Methylation CSV manifest reader (MET-002/003), raw M/U assembly with bead masking
(MET-005), pOOBAH detection p-values, noob background correction, linear/nonlinear dye
bias, beta and M-values (MET-010..012), the 21 methylation control metrics (MET-006,
bs-conv red-bg set option), per-sample ctrl/cgs tables, summary tsv/xlsx/html with the
detection histogram and a beta PCA, pcs.tsv.gz, controls_raw/controls_qc.tsv; methylation
datasets load in qc report (MET-014); qc controls --array-type methylation; minfi-style
Sentrix_ID/Sentrix_Position sheet keys. Vendor EPIC manifests carry a 5th field on some
control lines: >= 4 fields accepted. Runs on the public minfiDataEPIC set (3 x NA12878).
- genotype/clusters.py: EGT aligned to manifest order (float32 mean R)
- genotype/gencall.py: flair, six-case likelihood, priors/posteriors,
fuzzy sub-scores and score map, vectorised with the reference's
float/double evaluation order and libm transcendentals
- genotype/baf_lrr.py, sex.py (rules v1/v2), sample.py (IDAT -> Gtc)
- pipeline/inputs.py shared by ingest and genotype
- pipeline/genotype.py + CLI: GTC per sample, sample_summary.tsv/json
(OUT-060..063), run manifest
- GTCs from IDATs are byte-identical to the oracle for 36 GSA samples x
2 normalization versions (NaN sign canonicalised to the x86 pattern)
kemal