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#!/bin/sh -e
pkg=mapdamage
if [ "$ADTTMP" = "" ] ; then
ADTTMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
trap "rm -rf $ADTTMP" 0 INT QUIT ABRT PIPE TERM
fi
cd $ADTTMP
cp -a /usr/share/doc/${pkg}/tests/* .
cp -a /usr/share/doc/${pkg}/ref_T.fa .
gunzip -r *
python rescale_test.py
mapDamage -i rescale_test/pe_test/pe.sam -r ref_T.fa
pdf_result="results_pe/Fragmisincorporation_plot.pdf"
if [ -e "$pdf_result" ]; then
echo "pdf result exists"
else
echo "pdf result doesnt' exist"
exit 1
fi
mapDamage -d results_pe -y 0.1 --plot-only
echo "checking stdin redirect..."
cat rescale_test/pe_test/pe.sam | mapDamage -i - -r ref_T.fa
rm -rf results_pe
mapDamage -i rescale_test/pe_test/pe.sam -r ref_T.fa --rescale
mapDamage -d results_pe --forward --stats-only -v -r ref_T.fa
#asks for -r reference when it's not mentioned in examples
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