Base Quality Thresholding
Hello!  This tool is pretty cool, definitely faster than the one I wrote for Python a while back.  Anyways, I'm wondering about computing a Q30% value per BED interval.  This would essentially be the number of bases in a particular region with at least phred base quality of 30 divided by the total number of bases in the region.  Similar to your threshold option, I could see this as a raw count of the number of times this happens, leaving the final division to the end user.  Thoughts on this?