#!/bin/bash
set -e

pkg="kalign"

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 /usr/share/doc/${pkg}/examples/* $AUTOPKGTEST_TMP

cd $AUTOPKGTEST_TMP

echo "---test1---"
/usr/bin/kalign < example.fa > output1
cat output1
echo "---test2---"
/usr/bin/kalign -gpo 60 -gpe 9 -tgpe 0 -bonus 0 < example.fa  > output2
cat output2

echo "PASS"
