/// <summary>
/// Parses ScaffoldGeneration command line parameters.
/// </summary>
/// <param name="args">The arguments.</param>
private static void ScaffoldGeneration(string[] args)
{
ScaffoldArguments arguments = new ScaffoldArguments();
CommandLineArguments parser = new CommandLineArguments();
// Add scaffold parameters
parser.Parameter(ArgumentType.DefaultArgument, "FilePath", ArgumentValueType.MultipleUniqueStrings, "", "File path");
parser.Parameter(ArgumentType.Optional, "Help", ArgumentValueType.Bool, "h", "Print the help information.");
parser.Parameter(ArgumentType.Optional, "OutputFile", ArgumentValueType.String, "o", "Output file");
parser.Parameter(ArgumentType.Optional, "Verbose", ArgumentValueType.Bool, "v", "Display verbose logging during processing.");
parser.Parameter(ArgumentType.Optional, "KmerLength", ArgumentValueType.Int, "k", "Length of k-mer");
parser.Parameter(ArgumentType.Optional, "Redundancy", ArgumentValueType.Int, "r", "Number of paired read required to connect two contigs.");
parser.Parameter(ArgumentType.Optional, "Depth", ArgumentValueType.Int, "d", "Depth for graph traversal.");
parser.Parameter(ArgumentType.Optional, "CloneLibraryName", ArgumentValueType.String, "n", "Clone Library Name");
parser.Parameter(ArgumentType.Optional, "MeanLengthOfInsert", ArgumentValueType.Int, "i", "Mean Length of clone library.");
parser.Parameter(ArgumentType.Optional, "StandardDeviationOfInsert", ArgumentValueType.Int, "sd", "Standard Deviation of Clone Library.");
if (args.Length > 1)
{
try
{
parser.Parse(args, arguments);
}
catch (ArgumentParserException ex)
{
DisplayErrorMessage(ex.Message);
DisplayErrorMessage(Resources.ScaffoldUtilHelp);
Environment.Exit(-1);
}
if (arguments.Help)
{
DisplayErrorMessage(Resources.ScaffoldUtilHelp);
}
else if (arguments.FilePath.Length == 2)
{
arguments.GenerateScaffolds();
}
else
{
DisplayErrorMessage(Resources.ScaffoldUtilHelp);
}
}
else
{
DisplayErrorMessage(Resources.ScaffoldUtilHelp);
}
}
/// <summary>
/// Parses ScaffoldGeneration command line parameters.
/// </summary>
/// <param name="args">The arguments.</param>
private static void ScaffoldGeneration(string[] args)
{
ScaffoldArguments arguments = new ScaffoldArguments();
CommandLineArguments parser = new CommandLineArguments();
// Add scaffold parameters
parser.Parameter(ArgumentType.DefaultArgument, "FilePath", ArgumentValueType.MultipleUniqueStrings, "", "File path");
parser.Parameter(ArgumentType.Optional, "Help", ArgumentValueType.Bool, "h", "Print the help information.");
parser.Parameter(ArgumentType.Optional, "OutputFile", ArgumentValueType.String, "o", "Output file");
parser.Parameter(ArgumentType.Optional, "Verbose", ArgumentValueType.Bool, "v", "Display verbose logging during processing.");
parser.Parameter(ArgumentType.Optional, "KmerLength", ArgumentValueType.Int, "k", "Length of k-mer");
parser.Parameter(ArgumentType.Optional, "Redundancy", ArgumentValueType.Int, "r", "Number of paired read required to connect two contigs.");
parser.Parameter(ArgumentType.Optional, "Depth", ArgumentValueType.Int, "d", "Depth for graph traversal.");
parser.Parameter(ArgumentType.Optional, "CloneLibraryName", ArgumentValueType.String, "n", "Clone Library Name");
parser.Parameter(ArgumentType.Optional, "MeanLengthOfInsert", ArgumentValueType.Int, "i", "Mean Length of clone library.");
parser.Parameter(ArgumentType.Optional, "StandardDeviationOfInsert", ArgumentValueType.Int, "sd", "Standard Deviation of Clone Library.");
if (args.Length > 1)
{
try
{
parser.Parse(args, arguments);
}
catch (ArgumentParserException ex)
{
DisplayErrorMessage(ex.Message);
DisplayErrorMessage(Resources.ScaffoldUtilHelp);
Environment.Exit(-1);
}
if (arguments.Help)
{
DisplayErrorMessage(Resources.ScaffoldUtilHelp);
}
else if (arguments.FilePath.Length == 2)
{
arguments.GenerateScaffolds();
}
else
{
DisplayErrorMessage(Resources.ScaffoldUtilHelp);
}
}
else
{
DisplayErrorMessage(Resources.ScaffoldUtilHelp);
}
}
/// <summary>
/// Parses ScaffoldGeneration command line parameters.
/// </summary>
/// <param name="args">The arguments.</param>
private static void ScaffoldGeneration(string[] args)
{
ScaffoldArguments arguments = new ScaffoldArguments();
if (args.Length > 1 && Parser.ParseArguments(args, arguments))
{
if (arguments.FilePath.Length == 2)
{
arguments.GenerateScaffolds();
}
else
{
DisplayErrorMessage(Resources.ScaffoldUtilHelp);
}
}
else
{
DisplayErrorMessage(Resources.ScaffoldUtilHelp);
}
}