included .#* for temporary open files
Update: use of the gfServer
ADDED: gfrPseudogenesFilter
FIX: measuring the number of overlapping nucleotids is now properly counting only the overlapping intervals
UPDATE: the number of attempts is now increased to 5000 to ensure that the reads are blatted against the reference
UPDATE: modified the way it checks the status of the gfServers
UPDATE: modified the use of gfServers and the way overlap is computed