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P3: normalization fit (1.2.0 and 1.1.2), apply, polar, simurg normalize
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- 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).

Co-Authored-By: Claude Opus 5.5 <[email protected]>
Claude-Session: https://claude.ai/code/session_01814GKVzZVL3FuF3DeiZXhv
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kemalandClaude Opus 5.5 committed 2026-09-27 22:51:06 +01:00
1 parent 5c93e194e0
commit 314fdc40d1
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+1097 -14
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tests/conftest.py
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@@ -24,7 +24,8 @@ GDA_EGT = DATA / "gda_v1" / "infinium-global-diversity-array-8-v1-0-D1-cluster-f
GDA_BPM = DATA / "gda_v1" / "infinium-global-diversity-array-8-v1-0-D1-manifest-file-bpm" / "GDA-8v1-0_D1.bpm"
GDA_SHEET = DATA / "gda_v1" / "infinium-global-diversity-array-8-v1-0_D1_SampleSheet_Demo_36.csv"
BIOC_IDATS = DATA / "bioc" / "IlluminaDataTestFiles_1.50.0" / "IlluminaDataTestFiles" / "inst" / "extdata" / "idat"
ORACLE_GTCS = DATA / "oracle" / "gsa_gtc_gtc2vcf"
ORACLE_GTCS = DATA / "oracle" / "gsa_gt3_nofma" # gtc2vcf, normalization 1.2.0, no FMA
ORACLE_GTCS_GT2 = DATA / "oracle" / "gsa_gt2_nofma" # normalization 1.1.2
def need(*paths: Path) -> None: