Move removing nearby or correlated snps to second pass

Final piece of #147 pulled out  - includes #163 but will rebase once that is merged in 

- Removed check for correlated (nearby) SNVs from caller - moved this to a second pass over genotypes in some window
- Adding average mapping quality filter
- Adding average base quality filter
any comment on why these loci are not relevant?

if our algorithm is just remove loci that fail, that doesn't bode well for this test being useful :-\