private void testRBPCounts(final ReadBackedPileup rbp, RBPCountTest expected) {
for (int cycles = 0; cycles < 3; cycles++) {
// multiple cycles to make sure caching is working
Assert.assertEquals(rbp.getNumberOfElements(), expected.nReads);
Assert.assertEquals(rbp.depthOfCoverage(), expected.nReads);
Assert.assertEquals(rbp.getNumberOfDeletions(), expected.nDeletions);
Assert.assertEquals(rbp.getNumberOfMappingQualityZeroReads(), expected.nMapq0);
}
}
@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);
}
/** Ensure that splitting read groups still works when dealing with null read groups. */
@Test
public void testSplitByNullReadGroups() {
SAMFileHeader header = ArtificialSAMUtils.createArtificialSamHeader(1, 1, 1000);
GATKSAMRecord read1 = ArtificialSAMUtils.createArtificialRead(header, "read1", 0, 1, 10);
GATKSAMRecord read2 = ArtificialSAMUtils.createArtificialRead(header, "read2", 0, 1, 10);
GATKSAMRecord read3 = ArtificialSAMUtils.createArtificialRead(header, "read3", 0, 1, 10);
ReadBackedPileup pileup =
new ReadBackedPileupImpl(null, Arrays.asList(read1, read2, read3), Arrays.asList(1, 1, 1));
ReadBackedPileup nullRgPileup = pileup.getPileupForReadGroup(null);
List<GATKSAMRecord> nullRgReads = nullRgPileup.getReads();
Assert.assertEquals(
nullRgPileup.getNumberOfElements(), 3, "Wrong number of reads in null read group");
Assert.assertEquals(
nullRgReads.get(0),
read1,
"Read " + read1.getReadName() + " should be in null rg but isn't");
Assert.assertEquals(
nullRgReads.get(1),
read2,
"Read " + read2.getReadName() + " should be in null rg but isn't");
Assert.assertEquals(
nullRgReads.get(2),
read3,
"Read " + read3.getReadName() + " should be in null rg but isn't");
ReadBackedPileup rg1Pileup = pileup.getPileupForReadGroup("rg1");
Assert.assertNull(rg1Pileup, "Pileup for non-existent read group should return null");
}
/** Ensure that basic read group splitting works. */
@Test
public void testSplitByReadGroup() {
SAMReadGroupRecord readGroupOne = new SAMReadGroupRecord("rg1");
SAMReadGroupRecord readGroupTwo = new SAMReadGroupRecord("rg2");
SAMFileHeader header = ArtificialSAMUtils.createArtificialSamHeader(1, 1, 1000);
header.addReadGroup(readGroupOne);
header.addReadGroup(readGroupTwo);
GATKSAMRecord read1 = ArtificialSAMUtils.createArtificialRead(header, "read1", 0, 1, 10);
read1.setAttribute("RG", readGroupOne.getId());
GATKSAMRecord read2 = ArtificialSAMUtils.createArtificialRead(header, "read2", 0, 1, 10);
read2.setAttribute("RG", readGroupTwo.getId());
GATKSAMRecord read3 = ArtificialSAMUtils.createArtificialRead(header, "read3", 0, 1, 10);
read3.setAttribute("RG", readGroupOne.getId());
GATKSAMRecord read4 = ArtificialSAMUtils.createArtificialRead(header, "read4", 0, 1, 10);
read4.setAttribute("RG", readGroupTwo.getId());
GATKSAMRecord read5 = ArtificialSAMUtils.createArtificialRead(header, "read5", 0, 1, 10);
read5.setAttribute("RG", readGroupTwo.getId());
GATKSAMRecord read6 = ArtificialSAMUtils.createArtificialRead(header, "read6", 0, 1, 10);
read6.setAttribute("RG", readGroupOne.getId());
GATKSAMRecord read7 = ArtificialSAMUtils.createArtificialRead(header, "read7", 0, 1, 10);
read7.setAttribute("RG", readGroupOne.getId());
ReadBackedPileup pileup =
new ReadBackedPileupImpl(
null,
Arrays.asList(read1, read2, read3, read4, read5, read6, read7),
Arrays.asList(1, 1, 1, 1, 1, 1, 1));
ReadBackedPileup rg1Pileup = pileup.getPileupForReadGroup("rg1");
List<GATKSAMRecord> rg1Reads = rg1Pileup.getReads();
Assert.assertEquals(rg1Reads.size(), 4, "Wrong number of reads in read group rg1");
Assert.assertEquals(
rg1Reads.get(0), read1, "Read " + read1.getReadName() + " should be in rg1 but isn't");
Assert.assertEquals(
rg1Reads.get(1), read3, "Read " + read3.getReadName() + " should be in rg1 but isn't");
Assert.assertEquals(
rg1Reads.get(2), read6, "Read " + read6.getReadName() + " should be in rg1 but isn't");
Assert.assertEquals(
rg1Reads.get(3), read7, "Read " + read7.getReadName() + " should be in rg1 but isn't");
ReadBackedPileup rg2Pileup = pileup.getPileupForReadGroup("rg2");
List<GATKSAMRecord> rg2Reads = rg2Pileup.getReads();
Assert.assertEquals(rg2Reads.size(), 3, "Wrong number of reads in read group rg2");
Assert.assertEquals(
rg2Reads.get(0), read2, "Read " + read2.getReadName() + " should be in rg2 but isn't");
Assert.assertEquals(
