Configure UART GPS module for Friendlyarm nanopc-t1 on Android
I figured it out, the problem was originating from NanoPC-t1 config which used the USART port for output debug. It was over-writing the gps output.

I used Android Serial Port API, and rooted my device. Because accessing ttySAC0 port, needs root access.

I wrote my own NMEA parser to receive GPS fixes.