Program: 13699
Project: 13699
Buggy source:
protected int runCombineJob(String halvadeOutDir,String mergeOutDir,boolean featureCount) throws IOException, URISyntaxException, InterruptedException, ClassNotFoundException {
  Configuration combineConf=getConf();
  if (!halvadeOpts.out.endsWith("String_Node_Str"))   halvadeOpts.out+="String_Node_Str";
  HalvadeConf.setInputDir(combineConf,halvadeOutDir);
  HalvadeConf.setOutDir(combineConf,mergeOutDir);
  FileSystem outFs=FileSystem.get(new URI(mergeOutDir),combineConf);
  if (outFs.exists(new Path(mergeOutDir))) {
    Logger.INFO("String_Node_Str" + mergeOutDir + "String_Node_Str");
    Logger.INFO("String_Node_Str");
    System.exit(-2);
  }
  HalvadeConf.setReportAllVariant(combineConf,halvadeOpts.reportAll);
  HalvadeResourceManager.setJobResources(halvadeOpts,combineConf,HalvadeResourceManager.COMBINE,false,halvadeOpts.useBamInput);
  halvadeOpts.splitChromosomes(combineConf);
  Job combineJob=Job.getInstance(combineConf,"String_Node_Str");
  combineJob.setJarByClass(be.ugent.intec.halvade.hadoop.mapreduce.VCFCombineMapper.class);
  addInputFiles(halvadeOutDir,combineConf,combineJob,featureCount ? "String_Node_Str" : "String_Node_Str");
  FileOutputFormat.setOutputPath(combineJob,new Path(mergeOutDir));
  combineJob.setMapperClass(featureCount ? be.ugent.intec.halvade.hadoop.mapreduce.HTSeqCombineMapper.class : be.ugent.intec.halvade.hadoop.mapreduce.VCFCombineMapper.class);
  combineJob.setMapOutputKeyClass(featureCount ? Text.class : LongWritable.class);
  combineJob.setMapOutputValueClass(featureCount ? LongWritable.class : VariantContextWritable.class);
  combineJob.setInputFormatClass(featureCount ? TextInputFormat.class : VCFInputFormat.class);
  combineJob.setNumReduceTasks(1);
  combineJob.setReducerClass(featureCount ? be.ugent.intec.halvade.hadoop.mapreduce.HTSeqCombineReducer.class : be.ugent.intec.halvade.hadoop.mapreduce.VCFCombineReducer.class);
  combineJob.setOutputKeyClass(Text.class);
  combineJob.setOutputValueClass(featureCount ? LongWritable.class : VariantContextWritable.class);
  return runTimedJob(combineJob,(featureCount ? "String_Node_Str" : "String_Node_Str") + "String_Node_Str");
}

Fixed version (ground truth):
protected int runCombineJob(String halvadeOutDir,String mergeOutDir,boolean featureCount) throws IOException, URISyntaxException, InterruptedException, ClassNotFoundException {
  Configuration combineConf=getConf();
  if (!halvadeOpts.out.endsWith("String_Node_Str"))   halvadeOpts.out+="String_Node_Str";
  HalvadeConf.setInputDir(combineConf,halvadeOutDir);
  HalvadeConf.setOutDir(combineConf,mergeOutDir);
  FileSystem outFs=FileSystem.get(new URI(mergeOutDir),combineConf);
  if (outFs.exists(new Path(mergeOutDir))) {
    Logger.INFO("String_Node_Str" + mergeOutDir + "String_Node_Str");
    Logger.INFO("String_Node_Str");
    System.exit(-2);
  }
  HalvadeConf.setReportAllVariant(combineConf,halvadeOpts.reportAll);
  HalvadeResourceManager.setJobResources(halvadeOpts,combineConf,HalvadeResourceManager.COMBINE,false,halvadeOpts.useBamInput);
  Job combineJob=Job.getInstance(combineConf,"String_Node_Str");
  combineJob.setJarByClass(be.ugent.intec.halvade.hadoop.mapreduce.VCFCombineMapper.class);
  addInputFiles(halvadeOutDir,combineConf,combineJob,featureCount ? "String_Node_Str" : "String_Node_Str");
  FileOutputFormat.setOutputPath(combineJob,new Path(mergeOutDir));
  combineJob.setMapperClass(featureCount ? be.ugent.intec.halvade.hadoop.mapreduce.HTSeqCombineMapper.class : be.ugent.intec.halvade.hadoop.mapreduce.VCFCombineMapper.class);
  combineJob.setMapOutputKeyClass(featureCount ? Text.class : LongWritable.class);
  combineJob.setMapOutputValueClass(featureCount ? LongWritable.class : VariantContextWritable.class);
  combineJob.setInputFormatClass(featureCount ? TextInputFormat.class : VCFInputFormat.class);
  combineJob.setNumReduceTasks(1);
  combineJob.setReducerClass(featureCount ? be.ugent.intec.halvade.hadoop.mapreduce.HTSeqCombineReducer.class : be.ugent.intec.halvade.hadoop.mapreduce.VCFCombineReducer.class);
  combineJob.setOutputKeyClass(Text.class);
  combineJob.setOutputValueClass(featureCount ? LongWritable.class : VariantContextWritable.class);
  return runTimedJob(combineJob,(featureCount ? "String_Node_Str" : "String_Node_Str") + "String_Node_Str");
}