167 lines
8.9 KiB
Java
167 lines
8.9 KiB
Java
/*
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* Copyright (c) 2010, The Broad Institute
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*
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* Permission is hereby granted, free of charge, to any person
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* obtaining a copy of this software and associated documentation
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* files (the "Software"), to deal in the Software without
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* restriction, including without limitation the rights to use,
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* copy, modify, merge, publish, distribute, sublicense, and/or sell
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* copies of the Software, and to permit persons to whom the
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* Software is furnished to do so, subject to the following
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* conditions:
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*
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* The above copyright notice and this permission notice shall be
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* included in all copies or substantial portions of the Software.
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* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
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* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
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* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
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* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
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* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
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* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
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* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
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* OTHER DEALINGS IN THE SOFTWARE.
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*/
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package org.broadinstitute.sting.utils.pileup;
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import net.sf.samtools.SAMFileHeader;
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import net.sf.samtools.SAMReadGroupRecord;
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import net.sf.samtools.SAMRecord;
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import org.testng.Assert;
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import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils;
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import org.testng.annotations.Test;
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import java.util.Arrays;
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import java.util.HashMap;
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import java.util.List;
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import java.util.Map;
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/**
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* Test routines for read-backed pileup.
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*/
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public class ReadBackedPileupUnitTest {
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/**
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* Ensure that basic read group splitting works.
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*/
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@Test
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public void testSplitByReadGroup() {
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SAMReadGroupRecord readGroupOne = new SAMReadGroupRecord("rg1");
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SAMReadGroupRecord readGroupTwo = new SAMReadGroupRecord("rg2");
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SAMFileHeader header = ArtificialSAMUtils.createArtificialSamHeader(1,1,1000);
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header.addReadGroup(readGroupOne);
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header.addReadGroup(readGroupTwo);
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SAMRecord read1 = ArtificialSAMUtils.createArtificialRead(header,"read1",0,1,10);
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read1.setAttribute("RG",readGroupOne.getId());
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SAMRecord read2 = ArtificialSAMUtils.createArtificialRead(header,"read2",0,1,10);
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read2.setAttribute("RG",readGroupTwo.getId());
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SAMRecord read3 = ArtificialSAMUtils.createArtificialRead(header,"read3",0,1,10);
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read3.setAttribute("RG",readGroupOne.getId());
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SAMRecord read4 = ArtificialSAMUtils.createArtificialRead(header,"read4",0,1,10);
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read4.setAttribute("RG",readGroupTwo.getId());
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SAMRecord read5 = ArtificialSAMUtils.createArtificialRead(header,"read5",0,1,10);
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read5.setAttribute("RG",readGroupTwo.getId());
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SAMRecord read6 = ArtificialSAMUtils.createArtificialRead(header,"read6",0,1,10);
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read6.setAttribute("RG",readGroupOne.getId());
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SAMRecord read7 = ArtificialSAMUtils.createArtificialRead(header,"read7",0,1,10);
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read7.setAttribute("RG",readGroupOne.getId());
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ReadBackedPileup pileup = new ReadBackedPileupImpl(null,
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Arrays.asList(read1,read2,read3,read4,read5,read6,read7),
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Arrays.asList(1,1,1,1,1,1,1));
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ReadBackedPileup rg1Pileup = pileup.getPileupForReadGroup("rg1");
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List<SAMRecord> rg1Reads = rg1Pileup.getReads();
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Assert.assertEquals(rg1Reads.size(), 4, "Wrong number of reads in read group rg1");
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Assert.assertEquals(rg1Reads.get(0), read1, "Read " + read1.getReadName() + " should be in rg1 but isn't");
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Assert.assertEquals(rg1Reads.get(1), read3, "Read " + read3.getReadName() + " should be in rg1 but isn't");
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Assert.assertEquals(rg1Reads.get(2), read6, "Read " + read6.getReadName() + " should be in rg1 but isn't");
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Assert.assertEquals(rg1Reads.get(3), read7, "Read " + read7.getReadName() + " should be in rg1 but isn't");
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ReadBackedPileup rg2Pileup = pileup.getPileupForReadGroup("rg2");
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List<SAMRecord> rg2Reads = rg2Pileup.getReads();
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Assert.assertEquals(rg2Reads.size(), 3, "Wrong number of reads in read group rg2");
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Assert.assertEquals(rg2Reads.get(0), read2, "Read " + read2.getReadName() + " should be in rg2 but isn't");
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Assert.assertEquals(rg2Reads.get(1), read4, "Read " + read4.getReadName() + " should be in rg2 but isn't");
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Assert.assertEquals(rg2Reads.get(2), read5, "Read " + read5.getReadName() + " should be in rg2 but isn't");
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}
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/**
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* Ensure that splitting read groups still works when dealing with null read groups.
