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.

	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

	Added windowBed, which scans for overlaps within a requested widow size.

	-wa allows the original A entry to be written for each overlap with B.

	1. Changed intersectMain.cpp, complementMain.cpp and mergeMain.cpp to
	   include information on how to run using stdin.

	1.  Changed BedFile::loadBedFileIntoMapNoBin() to allow either "" or "stdin".
	2.  Consequently, this allows mergeBed to accept stdin as well.

	1.  Changed the cout statements for the last entries for a chromosome.
	2.  I had forgotten to report the number of merged entries when -n is requested.
	3.  I also fixed a bug that occassionally caused the last entry for a chromosome
	    to report the chrom twice in the output.

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

	1.  Fixed a bug that caused genomeCoverageBed to crash on Linux systems.
	2.  Refined the algorithm to use less memory.  It's a bit slower now, but uses 1/3 the memory.
	3.  Changed the logic for computing depth to conform to the UCSC coordinate system.