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Reading PACS (raw Wiegand) data with Omnikey 5022

I'm developing a Java application that connects to HID Omnikey 5022 card reader. What I need is reading PACS bits (raw Wiegand data).
I have exactly the same problem with this question, I also can see the data with PACS Probe application:
How to read Smart Card data
Unfortunately the provided answer to that is not working for me.
This is what I get from PACS Probe:
Card Reader: HID Global OMNIKEY 5022 Smart Card Reader 0
Card type: PicoPass 32KS (8x2 + 16)
Card serial number (CSN, UID): 32966202F8FF12E0 (hex)
PACS bits (raw Wiegand) data: 000000310BC53938 (hex)
I have already tried the command I found in Omnikey 5023 guide, surprisingly it returns some data but it's not what I need.
That command is:
commandAPDU = new CommandAPDU(new byte[] { (byte) 0xFF, (byte) 0x70, (byte) 0x07, (byte) 0x6B, (byte) 0x07,
(byte) 0xA0, (byte) 0x05, (byte) 0xBE, (byte) 0x03, (byte) 0x80, (byte) 0x01, (byte) 0x04, (byte) 0x00 }); // Read PACS 5023
It returns this:
9E020003
// I need 000000310BC53938
Any help is appreciated since I am new to smart card development.
Thanks in advance.

The response APDU you are getting from the reader is an error code for unsupported proprietary command.
You will need a secure session to access PACS bit data using OMNIKEY 5022 or OMNIKEY 5023 readers.
Unless you have the appropriate documentation for this reader, I would probably stick to the card serial number (UID, CSN) and use a Java wrapper for PC/SC (or pcsclite) to connect to reader and card.
Then issue (via SCardTransmit(FFCA0000 APDU) to get the UID (32966202F8FF12E0) shown in your the sample output from https://PACSprobe.com
As for Java: use smartcardio lib. That's a good wrapper for native PC/SC
It's a lot of work porting the secure channel protocols to Java. Calling a third-party library may be easier.

I was able to use javax.smartcardio, and get the Wiegand data using code like below. At the end you can see the facility code and card number are printed.
TerminalFactory terminalFactory = TerminalFactory.getDefault();
CardTerminals cardTerminals = terminalFactory.terminals();
List<CardTerminal> terminalList = cardTerminals.list();
CardTerminal cardTerminal = terminalList.get(0);
cardTerminal.waitForCardPresent(10 * 1000); // wait 10 seconds
Card card = cardTerminal.connect("*");
System.out.println("Card: " + card);
CardChannel channel = card.getBasicChannel();
byte[] aid = { (byte) 0xA0, (byte) 0x05, (byte) 0xA1, (byte) 0x03, (byte) 0x80, (byte) 0x01, (byte) 0x04 };
CommandAPDU apdu = new CommandAPDU(0xFF, (byte) 112, (byte) 7, (byte) 107, aid, 256);
ResponseAPDU r = channel.transmit(apdu);
byte[] bytesOut = r.getBytes();
int num1 = (int) bytesOut[3];
if (bytesOut.length - 6 != num1)
System.out.println("problem");
int numberOfBitsShifted = (int) bytesOut[4];
int num2 = num1 - 1;
byte[] newBytesArr = Arrays.copyOfRange(bytesOut, 5, 5 + num2);
if (newBytesArr.length != num2)
System.out.println("problem");
ByteBuffer wrapped = ByteBuffer.wrap(newBytesArr);
int num = wrapped.getInt();
int first26 = num >> 6;
int withoutParity = first26 >> 1;
int cardNumber = withoutParity & 0xffff;
int facilityCode = (withoutParity >> 16) & 0xff;
System.out.println(facilityCode);
System.out.println(cardNumber);

Weird "illegal start of expression" error in Netbeans

In the following programs, command is a byte array field in Apdu class. The problem is that my IDE (Netbeans) mark the line of
apdu.command = {(byte) 0x00, (byte)0xa4, (byte) 0x00, (byte) 0x00};
As error, with the message illegal start of expression, while it is okay to use the following instead:
byte[] bytes = {(byte) 0x00, (byte) 0xa4, (byte) 0x00, (byte) 0x00};
apdu.command = bytes;
What's wrong with the first programs?
First program:
Second Program:

