From 10961db3ce04c46ac1370f40ee9640824fc30aaa Mon Sep 17 00:00:00 2001
From: Ryan Poplin <rpoplin@broadinstitute.org>
Date: Tue, 21 Aug 2012 09:35:55 -0400
Subject: [PATCH] Another round of FindBugs fixes. Object returns its internal
 reference to an externally mutable array. Very dangerous.

---
 .../sting/gatk/walkers/haplotypecaller/DeBruijnVertex.java    | 2 +-
 public/java/src/org/broadinstitute/sting/utils/Haplotype.java | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/DeBruijnVertex.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/DeBruijnVertex.java
index 358bd0c38..4da3251bc 100755
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/DeBruijnVertex.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/DeBruijnVertex.java
@@ -37,7 +37,7 @@ public class DeBruijnVertex {
     }
 
     public byte[] getSequence() {
-        return sequence;
+        return sequence.clone();
     }
 
     public byte[] getSuffix() {
diff --git a/public/java/src/org/broadinstitute/sting/utils/Haplotype.java b/public/java/src/org/broadinstitute/sting/utils/Haplotype.java
index efddf1468..befd24307 100755
--- a/public/java/src/org/broadinstitute/sting/utils/Haplotype.java
+++ b/public/java/src/org/broadinstitute/sting/utils/Haplotype.java
@@ -140,10 +140,10 @@ public class Haplotype {
     }
 
     public double[] getQuals() {
-        return quals;
+        return quals.clone();
     }
     public byte[] getBases() {
-        return bases;
+        return bases.clone();
     }
 
     public long getStartPosition() {