From e5f88b5ba997e9b4327c0188c5ebf094ff62e869 Mon Sep 17 00:00:00 2001
From: Matt Massie <massie@cs.berkeley.edu>
Date: Sun, 2 Nov 2014 07:13:18 -0800
Subject: [PATCH] Better null handling for isSameContig utility

---
 .../scala/org/bdgenomics/adam/util/Util.scala |  7 ++-
 .../org/bdgenomics/adam/util/UtilSuite.scala  | 43 +++++++++++++++++++
 2 files changed, 48 insertions(+), 2 deletions(-)
 create mode 100644 adam-core/src/test/scala/org/bdgenomics/adam/util/UtilSuite.scala

diff --git a/adam-core/src/main/scala/org/bdgenomics/adam/util/Util.scala b/adam-core/src/main/scala/org/bdgenomics/adam/util/Util.scala
index 7eff4e2a51..2010ebc760 100644
--- a/adam-core/src/main/scala/org/bdgenomics/adam/util/Util.scala
+++ b/adam-core/src/main/scala/org/bdgenomics/adam/util/Util.scala
@@ -21,8 +21,11 @@ import org.bdgenomics.formats.avro.Contig
 
 object Util {
   def isSameContig(left: Contig, right: Contig): Boolean = {
-    left.getContigName == right.getContigName && (
-      left.getContigMD5 == null || right.getContigMD5 == null || left.getContigMD5 == right.getContigMD5)
+    val leftName = Option(left).map(_.getContigName)
+    val leftMD5 = Option(left).map(_.getContigMD5)
+    val rightName = Option(right).map(_.getContigName)
+    val rightMD5 = Option(right).map(_.getContigMD5)
+    leftName == rightName && (leftMD5.isEmpty || rightMD5.isEmpty || leftMD5 == rightMD5)
   }
 
   def hashCombine(parts: Int*): Int =
diff --git a/adam-core/src/test/scala/org/bdgenomics/adam/util/UtilSuite.scala b/adam-core/src/test/scala/org/bdgenomics/adam/util/UtilSuite.scala
new file mode 100644
index 0000000000..9a44ae8cad
--- /dev/null
+++ b/adam-core/src/test/scala/org/bdgenomics/adam/util/UtilSuite.scala
@@ -0,0 +1,43 @@
+/**
+ * Licensed to Big Data Genomics (BDG) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The BDG licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.  You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.bdgenomics.adam.util
+
+import org.bdgenomics.formats.avro.Contig
+
+class UtilSuite extends SparkFunSuite {
+
+  test("isSameConfig") {
+    val a = Contig.newBuilder().setContigName("foo")
+    val b = Contig.newBuilder().setContigName("bar")
+    assert(!Util.isSameContig(a.build(), b.build()))
+    b.setContigName("foo")
+    assert(Util.isSameContig(a.build(), b.build()))
+
+    // proper null handling
+    assert(Util.isSameContig(null, null))
+    assert(!Util.isSameContig(null, b.build()))
+    assert(!Util.isSameContig(a.build(), null))
+
+    a.setContigMD5("md5")
+    // both md5s need to be set to change equality
+    assert(!Util.isSameContig(a.build(), b.build()))
+    b.setContigMD5("md5")
+    assert(Util.isSameContig(a.build(), b.build()))
+  }
+
+}