Merge branch 'fix-short-custom-bcs' of github.com:TomKellyGenetics/universc...

    echo " setting whitelist barcode file."

fi

custombarcodes=false

if [[ -n "$barcodefile" ]]; then

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

        echo "Error: File selected for option --barcodefile does not exist"

    else

        #getting absolute path

        barcodefile=$(readlink -f $barcodefile)

        custombarcodes=true

        #allowing WellList from ICELL8 and other well-based techniques

        if [[ "$technology" == "icell8" ]] || [[ "$technology" == "quartz-seq2*" ]] || [[ "$technology" == "splitseq" ]] || [[ "$technology" == "smartseq*" ]] || [[ "$technology" == "seqwell" ]] || [[ "$technology" == "sciseq" ]] || [[ "$technology" == "custom" ]]; then

            seg=$'\t'

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

        done

    fi

    #check for custom whitelist

    if [[ $custombarcodes == "true" ]]; then

        #disable detect chemistry check for custom whitelist

        if [[ $verbose ]]; then

            echo "disable detect chemistry check..."

        fi

        sed -i "s/ raise NoChemistryFoundException/ return best_chem #raise NoChemistryFoundException/g" ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/chemistry.py

        sed -i "s/ (100\.0 \* best_frac/ #(100.0 * best_frac/g" ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/chemistry.py

    else

         if [[ $verbose ]]; then

             echo "restore detect chemistry check..."

        fi

        #restore detect chemistry check for custom whitelist

        sed -i "s/ return best_chem \#raise NoChemistryFoundException/ raise NoChemistryFoundException/g" ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/chemistry.py

        sed -i "s/ \#(100\.0 \* best_frac/ (100.0 * best_frac/g" ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/chemistry.py

    fi

    echo " ${cellrangerpath} set for $technology"

    #whitelist file name