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#!/bin/bash
set -e
pkg=mosdepth
if [ "${AUTOPKGTEST_TMP}" = "" ] ; then
AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
# Double quote below to expand the temporary directory variable now versus
# later is on purpose.
# shellcheck disable=SC2064
trap "rm -rf ${AUTOPKGTEST_TMP}" 0 INT QUIT ABRT PIPE TERM
fi
cp -a /usr/share/doc/${pkg}-examples/* "${AUTOPKGTEST_TMP}"
cd "${AUTOPKGTEST_TMP}"
gunzip -r *.gz
echo "Test 1"
mosdepth --by empty-tids.bed --thresholds 1,10,20,30 test1 empty-tids.bam
for f in test1*
do
[ -s $f ] || exit 1
done
cat test1.*.txt | tail -20
rm test1*
echo "PASS"
echo "Test 2"
mosdepth --by empty-tids.bed --quantize 0:1:4:100:200 test2 empty-tids.bam
for f in test2*
do
[ -s $f ] || exit 1
done
cat test2.*.txt | tail -20
echo "PASS"
echo "Tet 3"
python3 plot-dist.py test2.mosdepth.global.dist.txt
[ -s dist.html ]
echo "PASS"
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