Merge branch 'master' of https://github.com/compomics/ThermoRawFileParser

Author: nielshulstaert

README.md

@@ -1,7 +1,7 @@
 # ThermoRawFileParser
 
 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: only MS2 spectra
+* MGF: only MS2 and MS3 spectra
 * mzML and indexed mzML: both MS1 and MS2 spectra
 * Apache Parquet: under development
 
@@ -20,6 +20,7 @@ For running on Windows, omit `mono`. The optional parameters only work in the -o
 ThermoRawFileParser.exe --help
  usage is (use -option=value for the optional arguments):
   -h, --help                 Prints out the options.
+      --version              Prints out the library version.
   -i, --input=VALUE          The raw file input.
   -o, --output=VALUE         The output directory. Specify this or an output
                                file.
@@ -62,7 +63,33 @@ If you want to build the project using nuget, put the ThermoFisher.CommonCore.Ra
 
 ## Logging
 
-The default log file is `ThermoRawFileParser.log`. The log settings can be changed in `log4net.config`.
+By default the parser only logs to console. To enable logging to file, uncomment the file appender in the `log4net.config` file.
+
+```
+<log4net>
+    <root>
+        <level value="INFO" />
+        <appender-ref ref="console" />
+        <!--<appender-ref ref="file" />-->
+    </root>
+    <appender name="console" type="log4net.Appender.ConsoleAppender">
+        <layout type="log4net.Layout.PatternLayout">
+            <conversionPattern value="%date %level %logger - %message%newline" />
+        </layout>
+    </appender>
+    <!--<appender name="file" type="log4net.Appender.RollingFileAppender">
+        <file value="ThermoRawFileParser.log" />
+        <appendToFile value="true" />
+        <rollingStyle value="Size" />
+        <maxSizeRollBackups value="5" />
+        <maximumFileSize value="10MB" />
+        <staticLogFileName value="true" />
+        <layout type="log4net.Layout.PatternLayout">
+            <conversionPattern value="%date [%thread] %level %logger - %message%newline" />
+        </layout>
+    </appender>-->
+</log4net>
+```
 
 ## Docker