The port register(s) (GPIO) always reflect the current value on the pins and the interrupt capture register (INTCAP) contains snapshot of the port at the time of the interrupt. Read the GPIO register(s) when interested in the current state. Read the capture register (INTCAP_ when interested in the state of the port when the interrupt occurred. The interrupt condition is cleared be reading either the port (GPIO) or the capture register (INTCAP).