- tests/unit/test_genotype.py: fuzzy memberships incl. NaN rules, calls
at cluster centres, intensity threshold, BAF/LRR interpolation and
NaN pattern, LogR-dev locus set, sex rules v1/v2, TOP-strand base
calls, invariant dates, end-to-end `simurg genotype` (summary schema,
pass-through columns, thread/layout determinism, overwrite refusal)
- tests/oracle/test_p4_genotype.py: 36 GSA samples x 2 versions
byte-identical to the oracle
- scripts/validate_p4_large.py + cloud task p4: compare every vendor
GTC field by field and as whole files; reports which sex rule matches
- 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