#!/bin/bash
set -e

pkg=bamclipper
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

cd "${AUTOPKGTEST_TMP}"
cp -a ${CUR_DIR}/debian/tests/*.sam .
cp -a ${CUR_DIR}/debian/tests/*.bedpe .

samtools view -S -b SRR2075598.sam > sample.bam
samtools index sample.bam sample.bam.bai
bamclipper.sh -b sample.bam -p trusight_myeloid.bedpe
ls -1
[ -s sample.primerclipped.bam ] || exit 1 
[ -s sample.primerclipped.bam.bai ] || exit 1

rm *.bam*
echo "PASS"
