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Up squared change a GPIO pin (HAT) from input to output (or reversed)?

I have 2 Up Squared boards and I can not change the state of any GPIO pins (HAT) from input to output (or reversed) on Linux.

I saw that GPIO pins are connected to an FPGA and the IO state must be redefined in the BIOS setting. Is it possible to change the GPIO state on the software/OS side?

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