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[WIP] filter psms for flashlfq only by qvalue and qvalue notch #2259

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this code was changed in a prior commit #2161
Files with values for PEP were filtered by PEP. But when assigning them to ProteinGroups, the filter was for qvalue and qvalue notch. Thus there was incosistency that produced UNDEFINED protein groups for some peptides. This messed up protein quantification.

@trishorts trishorts added Bug WIP Work in progress, not ready for review labels Feb 27, 2023
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codecov bot commented Feb 27, 2023

Codecov Report

Merging #2259 (e5158ee) into master (8d84c84) will decrease coverage by 0.01%.
The diff coverage is 100.00%.

Impacted file tree graph

@@            Coverage Diff             @@
##           master    #2259      +/-   ##
==========================================
- Coverage   91.44%   91.43%   -0.01%     
==========================================
  Files         134      134              
  Lines       20167    20158       -9     
  Branches     2809     2807       -2     
==========================================
- Hits        18441    18432       -9     
  Misses       1237     1237              
  Partials      489      489              
Impacted Files Coverage Δ
TaskLayer/SearchTask/PostSearchAnalysisTask.cs 92.50% <100.00%> (-0.06%) ⬇️

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