#! /bin/bash

test $# = 2 || {
    cat <<EOF
Usage: $0 x.fastq y.fastq
or:    $0 x.fastq.gz y.fastq.gz

Read 2 fastq files, and write them interleaved.  Keep just the first
word of header lines, and append "/1" and "/2" if they are otherwise
identical.  Assumes 1 fastq per 4 lines, i.e. no line wrapping.
EOF
    exit
}

fastqTab () {
    gzip -cdf "$@" |
	sed -e 's/^@  */@/' -e 's/ .*//' |
	paste - - - -
}

paste <(fastqTab "$1") <(fastqTab "$2") |
    awk '$1 == $5 {$1 = $1 "/1"; $5 = $5 "/2"} $1 = $1' OFS="\n"
