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I have a Pi3 flashed with Retropie connected to a Switch Controller via USB.

The controller mapping seems off.

I can't seem to play in KOF97 properly. I want to remapped it.

Right now it mapped to :

(X) - big kick
(Y) - big punch 
(A) - small kick
(B) - small punch 

I want to overwrite to :

(X) - big punch
(Y) - small punch 
(A) - big kick
(B) - small kick 

How would one configure a specific inputs for specific emulator or rom ?

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You should be able to start the game and then bring up RetroArch's RGUI menu using Select+X

On that menu use D-pad Up and Down buttons to highlight Controls and press A to open that. Then select Port 1 Controls.

Use the D-pad Up and Down buttons to highlight the control line you want, then use the D-pad Left and Right buttons to change which controller button is assigned to that line.

If the names on the left don't make sense see Mapping gamepad controls in RetroPie (for MAME2003 arcade games) which may help (just ignore the MAME stuff).

You must save the configuration back at the RGUI menu.

Some of this is explained at RetroArch Controller Configuration which covers global, per-emulator ("system-specific") and per-game ("ROM-specific") remapping.

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