#!/bin/bash
set -e

pkg=python3-nanoget

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}"

gunzip nanotest/[as]*.gz
gunzip nanotest/reads-mixed-timestamp.fastq.gz

python3 test.py

if diff nanotest/alignment.bam.bai_orig nanotest/alignment.bam.bai ; then
    echo "Pass"
else
    echo "Fail"
    exit 1
fi
