/
LeftOuterShuffleRegionJoinSuite.scala
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/
LeftOuterShuffleRegionJoinSuite.scala
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/**
* 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.ds
import org.apache.spark.rdd.RDD
import org.bdgenomics.adam.models.{
ReferenceRegion,
SequenceDictionary,
SequenceRecord
}
import org.bdgenomics.formats.avro.Alignment
class LeftOuterShuffleRegionJoinSuite(partitionMap: Seq[Option[(ReferenceRegion, ReferenceRegion)]])
extends OuterRegionJoinSuite {
val partitionSize = 3
var seqDict: SequenceDictionary = _
before {
seqDict = SequenceDictionary(
SequenceRecord("chr1", 15, url = "test://chrom1"),
SequenceRecord("chr2", 15, url = "test://chrom2"))
}
def runJoin(leftRdd: RDD[(ReferenceRegion, Alignment)],
rightRdd: RDD[(ReferenceRegion, Alignment)]): RDD[(Option[Alignment], Alignment)] = {
LeftOuterShuffleRegionJoin[Alignment, Alignment](rightRdd, leftRdd)
.compute().map(_.swap)
}
}