From f0c54d99ed2e6b2feaaa0025f917c6783c21d6c1 Mon Sep 17 00:00:00 2001
From: Joel Thibault <thibault@broadinstitute.org>
Date: Fri, 22 Jun 2012 16:56:04 -0400
Subject: [PATCH] Account for a null attributes object

* field attributesCanBeModified - a null attributes object can't be modified in its current state
* method makeAttributesModifiable() - initialize a null attributes object to empty
---
 .../utils/variantcontext/VariantContextBuilder.java      | 9 ++++++++-
 1 file changed, 8 insertions(+), 1 deletion(-)

diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextBuilder.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextBuilder.java
index c6c2ac2c7..83ddd2a1f 100644
--- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextBuilder.java
+++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextBuilder.java
@@ -182,7 +182,13 @@ public class VariantContextBuilder {
      * @param attributes
      */
     public VariantContextBuilder attributes(final Map<String, Object> attributes) {
-        this.attributes = attributes;
+        if (attributes != null) {
+            this.attributes = attributes;
+        }
+        else {
+            this.attributes = new HashMap<String, Object>();
+        }
+
         this.attributesCanBeModified = true;
         return this;
     }
@@ -220,6 +226,7 @@ public class VariantContextBuilder {
      * Makes the attributes field modifiable.  In many cases attributes is just a pointer to an immutable
      * collection, so methods that want to add / remove records require the attributes to be copied to a
      */
+    @Ensures({"this.attributesCanBeModified"})
     private void makeAttributesModifiable() {
         if ( ! attributesCanBeModified ) {
             this.attributesCanBeModified = true;