Modified ParseGTF function to remove quotes around tags.

These are added back by FlattenGTF, which was resulting in double quotes.
Added FixTranscripts.pl which modifies GTF files to group exons from the same gene and indicate paralogs
Modified the split function in ParseGTF to catch white space surrounding tabs
Functionality of CompareColumns.pl is included in CompareSets.pl
modified to use Bioperl IO

I have recently figured out how to read/write Bioperl objects to/from STDIN/STDOUT, so
I have modified this script to use this method rather than the custom parser I hade been using
Added a second sequence that is the reverse complement of the first

Sequences were also given names that correspond to the hits in test.bl
modified to use Bioperl IO

I have recently figured out how to read/write Bioperl objects to/from STDIN/STDOUT, so
I have modified this script to use this method rather than the custom parser I hade been using
first commit
new test files
Modified to include recently added scripts and test files