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We pointed several solutions for accessing the USB connector.
The easiest is by far using TCL scripts, but then it is probably the slowest.
A second choice would be to use the unofficially documented (seems more like not officially supported, rather than undocumented) jtag-uart interface using the atlantic DLL. Or you can use one of the undocumented interfaces, including direct access to the USB-Blaster using FTDI DLL API.
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After reading the topic I am still not sure what's the best way to get FTDI USB to work. Did anybody really try to use FTDI D2XX DLL API for USB to PC communication?
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