code: public static void main(final String[] args) {
          Switch about = new Switch("a", "about", "display about message");
          Switch help = new Switch("h", "help", "display help message");
          FileArgument referenceFastaFile = new FileArgument("r", "reference", "input reference FASTA file", true);
          FileArgument scaffoldsFastaFile = new FileArgument("s", "scaffolds", "input scaffolds FASTA file", true);
          FileArgument evalFile = new FileArgument("e", "eval", "output eval file, default stdout", false);
  
          ArgumentList arguments = new ArgumentList(about, help, referenceFastaFile, scaffoldsFastaFile, evalFile);
          CommandLine commandLine = new CommandLine(args);
  
          EvaluateScaffolds evaluateScaffolds = null;
          try {
              CommandLineParser.parse(commandLine, arguments);
              if (about.wasFound()) {
                  About.about(System.out);
                  System.exit(0);
              }
              if (help.wasFound()) {
                  Usage.usage(USAGE, null, commandLine, arguments, System.out);
                  System.exit(0);
              }
              evaluateScaffolds = new EvaluateScaffolds(referenceFastaFile.getValue(), scaffoldsFastaFile.getValue(), evalFile.getValue());
          }
          catch (CommandLineParseException e) {
              if (about.wasFound()) {
                  About.about(System.out);
                  System.exit(0);
              }
              if (help.wasFound()) {
                  Usage.usage(USAGE, null, commandLine, arguments, System.out);
                  System.exit(0);
              }
              Usage.usage(USAGE, e, commandLine, arguments, System.err);
              System.exit(-1);
          }
          try {
              System.exit(evaluateScaffolds.call());
          }
          catch (Exception e) {
              e.printStackTrace();
              System.exit(1);
          }
      }
docs: Main.
  
  @param args command line args