/** This method will process each argument and assign new varibles */
  public void processArgs(String[] args) {
    File file = null;
    Pattern pat = Pattern.compile("-[a-z]");
    for (int i = 0; i < args.length; i++) {
      String lcArg = args[i].toLowerCase();
      Matcher mat = pat.matcher(lcArg);
      if (mat.matches()) {
        char test = args[i].charAt(1);
        try {
          switch (test) {
            case 'f':
              file = new File(args[i + 1]);
              i++;
              break;
            case 'v':
              genomeVersion = args[i + 1];
              i++;
              break;
            case 's':
              sumScores = true;
              break;
            case 't':
              threshold = Float.parseFloat(args[++i]);
              break;
            case 'h':
              printDocs();
              System.exit(0);
            default:
              Misc.printExit("\nError, unknown option! " + mat.group());
          }
        } catch (Exception e) {
          System.out.print("\nSorry, something doesn't look right with this parameter: -" + test);
          System.out.println();
          System.exit(0);
        }
      }
    }
    if (file == null || file.exists() == false)
      Misc.printErrAndExit("Problem finding your bed files!\n");
    // pull files
    File[][] tot = new File[3][];
    tot[0] = IO.extractFiles(file, ".bed");
    tot[1] = IO.extractFiles(file, ".bed.zip");
    tot[2] = IO.extractFiles(file, ".bed.gz");
    bedFiles = IO.collapseFileArray(tot);
    if (bedFiles == null || bedFiles.length == 0)
      Misc.printErrAndExit("Problem finding your xxx.bed(.zip/.gz OK) files!\n");

    // genome version
    if (genomeVersion == null)
      Misc.printErrAndExit(
          "Please enter a genome version (e.g. H_sapiens_Mar_2006, see http://genome.ucsc.edu/FAQ/FAQreleases\n");
  }
 public static void main(String[] args) {
   if (args.length == 0) {
     printDocs();
     System.exit(0);
   }
   new Bed2Bar(args);
 }