You need to initialize the array variable with :
apdu.command = new byte[] {(byte) 0x00, (byte)0xa4, (byte) 0x00, (byte) 0x00};
The initialization you tried is only valid in array declaration expressions.

array syntax {} can only be used for initialization not for assignment.
you need to use apdu.command =new byte[] {(byte) 0x00, (byte)0xa4, (byte) 0x00, (byte) 0x00};.

possibly lossy conversion from int to byte

I am trying to write hexadecimal data into my serial port using java, but now I cant convert the hexadecimal data into the byte array.
Here is the code which shows the error message:
static byte[] bytearray = {0x02, 0x08, 0x16, 0x0, 0x00, 0x33, 0xC6, 0x1B};
This is the code writing into the serial port:
try {
outputStream = serialPort.getOutputStream();
// Write the stream of data conforming to PC to reader protocol
outputStream.write(bytearray);
outputStream.flush();
System.out.println("The following bytes are being written");
for(int i=0; i<bytearray.length; i++){
System.out.println(bytearray[i]);
System.out.println("Tag will be read when its in the field of the reader");
}
} catch (IOException e) {}
Can I know how can I solve this problem. Currently I am using the javax.comm plugin. Thank you.

If you look at the error message:
Main.java:10: error: incompatible types: possible lossy conversion from int to byte
static byte[] bytearray = {0x02, 0x08, 0x16, 0x0, 0x00, 0x33, 0xC6, 0x1B};
^
There is a small caret pointing to the value 0xC6. The reason for the issue is that java's byte is signed, meaning that its range is from -0x80 to 0x7F. You can fix this by casting:
static byte[] bytearray = {0x02, 0x08, 0x16, 0x0, 0x00, 0x33, (byte) 0xC6, 0x1B};
Or, you can use the negative, in-range value of -0x3A (which is equivalent to 0x36 in two's-complement notation).

Try to cast 0xC6 like this as byte range is from -0x80 to 0x7F:
static byte[] bytearray = {0x02, 0x08, 0x16, 0x0, 0x00, 0x33, (byte) 0xC6, 0x1B};

Java int to hex with 0x

I'm trying to convert int to hex with format 0x12 0x2B and so on. Is there anything similar like python: https://docs.python.org/2/library/functions.html#hex
to accomplish this or i will need to work around this with many unnecessary steps?
I need to get something like this below:
int []hexInt={0x00, 0x00, 0x00, 0x10, 0x00, 0x00, 0x00, 0x15, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x02, 0x01};

You could declare a String which will be equal to "0x" + Integer.toHexString(int)

public static String intToHexStr(int i){
return "0x"+String.format("%2s", Integer.toHexString(i)).replace(' ', '0');
}

Maybe this is very late but here is the answer to your question:
Integer.parseInt(String.format("%X", intValue),16)

Mifare Classic 1k APDU command for retrieving tag UID

As the title says; is there a APDU command for retrieving the UID of a tag? I am using Java, with an ACR122-u cardreader and the javax.smartcardio.* package and I want to get the UID from a tag on the scanner. The smartcardio library can send CommandAPDU's but I need to figure out what APDU to send. Google has not been very friendly to me on this one, providing me with thousands of unhelpful datasheets of some sort...
Any help would be great :)

Better late than never but there is actually an APDU to JUST retrieve the UID: (byte) 0xFF, (byte) 0xCA, (byte) 0x00, (byte) 0x00, (byte) 0x00
FF CA 00 00 00
In Java: byte[] getuid = new byte[] { (byte) 0xFF, (byte) 0xCA, (byte) 0x00,
(byte) 0x00, (byte) 0x00 };
If you send this APDU, the response data will be just the UID of the card :) (Much easier than having more info and having to set an offset to get just the info you need...)

The APDU Command for Read UID is
byte[] baReadUID = new byte[5];
baReadUID = new byte[] { (byte) 0xFF, (byte) 0xCA, (byte) 0x00,
(byte) 0x00, (byte) 0x00 };
All Complete code is here....