From 3eb895c3e71c7d4dbafa2a01320d723ab31c0a53 Mon Sep 17 00:00:00 2001
From: Thomas Moerman <thomas.moerman@gmail.com>
Date: Mon, 4 May 2015 15:44:15 +0200
Subject: [PATCH 1/2] - fixed pattern matching bug in
 ReferenceUtils.unionReferenceSet - added test suite

---
 .../org/bdgenomics/adam/models/Gene.scala     |  6 +--
 .../adam/models/ReferenceUtilsSuite.scala     | 44 +++++++++++++++++++
 2 files changed, 47 insertions(+), 3 deletions(-)
 create mode 100644 adam-core/src/test/scala/org/bdgenomics/adam/models/ReferenceUtilsSuite.scala

diff --git a/adam-core/src/main/scala/org/bdgenomics/adam/models/Gene.scala b/adam-core/src/main/scala/org/bdgenomics/adam/models/Gene.scala
index e931d7adec..56aaf3c55a 100644
--- a/adam-core/src/main/scala/org/bdgenomics/adam/models/Gene.scala
+++ b/adam-core/src/main/scala/org/bdgenomics/adam/models/Gene.scala
@@ -222,11 +222,11 @@ object ReferenceUtils {
     def folder(acc: Seq[ReferenceRegion], tref: ReferenceRegion): Seq[ReferenceRegion] =
       acc match {
         case Seq() => Seq(tref)
-        case (first: ReferenceRegion) +: Seq(rest) =>
+        case (first: ReferenceRegion) +: rest =>
           if (first.overlaps(tref))
-            first.hull(tref) +: Seq(rest)
+            first.hull(tref) +: rest
           else
-            tref +: first +: Seq(rest)
+            tref +: first +: rest
       }
 
     refs.toSeq.sorted.foldLeft(Seq[ReferenceRegion]())(folder)
diff --git a/adam-core/src/test/scala/org/bdgenomics/adam/models/ReferenceUtilsSuite.scala b/adam-core/src/test/scala/org/bdgenomics/adam/models/ReferenceUtilsSuite.scala
new file mode 100644
index 0000000000..670e685bea
--- /dev/null
+++ b/adam-core/src/test/scala/org/bdgenomics/adam/models/ReferenceUtilsSuite.scala
@@ -0,0 +1,44 @@
+package org.bdgenomics.adam.models
+
+import org.bdgenomics.adam.models.ReferenceUtils._
+import org.bdgenomics.adam.util.ADAMFunSuite
+
+class ReferenceUtilsSuite extends ADAMFunSuite {
+
+  test("unionReferenceSet: empty") {
+    val regions = Seq()
+
+    assert(unionReferenceSet(regions) === regions)
+  }
+
+  test("unionReferenceSet: one region") {
+    val regions = Seq(ReferenceRegion("1", 3, 7))
+
+    assert(unionReferenceSet(regions) === regions)
+  }
+
+  test("unionReferenceSet: multiple regions on one contig, all overlap") {
+    val regions = Seq(ReferenceRegion("1", 3, 7),
+      ReferenceRegion("1", 1, 5),
+      ReferenceRegion("1", 6, 10))
+
+    assert(unionReferenceSet(regions) === Seq(ReferenceRegion("1", 1, 10)))
+  }
+
+  test("unionReferenceSet: multiple regions on one contig, some overlap") {
+    val regions = Seq(ReferenceRegion("1", 3, 7),
+      ReferenceRegion("1", 1, 5),
+      ReferenceRegion("1", 8, 10))
+
+    assert(unionReferenceSet(regions) === Seq(ReferenceRegion("1", 8, 10), ReferenceRegion("1", 1, 7)))
+  }
+
+  test("unionReferenceSet: multiple regions on multiple contigs") {
+    val regions = Seq(ReferenceRegion("1", 3, 7),
+      ReferenceRegion("1", 1, 5),
+      ReferenceRegion("2", 4, 8))
+
+    assert(unionReferenceSet(regions) === Seq(ReferenceRegion("2", 4, 8), ReferenceRegion("1", 1, 7)))
+  }
+
+}

From 9dc6a6cb2229aae0bca406f5656e97a1210a87e9 Mon Sep 17 00:00:00 2001
From: Thomas Moerman <thomas.moerman@gmail.com>
Date: Mon, 4 May 2015 17:30:31 +0200
Subject: [PATCH 2/2] now with proper header ./scripts/format-source

---
 .../adam/models/ReferenceUtilsSuite.scala       | 17 +++++++++++++++++
 1 file changed, 17 insertions(+)

diff --git a/adam-core/src/test/scala/org/bdgenomics/adam/models/ReferenceUtilsSuite.scala b/adam-core/src/test/scala/org/bdgenomics/adam/models/ReferenceUtilsSuite.scala
index 670e685bea..9f1ca9eb1a 100644
--- a/adam-core/src/test/scala/org/bdgenomics/adam/models/ReferenceUtilsSuite.scala
+++ b/adam-core/src/test/scala/org/bdgenomics/adam/models/ReferenceUtilsSuite.scala
@@ -1,3 +1,20 @@
+/**
+ * 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.models
 
 import org.bdgenomics.adam.models.ReferenceUtils._