/**
* 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.apis.java;
import java.io.IOException;
import java.nio.file.Files;
import java.nio.file.Path;
import org.apache.spark.api.java.JavaRDD;
import org.bdgenomics.adam.apis.java.JavaADAMContext;
import org.bdgenomics.formats.avro.AlignmentRecord;
/**
* A simple test class for the JavaADAMRDD/Context. Writes an RDD to
* disk and reads it back.
*/
public class JavaADAMConduit {
public static JavaAlignmentRecordRDD conduit(JavaRDD<AlignmentRecord> rdd) throws IOException {
JavaAlignmentRecordRDD recordRdd = new JavaAlignmentRecordRDD(rdd);
// make temp directory and save file
Path tempDir = Files.createTempDirectory("javaAC");
String fileName = tempDir.toString() + "/testRdd";
recordRdd.adamSave(fileName);
// create a new adam context and load the file
JavaADAMContext jac = new JavaADAMContext(rdd.context());
return jac.adamRecordLoad(fileName);
}
}