#!/bin/bash
set -e

pkg=parsnp

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 *

echo -e "\e[93m\e[1mTest 1: With GenBank Annotations\e[0m"
parsnp -g mers_virus/ref/England1.gbk -d mers_virus/genomes -c
echo -e "\e[92m\e[1mPassed\e[0m"
echo

echo -e "\e[93m\e[1mTest 2: Without GenBank Annotations\e[0m"
parsnp -r mers_virus/ref/England1.fna -d mers_virus/genomes -c
echo -e "\e[92m\e[1mPassed\e[0m"
echo
