run_tests

#!/bin/bash

cd data

#
# Create tests
#
../simtools create --infile example.json --outfile test.sim --man_file example.bpm.csv
if [ $? -ne 0 ]; then
	echo simtools create: TEST FAILED
	exit;
fi

diff test.sim example.raw.sim
if [ $? -ne 0 ]; then
	echo simtools create: check output file: TEST FAILED
	exit;
fi

#
# illuminus tests
#
../simtools illuminus --infile test.sim --outfile test.iln --man_file example.bpm.csv
if [ $? -ne 0 ]; then
	echo simtools illuminus: TEST FAILED
	exit;
fi

diff test.iln example_1.iln
if [ $? -ne 0 ]; then
	echo simtools illuminus: check output file: TEST FAILED
	exit;
fi

../simtools illuminus --end 3 --infile test.sim --outfile test.iln --man_file example.bpm.csv
if [ $? -ne 0 ]; then
	echo simtools illuminus2: TEST FAILED
	exit;
fi

diff test.iln example_2.iln
if [ $? -ne 0 ]; then
	echo simtools illuminus2: check output file: TEST FAILED
	exit;
fi

../simtools illuminus --start 3 --infile test.sim --outfile test.iln --man_file example.bpm.csv
if [ $? -ne 0 ]; then
	echo simtools illuminus3: TEST FAILED
	exit;
fi

diff test.iln example_3.iln
if [ $? -ne 0 ]; then
	echo simtools illuminus3: check output file: TEST FAILED
	exit;
fi

../simtools illuminus --end 3 --start 3 --infile test.sim --outfile test.iln --man_file example.bpm.csv
if [ $? -ne 0 ]; then
	echo simtools illuminus4: TEST FAILED
	exit;
fi

diff test.iln example_4.iln
if [ $? -ne 0 ]; then
	echo simtools illuminus4: check output file: TEST FAILED
	exit;
fi


#
# genosnp tests
#
../simtools genosnp --infile test.sim --outfile test.gsn --man_file example.bpm.csv
if [ $? -ne 0 ]; then
	echo simtools genosnp: TEST FAILED
	exit;
fi

diff test.gsn example_1.gsn
if [ $? -ne 0 ]; then
	echo simtools genosnp: check output file: TEST FAILED
	exit;
fi

../simtools genosnp --start 1 --infile test.sim --outfile test.gsn --man_file example.bpm.csv
if [ $? -ne 0 ]; then
	echo simtools genosnp2: TEST FAILED
	exit;
fi

diff test.gsn example_2.gsn
if [ $? -ne 0 ]; then
	echo simtools genosnp2: check output file: TEST FAILED
	exit;
fi

../simtools genosnp --end 3 --infile test.sim --outfile test.gsn --man_file example.bpm.csv
if [ $? -ne 0 ]; then
	echo simtools genosnp3: TEST FAILED
	exit;
fi

diff test.gsn example_3.gsn
if [ $? -ne 0 ]; then
	echo simtools genosnp3: check output file: TEST FAILED
	exit;
fi

../simtools genosnp --end 3 --start 2 --infile test.sim --outfile test.gsn --man_file example.bpm.csv
if [ $? -ne 0 ]; then
	echo simtools genosnp4: TEST FAILED
	exit;
fi

diff test.gsn example_4.gsn
if [ $? -ne 0 ]; then
	echo simtools genosnp4: check output file: TEST FAILED
	exit;
fi

rm test.sim test.iln test.gsn

echo All tests successful