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TFP401AMPZPEP, changing configuration post-startup

Hi,

I have the TFP401AMPZPEP digital input lines connected to the outputs of my FPGA (spartan-6). during startup, the FPGA lines are held high due to pullups (~10k), which means that the device will be configured with all of the digital inputs pulled high. 

What is the process of changing the digital input configuration after the startup has occurred?

Thank you!

Stacey