Inconsistent use of mismatches in thresholds

[lweasel]

In hits_checker.py , the method check_hits() compares the maximum number of mismatches for a set of mappings for a read against the mismatch threshold. But _check_thresholds compares the minimum number of mismatches against the threshold. I think that these should both use the minimum number of mismatches?

[hxin]

in the branch but need to be tested to see the effect.
#59

The continuous-integration check fails but this is expected since the desition making structure has been changed.