Pointing auto-optimize at genomics code: tomtom made 7.8x faster, bit-identical output
jmschreiber91 · x · 2026-10-11
The author describes going deep into "auto-optimization"—a bubble-wrapped auto-research loop that keeps yielding massive speed/memory gains, arguing the genomics ecosystem has huge room for improvement.
First target: tomtom-lite (already 10-1000x faster than original tomtom). By clearing only rows actually written, blocking across query columns, and batching same-width queries, benchmark time fell from 5.455s to 0.7004s (7.8x) with bit-identical output. The PR is merged.
Related event: Auto-Optimization Loop Delivers Big Speedups Across Genomics Tools(2 posts)→
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