correct syntax for fix setup call and barcode adjust

#barcode and umi lengths given by options

barcodelength=""

if [[ $verbose ]]; then

    echo "barcodelength before $barcodelength"

fi

umilength=""

minlength=""

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

    barcodelength=19 

    umilength=6

    minlength=16

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

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

    barcodelength=11

    umilength=6

    minlength=8

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

#adjustment lengths

if [[ $verbose ]]; then

   echo "barcode length: $barcodelength"

   echo "barcode default: $barcode_default"

fi

barcodeadjust=`echo $(($barcodelength-$barcode_default))`

umiadjust=`echo $(($umilength-$umi_default))`

if [[ $verbose ]]; then

   echo "barcode adjust: $barcodeadjust "

fi

if [[ $verbose ]]; then

    echo " chemisty set to ${chemistry}"

    echo " chemistry set to ${chemistry}"

fi

##########

             fi

             #Note that R2 and R1 are inverted below (thus [I1, I2]R2 or [R2, R3]R4 are converted to R1)

        done

    fi

    #checking inDrops-v3 indexes are accepted (by checking that index 2 is correct)

    ##note that index 1 will be detected as I1 OR R2

    ##note that read1 will be detected R2 or R4

    if [[ ${#index2[@]} -eq ${#read1[@]} ]] && [[ ${#index2[@]} -ge 1 ]]; then

        echo " indexes ${index1[@]} and ${index2[@]} found for ${technology}"

    else

        if [[ $setup == "false" ]]; then

            echo "ERROR: note that ${technology} expects dual indexes: I1 and I2 OR R2 and R3"

            exit 1

        fi

    fi

fi

if [[ $verbose = "true" ]]; then

    echo "${#read1[@]} read1s: ${read1[@]}"

    if [[ $verbose ]]; then

        echo "  barcodefile file exists"

    fi

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

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

        if [[ $verbose ]]; then

            echo "  ensuring all barcode within selected whitelist are in upper case"

        fi

else

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

        if [[ $verbose ]]; then

            echo "  default 10x barcoe whitelist will be used"

            echo "  default 10x barcode whitelist will be used"

        fi

    elif ! [[ "${barcodefile}" == "${whitelistdir}"* ]]; then

        echo "Error: user selected barcode file (${barcodefile}) does not exist"

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

                ${MAKEINDROPBARCODES} ${whitelistdir}/inDrop_gel_barcode1_list.txt ${whitelistdir}/inDrop_gel_barcode2_list.txt v2 ${whitelistdir}

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

                ${MAKEINDROPBARCODES} ${whitelistdir}/inDrop_gel_barcode1_list.txt ${whitelistdir}/inDrop_gel_barcode2_list.txt v3 ${whitelistdir}

                #ignore barcodes in index (R1 only)

                cp ${whitelistdir}/inDrop_gel_barcode2_list.txt ${whitelistdir}/inDrop-v3_barcodes.txt

                #${MAKEINDROPBARCODES} ${whitelistdir}/inDrop_gel_barcode1_list.txt ${whitelistdir}/inDrop_gel_barcode2_list.txt v3 ${whitelistdir}

            fi

        else

            #generating permutations of ATCG of barcode length (non-standard evaluation required to run in script)

            sed -i "s/assert barcode_idx >= prev_barcode_idx/#assert barcode_idx >= prev_barcode_idx/g" ${cellrangerpath}-cs/${cellrangerversion}/mro/stages/counter/report_molecules/__init__.py

            sed -i "s/assert np.array_equal(in_mc.get_barcodes(), barcodes)/#assert np.array_equal(in_mc.get_barcodes(), barcodes)/g" ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/molecule_counter.py

            #disable cloupe generation

            sed -i '/output_for_cloupe/s/^#//g' ${cellrangerpath}-cs/${cellrangerversion}/mro/*mro

            sed -i '/out cloupe cloupe/ {s/^#//g}' ${cellrangerpath}-cs/${cellrangerversion}/mro/*mro

#            sed -i '/output_for_cloupe/s/^/#/g' ${cellrangerpath}-cs/${cellrangerversion}/mro/*mro 

#            sed -i '/out cloupe cloupe/ {s/^/#/g}' ${cellrangerpath}-cs/${cellrangerversion}/mro/*mro

#            sed -i '/output_for_cloupe/s/^#//g' ${cellrangerpath}-cs/${cellrangerversion}/mro/*mro

#            sed -i '/out cloupe cloupe/ {s/^#//g}' ${cellrangerpath}-cs/${cellrangerversion}/mro/*mro

            sed -i '/output_for_cloupe/s/^/#/g' ${cellrangerpath}-cs/${cellrangerversion}/mro/*mro 

            sed -i '/out cloupe cloupe/ {s/^/#/g}' ${cellrangerpath}-cs/${cellrangerversion}/mro/*mro

        fi

        echo " ${cellrangerpath} set for $technology"

    fi

        echo " backup generated"

    fi

    #convert whitelist to the apropriate barcode

    #convert whitelist to the appropriate barcode

    echo " converting whitelist"

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

        #for version 2

    else

        #for version 2

        cat ${barcodefile} > ${v2}

        echo "barcode adjust: $barcodeadjust "

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

            sed -i "s/^.{${barcodeadjust}}//" ${v2} #Trim the first n characters from the beginning of the sequence and quality

        elif [[ 0 -gt $barcodeadjust ]]; then

            As=`printf '%0.sA' $(seq 1 $(($barcodeadjust * -1)))`

            echo As: $As

            sed -i "s/^/$As/" ${v2} #Trim the first n characters from the beginning of the quality

        fi

        #for version 3