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Enable users to limit the number of chimeric identifications per spectra #2364

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@nbollis nbollis commented May 3, 2024

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.

@nbollis nbollis added Validation WIP Work in progress, not ready for review labels May 3, 2024
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codecov bot commented May 3, 2024

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).

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@@            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 Coverage Δ
MetaMorpheus/EngineLayer/CommonParameters.cs 95.60% <100.00%> (+0.08%) ⬆️
...eus/TaskLayer/SearchTask/PostSearchAnalysisTask.cs 93.43% <100.00%> (+0.17%) ⬆️
...Morpheus/EngineLayer/FdrAnalysis/CustomComparer.cs 73.80% <73.80%> (ø)

... and 4 files with indirect coverage changes

@nbollis nbollis closed this May 30, 2024
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