tweaks for usability with hg19/GRCh37, awk one liner style
tweaks for usability with hg19/GRCh37, awk one liner style

moved most of the logic required for compatibility into an awk one liner.
chapmanb/cloudbiolinux,chapmanb/cloudbiolinux,rchekaluk/cloudbiolinux,chapmanb/cloudbiolinux,rchekaluk/cloudbiolinux,chapmanb/cloudbiolinux,rchekaluk/cloudbiolinux,rchekaluk/cloudbiolinux