@Test
public void testRBPMappingQuals() {
// create a read with high MQ
final GATKSAMRecord read = ArtificialSAMUtils.createArtificialRead(header, "read", 0, 1, 10);
read.setReadBases(Utils.dupBytes((byte) 'A', 10));
read.setBaseQualities(Utils.dupBytes((byte) 30, 10));
read.setCigarString("10M");
read.setMappingQuality(200); // set a MQ higher than max signed byte
// now create the RBP
final List<PileupElement> elts = new LinkedList<>();
elts.add(new PileupElement(read, 0, read.getCigar().getCigarElement(0), 0, 0));
final Map<String, ReadBackedPileupImpl> pileupsBySample = new HashMap<>();
pileupsBySample.put("foo", new ReadBackedPileupImpl(loc, elts));
final ReadBackedPileup pileup = new ReadBackedPileupImpl(loc, pileupsBySample);
Assert.assertEquals(pileup.getMappingQuals()[0], 200);
}
