#!/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. 

