/** 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 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 realignAtContigBorderTest() {
final int contigEnd = header.getSequence(0).getSequenceLength();
final GATKSAMRecord read =
ArtificialSAMUtils.createArtificialRead(header, "goodRead", 0, contigEnd - 1, 2);
read.setCigarString("2M");
Assert.assertEquals(IndelRealigner.realignmentProducesBadAlignment(read, contigEnd), false);
read.setCigarString("1M1D1M");
Assert.assertEquals(IndelRealigner.realignmentProducesBadAlignment(read, contigEnd), true);
}
/** 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");
}
@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");
}
@Test(dataProvider = "DanglingHeads")
public void testDanglingHeads(
final String ref, final String alt, final String cigar, final boolean shouldBeMerged) {
final int kmerSize = 5;
// create the graph and populate it
final ReadThreadingGraph rtgraph = new ReadThreadingGraph(kmerSize);
rtgraph.addSequence("ref", ref.getBytes(), true);
final GATKSAMRecord read =
ArtificialSAMUtils.createArtificialRead(
alt.getBytes(), Utils.dupBytes((byte) 30, alt.length()), alt.length() + "M");
rtgraph.addRead(read);
rtgraph.setMaxMismatchesInDanglingHead(10);
rtgraph.buildGraphIfNecessary();
// confirm that we have just a single dangling head
MultiDeBruijnVertex altSource = null;
for (final MultiDeBruijnVertex v : rtgraph.vertexSet()) {
if (rtgraph.isSource(v) && !rtgraph.isReferenceNode(v)) {
Assert.assertTrue(altSource == null, "We found more than one non-reference source");
altSource = v;
}
}
Assert.assertTrue(altSource != null, "We did not find a non-reference source");
// confirm that the SW alignment agrees with our expectations
final ReadThreadingGraph.DanglingChainMergeHelper result =
rtgraph.generateCigarAgainstUpwardsReferencePath(altSource, 0, 1);
if (result == null) {
Assert.assertFalse(shouldBeMerged);
return;
}
Assert.assertTrue(
cigar.equals(result.cigar.toString()), "SW generated cigar = " + result.cigar.toString());
// confirm that the tail merging works as expected
final int mergeResult = rtgraph.mergeDanglingHead(result);
Assert.assertTrue(mergeResult > 0 || !shouldBeMerged);
// confirm that we created the appropriate bubble in the graph only if expected
rtgraph.cleanNonRefPaths();
final SeqGraph seqGraph = rtgraph.convertToSequenceGraph();
final List<KBestHaplotype> paths =
new KBestHaplotypeFinder(
seqGraph, seqGraph.getReferenceSourceVertex(), seqGraph.getReferenceSinkVertex());
Assert.assertEquals(paths.size(), shouldBeMerged ? 2 : 1);
}
private List<PileupElement> makeReads(final int n, final int mapq, final String op) {
final int readLength = 3;
final List<PileupElement> elts = new LinkedList<PileupElement>();
for (int i = 0; i < n; i++) {
GATKSAMRecord read =
ArtificialSAMUtils.createArtificialRead(header, "read", 0, 1, readLength);
read.setReadBases(Utils.dupBytes((byte) 'A', readLength));
read.setBaseQualities(Utils.dupBytes((byte) 30, readLength));
read.setCigarString("1M1" + op + "1M");
read.setMappingQuality(mapq);
final int baseOffset = op.equals("M") ? 1 : 0;
final CigarElement cigarElement = read.getCigar().getCigarElement(1);
elts.add(new PileupElement(read, baseOffset, cigarElement, 1, 0));
}
return elts;
}
@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);
}
@Test(dataProvider = "DanglingTails")
public void testDanglingTails(
final String refEnd,
final String altEnd,
final String cigar,
final boolean cigarIsGood,
final int mergePointDistanceFromSink) {
final int kmerSize = 15;
// construct the haplotypes
final String commonPrefix = "AAAAAAAAAACCCCCCCCCCGGGGGGGGGGTTTTTTTTTT";
final String ref = commonPrefix + refEnd;
final String alt = commonPrefix + altEnd;
// create the graph and populate it
final ReadThreadingGraph rtgraph = new ReadThreadingGraph(kmerSize);
rtgraph.addSequence("ref", ref.getBytes(), true);
final GATKSAMRecord read =
ArtificialSAMUtils.createArtificialRead(
alt.getBytes(), Utils.dupBytes((byte) 30, alt.length()), alt.length() + "M");
rtgraph.addRead(read);
rtgraph.buildGraphIfNecessary();
// confirm that we have just a single dangling tail
MultiDeBruijnVertex altSink = null;
for (final MultiDeBruijnVertex v : rtgraph.vertexSet()) {
if (rtgraph.isSink(v) && !rtgraph.isReferenceNode(v)) {
Assert.assertTrue(altSink == null, "We found more than one non-reference sink");
altSink = v;
}
}
Assert.assertTrue(altSink != null, "We did not find a non-reference sink");
// confirm that the SW alignment agrees with our expectations
final ReadThreadingGraph.DanglingChainMergeHelper result =
rtgraph.generateCigarAgainstDownwardsReferencePath(altSink, 0, 4);
if (result == null) {
Assert.assertFalse(cigarIsGood);
return;
}
Assert.assertTrue(
cigar.equals(result.cigar.toString()), "SW generated cigar = " + result.cigar.toString());
// confirm that the goodness of the cigar agrees with our expectations
Assert.assertEquals(rtgraph.cigarIsOkayToMerge(result.cigar, false, true), cigarIsGood);
// confirm that the tail merging works as expected
if (cigarIsGood) {
final int mergeResult = rtgraph.mergeDanglingTail(result);
Assert.assertTrue(mergeResult == 1 || mergePointDistanceFromSink == -1);
// confirm that we created the appropriate edge
if (mergePointDistanceFromSink >= 0) {
MultiDeBruijnVertex v = altSink;
for (int i = 0; i < mergePointDistanceFromSink; i++) {
if (rtgraph.inDegreeOf(v) != 1) Assert.fail("Encountered vertex with multiple edges");
v = rtgraph.getEdgeSource(rtgraph.incomingEdgeOf(v));
}
Assert.assertTrue(rtgraph.outDegreeOf(v) > 1);
}
}
}
@BeforeClass
public void beforeClass() {
header = ArtificialSAMUtils.createArtificialSamHeader(1, 1, 1000);
genomeLocParser = new GenomeLocParser(header.getSequenceDictionary());
loc = genomeLocParser.createGenomeLoc("chr1", 1);
}
@BeforeClass
public void setup() throws FileNotFoundException {
final ReferenceSequenceFile seq = new CachingIndexedFastaSequenceFile(new File(b37KGReference));
header = ArtificialSAMUtils.createArtificialSamHeader(seq.getSequenceDictionary());
}