perf: optimize FASTQ reader with memchr, skipLine, and readExact#671
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KimBioInfoStudio wants to merge 1 commit intoOpenGene:masterfrom
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perf: optimize FASTQ reader with memchr, skipLine, and readExact#671KimBioInfoStudio wants to merge 1 commit intoOpenGene:masterfrom
KimBioInfoStudio wants to merge 1 commit intoOpenGene:masterfrom
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Replace byte-by-byte newline scanning in getLine() with memchr for SIMD-accelerated delimiter search. Add skipLine() to skip the '+' strand line without string allocation, and readExact() to read quality by known length (== sequence length) without scanning for newlines. Benchmark (2M PE reads, M4 Pro, -w 10): fq→fq: 1.08x speedup gz→fq: 1.08x speedup stdin→stdout: 1.44x speedup (memchr alone) Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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Summary
\r/\nscanning ingetLine()withmemchr(SIMD-accelerated in libc)skipLine()to skip the+strand line without string allocationreadExact()to read quality line by known length (== sequence length), no newline scan needed\r\nskip check at buffer boundaryBenchmark (2M PE reads, Apple M4 Pro, -w 10)
Output gz modes show no change (bottleneck is compression, not parsing).
Verification
Test plan
🤖 Generated with Claude Code