add GFF source argument

PIGPEN requires relating transcripts and genes. This is done using a supplied GFF file. The locations of the information in this file that are important for relating transcripts and genes (i.e. tags in annotations that denote transcript, parent and gene IDs) are slightly different depending on where this GFF came from. For mouse and human samples, we recommend using GENCODE gffs, but these are not available for other species. This release includes a --gfftype argument to handle this. The string supplied to this argument changes the getpostmasterassignments, assigntotxs, collapsetogene, readspergene, and writeOutput functions used. None of this comes into play if instead a bed file of genomic regions of interest is supplied via --ROIbed.