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It's an optional pin function, that takes effect after entering user mode. It's ignored before and during configuration read.
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Hey Frank, thanks for the correction. I was going to recommend he use the IO_PULLUP# option that is present on the Stratix devices to enable the weak pull-ups during configuration, however, the Cyclone device does not have that pin. I incorrectly assumed that DEV_OE performed a similar function (with respect to tri-stating during configuration). However, you're right, the device pins are tri-stated during configuration anyway, so the DEV_OE pin function is not required until after configuration.
Cheers,
Dave