set -e

pkg=bitseq

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 "$(dirname "$0")/Data/"* "${AUTOPKGTEST_TMP}/"

cd "${AUTOPKGTEST_TMP}"

bowtie-build -f Ref.fasta index
bowtie -q -v 3 --all -m 100 --sam index Reads.fastq  -S out.sam

[ -s out.sam ] && echo "Test passed!" || { echo "Output missing or empty"; exit 1; }

parseAlignment out.sam \
  -o result.prob \
  --trSeqFile Ref.fasta \
  --trInfoFile Ref.tr \
  --uniform --verbose
  
if [ -s result.prob ] && [ -s Ref.tr ]; then
  echo "parseAlignment test passed"
else
  echo "parseAlignment test failed"
  exit 1
fi
