@Override
	public void parseArgs(String[] args) {
		if (args.length < 1) usage(null);

		// Parse command line arguments
		for (int i = 0; i < args.length; i++) {
			if (args[i].equals("-f")) {
				// List in a file?
				if ((i + 1) < args.length) fileName = args[++i];
				else usage("Option '-f' without file argument");
			} else if (args[i].equals("-pc")) {
				// Use only protein coding genes
				onlyProteinCoding = true;
			} else if (args[i].equals("-ud")) {
				// Expand upstream & downstream 
				if ((i + 1) < args.length) expandUpstreamDownstream = Gpr.parseIntSafe(args[++i]);
				else usage("Option '-ud' without file argument");
			} else if ((genomeVer == null) || genomeVer.isEmpty()) {
				// Genome version
				genomeVer = args[i];
			} else geneIds.add(args[i]);
		}
	}