[UTILS-114] Add abstract duplicate method to IntervalArray.

Resolves #114.
bigdatagenomics · Mar 17, 2017 · 56c4849 · 56c4849
1 parent 2431d6c
commit 56c4849
Showing 1 changed file with 10 additions and 0 deletions.
diff --git a/utils-intervalrdd/src/main/scala/org/bdgenomics/utils/interval/array/IntervalArray.scala b/utils-intervalrdd/src/main/scala/org/bdgenomics/utils/interval/array/IntervalArray.scala
@@ -127,6 +127,12 @@ trait IntervalArray[K <: Interval[K], T] extends Serializable {
 
   protected def replace(arr: Array[(K, T)], maxWidth: Long): IntervalArray[K, T]
 
+  /**
+   * @return Makes a copy of the interval array. The underlying array is shallow
+   *   copied, but the thread unsafe optLastIndex variable is not shared.
+   */
+  def duplicate(): IntervalArray[K, T]
+
   @tailrec private def pow2ceil(i: Int = 1): Int = {
     if (2 * i >= length) {
       i
@@ -493,6 +499,10 @@ case class ConcreteIntervalArray[K <: Interval[K], T: ClassTag](
     array: Array[(K, T)],
     maxIntervalWidth: Long) extends IntervalArray[K, T] {
 
+  def duplicate(): IntervalArray[K, T] = {
+    new ConcreteIntervalArray(array, maxIntervalWidth)
+  }
+
   protected def replace(arr: Array[(K, T)],
                         maxWidth: Long): IntervalArray[K, T] = {
     new ConcreteIntervalArray(arr, maxWidth)