implement smart-seq3 UMI filtering for all reads to convert (matched to R1)

            exit 1

        else

            if [[ $verbose ]]; then

                echo " No index files given. Automatically detecing from R1 and R2 file names..."

                echo " No index files given. Automatically detecting from R1 and R2 file names..."

            fi

            r1_list=("${read1[@]}")

            r2_list=("${read2[@]}")

               exit 1

            else

                if [[ $verbose ]]; then

                    echo " No index files given. Automatically detecing from R1 and R2 file names..."

                    echo " No index files given. Automatically detecting from R1 and R2 file names..."

                fi

                r1_list=("${read1[@]}")

                r2_list=("${read2[@]}")

    #Smart-Seq3

    if [[ "$technology" == "smartseq"* ]];then

        R2_file=$(echo $read | perl -pne 's/(.*)_R1/$1_R2/' )

        echo "Note: SmartSeq-3 requires additional dependencies, install fastq_pair and bbduk.sh and add these to the PATH"

        for convFile in "${convFiles[@]}"; do

            read=$convFile

            convR1=$read

            convR2=$(echo $read | perl -pne 's/(.*)_R1/$1_R2/' )

            convI1=$(echo $read | perl -pne 's/(.*)_R1/$1_I1/' )

            convI2=$(echo $read | perl -pne 's/(.*)_R1/$1_I2/' )

            # reads matching adapter sequence for R1

        grep -A 2 -B 1 ATTGCGCAATG test_R1.fastq  | sed '/--/d' > test_R1_umi.fastq

            grep -A 2 -B 1 ATTGCGCAATG $convR1  | sed '/--/d' > ${convR1}.umi.fastq

            #match R2 to R1 containing UMI

        fastq_pair  test_R1_umi.fastq test_R2.fastq

            fastq_pair  ${convR1}.umi.fastq $convR2

            # uses bbduk (decontamination using k=mers) from BBMap(BBTools) vesion 38.87

            # step 1: process as paired ends to match k-mers (adapters matched are filtered)

        bbduk.sh in1=test_R1.fastq in2=test_R2.fastq outu1=clean_R1.fq outu2=clean_R2.fq outm1=fail_R2.fastq outm2=fail_R1.fastq outs=pass_singletons.fq literal=ATTGCGCAATG k=10

            bbduk.sh in1=${convR1}.umi.fastq.paired.fq in2=${convR2}.paired.fq outu1=$crIN/clean_R1.fq outu2=$crIN/clean_R2.fq outm1=$crIN/fail_R2.fq outm2=$crIN/fail_R1.fq outs=$crIN/pass_singletons.fq literal=ATTGCGCAATG k=10

            # step 2: take matched (adapter filtered) reads and remove adapter (and all bases to the left)

        bbduk.sh in1=fail_R1.fq in2=fail_R2.fq out1=trimmed_R1.fq out2=trimmed_R2.fq literal=ATTGCGCAATG ktrim=l k=11

            bbduk.sh in1=$crIN/fail_R1.fq in2=$crIN/fail_R2.fq out1=$crIN/trimmed_R1.fq out2=$crIN/trimmed_R2.fq literal=ATTGCGCAATG ktrim=l k=11

            # match indexes to R1

       fastq_pair  test_R1_umi.fastq test_I1.fastq

       fastq_pair  test_R1_umi.fastq test_I2.fastq

            fastq_pair  ${convR1}.umi.fastq ${convI1}

            fastq_pair  ${convR1}.umi.fastq ${convI2}

            #replace original files

       mv test_I1.fastq.paired.fq test_I1.fastq

       mv test_I2.fastq.paired.fq test_I2.fastq

       mv trimmed_R1.fq test_R1.fastq

       mv trimmed_R2.fq test_R2.fastq

       rm *fastq.paired.fq *fastq.single.fq clean_R1.fq clean_R2.fq fail_R1.fastq fail_R2.fastq pass_singletons.fq  test_R1_umi.fastq

            mv ${convI1}.fastq.paired.fq ${convI1}

            mv ${convI2}.fastq.paired.fq ${convI2}

            mv $crIN/trimmed_R1.fq ${convR1}

            mv $crIN/trimmed_R2.fq ${convR2}

            rm $crIN/*fastq.paired.fq $crIN/*fastq.single.fq $crIN/clean_R1.fq $crIN/clean_R2.fq $crIN/fail_R1.fq $crIN/fail_R2.fq $crIN/pass_singletons.fq ${convR1}.umi.fastq

        done

    fi

    #converting barcodes