define UMI subroutine

    #UMI

    echo " adjusting UMIs of R1 files"

    # check if original UMI is shorter than default

    if [[ 0 -gt $umiadjust ]]; then

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

            echo " handling $convFile ..."

            toQ=`printf '%0.sI' $(seq 1 $(($umiadjust * -1)))`

            #compute length of adjusted barcode + original UMI

            keeplength=`echo $((${barcode_default}+${umi_default}-($umiadjust * -1)))`

            if [[ $chemistry != "SC5P"* ]] && [[ $chemistry != "five"* ]]; then

                echo "UMI trimming disabled"

                #sed -i "2~2s/^\(.\{${keeplength}\}\).*/\1/" $convFile #Trim off everything beyond what is needed

            fi

            #Add n characters to the end of the sequence

            sed -E "2~4s/(.{$keeplength})(.*)/\1$toS\2/"  $convFile > ${crIN}/.temp

            mv ${crIN}/.temp $convFile