Merge branch 'master' of dgt-gitlab.gsc.riken.jp:tom/cellranger_convert

    echo " restoring cellranger"

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

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

            #restore checking barcodes

            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

            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

            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

            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

#####process output#####

cloupefile=${SDIR}/${id}/outs/cloupe.cloupe

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

    #should not be necessary if setup is run correctly (will be omitted from Martian output)

    #this is kept to comply with the 10x End User License Agreement

    ###do not remove this code###

    if [[ -f $cloupefile ]]; then

        echo "Removing file ${cloupefile}"

        rm -rf $cloupefile

    fi

    echo "***Notice: Cloupe file cannot be computed for $technology"

    echo "           Cloupe files generated by this pipeline are corrupt"

    echo "           and cannot be read by the 10x Genomics Loupe Browser."

    echo "           We do not provide support for Cloupe files as this"

    echo "           requires software from 10x Genomics subject to their"

    echo "           End User License Agreement."

    echo "           Cloupe files are disabled in compliance with this."

fi

##########

#####remove files if convert is not running elsewhere#####

echo "updating .lock file"