minor bug fixes

#####Input file curation 2: Check R1, R2, I1, and I2 files for their extensions#####

##allows incomplete file names and processing compressed files

if [[ $verbose ]]; then

    echo "key: ${keys[@]}"

fi

for key in ${keys[@]}; do

    readkey=$key

    list=()

    read12=("${read1[@]}" "${read2[@]}" "${index1[@]}")

fi

if [[ $verbose ]]; then

    echo "reads:" ${read12[@]}

fi

for fq in "${read12[@]}"; do

    if [[ $verbose ]]; then

        echo "read: $fq"

    fi

    name=`basename $fq`

    name=${name%.*}

    fields=`echo ${name} | grep -o "_" | wc -l`

	exit 1

    fi

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

       echo "SAMPLE: $SAMPLE"

       echo "sample (field): $sn"

    fi

    if [[ ${sn} != $SAMPLE ]]; then

        if [[ -z $SAMPLE ]]; then

            SAMPLE=${sn}