Added code to accept index file for merging mate-pairs.  Also accepting option for removing or retaining non-overlapping mate-pairs.
Added code to accept index file for merging mate-pairs.  Also accepting option for removing or retaining non-overlapping mate-pairs.

paczian/MG-RAST,wilke/MG-RAST,MG-RAST/MG-RAST,MG-RAST/MG-RAST,teharrison/MG-RAST,MG-RAST/MG-RAST,MG-RAST/MG-RAST,teharrison/MG-RAST,paczian/MG-RAST,paczian/MG-RAST,MG-RAST/MG-RAST,paczian/MG-RAST,wilke/MG-RAST,wilke/MG-RAST,teharrison/MG-RAST,wilke/MG-RAST,teharrison/MG-RAST,wilke/MG-RAST,teharrison/MG-RAST,teharrison/MG-RAST,wilke/MG-RAST,wilke/MG-RAST,paczian/MG-RAST,paczian/MG-RAST