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Stop RBP.getPileupBySample() from throwing a NullPointerException if the 

sample doesn't exist -- now returns null.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4719 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2010-11-23 05:17:06 +00:00
parent d2fc30d188
commit 082073ca3c
2 changed files with 45 additions and 6 deletions
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6
java/src/org/broadinstitute/sting/utils/pileup/AbstractReadBackedPileup.java
View File

@ -612,7 +612,8 @@ public abstract class AbstractReadBackedPileup<RBP extends AbstractReadBackedPil
public RBP getPileupForSampleName(String sampleName) {
if(pileupElementTracker instanceof PerSamplePileupElementTracker) {
PerSamplePileupElementTracker<PE> tracker = (PerSamplePileupElementTracker<PE>)pileupElementTracker;
return (RBP)createNewPileup(loc,tracker.getElements(sampleName));
PileupElementTracker<PE> filteredElements = tracker.getElements(sampleName);
return filteredElements != null ? (RBP)createNewPileup(loc,filteredElements) : null;
}
else {
UnifiedPileupElementTracker<PE> filteredTracker = new UnifiedPileupElementTracker<PE>();
@ -635,7 +636,8 @@ public abstract class AbstractReadBackedPileup<RBP extends AbstractReadBackedPil
public RBP getPileupForSample(Sample sample) {
if(pileupElementTracker instanceof PerSamplePileupElementTracker) {
PerSamplePileupElementTracker<PE> tracker = (PerSamplePileupElementTracker<PE>)pileupElementTracker;
return (RBP)createNewPileup(loc,tracker.getElements(sample));
PileupElementTracker<PE> filteredElements = tracker.getElements(sample);
return filteredElements != null ? (RBP)createNewPileup(loc,filteredElements) : null;
}
else {
UnifiedPileupElementTracker<PE> filteredTracker = new UnifiedPileupElementTracker<PE>();

45
java/test/org/broadinstitute/sting/utils/pileup/ReadBackedPileupUnitTest.java
View File

@ -33,10 +33,7 @@ import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils;
import org.testng.annotations.Test;
import java.util.Arrays;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.*;
/**
* Test routines for read-backed pileup.
@ -164,4 +161,44 @@ public class ReadBackedPileupUnitTest {
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<Sample,ReadBackedPileupImpl> sampleToPileupMap = new HashMap<Sample,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 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");
}
}