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#!/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"
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