/// <summary> /// Parses ScaffoldGeneration command line parameters. /// </summary> /// <param name="args">The arguments.</param> private static void ScaffoldGeneration(string[] args) { ScaffoldArguments arguments = new ScaffoldArguments(); CommandLineArguments parser = new CommandLineArguments(); // Add scaffold parameters parser.Parameter(ArgumentType.DefaultArgument, "FilePath", ArgumentValueType.MultipleUniqueStrings, "", "File path"); parser.Parameter(ArgumentType.Optional, "Help", ArgumentValueType.Bool, "h", "Print the help information."); parser.Parameter(ArgumentType.Optional, "OutputFile", ArgumentValueType.String, "o", "Output file"); parser.Parameter(ArgumentType.Optional, "Verbose", ArgumentValueType.Bool, "v", "Display verbose logging during processing."); parser.Parameter(ArgumentType.Optional, "KmerLength", ArgumentValueType.Int, "k", "Length of k-mer"); 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, "CloneLibraryName", ArgumentValueType.String, "n", "Clone Library Name"); parser.Parameter(ArgumentType.Optional, "MeanLengthOfInsert", ArgumentValueType.Int, "i", "Mean Length of clone library."); parser.Parameter(ArgumentType.Optional, "StandardDeviationOfInsert", ArgumentValueType.Int, "sd", "Standard Deviation of Clone Library."); if (args.Length > 1) { try { parser.Parse(args, arguments); } catch (ArgumentParserException ex) { DisplayErrorMessage(ex.Message); DisplayErrorMessage(Resources.ScaffoldUtilHelp); Environment.Exit(-1); } if (arguments.Help) { DisplayErrorMessage(Resources.ScaffoldUtilHelp); } else if (arguments.FilePath.Length == 2) { arguments.GenerateScaffolds(); } else { DisplayErrorMessage(Resources.ScaffoldUtilHelp); } } else { DisplayErrorMessage(Resources.ScaffoldUtilHelp); } }
/// <summary> /// Parses ScaffoldGeneration command line parameters. /// </summary> /// <param name="args">The arguments.</param> private static void ScaffoldGeneration(string[] args) { ScaffoldArguments arguments = new ScaffoldArguments(); if (args.Length > 1 && Parser.ParseArguments(args, arguments)) { if (arguments.FilePath.Length == 2) { arguments.GenerateScaffolds(); } else { DisplayErrorMessage(Resources.ScaffoldUtilHelp); } } else { DisplayErrorMessage(Resources.ScaffoldUtilHelp); } }