1. Fixed bug to "re-allow" track and "browser" lines.
	2. Fixed bug in reporting BEDPE overlaps.
	3. Fixed bug when using type "notboth" with BAM files in pairToBed.
	4. When comparing BAM files to BED/GFF annotations with intersectBed or pairToBed, the __aligned__ sequence is used, rather than the __original__ sequence.
	5. Greatly increased the speed of pairToBed when using BAM alignments.
	6. Fixed a bug in bamToBed when reporting edit distance from certain aligners.

	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.

	1. atoi fails in parseLine when start = 0.  Changed to strtol.
	2. modified parseBedLine and parseGffLine to do better sanity checking.

  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 closestBed that caused all nearby (not just closest) features to be returned.

	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.

=== 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. 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. 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