ac8788898448a1442aaa142060191071cb251c02,src/org/broad/igv/ui/Main.java,IGVArgs,parseArgs,#String[]#,408

Before Change


            genomeId = (String) parser.getOptionValue(genomeOption);
            dataServerURL = (String) parser.getOptionValue(dataServerOption);
            genomeServerURL = (String) parser.getOptionValue(genomeServerOption);
            indexFile = (String) parser.getOptionValue(indexFileOption);
            coverageFile = (String) parser.getOptionValue(coverageFileOption);
            name = (String) parser.getOptionValue(nameOption);
            igvDirectory = (String) parser.getOptionValue(igvDirectoryOption);

            String[] nonOptionArgs = parser.getRemainingArgs();
            if (nonOptionArgs != null && nonOptionArgs.length > 0) {

After Change


         * firstArg  locusString  -b batchFile -p preferences
         */
        private void parseArgs(String[] args) {
            CmdLineParser parser = new CmdLineParser();
            CmdLineParser.Option propertyFileOption = parser.addStringOption('o', "preferences");
            CmdLineParser.Option batchFileOption = parser.addStringOption('b', "batch");
            CmdLineParser.Option portOption = parser.addStringOption('p', "port");
            CmdLineParser.Option genomeOption = parser.addStringOption('g', "genome");
            CmdLineParser.Option dataServerOption = parser.addStringOption('d', "dataServerURL");
            CmdLineParser.Option genomeServerOption = parser.addStringOption('u', "genomeServerURL");
            CmdLineParser.Option indexFileOption = parser.addStringOption('i', "indexFile");
            CmdLineParser.Option coverageFileOption = parser.addStringOption('c', "coverageFile");
            CmdLineParser.Option nameOption = parser.addStringOption('n', "name");
            CmdLineParser.Option igvDirectoryOption = parser.addStringOption("igvDirectory");

            try {
                parser.parse(args);
            } catch (CmdLineParser.IllegalOptionValueException e) {
                e.printStackTrace();  // This is not logged because the logger is not initialized yet.
            } catch (CmdLineParser.UnknownOptionException e) {
                e.printStackTrace();
            }
            propertyOverrides = getDecodedValue(parser, propertyFileOption);
            batchFile = getDecodedValue(parser, batchFileOption);
            port = (String) parser.getOptionValue(portOption);
            genomeId = (String) parser.getOptionValue(genomeOption);
            dataServerURL = getDecodedValue(parser, dataServerOption);
            genomeServerURL = getDecodedValue(parser, genomeServerOption);
            indexFile = getDecodedValue(parser, indexFileOption);
            coverageFile = getDecodedValue(parser, coverageFileOption);
            name = (String) parser.getOptionValue(nameOption);
            igvDirectory = getDecodedValue(parser, igvDirectoryOption);

            String[] nonOptionArgs = parser.getRemainingArgs();
            if (nonOptionArgs != null && nonOptionArgs.length > 0) {