Updates to the MQM code based on valgrind output

Hey Karl,

I fixed one of the major memory leaks (10mb) in mqmaugment line 633, I was freeing a matrix like it was a vector causing a loss of the whole augmented genotype matrix. I still have to fix more, but I think this is the major one. 

The biggest issue is I have to re-run the valgrind test every time I change the code, which takes around 2 hours (there is no way to do the valgrind test multi-core)

Gr,
Danny