/// <summary>
/// Assemble With Scaffolding.
/// </summary>
/// <param name="args">Arguments to Scaffolding.</param>
private static void AssembleWithScaffolding(string[] args)
{
AssembleWithScaffoldArguments options = new AssembleWithScaffoldArguments();
CommandLineArguments parser = new CommandLineArguments();
// add assemble related parameters.
AddAssembleParameters(parser);
// Add scaffold parameters
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, "b", "Number of paired read required to connect two contigs.");
parser.Parameter(ArgumentType.Optional, "Depth", ArgumentValueType.Int, "f", "Depth for graph traversal.");
if (args.Length > 0)
{
try
{
parser.Parse(args, options);
}
catch (ArgumentParserException ex)
{
Output.WriteLine(OutputLevel.Error, ex.Message);
Output.WriteLine(OutputLevel.Required, Resources.AssembleWithScaffoldHelp);
Environment.Exit(-1);
}
if (options.Help)
{
Output.WriteLine(OutputLevel.Required, Resources.AssembleWithScaffoldHelp);
}
else
{
if (!options.ForceKmer)
{
ValidateKmerLength(options.KmerLength, options.AllowKmerLengthEstimation);
}
if (options.Verbose)
{
Output.TraceLevel = OutputLevel.Information | OutputLevel.Verbose;
}
else if (!options.Quiet)
{
Output.TraceLevel = OutputLevel.Information;
}
options.AssembleSequences();
}
}
else
{
Output.WriteLine(OutputLevel.Required, Resources.AssembleWithScaffoldHelp);
}
}
/// <summary>
/// Assemble With Scaffolding.
/// </summary>
/// <param name="args">Arguments to Scaffolding.</param>
private static void AssembleWithScaffolding(string[] args)
{
AssembleWithScaffoldArguments options = new AssembleWithScaffoldArguments();
CommandLineArguments parser = new CommandLineArguments();
// add assemble related paraemeters.
AddAssembleParameters(parser);
// Add scaffold parameters
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, "b", "Number of paired read required to connect two contigs.");
parser.Parameter(ArgumentType.Optional, "Depth", ArgumentValueType.Int, "f", "Depth for graph traversal.");
if (args.Length > 0)
{
try
{
parser.Parse(args, options);
}
catch (ArgumentParserException ex)
{
DisplayErrorMessage(ex.Message);
DisplayErrorMessage(Resources.AssembleWithScaffoldHelp);
Environment.Exit(-1);
}
if (options.Help)
{
DisplayErrorMessage(Resources.AssembleWithScaffoldHelp);
}
else
{
options.AssembleSequences();
}
}
else
{
DisplayErrorMessage(Resources.AssembleWithScaffoldHelp);
}
}
/// <summary>
/// Assemble With Scaffolding.
/// </summary>
/// <param name="args">Arguments to Scaffolding.</param>
private static void AssembleWithScaffolding(string[] args)
{
AssembleWithScaffoldArguments options = new AssembleWithScaffoldArguments();
if (args.Length > 0 && Parser.ParseArguments(args, options))
{
if (options.Help)
{
DisplayErrorMessage(Resources.AssembleWithScaffoldHelp);
}
else
{
options.AssembleSequences();
}
}
else
{
DisplayErrorMessage(Resources.AssembleWithScaffoldHelp);
}
}
/// <summary>
/// Assemble With Scaffolding.
/// </summary>
/// <param name="args">Arguments to Scaffolding.</param>
private static void AssembleWithScaffolding(string[] args)
{
AssembleWithScaffoldArguments options = new AssembleWithScaffoldArguments();
CommandLineArguments parser = new CommandLineArguments();
// add assemble related parameters.
AddAssembleParameters(parser);
// Add scaffold parameters
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, "b", "Number of paired read required to connect two contigs.");
parser.Parameter(ArgumentType.Optional, "Depth", ArgumentValueType.Int, "f", "Depth for graph traversal.");
if (args.Length > 0)
{
try
{
parser.Parse(args, options);
}
catch (ArgumentParserException ex)
{
Output.WriteLine(OutputLevel.Error, ex.Message);
Output.WriteLine(OutputLevel.Required, Resources.AssembleWithScaffoldHelp);
Environment.Exit(-1);
}
if (options.Help)
{
Output.WriteLine(OutputLevel.Required, Resources.AssembleWithScaffoldHelp);
}
else
{
if (!options.ForceKmer)
ValidateKmerLength(options.KmerLength, options.AllowKmerLengthEstimation);
if (options.Verbose)
Output.TraceLevel = OutputLevel.Information | OutputLevel.Verbose;
else if (!options.Quiet)
Output.TraceLevel = OutputLevel.Information;
options.AssembleSequences();
}
}
else
{
Output.WriteLine(OutputLevel.Required, Resources.AssembleWithScaffoldHelp);
}
}