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).
kemal
6524a6d1b0