remove and replace UMI with mock (read-only counts) for any technology

        fi

    fi

    #replace UMI with mock UMI to count reads (for technologies not already containing mock UMI)

    if [[ $technology != "icell8" ]] && [[ $technology != "ramda-seq" ]] && [[ $technology != "quartz-seq" ]] && [[ $technology != "smartseq" ]] && [[ $technology != "smartseq2" ]] && [[ $technology != "strt-seq" ]]; then

        if [[ $nonUMI ]]; then

             echo "WARNING: removing true UMI and replacing with Mock UMI"

             echo "NOTICE: results will result read counts not UMI"

             echo "## this behaviour is not recommended unless integrating with non-UMI data ##"

                            #remove inflated umi (to replace with mock and count as reads)

                sed -E '

                    /^(.{11})(.{14})(.*)/ {

                    s/^(.{11})(.{14})(.*)/\1\3/g

                    n

                    n

                    s/^(.{11})(.{14})(.*)/\1\3/g

                    }' $convFile > ${crIN}/.temp

                mv ${crIN}/.temp $convFile

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

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

                umilength=$umi_default

                umiadjust=0

                if [[ $chemistry == "SC3Pv3"]; then

                    chemistry="SC3Pv2"

                fi

                #returns a combined R1 file with barcode and mock UMI

                ## barcode, 10 bp UMI, followed by TSO (if applicable)

                mv $crIN/mock_UMI.fastq ${convR1}

            fi

        fi

    fi

    #UMI

    echo " adjusting UMIs of R1 files"

    # check if original UMI is shorter than default