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#!/bin/sh
set -e
pkg=bitseq
export LC_ALL=C.UTF-8
CUR_DIR=`pwd`
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 ${CUR_DIR}/debian-tests-data/* -a "${AUTOPKGTEST_TMP}"
cd "${AUTOPKGTEST_TMP}"
# Check for pre-generated input
if [ ! -s out.sam ]; then
echo "out.sam not found"
exit 1
fi
parseAlignment out.sam -o result.prob --trSeqFile Ref.fasta --trInfoFile Ref.tr --uniform --verbose
if [ -s result.prob ] && [ -s Ref.tr ]; then
echo " test passed"
else
exit 1
fi
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