1. Assumes stdin when no -i is given.  Credit = Assaf Gordon
	2. New freqasc and freqdesc options.
	3. Better command line parsing.  Credit = Assaf Gordon.

	1. Added new version of BamTools supporting uncompressed BAM.
	2. Added -ubam option to intersectBed.
	3. First functional release of annotateBed.
	4. Updated GetEditDistance calls to GetTag(NM) per the new API change in BamTools.

	1. Fixed bug where an extra tab is inserted prior to \n in the report*Newline methods.
	2. Fixed bug causing incorrect behavior when first bed feature has stant and end = 0.

Tweaks to processHits in intersectBed for speed.

	The overlap variable was a CHRPOS.  The negative overlaps were reported as positive causing
        false hits when using BAM input.