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.

	1. Fixed bugs in parsing command line booleans in fastaFromBed and maskFastaFromBed
	2. Added tabular output to fastaFromBed

extract beyond the length of a chromosome.

	1. If intrachromosomal, choose the leftmost end.
	2. Else, choose the first mate.

	- also added map quality as score in pairToBed