Only quantify peptides that clear the q-value threshold

[Alexander-Sol]

Previously, when we wrote the AllQuantifiedPeptides output, we filtered based off of PSM q-value. So you would have some peptides with high q-values reported in the quant results. This fixes that!

In order to fix that, I had to reconfigure FDR calculation at the PSM and Peptide level. I did this by adding two new fields to SpectralMatch: PsmFdrInfo and PeptideFdrInfo. The names are self explanatory. There are a variety of toggles that were added to specify when Psm level FDR info should be used and peptide level info should be used.

[codecov]

Codecov Report

Attention: Patch coverage is 96.94656% with 4 lines in your changes missing coverage. Please review.

Project coverage is 92.90%. Comparing base (9b3118c) to head (454d20c).

Additional details and impacted files

@@           Coverage Diff           @@
##           master    #2375   +/-   ##
=======================================
  Coverage   92.89%   92.90%           
=======================================
  Files         139      139           
  Lines       21435    21498   +63     
  Branches     2944     2952    +8     
=======================================
+ Hits        19913    19973   +60     
- Misses       1043     1045    +2     
- Partials      479      480    +1     

Files	Coverage Δ
MetaMorpheus/EngineLayer/PsmTsv/PsmTsvWriter.cs	97.54% <100.00%> (ø)
MetaMorpheus/EngineLayer/SpectralMatch.cs	99.73% <100.00%> (+0.01%)	⬆️
MetaMorpheus/TaskLayer/MetaMorpheusTask.cs	88.49% <100.00%> (ø)
...aMorpheus/TaskLayer/SearchTask/SearchParameters.cs	100.00% <100.00%> (ø)
...EngineLayer/FdrAnalysis/PEPValueAnalysisGeneric.cs	95.72% <83.33%> (+<0.01%)	⬆️
...eus/TaskLayer/SearchTask/PostSearchAnalysisTask.cs	93.42% <98.36%> (+0.16%)	⬆️
...pheus/EngineLayer/FdrAnalysis/FdrAnalysisEngine.cs	96.57% <90.90%> (+0.04%)	⬆️

... and 1 file with indirect coverage changes