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I'm not sure at which app note you're looking (although I suspect) but trust me on this: you just fire up the "Convert Programming File" dialog, make a .JIC from the .SOF and program it using the Programmer tool. No changes to your design are needed.
JTAG allows you to download configurations directly into the FPGA (much faster than programming the PROM), to use SignalTap for debugging, etc.
Quite honestly, not having JTAG is... insane.
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I think I see the misunderstanding. JTAG will program the FPGA directly which is fine but if you want to program the EPCS serial flash device through JTAG then you need to go through a lot as described in this app note (I forgot the link last time):
http://www.altera.com/literature/an/an370.pdf I may be able to squeeze in both connectors. In later revs perhaps I can get rid of the one for AS programming after I get the indirect programming working..
Rich
Honored Contributor
