fixed the function         for i in xrange(len(lines_out_markers1)):clean up after completed test run - will remove the slow checks at the end of the function BEAGLE_divide at a later stage
1) fixed the function remove_duplicate_lines called by the function BEAGLE_divide, whenever a fragment is appended to the previous fragments (e.g. at the centromeres), 2) clean up after completed test run, 3) will remove the slow checks at the end of the function BEAGLE_divide at a later stage