#!/usr/bin/env bash
#
# orthologer - Pipeline for deducing orthology from fasta files.
# Copyright (C) 2005-2023 E. Zdobnov lab: F. Tegenfeldt
# <fredrik.tegenfeldt@unige.ch> based on code by E. Kriventseva
#
# This file is part of orthologer.
#
# orthologer is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# orthologer is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with orthologer.  If not, see <http://www.gnu.org/licenses/>.
#
#--- check if environment is ok -----------------
[ "${LOADED_COMMON_PIPELINE_SH+1}" == "" ] && echo "ERROR $0 : main config has not been loaded" 1>&2 && exit 255
#------------------------------------------------

# get args
if [ $# != 3 ]; then
    echo "Usage $0 <masked fasta> <cleaned fasta> <output>"
    exit 1;
fi

masked="$1"
cleaned="$2" # not used here
output="$3"

# remove output file
rm -f "$output"

# link output to masked file
copy_file 0 "$output" "$masked"
[ $? -eq 0 ] || exit 255

# create a dummy clstr file
rm -f "${output}.clstr"
echo "# No clustering of similar genes is present since select step used label NONE" > "${output}.clstr"

# set permissions
chmod 644 "$output"
chmod 644 "${output}.clstr"
