add TSO with non-standard eval based on variables for Smart-Seq3

    technology="seqwell"

elif [[ "$technology" == "smartseq" ]] || [[ "$technology" == "smart-seq" ]] || [[ "$technology" == "smartseq2" ]] || [[ "$technology" == "smart-seq2" ]]; then

    technology="smartseq2"

elif [[ "$technology" == "smartseq2-umi" ]] || [[ "$technology" == "smart-seq2-umi" ]] ||  [[ "$technology" == "smartseq3" ]] || [[ "$technology" == "smart-seq3" ]]; then

    technology="smartseq"

    nonUMI=true

elif [[ "$technology" == "smartseq2-umi" ]] || [[ "$technology" == "smart-seq2-umi" ]]; then

    technology="smartseq2-umi"

    nonUMI=false

elif [[ "$technology" == "smartseq3" ]] || [[ "$technology" == "smart-seq3" ]]; then

    technology="smartseq3"

    nonUMI=false

elif [[ "$technology" == "splitseq" ]] || [[ "$technology" == "split-seq" ]]; then

    technology="splitseq"

elif [[ "$technology" == "surecell" ]] || [[ "$technology" == "surecellseq" ]] || [[ "$technology" == "surecell-seq" ]] || [[ "$technology" == "ddseq" ]] || [[ "$technology" == "dd-seq" ]] || [[ "$technology" == "bioraad" ]]; then

#index 2

if [[ $setup == "false" ]]; then

    #only check I2 for dual-indexed techniques

    if [[ "$technology" == "indrop-v3" ]] || [[ "$technology" == "sci-seq" ]] || [[ "$technology" == "smartseq" ]]; then

    if [[ "$technology" == "indrop-v3" ]] || [[ "$technology" == "sci-seq" ]] || [[ "$technology" == "smartseq"* ]]; then

        if [[ ${#index2[@]} -ne ${#read1[@]} ]]; then

            if [[ ${#index2[@]} -gt 0 ]]; then

               echo " Error: number of index1 files is not matching the number of index2 files"

            tsoS="TTTCTTATATGGG"

            tsoQ="IIIIIIIIIIIII"

            #Add 10x TSO characters to the end of the sequence

            # echo 'sed -E "4~4s/(.{$barcodelength})(.{$umilength})(.{3})/\1\2$tsoS/"  $convFile > ${crIN}/.temp'

            # sed -E "4~4s/(.{$barcodelength})(.{$umilength})(.{3})/\1\2$tsoS/"  $convFile > ${crIN}/.temp

            echo 'sed -E "2~4s/(.{16})(.{8})(.{3})(.*)/\1\2$tsoS\4/"  $convFile > ${crIN}/.temp'

            sed -E "2~4s/(.{16})(.{8})(.{3})(.*)/\1\2$tsoS\4/"  $convFile > ${crIN}/.temp

            cmd=$(echo 'sed -E "2~4s/(.{'$barcodelength'})(.{'${umilength}'})(.{3})/\1\2'$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

            # sed -E "4~4s/(.{$barcodelength})(.{$umilength})(.{3})(.*)/\1\2$tsoQ\4/"  $convFile > ${crIN}/.temp

            sed -E "4~4s/(.{16})(.{8})(.{3})(.*)/\1\2$tsoQ\4/"  $convFile > ${crIN}/.temp

            cmd=$(echo 'sed -E "4~4s/(.{'$barcodelength'})(.{'${umilength}'})(.{3})/\1\2'$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

            echo "  ${convFile} adjusted"

        done