1. Fixed a bug in peIntersectBed that prevented -a from being correctly handled when passed via stdin.
	2. Added new functionality to coverageBed that calculates the density of coverage.
	3. Fixed bug in genomeCoverageBed.

	1. When using stdin, the "inspan" annd "outspan" modes were not working.
	   Simple bug in the if statement...copy and paste error.

	1.  Changed master Makefile to compile utils first.
	2.  Fixed obvious bug in calculating discrete DOC in genomeCoverageBed
		--Identified by Scott Dewell, Rockefeller University.  Thanks!

	1. Added strandedness to relevant programs (e.g. intersectBed, mergeBed, etc.)
	2. Moved reportBed and reportBedRange to bedFile.cpp to clean up code
	3. Sped up file parsing.  Added lineFileUtilities.cpp
	4. Added peIntersectBed

	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.  Cleaned up the whitespace in bedFile.cpp and bedFile.h
	2.  Added a check in bedFile.cpp to detect if the BED file is space-delimited.

	1.  Thanks to Loyal Goff at CSAIL/Broad for help identifying misssing includes.
	2.  Updated README to reflect this.