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*/
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@Test
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public void testSplitByNullReadGroups() {
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SAMFileHeader header = ArtificialSAMUtils.createArtificialSamHeader(1,1,1000);
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SAMRecord read1 = ArtificialSAMUtils.createArtificialRead(header,"read1",0,1,10);
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SAMRecord read2 = ArtificialSAMUtils.createArtificialRead(header,"read2",0,1,10);
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SAMRecord read3 = ArtificialSAMUtils.createArtificialRead(header,"read3",0,1,10);
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ReadBackedPileup pileup = new ReadBackedPileupImpl(null,
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Arrays.asList(read1,read2,read3),
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Arrays.asList(1,1,1));
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ReadBackedPileup nullRgPileup = pileup.getPileupForReadGroup(null);
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List<SAMRecord> nullRgReads = nullRgPileup.getReads();
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Assert.assertEquals(nullRgPileup.size(), 3, "Wrong number of reads in null read group");
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Assert.assertEquals(nullRgReads.get(0), read1, "Read " + read1.getReadName() + " should be in null rg but isn't");
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Assert.assertEquals(nullRgReads.get(1), read2, "Read " + read2.getReadName() + " should be in null rg but isn't");
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Assert.assertEquals(nullRgReads.get(2), read3, "Read " + read3.getReadName() + " should be in null rg but isn't");
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ReadBackedPileup rg1Pileup = pileup.getPileupForReadGroup("rg1");
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Assert.assertNull(rg1Pileup, "Pileup for non-existent read group should return null");
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}
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/**
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* Ensure that splitting read groups still works when dealing with a sample-split pileup.
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*/
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@Test
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public void testSplitBySample() {
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SAMReadGroupRecord readGroupOne = new SAMReadGroupRecord("rg1");
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readGroupOne.setSample("sample1");
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SAMReadGroupRecord readGroupTwo = new SAMReadGroupRecord("rg2");
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readGroupTwo.setSample("sample2");
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SAMFileHeader header = ArtificialSAMUtils.createArtificialSamHeader(1,1,1000);
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header.addReadGroup(readGroupOne);
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header.addReadGroup(readGroupTwo);
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SAMRecord read1 = ArtificialSAMUtils.createArtificialRead(header,"read1",0,1,10);
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read1.setAttribute("RG",readGroupOne.getId());
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SAMRecord read2 = ArtificialSAMUtils.createArtificialRead(header,"read2",0,1,10);
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read2.setAttribute("RG",readGroupTwo.getId());
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SAMRecord read3 = ArtificialSAMUtils.createArtificialRead(header,"read3",0,1,10);
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read3.setAttribute("RG",readGroupOne.getId());
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SAMRecord read4 = ArtificialSAMUtils.createArtificialRead(header,"read4",0,1,10);
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read4.setAttribute("RG",readGroupTwo.getId());
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ReadBackedPileupImpl sample1Pileup = new ReadBackedPileupImpl(null,
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Arrays.asList(read1,read3),
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Arrays.asList(1,1));
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ReadBackedPileupImpl sample2Pileup = new ReadBackedPileupImpl(null,
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Arrays.asList(read2,read4),
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Arrays.asList(1,1));
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Map<String,ReadBackedPileupImpl> sampleToPileupMap = new HashMap<String,ReadBackedPileupImpl>();
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sampleToPileupMap.put(readGroupOne.getSample(),sample1Pileup);
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sampleToPileupMap.put(readGroupTwo.getSample(),sample2Pileup);
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ReadBackedPileup compositePileup = new ReadBackedPileupImpl(null,sampleToPileupMap);
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ReadBackedPileup rg1Pileup = compositePileup.getPileupForReadGroup("rg1");
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List<SAMRecord> rg1Reads = rg1Pileup.getReads();
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Assert.assertEquals(rg1Reads.size(), 2, "Wrong number of reads in read group rg1");
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Assert.assertEquals(rg1Reads.get(0), read1, "Read " + read1.getReadName() + " should be in rg1 but isn't");
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Assert.assertEquals(rg1Reads.get(1), read3, "Read " + read3.getReadName() + " should be in rg1 but isn't");
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ReadBackedPileup rg2Pileup = compositePileup.getPileupForReadGroup("rg2");
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List<SAMRecord> rg2Reads = rg2Pileup.getReads();
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Assert.assertEquals(rg1Reads.size(), 2, "Wrong number of reads in read group rg2");
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Assert.assertEquals(rg2Reads.get(0), read2, "Read " + read2.getReadName() + " should be in rg2 but isn't");
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Assert.assertEquals(rg2Reads.get(1), read4, "Read " + read4.getReadName() + " should be in rg2 but isn't");
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}
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}
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