Another round of FindBugs fixes. Object returns its internal reference to an externally mutable array. Very dangerous.

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() {

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() {