@Override
  public boolean parseArgument(String arg, String a, String b) {
    //		System.err.println("Calling parseArgument("+arg+","+a+","+b+")");
    if (a.equals("minq")) {
      minq = (int) Tools.parseKMG(b);
      return true;
    } else if (a.equals("maxq")) {
      maxq = (int) Tools.parseKMG(b);
      return true;
    } else if (a.equals("keepperfect")) {
      keepPerfect = Tools.parseBoolean(b);
      return true;
    } else if (a.equals("countindels")) {
      countIndels = Tools.parseBoolean(b);
      return true;
    }

    // There was no match to the argument
    return false;
  }
  public static void main(String[] args) {
    System.err.println(
        "Executing "
            + (new Object() {}.getClass().getEnclosingClass().getName())
            + " "
            + Arrays.toString(args)
            + "\n");
    Timer t = new Timer();

    String inPattern = args[0];

    int minChrom = -1;
    int maxChrom = -1;
    int outgenome = -1;
    Data.GENOME_BUILD = -1;
    String name = null;

    for (int i = 1; i < args.length; i++) {
      final String arg = args[i].toLowerCase();
      String[] split = arg.split("=");
      String a = split[0];
      String b = (split.length > 1 ? split[1] : null);

      if (a.equals("ingenome")) {
        Data.setGenome(Integer.parseInt(b));
        if (minChrom == -1) {
          minChrom = 1;
        }
        if (maxChrom == -1) {
          maxChrom = Data.numChroms;
        }
      } else if (a.equals("outgenome")) {
        outgenome = Integer.parseInt(b);
      } else if (a.equals("minchrom")) {
        minChrom = Integer.parseInt(b);
      } else if (a.equals("maxchrom")) {
        maxChrom = Integer.parseInt(b);
      } else if (a.equals("threads") || a.equals("t")) {
        THREADS = Integer.parseInt(b);
      } else if (a.equals("nblocksize")) {
        N_BLOCK_SIZE = Integer.parseInt(b);
      } else if (a.equals("nblocktrigger")) {
        N_BLOCK_TRIGGER = Integer.parseInt(b);
      } else if (a.equals("staynearref")) {
        STAY_NEAR_REF = Tools.parseBoolean(b);
      } else if (a.equals("append") || a.equals("app")) {
        append = ReadStats.append = Tools.parseBoolean(b);
      } else if (a.equals("overwrite") || a.equals("ow")) {
        overwrite = Tools.parseBoolean(b);
      } else if (a.startsWith("regen")) {
        REGEN_N_BLOCKS = Tools.parseBoolean(b);
      } else if (a.startsWith("name=")) {
        REGEN_N_BLOCKS = Tools.parseBoolean(b);
      } else {
        System.err.println("Unknown argument " + arg);
      }
    }

    assert (Data.GENOME_BUILD > -1);
    assert (outgenome > -1);
    //		assert(Data.GENOME_BUILD!=outgenome);
    if (Data.GENOME_BUILD == outgenome) {
      System.out.println("Warning! Overwriting input genome " + outgenome);
    }

    String fname = Data.chromFname(minChrom, outgenome);
    File f = new File(fname.substring(0, fname.lastIndexOf('/')));
    //		assert(false) : f.getAbsolutePath();
    if (!f.exists()) {
      f.mkdirs();
    }

    for (int chrom = minChrom; chrom <= maxChrom; chrom++) {
      String outName = Data.chromFname(chrom, outgenome);
      assert (overwrite || !new File(outName).exists())
          : "Destination " + outName + " already exists.";
      //			assert(false) : inPattern+", "+outName;
      process(inPattern.replaceFirst("#", "" + chrom), outName, chrom);
    }

    FastaToChromArrays2.writeInfo(
        outgenome,
        maxChrom,
        (name == null ? Data.name : name),
        "" + Data.GENOME_BUILD + "_plus_variations",
        false,
        false);

    t.stop();

    {
      String path = IndexMaker4.fname(1, 1, 12, 1);
      int lastSlash = path.lastIndexOf('/');
      path = path.substring(0, lastSlash);
      File dir = new File(path);
      if (dir.exists()) {
        System.out.println("Deleting old index for " + outgenome);
        for (File f2 : dir.listFiles()) {
          if (f2.isFile() && (f2.getName().contains(".int2d") || f2.getName().endsWith(".txt"))) {
            f2.delete();
          }
        }
      }
    }

    //		System.out.println("Vars in: \t"+VARS_IN);
    //		System.out.println("Vars out:\t"+VARS_OUT);
    System.out.println();
    System.out.println("Time: \t" + t);
  }