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4 Commits
Author SHA1 Message Date
kemal bf00b0e453 P3: vectorised nearest-neighbour search; task-driven cloud trials 
- 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)
 2026-09-27 22:57:03 +01:00
kemal 95e4e41560 P3: normalization fit (1.2.0 and 1.1.2), apply, polar, simurg normalize 
- 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).
 2026-09-27 22:51:06 +01:00
kemal 87f9b3499c P2 (WIP): raw X/Y assembly, canonical Parquet model, simurg ingest 
- signal/raw_xy.py: vectorised Infinium I/II raw X/Y and control assembly
  (plan §7.1) with a per-chip address-map cache; IN-027 coverage gate
- core/schemas.py: Arrow schemas (loci, sample_intensity, controls),
  deterministic atomic Parquet writing
- pipeline/ingest.py + CLI: discovery, sheet, IN-010 naming, overwrite
  check before any work, spawn-based workers, per-sample isolation,
  --resume by input hashes, run manifest, exit codes 0/3/4
- matches gtc2vcf raw X/Y and controls exactly on 18 GSA samples;
  outputs byte-identical across thread counts and layouts
 2026-09-27 20:54:06 +01:00
kemal 8cd092460f P1: file parsers, sample sheet, discovery, CLI inspect 
Readers for IDAT v3, BPM (locus entries v4-v8), CSV manifest, EGT
(data blocks 5-9) and GTC v3-v5 (plus a layout-preserving GTC writer);
sample-sheet validation (IN-001..IN-014), IDAT discovery and pairing
(IN-020..IN-022), message catalogue and exit codes (CLI-014/016),
JSON Lines logging (CLI-007/008), atomic writes (CLI-011), run manifest,
and `simurg inspect`.

Validation (docs/validation/P1.md): GTC, BPM and EGT readers agree
exactly with Illumina BeadArrayFiles on GSA v4 / GDA v1 files; GTCs
round-trip byte-identically; BPM and CSV manifests are consistent.
 2026-09-27 16:56:39 +01:00