File: fastq-interleave

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#! /bin/bash

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

Read 2 fastq files, and write them interleaved.
Assumes 1 fastq per 4 lines, i.e. no line wrapping.
EOF
    exit
}

paste <(cat "$1" | paste - - - -) <(cat "$2" | paste - - - -) | tr '\t' '\n'

# Is this better?
#paste <(zcat -f "$1"|paste - - - -) <(zcat -f "$2"|paste - - - -)|tr '\t' '\n'

# This does not interpret "-" as stdin:
#paste <(paste - - - - < "$1") <(paste - - - - < "$2") | tr '\t' '\n'