The SWDIO and SWCLK pins don't appear to be GPIO pins.
According to the data sheet and schematics, the SWDIO and the SWCLK pins are attached to PA30 and PA31 of the SAMD21.
The I/O multiplexing table on page 21/22 of the data sheet show that these pins can be connected to:
MUX A - EXTINT / EXTINT
MUX D - SECOM PAD / SECOM PAD
MUX E - TCC1 WO / TCC1 WO
MUX G - SWDIO / SWCLK
MUX H - GCLK_IO / N/A
This suggests that those pins could indeed be used as some kind of I/O, using the EXTINTs perhaps?
But its MUX B that includes the ADC and AC operations, which means that you wouldn't be able to do an analogue read or write of those pins.
Perhaps somebody else could expand more on this.
What is it you were wanting to use these pins for?