/// <summary>
/// Parse command line arguments for Orphan regions command
/// </summary>
/// <param name="args">Array of command line arguments.</param>
private static void OrphanRegionOption(string[] args)
{
Orphans options = new Orphans();
CommandLineArguments parser = new CommandLineArguments();
// Add the parameters
parser.Parameter(ArgumentType.Optional, "SAMInput", ArgumentValueType.Bool, "S", "Input is SAM format");
parser.Parameter(ArgumentType.Optional, "Help", ArgumentValueType.Bool, "", "");
try
{
parser.Parse(args, options);
}
catch (ArgumentParserException ex)
{
DisplayErrorMessage(ex.Message);
DisplayErrorMessage(Resources.OrphanRegionsHelp);
Environment.Exit(-1);
}
if (options.Help)
{
DisplayErrorMessage(Resources.OrphanRegionsHelp);
}
else
{
options.DisplayOrpanChromosomes(args[0]);
}
}
/// <summary>
/// Parse command line arguments for Orphan regions command
/// </summary>
/// <param name="args">Array of command line arguments.</param>
private static void OrphanRegionOption(string[] args)
{
Orphans options = new Orphans();
if (options.Usage)
{
DisplayErrorMessage(Resources.OrphanRegionsHelp);
}
else
{
options.DisplayOrpanChromosomes(args[0]);
}
}
/// <summary>
/// Parse command line arguments for Orphan regions command
/// </summary>
/// <param name="args">Array of command line arguments.</param>
private static void OrphanRegionOption(string[] args)
{
Orphans options = new Orphans();
CommandLineArguments parser = new CommandLineArguments();
// Add the parameters
parser.Parameter(ArgumentType.Optional, "SAMInput", ArgumentValueType.Bool, "S", "Input is SAM format");
parser.Parameter(ArgumentType.Optional, "Help", ArgumentValueType.Bool, "", "");
try
{
parser.Parse(args, options);
}
catch (ArgumentParserException ex)
{
DisplayErrorMessage(ex.Message);
DisplayErrorMessage(Resources.OrphanRegionsHelp);
Environment.Exit(-1);
}
if (options.Help)
{
DisplayErrorMessage(Resources.OrphanRegionsHelp);
}
else
{
options.DisplayOrpanChromosomes(args[0]);
}
}
