Reflecting newest changes

bigdatagenomics · Sep 26, 2017 · 7f12ed2 · 7f12ed2
1 parent 9445658
commit 7f12ed2
Showing 1 changed file with 8 additions and 7 deletions.
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
@@ -1540,7 +1540,7 @@ trait GenomicRDD[T, U <: GenomicRDD[T, U]] extends Logging {
    * @param genomicRdd The right RDD in the join.
    * @param optPartitions Optionally sets the number of output partitions. If
    *   None, the number of partitions on the resulting RDD does not change.
-   * @param threshold Sets a threshold for the distance between elements to be
+   * @param flankSize Sets a flankSize for the distance between elements to be
    *   joined. If set to 0, an overlap is required to join two elements.
    * @return Returns a new genomic RDD containing all pairs of keys that
    *   overlapped in the genomic coordinate space, and all keys from the
@@ -1549,13 +1549,13 @@ trait GenomicRDD[T, U <: GenomicRDD[T, U]] extends Logging {
   def leftOuterShuffleRegionJoinAndGroupByLeft[X, Y <: GenomicRDD[X, Y]](
     genomicRdd: GenomicRDD[X, Y],
     optPartitions: Option[Int],
-    threshold: Long)(
+    flankSize: Long)(
       implicit tTag: ClassTag[T],
       xTag: ClassTag[X],
       toxTag: ClassTag[(T, Iterable[X])]): GenericGenomicRDD[(T, Iterable[X])] = LeftOuterShuffleJoin.time {
 
     val (leftRddToJoin, rightRddToJoin) =
-      prepareForShuffleRegionJoin(genomicRdd, optPartitions, threshold)
+      prepareForShuffleRegionJoin(genomicRdd, optPartitions, flankSize)
 
     // what sequences do we wind up with at the end?
     val combinedSequences = sequences ++ genomicRdd.sequences
@@ -1565,7 +1565,8 @@ trait GenomicRDD[T, U <: GenomicRDD[T, U]] extends Logging {
         .compute(),
       combinedSequences,
       kv => {
-        getReferenceRegions(kv._1).map(_.pad(-1 * threshold)) ++
+        // pad by -1 * flankSize to undo flank from preprocessing
+        getReferenceRegions(kv._1).map(_.pad(-1 * flankSize)) ++
           Seq(kv._2.map(v => genomicRdd.getReferenceRegions(v))).flatten.flatten
       })
   }
@@ -1610,20 +1611,20 @@ trait GenomicRDD[T, U <: GenomicRDD[T, U]] extends Logging {
    * RDD, it will be paired with a `None` in the product of the join.
    *
    * @param genomicRdd The right RDD in the join.
-   * @param threshold Sets a threshold for the distance between elements to be
+   * @param flankSize Sets a flankSize for the distance between elements to be
    *   joined. If set to 0, an overlap is required to join two elements.
    * @return Returns a new genomic RDD containing all pairs of keys that
    *   overlapped in the genomic coordinate space, and all keys from the
    *   left RDD that did not overlap a key in the right RDD.
    */
   def leftOuterShuffleRegionJoinAndGroupByLeft[X, Y <: GenomicRDD[X, Y]](
     genomicRdd: GenomicRDD[X, Y],
-    threshold: Long)(
+    flankSize: Long)(
       implicit tTag: ClassTag[T],
       xTag: ClassTag[X],
       toxTag: ClassTag[(T, Iterable[X])]): GenericGenomicRDD[(T, Iterable[X])] = {
 
-    leftOuterShuffleRegionJoinAndGroupByLeft(genomicRdd, None, threshold)
+    leftOuterShuffleRegionJoinAndGroupByLeft(genomicRdd, None, flankSize)
   }
 
   /**