* to be included:

Makefile (added gfrWhiteListFilter )
export2mrf (using exportPEParser)
bp2alignment (using correct size)
bp2fasta (extract the junction in fasta format)
bpClustering (cluster bpjunction with the same central sequence)
bpValidate (validating the junctions against the reference, need to run bp2fasta, bowtie to the reference and read the results)