@Test
public void testWholeIndelReadInIsolation() {
final int firstLocus = 44367789;
// create a test version of the Reads object
ReadProperties readAttributes = createTestReadProperties();
SAMRecord indelOnlyRead =
ArtificialSAMUtils.createArtificialRead(header, "indelOnly", 0, firstLocus, 76);
indelOnlyRead.setReadBases(Utils.dupBytes((byte) 'A', 76));
indelOnlyRead.setBaseQualities(Utils.dupBytes((byte) '@', 76));
indelOnlyRead.setCigarString("76I");
List<SAMRecord> reads = Arrays.asList(indelOnlyRead);
// create the iterator by state with the fake reads and fake records
li = makeLTBS(reads, readAttributes);
// Traditionally, reads that end with indels bleed into the pileup at the following locus.
// Verify that the next pileup contains this read
// and considers it to be an indel-containing read.
Assert.assertTrue(
li.hasNext(),
"Should have found a whole-indel read in the normal base pileup without extended events enabled");
AlignmentContext alignmentContext = li.next();
Assert.assertEquals(
alignmentContext.getLocation().getStart(),
firstLocus,
"Base pileup is at incorrect location.");
ReadBackedPileup basePileup = alignmentContext.getBasePileup();
Assert.assertEquals(basePileup.getReads().size(), 1, "Pileup is of incorrect size");
Assert.assertSame(basePileup.getReads().get(0), indelOnlyRead, "Read in pileup is incorrect");
}
