Fixing after merge

Author: caetera

MainClass.cs

@@ -574,8 +574,7 @@ private static void RegularParametersParsing(string[] args)
                         "-o, --output");
                 }
 
-                if (metadataFormatString == null && parseInput.DepositionMetadataFile == null
-                    && parseInput.ExperimentMetadataFile == null && outputFormatString == null)
+                if (metadataFormatString == null && outputFormatString == null)
                 {
                     parseInput.OutputFormat = OutputFormat.IndexMzML;
                 }

ParseInput.cs

@@ -29,6 +29,7 @@ public string RawFilePath
                 if (value != null)
                 {
                     RawFileNameWithoutExtension = Path.GetFileNameWithoutExtension(value);
+                    //do we need it?
                     var splittedPath = value.Split('/');
                     _rawFileName = splittedPath[splittedPath.Length - 1];
                 }
@@ -93,6 +94,7 @@ public string RawFilePath
 
         public string BucketName { get; set; }
 
+        //this property assigned but never used
         /// <summary>
         /// The raw file name.
         /// </summary>

Writer/MzMlSpectrumWriter.cs

@@ -1181,7 +1181,7 @@ private SpectrumType ConstructMSSpectrum(int scanNumber)
             //tune version < 3
             if (trailerData.Has("SPS Mass 1:"))
             {
-                foreach (var label in trailerData.MatchKeys(SPSentry))
+                foreach (var label in trailerData.MatchKeys(_spSentry))
                 {
                     var mass = trailerData.AsDouble(label).GetValueOrDefault(0);
                     if (mass > 0) SPSMasses.Add((double)mass); //zero means mass does not exist
@@ -1191,7 +1191,7 @@ private SpectrumType ConstructMSSpectrum(int scanNumber)
             //tune version == 3
             if (trailerData.Has("SPS Masses:"))
             {
-                foreach (var labelvalue in trailerData.MatchValues(SPSentry3))
+                foreach (var labelvalue in trailerData.MatchValues(_spSentry3))
                 {
                     foreach (var mass in labelvalue.Trim().Split(new char[] { ',' }, StringSplitOptions.RemoveEmptyEntries))
                     {
@@ -1372,7 +1372,7 @@ private SpectrumType ConstructMSSpectrum(int scanNumber)
             });
 
             // FAIMS
-            if(FAIMSCV != null && FAIMSON)
+            if(FAIMSCV != null)
             {
                 spectrumCvParams.Add(new CVParamType
                 {