Try to fix gcms alignment processing bugs#708
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Pull request overview
This PR adjusts GC-MS alignment logic to use the correct retention-index (RI) tolerance during EI-MS scan comparisons, and tweaks spot-cleaning behavior to treat “Putative” identifications differently during refinement.
Changes:
- Fix EI-MS scan comparison calls to use
RetentionIndexAlignmentTolerance(instead of reusing RT tolerance) for RI matching/scoring. - Update GC-MS alignment refinement to exclude reference-matched spots whose names start with
"Putative"from the initial “clean” set and reprocess them in the deduplication pass.
Reviewed changes
Copilot reviewed 2 out of 2 changed files in this pull request and generated no comments.
| File | Description |
|---|---|
src/MSDIAL5/MsdialGcMsApi/Algorithm/Alignment/GcmsPeakJoiner.cs |
Corrects RI tolerance passed into EI-MS scan comparison so RI-based alignment uses the intended tolerance. |
src/MSDIAL5/MsdialGcMsApi/Algorithm/Alignment/GcmsAlignmentRefiner.cs |
Changes cleaned-spot selection/deduping rules to handle "Putative"-prefixed names specially. |
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