join I1 barcodes for Quartz-Seq and RamDA-Seq before mock UMI

    if [[ "$technology" == "quartz-seq" ]] && [[ "$technology" == "ramda-seq" ]]; then

        echo "  ...processsing for ${technology}"

        if [[ $verbose ]]; then

            echo "Note: ICELL8 v2 does not contain UMIs"

            echo "Note: ${technology} does not contain UMIs"

        fi

        for convFile in "${convFiles[@]}"; do

            read=$convFile

            convR1=$read

            convR2=$(echo $read | perl -pne 's/(.*)_R1/$1_R2/' )

            convI1=$(echo $read | perl -pne 's/(.*)_R1/$1_I1/' )

            #detect index length

            indexlength=$(($(head $I1_file -n 2 | tail -n 1 | wc -c) -1))

            barcodelength=$indexlength

            echo "  ...concatencate barcodes to R1 from I1 index files"

            # concatenate barcocdes from index to R1 as (bases 1-6 of the) barcode, moving (read to start at base 7-)

            perl sub/ConcatenateDualIndexBarcodes.pl --additive=${convI1} --ref_fastq=${convR1} --out_dir $crIN

            #returns a combined R1 file with I1-R1 concatenated (I1 is cell barcode)

            mv $crIN/Concatenated_File.fastq ${convR1}

            if [[ $nonUMI ]]; then

                # add mock UMI (count reads instead of UMI) barcodelength=16, umi_default=10

                # add mock UMI (count reads instead of UMI) barcodelength=6, umi_default=10

                perl sub/AddMockUMI.pl --fastq=${convR1} --out_dir $crIN --head_length=$barcodelength --umi_length=$umi_default

                umilength=$umi_default

                umiadjust=0

                    chemistry="SC3Pv2"

                fi

                #returns a combined R1 file with barcode and mock UMI

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

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

                mv $crIN/mock_UMI.fastq ${convR1}

            fi

        done