#!/bin/bash
set -e

pkg=TVC

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/${pkg}/examples/example1/* "${AUTOPKGTEST_TMP}"

cd "${AUTOPKGTEST_TMP}"

echo -e "Running Tests"

variant_caller_pipeline.py \
    --input-bam      test.bam \
    --reference-fasta reference.fasta \
    --region-bed      test_merged_plain.bed \
    --primer-trim-bed test_unmerged_detail.bed

if [ -f TSVC_variants.vcf ] && \
   [ -f small_variants.vcf ] && \
   [ -f small_variants_filtered.vcf ]; then

   echo "PASS"

else
   echo "FAIL"
   exit 1
fi
