3 Commits

Include renames

Author	SHA1	Message	Date
kemalandClaude Opus 5.5	febdd121ef	P4 (WIP): GenCall-equivalent calling, BAF/LRR, sex, GTC v5, simurg genotype ... - 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	a4faead6d7	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 Co-Authored-By: Claude Opus 5.5 <[email protected]> Claude-Session: https://claude.ai/code/session_01814GKVzZVL3FuF3DeiZXhv	2026-09-27 20:54:06 +01:00
kemalandClaude Opus 5.5	4357d3deef	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. 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