コード例 #1
0
  /** 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");
  }
コード例 #2
0
 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);
   }
 }
コード例 #3
0
  @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");
  }