1. Got parseGffLine working
	2. Added GFF support to the reportBed* methods.
	3. Cleaned up the stdin / parsing logic and centralized it within bedFile.cpp.
	This removes some of the complexity from each of the tools and tidies the codebase
	overall.

   This becomes the new model for handling files/stdin,
   rather than duplicating the main logic of each porgram
   in a block for files and a block for stdin.

   Much slicker.