update defaults for 10x auto chemistry and correct v3 detection

        #use SC3Pv2 (umi length 10)

        echo "Using 10x version 2 chemistry to support UMIs"

        chemistry="SC3Pv2"

        umi_default=10

    elif [[ "$chemistry" != "auto" ]];then

        #use automatic chemistry detection

        echo "Detecting 10x chemistry automatically"

        chemistry="auto"

        #do not convert UMI

        umi_default=12

        umilength=${umi_default}

        umiadjust=0

    fi

    if [[ "$chemistry" != "threeprime" ]] && [[ "$chemistry" != "fiveprime" ]] && [[ "$chemistry" != "SC3Pv1" ]] && [[ "$chemistry" != "SC3Pv2" ]] && [[ "$chemistry" != "SC3Pv3" ]] && [[ "$chemistry" != "SC5P-PE" ]] && [[ "$chemistry" != "SC5P-R1" ]] && [[ "$chemistry" != "SC5P-R2" ]]; then

       echo "Error: option --chemistry must be SC3Pv3, SC3Pv2, SC5P-PE, SC5P-R1, or SC5P-R2"

        fi

        if [[ -f translation/${v3}.gz ]]; then

            rm translation/${v3}.gz

            zcat ${v3}.gz | awk -F , -v OFS="\t" '{print $1, "\t", $1}' > translation/${v3}

            zcat ${v3}.gz | awk -F , -v OFS="\t" '{print $1, "\t\t\t", $1}' > translation/${v3}

            gzip -f translation/${v3}

        fi

    echo " whitelist converted"