/// <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); } }