Exemplos de SamUtil SequenceCoverage em C# (CSharp)

Exemplo n.º 1

        /// <summary>
        /// Parse command line arguments for Sequence Item Possible Occurence
        /// </summary>
        /// <param name="args">Array of command line arguments.</param>
        private static void SeqPossibleOccurence(string[] args)
        {
            SequenceCoverage     options = new SequenceCoverage();
            CommandLineArguments parser  = new CommandLineArguments();

            // Add the parameters
            parser.Parameter(ArgumentType.Optional, "SAMInput", ArgumentValueType.Bool, "S", "Input is SAM format");
            parser.Parameter(ArgumentType.Optional, "Help", ArgumentValueType.Bool, "", "");

            try
            {
                parser.Parse(args, options);
            }
            catch (ArgumentParserException ex)
            {
                DisplayErrorMessage(ex.Message);
                DisplayErrorMessage(Resources.DNAPossibleOccurenceHelp);
                Environment.Exit(-1);
            }

            if (options.Help)
            {
                DisplayErrorMessage(Resources.DNAPossibleOccurenceHelp);
            }

            else
            {
                options.DisplaySequenceItemOccurences(args[0], true);
            }
        }

Exemplo n.º 2

        /// <summary>
        /// Parse command line arguments for Sequence Distribution table for DNA
        /// </summary>
        /// <param name="args">Array of command line arguments.</param>
        private static void SeqDistributionOption(string[] args)
        {
            SequenceCoverage options = new SequenceCoverage();

            if (options.Usage)
            {
                DisplayErrorMessage(Resources.DNACoverageHelp);
            }
            else
            {
                options.DisplaySequenceItemOccurences(args[0], false);
            }
        }

Exemplo n.º 3

        /// <summary>
        /// Parse command line arguments for Sequence Item Possible Occurence
        /// </summary>
        /// <param name="args">Array of command line arguments.</param>
        private static void SeqPossibleOccurence(string[] args)
        {
            SequenceCoverage options = new SequenceCoverage();

            if (options.Usage)
            {
                DisplayErrorMessage(Resources.DNAPossibleOccurenceHelp);
            }

            else
            {
                options.DisplaySequenceItemOccurences(args[0], true);
            }
        }

Exemplo n.º 4

Arquivo: Program.cs Projeto: cpatmoore/bio

        /// <summary>
        /// Parse command line arguments for Sequence Item Possible Occurence
        /// </summary>
        /// <param name="args">Array of command line arguments.</param>
        private static void SeqPossibleOccurence(string[] args)
        {

            SequenceCoverage options = new SequenceCoverage();
            CommandLineArguments parser = new CommandLineArguments();

            // Add the parameters
            parser.Parameter(ArgumentType.Optional, "SAMInput", ArgumentValueType.Bool, "S", "Input is SAM format");
            parser.Parameter(ArgumentType.Optional, "Help", ArgumentValueType.Bool, "", "");

            try
            {
                parser.Parse(args, options);
            }
            catch (ArgumentParserException ex)
            {
                DisplayErrorMessage(ex.Message);
                DisplayErrorMessage(Resources.DNAPossibleOccurenceHelp);
                Environment.Exit(-1);
            }

            if (options.Help)
            {
                DisplayErrorMessage(Resources.DNAPossibleOccurenceHelp);
            }

            else
            {
                options.DisplaySequenceItemOccurences(args[0], true);
            }

        }