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#!/bin/sh -e
pkg=bamtools
if [ "$AUTOPKGTEST_TMP" = "" ] ; then
AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
trap "rm -rf $AUTOPKGTEST_TMP" 0 INT QUIT ABRT PIPE TERM
fi
cd $AUTOPKGTEST_TMP
cp -a /usr/share/doc/${pkg}/sam_spec_example.bam .
cp -a /usr/share/doc/${pkg}/filter_script .
gunzip -r *
bamtools convert -format fastq -in sam_spec_example.bam -out test.fastq
bamtools convert -format json -in sam_spec_example.bam -out test.json
bamtools count -in sam_spec_example.bam
bamtools coverage -in sam_spec_example.bam -out out
# This test fails on ppc64el for whatever reason and is for the moment (see bug #933505)
# The test is also problematic for armel (see bug #992143)
ARCH=$(dpkg --print-architecture)
if [ "$ARCH" != "ppc64el" -a "$ARCH" != "arm64" -a "$ARCH" != "armel"-a "$ARCH" != "armhf" -a "$ARCH" != "s390x" ] ; then
bamtools filter -script filter_script -in sam_spec_example.bam -out out.bam
else
if [ "$ARCH" = "ppc64el" ] ; then
echo "The following test is known to fail on ppc64el architecture (see bug #933505)"
else
echo "The following test is known to time out on $ARCH architecture (see bug #953939)"
fi
echo "bamtools filter -script filter_script -in sam_spec_example.bam -out out.bam"
fi
bamtools header -in sam_spec_example.bam
bamtools index -in sam_spec_example.bam
bamtools random -n 100 -in sam_spec_example.bam -out out.bam
bamtools revert -in sam_spec_example.bam -out out.bam
bamtools sort -in sam_spec_example.bam -out out.bam
bamtools split -mapped -in sam_spec_example.bam
bamtools stats -in sam_spec_example.bam
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