alter cellranger chemistry parameters

            eval "sed -i '$(echo "${num},${num2}s/^/#/g")' $file"

        done

    fi

    #determine last barcode and UMI

    if [[ lastcall_b == "" ]]; then

        old_bc_length=16

    else

        old_bc_length=$lastcall_b

    fi

    if [[ lastcall_u == "" ]]; then

       old_umi_length=10

    else

       old_umi_length=$lastcall_u

    fi

    # 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

    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

    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

    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

    fi

    echo " ${cellrangerpath} set for $technology"

    #whitelist file name