#!/bin/bash
set -e

pkg=bio-rainbow

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}"

gunzip -r *

bio-rainbow cluster -1 R.1.fastq -2 R.2.fastq > rbcluster.out 2> log
bio-rainbow div -i rbcluster.out -o rbdiv.out
bio-rainbow merge -o rbasm.out -a -i rbdiv.out -N50000

echo "4f0a35450f64adc3bfd6f4b664887631  rbasm.out" >> checksums
echo "29a755de547ac393328c8b31d5f6e26d  rbcluster.out" >> checksums
echo "b7dfd0cfd2f0eade15487a72632e972d  rbdiv.out" >> checksums

md5sum --check checksums