/** 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");
  }
 @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());
 }