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I'm doing some analysis with SignalTap and I'm wondering if I can set some sort of flag in the compiler to make it not synthesize away some signals that are currently not routed anywhere in the design but I would still like to view their values.
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take a look at the noprune synthesis attribute
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And where do I set that in Quartus II?
My design is all VHDL. Nevermind, found it. http://quartushelp.altera.com/current/mergedprojects/hdl/vhdl/vhdl_file_dir_noprune.htm- Mark as New
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Don't forget to open your VHDL/Verilog in Quartus II and go to Edit -> Insert Template. I find this the best place to look at what's possible. I also put "keep" attributes on a combinatorial node that won't get synthesized out, but might get merged with other combinatorial logic and hence something I can't find in the post-fit netlist.

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