/* * Copyright (c) 2010, The Broad Institute * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation * files (the "Software"), to deal in the Software without * restriction, including without limitation the rights to use, * copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the * Software is furnished to do so, subject to the following * conditions: * * The above copyright notice and this permission notice shall be * included in all copies or substantial portions of the Software. * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR * OTHER DEALINGS IN THE SOFTWARE. */ package org.broadinstitute.sting.utils.pileup; import net.sf.samtools.SAMFileHeader; import net.sf.samtools.SAMReadGroupRecord; import net.sf.samtools.SAMRecord; import org.testng.Assert; import org.broadinstitute.sting.gatk.datasources.sample.Sample; import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils; import org.testng.annotations.Test; import java.util.*; /** * Test routines for read-backed pileup. */ public class ReadBackedPileupUnitTest { /** * 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); SAMRecord read1 = ArtificialSAMUtils.createArtificialRead(header,"read1",0,1,10); read1.setAttribute("RG",readGroupOne.getId()); SAMRecord read2 = ArtificialSAMUtils.createArtificialRead(header,"read2",0,1,10); read2.setAttribute("RG",readGroupTwo.getId()); SAMRecord read3 = ArtificialSAMUtils.createArtificialRead(header,"read3",0,1,10); read3.setAttribute("RG",readGroupOne.getId()); SAMRecord read4 = ArtificialSAMUtils.createArtificialRead(header,"read4",0,1,10); read4.setAttribute("RG",readGroupTwo.getId()); SAMRecord read5 = ArtificialSAMUtils.createArtificialRead(header,"read5",0,1,10); read5.setAttribute("RG",readGroupTwo.getId()); SAMRecord read6 = ArtificialSAMUtils.createArtificialRead(header,"read6",0,1,10); read6.setAttribute("RG",readGroupOne.getId()); SAMRecord 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 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 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 null read groups. */ @Test public void testSplitByNullReadGroups() { SAMFileHeader header = ArtificialSAMUtils.createArtificialSamHeader(1,1,1000); SAMRecord read1 = ArtificialSAMUtils.createArtificialRead(header,"read1",0,1,10); SAMRecord read2 = ArtificialSAMUtils.createArtificialRead(header,"read2",0,1,10); SAMRecord 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 nullRgReads = nullRgPileup.getReads(); Assert.assertEquals(nullRgPileup.size(), 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); SAMRecord read1 = ArtificialSAMUtils.createArtificialRead(header,"read1",0,1,10); read1.setAttribute("RG",readGroupOne.getId()); SAMRecord read2 = ArtificialSAMUtils.createArtificialRead(header,"read2",0,1,10); read2.setAttribute("RG",readGroupTwo.getId()); SAMRecord read3 = ArtificialSAMUtils.createArtificialRead(header,"read3",0,1,10); read3.setAttribute("RG",readGroupOne.getId()); SAMRecord 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 sampleToPileupMap = new HashMap(); sampleToPileupMap.put(new Sample(readGroupOne.getSample()),sample1Pileup); sampleToPileupMap.put(new Sample(readGroupTwo.getSample()),sample2Pileup); ReadBackedPileup compositePileup = new ReadBackedPileupImpl(null,sampleToPileupMap); ReadBackedPileup rg1Pileup = compositePileup.getPileupForReadGroup("rg1"); List 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 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() { Sample sample1 = new Sample("sample1"); Sample sample2 = new Sample("sample2"); SAMReadGroupRecord readGroupOne = new SAMReadGroupRecord("rg1"); readGroupOne.setSample(sample1.getId()); SAMReadGroupRecord readGroupTwo = new SAMReadGroupRecord("rg2"); readGroupTwo.setSample(sample2.getId()); SAMFileHeader header = ArtificialSAMUtils.createArtificialSamHeader(1,1,1000); header.addReadGroup(readGroupOne); header.addReadGroup(readGroupTwo); SAMRecord read1 = ArtificialSAMUtils.createArtificialRead(header,"read1",0,1,10); read1.setAttribute("RG",readGroupOne.getId()); SAMRecord read2 = ArtificialSAMUtils.createArtificialRead(header,"read2",0,1,10); read2.setAttribute("RG",readGroupTwo.getId()); Map sampleToPileupMap = new HashMap(); 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 sample1Pileup = pileup.getPileupForSample(sample1); Assert.assertEquals(sample1Pileup.size(),1,"Sample 1 pileup has wrong number of elements"); Assert.assertEquals(sample1Pileup.getReads().get(0),read1,"Sample 1 pileup has incorrect read"); ReadBackedPileup sample2Pileup = pileup.getPileupForSampleName(sample2.getId()); Assert.assertEquals(sample2Pileup.size(),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(new Sample("missing")); Assert.assertNull(missingSamplePileup,"Pileup for sample 'missing' should be null but isn't"); missingSamplePileup = pileup.getPileupForSampleName("not here"); Assert.assertNull(missingSamplePileup,"Pileup for sample 'not here' should be null but isn't"); } }