes oracle GTCs
uv run pytest tests/oracle # real-data acceptance tests (add -m "not slow" to skip the long ones)
uv run simurg inspect data/p0/gsa_v4_pgx/idats_Demo_36/idats_Demo_36/207895980019/207895980019_R03C01_Grn.idat
Vendor data files are downloaded for personal research use only and are never committed. See THIRD_PARTY_NOTICES.md.