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

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

	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.

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

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

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

	1. Got parseGffLine working
	2. Added GFF support to the reportBed* methods.
	3. Cleaned up the stdin / parsing logic and centralized it within bedFile.cpp.
	This removes some of the complexity from each of the tools and tidies the codebase
	overall.

	Not thoroughly tested but looks good so far.
	Initial cut at a GFF parser...needs work.

  Rewrote complementBed to use a slower but much simpler approach. This resolves several bugs with the previous logic.

   This becomes the new model for handling files/stdin,
   rather than duplicating the main logic of each porgram
   in a block for files and a block for stdin.

   Much slicker.

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

	Fixed a bug in closestBed that caused all nearby (not just closest) features to be returned.

1

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

	Working on maskFastaFromBed, permuteBed and addFlanksBed

	Forced an exit if negative coordinates are encountered.

	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).

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