From 082073ca3c622a89cc605804af8bce43bf53404c Mon Sep 17 00:00:00 2001
From: hanna <hanna@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Tue, 23 Nov 2010 05:17:06 +0000
Subject: [PATCH] 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
---
 .../pileup/AbstractReadBackedPileup.java      |  6 ++-
 .../pileup/ReadBackedPileupUnitTest.java      | 45 +++++++++++++++++--
 2 files changed, 45 insertions(+), 6 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/utils/pileup/AbstractReadBackedPileup.java b/java/src/org/broadinstitute/sting/utils/pileup/AbstractReadBackedPileup.java
index f50d7a5af..85156abf1 100644
--- a/java/src/org/broadinstitute/sting/utils/pileup/AbstractReadBackedPileup.java
+++ b/java/src/org/broadinstitute/sting/utils/pileup/AbstractReadBackedPileup.java
@@ -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>();
diff --git a/java/test/org/broadinstitute/sting/utils/pileup/ReadBackedPileupUnitTest.java b/java/test/org/broadinstitute/sting/utils/pileup/ReadBackedPileupUnitTest.java
index c031aa2da..fb479ab47 100644
--- a/java/test/org/broadinstitute/sting/utils/pileup/ReadBackedPileupUnitTest.java
+++ b/java/test/org/broadinstitute/sting/utils/pileup/ReadBackedPileupUnitTest.java
@@ -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");
+    }
 }