add end-to-end benchmark suite#677
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Split the monolithic bench_e2e.py into a modular benchmark/ package with focused modules (modes, datagen, runner, verify, report, sysinfo). Added 7 feature test modes (merge, correction, dedup, qualcut, high-thread) that exercise fastp code paths beyond default filtering, including overlapping PE data generation for merge/correction testing. Supports custom FASTQ input via --r1/--r2 with automatic format conversion. Co-Authored-By: Claude Opus 4.6 (1M context) <[email protected]>
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Summary
benchmark/) with 8 focused modules--r1/--r2flags for custom FASTQ input with automatic format conversion (gz<->fq)all(9 I/O),all-feat(7 feature),everything(16 total)Test plan
python3 -m benchmark --helpshows all modes and optionspython3 -m benchmark --mode all-feat --opt ./fastpruns all feature modespython3 -m benchmark --r1 real_R1.fq.gz --r2 real_R2.fq.gz --mode merge --opt ./fastpworks with custom datapython3 -m benchmark --mode everything --opt ./fastp --orig ./fastp_baselinefull regression test with verification🤖 Generated with Claude Code