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I always bring out a full MICTOR connector worth of test pins.
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There are a couple of additional Quartus features that can be used with test pins.
[LIST]SignalProbe lets you bring out internal signals to device pins. You can change which signals are probed with recompiles that are faster than a regular Fitter runtime.[/LIST]
[LIST]The Logic Analyzer Interface lets you preselect a large number of internal signals to bring out to a relatively small number of device pins. You can dynamically change which internal signals are currently being monitored on the test pins using a GUI that communicates with the Logic Analyzer Interface by JTAG.
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Another JTAG-controlled debugging feature is In-System Sources and Probes.
Information on all these debugging features is in the Quartus handbook, Volume 3, Section V: In-System Design Debugging.
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