correct check for cellranger >= 3.0.0

    echo "cellranger command is not found."

    exit 1

fi

cellrangerversion=`cellranger count --version | head -n 2 | tail -n 1 | cut -f2 -d'(' | cut -f1 -d')'`

cellrangerversion=$(cellranger count --version | head -n 2 | tail -n 1 | cut -f2 -d'(' | cut -f1 -d')')

##########

    #restore assert functions if cellranger version is 3 or greater

    echo " restoring cellranger"

    if [[ `printf '%s\n' '${cellrangerversion} 3.0.0' | sort -V | head -n 1` != ${cellrangerversion} ]]; then

        if [[ $technology == "10x" ]] && [[ -z $barcodefile ]]; then

    if [[ $verbose  ]]; then

        echo "${cellrangerversion}"

        echo "${cellrangerversion} 3.0.0" | tr " " "\n" | sort -V | head -n 1

    fi

    if [[ $(echo "${cellrangerversion} 3.0.0" | tr " " "\n" | sort -V | tail -n 1)  == ${cellrangerversion} ]]; then

        if [[ $verbose  ]]; then

            echo "cellranger version 3.0.0 or greater"

        fi

        if [[ ! -z $barcodefile ]] && [[ $verbose  ]]; then

            echo "barcodefile: $barcodefile"

        fi

        if [[ $technology == "10x" ]] && [[ $barcodefile == "default:10x" ]]; then

            #restore checking barcodes

            if [[ $verbose  ]]; then

                echo "restore barcode checks"

            fi

            sed -i "s/#if gem_group == prev_gem_group/if gem_group == prev_gem_group/g" ${cellrangerpath}-cs/${cellrangerversion}/mro/stages/counter/report_molecules/__init__.py

            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

            #restore cloupe generation

            if [[ $verbose  ]]; then

                echo "restore cloupe"

            fi

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

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

        elif [[ $lastcall == "10x" ]] || [[ ! -f $lastcallfile ]]; then

            #disable checking barcodes

            if [[ $verbose  ]]; then

                 echo "disable barcode checks"

            fi

            sed -i "s/if gem_group == prev_gem_group/#if gem_group == prev_gem_group/g" ${cellrangerpath}-cs/${cellrangerversion}/mro/stages/counter/report_molecules/__init__.py

            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

            if [[ $verbose  ]]; then

                echo "diasble cloupe"

            fi

#            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