Hello Christian and Jeremy,

Thanks very much, indeed in my IDE (IDEA) it was printing:

PID|||123456||Doe^John

But when ran from a standard shell it printed:

PID|||123456||Doe^Johnstem||||200701011539||ADT^A01^ADT A01||||123

And of course at the hint replacing \r in java or piping it to tr '\r'
'\n' in shell gave me the output I was expecting.

Thanks again, I'm sure I would have never realized that on my own!

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