account for longer UMI than compatible while preserving R1 for 5' chemistry

            echo "  ${convFile} adjusted"

        done

    fi

    # check if original UMI is longer than default

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

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

            echo " handling $convFile ..."

            #compute length of adjusted barcode + original UMI

            targetlength=`echo $((${barcode_default}+${umi_default}))`

            #Remove n characters to the end of the sequence and quality score

            sed -E "2~2s/(.{$targetlength})(.{$umiadjust})(.*)/\1\3/"  $convFile > ${crIN}/.temp

            mv ${crIN}/.temp $convFile

            echo "  ${convFile} adjusted"

        done

    fi

fi

##########