#!/bin/bash
set -e

examplepkg=vcftools

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 /usr/share/doc/${examplepkg}/examples/testdata/annotate-test.vcf "${AUTOPKGTEST_TMP}"

cd "${AUTOPKGTEST_TMP}"

echo "Test 1"
SURVIVOR vcftobed annotate-test.vcf 0 -1 test1.bed
[ -s test1.bed ] || exit 1
echo "PASS"

echo "Test 2"
SURVIVOR bedpetovcf test1.bed test2.vcf
[ -s test2.vcf ] || exit 1
echo "PASS"

echo "Test 3"
SURVIVOR stats annotate-test.vcf -1 10 -1 test3
[ -s test3 ] || exit 1
echo "PASS"

echo "Test 4"
SURVIVOR bedtovcf test1.bed DEL test4.bed
[ -s test4.bed ] || exit 1
echo "PASS"

echo "Test 5"
SURVIVOR filter annotate-test.vcf test4.bed 50 -1 0.01 10 test5.vcf
[ -s test5.vcf ] || exit 1
echo "PASS"
