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The Quartus programmer isn't designed to perform general JTAG boundary scan tasks (although it would be a nice feature). Lookout for tools like TopJTAG http://www.topjtag.com/flash-programmer/
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I didn't use the tool, but I guess, you may need the BSDL description file, that shows the assignment of indidvidual IO pins to the boundary scan JTAG chain. It can be downloaded from Altera.
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--- Quote Start --- It wants to know which pins of the EPM 3064a is connected to the flash chips CE, WE , OE ,A0> a31 and D0 > D31 pins. --- Quote End --- Your questions are very unclear. You didn't mention before, that you are dealing with a hardware which circuit is apparently unknown. This problem hasn't anything to do with Altera CPLDs or programming tools.
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