Unmapped BAM alignments are now captured by -v in intersectBed and windowBed. Thanks to Davide Cittaro.

Fixed casting issue in windowBed.AddWindow() that cuased slop positions to run off the end of the chromosome.

	1. Reset BED.strand to be string instead of char in the interest of generality.
	2. Fixed bug in genomeCoverageBed where NULL entries where genome summaries were err. reported with -bga.
	3. Fixed bug in closestBed where NULL entries were err. reported when BED > 6.
	4. Standardized the Open, Get, Close idiom per improvements from Gordon Assaf.
	5. Add "split" logic to bamToBed.

	1. Added BAM support to windowBed.
	2. Forced correct BEDPE ordering for bamToBed.
	3. Added default overlapFraction = 0.0 to bedFile prototype.

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

	1. Added GPLv2 license to entire distribution
	2. Added GPL headers to intersect and window
	3. Added new stdin logic to windowBed

   Changed windowBed to optionally define the left and right windows according to
   strandedness.

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

	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 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.