/// <summary>
/// Scaffold function.
/// </summary>
/// <param name="args">Arguments to Scaffold function.</param>
private static void Scaffold(string[] args)
{
ScaffoldArguments options = new ScaffoldArguments();
CommandLineArguments parser = new CommandLineArguments();
// Add the parameters
parser.Parameter(ArgumentType.Required, "KmerLength", ArgumentValueType.OptionalInt, "k", "Length of k-mer");
parser.Parameter(ArgumentType.Optional, "Help", ArgumentValueType.Bool, "h", "");
parser.Parameter(ArgumentType.Optional, "OutputFile", ArgumentValueType.String, "o", "Output file");
parser.Parameter(ArgumentType.DefaultArgument, "Filenames", ArgumentValueType.MultipleUniqueStrings, "", "Input file of reads and contigs.");
parser.Parameter(ArgumentType.Optional, "CloneLibraryName", ArgumentValueType.String, "n", "Clone Library Name");
parser.Parameter(ArgumentType.Optional, "MeanLengthOfInsert", ArgumentValueType.Int, "m", "Mean Length of clone library.");
parser.Parameter(ArgumentType.Optional, "StandardDeviationOfInsert", ArgumentValueType.Int, "s", "Standard Deviation of Clone Library.");
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, "Verbose", ArgumentValueType.Bool, "v", "Display verbose logging during processing.");
if (args.Length > 0)
{
try
{
parser.Parse(args, options);
}
catch (ArgumentParserException ex)
{
Console.Error.WriteLine(ex.Message);
Console.Error.WriteLine(Resources.ScaffoldHelp);
Environment.Exit(-1);
}
if (options.Help)
{
DisplayErrorMessage(Resources.ScaffoldHelp);
}
else if (options.FileNames != null)
{
options.GenerateScaffold();
}
else
{
DisplayErrorMessage(Resources.ScaffoldHelp);
}
}
else
{
DisplayErrorMessage(Resources.ScaffoldHelp);
}
}
/// <summary>
/// Scaffold function.
/// </summary>
/// <param name="args">Arguments to Scaffold function.</param>
private static void Scaffold(string[] args)
{
ScaffoldArguments options = new ScaffoldArguments();
if (args.Length > 0 && Parser.ParseArguments(args, options))
{
if (options.FileNames != null)
{
options.GenerateScaffold();
}
else
{
DisplayErrorMessage(Resources.ScaffoldHelp);
}
}
else
{
DisplayErrorMessage(Resources.ScaffoldHelp);
}
}
/// <summary>
/// Scaffold function.
/// </summary>
/// <param name="args">Arguments to Scaffold function.</param>
private static void Scaffold(string[] args)
{
ScaffoldArguments options = new ScaffoldArguments();
CommandLineArguments parser = new CommandLineArguments();
// Add the parameters
parser.Parameter(ArgumentType.Optional, "Quiet", ArgumentValueType.Bool, "q", "Display minimal output during processing.");
parser.Parameter(ArgumentType.Required, "KmerLength", ArgumentValueType.OptionalInt, "k", "Length of k-mer");
parser.Parameter(ArgumentType.Optional, "Help", ArgumentValueType.Bool, "h", "");
parser.Parameter(ArgumentType.Optional, "OutputFile", ArgumentValueType.String, "o", "Output file");
parser.Parameter(ArgumentType.DefaultArgument, "Filenames", ArgumentValueType.MultipleUniqueStrings, "", "Input file of reads and contigs.");
parser.Parameter(ArgumentType.Optional, "CloneLibraryName", ArgumentValueType.String, "n", "Clone Library Name");
parser.Parameter(ArgumentType.Optional, "MeanLengthOfInsert", ArgumentValueType.Int, "m", "Mean Length of clone library.");
parser.Parameter(ArgumentType.Optional, "StandardDeviationOfInsert", ArgumentValueType.Int, "s", "Standard Deviation of Clone Library.");
