From e3540ac69146a122933c79152b93c7a4cbf7875d Mon Sep 17 00:00:00 2001
From: Alyssa Morrow <akmorrow@berkeley.edu>
Date: Mon, 29 Jan 2018 16:44:44 -0800
Subject: [PATCH] added java friendly version of filterByOverlappingRegions

---
 .../adam/cli/TransformAlignments.scala        |  3 +--
 .../org/bdgenomics/adam/rdd/GenomicRDD.scala  | 19 +++++++++++++++++++
 2 files changed, 20 insertions(+), 2 deletions(-)

diff --git a/adam-cli/src/main/scala/org/bdgenomics/adam/cli/TransformAlignments.scala b/adam-cli/src/main/scala/org/bdgenomics/adam/cli/TransformAlignments.scala
index c685b3c1f2..dfc332d081 100644
--- a/adam-cli/src/main/scala/org/bdgenomics/adam/cli/TransformAlignments.scala
+++ b/adam-cli/src/main/scala/org/bdgenomics/adam/cli/TransformAlignments.scala
@@ -17,7 +17,6 @@
  */
 package org.bdgenomics.adam.cli
 
-import scala.collection.JavaConverters._
 import htsjdk.samtools.ValidationStringency
 import java.time.Instant
 import org.apache.parquet.filter2.dsl.Dsl._
@@ -488,7 +487,7 @@ class TransformAlignments(protected val args: TransformAlignmentsArgs) extends B
 
         if (args.regionPredicate != null) {
           val loci = ReferenceRegion.fromString(args.regionPredicate)
-          loadedReads.filterByOverlappingRegions(loci.asJava)
+          loadedReads.filterByOverlappingRegions(loci)
         } else {
           loadedReads
         }
diff --git a/adam-core/src/main/scala/org/bdgenomics/adam/rdd/GenomicRDD.scala b/adam-core/src/main/scala/org/bdgenomics/adam/rdd/GenomicRDD.scala
index 1ab732f71e..90b0fa94e4 100644
--- a/adam-core/src/main/scala/org/bdgenomics/adam/rdd/GenomicRDD.scala
+++ b/adam-core/src/main/scala/org/bdgenomics/adam/rdd/GenomicRDD.scala
@@ -725,6 +725,25 @@ trait GenomicRDD[T, U <: GenomicRDD[T, U]] extends Logging {
    * @return Returns a new GenomicRDD containing only data that overlaps the
    *   querys region.
    */
+  def filterByOverlappingRegions(querys: Iterable[ReferenceRegion]): U = {
+    replaceRdd(rdd.filter(elem => {
+
+      val regions = getReferenceRegions(elem)
+
+      querys.exists(query => {
+        regions.exists(_.overlaps(query))
+      })
+    }), optPartitionMap)
+  }
+
+  /**
+   * Runs a filter that selects data in the underlying RDD that overlaps
+   * several genomic regions. Java friendly version.
+   *
+   * @param querys The regions to query for.
+   * @return Returns a new GenomicRDD containing only data that overlaps the
+   *   querys region.
+   */
   def filterByOverlappingRegions(querys: java.lang.Iterable[ReferenceRegion]): U = {
     replaceRdd(rdd.filter(elem => {