AI-Driven auto-optimize Makes MACS3 Peak Calling 41-64x Faster in One Weekend
jmschreiber91 · x · 2026-10-22
MACS3 v3.1.0 ships with Jacob Schreiber's auto-optimize contribution, delivering 41-64x faster callpeak runs in 8-core benchmarks (medians of three runs: BAM 41x, FRAG 64x, BAM with control 49x, BAMPE 57x). The maintainer credits AI with achieving in a weekend what he'd hoped for over years. The release also adds --threads/MACS3NUMTHREADS CPU budget controls, a --process-backend execution policy option, and fixes to control-sample duplicate filtering. Speedups are workload-specific; large inputs may use more peak memory.
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