/// <summary>
/// Parse command line arguments
/// </summary>
/// <param name="args"></param>
/// <returns></returns>
static CommandLineOptions ProcessCommandLine(string[] args)
{
CommandLineOptions myArgs = new CommandLineOptions();
CommandLineArguments parser = new CommandLineArguments();
AddParameters(parser);
try
{
parser.Parse(args, myArgs);
}
catch (Exception e)
{
Console.Error.WriteLine("\nException while processing command line arguments [{0}]", e.Message);
Environment.Exit(-1);
}
if (myArgs.Help)
{
const string helpString = "Usage: SeqcosDiscarderUtil.exe [options] <input file> <output file>\n"
+ "\nDescription: Discard reads based on length (option -l) or quality (-q).\n"
+ "\n\n/Help (/h)\n Show this Help information"
+ "\n\n/Verbose (/v)\n Display more information"
+ "\n\n/DiscardedFile:<String> (/D)\n Filename to store discarded reads [optional]."
+ "\n\n*** Discard modes ***"
+ "\n\n/DiscardByLength:<INT > 0> (/l)\n Discard reads with length less than INT."
+ "\n\n/DiscardByQuality:<INT > 0> (/q)\n Discard reads with mean Phred-based quality score less than INT."
+ "\n\n/DiscardByRegex:<Pattern> (/r)\n Discard reads based a .NET Framework regular expression pattern. "
+ "For more information on .NET supported regular expressions, please visit: http://msdn.microsoft.com/en-us/library/az24scfc.aspx"
;
Console.WriteLine(helpString);
Environment.Exit(-1);
}
// Process all the arguments
if (!File.Exists(myArgs.FileList[0]))
{
Console.Error.WriteLine("Error: The file {0} could not be found.", myArgs.FileList[0]);
Environment.Exit(-1);
}
if ((myArgs.FileList == null) || (myArgs.FileList.Length < 2))
{
Console.Error.WriteLine("Error: Must specify an input and output file.");
Environment.Exit(-1);
}
if ((myArgs.DiscardByLength == 0 && myArgs.DiscardByQuality == 0) || (myArgs.DiscardByLength > 0 && myArgs.DiscardByQuality > 0))
{
Console.Error.WriteLine("Error: You must choose either -l or -q discard modes.");
Environment.Exit(-1);
}
if (myArgs.DiscardByRegex != null && !RegexTools.IsValidRegexPattern(myArgs.DiscardByRegex))
{
Console.Error.WriteLine("Error: unable to verify your regular expression pattern.");
Environment.Exit(-1);
}
return(myArgs);
}
/// <summary>
/// Parse command line arguments
/// </summary>
/// <param name="args"></param>
/// <returns></returns>
static CommandLineOptions ProcessCommandLine(string[] args)
{
CommandLineOptions myArgs = new CommandLineOptions();
CommandLineArguments parser = new CommandLineArguments();
AddParameters(parser);
try
{
parser.Parse(args, myArgs);
}
catch (Exception e)
{
Console.Error.WriteLine("\nException while processing command line arguments [{0}]", e.Message);
Environment.Exit(-1);
}
if (myArgs.Help)
{
const string helpString = "Usage: SeqcosTrimmerUtil.exe [options] <input file> <output file>\n"
+ "\nDescription: Trim reads based on length (use option -l) or quality (use option -q and optionally -l).\n"
+ "\n/Help (/h)\n Show this Help information"
+ "\n/Verbose (/v)\n Display more information"
+ "\n\n*** Trim modes ***"
+ "\n\n/TrimByLength:<INT > 0> (/l)\n Minimum length that reads will be trimmed to. Reads whose original length is less than INT will not be discarded."
+ "\n\n/TrimByQuality:<INT > 0> (/q)\n Minimum Phred-based quality score that reads will be trimmed to. Trimming is done by finding the subsequence whose "
+ "sum of differences between base quality score and cutoff is maximized. If a subsequence cannot be found due to poor quality, the entire read will be "
+ "discarded. \n\n Can be combined with /l option to set a minimum trimming length (e.g. if '/q 15 /l 10', any read that gets trimmed to a length less than "
+ "10 will be discarded."
+ "\n\n/TrimByRegex:<Pattern> (/r)\n Trim reads based on a .NET Framework regular expression pattern. Any matches found, will be stripped from the sequence. "
+ "For more information on .NET supported regular expressions, please visit: http://msdn.microsoft.com/en-us/library/az24scfc.aspx"
+ "\n\n*** Trim options ***\n"
+ "\n\n/Left (/L)\n When combined with /l, trimming occurs from the beginning of the read. When combined with /q, "
+ "trimming occurs at both ends of the read. For both modes, this option is OFF (i.e. only trim from right side)."
+ "\n\n/DiscardedFilename:<String> (/D)\n Filename to store discarded reads [optional]."
;
Console.WriteLine(helpString);
Environment.Exit(-1);
}
// Process all the arguments
if (!File.Exists(myArgs.InputFile))
{
Console.Error.WriteLine("Error: The file {0} could not be found.", myArgs.InputFile);
Environment.Exit(-1);
}
if (myArgs.TrimByLength == 0 && myArgs.TrimByQuality == 0 && myArgs.TrimByRegex != null)
{
Console.Error.WriteLine("You must choose a trim mode.");
Environment.Exit(-1);
}
if (myArgs.TrimByLength < 0)
{
Console.Error.WriteLine("Trim length must be greater than zero");
Environment.Exit(-1);
}
if (myArgs.TrimByQuality < 0)
{
Console.Error.WriteLine("Quality score threshold must be greater than zero");
Environment.Exit(-1);
}
if (myArgs.TrimByRegex != null && !RegexTools.IsValidRegexPattern(myArgs.TrimByRegex))
{
Console.Error.WriteLine("Error: unable to verify your regular expression pattern.");
Environment.Exit(-1);
}
return(myArgs);
}