#!/bin/bash
set -e

pkg=segemehl

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

cd "${AUTOPKGTEST_TMP}"

segemehl -x index.idx -d seq1.fa
segemehl -i index.idx -d seq1.fa -q myseq.fa > mymap.sam
segemehl -S -i index.idx -d seq1.fa -q seq2.fa > my.sngl.bed
[ -s "mymap.sam" ] && [ -s "index.idx" ] && [ -s "my.sngl.bed" ] || exit 1 && echo "PASS Test"
