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.

	Fixed an insidious bug that caused malformed BAM output from intersectBed and pairToBed.  The previous BAM files worked fine with samtools as BAM input, but when piped in as SAM, there was an extra tab that thwarted conversion from SAM back to BAM.  Many thanks to Ivan Gregoretti for reporting this bug.  I had never used the BAM output in this way and thus never caught the bug!

	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.
	5. Greatly increased the speed of pairToBed when using BAM alignments.
	6. Fixed a bug in bamToBed when reporting edit distance from certain aligners.

	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.

Changed "notboth" logic in pairToBed when inout is BAM.
Changed "notboth" logic in pairToBed when inout is BAM.
Changed "notboth" logic in pairToBed when inout is BAM.
Changed "notboth" logic in pairToBed when inout is BAM.
Changed "notboth" logic in pairToBed when inout is BAM.
Changed "notboth" logic in pairToBed when inout is BAM.
Changed "notboth" logic in pairToBed when inout is BAM.

	1. The start and end coordinates for BED and BEDPE entries created by bamToBed are now based on the __aligned__ sequence, rather than the original sequence.  It's obvious, but I missed it originally...sorry.
	2. Fixed a bug in bamToBed that caused a crash when created BED / BEDPE from "spliced" BAM alignments.
	3. Added an error message to mergeBed preventing one from using "-n" and "-nms" together.
	4. Fixed a bug in pairToBed that caused neither -type "notispan" nor "notospan" to behave as described.

	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.

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