even when there is no overlapping features in B.

Unmapped BAM alignments are now captured by -v in intersectBed and windowBed. Thanks to Davide Cittaro.

	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.

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.

	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. 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. 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. 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

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