allow calling of calmd with flag
allow calling of calmd with flag

dariober/bwa-meth,brentp/bwa-meth,dariober/bwa-meth,brentp/bwa-meth,PeteHaitch/bwa-parclip,dariober/bwa-meth,PeteHaitch/bwa-parclip,PeteHaitch/bwa-parclip,brentp/bwa-meth