#!/bin/bash

CUR_DIR=`pwd`

if [ "$AUTOPKGTEST_TMP" = "" ]; then
	AUTOPKGTEST_TMP=`mktemp -d /tmp/${pkg}-test.XXXX`

	trap "rm -rf $AUTOPKG_TMP" 0 INT QUIT ABRT PIPE TERM

fi

mkdir -p "$AUTOPKGTEST_TMP"/tests

# Copy test dataset
cp -a "${CUR_DIR}"/debian-tests-data/* "$AUTOPKGTEST_TMP"/tests


cd "$AUTOPKGTEST_TMP"/tests/

# Extract demo dataset
tar -xvf demo.tar.gz

# Change directory to a dataset dir
cd demo/data/HEK293T-METTL3-KO-rep1/

# Run within the dataset dir
xpore dataprep --eventalign nanopolish/eventalign.txt --gtf_or_gff ../../demo.gtf --transcript_fasta ../../demo.fa --out_dir dataprep --genome

# Check output directory
if [ -d "./dataprep" ]; then

    echo "Output Directory Generated"
    echo "PASS"

else

    echo "Output Directory Not Generated"
    exit 1

fi