[WIP] filter psms for flashlfq only by qvalue and qvalue notch #2259
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Codecov Report
@@ Coverage Diff @@
## master #2259 +/- ##
==========================================
- Coverage 91.44% 91.43% -0.01%
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Files 134 134
Lines 20167 20158 -9
Branches 2809 2807 -2
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- Hits 18441 18432 -9
Misses 1237 1237
Partials 489 489
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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.