Hi
The OTP memory can't be programmed via EzPort.
It can be programmed via Jtag/SWD, however the controlling device needs to load a program to do it into SRAM (as it needs to do to program Flash). I see no reference to the PEMicro Cyclone programming tools supporting this but it is possible if the tools are give the capability - you should contact PEMicro to ask specifically.
Regards
Mark