Flag in-source fragments and re-inject for quantification (--flag_in_source)#3
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jonasscheid wants to merge 5 commits into
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Flag in-source fragments and re-inject for quantification (--flag_in_source)#3jonasscheid wants to merge 5 commits into
jonasscheid wants to merge 5 commits into
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…them into quantification Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
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…lagging, snapshot versions in test, honor --min-len Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
…g survives the QUANT consensus into the final TSV Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
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Description
Adds
--flag_in_source(defaultfalse). After rescoring, flags in-source fragments among the 100% FDR PSMs using the FDR-filtered peptides as parents (strict per-run co-elution in observed RT + DeepLC RT-prediction mismatch), tags every PeptideHit with anis_isfUserParam, and re-injects the flagged fragments into the FDR-filtered set so their signal reaches quantification.is_isfis exported to the final TSV.New module
PYOPENMS_FLAGINSOURCE(bin/flag_in_source_fragments.py); when the flag is off, behaviour is unchanged.PR checklist
CHANGELOG.mdis updated.nf-core pipelines lint).nextflow run . -profile test,docker --outdir <OUTDIR>).docs/usage.mdis updated.docs/output.mdis updated.