generate automatic whitelist of barcode length for custom inputs

    elif [[ "$technology" == "nadia" ]]; then

        barcodefile=${SDIR}/nadia_barcode.txt

        if [[ ! -f ${barcodefile} ]]; then

            #creat a nadia barcode file

            #create a nadia barcode file

            echo "No barcodes whitelists available for Drop-Seq or Nadia: all possible barcodes accepted (valid barcodes will be 100% as a result)"

            echo {A,T,C,G}{A,T,C,G}{A,T,C,G}{A,T,C,G}{A,T,C,G}{A,T,C,G}{A,T,C,G}{A,T,C,G}{A,T,C,G}{A,T,C,G}{A,T,C,G}{A,T,C,G} | sed 's/ /\n/g' | sort | uniq > ${barcodefile}

        fi

    elif [[ "$technology" == "icell8" ]]; then

        barcodefile=${SDIR}/iCell8_barcode.txt

    elif [[ "$technology" != "custom"* ]]; then

        custom=`echo $technology | grep -o "_" | wc -l`

        custom=$(($custom+1))

        customname=`echo $technology | cut -f1-$((${custom}-2))  -d'_'`

        barcodelength=`echo $technology | cut -f$((${custom}-1))  -d'_'`

        #check whether barcodes exceed 16bp (and reuse 16bp whitelist for all greater than 16bp)

        if [[  $barcodelength -ge 16 ]]; then

            echo "Barcode length ($barcodelength) of 16 or more:"

            echo "    ...using barcode whitelist of 16bp"

        fi

        minlength = `echo $(( $barcodelength < 16 ? $barcodelength : 16 ))`

        # compute custom barcodes if barcode length is different

        barcodefile=${SDIR}/${customname}_${minlength}_barcode.txt

        if [[ ! -f ${barcodefile} ]]; then

            echo "No barcodes whitelists available for ${customname}: all possible barcodes accepted (valid barcodes will be 100% as a result)"

            echo "***Warning: giving a barcode whitelist --barcodefile is recommended where available.***"

            if [[ -f ${SDIR}/*${barcodelength}_barcode.txt ]]

                pregeneratedfile=`ls ${SDIR}/*${barcodelength}_barcode.txt | awk '{print $1;}' | head -n 1`

                echo "$pregeneratedfile for barcode(${barcodelength}) generated already"

                ln -s $pregeneratedfile $barcodefile

                echo "    ...using this as $barcodefile"

            else

                echo "generating $barcodefile of barcode length $minlength"

                strings=`for ii in {1..${minlength}}

                             do

                             echo "{A,T,C,G}"

                             done |  tr "\n" " " | sed "s/ //g" | xargs -I {} echo {} | xargs -I {} echo {}`

                eval "echo ${strings}" | sed 's/ /\n/g' | sort | uniq > ${barcodefile}

            fi

        fi 

    fi

fi

    barcodelength=15

    umilength=8 

else

    barcodelength=`echo $technology | cut -f 2 -d'_'`

    umilength=`echo $technology | cut -f 3 -d'_'`

    custom=`echo $technology | grep -o "_" | wc -l`

    custom=$(($custom+1))

    barcodelength=`echo $technology | cut -f$((${custom}-1))  -d'_'`

    umilength=`echo $technology | cut -f$((${custom}))  -d'_'`

fi

#adjustment lengths