1. Added new version of BamTools supporting uncompressed BAM.
	2. Added -ubam option to intersectBed.
	3. First functional release of annotateBed.
	4. Updated GetEditDistance calls to GetTag(NM) per the new API change in BamTools.

	1. Fixed bug where an extra tab is inserted prior to \n in the report*Newline methods.
	2. Fixed bug causing incorrect behavior when first bed feature has stant and end = 0.

Tweaks to processHits in intersectBed for speed.

	The overlap variable was a CHRPOS.  The negative overlaps were reported as positive causing
        false hits when using BAM input.

	A. Fixed massive bug in parseBedLine that disallowed BED features with start = 0.  Bad news.
	1. Moved ToString to lineFileUtilities
	2. Added tabFile class.  Works with gzip as well.
	3. Changed groupBy to use the new TabFile class.
	4. Added new collapse feature to groupBy.

	1. Fixed bug in BamAncillary::getBamBlocks where the switch statement was misbehaving.  Changed to if/else
	2. Added countSplitHits to bedFile class to proper count coverage from "blocked" alignments. Previously, coverage
           was counted separately for __each__ block yet what we actually want is the base coverage to be counted for each block,
           but we only want the blocks to be treated as __one__ alignment or feature.
	3. Updated coverageBed to use getBamBlocks.

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

	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.