From c77c60005b8d61cfade532f370359f1282a79531 Mon Sep 17 00:00:00 2001
From: devin-petersohn <devin.petersohn@gmail.com>
Date: Fri, 5 May 2017 11:51:43 -0700
Subject: [PATCH] Making TreeRegionJoin consistent with ShuffleRegionJoin

---
 .../org/bdgenomics/adam/rdd/TreeRegionJoin.scala    | 13 +++++--------
 .../bdgenomics/adam/rdd/TreeRegionJoinSuite.scala   |  5 +----
 2 files changed, 6 insertions(+), 12 deletions(-)

diff --git a/adam-core/src/main/scala/org/bdgenomics/adam/rdd/TreeRegionJoin.scala b/adam-core/src/main/scala/org/bdgenomics/adam/rdd/TreeRegionJoin.scala
index 46cea8345b..22642a5afa 100644
--- a/adam-core/src/main/scala/org/bdgenomics/adam/rdd/TreeRegionJoin.scala
+++ b/adam-core/src/main/scala/org/bdgenomics/adam/rdd/TreeRegionJoin.scala
@@ -29,7 +29,7 @@ import scala.reflect.ClassTag
  * The broadcast values are stored in a sorted array. It was going to be an
  * ensemble of interval trees, but, that didn't work out.
  */
-trait TreeRegionJoin[T, U] {
+trait TreeRegionJoin[T, U, RT, RU] extends RegionJoin[T, U, RT, RU] {
 
   private[rdd] def runJoinAndGroupByRightWithTree(
     tree: IntervalArray[ReferenceRegion, T],
@@ -84,7 +84,7 @@ trait TreeRegionJoin[T, U] {
 /**
  * Implements an inner region join where the left side of the join is broadcast.
  */
-case class InnerTreeRegionJoin[T: ClassTag, U: ClassTag]() extends RegionJoin[T, U, T, U] with TreeRegionJoin[T, U] {
+case class InnerTreeRegionJoin[T: ClassTag, U: ClassTag]() extends TreeRegionJoin[T, U, T, U] {
 
   def broadcastAndJoin(tree: IntervalArray[ReferenceRegion, T],
                        joinedRDD: RDD[(ReferenceRegion, U)]): RDD[(T, U)] = {
@@ -119,8 +119,7 @@ case class InnerTreeRegionJoin[T: ClassTag, U: ClassTag]() extends RegionJoin[T,
  * broadcast.
  */
 case class RightOuterTreeRegionJoin[T: ClassTag, U: ClassTag]()
-    extends RegionJoin[T, U, Option[T], U]
-    with TreeRegionJoin[T, U] {
+    extends TreeRegionJoin[T, U, Option[T], U] {
 
   def broadcastAndJoin(tree: IntervalArray[ReferenceRegion, T],
                        joinedRDD: RDD[(ReferenceRegion, U)]): RDD[(Option[T], U)] = {
@@ -168,8 +167,7 @@ case class RightOuterTreeRegionJoin[T: ClassTag, U: ClassTag]()
  * values on the left grouped by the right value.
  */
 case class InnerTreeRegionJoinAndGroupByRight[T: ClassTag, U: ClassTag]()
-    extends RegionJoin[T, U, Iterable[T], U]
-    with TreeRegionJoin[T, U] {
+    extends TreeRegionJoin[T, U, Iterable[T], U] {
 
   def broadcastAndJoin(tree: IntervalArray[ReferenceRegion, T],
                        joinedRDD: RDD[(ReferenceRegion, U)]): RDD[(Iterable[T], U)] = {
@@ -203,8 +201,7 @@ case class InnerTreeRegionJoinAndGroupByRight[T: ClassTag, U: ClassTag]()
  * collections on the left side of the join are kept.
  */
 case class RightOuterTreeRegionJoinAndGroupByRight[T: ClassTag, U: ClassTag]()
-    extends RegionJoin[T, U, Iterable[T], U]
-    with TreeRegionJoin[T, U] {
+    extends TreeRegionJoin[T, U, Iterable[T], U] {
 
   def broadcastAndJoin(tree: IntervalArray[ReferenceRegion, T],
                        joinedRDD: RDD[(ReferenceRegion, U)]): RDD[(Iterable[T], U)] = {
diff --git a/adam-core/src/test/scala/org/bdgenomics/adam/rdd/TreeRegionJoinSuite.scala b/adam-core/src/test/scala/org/bdgenomics/adam/rdd/TreeRegionJoinSuite.scala
index 51701bad8b..4cfdaf4bbf 100644
--- a/adam-core/src/test/scala/org/bdgenomics/adam/rdd/TreeRegionJoinSuite.scala
+++ b/adam-core/src/test/scala/org/bdgenomics/adam/rdd/TreeRegionJoinSuite.scala
@@ -24,9 +24,6 @@ import org.bdgenomics.formats.avro.{ AlignmentRecord, Variant }
 import org.bdgenomics.utils.interval.array.IntervalArray
 import scala.reflect.ClassTag
 
-private case class ConcreteTreeRegionJoin[T: ClassTag, U]() extends TreeRegionJoin[T, U] {
-}
-
 class TreeRegionJoinSuite extends ADAMFunSuite {
 
   sparkTest("run a join between data on a single contig") {
@@ -62,7 +59,7 @@ class TreeRegionJoinSuite extends ADAMFunSuite {
           .build)
       })
 
-    val joinData = ConcreteTreeRegionJoin().runJoinAndGroupByRightWithTree(tree,
+    val joinData = InnerTreeRegionJoin().runJoinAndGroupByRightWithTree(tree,
       leftRdd)
       .map(kv => {
         val (k, v) = kv