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How about TCK? Does it also the output of the virtual jtag(vji)? I think we should generate a clock which we feed into the vji(not sure either).
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The Virtual JTAG component ports TCK/TMS/TDI are outputs, and the TDO signal is an input. These pins correspond to the signals coming from the FPGA pins via the Virtual JTAG component into your design.
For your first design, you can ignore all of these signals, and just wire ir_in to your LEDs, and ir_out to some push buttons. You can then use quartus_stp and device_virtual_ir_shift to write to the LEDs and read from the push buttons.
Cheers,
Dave