Program: 141337
Project: 141337
Buggy source:
/** 
 * Create the JobConf object for a sample
 * @param basePath base path of data
 * @param sample sample to process
 * @return a new JobConf object
 * @throws IOException
 */
private Job createJobConf(final Configuration parentConf,final Context context,final Sample sample) throws IOException {
  final Configuration jobConf=new Configuration(parentConf);
  final Path inputPath=new Path(context.getDataFilename(DataFormats.FILTERED_READS_TFQ,sample));
  final Path genomeIndex=new Path(context.getDataFile(getMapper().getArchiveFormat(),sample).getSource());
  DistributedCache.addCacheFile(genomeIndex.toUri(),jobConf);
  jobConf.set(ReadsMapperMapper.MAPPER_NAME_KEY,getMapperName());
  jobConf.set(ReadsMapperMapper.PAIR_END_KEY,Boolean.FALSE.toString());
  if (getMapperThreads() < 0) {
    jobConf.set(ReadsMapperMapper.MAPPER_THREADS_KEY,"String_Node_Str" + getMapperThreads());
  }
  if (getMapperArguments() != null) {
    jobConf.set(ReadsMapperMapper.MAPPER_ARGS_KEY,getMapperArguments());
  }
  jobConf.set(CommonHadoop.COUNTER_GROUP_KEY,COUNTER_GROUP);
  jobConf.set("String_Node_Str","String_Node_Str" + HADOOP_TIMEOUT);
  final Job job=new Job(jobConf,"String_Node_Str" + getMapperName() + "String_Node_Str"+ sample.getName()+ "String_Node_Str"+ inputPath.getName()+ "String_Node_Str");
  job.setJarByClass(ReadsMapperHadoopStep.class);
  FileInputFormat.addInputPath(job,inputPath);
  if (sample.getSource().endsWith(READS_FASTQ.getDefaultExtention()))   job.setInputFormatClass(FastQFormatNew.class);
  job.setMapperClass(ReadsMapperMapper.class);
  job.setOutputKeyClass(Text.class);
  job.setOutputValueClass(Text.class);
  FileOutputFormat.setOutputPath(job,new Path(context.getDataFile(MAPPER_RESULTS_SAM,sample).getSource()));
  return job;
}

Fixed version (ground truth):
/** 
 * Create the JobConf object for a sample
 * @param basePath base path of data
 * @param sample sample to process
 * @return a new JobConf object
 * @throws IOException
 */
private Job createJobConf(final Configuration parentConf,final Context context,final Sample sample) throws IOException {
  final Configuration jobConf=new Configuration(parentConf);
  final Path inputPath=new Path(context.getDataFilename(DataFormats.FILTERED_READS_TFQ,sample));
  final Path genomeIndex=new Path(context.getDataFile(getMapper().getArchiveFormat(),sample).getSource());
  DistributedCache.addCacheFile(genomeIndex.toUri(),jobConf);
  jobConf.set(ReadsMapperMapper.MAPPER_NAME_KEY,getMapperName());
  jobConf.set(ReadsMapperMapper.PAIR_END_KEY,Boolean.FALSE.toString());
  if (getMapperThreads() < 0) {
    jobConf.set(ReadsMapperMapper.MAPPER_THREADS_KEY,"String_Node_Str" + getMapperThreads());
  }
  if (getMapperArguments() != null) {
    jobConf.set(ReadsMapperMapper.MAPPER_ARGS_KEY,getMapperArguments());
  }
  jobConf.set(CommonHadoop.COUNTER_GROUP_KEY,COUNTER_GROUP);
  jobConf.set("String_Node_Str","String_Node_Str" + HADOOP_TIMEOUT);
  jobConf.set("String_Node_Str","String_Node_Str" + 1);
  final Job job=new Job(jobConf,"String_Node_Str" + getMapperName() + "String_Node_Str"+ sample.getName()+ "String_Node_Str"+ inputPath.getName()+ "String_Node_Str");
  job.setJarByClass(ReadsMapperHadoopStep.class);
  FileInputFormat.addInputPath(job,inputPath);
  if (sample.getSource().endsWith(READS_FASTQ.getDefaultExtention()))   job.setInputFormatClass(FastQFormatNew.class);
  job.setMapperClass(ReadsMapperMapper.class);
  job.setOutputKeyClass(Text.class);
  job.setOutputValueClass(Text.class);
  FileOutputFormat.setOutputPath(job,new Path(context.getDataFile(MAPPER_RESULTS_SAM,sample).getSource()));
  return job;
}