Max_mismatch almost ready
Max_mismatch cleanup; generalize to any # of masks
Minor readability improvements
Update setup.sh for new method
Move max_mismatch to the flowcells dir

Should have put it there from the beginning!
Merge pull request #13 from fwip/rewrite_max_mismatch

Rewrite max mismatch

Now actually works for more than the trivial case!
Fix bug where Picard reports uploaded to wrong alignment object