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. Eliminated redundant code.
	2. Allowed writing to stdout.

	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.

	Open and Close were omitted by mistake.

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

	- added more details about -bga option.

	1. Updated intersectBed, coverageBed and genomeCoverageBed to correctly compute alignment end coordinates in BAM.
	2. Changed the logic for handling BAM alignments in pairToBed
	3. Allowed the use of minMappingQuality or totalEdit distance in pairToBed.

	1. Writing BEDPE now requires a BAM sorted/grouped by query.
	2. BEDPE output respects CIGARs on both ends.
	3. End coordinates for all output formats respect CIGAR.
	4. Default score for BEDPE is min mapping quality.

	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.

Added new version of BamTools and fixed a couple minor bugs in intersectBed that were caused by the branchmerge.