/// <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); } }