/// <summary>
/// Parse command line arguments for Sequence Item Possible Occurence
/// </summary>
/// <param name="args">Array of command line arguments.</param>
private static void SeqPossibleOccurence(string[] args)
{
SequenceCoverage options = new SequenceCoverage();
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.DNAPossibleOccurenceHelp);
Environment.Exit(-1);
}
if (options.Help)
{
DisplayErrorMessage(Resources.DNAPossibleOccurenceHelp);
}
else
{
options.DisplaySequenceItemOccurences(args[0], true);
}
}
/// <summary>
/// Parse command line arguments for Sequence Distribution table for DNA
/// </summary>
/// <param name="args">Array of command line arguments.</param>
private static void SeqDistributionOption(string[] args)
{
SequenceCoverage options = new SequenceCoverage();
if (options.Usage)
{
DisplayErrorMessage(Resources.DNACoverageHelp);
}
else
{
options.DisplaySequenceItemOccurences(args[0], false);
}
}
/// <summary>
/// Parse command line arguments for Sequence Item Possible Occurence
/// </summary>
/// <param name="args">Array of command line arguments.</param>
private static void SeqPossibleOccurence(string[] args)
{
SequenceCoverage options = new SequenceCoverage();
if (options.Usage)
{
DisplayErrorMessage(Resources.DNAPossibleOccurenceHelp);
}
else
{
options.DisplaySequenceItemOccurences(args[0], true);
}
}
/// <summary>
/// Parse command line arguments for Sequence Item Possible Occurence
/// </summary>
/// <param name="args">Array of command line arguments.</param>
private static void SeqPossibleOccurence(string[] args)
{
SequenceCoverage options = new SequenceCoverage();
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.DNAPossibleOccurenceHelp);
Environment.Exit(-1);
}
if (options.Help)
{
DisplayErrorMessage(Resources.DNAPossibleOccurenceHelp);
}
else
{
options.DisplaySequenceItemOccurences(args[0], true);
}
}