fixed some undefined variable errors caused by splitting off normalize function
fixed some undefined variable errors caused by splitting off normalize function

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