- also standardized the naming convention for private variables.
	- loadIntoMap methods use Open/Get/Close idiom.

	1. Revised usage to 80 chars
	2. GPL headers
	3. Added new stdin logic

	Fixed a bug in subtractBed that prevent a file from subtracting itself when the following is used:
	$ subtractBed -a test.bed -b test.bed

The memory usage is now less than 2.0 Gb.

	Fixed an obvious bug in subtractBed causing incorrect behavior when
	two features in B overlapped with a feature in A.

1. Fixed yet another bug in the parsing of "track" or "browser" lines.  Sigh...
2. Change the "score" column (i.e. column 5) to b stored as a string.  While this deviates
   from the UCSC convention, it allows significantly more information to be packed into the column.

	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.  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

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

	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.