Update: minor added documentation
Update: numInter is now float
Update: added documentation and the use of configuration information
Update: added documentation
Update: added documentation and generalized the use of gfServer

The program now uses gfServer to speed up the alignement. The
information needs to be present in the configuration file
Update: the overlap with repetitive regions is now based on nucleotides

The overlap is properly computed by accounting for the actual
nucleotides that overlap a repetitive region.