Hi,
Let's just say I screwed up and designed a board that had d- and d+ swapped by mistake. Is there any way to solve this by software? How can I swap SAMD21's d- and d+ pins?
If anyone can help, it would a life saved for me!
I don't think you can. I checked the pin multiplexing and it looks like you can't even swap the USB signals to another set of pins. Also the USB won't work if those signals are reversed.
Have you considered cutting open a USB cable and swapping the signal wires there? This might not help you if you have a bunch of boards manufactured for others to use, but if this is just a one off project for yourself it would be a simple solution.
Thanks for your reply, I figured that this it was hardwired 
I ended up cutting the PCB traces.