Initial update

.gitignore to remove the generate files from consideration
Update: use of gfServer to perform the analysis

gfServer (part of the blatSuite) speeds up the alignment of the
sequences to the reference. Here an instance of the server is generated
and the fasta files are rapidily aligned.
The Mitochondrial filter now checks for similarity to chrM, similarly
to what the Ribosomal filter does.
TO DO: update the documentation and the Requirements for FusionSeq (and
.fusionseqrc)
Update: only 1 bed file per fusion is now generated

A single bed file is now generate per candidate fusion. The reads are
identified by R1 and R2 for transcript1 or transcript2, respectively.
Inital update: hash library

Used by RandomPairing Filter
Minor: added *.la