"No output" explained

Update to readme and internal help to include no output (None) option for file and metadata format (#172)

Author: caetera

MainClass.cs

@@ -526,11 +526,11 @@ private static void RegularParametersParsing(string[] args)
                 },
                 {
                     "f=|format=",
-                    "The spectra output format: 0 for MGF, 1 for mzML, 2 for indexed mzML, 3 for Parquet; both numeric and text (case insensitive) value recognized. Defaults to indexed mzML if no format is specified.",
+                    "The spectra output format: 0 for MGF, 1 for mzML, 2 for indexed mzML, 3 for Parquet, 4 for None (no output); both numeric and text (case insensitive) value recognized. Defaults to indexed mzML if no format is specified.",
                     v => outputFormatString = v
                 },
                 {
-                    "m=|metadata=", "The metadata output format: 0 for JSON, 1 for TXT; both numeric and text (case insensitive) value recognized",
+                    "m=|metadata=", "The metadata output format: 0 for JSON, 1 for TXT, 2 for None (no output); both numeric and text (case insensitive) value recognized. Defaults to None",
                     v => metadataFormatString = v
                 },
                 {
@@ -740,7 +740,7 @@ private static void RegularParametersParsing(string[] args)
                         "-c, --metadata_output_file");
                 }
 
-                if (parseInput.MetadataOutputFile != null && parseInput.MetadataFormat == MetadataFormat.NONE)
+                if (parseInput.MetadataOutputFile != null && parseInput.MetadataFormat == MetadataFormat.None)
                 {
                     throw new OptionException("specify a metadata format (0 for JSON, 1 for TXT)",
                         "-m, --metadata");

OutputFormat.cs

@@ -6,13 +6,13 @@ public enum OutputFormat
         MzML,
         IndexMzML,
         Parquet,
-        NONE
+        None
     }
 
     public enum MetadataFormat
     {
         JSON,
         TXT,
-        NONE
+        None
     }
 }

ParseInput.cs

@@ -121,8 +121,8 @@ public int Warnings
 
         public ParseInput()
         {
-            MetadataFormat = MetadataFormat.NONE;
-            OutputFormat = OutputFormat.NONE;
+            MetadataFormat = MetadataFormat.None;
+            OutputFormat = OutputFormat.None;
             Gzip = false;
             NoPeakPicking = new HashSet<int>();
             NoZlibCompression = false;

README.md

@@ -47,10 +47,9 @@ or
 mono ThermoRawFileParser.exe -d=/home/user/data_input/
 ```
 
-For running on Windows, omit `mono`. The optional parameters only work in the -option=value format. The tool can output some RAW file metadata `-m=0|1` (0 for JSON, 1 for TXT) and the spectra file `-f=0|1|2|3` (0 for MGF, 1 for mzML, 2 for indexed mzML, 3 for Parquet) or both. Use the `-p` flag to disable the thermo native peak picking. 
+For running on Windows, omit `mono`. The optional parameters only work in the -option=value format. The tool can output some RAW file metadata `-m=0|1` (0 for JSON, 1 for TXT) and the spectra file `-f=0|1|2|3|4` (0 for MGF, 1 for mzML, 2 for indexed mzML, 3 for Parquet, 4 for no output) or both. Use the `-p` flag to disable the thermo native peak picking. 
 
 ```
-ThermoRawFileParser.exe --help
 Usage is ThermoRawFileParser.exe [subcommand] [options]
 optional subcommands are xic|query (use [subcommand] -h for more info]):
   -h, --help                 Prints out the options.
@@ -70,13 +69,14 @@ optional subcommands are xic|query (use [subcommand] -h for more info]):
                                file or directory output. Implies silent logging,
                                 i.e. logging level 0
   -f, --format=VALUE         The spectra output format: 0 for MGF, 1 for mzML,
-                               2 for indexed mzML, 3 for Parquet; both numeric
-                               and text (case insensitive) value recognized.
-                               Defaults to indexed mzML if no format is
-                               specified.
-  -m, --metadata=VALUE       The metadata output format: 0 for JSON, 1 for TXT;
-                               both numeric and text (case insensitive) value
-                               recognized
+                               2 for indexed mzML, 3 for Parquet, 4 for None (
+                               no output); both numeric and text (case
+                               insensitive) value recognized. Defaults to
+                               indexed mzML if no format is specified.
+  -m, --metadata=VALUE       The metadata output format: 0 for JSON, 1 for TXT,
+                               2 for None (no output); both numeric and text (
+                               case insensitive) value recognized. Defaults to
+                               None
   -c, --metadata_output_file=VALUE
                              The metadata output file. By default the metadata
                                file is written to the output directory.

RawFileParser.cs

@@ -155,13 +155,13 @@ private static void ProcessFile(ParseInput parseInput)
                     }
                 }
 
-                if (parseInput.MetadataFormat != MetadataFormat.NONE)
+                if (parseInput.MetadataFormat != MetadataFormat.None)
                 {
                     MetadataWriter metadataWriter = new MetadataWriter(parseInput);
                     metadataWriter.WriteMetadata(rawFile, firstScanNumber, lastScanNumber);
                 }
 
-                if (parseInput.OutputFormat != OutputFormat.NONE)
+                if (parseInput.OutputFormat != OutputFormat.None)
                 {
                     SpectrumWriter spectrumWriter;
                     switch (parseInput.OutputFormat)