BLAT plugin fixes

This proposed update to the BLAT plugin allows the user to specify a minimum percent identity---the default of 90 can be too stringent for cross-species alignment---and allows the user to select whether the query is dna or rna (previously, the query type was hard-coded to dna, and we tend to use the BLAT plugin to align transcripts).

![q_minidentity](https://cloud.githubusercontent.com/assets/1800812/3690410/88cd7df4-1348-11e4-9186-521e41eff289.png)

In addition, the proposed update fixes several issues:

* BLAT hits are not necessarily reported in best-to-worst order.

The BLAT plugin currently keeps the first "Number of Hits to Return" hits in the PSL output (default 5). BLAT doesn't necessarily report hits in best-to-worst order, however. Compare the results from "Number of Hits to Return: 5":

![orig-keep5](https://cloud.githubusercontent.com/assets/1800812/3000062/e905c934-dd1e-11e3-8985-6cfb19ecd471.png)

with "Number of Hits to Return: 10":

![orig-keep10](https://cloud.githubusercontent.com/assets/1800812/3000069/f6d3e3a2-dd1e-11e3-98c3-fbcc614fce43.png)

The best hit was only reported in the second set, as it did not appear in the first 5 reported hits in the BLAT PSL file. The erroneous start coordinate of the best hit, which starts at the beginning of the sequence, is a side effect of issue #2:

* Start coordinates in PSL output are 0-based, not 1-based.

The proposed patch reads all BLAT hits and sorts them by the calculated score (which appears to be percent query coverage---a separate issue is whether it would be better to exclude mismatches) and adds one to all start coordinates, resulting in the following results with "Number of Hits to Return: 5":

![fixed-keep5](https://cloud.githubusercontent.com/assets/1800812/3000137/eaa6d00c-dd1f-11e3-9d63-056d4944e685.png)

This patch also changes the strand argument to Bio::Graphics::Feature to 1 or -1 instead of the "+" or "-" that is read from the PSL file, as the base class Bio::SeqFeature::Lite doesn't correctly handle "+" or "-", resulting in a 0 (".") for the strand (though I submitted a pull request to fix this: https://github.com/bioperl/bioperl-live/pull/71)

* Bio::Graphics::Browser2::Render does not handle "-" strand features in FeatureFile output

Even with the strand update to Blat.pm, the strand information isn't propagated to the resulting custom track that is created from the BLAT alignments; e.g., the following transcript alignment is on the "+" strand, while the gene model it was generated from is on the "-" strand:

![orig](https://cloud.githubusercontent.com/assets/1800812/3000527/0c6fcaea-dd25-11e3-946f-8e6f55c9340a.png)

The $userdata_base/*/My_Track/SOURCES/My_Track FeatureFile that was created from the BLAT alignments contains the following for that alignment:
```
reference=Gm01
"BLAT"  "Alignment1"    27946273..27946807,27950756..27950884,27952415..27952503,27952612..27956334,27957232..27957520
```
The documentation for Bio::DB::SeqFeature::Store::FeatureFileLoader states:
```
  Column 3: The position of this feature in base pair
            coordinates... Minus-strand features are indicated by specifying a start > end.
```

The proposed mod to Bio::Graphics::Browser2::Render uses end..start instead of start..end if the feature's strand is "-". The resulting alignment is then rendered on the correct strand:
![fixed](https://cloud.githubusercontent.com/assets/1800812/3000596/c2f3e210-dd25-11e3-93e7-66f7febd9054.png)