adjust UMI while preserving R1 for 5' chemistry

            echo " handling $convFile ..."

            toS=`printf '%0.sA' $(seq 1 $(($umiadjust * -1)))`

            toQ=`printf '%0.sI' $(seq 1 $(($umiadjust * -1)))`

            if [[ $chemistry == "SC5P"* ]] || [[ $chemistry == "five"* ]]; then

            #compute length of adjusted barcode + original UMI

            keeplength=`echo $((${barcode_default}+${umi_default}-($umiadjust * -1)))`

                sed -i "2~2s/^\(.\{${keeplength}\}\).*/\1/" $convFile #Trim off everything beyond what is needed

            if [[ $chemistry != "SC5P"* ]] && [[ $chemistry != "five"* ]]; then

                echo "UMI trimming disabled"

                #sed -i "2~2s/^\(.\{${keeplength}\}\).*/\1/" $convFile #Trim off everything beyond what is needed

            fi

            sed -i "2~4s/$/$toS/" $convFile #Add n characters to the end of the sequence

            sed -i "4~4s/$/$toQ/" $convFile #Add n characters to the end of the quality

            #Add n characters to the end of the sequence

            sed -E "2~4s/(.{$keeplength})(.*)/\1$toS\2/"  $convFile > ${crIN}/.temp

            mv ${crIN}/.temp $convFile

            #Add n characters to the end of the quality

            sed -E "4~4s/(.{$keeplength})(.*)/\1$toQ\2/"  $convFile > ${crIN}/.temp

            mv ${crIN}/.temp $convFile

            echo "  ${convFile} adjusted"

        done

    fi