1.  Added support for VCF 4.0.  BED.end is based on the size of the REF allele in the VCF entry.
	2.  Fixed a bug in BamReader.cpp that bombed when seq and qual are == "*"
	3.  Changed the Makefiles to inherit flags from the master Makefile in the root directory.
	4.  Fixed a bug in bedToBam to created incorrect CIGAR strings for the first block.

	1. Reset BED.strand to be string instead of char in the interest of generality.
	2. Fixed bug in genomeCoverageBed where NULL entries where genome summaries were err. reported with -bga.
	3. Fixed bug in closestBed where NULL entries were err. reported when BED > 6.
	4. Standardized the Open, Get, Close idiom per improvements from Gordon Assaf.
	5. Add "split" logic to bamToBed.

	1. Created separate structs for BED and BEDCOV in order to reduce memory consumption.  Savings of ~30%.
	2. Changed the binning approach to make 16kb bins the most granular.  IntersectBed is now 1/3 faster as a result.
	3. Templated the parsing and reporting functions in bedFile.  Had to move them to the header file to avoid linker complications.
	4. Added CHRPOS as a common type.

	1. Added BAM support to windowBed.
	2. Forced correct BEDPE ordering for bamToBed.
	3. Added default overlapFraction = 0.0 to bedFile prototype.

	1. Added an enum for BED line status in an effort to handle
           header and blank lines in an input file.
	2. Modified the Open/Get/Close idiom to only test against
           BED_INVALID status.  Only intersectBed and bedFile.cpp
           were updated.
	3. Added AddBamTag to BaumAux.h
	4. Wrote bamFillMateSeq

	- also standardized the naming convention for private variables.
	- loadIntoMap methods use Open/Get/Close idiom.

	- Allows one to report 0 overlap for non-overlapping A features
	- Changed all private memeber variables to use "_VAR" notation.
	- Added convenience functions for reporting overlaps.

	1. Added the -hist option (credit to Jose Bras).
	2. Substantially improved the speed by using a depth iterator instead of copying the depth map for each feature in B when computing coverage.

	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.

	1. pairToBed had a bug in the way it parsed -a
	2. extraneous tr1/unordered_map include in bedfile.h causes compile issues on some machines.

	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

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