pre merge commit

Author: nielshulstaert

MainClass.cs

@@ -782,7 +782,7 @@ private static HashSet<int> ParseMsLevel(string inputString)
             if (!valid.IsMatch(inputString))
                 throw new OptionException("Invalid characters in msLevel key", "msLevel");
 
-            foreach (var piece in inputString.Split(new char[] { ',' }))
+            foreach (var piece in inputString.Split(new char[] {','}))
             {
                 try
                 {
@@ -825,7 +825,8 @@ private static HashSet<int> ParseMsLevel(string inputString)
 
                 catch (Exception ex)
                 {
-                    throw new OptionException(String.Format("Cannot parse part of msLevel input: '{0}'", piece), "msLevel", ex);
+                    throw new OptionException(String.Format("Cannot parse part of msLevel input: '{0}'", piece),
+                        "msLevel", ex);
                 }
             }
 

README.md

@@ -2,7 +2,7 @@
 
 Wrapper around the .net (C#) ThermoFisher ThermoRawFileReader library for running on Linux with mono (works on Windows too). It takes a thermo RAW file as input and outputs a metadata file and the spectra in 3 possible formats:
 * MGF: MS2 and MS3 spectra
-* mzML and indexed mzML: both MS1, MS2 and MS3 spectra
+* mzML and indexed mzML: MS1, MS2 and MS3 spectra
 * Apache Parquet: under development
 
 As of version 1.2.0, 2 subcommands are available (shoutout to the [eubic 2020 developers meeting](https://eubic-ms.org/events/2020-developers-meeting/), see [usage](#usage) for examples):
@@ -113,7 +113,7 @@ usage is:
                                Thermo library. By default peak picking is
                                enabled.
   -s, --stdout               Pipes the output into standard output. Logging is
-                               being turned off
+                               being turned off.
 ```
 ### xic subcommand
 Return one or more chromatograms based on query JSON input.

RawFileParser.cs

@@ -24,7 +24,9 @@ public static void Parse(ParseInput parseInput)
             {
                 Log.Info("Started analyzing folder " + parseInput.RawDirectoryPath);
 
-                var rawFilesPath = Directory.EnumerateFiles(parseInput.RawDirectoryPath, "*", SearchOption.TopDirectoryOnly).Where(s => s.ToLower().EndsWith("raw")).ToArray();
+                var rawFilesPath = Directory
+                    .EnumerateFiles(parseInput.RawDirectoryPath, "*", SearchOption.TopDirectoryOnly)
+                    .Where(s => s.ToLower().EndsWith("raw")).ToArray();
                 Log.Info(String.Format("The folder contains {0} RAW files", rawFilesPath.Length));
 
                 if (rawFilesPath.Length == 0)

ThermoRawFileParserTest/WriterTests.cs

@@ -44,8 +44,8 @@ public void TestFolderMgfs()
 
             RawFileParser.Parse(parseInput);
 
-            var numfiles = Directory.GetFiles(tempFilePath, "*.mgf");
-            Assert.AreEqual(numfiles.Length, 2);
+            var numFiles = Directory.GetFiles(tempFilePath, "*.mgf");
+            Assert.AreEqual(numFiles.Length, 2);
 
             var mgfData = Mgf.LoadAllStaticData(Path.Combine(tempFilePath, "small1.mgf"));
             Assert.AreEqual(34, mgfData.NumSpectra);

Writer/MzMlSpectrumWriter.cs

@@ -1177,7 +1177,7 @@ private SpectrumType ConstructMSSpectrum(int scanNumber)
                 //tune version < 3 produced trailer entry like "SPS Mass #", one entry per mass
                 if (SPSentry.IsMatch(trailerData.Labels[i]))
                 {
-                    var mass = Double.Parse(trailerData.Values[i]);
+                    var mass = double.Parse(trailerData.Values[i]);
                     if (mass > 0)  SPSMasses.Add(mass); //zero means mass does not exist
                 }
 
@@ -1186,7 +1186,7 @@ private SpectrumType ConstructMSSpectrum(int scanNumber)
                 {
                     foreach (var mass in trailerData.Values[i].Trim().Split(new char[] { ',' }, StringSplitOptions.RemoveEmptyEntries))
                     {
-                        SPSMasses.Add(Double.Parse(mass));
+                        SPSMasses.Add(double.Parse(mass));
                     }
 
                 }