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|
#! /bin/sh
set -e
if ! dpkg --listfiles freebayes > /dev/null 2>&1
then
cat >&2 <<-END
error: package freebayes needed: provides test data for cuteSV.
END
exit 1
fi
if [ "$AUTOPKGTEST_TMP" = "" ]
then
AUTOPKGTEST_TMP="$(mktemp -d /tmp/cutesv-test.XXXXXX)"
trap "rm -rf $AUTOPKGTEST_TMP" 0 INT QUIT ABRT PIPE TERM
fi
cd "$AUTOPKGTEST_TMP"
set -x
cuteSV --version
cuteSV --help
cuteSV \
/usr/share/doc/freebayes/examples/tiny/NA12878.chr22.tiny.hla.bam \
/usr/share/doc/freebayes/examples/tiny/hla.fa \
out1.vcf .
cuteSV -t "$(nproc)" \
/usr/share/doc/freebayes/examples/tiny/1read.bam \
/usr/share/doc/freebayes/examples/tiny/hla.fa \
out2.vcf .
cuteSV --genotype \
/usr/share/doc/freebayes/examples/tiny/NA12878.chr22.tiny.bam \
/usr/share/doc/freebayes/examples/tiny/q.fa \
out3.vcf .
cuteSV -t "$(nproc)" --genotype \
/usr/share/doc/freebayes/examples/splice/1:883884-887618.bam \
/usr/share/doc/freebayes/examples/splice/1:883884-887618.fa \
out4.vcf .
for vcf in out*.vcf
do
test "$(sed -n '1s/v[0-9.]\+$//p' "$vcf")" = "##fileformat=VCF"
test "$(sed -n '2s/-[0-9.]\+$//p' "$vcf")" = "##source=cuteSV"
done
set +x
echo PASS
|
