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.

	Open and Close were omitted by mistake.

	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 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.

	There was a problem with the way args with a value were being parsed.

	1. Revised usage to 80 chars
	2. GPL headers
	3. Added new stdin logic
	4. Changes logo.
	5. Revised the usage statement.

	1. Revised usage to 80 chars
	2. GPL headers
	3. Added new stdin logic
	4. Changes logo.
	5. Updated bedFile.cpp's loadBedIntoMapBin to support stdin.

	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.