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#!/bin/bash
set -e
pkg=dascrubber
export LC_ALL=C.UTF-8
if [ "${AUTOPKGTEST_TMP}" = "" ] ; then
AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
trap "rm -rf ${AUTOPKGTEST_TMP}" 0 INT QUIT ABRT PIPE TERM
fi
#cp -a /usr/share/doc/${pkg}/examples/* "${AUTOPKGTEST_TMP}"
cd "${AUTOPKGTEST_TMP}"
#do_stuff_to_test_package#
rangen 1.0 -r2020 >R.fasta
fasta2DAM R R.fasta
dsimulator R -c20. -r2020 >G.fasta
fasta2DB G G.fasta
rm G.fasta
DBsplit -s11 G
DBdust G.1
DBdust G.2
DBstats -mdust G
cat G.db
HPC.daligner -mdust -t5 G | sh -v
DAScover -v G G.1 G.2
Catrack G covr
DASqv -c20 -v G G.1 G.2
Catrack -v G qual
DAStrim -v -g20 -b20 G G.1 G.2
Catrack -v G trim
DASpatch -v G G.1 G.2
Catrack G patch
DASedit -v G G1
DASmap G1
# Since the output is not consistent.
#It cannot be compared with the reference.
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