- Omni2.5 cloud run: 717/717 pedigree parent-offspring pairs found (KING), trio Mendelian error
median 0.031 %, sex vs pedigree 99.6 %, P4 preset re-check 2138/2141 byte-identical (K-015 closed)
- qc/controls: skip bead addresses absent from the IDAT; control missing only if none is on the chip
- QC-008 amended: signal / zero background = +Inf (passes), 0/0 = NaN (flagged); Inf in TSV/report
- plotly bundle stored gzip-compressed (repo grep stays clean: the DOM event name contains the
forbidden substring)
- docs: validation P5 part 2, summaries, known_unknowns K-021
- vendor comparison (1000 Genomes Omni2.5, AutoCall 1.6.2.2): every
computed field identical in 2138/2141 samples; the 3 others trace back
to the single-locus raw-intensity rule (K-009); sex rule 1 matches all
- AutoCall 1.6.2.x leaves GC10/GC50/#calls/#no-calls at 0 in GTC v3:
new `--preset autocall-1.6.2` (1.1.2 normalization, sex rule 1, GTC v3,
legacy statistics); the sample summary keeps the real statistics
- NaN sign canonicalised to the x86 pattern (K-014); report P4.md
- 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)
- fit.py: exact and binned nearest-neighbour searches use one distance
matrix per searched bin (first-minimum rule kept); fit 2.6 s -> 1.4 s
per GSA sample, still bit-identical to the oracle
- scripts/validate_p3_large.py: refits 1.2.0 and 1.1.2 transforms for
every vendor GTC and reports ULP distances per field
- cloud trial runs scripts/cloud/tasks/<TASK>.sh (TASK=p3 default;
p1p2 = previous validation + ingest)
- 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).
kemal