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Replaced placeholder support for splitting by read group with read support (sorry everyone), and added relatively comprehensive unit tests to ensure that splitting by read group works. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4190 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2010-09-01 22:24:50 +00:00
parent b28f63a948
commit dc5f858d29
2 changed files with 196 additions and 6 deletions
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35
java/src/org/broadinstitute/sting/utils/pileup/AbstractReadBackedPileup.java
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@ -24,6 +24,7 @@
package org.broadinstitute.sting.utils.pileup; package org.broadinstitute.sting.utils.pileup;
import net.sf.samtools.SAMReadGroupRecord;
import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.StingException; import org.broadinstitute.sting.utils.StingException;
import org.broadinstitute.sting.utils.BaseUtils; import org.broadinstitute.sting.utils.BaseUtils;
@ -482,15 +483,39 @@ public abstract class AbstractReadBackedPileup<RBP extends AbstractReadBackedPil
/** /**
* Gets the pileup for a given read group. Horrendously inefficient at this point. * Gets the pileup for a given read group. Horrendously inefficient at this point.
* @param readGroupId Identifier for the read group. * @param targetReadGroupId Identifier for the read group.
* @return A read-backed pileup containing only the reads in the given read group. * @return A read-backed pileup containing only the reads in the given read group.
*/ */
@Override @Override
public RBP getPileupForReadGroup(String readGroupId) { public RBP getPileupForReadGroup(String targetReadGroupId) {
UnifiedPileupElementTracker<PE> filteredTracker = new UnifiedPileupElementTracker<PE>(); if(pileupElementTracker instanceof PerSamplePileupElementTracker) {
for(PileupElement pileupElement: this) PerSamplePileupElementTracker<PE> tracker = (PerSamplePileupElementTracker<PE>)pileupElementTracker;
filteredTracker.add((PE)pileupElement); PerSamplePileupElementTracker<PE> filteredTracker = new PerSamplePileupElementTracker<PE>();
for(String sampleName: tracker.getSamples()) {
PileupElementTracker<PE> perSampleElements = tracker.getElements(sampleName);
AbstractReadBackedPileup<RBP,PE> pileup = createNewPileup(loc,perSampleElements).getPileupForReadGroup(targetReadGroupId);
if(pileup != null)
filteredTracker.addElements(sampleName,pileup.pileupElementTracker);
}
return (RBP)createNewPileup(loc,filteredTracker); return (RBP)createNewPileup(loc,filteredTracker);
}
else {
UnifiedPileupElementTracker<PE> filteredTracker = new UnifiedPileupElementTracker<PE>();
for(PE p: pileupElementTracker) {
SAMRecord read = p.getRead();
if(targetReadGroupId != null) {
if(read.getReadGroup() != null && targetReadGroupId.equals(read.getReadGroup().getReadGroupId()))
filteredTracker.add(p);
}
else {
if(read.getReadGroup() == null || read.getReadGroup().getReadGroupId() == null)
filteredTracker.add(p);
}
}
return filteredTracker.size()>0 ? (RBP)createNewPileup(loc,filteredTracker) : null;
}
} }
public Collection<String> getSamples() { public Collection<String> getSamples() {

165
java/test/org/broadinstitute/sting/utils/pileup/ReadBackedPileupTest.java 100644
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@ -0,0 +1,165 @@
/*
* 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.broadinstitute.sting.utils.sam.ArtificialSAMUtils;
import org.junit.Assert;
import org.junit.Test;
import java.util.Arrays;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
/**
* Test routines for read-backed pileup.
*/
public class ReadBackedPileupTest {
/**
* 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<SAMRecord> rg1Reads = rg1Pileup.getReads();
Assert.assertEquals("Wrong number of reads in read group rg1",4,rg1Reads.size());
Assert.assertEquals("Read " + read1.getReadName() + " should be in rg1 but isn't",read1,rg1Reads.get(0));
Assert.assertEquals("Read " + read3.getReadName() + " should be in rg1 but isn't",read3,rg1Reads.get(1));
Assert.assertEquals("Read " + read6.getReadName() + " should be in rg1 but isn't",read6,rg1Reads.get(2));
Assert.assertEquals("Read " + read7.getReadName() + " should be in rg1 but isn't",read7,rg1Reads.get(3));
ReadBackedPileup rg2Pileup = pileup.getPileupForReadGroup("rg2");
List<SAMRecord> rg2Reads = rg2Pileup.getReads();
Assert.assertEquals("Wrong number of reads in read group rg2",3,rg2Reads.size());
Assert.assertEquals("Read " + read2.getReadName() + " should be in rg2 but isn't",read2,rg2Reads.get(0));
Assert.assertEquals("Read " + read4.getReadName() + " should be in rg2 but isn't",read4,rg2Reads.get(1));
Assert.assertEquals("Read " + read5.getReadName() + " should be in rg2 but isn't",read5,rg2Reads.get(2));
}
/**
* 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<SAMRecord> nullRgReads = nullRgPileup.getReads();
Assert.assertEquals("Wrong number of reads in null read group",3,nullRgPileup.size());
Assert.assertEquals("Read " + read1.getReadName() + " should be in null rg but isn't",read1,nullRgReads.get(0));
Assert.assertEquals("Read " + read2.getReadName() + " should be in null rg but isn't",read2,nullRgReads.get(1));
Assert.assertEquals("Read " + read3.getReadName() + " should be in null rg but isn't",read3,nullRgReads.get(2));
ReadBackedPileup rg1Pileup = pileup.getPileupForReadGroup("rg1");
Assert.assertNull("Pileup for non-existent read group should return null",rg1Pileup);
}
/**
* 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<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<SAMRecord> rg1Reads = rg1Pileup.getReads();
Assert.assertEquals("Wrong number of reads in read group rg1",2,rg1Reads.size());
Assert.assertEquals("Read " + read1.getReadName() + " should be in rg1 but isn't",read1,rg1Reads.get(0));
Assert.assertEquals("Read " + read3.getReadName() + " should be in rg1 but isn't",read3,rg1Reads.get(1));
ReadBackedPileup rg2Pileup = compositePileup.getPileupForReadGroup("rg2");
List<SAMRecord> rg2Reads = rg2Pileup.getReads();
Assert.assertEquals("Wrong number of reads in read group rg2",2,rg1Reads.size());
Assert.assertEquals("Read " + read2.getReadName() + " should be in rg2 but isn't",read2,rg2Reads.get(0));
Assert.assertEquals("Read " + read4.getReadName() + " should be in rg2 but isn't",read4,rg2Reads.get(1));
}
}