support 5' chemistry with C1 CAGE with TSO conversion

                ## 6 bp barcode, 10 bp UMI (TSO not handled yet)

                mv $crIN/mock_UMI.fastq ${convR1}

           fi

            if [[ "$technology" == "c1-cage" ]]; then

                #convert TSO to expected length for 10x 5' (TSS in R1 from base 39)

                echo " handling $convFile ..."

                tsoS="TTTCTTATATGGG"

                tsoQ="IIIIIIIIIIIII"

                chemistry="SC5P-PE"

                #Add 10x TSO characters to the end of the sequence (removes 'NNNNNNNNTATAGGG')

                cmd=$(echo 'sed -E "2~4s/(.{'$barcodelength'})(.{'${umilength}'})(.{8})TATAGGG/\1\2'$tsoS'/" '$convFile' > '${crIN}'/.temp')

                if [[ $verbose ]]; then

                    echo technology $technology

                    echo barcode: $barcodelength

                    echo umi: $umilength

                    echo $cmd

                fi

                # run command with barcode and umi length, e.g.,: sed -E "2~4s/(.{16})(.{8})(.{3})(.*)/\1\2$tsoS\4/"  $convFile > ${crIN}/.temp

                eval $cmd

                mv ${crIN}/.temp $convFile

                #Add n characters to the end of the quality

                cmd=$(echo 'sed -E "4~4s/(.{'$barcodelength'})(.{'${umilength}'})(.{8})(.{7})/\1\2'$tsoQ'/" '$convFile' > '${crIN}'/.temp')

                # run command with barcode and umi length, e.g.,: sed -E "4~4s/(.{16})(.{8})(.{3})(.*)/\1\2$tsoQ\4/"  $convFile > ${crIN}/.temp

                eval $cmd

                mv ${crIN}/.temp $convFile

            fi

            echo "  ${convFile} adjusted"

        done

    fi