Set the flag 'filter_duplicates_net' to 1 for filter_duplicates analysis at the netting step.

Set the flag 'filter_duplicates_net' to 1 for analysis, 'filter_duplicates_net' and 'filter_duplicates_net_himem', as done in EGPairAligner.pm, to make sure the filtering duplicates logic, at the net step, is consistent.