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
Yea, I agree, the test fails because it will be ruled out for not being a reasonable variant, but other things (low mapping quality) which we aren't testing here.  

I think the tests need to be reworked significantly.  Also the variant should be split up a bit more as there should some tests that are absolute no-brainer callers that we should make as basic regression tests and then perhaps more separated tests for the invidual filters.  

Also this was not representative sample of variants so getting one wrong here was likely meant we were getting many others right now, but weren't in the original tests.

TLDR - I plan to break the tests into 3 groups - obvious basic varaints, possible variants that are filtered out to test the filters and 4 some set of variants that we should keep respectable precision/recall on.