#!/bin/sh
set -e

pkg="clearcut"

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}"

# Compute tree by supplying alignment of DNA sequences from a file
clearcut --alignment --DNA --in=alignment1.dist --out=treefile.tre
# Compute tree from matrix
clearcut --distance --in=symmetric.dist --out=symmtree.tre
# Run clearcut with properly formatted stdin input
cat lower_diag.dist | clearcut

echo "test pass"
