#!/bin/bash
set -e

pkg=fastani
CUR_DIR=`pwd`

export LC_ALL=C.UTF-8
if [ "${AUTOPKGTEST_TMP}" = "" ] ; then
  AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
  trap "rm -rf ${AUTOPKGTEST_TMP}" 0 INT QUIT ABRT PIPE TERM
fi

cp -a ${CUR_DIR}/data/* "${AUTOPKGTEST_TMP}"

cd "${AUTOPKGTEST_TMP}"

echo "Test functionality"
fastANI -q Shigella_flexneri_2a_01.fna -r Escherichia_coli_str_K12_MG1655.fna --visualize -o fastani.out
cat fastani.out
[ -s fastani.out ] || exit 1

Rscript /usr/share/fastani/visualize.R Shigella_flexneri_2a_01.fna Escherichia_coli_str_K12_MG1655.fna fastani.out.visual
[ -s fastani.out.visual.pdf ] || exit 1
echo "PASS"
