public void count() {
		genome = snpEffectPredictor.getGenome();

		readLengthSum = 0;
		readLengthCount = 0;

		// Iterate over all BAM/SAM files
		try {
			if (verbose) Timer.showStdErr("Reading file '" + fileName + "'");
			countReads = new CountByKey<Marker>();
			countBases = new CountByKey<Marker>();
			countTypes = new CountByType();
			coverageByType = new CoverageByType();
			countFile(fileName);
		} catch (Exception e) {
			e.printStackTrace();
		}

		if (verbose) {
			System.err.println("");
			Timer.showStdErr("Finished reding file " + fileName + "\n\tTotal reads: " + countTotalReads);
		}
		if (verbose) Timer.showStdErr("Done.");
	}