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PORT IS NOT GETTING RESET[tiva]

Hi, 

I'm using the TIVA TM4C123 series board.My objective is to generate the 4 pulses signal,

Here, I facing the problem with port. > I used one dedicated port for my application of pulse generations,

For that, > I enabled port,

 >Port is configure as timer like GPIPintpyeTimer

> Setting values to the timers,

After, based on my requirement, i used different functions, to generate the 2 pulse signal for each functions.other 2 pulse pins are disabled.

> I observed that, the time of transition between the functions, it's holding the values, I felt the port register is problem. After, I tired the software reset on the specific port. its restored the original values. Also, I diabled the corresponding pins.

Without the software reset, is that possible to restore/change the timer values are stored in port registers.