Added two new options:
Added two new options:

-gapped : creates one DnaDnaAlignFeature for each BLAT line (as opposed to
   one feature for each ungapped block)
-queryhseq : interprets the query side of the alignment as the hit sequence
   (as opposed to the genome sequence)

Both of these are to allow the resulting align features to be stored in
a core database)

mn1/ensembl-analysis,mn1/ensembl-analysis,kiwiroy/ensembl-analysis,Ensembl/ensembl-analysis,Ensembl/ensembl-analysis,Ensembl/ensembl-analysis,james-monkeyshines/ensembl-analysis,kiwiroy/ensembl-analysis,james-monkeyshines/ensembl-analysis,james-monkeyshines/ensembl-analysis,mn1/ensembl-analysis