set up SCI-Seq barcode whitelist

            barcodefile=${whitelistdir}/inDrop-v3_barcodes.txt

            echo "***WARNING: ***combination of list1 and list2 from indrop-v2 (https://github.com/indrops/indrops/issues/32)***"  

        fi

    elif [[ "$technology" == "sciseq" ]]; then

             barcodefile=${whitelistdir}/sciseq3_barcode.txt

             if [[ ! -f ${whitelistdir}/sciseq3_barcode.txt ]]; then

                 echo "  ...generating combination of I1, I2, and RT barcodes..."

             fi

    elif [[ "$technology" == "smartseq3" ]]; then

        barcodefile=${whitelistdir}/SmartSeq3_barcode.txt

    else

                #allow for barcodes in index (I1) and R1

                perl ${MAKEINDROPBARCODES} ${whitelistdir}/inDrop_gel_barcode1_list.txt ${whitelistdir}/inDrop_gel_barcode2_list.txt v3 ${whitelistdir}

            fi

        elif [[ "$technology" == "sciseq" ]]; then

             #generates all combinations of I1-I2-R1 barcodes

             join -j 9999 ${whitelistdir}/sci-seq3_i5_barcodes.txt ${whitelistdir}/sci-seq3_i7_barcodes.txt | join -j 9999 - ${whitelistdir}/sci-seq3_rt_barcodes.txt | sed "s/ //g"  > ${whitelistdir}/sciseq3_barcode.txt

        else

            #generating permutations of ATCG of barcode length (non-standard evaluation required to run in script)

            echo $(eval echo $(for ii in $(eval echo {1..${barcodelength}}); do echo "{A,T,C,G}"; done | tr "\n" " " | sed "s/ //g" | xargs -I {} echo {})) | sed 's/ /\n/g' | sort | uniq > ${barcodefile}

    fi

    #determine last barcode and UMI

    if [[ lastcall_b == "" ]]; then

    if [[ $lastcall_b == "" ]]; then

        old_bc_length=16

    else

        old_bc_length=$lastcall_b

    fi

    if [[ lastcall_u == "" ]]; then

    if [[ $lastcall_u == "" ]]; then

       old_umi_length=10

    else

       old_umi_length=$lastcall_u

    fi

    old_rna_offset=`echo $((${lastcall_b}+${last_call_u}))`

    if [[ $verbose ]]; then

        echo b ${lastcall_b} u ${lastcall_u} b ${barcodelength} u ${umilength}

    fi

    old_rna_offset=`echo $((${lastcall_b}+${lastcall_u})) || 26`

    new_rna_offset=`echo $((${barcodelength}+${umilength}))`

    # convert barcodes back if last technology barcode greater than 16 bp

    if [[ $old_bc_length -gt 16 ]]; then