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
long line; I have a commit somewhere that chops it up though so don't need to fix it here