Minnowboard gpio

The minnowboard is the only board I can find that:
Runs Linux
Has GPIO header
Supports opengl (rather than exclusively opengl es that arm devices do)

The only tutorial I could find on GPIO for the minnowboard, is for the terminal. But it seems it operates through changing text in a sys/class/ file. Can I do this from a C++ program if run with sudo? Is there an easier way? Is there a better board that could replace the minnowboard? It has to comply with the above three terms.
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