rg2Reads.get(1), read4, "Read " + read4.getReadName() + " should be in rg2 but isn't");
Assert.assertEquals(
rg2Reads.get(2), read5, "Read " + read5.getReadName() + " should be in rg2 but isn't");
}
/** Ensure that splitting read groups still works when dealing with a sample-split pileup. */
@Test
public void testSplitBySample() {
SAMReadGroupRecord readGroupOne = new SAMReadGroupRecord("rg1");
readGroupOne.setSample("sample1");
SAMReadGroupRecord readGroupTwo = new SAMReadGroupRecord("rg2");
readGroupTwo.setSample("sample2");
SAMFileHeader header = ArtificialSAMUtils.createArtificialSamHeader(1, 1, 1000);
header.addReadGroup(readGroupOne);
header.addReadGroup(readGroupTwo);
GATKSAMRecord read1 = ArtificialSAMUtils.createArtificialRead(header, "read1", 0, 1, 10);
read1.setAttribute("RG", readGroupOne.getId());
GATKSAMRecord read2 = ArtificialSAMUtils.createArtificialRead(header, "read2", 0, 1, 10);
read2.setAttribute("RG", readGroupTwo.getId());
GATKSAMRecord read3 = ArtificialSAMUtils.createArtificialRead(header, "read3", 0, 1, 10);
read3.setAttribute("RG", readGroupOne.getId());
GATKSAMRecord read4 = ArtificialSAMUtils.createArtificialRead(header, "read4", 0, 1, 10);
read4.setAttribute("RG", readGroupTwo.getId());
ReadBackedPileupImpl sample1Pileup =
new ReadBackedPileupImpl(null, Arrays.asList(read1, read3), Arrays.asList(1, 1));
ReadBackedPileupImpl sample2Pileup =
new ReadBackedPileupImpl(null, Arrays.asList(read2, read4), Arrays.asList(1, 1));
Map<String, ReadBackedPileupImpl> sampleToPileupMap =
new HashMap<String, ReadBackedPileupImpl>();
sampleToPileupMap.put(readGroupOne.getSample(), sample1Pileup);
sampleToPileupMap.put(readGroupTwo.getSample(), sample2Pileup);
ReadBackedPileup compositePileup = new ReadBackedPileupImpl(null, sampleToPileupMap);
ReadBackedPileup rg1Pileup = compositePileup.getPileupForReadGroup("rg1");
List<GATKSAMRecord> rg1Reads = rg1Pileup.getReads();
Assert.assertEquals(rg1Reads.size(), 2, "Wrong number of reads in read group rg1");
Assert.assertEquals(
rg1Reads.get(0), read1, "Read " + read1.getReadName() + " should be in rg1 but isn't");
Assert.assertEquals(
rg1Reads.get(1), read3, "Read " + read3.getReadName() + " should be in rg1 but isn't");
ReadBackedPileup rg2Pileup = compositePileup.getPileupForReadGroup("rg2");
List<GATKSAMRecord> rg2Reads = rg2Pileup.getReads();
Assert.assertEquals(rg1Reads.size(), 2, "Wrong number of reads in read group rg2");
Assert.assertEquals(
rg2Reads.get(0), read2, "Read " + read2.getReadName() + " should be in rg2 but isn't");
Assert.assertEquals(
rg2Reads.get(1), read4, "Read " + read4.getReadName() + " should be in rg2 but isn't");
}
@Test
public void testGetPileupForSample() {
String sample1 = "sample1";
String sample2 = "sample2";
SAMReadGroupRecord readGroupOne = new SAMReadGroupRecord("rg1");
readGroupOne.setSample(sample1);
SAMReadGroupRecord readGroupTwo = new SAMReadGroupRecord("rg2");
readGroupTwo.setSample(sample2);
SAMFileHeader header = ArtificialSAMUtils.createArtificialSamHeader(1, 1, 1000);
header.addReadGroup(readGroupOne);
header.addReadGroup(readGroupTwo);
GATKSAMRecord read1 = ArtificialSAMUtils.createArtificialRead(header, "read1", 0, 1, 10);
read1.setAttribute("RG", readGroupOne.getId());
GATKSAMRecord read2 = ArtificialSAMUtils.createArtificialRead(header, "read2", 0, 1, 10);
read2.setAttribute("RG", readGroupTwo.getId());
Map<String, ReadBackedPileupImpl> sampleToPileupMap =
new HashMap<String, ReadBackedPileupImpl>();
sampleToPileupMap.put(
sample1, new ReadBackedPileupImpl(null, Collections.singletonList(read1), 0));
sampleToPileupMap.put(
sample2, new ReadBackedPileupImpl(null, Collections.singletonList(read2), 0));
ReadBackedPileup pileup = new ReadBackedPileupImpl(null, sampleToPileupMap);
ReadBackedPileup sample2Pileup = pileup.getPileupForSample(sample2);
Assert.assertEquals(
sample2Pileup.getNumberOfElements(), 1, "Sample 2 pileup has wrong number of elements");
Assert.assertEquals(
sample2Pileup.getReads().get(0), read2, "Sample 2 pileup has incorrect read");
ReadBackedPileup missingSamplePileup = pileup.getPileupForSample("missing");
Assert.assertNull(missingSamplePileup, "Pileup for sample 'missing' should be null but isn't");
missingSamplePileup = pileup.getPileupForSample("not here");
Assert.assertNull(missingSamplePileup, "Pileup for sample 'not here' should be null but isn't");
}