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.

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.

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

=== 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.

	- Added the -name parameter.  It was missing, so users had no idea it existed.

	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