Program: 141335
Project: 141335
Buggy source:
/** 
 * Create a filter reads job
 * @param basePath bas epath
 * @param sample Sample to filter
 * @return a 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.getBasePathname(),sample.getSource());
  jobConf.set(CommonHadoop.COUNTER_GROUP_KEY,getCounterGroup());
  jobConf.set("String_Node_Str","String_Node_Str" + HADOOP_TIMEOUT);
  if (getLengthThreshold() >= 0)   jobConf.set(ReadsFilterMapper.LENGTH_THRESHOLD_KEY,"String_Node_Str" + getLengthThreshold());
  if (getQualityThreshold() >= 0)   jobConf.set(ReadsFilterMapper.QUALITY_THRESHOLD_KEY,"String_Node_Str" + getQualityThreshold());
  jobConf.set(ReadsFilterMapper.PAIR_END_KEY,"String_Node_Str" + isPairend());
  final Path genomeIndex=new Path(context.getDataFile(getMapper().getArchiveFormat(),sample).getSource());
  DistributedCache.addCacheFile(genomeIndex.toUri(),jobConf);
  jobConf.set(ReadsMapperMapper.MAPPER_NAME_KEY,getMapperName());
  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(SAMFilterMapper.MAPPING_QUALITY_THRESOLD_KEY,Integer.toString(getMappingQualityThreshold()));
  jobConf.set(SAMFilterMapper.GENOME_DESC_PATH_KEY,context.getDataFile(DataFormats.GENOME_DESC_TXT,sample).getSource());
  final Job job=new Job(jobConf,"String_Node_Str" + sample.getName() + "String_Node_Str"+ sample.getSource()+ "String_Node_Str");
  job.setJarByClass(ReadsFilterHadoopStep.class);
  FileInputFormat.addInputPath(job,inputPath);
  if (sample.getSource().endsWith(READS_FASTQ.getDefaultExtention()))   job.setInputFormatClass(FastQFormatNew.class);
  job.setMapperClass(FilterAndMapMapper.class);
  job.setReducerClass(SAMFilterReducer.class);
  job.setOutputKeyClass(Text.class);
  job.setOutputValueClass(Text.class);
  job.setNumReduceTasks(1);
  FileOutputFormat.setOutputPath(job,new Path(context.getDataFile(DataFormats.FILTERED_MAPPER_RESULTS_SAM,sample).getSource()));
  return job;
}

Fixed version (ground truth):
/** 
 * Create a filter reads job
 * @param basePath bas epath
 * @param sample Sample to filter
 * @return a 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.getBasePathname(),sample.getSource());
  jobConf.set(CommonHadoop.COUNTER_GROUP_KEY,getCounterGroup());
  jobConf.set("String_Node_Str","String_Node_Str" + HADOOP_TIMEOUT);
  jobConf.set("String_Node_Str","String_Node_Str" + 1);
  if (getLengthThreshold() >= 0)   jobConf.set(ReadsFilterMapper.LENGTH_THRESHOLD_KEY,"String_Node_Str" + getLengthThreshold());
  if (getQualityThreshold() >= 0)   jobConf.set(ReadsFilterMapper.QUALITY_THRESHOLD_KEY,"String_Node_Str" + getQualityThreshold());
  jobConf.set(ReadsFilterMapper.PAIR_END_KEY,"String_Node_Str" + isPairend());
  final Path genomeIndex=new Path(context.getDataFile(getMapper().getArchiveFormat(),sample).getSource());
  DistributedCache.addCacheFile(genomeIndex.toUri(),jobConf);
  jobConf.set(ReadsMapperMapper.MAPPER_NAME_KEY,getMapperName());
  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(SAMFilterMapper.MAPPING_QUALITY_THRESOLD_KEY,Integer.toString(getMappingQualityThreshold()));
  jobConf.set(SAMFilterMapper.GENOME_DESC_PATH_KEY,context.getDataFile(DataFormats.GENOME_DESC_TXT,sample).getSource());
  final Job job=new Job(jobConf,"String_Node_Str" + sample.getName() + "String_Node_Str"+ sample.getSource()+ "String_Node_Str");
  job.setJarByClass(ReadsFilterHadoopStep.class);
  FileInputFormat.addInputPath(job,inputPath);
  if (sample.getSource().endsWith(READS_FASTQ.getDefaultExtention()))   job.setInputFormatClass(FastQFormatNew.class);
  job.setMapperClass(FilterAndMapMapper.class);
  job.setReducerClass(SAMFilterReducer.class);
  job.setOutputKeyClass(Text.class);
  job.setOutputValueClass(Text.class);
  job.setNumReduceTasks(1);
  FileOutputFormat.setOutputPath(job,new Path(context.getDataFile(DataFormats.FILTERED_MAPPER_RESULTS_SAM,sample).getSource()));
  return job;
}