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.

	Working on maskFastaFromBed, permuteBed and addFlanksBed

	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).

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 limits.h to bedFile.h to prevent compilation errors on some systems.
	2. Fixed the bedFile.cpp parsing logic to allow proper parsing of track and browser lines

	1. Fixed a bug in peIntersectBed that prevented -a from being correctly handled when passed via stdin.
	2. Added new functionality to coverageBed that calculates the density of coverage.
	3. Fixed bug in genomeCoverageBed.

	1. When using stdin, the "inspan" annd "outspan" modes were not working.
	   Simple bug in the if statement...copy and paste error.

	1.  Changed master Makefile to compile utils first.
	2.  Fixed obvious bug in calculating discrete DOC in genomeCoverageBed
		--Identified by Scott Dewell, Rockefeller University.  Thanks!

	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