So will the GPS be handling Uart traffic until the Nios is ready to take over? If that's not the case then the Uart is probably overflowing. In order for the Nios to be ready to handle the Uart, it will need a few micro seconds to finish initializing.
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Any device that comes up before the NIOS, could be transmitting to it before it is ready to receive data. Imagine a handheld unit with a GPS connected to a NIOS/CCA is powered on. The GPS initializes and begins transmitting data before the NIOS is ready - then what?[/b]
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Will the Nios be used just for status messenges or is it acting as a controller/error checker between the Uart and the GPS device? If you want the Nios to be up and running very fast then you have to provide code to do the initialization manually (see the small hello world sample code in the Nios install directory).