Program: 153262
Project: 153262
Buggy source:
public void run(){
  boolean sendHashUpdates=Globals.localCache();
  System.out.println("String_Node_Str");
  ByteCircleBuffer bcb=new ByteCircleBuffer(20);
  boolean eof=false;
  byte[] buffer=new byte[131072];
  while (!eof && !super.killed()) {
    if (sendHashUpdates && !ptc.hashQueue.isEmpty()) {
      Long hash;
      UnitByte fakeId=new UnitByte();
      fakeId.setValue((byte)0x50);
      if (fakeId.write(out,ptc,this,false) == null) {
        eof=true;
        continue;
      }
      while ((hash=ptc.hashQueue.poll()) != null && synced.size() < 2048) {
        synced.add(hash);
      }
      UnitShort length=new UnitShort();
      length.setValue((short)synced.size());
      if (length.write(out,ptc,this,false) == null) {
        eof=true;
        continue;
      }
      UnitLong hashUnit=new UnitLong();
      while ((hash=synced.poll()) != null) {
        hashUnit.setValue(hash);
        if (hashUnit.write(out,ptc,this,false) == null) {
          eof=true;
          continue;
        }
      }
      ptc.savedData.addAndGet(-length.getValue() * 8);
    }
    Byte packetId=UnitByte.getByte(in,ptc,this);
    if (packetId == null) {
      if (!Globals.isQuiet()) {
        ptc.printLogMessage("String_Node_Str");
      }
      eof=true;
      continue;
    }
    if (packetId == (byte)0x50) {
      UnitShort length=new UnitShort();
      if (length.read(in,ptc,this,false,null) == null) {
        eof=true;
        continue;
      }
      short lengthPrim=length.getValue();
      UnitLong hashUnit=new UnitLong();
      for (short cnt=0; cnt < lengthPrim && !eof; cnt++) {
        if (hashUnit.read(in,ptc,this,false,null) == null) {
          eof=true;
        }
 else         if (ptc.setHashes.size() < 100000) {
          ptc.setHashes.add(hashUnit.getValue());
        }
      }
      if (eof) {
        continue;
      }
    }
 else {
      if (packetId == 0xFF) {
        ptc.printLogMessage("String_Node_Str");
        eof=true;
      }
      if (UnitByte.writeByte(out,packetId,ptc,this) == null) {
        ptc.printLogMessage("String_Node_Str");
        eof=true;
        continue;
      }
      Packet currentPacket=new Packet(packetId);
      bcb.write(packetId);
      if (currentPacket.critical) {
        ptc.printLogMessage("String_Node_Str" + bcb);
      }
      if (Globals.isVerbose()) {
        ptc.printLogMessage("String_Node_Str" + Integer.toHexString(packetId & 0xFF));
      }
      if (currentPacket.packetId == null || currentPacket.pass(in,out,ptc,this,false,buffer,null) == null) {
        if (!Globals.isQuiet()) {
          ptc.printLogMessage("String_Node_Str");
        }
        eof=true;
        continue;
      }
      if (packetId == 0x10) {
        Short holding=(Short)((UnitShort)(currentPacket.fields[0])).getValue();
        ptc.setHolding(holding);
      }
    }
  }
  ptc.interrupt();
}

Fixed version (ground truth):
public void run(){
  boolean sendHashUpdates=Globals.localCache();
  System.out.println("String_Node_Str");
  ByteCircleBuffer bcb=new ByteCircleBuffer(20);
  boolean eof=false;
  byte[] buffer=new byte[131072];
  while (!eof && !super.killed()) {
    if (sendHashUpdates && !ptc.hashQueue.isEmpty()) {
      Long hash;
      UnitByte fakeId=new UnitByte();
      fakeId.setValue((byte)0x50);
      if (fakeId.write(out,ptc,this,false) == null) {
        eof=true;
        continue;
      }
      while ((hash=ptc.hashQueue.poll()) != null && synced.size() < 2048) {
        synced.add(hash);
        ptc.hashesSentThisConnection.put(hash,true);
      }
      UnitShort length=new UnitShort();
      length.setValue((short)synced.size());
      if (length.write(out,ptc,this,false) == null) {
        eof=true;
        continue;
      }
      UnitLong hashUnit=new UnitLong();
      while ((hash=synced.poll()) != null) {
        hashUnit.setValue(hash);
        if (hashUnit.write(out,ptc,this,false) == null) {
          eof=true;
          continue;
        }
      }
      ptc.savedData.addAndGet(-length.getValue() * 8);
    }
    Byte packetId=UnitByte.getByte(in,ptc,this);
    if (packetId == null) {
      if (!Globals.isQuiet()) {
        ptc.printLogMessage("String_Node_Str");
      }
      eof=true;
      continue;
    }
    if (packetId == (byte)0x50) {
      UnitShort length=new UnitShort();
      if (length.read(in,ptc,this,false,null) == null) {
        eof=true;
        continue;
      }
      short lengthPrim=length.getValue();
      UnitLong hashUnit=new UnitLong();
      for (short cnt=0; cnt < lengthPrim && !eof; cnt++) {
        if (hashUnit.read(in,ptc,this,false,null) == null) {
          eof=true;
        }
 else         if (ptc.setHashes.size() < 100000) {
          ptc.setHashes.add(hashUnit.getValue());
        }
      }
      if (eof) {
        continue;
      }
    }
 else {
      if (packetId == 0xFF) {
        ptc.printLogMessage("String_Node_Str");
        eof=true;
      }
      if (UnitByte.writeByte(out,packetId,ptc,this) == null) {
        ptc.printLogMessage("String_Node_Str");
        eof=true;
        continue;
      }
      Packet currentPacket=new Packet(packetId);
      bcb.write(packetId);
      if (currentPacket.critical) {
        ptc.printLogMessage("String_Node_Str" + bcb);
      }
      if (Globals.isVerbose()) {
        ptc.printLogMessage("String_Node_Str" + Integer.toHexString(packetId & 0xFF));
      }
      if (currentPacket.packetId == null || currentPacket.pass(in,out,ptc,this,false,buffer,null) == null) {
        if (!Globals.isQuiet()) {
          ptc.printLogMessage("String_Node_Str");
        }
        eof=true;
        continue;
      }
      if (packetId == 0x10) {
        Short holding=(Short)((UnitShort)(currentPacket.fields[0])).getValue();
        ptc.setHolding(holding);
      }
    }
  }
  ptc.interrupt();
}