Program: 2121
Project: 2121
Buggy source:
public static byte[] combineTimelines(final List<byte[]> timesList){
  final ByteArrayOutputStream outputStream=new ByteArrayOutputStream();
  final DataOutputStream dataStream=new DataOutputStream(outputStream);
  try {
    int lastTime=0;
    int lastDelta=0;
    int repeatCount=0;
    int chunkCounter=0;
    for (    byte[] times : timesList) {
      final ByteArrayInputStream byteStream=new ByteArrayInputStream(times);
      final DataInputStream byteDataStream=new DataInputStream(byteStream);
      int byteCursor=0;
      while (true) {
        final int opcode=byteDataStream.read();
        if (opcode == -1) {
          break;
        }
        byteCursor++;
        int newTime=0;
        int newCount=0;
        int newDelta=0;
        if (opcode == TimelineOpcode.FULL_TIME.getOpcodeIndex()) {
          newTime=byteDataStream.readInt();
          byteCursor+=4;
          if (lastTime == 0) {
            writeTime(0,newTime,dataStream);
            lastTime=newTime;
            lastDelta=0;
            repeatCount=0;
            continue;
          }
 else {
            if (newTime - lastTime <= TimelineOpcode.MAX_DELTA_TIME) {
              newDelta=newTime - lastTime;
              newCount=1;
            }
          }
        }
 else         if (opcode <= TimelineOpcode.MAX_DELTA_TIME) {
          newTime=lastTime + opcode;
          newDelta=opcode;
          newCount=1;
        }
 else         if (opcode == TimelineOpcode.REPEATED_DELTA_TIME_BYTE.getOpcodeIndex()) {
          newCount=byteDataStream.read();
          newDelta=byteDataStream.read();
          byteCursor+=2;
          if (lastTime != 0) {
            newTime=lastTime + newDelta * newCount;
          }
 else {
            throw new IllegalStateException(String.format("String_Node_Str",opcode,byteCursor,chunkCounter,new String(Hex.encodeHex(times))));
          }
        }
 else         if (opcode == TimelineOpcode.REPEATED_DELTA_TIME_SHORT.getOpcodeIndex()) {
          newCount=byteDataStream.readUnsignedShort();
          newDelta=byteDataStream.read();
          byteCursor+=3;
          if (lastTime != 0) {
            newTime=lastTime + newDelta * newCount;
          }
        }
 else {
          throw new IllegalStateException(String.format("String_Node_Str",opcode,byteCursor,chunkCounter,new String(Hex.encodeHex(times))));
        }
        if (lastTime == 0) {
          log.error("String_Node_Str",byteCursor,chunkCounter,new String(Hex.encodeHex(times)));
        }
 else         if (repeatCount > 0) {
          if (lastDelta == newDelta) {
            if (newCount > 0) {
              repeatCount+=newCount;
              lastTime=newTime;
            }
 else {
              repeatCount++;
              lastTime+=lastDelta;
            }
          }
 else {
            writeRepeatedDelta(lastDelta,repeatCount,dataStream);
            if (newDelta > 0) {
              lastDelta=newDelta;
              repeatCount=newCount;
              lastTime=newTime;
            }
 else {
              writeTime(lastTime,newTime,dataStream);
              lastTime=newTime;
              lastDelta=0;
              repeatCount=0;
            }
          }
        }
 else         if (lastDelta == 0) {
          lastTime=newTime;
          repeatCount=newCount;
          lastDelta=newDelta;
        }
      }
      chunkCounter++;
    }
    if (repeatCount > 0) {
      writeRepeatedDelta(lastDelta,repeatCount,dataStream);
    }
    dataStream.flush();
    return outputStream.toByteArray();
  }
 catch (  Exception e) {
    log.error(e,"String_Node_Str");
    return new byte[0];
  }
}

Fixed version (ground truth):
public static byte[] combineTimelines(final List<byte[]> timesList){
  final ByteArrayOutputStream outputStream=new ByteArrayOutputStream();
  final DataOutputStream dataStream=new DataOutputStream(outputStream);
  try {
    int lastTime=0;
    int lastDelta=0;
    int repeatCount=0;
    int chunkCounter=0;
    for (    byte[] times : timesList) {
      final ByteArrayInputStream byteStream=new ByteArrayInputStream(times);
      final DataInputStream byteDataStream=new DataInputStream(byteStream);
      int byteCursor=0;
      while (true) {
        final int opcode=byteDataStream.read();
        if (opcode == -1) {
          break;
        }
        byteCursor++;
        int newTime=0;
        int newCount=0;
        int newDelta=0;
        if (opcode == TimelineOpcode.FULL_TIME.getOpcodeIndex()) {
          newTime=byteDataStream.readInt();
          newDelta=0;
          newCount=0;
          byteCursor+=4;
          if (lastTime == 0) {
            writeTime(0,newTime,dataStream);
            lastTime=newTime;
            lastDelta=0;
            repeatCount=0;
            continue;
          }
 else           if (newTime - lastTime <= TimelineOpcode.MAX_DELTA_TIME) {
            newDelta=newTime - lastTime;
            newCount=1;
          }
        }
 else         if (opcode <= TimelineOpcode.MAX_DELTA_TIME) {
          newTime=lastTime + opcode;
          newDelta=opcode;
          newCount=1;
        }
 else         if (opcode == TimelineOpcode.REPEATED_DELTA_TIME_BYTE.getOpcodeIndex()) {
          newCount=byteDataStream.read();
          newDelta=byteDataStream.read();
          byteCursor+=2;
          if (lastTime != 0) {
            newTime=lastTime + newDelta * newCount;
          }
 else {
            throw new IllegalStateException(String.format("String_Node_Str",opcode,byteCursor,chunkCounter,new String(Hex.encodeHex(times))));
          }
        }
 else         if (opcode == TimelineOpcode.REPEATED_DELTA_TIME_SHORT.getOpcodeIndex()) {
          newCount=byteDataStream.readUnsignedShort();
          newDelta=byteDataStream.read();
          byteCursor+=3;
          if (lastTime != 0) {
            newTime=lastTime + newDelta * newCount;
          }
        }
 else {
          throw new IllegalStateException(String.format("String_Node_Str",opcode,byteCursor,chunkCounter,new String(Hex.encodeHex(times))));
        }
        if (lastTime == 0) {
          log.error("String_Node_Str",byteCursor,chunkCounter,new String(Hex.encodeHex(times)));
        }
 else         if (repeatCount > 0) {
          if (lastDelta == newDelta && newCount > 0) {
            repeatCount+=newCount;
            lastTime=newTime;
          }
 else {
            writeRepeatedDelta(lastDelta,repeatCount,dataStream);
            if (newDelta > 0) {
              lastDelta=newDelta;
              repeatCount=newCount;
              lastTime=newTime;
            }
 else {
              writeTime(lastTime,newTime,dataStream);
              lastTime=newTime;
              lastDelta=0;
              repeatCount=0;
            }
          }
        }
 else         if (lastDelta == 0) {
          lastTime=newTime;
          repeatCount=newCount;
          lastDelta=newDelta;
        }
      }
      chunkCounter++;
    }
    if (repeatCount > 0) {
      writeRepeatedDelta(lastDelta,repeatCount,dataStream);
    }
    dataStream.flush();
    return outputStream.toByteArray();
  }
 catch (  Exception e) {
    log.error(e,"String_Node_Str");
    return new byte[0];
  }
}