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#!/bin/bash
set -e
pkg=stringtie
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}"
gunzip -r *
cat long_reads.sam| samtools view -Sb - > long_reads.bam
cat short_reads_and_superreads.sam| samtools view -Sb - > short_reads_and_superreads.bam
cat short_reads.sam| samtools view -Sb - > short_reads.bam
# skipping the first line because it differs due to location of compiled binary
function test_output()
{
# $1: Test Number
# $2: output file
# $3: input bam file
# $4: expected output file
echo "Test $1"
stringtie -o $2 $3
if [ "$1" = 3 ]
then
stringtie -L -o $2 $3
elif [ "$1" = 4 ]
then
stringtie -L -G human-chr19_P.gff -o $2 $3
fi
if [ $(dpkg-architecture -qDEB_BUILD_ARCH) = "amd64" ]
then
diff -u <(tail -n +3 $2) <(tail -n +3 $4)
echo "Expected output and generated output are same: PASS"
else
[ -s $2 ] || exit 1
echo "PASS"
fi
}
test_output 1 short_reads.out.gtf short_reads.bam short_reads.out_expected.gtf
test_output 2 short_reads_and_superreads.out.gtf short_reads_and_superreads.bam short_reads_and_superreads.out_expected.gtf
test_output 3 long_reads.out.gtf long_reads.bam long_reads.out_expected.gtf
test_output 4 long_reads_guided.out.gtf long_reads.bam long_reads_guided.out_expected.gtf
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