From 5a0617080483b4fb4076bdc915962a06ace255ea Mon Sep 17 00:00:00 2001
From: Laurent Francioli <lfran@broadinstitute.org>
Date: Fri, 9 Dec 2011 14:51:34 +0100
Subject: [PATCH] Corrected bug causing getChildrenWithParents() to not take
 the last family member into consideration.

---
 .../src/org/broadinstitute/sting/gatk/samples/SampleDB.java   | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/samples/SampleDB.java b/public/java/src/org/broadinstitute/sting/gatk/samples/SampleDB.java
index 1ed8dd7a3..a6f6b3481 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/samples/SampleDB.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/samples/SampleDB.java
@@ -200,7 +200,9 @@ public class SampleDB {
                 continue;
 
             sampleIterator = familyMembers.iterator();
-            for(Sample sample = sampleIterator.next(); sampleIterator.hasNext(); sample = sampleIterator.next()){
+            Sample sample;
+            while(sampleIterator.hasNext()){
+                sample = sampleIterator.next();
                 if(sample.getParents().size() == 2 && familyMembers.containsAll(sample.getParents()))
                     childrenWithParents.add(sample);
             }