#!/bin/bash
set -e

pkg=daligner

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

cd "${AUTOPKGTEST_TMP}"

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
LAshow -c G -w50 G.1 | head

# Since the output is not consistent.
#It cannot be compared with the reference. 
