test and debug toggling of long barcodes and UMIs

    fi

    if [[ $verbose ]]; then

        echo b ${lastcall_b} u ${lastcall_u} b ${barcodelength} u ${umilength}

        echo ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/chemistry.py

    fi

    old_rna_offset=`echo $((${lastcall_b}+${lastcall_u})) || 26`

    new_rna_offset=`echo $((${barcodelength}+${umilength}))`

    # convert barcodes back if last technology barcode greater than 16 bp

    if [[ $old_bc_length -gt 16 ]]; then

        sed -i "s/\'barcode_read_length\': ${old_bc_length},/\'barcode_read_length\': 16,/g" ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/chemistry.py

        sed -i "s/\'umi_read_offset\': ${old_bc_length},/\'umi_read_offset\': 16,/g" ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/chemistry.py

        if [[ $verbose ]]; then

           echo "barcode default restored to 16 bp"

        fi

        sed -i "s/'barcode_read_length': ${old_bc_length},/'barcode_read_length': 16,/g" ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/chemistry.py

        sed -i "s/'umi_read_offset': ${old_bc_length},/'umi_read_offset': 16,/g" ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/chemistry.py

    fi

    # convert UMI back if last technology UMI greater than 12 bp

    if [[ $old_umi_length -gt 12 ]]; then

        sed -i "s/\'umi_read_length\': ${old_umi_length},/\'umi_read_length\': 10/g" ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/chemistry.py

        if [[ $verbose ]]; then

           echo "umi default restored to 10 bp"

        fi

        sed -i "s/'umi_read_length': ${old_umi_length},/'umi_read_length': 10/g" ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/chemistry.py

    fi

    if [[ $old_rna_offset -gt 26 ]]; then

       sed -i "s/\'rna_read_offset\': ${old_rna_offset},/\'rna_read_offset\': 26,/g" ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/chemistry.py

       sed -i "s/\'umi_read_length\': ${old_umi_length},/\'umi_read_length\': 10/g" ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/chemistry.py

       if [[ $verbose ]]; then

           echo "RNA offset restored to 26 bp"

       fi

       sed -i "s/'rna_read_offset': ${old_rna_offset},/'rna_read_offset': 26,/g" ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/chemistry.py

       sed -i "s/'umi_read_length': ${old_umi_length},/'umi_read_length': 10/g" ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/chemistry.py

    fi

    # convert barcodes if new technology greater than 16 bp

    if [[ $minlength -gt 16 ]]; then

        sed -i "s/\'barcode_read_length\': 16,/\'barcode_read_length\': ${minlength},/g" ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/chemistry.py

        sed -i "s/\'umi_read_offset\': 16,/\'umi_read_offset\': ${minlength},/g" ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/chemistry.py

        if [[ $verbose ]]; then

            echo "barcode length set to $minlength"

        fi

        sed -i "s/'barcode_read_length': 16,/'barcode_read_length': ${minlength},/g" ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/chemistry.py

        sed -i "s/'umi_read_offset': 16,/'umi_read_offset': ${minlength},/g" ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/chemistry.py

    fi

    # convert UMI back if new technology greater than 12 bp

    if [[ $umilength -gt 12 ]]; then

        sed -i "s/\'umi_read_length\': 10,/\'umi_read_length\': ${umilength}/g" ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/chemistry.py

        if [[ $verbose ]]; then

            echo "umi length set to $umilength"

        fi

        sed -i "s/'umi_read_length': 10,/'umi_read_length': ${umilength}/g" ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/chemistry.py

    fi

    if [[ $new_rna_offset -gt 26 ]]; then

       sed -i "s/\'rna_read_offset\': 26,/\'rna_read_offset\': ${new_rna_offset},/g" ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/chemistry.py

       sed -i "s/\'umi_read_length\': 10,/\'umi_read_length\': ${umilength}/g" ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/chemistry.py

       if [[ $verbose ]]; then

           echo "RNA offset set to $new_rna_offset"

       fi

       sed -i "s/'rna_read_offset': 26,/'rna_read_offset': ${new_rna_offset},/g" ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/chemistry.py

       sed -i "s/'umi_read_length': 10,/'umi_read_length': ${umilength}/g" ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/chemistry.py

    fi

    echo " ${cellrangerpath} set for $technology"