@@ -0,0 +1,2476 @@
+/*%0A * Copyright (C) 2014 Google Inc.%0A *%0A * Licensed under the Apache License, Version 2.0 (the %22License%22); you may not%0A * use this file except in compliance with the License. You may obtain a copy of%0A * the License at%0A *%0A * http://www.apache.org/licenses/LICENSE-2.0%0A *%0A * Unless required by applicable law or agreed to in writing, software%0A * distributed under the License is distributed on an %22AS IS%22 BASIS, WITHOUT%0A * WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the%0A * License for the specific language governing permissions and limitations under%0A * the License.%0A */%0Apackage com.google.cloud.genomics.dataflow.pipelines;%0A%0Aimport com.google.api.services.genomics.model.SearchVariantsRequest;%0Aimport com.google.cloud.dataflow.sdk.Pipeline;%0Aimport com.google.cloud.dataflow.sdk.transforms.ParDo;%0Aimport com.google.cloud.dataflow.utils.OptionsParser;%0Aimport com.google.cloud.genomics.dataflow.functions.ExtractSimilarCallsets;%0Aimport com.google.cloud.genomics.dataflow.functions.OutputPCoAFile;%0Aimport com.google.cloud.genomics.dataflow.readers.VariantReader;%0Aimport com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds;%0Aimport com.google.cloud.genomics.dataflow.utils.GenomicsAuth;%0Aimport com.google.cloud.genomics.dataflow.utils.GenomicsDatasetOptions;%0A%0Aimport java.io.IOException;%0Aimport java.security.GeneralSecurityException;%0Aimport java.util.List;%0A%0A/**%0A * An pipeline that generates similarity data for variants in a dataset.%0A * See the README for running instructions.%0A */%0Apublic class VariantSimilarity %7B%0A  private static final String VARIANT_FIELDS%0A      = %22nextPageToken,variants(id,calls(genotype,callSetName))%22;%0A%0A  public static void main(String%5B%5D args) throws IOException, GeneralSecurityException %7B%0A    GenomicsDatasetOptions options = OptionsParser.parse(args, GenomicsDatasetOptions.class,%0A        VariantSimilarity.class.getSimpleName());%0A    options.validateOptions();%0A%0A    GenomicsAuth auth = options.getGenomicsAuth();%0A    List%3CSearchVariantsRequest%3E requests = options.getVariantRequests(auth);%0A%0A    Pipeline p = Pipeline.create(options);%0A    DataflowWorkarounds.registerGenomicsCoders(p);%0A    DataflowWorkarounds.getPCollection(requests, p, options.numWorkers)%0A        .apply(ParDo.named(%22VariantReader%22)%0A            .of(new VariantReader(auth, VARIANT_FIELDS)))%0A        .apply(ParDo.named(%22ExtractSimilarCallsets%22).of(new ExtractSimilarCallsets()))%0A        .apply(new OutputPCoAFile(options.output));%0A%0A    p.run();%0A  %7D%0A%7D%0A

Fix git screwup