Program: 132253
Project: 132253
Buggy source:
public static void main(String[] args) throws IOException, GeneralSecurityException {
  PipelineOptionsFactory.register(Options.class);
  Options options=PipelineOptionsFactory.fromArgs(args).withValidation().as(Options.class);
  Options.Methods.validateOptions(options);
  StreamVariantsRequest prototype=CallSetNamesOptions.Methods.getRequestPrototype(options);
  OfflineAuth auth=GenomicsOptions.Methods.getGenomicsAuth(options);
  ImmutableSet<String> callSetIds=ImmutableSet.<String>builder().addAll(CallSetNamesOptions.Methods.getCallSetIds(options)).build();
  LOG.info("String_Node_Str" + "String_Node_Str" + callSetIds.size() + "String_Node_Str"+ callSetIds);
  if (options.getIdentifyVariantsWithoutCalls()) {
    LOG.info("String_Node_Str");
  }
  List<StreamVariantsRequest> shardRequests=options.isAllReferences() ? ShardUtils.getVariantRequests(prototype,ShardUtils.SexChromosomeFilter.INCLUDE_XY,options.getBasesPerShard(),auth) : ShardUtils.getVariantRequests(prototype,options.getBasesPerShard(),options.getReferences());
  Pipeline p=Pipeline.create(options);
  PCollection<Variant> variants=p.begin().apply(Create.of(shardRequests)).apply(new VariantStreamer(auth,ShardBoundary.Requirement.STRICT,VARIANT_FIELDS)).apply(ParDo.of(new PrivateVariantsFilterFn(callSetIds,options.getIdentifyVariantsWithoutCalls())));
  variants.apply(ParDo.named("String_Node_Str").of(new DoFn<Variant,String>(){
    @Override public void processElement(    ProcessContext c){
      Variant v=c.element();
      c.output(Joiner.on("String_Node_Str").join(v.getId(),v.getReferenceName(),v.getStart(),v.getEnd(),v.getReferenceBases(),Joiner.on("String_Node_Str").join(v.getAlternateBasesList())));
    }
  }
)).apply(TextIO.Write.to(options.getOutput()));
  p.run();
}

Fixed version (ground truth):
public static void main(String[] args) throws IOException, GeneralSecurityException {
  PipelineOptionsFactory.register(Options.class);
  Options options=PipelineOptionsFactory.fromArgs(args).withValidation().as(Options.class);
  Options.Methods.validateOptions(options);
  StreamVariantsRequest prototype=StreamVariantsRequest.newBuilder(CallSetNamesOptions.Methods.getRequestPrototype(options)).clearCallSetIds().build();
  OfflineAuth auth=GenomicsOptions.Methods.getGenomicsAuth(options);
  ImmutableSet<String> callSetIds=ImmutableSet.<String>builder().addAll(CallSetNamesOptions.Methods.getCallSetIds(options)).build();
  LOG.info("String_Node_Str" + "String_Node_Str" + callSetIds.size() + "String_Node_Str"+ callSetIds);
  if (options.getIdentifyVariantsWithoutCalls()) {
    LOG.info("String_Node_Str");
  }
  List<StreamVariantsRequest> shardRequests=options.isAllReferences() ? ShardUtils.getVariantRequests(prototype,ShardUtils.SexChromosomeFilter.INCLUDE_XY,options.getBasesPerShard(),auth) : ShardUtils.getVariantRequests(prototype,options.getBasesPerShard(),options.getReferences());
  Pipeline p=Pipeline.create(options);
  PCollection<Variant> variants=p.begin().apply(Create.of(shardRequests)).apply(new VariantStreamer(auth,ShardBoundary.Requirement.STRICT,VARIANT_FIELDS)).apply(ParDo.of(new PrivateVariantsFilterFn(callSetIds,options.getIdentifyVariantsWithoutCalls())));
  variants.apply(ParDo.named("String_Node_Str").of(new DoFn<Variant,String>(){
    @Override public void processElement(    ProcessContext c){
      Variant v=c.element();
      c.output(Joiner.on("String_Node_Str").join(v.getId(),v.getReferenceName(),v.getStart(),v.getEnd(),v.getReferenceBases(),Joiner.on("String_Node_Str").join(v.getAlternateBasesList())));
    }
  }
)).apply(TextIO.Write.to(options.getOutput()));
  p.run();
}