Program: 81347
Project: 81347
Buggy source:
@Override public Sound transform(Sound sound){
  int threshold=100;
  Note silence=new Silence();
  int channelNum=sound.getChannelNum();
  Sound builtSound=new Sound(new long[sound.getSamples().length],sound.getNbBytesPerSample(),sound.getSampleRate(),channelNum);
  List<Integer> freqs;
  this.log(new LogEvent(LogLevel.VERBOSE,"String_Node_Str"));
  PeakFindWithHPSSoundTransformation peak=new PeakFindWithHPSSoundTransformation(threshold,-1);
  peak.setObservers(this.observers);
  peak.transform(sound);
  freqs=peak.getLoudestFreqs();
  double lastFreq=freqs.get(0);
  int lastBegining=0;
  for (int i=0; i < freqs.size(); i++) {
    this.log(new LogEvent(LogLevel.VERBOSE,"String_Node_Str" + i + "String_Node_Str"+ freqs.size()));
    float lengthInSeconds=(i - lastBegining < 1 ? freqs.size() * threshold : (i - 1 - lastBegining) * threshold) / sound.getSampleRate();
    if (i == freqs.size() - 1 || (Math.abs(freqs.get(i) - lastFreq) > freqs.get(i) / 100 && lengthInSeconds > 0.5)) {
      Note note=silence;
      if (lastFreq > 50 && Math.abs(sound.getSampleRate() - lastFreq) > 100) {
        note=this.pack.get(this.instrument).getNearestNote((int)lastFreq);
      }
      Sound attack=note.getAttack((int)lastFreq,channelNum,lengthInSeconds);
      Sound decay=note.getDecay((int)lastFreq,channelNum,lengthInSeconds);
      Sound sustain=note.getSustain((int)lastFreq,channelNum,lengthInSeconds);
      Sound release=note.getRelease((int)lastFreq,channelNum,lengthInSeconds);
      soundAppender.append(builtSound,threshold * lastBegining,attack,decay,sustain,release);
      lastBegining=i;
      lastFreq=freqs.get(i);
    }
  }
  return builtSound;
}

Fixed version (ground truth):
@Override public Sound transform(Sound sound){
  int threshold=100;
  Note silence=new Silence();
  int channelNum=sound.getChannelNum();
  Sound builtSound=new Sound(new long[sound.getSamples().length],sound.getNbBytesPerSample(),sound.getSampleRate(),channelNum);
  List<Integer> freqs;
  this.log(new LogEvent(LogLevel.VERBOSE,"String_Node_Str"));
  PeakFindWithHPSSoundTransformation peak=new PeakFindWithHPSSoundTransformation(threshold,-1);
  peak.setObservers(this.observers);
  peak.transform(sound);
  freqs=peak.getLoudestFreqs();
  double lastFreq=freqs.get(0);
  int lastBegining=0;
  int countZeros=0;
  for (int i=0; i < freqs.size(); i++) {
    this.log(new LogEvent(LogLevel.VERBOSE,"String_Node_Str" + i + "String_Node_Str"+ freqs.size()));
    float lengthInSeconds=(i - lastBegining < 1 ? freqs.size() * threshold : (i - 1 - lastBegining) * threshold * 1.0f) / sound.getSampleRate();
    boolean freqChanged=Math.abs(freqs.get(i) - lastFreq) > freqs.get(i) / 100 && lengthInSeconds > 0.5;
    if (freqChanged && freqs.get(i) == 0) {
      countZeros++;
    }
 else {
      countZeros=0;
    }
    if (i == freqs.size() - 1 || (freqChanged && (lastFreq == 0 || (freqs.get(i) == 0 && countZeros >= 3)))) {
      countZeros=0;
      Note note=silence;
      if (lastFreq > 50 && Math.abs(sound.getSampleRate() - lastFreq) > 100) {
        note=this.pack.get(this.instrument).getNearestNote((int)lastFreq);
      }
      Sound attack=note.getAttack((int)lastFreq,channelNum,lengthInSeconds);
      Sound decay=note.getDecay((int)lastFreq,channelNum,lengthInSeconds);
      Sound sustain=note.getSustain((int)lastFreq,channelNum,lengthInSeconds);
      Sound release=note.getRelease((int)lastFreq,channelNum,lengthInSeconds);
      soundAppender.append(builtSound,threshold * lastBegining,attack,decay,sustain,release);
      lastBegining=i;
      lastFreq=freqs.get(i);
    }
  }
  return builtSound;
}