1. The start and end coordinates for BED and BEDPE entries created by bamToBed are now based on the __aligned__ sequence, rather than the original sequence.  It's obvious, but I missed it originally...sorry.
	2. Fixed a bug in bamToBed that caused a crash when created BED / BEDPE from "spliced" BAM alignments.
	3. Added an error message to mergeBed preventing one from using "-n" and "-nms" together.
	4. Fixed a bug in pairToBed that caused neither -type "notispan" nor "notospan" to behave as described.

	There was a problem with the way args with a value were being parsed.

	1. Revised usage to 80 chars
	2. GPL headers
	3. Added new stdin logic
	4. Changes logo.
	5. Revised the usage statement.

	1. Revised usage to 80 chars
	2. GPL headers
	3. Added new stdin logic
	4. Changes logo.
	5. Updated bedFile.cpp's loadBedIntoMapBin to support stdin.

	1. Revised usage to 80 chars
	2. GPL headers
	3. Added new stdin logic
	4. Changes logo.
	5. Updated bedFile.cpp's loadBedIntoMapNoBin.  Bug in stdin logic.

	Ready for publication release.
	Checked all of the help messages.
	Cleaned up some inconsistencies.

	1. Updated the mergeBed documentation to describe the -names option which allows one to report the names of the
	features that were merged (separated by semicolons).

	This allows the names field from all merged intervals to be reported in the merged block.

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

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