skip conversion

LANE=$(echo "${LANE[@]}" | tr ' ' '\n' | sort -u | tr '\n' ',' | sed 's/,$//')

if [ convert ]

then

#create directory of modified files

echo "    creating a folder for all cellranger input files..."

crIN="cellranger"

    fi

done

if [[ $convert ]]

then

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

    echo "    10x files accepted without conversion"

else

    for fq in "${crR1s[@]}"; do

        echo "        handling $fq"

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

            echo "        converting barcodes of"

            echo "        converting barcodes"

            sed -i '2~4s/^/AAAA/' ${crIN}/$fq #Add AAAA to every read

            echo "        converting quality scores"

            sed -i '4~4s/^/IIII/'  ${crIN}/$fq #Add quality scores for added bases