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#!/bin/sh -e
#debug=1
if [ "$AUTOPKGTEST_TMP" = "" ] ; then
AUTOPKGTEST_TMP=`mktemp -d /tmp/smalt-test.XXXXXX`
fi
cd $AUTOPKGTEST_TMP
cp -a /usr/share/doc/smalt/test/* $AUTOPKGTEST_TMP
gunzip *.py.gz data/*.bam.gz
TESTS="splitReads_test.py
results_split_test.py
ouform_cigar_test.py
sample_test.py
cigar_test.py
mthread_test.py"
# since libbambamc is available we can dafely run all tests
TESTS=`ls *_test.py`
ln -s /usr/lib/smalt/test/sequenceReverseComplement_test .
for tst in $TESTS ; do
if [ $debug ] ; then
echo "Testing $tst ..."
fi
if [ "$tst" = "xali_test.py" ] ; then
if [ $debug ] ; then
echo "xali_test.py is using smalt built with different compile options"
echo "lets try, whether the test also runs with plain smalt"
echo "This fails with:"
echo " ERROR: wrong CIGAR string '44M44S' (target:'44M1X1M42S')"
fi
#ln -s /usr/bin/smalt smalt_Xali_test
#python $tst
#rm -f smalt_Xali_test
else
python3 $tst
fi
done
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