BLAT hits are not necessarily reported in best-to-worst order. Read all
blat hits and sort by calculated score (percent query coverage).

Add 1 to start coordinates, as Start coordinates in BLAT PSL output are
0-based, not 1-based.

Strand needs to be +1/-1 (rather than "+" or "-") in order for
Bio::SeqFeature::Lite (base class of Bio::Graphics::Feature) to
correctly interpret them (though there is a pull request to fix this:
    https://github.com/bioperl/bioperl-live/pull/71
Make end > start for - strand features in FeatureFile output.
Allow user to select dna/rna query & specify minimum percent identity.
Remove unused check_seq() subroutine.
Merge pull request #43 from nathanweeks/issue/blat-fix-sort-start-strand

BLAT plugin fixes