refactor inDrops-v3 R1-R4 barcode handling to check whether I1 and I2 detected

# check for indexes in R2 and R3 (R1 -> R2; R2 -> I1; R3 -> I2; R4 -> R1)

if [[ "$technology" == "indrop-v3" ]]; then

    if [[ ${#index2[@]} -eq ${#read1[@]} ]] && [[ ${#index2[@]} -ge 1 ]]; then

        echo " index I1 and I2 found for ${technology}"

    if [[ ${#index1[@]} -eq ${#read1[@]} ]] && [[ ${#index1[@]} -ge 1 ]]; then

        echo " index I1 found for ${technology}"

    else

        #checking for R2 and R3 index files

        echo " checking for index R2 and R3 files..."

        echo " checking for index I1 in R2 files..."

        for ii in $(seq 1 1 ${#read1[@]}); do

             #iterate over read1 inputs

             indexfile=${read1[$(( $ii -1 ))]}

             #derive I1 filename from R1 filename

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

             #only add index1 files to list variable if file exists

             #only add index2 files to list variable if file exists (this will only run if I1 not found above)

             if [[ -f $indexfile ]] || [[ -f ${indexfile}.gz ]] || [[ -f $indexfile.fastq ]] || [[ -f ${indexfile}.fastq.gz ]] || [[ -f $indexfile.fq ]] || [[ -f ${indexfile}.fq.gz ]]; then

                 index1+=("$indexfile")

             fi

        done

    fi

    if [[ ${#index2[@]} -eq ${#read1[@]} ]] && [[ ${#index2[@]} -ge 1 ]]; then

        echo " index I2 found for ${technology}"

    else

        #checking for R2 and R3 index files

        echo " checking for index I2 in R3 files..."

        for ii in $(seq 1 1 ${#read1[@]}); do  

             #iterate over read1 inputs

             indexfile=${read1[$(( $ii -1 ))]}

             #derive I2 filename from R1 filename

             indexfile=$(echo $indexfile | perl -pne 's/(.*)_R1/$1_R3/' )

             #only add index2 files to list variable if file exists

             #only add index2 files to list variable if file exists (this will only run if I2 not found above)

             if [[ -f $indexfile ]] || [[ -f ${indexfile}.gz ]] || [[ -f $indexfile.fastq ]] || [[ -f ${indexfile}.fastq.gz ]] || [[ -f $indexfile.fq ]] || [[ -f ${indexfile}.fq.gz ]]; then

                 index2+=("$indexfile")

             fi

        done

     fi

     #checking for R1 and R4 index files

        echo " checking for read R4 files..."

        for ii in $(seq 1 1 ${#read1[@]}); do

             #iterate over read1 inputs

             indexfile=${read1[$(( $ii -1 ))]}

             #derive I2 filename from R1 filename

             indexfile=$(echo $indexfile | perl -pne 's/(.*)_R1/$1_R4/' )

             #only replace R2 files with R4 variable if file exists

             #only replace R2 files with R4 variable if R4 file exists (otherwise keep R2)

             if [[ -f $indexfile ]] || [[ -f ${indexfile}.gz ]] || [[ -f $indexfile.fastq ]] || [[ -f ${indexfile}.fastq.gz ]] || [[ -f $indexfile.fq ]] || [[ -f ${indexfile}.fq.gz ]]; then

                 read2[$(( $ii -1 ))]=("$indexfile")

             fi

             #Note that R2 and R1 are inverted below (thus [I1, I2]R2 or [R2, R3]R4 are converted to R1)

        done

    fi

    #checking inDrops-v3 indexes are accepted (by checking that index 2 is correct)

    ##note that index 1 will be detected as I1 OR R2

    ##note that read1 will be detected R2 or R4

    if [[ ${#index2[@]} -eq ${#read1[@]} ]] && [[ ${#index2[@]} -ge 1 ]]; then

        echo " indexes ${index1[@]} and ${index2[@]} found for ${technology}"

    else

        echo "ERROR: note that ${technology} expects dual indexes: I1 and I2 OR R2 and R3"

        exit 1

    fi

fi

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