@Test
public void testCallPloidyDefault() throws Exception {

    Files.write(Resources.toByteArray(getClass().getResource("testfile2.bam")), bamFile);
    Files.write(Resources.toByteArray(getClass().getResource("hla-a.bed")), bedFile);
    new FilterConsensus(bamFile, bedFile, outputFile, gene, cdna, removeGaps, minimumBreadth, expectedPloidy).call();
    assertEquals(4, countLines(outputFile));
}