update directories for compatibility

barcodedir=${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/barcodes #folder within cellranger with the whitelist barcodes

if [[ $(echo "${cellrangerversion} 4.0.0" | tr " " "\n" | sort -V | tail -n 1)  == ${cellrangerversion} ]]; then

    barcodedir=$(dirname /home/tom/local/bin/cellranger-4.0.0/cellranger)/lib/python/cellranger/barcodes

    mkdir -p $(dirname /home/tom/local/bin/cellranger-4.0.0/cellranger)/${cellrangerpath}-cs/${cellrangerversion}

    ln -sf $(dirname /home/tom/local/bin/cellranger-4.0.0/cellranger)/mro/rna $(dirname /home/tom/local/bin/cellranger-4.0.0/cellranger)/${cellrangerpath}-cs/${cellrangerversion}/mro

fi

barcodefile=""

crIN=input4cellranger #name of the directory with all FASTQ and index files given to cellranger

        cat ${v2} > ${v3}

        gzip -f ${v3}

        rm translation/${v3}.gz

        ln -s ${v3}.gz translation/${v3}.gz

        ln -s ../${v3}.gz translation/${v3}.gz

    fi

    echo " whitelist converted"