Tumour only calling using FreeBayes falls back to single sample mode

Hi Brad,
We have in most studies singleton tumour samples and we'd like to be able produce output from FreeBayes for these samples too. At the moment it's not really simple and requires manual intervention. This change would produce output from FreeBayes, although unoptimal, but we could tune tumour-only calling in FreeBayes later on. 

My other proposal would be to possibly apply ``allelicprimitives`` on paired FreeBayes calling because complex variants cause errors in SnpEff downstream. I can implement this too given public aye :)