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#! /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"
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