automate detection of I1 index and R4 read

            echo " Error: number of index1 files is not matching the number of R1 and R2 files"

            echo " either give no index1 file, or give index1 file for each and every read1 file"

            exit 1

        else

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

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

            i1_list=()

            for j in ${!r1_list[@]}; do

                read=${r1_list[$j]}

                R1_file=$read

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

                R4_file=$(echo $indexfile | perl -pne 's/(.*)_R1/$1_R4/' )

                I1_file=$(echo $indexfile | perl -pne 's/(.*)_R1/$1_I1/' )

                if [[ -f $R4_file ]] || [[  -f $(find $(dirname ${read}) -name $(basename ${R4_file})'*.gz') ]] || [[  -f $(find $(dirname ${read}) -name $(basename ${R4_file})'*.fastq') ]] || [[  -f $(find $(dirname ${read}) -name $(basename ${R4_file})'*.fq') ]]; then

                    if [[ $verbose ]]; then

                        echo "file $R4_file found, replacing $R1_file ..." 

                    fi

                    r1_read=$R4_file

                    r1_list[$j]=$r1_read

                    if [[ $verbose ]]; then

                        echo "file $R1_file found, replacing $R2_file ..."

                    fi

                    r2_read=$R1_file

                    r2_list[$j]=$r2_read

                    if [[ $verbose ]]; then

                         echo "file $R2_file found, replacing $I1_file ..."

                    fi

                    i1_read=$R2_file

                    i1_list[$j]=$i1_read

                fi

                if [[ -f $I1_file ]] || [[  -f $(find $(dirname ${read}) -name $(basename ${I1_file})'*.gz') ]] || [[  -f $(find $(dirname ${read}) -name $(basename ${I1_file})'*.fastq') ]] || [[  -f $(find $(dirname ${read}) -name $(basename ${I1_file})'*.fq') ]]; then

                    if [[ $verbose ]]; then

                         echo "file $I1_file found..."

                    fi

                    i1_read=$I1_file

                    i1_list[$j]=$i1_read

                fi

            done

            read1=("$r1_{list[@]}")

            read2=("$r2_{list[@]}")

            if [ ${#i1_list[@]} -eq 0 ]; then

                if [[ $verbose ]]; then

                    echo "No index files found"

                fi

            else

            if [ ${#i1_list[@]} -eq 0 ]; then

                 if [[ $verbose ]]; then

                     echo "echo "  index files found ${#index1[@]} I1s: ${index1[@]}"

                 fi

            fi

        fi

    fi

fi