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smith-chem-wisc / MetaMorpheus

Proteomics search software with integrated calibration, PTM discovery, bottom-up, top-down and LFQ capabilities
MIT License
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Enable users to limit the number of chimeric identifications per spectra #2364

Closed nbollis closed 1 month ago

nbollis commented 2 months ago

Added a field to common parameters and the search task GUI enabling the user to limit the number of chimeric identifications per spectra.

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This new parameter does not have any affect on the search or FDR calculations. The filtering is only performed after FDR has been calculated. The chimeras are grouped then sorted by QValue, then PEP, then score, keeping the top n identifications before writing the output. The default is currently set to 7.

I also added a custom comparer class that can be used in linq statements to group or select by multiple properties and have created a custom chimera comparer for PsmFromTsv and SpectralMatch.

The FilterSpecificPSMs method inside PostSearchAnalysisTask was not functioning. A list was passed in and modified in place without being saved to the original list. This was corrected by adding the ref keyword to the passed in list.

codecov[bot] commented 2 months ago

Codecov Report

Attention: Patch coverage is 87.05882% with 11 lines in your changes are missing coverage. Please review.

Project coverage is 92.78%. Comparing base (5ee8567) to head (931b03a).

Additional details and impacted files [![Impacted file tree graph](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2364/graphs/tree.svg?width=650&height=150&src=pr&token=m0HXyK8tFy&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc)](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2364?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc) ```diff @@ Coverage Diff @@ ## master #2364 +/- ## ========================================== + Coverage 92.76% 92.78% +0.01% ========================================== Files 137 138 +1 Lines 21166 21235 +69 Branches 2924 2933 +9 ========================================== + Hits 19635 19702 +67 - Misses 1049 1053 +4 + Partials 482 480 -2 ``` | [Files](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2364?dropdown=coverage&src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc) | Coverage Δ | | |---|---|---| | [MetaMorpheus/EngineLayer/CommonParameters.cs](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2364?src=pr&el=tree&filepath=MetaMorpheus%2FEngineLayer%2FCommonParameters.cs&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc#diff-TWV0YU1vcnBoZXVzL0VuZ2luZUxheWVyL0NvbW1vblBhcmFtZXRlcnMuY3M=) | `95.60% <100.00%> (+0.08%)` | :arrow_up: | | [...eus/TaskLayer/SearchTask/PostSearchAnalysisTask.cs](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2364?src=pr&el=tree&filepath=MetaMorpheus%2FTaskLayer%2FSearchTask%2FPostSearchAnalysisTask.cs&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc#diff-TWV0YU1vcnBoZXVzL1Rhc2tMYXllci9TZWFyY2hUYXNrL1Bvc3RTZWFyY2hBbmFseXNpc1Rhc2suY3M=) | `93.43% <100.00%> (+0.17%)` | :arrow_up: | | [...Morpheus/EngineLayer/FdrAnalysis/CustomComparer.cs](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2364?src=pr&el=tree&filepath=MetaMorpheus%2FEngineLayer%2FFdrAnalysis%2FCustomComparer.cs&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc#diff-TWV0YU1vcnBoZXVzL0VuZ2luZUxheWVyL0ZkckFuYWx5c2lzL0N1c3RvbUNvbXBhcmVyLmNz) | `73.80% <73.80%> (ø)` | | ... and [4 files with indirect coverage changes](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2364/indirect-changes?src=pr&el=tree-more&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc)