Package jargs.gnu

Examples of jargs.gnu.CmdLineParser.addIntegerOption()

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    CmdLineParser parser = new CmdLineParser();
    CmdLineParser.Option help = parser.addBooleanOption('h', "help");
    CmdLineParser.Option output = parser.addStringOption('o', "output");
    CmdLineParser.Option iface = parser.addStringOption('i', "iface");
    CmdLineParser.Option seedTime = parser.addIntegerOption('s', "seed");
    CmdLineParser.Option maxUpload = parser.addDoubleOption('u', "max-upload");
    CmdLineParser.Option maxDownload = parser.addDoubleOption('d', "max-download");

    try {
      parser.parse(args);
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    BasicConfigurator.configure(new ConsoleAppender(
      new PatternLayout("%d [%-25t] %-5p: %m%n")));

    CmdLineParser parser = new CmdLineParser();
    CmdLineParser.Option help = parser.addBooleanOption('h', "help");
    CmdLineParser.Option port = parser.addIntegerOption('p', "port");

    try {
      parser.parse(args);
    } catch (CmdLineParser.OptionException oe) {
      System.err.println(oe.getMessage());
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    private CmdLineParser initParser(String command) {
        command = command.toLowerCase();
        CmdLineParser parser = new CmdLineParser();
        if (command.equals(CMD_SORT) || command.equals(CMD_TOTDF) || command.equals(CMD_TILE)) {
            maxRecordsOption = parser.addIntegerOption('m', "maxRecords");
            tmpDirOption = parser.addStringOption('t', "tmpDir");
        }

        if (command.equals(CMD_COUNT) || command.equals(CMD_TOTDF) || command.equals(CMD_TILE)) {
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        if (command.equals(CMD_COUNT) || command.equals(CMD_TOTDF) || command.equals(CMD_TILE)) {

            // general options
            windowFunctions = parser.addStringOption('f', "windowFunctions");
            maxZoomOption = parser.addIntegerOption('z', "maxZoom");

            // extended options for coverage
            if (command.equals(CMD_COUNT) || command.equals(CMD_BAMTOBED)) {

                extFactorOption = parser.addIntegerOption('e', "extFactor");
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            maxZoomOption = parser.addIntegerOption('z', "maxZoom");

            // extended options for coverage
            if (command.equals(CMD_COUNT) || command.equals(CMD_BAMTOBED)) {

                extFactorOption = parser.addIntegerOption('e', "extFactor");
                preExtFactorOption = parser.addIntegerOption("preExtFactor");
                postExtFactorOption = parser.addIntegerOption("postExtFactor");
                windowSizeOption = parser.addIntegerOption('w', "windowSize");

                separateBasesOption = parser.addBooleanOption("bases");
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            // extended options for coverage
            if (command.equals(CMD_COUNT) || command.equals(CMD_BAMTOBED)) {

                extFactorOption = parser.addIntegerOption('e', "extFactor");
                preExtFactorOption = parser.addIntegerOption("preExtFactor");
                postExtFactorOption = parser.addIntegerOption("postExtFactor");
                windowSizeOption = parser.addIntegerOption('w', "windowSize");

                separateBasesOption = parser.addBooleanOption("bases");
                strandOption = parser.addStringOption("strands");
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            // extended options for coverage
            if (command.equals(CMD_COUNT) || command.equals(CMD_BAMTOBED)) {

                extFactorOption = parser.addIntegerOption('e', "extFactor");
                preExtFactorOption = parser.addIntegerOption("preExtFactor");
                postExtFactorOption = parser.addIntegerOption("postExtFactor");
                windowSizeOption = parser.addIntegerOption('w', "windowSize");

                separateBasesOption = parser.addBooleanOption("bases");
                strandOption = parser.addStringOption("strands");
                queryStringOpt = parser.addStringOption("query");
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            if (command.equals(CMD_COUNT) || command.equals(CMD_BAMTOBED)) {

                extFactorOption = parser.addIntegerOption('e', "extFactor");
                preExtFactorOption = parser.addIntegerOption("preExtFactor");
                postExtFactorOption = parser.addIntegerOption("postExtFactor");
                windowSizeOption = parser.addIntegerOption('w', "windowSize");

                separateBasesOption = parser.addBooleanOption("bases");
                strandOption = parser.addStringOption("strands");
                queryStringOpt = parser.addStringOption("query");
                minMapQualityOpt = parser.addIntegerOption("minMapQuality");
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                windowSizeOption = parser.addIntegerOption('w', "windowSize");

                separateBasesOption = parser.addBooleanOption("bases");
                strandOption = parser.addStringOption("strands");
                queryStringOpt = parser.addStringOption("query");
                minMapQualityOpt = parser.addIntegerOption("minMapQuality");
                includeDupsOpt = parser.addBooleanOption("includeDuplicates");
                pairedCoverageOpt = parser.addBooleanOption("pairs");

                // Trackline
                colorOption = parser.addStringOption("color");
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                typeOption = parser.addStringOption("fileType");
            }
        }

        if (command.equals(CMD_INDEX)) {
            indexTypeOption = parser.addIntegerOption("indexType");
            binSizeOption = parser.addIntegerOption("binSize");
            outputDirOption = parser.addStringOption("outputDir");
        }

        return parser;
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