@Override
	public boolean run() {
		if (verbose) Timer.showStdErr("Calculating ACAT score on input: " + vcfFile);
		countByAcat = new CountByType();
		countByEff = new CountByType();

		VcfFileIterator vcf = new VcfFileIterator(vcfFile);
		for (VcfEntry ve : vcf) {
			if (vcf.isHeadeSection()) {
				addHeader(vcf); // Add header lines
				System.out.println(vcf.getVcfHeader()); // Show header
			}

			acat(ve); // Annotate ACAT
			t2dGenes(ve); // Annotate T2D-Genes

			// Show line
			if (!quiet) System.out.println(ve);
		}

		if (verbose) {
			System.err.println(countByAcat);
			System.err.println(countByEff);
			Timer.showStdErr("Done.");
		}

		return true;
	}