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.

	- 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. Can parse CIGAR string.
	2. Output looks roughly correct.  Need to continue testing.

	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. Added the -wo option to intersectBed.
	2. Added the -s option to fastaFromBed.

	Now using a map to track the unique names of the features in a merged block.
	The consequence is that names will not be reported in the order they were added.