/** 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()); }