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.

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

=== 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. 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.  Thanks to Loyal Goff at CSAIL/Broad for help identifying misssing includes.
	2.  Updated README to reflect this.

	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