Added functionality to call merge mate-pairs with or without retaining non-overlapping pairs and with or without an index (aka barcodes) file.
Added functionality to call merge mate-pairs with or without retaining non-overlapping pairs and with or without an index (aka barcodes) file.

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