Edited MSFragger Reader

[mzhastings]

Made changes to MSFraggerPsm class to fix errors when reading psm.tsv files returned by MSFragger.

• Added a new property RetentionTimeSeconds to map the raw "Retention" column from the psm.tsv file (reported in seconds).
• Modified the existing RetentionTime property to be computed from RetentionTimeSeconds, converting it to minutes
• Changed FileName property to use FileNameWithoutExtension instead of SpectrumFilePath (points to a .pep.xml file created by MSFragger, which appends the file name with interact-). The list of SpectrumFilePaths was thus inconsistent with the raw file names used in the dictionary mapping file names to their paths

Made changes to SpectrumMatchFromTsv class

• Added support for optional PEP and PEP_QValue columns for compatibility with different versions of MetaMorpheus that may or may not include these columns

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 78.68%. Comparing base (b83de70) to head (eb33927).

Additional details and impacted files

@@           Coverage Diff           @@
##           master     #871   +/-   ##
=======================================
  Coverage   78.67%   78.68%           
=======================================
  Files         251      251           
  Lines       36330    36331    +1     
  Branches     3873     3875    +2     
=======================================
+ Hits        28584    28586    +2     
  Misses       7082     7082           
+ Partials      664      663    -1     

Files with missing lines	Coverage Δ
...nalResults/IndividualResultRecords/MsFraggerPsm.cs	91.13% <100.00%> (+0.11%)	⬆️
...ts/IndividualResultRecords/SpectrumMatchFromTsv.cs	92.94% <100.00%> (+0.24%)	⬆️

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[Alexander-Sol]

You can get rid of the SmallCalibratibleYeast.mzml file, as it's not actually used for the tests