/*
 * 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.options.Default;
import com.google.cloud.dataflow.sdk.options.Description;

/**
 * A common options class for pipelines that shard by genomic region.
 */
public interface ShardOptions extends GenomicsOptions {

  @Description("By default, variants analyses will be run on BRCA1.  Pass this flag to run on all "
      + "references present in the dataset.  Note that certain jobs such as PCA and IBS "
      + "will automatically exclude X and Y chromosomes when this option is true.")
  boolean isAllReferences();
  void setAllReferences(boolean allReferences);

  @Description("Comma separated tuples of reference:start:end,... "
  + "Defaults to '17:41196311:41277499' for BRCA1.")
  @Default.String("17:41196311:41277499")
  String getReferences();
  void setReferences(String references);

  @Description("The maximum number of bases per shard.")
  @Default.Long(1000000)
  long getBasesPerShard();
  void setBasesPerShard(long basesPerShard);

}

@@ -1155,16 +1155,42 @@
 true.%22)%0A
+  @Default.Boolean(false)%0A
   boolea
@@ -1330,60 +1330,8 @@
 .. %22
-%0A  + %22Defaults to '17:41196311:41277499' for BRCA1.%22
 )%0A  

Update option help messages.