You don't need GPIOs. Instead analyse the pulse train by hardware. The eCAP modules in the PWMSS subsystems are designed for that purpose. The simplest (and most powerful) solution is to use libpruio <http://beagleboard.org/project/libpruio/>. Check out the example pwm_cap <http://users.freebasic-portal.de/tjf/Projekte/libpruio/doc/html/_cha_examples.html#SubSecExaPwmCap> .
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