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Hi,
Not possible through firmware because it is having dedicated pins &
function.It can be only done through hardware design.
For correcting it you required hardware change.
You can design a adapter with help of dot-matrix board and BergStik connectors with stack-up arrangements and use.
Best Regards,
Anand Raj Shankar
(This message was posted on behalf of Intel Corporation)
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Thanks.
I decided to download the bsdl file from the alteras site, replace there two contacts in places and try running jtag scanning. In a few hours I'll try