void init(String genomeVersion, String configFileName, String dataDir) {
		treatAllAsProteinCoding = false;
		onlyRegulation = false;
		errorOnMissingChromo = true;
		errorChromoHit = true;
		this.dataDir = dataDir;

		readConfig(genomeVersion, configFileName); // Read config file and get a genome
		genome = genomeByVersion.get(genomeVersion); // Set a genome
		if (!genomeVersion.isEmpty() && (genome == null)) throw new RuntimeException("No such genome '" + genomeVersion + "'");
		configInstance = this;
	}