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#!/bin/sh
# autopkgtest check: Run test data through Gubbins
# Author: Sascha Steinbiss <satta@debian.org>
set -e
TESTDIR=$(pwd)/tests/data
WORKDIR=$(mktemp -d)
HOME="$WORKDIR"
export HOME
trap "rm -rf $WORKDIR" 0 INT QUIT ABRT PIPE TERM
cd $WORKDIR
cp $TESTDIR/*aln .
for f in alignment_file_multiple_lines_per_sequence.aln alignment_file_one_line_per_sequence.aln alignment_file_with_n.aln multiple_recombinations.aln no_recombinations.aln one_recombination.aln; do
echo "##### $f #####"
cp $TESTDIR/$f .
run_gubbins $f
done
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