2 Commits

Include renames

Author	SHA1	Message	Date
kemalandClaude Opus 5.5	5bdd41b048	P9 (WIP): compiled kernels (rust/simurg-core, PyO3) with bit-identical pure-Python fallback ... Rust ports of the hot paths found by profiling: fused per-locus GenCall calling and scoring, BAF/LRR, libm maps with CPython math semantics, both nearest-neighbour searches of the normalization fit, and the BPM LocusEntry parser. Address coverage is memoised per IDAT layout. SIMURG_PURE_PYTHON=1 forces the pure paths. On the Pi: genotype_sample 3.4 s -> 1.1 s, 36-sample GSA run 131 s -> 46 s, BPM read 4x faster; 36 GSA + 6 Omni2.5 GTCs and QC tables byte-identical to the pure path; tests/unit/test_core_kernels.py checks every kernel on edge cases. bench/profile_genotype.py, bench/scaling.py, cloud task p9 (thread scaling). Co-Authored-By: Claude Opus 5.5 <[email protected]> Claude-Session: https://claude.ai/code/session_01814GKVzZVL3FuF3DeiZXhv	2026-09-28 21:28:55 +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