#!/bin/bash
set -e

pkg=jaligner

export LC_ALL=C.UTF-8
if [ "${AUTOPKGTEST_TMP}" = "" ] ; then
  AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
  # Double quote below to expand the temporary directory variable now versus
  # later is on purpose.
  # shellcheck disable=SC2064
  trap "rm -rf ${AUTOPKGTEST_TMP}" 0 INT QUIT ABRT PIPE TERM
fi

cp -a /usr/share/doc/${pkg}/examples/* "${AUTOPKGTEST_TMP}"

cd "${AUTOPKGTEST_TMP}"

gunzip -r *
tar -xf references.tar.xz
ls  -R
#do_stuff_to_test_package#
matrices=$(ls /usr/share/jaligner/jaligner/matrix/matrices)

for matrix in $matrices;
do
    jaligner p53_human.fasta p53_mouse.fasta ${matrix} 10 0.5 > result.${matrix}.txt
    diff reference.${matrix}.txt result.${matrix}.txt
done
