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.