added long-form options; fixed epilog crashing bug by adding metavar
added long-form options; fixed epilog crashing bug by adding metavar

Winterflower/khmer,F1000Research/khmer,kdmurray91/khmer,F1000Research/khmer,jas14/khmer,souravsingh/khmer,souravsingh/khmer,souravsingh/khmer,jas14/khmer,kdmurray91/khmer,kdmurray91/khmer,ged-lab/khmer,Winterflower/khmer,ged-lab/khmer,F1000Research/khmer,ged-lab/khmer,jas14/khmer,Winterflower/khmer