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#!/bin/sh
# autopkgtest check: Run sumatra on one single file with three sequences to
# test alignment against itself. We use a threshold of 0.5 and then a
# threshold of 0.6, and we check that
# * 3 sequences are read in the file;
# * 3 lines are output with a threshold of 0.5;
# * 1 line is output with a threshold of 1.
# (C) 2020 Pierre Gruet.
# Author: Pierre Gruet <pgt@debian.org>
set -e
WORKDIR=$(mktemp -d)
trap "rm -rf $WORKDIR" 0 INT QUIT ABRT PIPE TERM
cd $WORKDIR
cat <<EOF > input.fasta
>SEQ1
ATGTGATCAATGCTGCTAGCTGCTAGCTGCTACGCACACGTGCATCGCTGCATGCACTGCTGCTGATGCTCAGCTAG
>SEQ2
AGGTATCTCGATCGATCACTCGCATCGTGTGCTAGCTGCTAGCTGCTACGATCGCATCGC
>SEQ3
AGGTATCTCGATCGATCACTCGCATCGTGTGCTAGCTGCTAGCTGCTACGATCGCATCGC
EOF
sumatra -t 0.5 input.fasta 2>&1 | \
sed -n 's/^3.sequences//p' | \
wc -l |
grep -q "1"
if [ $? -ne 0 ]; then
exit 1
fi
sumatra -t 0.5 input.fasta 2>&1 | \
sed -n 's/^SEQ.*SEQ//p' | \
wc -l |
grep -q "3"
if [ $? -ne 0 ]; then
exit 1
fi
sumatra -t 0.6 input.fasta 2>&1 | \
sed -n 's/^SEQ.*SEQ//p' | \
wc -l |
grep -q "1"
if [ $? -ne 0 ]; then
exit 1
fi
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