use full paths only for custom barcodes and handle all_barcodes across projects

        read1=("${SDIR}/test/shared/mappa-test/test_FL_R1.fastq")

        read2=("${SDIR}/test/shared/mappa-test/test_FL_R2.fastq")

    else

        echo "Error: for test run, option --technology must be 10x, nadia, or icell8"

        echo "Error: option -t needs to be a technology listed or custom_<barcode>_<UMI>"

	exit 1

    fi

fi

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

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

        if ! [[ "$b" =~ ^[0-9]+$ ]] || ! [[ "$u" =~ ^[0-9]+$ ]]; then

            echo "Error: option -t needs to be 10x, nadia, icell8, or custom_<barcode>_<UMI>"

            echo "Error: option -t needs to be a technology listed or custom_<barcode>_<UMI>"

            exit 1

        fi

        if [[ -z $barcodefile ]]; then

        barcodefile=`readlink -f $barcodefile`

        #all barcodes upper case

        sed -i 's/.*/\U&/g' $barcodefile

        #full path for custom barcodes

        current_barcode=$barcodefile

    fi

else

    if [[ "$technology" == "10x" ]]; then

        barcodefile="default"

        barcodefile="default:10x"

        current_barcode=$barcodefile

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

        barcodefile=${SDIR}/nadia_barcode.txt

        barcodefile=${SDIR}/all_barcodes_12bp.txt

        if [[ ! -f ${SDIR}/nadia_barcodes.txt ]]; then

            ln -s ${SDIR}/all_barcodes_12bp.txt ${SDIR}/nadia_barcodes.txt

        fi

        current_barcode="default:all_barcodes_12bp.txt"

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

            #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)"

        fi

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

        barcodefile=${SDIR}/iCell8_barcode.txt

        current_barcode="default:iCell8_barcode.txt"

    elif [[ "$technology" == "indrop-v1" ]] || [[ "$technology" == "indrop-v2" ]]; then

        # use bustools whitelist for inDrops-v2 with adapters removed https://github.com/BUStools/bustools/issues/4 

        barcodefile=${SDIR}/inDrops_barcodes.txt

        current_barcode="default:inDrops_barcodes.txt"

    elif [[ "$technology" == "indrop-v3" ]]; then

        # inDrops-v3 whitelist is a combination of v2 whitelists https://github.com/indrops/indrops/issues/32

        ## version 2 whitelist will be used until dual indexing (i7) is supported for read I2: https://github.com/alexdobin/STAR/issues/825

        barcodefile=${SDIR}/inDrops-v2_barcodes.txt

        current_barcode="default:inDrops-v2_barcodes.txt"

    elif [[ "$technology" == "quartz-seq2-384" ]]; then

        barcodefile=${SDIR}/Quartz-Seq2-384_barcode.txt

        current_barcode="default:Quartz-Seq2-384_barcodes.txt"

    elif [[ "$technology" == "quartz-seq2-1536" ]]; then

        barcodefile=${SDIR}/Quartz-Seq2-1536_barcode.txt

        current_barcode="default:Quartz-Seq2-1536_barcodes.txt"

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

        echo "***WARNING: barcodes not available for Smart-Seq 2 or 3, using iCELL8 whitelist (version 3)***"

        echo "...valid barcodes may be an overestimate"

        barcodefile=${SDIR}/iCell8_barcode.txt

        current_barcode="default:iCell8_barcode.txt"

    elif [[ "$technology" == "custom"* ]] || [[ "$technology" == "celseq"* ]] ||  [[ "$technology" == "sciseq" ]] || [[ "$technology" == "scrbseq" ]] || [[ "$technology" == "seqwell" ]] || [[ "$technology" == "surecell" ]]; then

        if [[ "$technology" == "celseq" ]]; then

            customname="celseq"

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

        fi

        # compute custom barcodes if barcode length is different

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

        barcodefile=${SDIR}/all_barcodes_${minlength}bp.txt

        if [[ ! -f ${SDIR}/${customname}_barcodes.txt ]]; then

            ln -s ${SDIR}/all_barcodes_${minlength}bp.txt ${SDIR}/${customname}_barcodes.txt

        fi

        current_barcode=`echo "default:all_barcodes_${minlength}bp.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 ]]; then

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

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

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

                ln -s $pregeneratedfile $barcodefile

                echo "    ...using this as $barcodefile"

    fi

fi

#full path for other barcodes

if [[ -z $current_barcode ]]; then

    current_barcode=$barcodefile

fi

#check if reference is present

if [[ -z $reference ]]; then

    if [[ $setup == "false" ]] || [[ ${#read1[@]} -ne 0 ]] || [[ ${#read2[@]} -ne 0 ]]; then

	    echo " total of $lock cellranger ${cellrangerversion} jobs are already running in ${cellrangerpath} with barcode length (${lastcall_b}), UMI length (${lastcall_u}), and whitelist barcodes (${lastcall_p})"

	    #check if a custom barcode is used for a run (which cannot be run in parallel)

            if [[ ${barcodelength} == ${lastcall_b} ]] && [[ ${umilength} == ${lastcall_u} ]] && [[ ${barcodefile} == ${lastcall_p} ]]; then

            if [[ ${barcodelength} == ${lastcall_b} ]] && [[ ${umilength} == ${lastcall_u} ]] && [[ ${current_barcode} == ${lastcall_p} ]]; then

                echo " call accepted: no conflict detected with other jobs currently running"

                #add current job to lock

                lock=$(($lock+1))

    #convert whitelist to the apropriate barcode

    echo " converting whitelist"

    if [[ ${barcodefile} == "default" ]]; then

    if [[ ${barcodefile} == "default:10x" ]]; then

        #for version 2

        cp ${v2}.backup ${v2}

        #for version 3

    echo " whitelist converted"

    #change last call file

    echo "${barcodelength} ${umilength} ${barcodefile}" > $lastcallfile

    echo "${barcodelength} ${umilength} ${current_barcode}" > $lastcallfile

    cd - > /dev/null

#####Readjusting the barcodes in the cellranger output back to its original state##### 

if [[ ${barcodefile} != "default" ]]; then

if [[ ${barcodefile} != "default:10x" ]]; then

    echo "replacing modified barcodes with the original in the output gene barcode matrix"

    perl ${BARCODERECOVER} ${barcodefile} ${barcodeadjust} ${id}

    echo "barcodes recovered"