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, "Verbose", ArgumentValueType.Bool, "v", "Display verbose logging during processing.");
parser.Parameter(ArgumentType.Optional, "ForceKmer", ArgumentValueType.Bool, "fk", "Force specified k-mer to be used without a warning prompt.");
if (args.Length > 0)
{
try
{
parser.Parse(args, options);
}
catch (ArgumentParserException ex)
{
Output.WriteLine(OutputLevel.Error, ex.Message);
Output.WriteLine(OutputLevel.Required, Resources.ScaffoldHelp);
Environment.Exit(-1);
}
if (options.Help)
{
Output.WriteLine(OutputLevel.Required, Resources.ScaffoldHelp);
}
else if (options.FileNames != null)
{
if (!options.ForceKmer)
{
ValidateKmerLength(options.KmerLength, false);
}
if (options.Verbose)
{
Output.TraceLevel = OutputLevel.Information | OutputLevel.Verbose;
}
else if (!options.Quiet)
{
Output.TraceLevel = OutputLevel.Information;
}
options.GenerateScaffold();
}
else
{
Output.WriteLine(OutputLevel.Required, Resources.ScaffoldHelp);
}
}
else
{
Output.WriteLine(OutputLevel.Required, Resources.ScaffoldHelp);
}
}
/// <summary>
/// Scaffold function.
/// </summary>
/// <param name="args">Arguments to Scaffold function.</param>
private static void Scaffold(string[] args)
{
ScaffoldArguments options = new ScaffoldArguments();
CommandLineArguments parser = new CommandLineArguments();
// Add the parameters
parser.Parameter(ArgumentType.Optional, "Quiet", ArgumentValueType.Bool, "q", "Display minimal output during processing.");
parser.Parameter(ArgumentType.Required, "KmerLength", ArgumentValueType.OptionalInt, "k", "Length of k-mer");
parser.Parameter(ArgumentType.Optional, "Help", ArgumentValueType.Bool, "h", "");
parser.Parameter(ArgumentType.Optional, "OutputFile", ArgumentValueType.String, "o", "Output file");
parser.Parameter(ArgumentType.DefaultArgument, "Filenames", ArgumentValueType.MultipleUniqueStrings, "", "Input file of reads and contigs.");
parser.Parameter(ArgumentType.Optional, "CloneLibraryName", ArgumentValueType.String, "n", "Clone Library Name");
parser.Parameter(ArgumentType.Optional, "MeanLengthOfInsert", ArgumentValueType.Int, "m", "Mean Length of clone library.");
parser.Parameter(ArgumentType.Optional, "StandardDeviationOfInsert", ArgumentValueType.Int, "s", "Standard Deviation of Clone Library.");
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, "Verbose", ArgumentValueType.Bool, "v", "Display verbose logging during processing.");
parser.Parameter(ArgumentType.Optional, "ForceKmer", ArgumentValueType.Bool, "fk", "Force specified k-mer to be used without a warning prompt.");
if (args.Length > 0)
{
try
{
parser.Parse(args, options);
}
catch (ArgumentParserException ex)
{
Output.WriteLine(OutputLevel.Error, ex.Message);
Output.WriteLine(OutputLevel.Required, Resources.ScaffoldHelp);
Environment.Exit(-1);
}
if (options.Help)
{
Output.WriteLine(OutputLevel.Required, Resources.ScaffoldHelp);
}
else if (options.FileNames != null)
{
if (!options.ForceKmer)
ValidateKmerLength(options.KmerLength, false);
if (options.Verbose)
Output.TraceLevel = OutputLevel.Information | OutputLevel.Verbose;
else if (!options.Quiet)
Output.TraceLevel = OutputLevel.Information;
options.GenerateScaffold();
}
else
{
Output.WriteLine(OutputLevel.Required, Resources.ScaffoldHelp);
}
}
else
{
Output.WriteLine(OutputLevel.Required, Resources.ScaffoldHelp);
}
}
