#!/bin/bash
set -e

pkg=centrifuge
CUR_DIR=`pwd`

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

cd "${AUTOPKGTEST_TMP}"
gunzip -r *

echo 'Test 1'
centrifuge-build --conversion-table reference/gi_to_tid.dmp --taxonomy-tree reference/nodes.dmp --name-table reference/names.dmp reference/test.fa test
for f in *.cf
do
	[ -s $f ] || exit 1
done
echo "PASS"

echo 'Test 2'
centrifuge -f -x test reads/input.fa
cat *.tsv
echo "PASS"
