Program: 3209
Project: 3209
Buggy source:
public static void cycle(long numCycles){
  totalCycles+=numCycles;
  sinceLastScanline+=numCycles;
  if (sinceLastScanline >= 536 && !wramRefreshed) {
    numCycles+=40;
    totalCycles+=40;
    wramRefreshed=true;
  }
  if (currentScanline == 0 && !hdmaStarted) {
    DMA.HDMAInit();
    hdmaStarted=true;
  }
  PPU.renderCycles(numCycles);
  checkIRQ();
  while (sinceLastScanline > cyclesPerScanLine) {
    sinceLastScanline-=cyclesPerScanLine;
    currentScanline++;
    irqOnCurrentLine=false;
    PPU.scanline();
    DMA.HDMARun();
    if (currentScanline == 0xE1) {
      CPU.triggerVBlank();
      PPU.vBlank();
      Core.advanceFrameOnce=false;
      break;
    }
  }
  if (currentScanline == 0xE3 && CPU.standardControllerRead) {
    Input.autoRead();
  }
  if (currentScanline >= scanlines) {
    currentScanline=0;
    wramRefreshed=false;
    PPU.vBlanking=false;
    hdmaStarted=false;
  }
  if (currentScanline >= 0xE1) {
    CPURegisters.rdnmi.val|=0x80;
  }
 else {
    CPURegisters.rdnmi.val&=0x7F;
  }
  toremove.clear();
  for (  TimerCallback t : callbacks) {
    if (t.callbackTime <= totalCycles) {
      System.out.println("String_Node_Str" + t);
      t.callback();
      toremove.add(t);
    }
  }
  for (  TimerCallback t : toremove)   callbacks.remove(t);
  cyclesToCatchup+=numCycles;
  if (limitSpeed && currentScanline == 1) {
    long sleep, elapsed;
    do {
      elapsed=System.nanoTime() - lastTime;
      sleep=cyclesToCatchup * cycleTimeNS - elapsed;
    }
 while (sleep > cycleTimeNS);
    lastTime=System.nanoTime();
    cyclesToCatchup=0;
  }
  if (autoFrameSkip) {
    long duration=numCycles * cycleTimeNS;
    long actualDuration=System.nanoTime() - lastTime;
    if (actualDuration > duration) {
      PPU.renderFrames=false;
    }
 else {
      PPU.renderFrames=true;
    }
  }
}

Fixed version (ground truth):
public static void cycle(long numCycles){
  totalCycles+=numCycles;
  sinceLastScanline+=numCycles;
  if (sinceLastScanline >= 536 && !wramRefreshed) {
    numCycles+=40;
    totalCycles+=40;
    wramRefreshed=true;
  }
  if (currentScanline == 0 && !hdmaStarted) {
    DMA.HDMAInit();
    hdmaStarted=true;
  }
  PPU.renderCycles(numCycles);
  checkIRQ();
  while (sinceLastScanline > cyclesPerScanLine) {
    sinceLastScanline-=cyclesPerScanLine;
    currentScanline++;
    irqOnCurrentLine=false;
    PPU.scanline();
    DMA.HDMARun();
    if (currentScanline == 0xE1) {
      CPU.triggerVBlank();
      PPU.vBlank();
      Core.advanceFrameOnce=false;
      break;
    }
    if (currentScanline == 0xE3 && CPU.standardControllerRead) {
      Input.autoRead();
    }
  }
  if (currentScanline >= scanlines) {
    currentScanline=0;
    wramRefreshed=false;
    PPU.vBlanking=false;
    hdmaStarted=false;
  }
  if (currentScanline >= 0xE1) {
    CPURegisters.rdnmi.val|=0x80;
  }
 else {
    CPURegisters.rdnmi.val&=0x7F;
  }
  toremove.clear();
  for (  TimerCallback t : callbacks) {
    if (t.callbackTime <= totalCycles) {
      System.out.println("String_Node_Str" + t);
      t.callback();
      toremove.add(t);
    }
  }
  for (  TimerCallback t : toremove)   callbacks.remove(t);
  cyclesToCatchup+=numCycles;
  if (limitSpeed && currentScanline == 1) {
    long sleep, elapsed;
    do {
      elapsed=System.nanoTime() - lastTime;
      sleep=cyclesToCatchup * cycleTimeNS - elapsed;
    }
 while (sleep > cycleTimeNS);
    lastTime=System.nanoTime();
    cyclesToCatchup=0;
  }
  if (autoFrameSkip) {
    long duration=numCycles * cycleTimeNS;
    long actualDuration=System.nanoTime() - lastTime;
    if (actualDuration > duration) {
      PPU.renderFrames=false;
    }
 else {
      PPU.renderFrames=true;
    }
  }
}