From 605acaae9cf0b9de4f55dcd7891c7243fb555bab Mon Sep 17 00:00:00 2001
From: Ryan Poplin <rpoplin@broadinstitute.org>
Date: Tue, 21 Aug 2012 09:33:58 -0400
Subject: [PATCH] Another round of FindBugs fixes. Object internally stores a
 reference to an externally mutable array. Very dangerous.

---
 .../walkers/haplotypecaller/DeBruijnVertex.java    |  2 +-
 .../walkers/bqsr/StandardRecalibrationEngine.java  |  2 +-
 .../org/broadinstitute/sting/utils/Haplotype.java  | 14 +++++++-------
 3 files changed, 9 insertions(+), 9 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 39833613d..358bd0c38 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
@@ -14,7 +14,7 @@ public class DeBruijnVertex {
     public final int kmer;
 
     public DeBruijnVertex( final byte[] sequence, final int kmer ) {
-        this.sequence = sequence;
+        this.sequence = sequence.clone();
         this.kmer = kmer;
     }
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/StandardRecalibrationEngine.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/StandardRecalibrationEngine.java
index 08c7da754..aec1bf7a8 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/StandardRecalibrationEngine.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/StandardRecalibrationEngine.java
@@ -42,7 +42,7 @@ public class StandardRecalibrationEngine implements RecalibrationEngine, PublicP
     protected RecalibrationTables recalibrationTables;
 
     public void initialize(final Covariate[] covariates, final RecalibrationTables recalibrationTables) {
-        this.covariates = covariates;
+        this.covariates = covariates.clone();
         this.recalibrationTables = recalibrationTables;
     }
 
diff --git a/public/java/src/org/broadinstitute/sting/utils/Haplotype.java b/public/java/src/org/broadinstitute/sting/utils/Haplotype.java
index fcde1f419..efddf1468 100755
--- a/public/java/src/org/broadinstitute/sting/utils/Haplotype.java
+++ b/public/java/src/org/broadinstitute/sting/utils/Haplotype.java
@@ -55,22 +55,22 @@ public class Haplotype {
      * @param bases bases
      * @param qual  qual
      */
-    public Haplotype(byte[] bases, int qual) {
-        this.bases = bases;
+    public Haplotype( final byte[] bases, final int qual ) {
+        this.bases = bases.clone();
         quals = new double[bases.length];
         Arrays.fill(quals, (double)qual);
     }
 
-    public Haplotype(byte[] bases, double[] quals) {
-        this.bases = bases;
-        this.quals = quals;
+    public Haplotype( final byte[] bases, final double[] quals ) {
+        this.bases = bases.clone();
+        this.quals = quals.clone();
     }
 
-    public Haplotype(byte[] bases) {
+    public Haplotype( final byte[] bases ) {
         this(bases, 0);
     }
 
-    public Haplotype(byte[] bases, GenomeLoc loc) {
+    public Haplotype( final byte[] bases, final GenomeLoc loc ) {
         this(bases);
         this.genomeLocation = loc;
     }