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#!/bin/bash
cmd="$@"
interleaved_file=`echo $cmd | sed -n 's/.*--interleaved\s\+\(\S\+\)\s\+.*/\1/p'`
if [ -z "$interleaved_file" ]
then
#Run normally in this branch
${@}
else
new_cmd=`echo $cmd | sed 's/--interleaved\s\+\S\+\s\+//'`
tmpdir=$(mktemp -d)
# Cleanup on exit
trap 'rm -rf "$tmpdir"' EXIT INT TERM HUP
p1="$tmpdir/p1.fq"
p2="$tmpdir/p2.fq"
mkfifo $p1
mkfifo $p2
# The following interleaved to split conversion is courtesy of
# https://gist.github.com/nathanhaigh/3521724
(paste - - - - - - - - | tee >(cut -f 1-4 | tr '\t' '\n' > $p1) | cut -f 5-8 | tr '\t' '\n' > $p2) < $interleaved_file &
echo "Running command [${new_cmd} -1 $p1 -2 $p2]"
${new_cmd} -1 $p1 -2 $p2
fi
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