com.google.cloud.genomics.dataflow.utils.ShardReadsTransform Maven / Gradle / Ivy

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/*
 * Copyright (C) 2014 Google Inc.
 *
 * Licensed 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 com.google.cloud.genomics.dataflow.utils;

import com.google.cloud.dataflow.sdk.transforms.GroupByKey;
import com.google.cloud.dataflow.sdk.transforms.ParDo;
import com.google.cloud.dataflow.sdk.transforms.PTransform;
import com.google.cloud.dataflow.sdk.values.PCollection;
import com.google.cloud.dataflow.sdk.values.KV;
import com.google.cloud.genomics.utils.Contig;
import com.google.genomics.v1.Read;
import com.google.cloud.genomics.dataflow.functions.KeyReadsFn;

/*
 * Takes a collection of reads and shards them out by Contig.
 * Can be used to prepare reads for being written to disk in parallel.
 */
public class ShardReadsTransform extends PTransform, PCollection>>> {

  static public interface Options extends KeyReadsFn.Options {}

  @Override
  public PCollection>> apply(PCollection reads) {
    return reads
      .apply(ParDo.named("KeyReads").of(new KeyReadsFn()))
      .apply(GroupByKey.create());
  }

  public static PCollection>> shard(PCollection reads) {
    return (new ShardReadsTransform()).apply(reads);
  }
}