-x flag

Add reference and exception data

Author: caetera

MainClass.cs

@@ -19,7 +19,7 @@ public static class MainClass
         private static readonly ILog Log =
             LogManager.GetLogger(System.Reflection.MethodBase.GetCurrentMethod().DeclaringType);
 
-        public const string Version = "1.3.1";
+        public const string Version = "1.3.2";
 
         public static void Main(string[] args)
         {
@@ -424,6 +424,10 @@ private static void RegularParametersParsing(string[] args)
                     "e|ignoreInstrumentErrors", "Ignore missing properties by the instrument.",
                     v => parseInput.IgnoreInstrumentErrors = v != null
                 },
+                {
+                    "x|includeExceptionData", "Include reference and exception data",
+                    v => parseInput.ExData = v != null
+                },
                 {
                     "L=|msLevel=",
                     "Select MS levels (MS1, MS2, etc) included in the output, should be a comma-separated list of integers ( 1,2,3 ) and/or intervals ( 1-3 ), open-end intervals ( 1- ) are allowed",

ParseInput.cs

@@ -75,6 +75,8 @@ public string RawFilePath
 
         public bool IgnoreInstrumentErrors { get; set; }
 
+        public bool ExData { get; set; }
+
         public HashSet<int> MsLevel { get; set; }
 
         public bool MGFPrecursor { get; set; }

Properties/AssemblyInfo.cs

@@ -5,7 +5,7 @@
 // set of attributes. Change these attribute values to modify the information
 // associated with an assembly.
 [assembly: AssemblyTitle("ThermoRawFileParser")]
-[assembly: AssemblyDescription("")]
+[assembly: AssemblyDescription("Modular, Scalable, and Cross-Platform RAW File Conversion [PMID 31755270]")]
 [assembly: AssemblyConfiguration("")]
 [assembly: AssemblyCompany("")]
 [assembly: AssemblyProduct("ThermoRawFileParser")]
@@ -31,7 +31,7 @@
 // You can specify all the values or you can default the Build and Revision Numbers 
 // by using the '*' as shown below:
 // [assembly: AssemblyVersion("1.0.*")]
-[assembly: AssemblyVersion("1.3.1.0")]
-[assembly: AssemblyFileVersion("1.3.1.0")]
+[assembly: AssemblyVersion("1.3.2.0")]
+[assembly: AssemblyFileVersion("1.3.2.0")]
 
 [assembly: log4net.Config.XmlConfigurator(ConfigFile = "log4net.config")]

README.md

@@ -76,6 +76,7 @@ optional subcommands are xic|query (use [subcommand] -h for more info]):
                                verbose.
   -e, --ignoreInstrumentErrors
                              Ignore missing properties by the instrument.
+  -x, --includeExceptionData Include reference and exception data
   -L, --msLevel=VALUE        Select MS levels (MS1, MS2, etc) included in the
                                output, should be a comma-separated list of
                                integers ( 1,2,3 ) and/or intervals ( 1-3 ),

RawFileParser.cs

@@ -99,6 +99,8 @@ private static void ProcessFile(ParseInput parseInput)
                 // selected instrument to the MS instrument, first instance of it
                 rawFile.SelectInstrument(Device.MS, 1);
 
+                rawFile.IncludeReferenceAndExceptionData = parseInput.ExData;
+
                 // Get the first and last scan from the RAW file
                 var firstScanNumber = rawFile.RunHeaderEx.FirstSpectrum;
                 var lastScanNumber = rawFile.RunHeaderEx.LastSpectrum;