1.  Added subtractBed.
		A. Fixed bug that prevented "split" overlaps from being reported.
		B. Prevented A from being reported if >=1 feature in B completely spans it.
	2.  Added linksBed.
	3.  Added the ability to define separate windows for upstream and downstream to windowBed.

	1.  Added a README for installation
	2.  Modified intersectBed and windowBed to call one function for
	    finding overlaps.  This function is now called when reading
	    from cin or from a file.
	3.  Added acknowledgements.
	4.  Corrected the PROGRAM_NAME in coverageBed

	Rather self-explanatory.  Affects *Main.cpp files.
	Also affects the bedFile.cpp file.
		All of the BED entry checks now write to stderr.

	Changed the include from graphBed.h to coverageBed.h
coverageMain.cpp:
        Changed the include from graphBed.h to coverageBed.h