Add GFF Support for Window Specification

[ritster]

Current implementation only supports BED window specification, so add support for specifying windows via GFF annotations. Also consider: GTF support, other file formats.

[cmdcolin]

sticking with just BED might be fine. a GFF or GTF can be "trivially" converted to bed by running "cut -f1,4,5 file.gff > out.bed" (and you might also have to "grep" the gff to only get gene level features....stuff like that makes you have to "guess" at what a user wants from inputting a GFF also...bed, it is more clear: just run over each row :))