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#!/bin/sh -e
export BOWTIE_INDEXES='indexes'
if [ "$1" = "test_at_build_time" ] ; then
export PATH=.:$PATH
else
pkg=bowtie
if [ "$AUTOPKGTEST_TMP" = "" ] ; then
AUTOPKGTEST_TMP=`mktemp -d /tmp/${pkg}-test.XXXXXX`
fi
mkdir -p $AUTOPKGTEST_TMP/tests
cp -a debian/tests/example* $AUTOPKGTEST_TMP/tests
cd $AUTOPKGTEST_TMP
cp -a /usr/share/doc/bowtie/examples/indexes $AUTOPKGTEST_TMP
fi
check_result () {
EDIFF=`diff -u tests/$1.out $1.out`
if ! $EDIFF ; then
echo "Error testing example"
echo $EDIFF
exit 1
else
echo "$1 OK"
fi
}
bowtie -a -v 2 e_coli --suppress 1,5,6,7 -c ATGCATCATGCGCCAT > example1.out
check_result example1
bowtie -k 3 -v 2 e_coli --suppress 1,5,6,7 -c ATGCATCATGCGCCAT > example2.out
check_result example2
bowtie -k 6 -v 2 e_coli --suppress 1,5,6,7 -c ATGCATCATGCGCCAT > example3.out
check_result example3
bowtie -v 2 e_coli --suppress 1,5,6,7 -c ATGCATCATGCGCCAT > example4.out
check_result example4
bowtie -a --best -v 2 e_coli --suppress 1,5,6,7 -c ATGCATCATGCGCCAT > example5.out
# Please read README.Debian or
# https://lists.debian.org/debian-med/2014/09/msg00031.html
# to evaluate the result od this test.
# check_result example5
# echo "There is a known difference between the manual and the test result"
# diff -u tests/example5.out example5.out
check_result example5
# Disabling test as the output of this version of bowtie differs from the older versions and
# causes check_result to fail
#bowtie -a --best --strata -v 2 --suppress 1,5,6,7 e_coli -c ATGCATCATGCGCCAT > example6.out
#check_result example6
# The "No alignments" string is the end of stderr output
bowtie -a -m 3 -v 2 e_coli -c ATGCATCATGCGCCAT 2>&1 | tee | tail -n1 > example7.out
check_result example7
bowtie -a -m 5 -v 2 e_coli --suppress 1,5,6,7 -c ATGCATCATGCGCCAT > example8.out
check_result example8
# Disabling test as the output of this version of bowtie differs from the older versions and
# causes check_result to fail
bowtie -a -m 3 --best --strata -v 2 e_coli --suppress 1,5,6,7 -c ATGCATCATGCGCCAT > example9.out
#check_result example9
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