/**
* Test to make sure that reads supporting only an indel (example cigar string: 76I) are
* represented properly
*/
@Test
public void testWholeIndelReadRepresentedTest() {
final int firstLocus = 44367788, secondLocus = firstLocus + 1;
SAMRecord read1 = ArtificialSAMUtils.createArtificialRead(header, "read1", 0, secondLocus, 1);
read1.setReadBases(Utils.dupBytes((byte) 'A', 1));
read1.setBaseQualities(Utils.dupBytes((byte) '@', 1));
read1.setCigarString("1I");
List<SAMRecord> reads = Arrays.asList(read1);
// create the iterator by state with the fake reads and fake records
li = makeLTBS(reads, createTestReadProperties());
while (li.hasNext()) {
AlignmentContext alignmentContext = li.next();
ReadBackedPileup p = alignmentContext.getBasePileup();
Assert.assertTrue(p.getNumberOfElements() == 1);
PileupElement pe = p.iterator().next();
Assert.assertTrue(pe.isBeforeInsertion());
Assert.assertFalse(pe.isAfterInsertion());
Assert.assertEquals(pe.getEventBases(), "A");
}
SAMRecord read2 = ArtificialSAMUtils.createArtificialRead(header, "read2", 0, secondLocus, 10);
read2.setReadBases(Utils.dupBytes((byte) 'A', 10));
read2.setBaseQualities(Utils.dupBytes((byte) '@', 10));
read2.setCigarString("10I");
reads = Arrays.asList(read2);
// create the iterator by state with the fake reads and fake records
li = makeLTBS(reads, createTestReadProperties());
while (li.hasNext()) {
AlignmentContext alignmentContext = li.next();
ReadBackedPileup p = alignmentContext.getBasePileup();
Assert.assertTrue(p.getNumberOfElements() == 1);
PileupElement pe = p.iterator().next();
Assert.assertTrue(pe.isBeforeInsertion());
Assert.assertFalse(pe.isAfterInsertion());
Assert.assertEquals(pe.getEventBases(), "AAAAAAAAAA");
}
}
@Test
public void testIndelsInRegularPileup() {
final byte[] bases = new byte[] {'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A'};
final byte[] indelBases =
new byte[] {'A', 'A', 'A', 'A', 'C', 'T', 'A', 'A', 'A', 'A', 'A', 'A'};
// create a test version of the Reads object
ReadProperties readAttributes = createTestReadProperties();
SAMRecord before = ArtificialSAMUtils.createArtificialRead(header, "before", 0, 1, 10);
before.setReadBases(bases);
before.setBaseQualities(new byte[] {20, 20, 20, 20, 20, 20, 20, 20, 20, 20});
before.setCigarString("10M");
SAMRecord during = ArtificialSAMUtils.createArtificialRead(header, "during", 0, 2, 10);
during.setReadBases(indelBases);
during.setBaseQualities(new byte[] {20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20});
during.setCigarString("4M2I6M");
SAMRecord after = ArtificialSAMUtils.createArtificialRead(header, "after", 0, 3, 10);
after.setReadBases(bases);
after.setBaseQualities(new byte[] {20, 20, 20, 20, 20, 20, 20, 20, 20, 20});
after.setCigarString("10M");
List<SAMRecord> reads = Arrays.asList(before, during, after);
// create the iterator by state with the fake reads and fake records
li = makeLTBS(reads, readAttributes);
boolean foundIndel = false;
while (li.hasNext()) {
AlignmentContext context = li.next();
ReadBackedPileup pileup = context.getBasePileup().getBaseFilteredPileup(10);
for (PileupElement p : pileup) {
if (p.isBeforeInsertion()) {
foundIndel = true;
Assert.assertEquals(p.getEventLength(), 2, "Wrong event length");
Assert.assertEquals(p.getEventBases(), "CT", "Inserted bases are incorrect");
break;
}
}
}
Assert.assertTrue(foundIndel, "Indel in pileup not found");
}