zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

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
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

37
java/src/org/broadinstitute/sting/utils/pileup/AbstractReadBackedPileup.java
View File

@ -24,6 +24,7 @@
package org.broadinstitute.sting.utils.pileup;
import net.sf.samtools.SAMReadGroupRecord;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.StingException;
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.
* @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.
*/
@Override
public RBP getPileupForReadGroup(String readGroupId) {
UnifiedPileupElementTracker<PE> filteredTracker = new UnifiedPileupElementTracker<PE>();
for(PileupElement pileupElement: this)
filteredTracker.add((PE)pileupElement);
return (RBP)createNewPileup(loc,filteredTracker);
public RBP getPileupForReadGroup(String targetReadGroupId) {
if(pileupElementTracker instanceof PerSamplePileupElementTracker) {
PerSamplePileupElementTracker<PE> tracker = (PerSamplePileupElementTracker<PE>)pileupElementTracker;
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);
}
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() {

165
java/test/org/broadinstitute/sting/utils/pileup/ReadBackedPileupTest.java 100644
View File

@ -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));
}
}