Bug fixes.

    echo "cellranger command is not found."

    exit 1

fi

ver_info=`paste -d "\n" <(cellranger count --version) <(echo conversion script version 0.3.0.9001) | head -n 3 | tail -n 2`

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

##########

fi

#check if cellranger is writable

if [[ ! -w $barcodedir ]]; then

if ! [[ -w "$barcodedir" ]]; then

    echo "Kai $barcodedir"

    echo "Error: Trying to run cellranger installed at ${cellrangerpath}"

    echo "launch_universc.sh can only run with cellranger installed locally"

    echo "Install cellranger in a directory with write permissions such as /home/`whoami`/local and export to the PATH"

    echo " `whereis cellranger`"

    exit 1

fi

exit 0

#check if technology matches expected inputs

if [[ "$technology" != "10x" ]] && [[ "$technology" != "nadia" ]] && [[ "$technology" != "icell8" ]]; then

    if [[ "$technology" != "custom"* ]]; then

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

            #create an iCell8 barcode file by copying from convert repo

            cat ${SDIR}/iCell8_barcode.txt > $barcodefile

            sed -i 's/^/AAAAA/g' ${barcodefile} | sort | uniq > $barcodefile

            sed -i 's/^/AAAAA/g' ${barcodefile}

	    sort -u -o ${barcodefile} ${barcodefile}

        fi

    fi

elif [[ ! -z $barcodefile ]]; then

            echo " total of $lock cellranger ${cellrangerversion} jobs already running in ${cellrangerpath} with technology $lastcall"

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

            if [[ $lastcall == "custom"* ]]; then

            if [[ $lastcall == "custom" ]]; then

                echo "Error: cellranger is currently running with a custom barcode list"

                echo "other jobs cannot be run until the current job is complete"

                echo "remove $lockfile if $lastcall jobs have completed or aborted"

    #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" ]]; then

            #restore functions if other technology run previously

            if [[ $lastcall != $technology ]]; then

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

            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

                echo " ${cellrangerpath} restored for $technology"

            else

                echo " ${cellrangerpath} ready for $technology"

            fi

        else

            #disable functions if 10x technology run previously

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

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

            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" ${cellrangerpath}-cs/${cellragerversion}/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

                echo " ${cellrangerpath} restored for $technology"

            else

                echo " ${cellrangerpath} ready for $technology"

        fi

        echo " ${cellrangerpath} set for $technology"

    fi

    #generate backup for the default 10x whitelist

    if [[ ! -f 737K-august-2016.txt.backup ]] || [[ ! -f 3M-february-2018.txt.backup.gz ]]; then

        echo " generating backups for default 10x whitelist"

        cp -f 737K-august-2016.txt 737K-august-2016.txt.backup

       	cp -f 3M-february-2018.txt.gz 3M-february-2018.txt.backup.gz

        echo " backup generated"

    fi

    #restore whitelist for 10x compatibility

    echo " restoring whitelist for 10x compatibility"

    if [[ -f nadia_barcode.txt ]] || [[ -f iCell8_barcode.txt ]] || [[ -f custom_barcodes.txt ]]; then

        echo " restoring 10x barcodes for version 2 kit ..."

    #convert whitelist to the apropriate barcode

    echo " converting whitelist"

    if [[ -z ${barcodefile} ]]; then

        #for version 2

        cp 737K-august-2016.txt.backup 737K-august-2016.txt

        echo " restoring 10x barcodes for version 3 kit ..."

        #for version 3

        cp 3M-february-2018.txt.backup.gz 3M-february-2018.txt.gz

    else

        cp 737K-august-2016.txt 737K-august-2016.txt.backup

       	cp 3M-february-2018.txt.gz 3M-february.txt.backup.gz

    fi

    echo " whitelist restored for 10x compatibility with version 2 kit and version 3 kit"

    #converting whitelist for specific barcode file

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

        echo "converting whitelist for the selected custom barcode list"

        #for version 2

        cat $barcodefile > 737K-august-2016.txt

        #for version 3

        if [[ -f 3M-february-2018.txt.gz ]] && [[ -d translation ]]; then

            rm 3M-february-2018.txt.gz

            cp 737K-august-2016.txt 3M-february-2018.txt

        cat 737K-august-2016.txt > 3M-february-2018.txt

        gzip -f 3M-february-2018.txt

        rm translation/3M-february-2018.txt.gz

        ln -s 3M-february-2018.txt.gz translation/3M-february-2018.txt.gz

    fi

    echo " whitelist converted"

    fi

    #change last call file

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

echo " adjusting UMIs of R1 files"

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

    for convFile in "${convFiles[@]}"; do

<<<<<<< HEAD

<<<<<<< HEAD

        toS=`printf '%0.sA' $(seq 1 $(($umiadjust * -1)))`

        toQ=`printf '%0.sI' $(seq 1 $(($umiadjust * -1)))`

	keeplength=`echo $((${barcode_default}+${umi_default}-($umiadjust * -1)))`

	sed -i "2~2s/^\(.\{${keeplength}\}\).*/\1/" $convFile #Trim off everything beyond what is needed

        sed -i "2~4s/$/$toS/" $convFile #Add n characters to the end of the sequence

        sed -i "4~4s/$/$toQ/" $convFile #Add n characters to the end of the quality

        echo "  ${convFile} adjusted"

=======

=======

>>>>>>> 1adfb361a1bc38c600bff617ac8877ca5cc3fdaa

        echo " handling $convFile ..."

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

            echo "  converting barcodes"

            sed -i '2~4s/^/AAAA/' $convFile #Add AAAA to every read

            echo "  converting quality scores"

            sed -i '4~4s/^/IIII/' $convFile #Add quality scores for added bases

            echo "  converting UMI"

            sed -i '2~4s/[NATCG][NATCG][NATCG][NATCG]$//' $convFile #Remove last 4 bases

            echo "  converting quality scores"

            sed -i '4~4s/....$//' $convFile #Replace quality scores for last 4 bases

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

            echo "  converting barcodes"

            sed -i '2~4s/^/AAAAA/' $convFile #Add AAAAA to every read

            echo "  converting quality scores"

            sed -i '4~4s/^/IIIII/' $convFile #Add quality scores for added bases

        fi

<<<<<<< HEAD

>>>>>>> e05b998d17d2c79ec3eec9784858acde747671ae

=======

=======

        toS=`printf '%0.sA' $(seq 1 $(($umiadjust * -1)))`

        toQ=`printf '%0.sI' $(seq 1 $(($umiadjust * -1)))`

        keeplength=`echo $((${barcode_default}+${umi_default}-($umiadjust * -1)))`

        sed -i "2~4s/$/$toS/" $convFile #Add n characters to the end of the sequence

        sed -i "4~4s/$/$toQ/" $convFile #Add n characters to the end of the quality

        echo "  ${convFile} adjusted"

>>>>>>> 630f098064d4535f192e5fd4ca68bfdc6dd1d966

>>>>>>> 1adfb361a1bc38c600bff617ac8877ca5cc3fdaa

    done

fi

##########