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configure PIO of ARM9 as input.

hi all,
I am Kirti Patel from india.
i am using AT91RM9200+FPGA SBC board made by darell harmon...
in this board when i read the status of the pio pins during execution ..at that time i am not getting the good response as on the pins.i.e.wrong response.and if i made changes through key pad to this particular pins at that time i did't get good response....
now in addition to this i want to start FPGA working on this board and send bitstream file through ARM9 controller.

so what i have to do??can any one help me about my problem..
Thanks.

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