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perf(extract): skip the MS1 traces a retrace skeleton zeroes - #205
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RobbinBouwmeester merged 9 commits intoOct 17, 2026
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Extract writes three MS1 isotope traces (mono, +1, +2) per candidate, each read on the candidate's grid as the maximum over the nearest MS1 scan and its ms1_scan_halfwidth neighbours. When retrace follows, the skeleton then zeroed every one of those rows, because retrace rebuilds them from the raw events. gdb samples of a standalone extract of a HYE diaPASEF run put about half of extract's busy time in those MS1 reads (ms1_near). The skeleton decision reads only the row's identity (Skeleton::zeroes, the rule retrace classifies by), so it is now taken first, and a row it zeroes is written as zeros without being read. The chromatogram table is the one the reading-then-zeroing wrote, and the apex MS1 reads that feed the features are unchanged. Without retrace, or under retrace.ms1 = false, nothing changes. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
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Part of a stack on #196; merge in order: 9 -> 10 -> 11 -> 12 -> 13 -> 14 -> 15 -> 16 -> 17. Measured on the six ProteoBench HYE diaPASEF runs (60 min, timsTOF SCP) on a 128-core host at 120 threads, NN seed 0,
MUMDIA_CACHE_DIR=off; docs/35_diapasef.md section 16 has the details.Summary
About half of extract's busy time on a HYE diaPASEF run (gdb samples,
ms1_near) was the MS1 reads of the three isotope traces per candidate, which the retrace skeleton then zeroed because retrace rebuilds those rows. The skeleton decision reads only a row's identity, so it is taken first and a zeroed row is written without being read; the table is unchanged. Part of the six-run measurement in the run-order PR (output bit-identical).Checks
cargo fmt --check,cargo clippy --workspace --all-targets -D warnings,cargo test --workspace,ci/gen_config_reference.py --check,ci/check_doc_refs.py,python -m compileall scripts.🤖 Generated with Claude Code