#!/bin/bash
set -e

pkg=nanook

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}"

tar xf data.tar.gz
tar xf ref.tar.gz
#do_stuff_to_test_package#
cd data/nanook_ecoli_500/references
lastdb -Q 0 ecoli_dh10b_cs ecoli_dh10b_cs.fasta
cd ..
nanook extract -s N79596_dh10b_8kb_11022015
nanook align -s N79596_dh10b_8kb_11022015 -r references/ecoli_dh10b_cs.fasta
nanook analyse -s N79596_dh10b_8kb_11022015 -r references/ecoli_dh10b_cs.fasta -passonly

cd ../..
for file in ref/*; do
  if [[ -f $file ]]; then
    output=data${file#ref}
    diff $file $output
  fi
done
