kemal/SimurgArray
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4 Commits
Author SHA1 Message Date
kemalandClaude Opus 5.5 febdd121ef P4 (WIP): GenCall-equivalent calling, BAF/LRR, sex, GTC v5, simurg genotype
ci / test (3.12) (push) Failing after 8s
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- 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)

Co-Authored-By: Claude Opus 5.5 <[email protected]>
Claude-Session: https://claude.ai/code/session_01814GKVzZVL3FuF3DeiZXhv
 2026-09-28 00:07:37 +01:00
kemalandClaude Opus 5.5 314fdc40d1 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
 2026-09-27 22:51:06 +01:00
kemalandClaude Opus 5.5 2e75345a30 P2 validation: oracle test and large-scale raw X/Y check
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- tests/oracle/test_p2_raw_xy.py: IDAT-assembled raw X/Y and controls
  equal the arrays in oracle GTCs
- validate_p1_large.py: phase-P2 comparison against vendor GTCs with
  diagnostics (channel swap, bead-count disagreements)
- cloud trial: also runs `simurg ingest` on all samples (time/memory),
  disk 250 GB

Co-Authored-By: Claude Opus 5.5 <[email protected]>
Claude-Session: https://claude.ai/code/session_01814GKVzZVL3FuF3DeiZXhv
 2026-09-27 20:57:42 +01:00
kemalandClaude Opus 5.5 4357d3deef P1: file parsers, sample sheet, discovery, CLI inspect
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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.

Co-Authored-By: Claude Opus 5.5 <[email protected]>
Claude-Session: https://claude.ai/code/session_01814GKVzZVL3FuF3DeiZXhv
 2026-09-27 16:56:39 +01:00