#!/bin/bash
set -e

pkg=delly
CUR_DIR=`pwd`
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 ${CUR_DIR}/example/* "${AUTOPKGTEST_TMP}"

cd "${AUTOPKGTEST_TMP}"

echo -e "\e[93m\e[1mRunning Tests\e[0m"

echo -e "\e[93m\e[1mTest 1\e[0m"

delly call -o sr.bcf -g ref.fa sr.bam

echo -e "\e[93m\e[1mTest 2\e[0m"

delly lr -g ref.fa lr.bam -o lr.vcf
echo -e "\e[93m\e[1mTest 3\e[0m"

delly cnv -g ref.fa -m map.fa.gz sr.bam -o cnv.vcf

if [[ -f sr.bcf ]] && [[ -f lr.vcf ]] && [[ -f cnv.vcf ]]
then
    echo -e "\e[92m\e[1mPASS\e[0m"
else
    echo -e "\e[1;31mFAILED!"
fi

