Program: 132263
Project: 132263
Buggy source:
public static void main(String[] args) throws GeneralSecurityException, IOException {
  PipelineOptionsFactory.register(CountReadsOptions.class);
  options=PipelineOptionsFactory.fromArgs(args).withValidation().as(CountReadsOptions.class);
  GenomicsDatasetOptions.Methods.validateOptions(options);
  auth=GenomicsOptions.Methods.getGenomicsAuth(options);
  p=Pipeline.create(options);
  DataflowWorkarounds.registerGenomicsCoders(p);
  String BAMFilePath=options.getBAMFilePath();
  if (!Strings.isNullOrEmpty(BAMFilePath)) {
    if (GCSURLExists(BAMFilePath)) {
      System.out.println(BAMFilePath + "String_Node_Str");
    }
 else {
      System.out.println("String_Node_Str" + BAMFilePath + "String_Node_Str");
      return;
    }
    if (options.getShardBAMReading()) {
      String BAMIndexPath=BAMFilePath + "String_Node_Str";
      if (GCSURLExists(BAMIndexPath)) {
        System.out.println(BAMIndexPath + "String_Node_Str");
      }
 else {
        System.out.println("String_Node_Str" + BAMIndexPath + "String_Node_Str");
        return;
      }
    }
  }
  System.out.println("String_Node_Str" + options.getOutput());
  PCollection<Read> reads=getReads();
  PCollection<Long> readCount=reads.apply(Count.<Read>globally());
  PCollection<String> readCountText=readCount.apply(ParDo.of(new DoFn<Long,String>(){
    @Override public void processElement(    DoFn<Long,String>.ProcessContext c) throws Exception {
      c.output(String.valueOf(c.element()));
    }
  }
).named("String_Node_Str"));
  readCountText.apply(TextIO.Write.to(options.getOutput()).named("String_Node_Str").withoutSharding());
  p.run();
}

Fixed version (ground truth):
public static void main(String[] args) throws GeneralSecurityException, IOException {
  PipelineOptionsFactory.register(CountReadsOptions.class);
  options=PipelineOptionsFactory.fromArgs(args).withValidation().as(CountReadsOptions.class);
  GenomicsDatasetOptions.Methods.validateOptions(options);
  auth=GenomicsOptions.Methods.getGenomicsAuth(options);
  p=Pipeline.create(options);
  DataflowWorkarounds.registerGenomicsCoders(p);
  String BAMFilePath=options.getBAMFilePath();
  if (!Strings.isNullOrEmpty(BAMFilePath)) {
    if (GCSURLExists(BAMFilePath)) {
      System.out.println(BAMFilePath + "String_Node_Str");
    }
 else {
      System.out.println("String_Node_Str" + BAMFilePath + "String_Node_Str");
      return;
    }
    if (options.isShardBAMReading()) {
      String BAMIndexPath=BAMFilePath + "String_Node_Str";
      if (GCSURLExists(BAMIndexPath)) {
        System.out.println(BAMIndexPath + "String_Node_Str");
      }
 else {
        System.out.println("String_Node_Str" + BAMIndexPath + "String_Node_Str");
        return;
      }
    }
  }
  System.out.println("String_Node_Str" + options.getOutput());
  PCollection<Read> reads=getReads();
  PCollection<Long> readCount=reads.apply(Count.<Read>globally());
  PCollection<String> readCountText=readCount.apply(ParDo.of(new DoFn<Long,String>(){
    @Override public void processElement(    DoFn<Long,String>.ProcessContext c) throws Exception {
      c.output(String.valueOf(c.element()));
    }
  }
).named("String_Node_Str"));
  readCountText.apply(TextIO.Write.to(options.getOutput()).named("String_Node_Str").withoutSharding());
  p.run();
}