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. 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.

	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.

=== Notable changes in this release ===
1.  coverageBed will optionally only count features in BED file A (e.g. sequencing reads) that overlap with
	the intervals/windows in BED file B.  This has been requested several times recently and facilitates CHiP-Seq and
	RNA-Seq experiments.

2.  intersectBed can now require a minimum __reciprocal__ overlap between intervals in BED A and BED B.  For example,
	previously, if one used -f 0.90, it required that a feature in B overlap 90% of the feature in A for the "hit"
	to be reported.  If one adds the -r (reciprocal) option, the hit must also cover 90% of the feature in B.  This helps
	to exclude overlaps between say small features in A and large features in B:

	A ==========
	B  **********************************************************

	-f 0.50 (Reported), whereas -f 0.50 -r (Not reported)

3.  The score field has been changed to be a string.  While this deviates from the UCSC definition, it allows one to track
	much more meaningful information about a feature/interval.  For example, score could now be:

	7.31E-05  (a p-value)
	0.334577  (mean enrichment)
	2:2.2:40:2 (several values encoded in a string)

4.  closestBed now, by default, reports __all__ intervals in B that overlap equally with an interval in A.  Previously, it
	merely reported the first such feature that appeared in B.  Here's a cartoon explaining the difference.

	**Prior behavior**

	A	 ==============
	B.1        				++++++++++++++
	B.2       				++++++++++++++
	B.3               				+++++++++

	-----------------------------------------
	Result = B.1 			++++++++++++++

	**Current behavior**

	A	 ==============
	B.1        				++++++++++++++
	B.2       				++++++++++++++
	B.3               				+++++++++

	-----------------------------------------
	Result = B.1 			++++++++++++++
			 B.2 			++++++++++++++

	Using the -t option, one can also choose to report either the first or the last entry in B in the event of a tie.

5.  Several other minor changes to the algorithms have been made to increase speed a bit.

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.  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

	1.  Cleaned up the whitespace in bedFile.cpp and bedFile.h
	2.  Added a check in bedFile.cpp to detect if the BED file is space-delimited.

	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

	1.  Changed BedFile::loadBedFileIntoMapNoBin() to allow either "" or "stdin".
	2.  Consequently, this allows mergeBed to accept stdin as well.

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

Changed sortBed to allow input from stdin.