Program: 20175
Project: 20175
Buggy source:
public static void main(String[] args) throws FileNotFoundException, IOException {
  CommandOption.setSummary(SvmLight2Vectors.class,"String_Node_Str");
  CommandOption.process(SvmLight2Vectors.class,args);
  if (args.length == 0) {
    CommandOption.getList(SvmLight2Vectors.class).printUsage(false);
    System.exit(-1);
  }
  if (inputFiles == null) {
    throw new IllegalArgumentException("String_Node_Str" + "String_Node_Str");
  }
  Pipe instancePipe;
  InstanceList previousInstanceList=null;
  if (usePipeFromVectorsFile.wasInvoked()) {
    previousInstanceList=InstanceList.load(usePipeFromVectorsFile.value);
    instancePipe=previousInstanceList.getPipe();
  }
 else {
    ArrayList<Pipe> pipeList=new ArrayList<Pipe>();
    pipeList.add(new SvmLight2FeatureVectorAndLabel());
    if (printOutput.value) {
      pipeList.add(new PrintInputAndTarget());
    }
    instancePipe=new SerialPipes(pipeList);
  }
  if (inputFiles.value.length != outputFiles.value.length) {
    throw new RuntimeException("String_Node_Str");
  }
  for (int fileIndex=0; fileIndex < inputFiles.value.length; fileIndex++) {
    InstanceList instances=new InstanceList(instancePipe);
    Reader fileReader;
    if (inputFiles.value[fileIndex].equals("String_Node_Str")) {
      fileReader=new InputStreamReader(System.in);
    }
 else {
      fileReader=new InputStreamReader(new FileInputStream(inputFiles.value[fileIndex]),encoding.value);
    }
    instances.addThruPipe(new SelectiveFileLineIterator(fileReader,"String_Node_Str"));
    ObjectOutputStream oos;
    if (outputFiles.value[fileIndex].toString().equals("String_Node_Str")) {
      oos=new ObjectOutputStream(System.out);
    }
 else {
      oos=new ObjectOutputStream(new FileOutputStream(outputFiles.value[fileIndex]));
    }
    oos.writeObject(instances);
    oos.close();
  }
  if (usePipeFromVectorsFile.wasInvoked()) {
    System.out.println("String_Node_Str" + usePipeFromVectorsFile.value);
    System.out.println("String_Node_Str" + previousInstanceList.getPipe().getInstanceId());
    ObjectOutputStream oos=new ObjectOutputStream(new FileOutputStream(usePipeFromVectorsFile.value));
    oos.writeObject(previousInstanceList);
    oos.close();
  }
}

Fixed version (ground truth):
public static void main(String[] args) throws FileNotFoundException, IOException {
  CommandOption.setSummary(SvmLight2Vectors.class,"String_Node_Str");
  CommandOption.process(SvmLight2Vectors.class,args);
  if (args.length == 0) {
    CommandOption.getList(SvmLight2Vectors.class).printUsage(false);
    System.exit(-1);
  }
  if (inputFiles == null) {
    throw new IllegalArgumentException("String_Node_Str" + "String_Node_Str");
  }
  Pipe instancePipe;
  InstanceList previousInstanceList=null;
  if (usePipeFromVectorsFile.wasInvoked()) {
    previousInstanceList=InstanceList.load(usePipeFromVectorsFile.value);
    instancePipe=previousInstanceList.getPipe();
  }
 else {
    ArrayList<Pipe> pipeList=new ArrayList<Pipe>();
    pipeList.add(new SvmLight2FeatureVectorAndLabel());
    if (printOutput.value) {
      pipeList.add(new PrintInputAndTarget());
    }
    instancePipe=new SerialPipes(pipeList);
  }
  if (inputFiles.value.length != outputFiles.value.length) {
    throw new RuntimeException("String_Node_Str");
  }
  InstanceList[] instances=new InstanceList[inputFiles.value.length];
  for (int fileIndex=0; fileIndex < inputFiles.value.length; fileIndex++) {
    instances[fileIndex]=new InstanceList(instancePipe);
    Reader fileReader;
    if (inputFiles.value[fileIndex].equals("String_Node_Str")) {
      fileReader=new InputStreamReader(System.in);
    }
 else {
      fileReader=new InputStreamReader(new FileInputStream(inputFiles.value[fileIndex]),encoding.value);
    }
    instances[fileIndex].addThruPipe(new SelectiveFileLineIterator(fileReader,"String_Node_Str"));
  }
  for (int fileIndex=0; fileIndex < inputFiles.value.length; fileIndex++) {
    instances[fileIndex].save(new File(outputFiles.value[fileIndex]));
  }
  if (usePipeFromVectorsFile.wasInvoked()) {
    logger.info("String_Node_Str" + usePipeFromVectorsFile.value);
    logger.info("String_Node_Str" + previousInstanceList.getPipe().getInstanceId());
    ObjectOutputStream oos=new ObjectOutputStream(new FileOutputStream(usePipeFromVectorsFile.value));
    oos.writeObject(previousInstanceList);
    oos.close();
  }
}