replace UMI with work (removes hardcoded barcode length)

             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

             cmd=$(echo 'sed -E "

                             /^(.{'$barcodelength'})(.{'${umilength}'})(.*)/ {

                            s/^(.{'$barcodelength'})(.{'${umilength}'})(.*)/\1\3/g

                            n

                            n

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

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

                mv ${crIN}/.temp $convFile

                            s/^(.{'$barcodelength'})(.{'${umilength}'})(.*)/\1\3/g

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

                         mv ${crIN}/.temp $convFile')

            if [[ $verbose ]]; then

                 echo technology $technology

                 echo barcode: $barcodelength

                 echo umi: $umilength

                 echo $cmd

             fi

             eval $cmd

             # 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

             mv $crIN/mock_UMI.fastq ${convR1}

        fi

    fi

    fi

    #UMI

    echo " adjusting UMIs of R1 files"