Some minore changes to ad hocs and new split bam ad hoc
Added Quality Score distribution to script
Added lines to generate the collation directories AllBamsDir and RrBamsDir
Adjusted script to generate hg19 and b37 format bed files (i.e. at chr to hg19)
Added option to allow misencoded quality scores
Additions and adjustments to accommodate hg19 format (chr)
Deleted unwanted annotation scripts. Adjusted names to remove BISR