#!/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
[ $# -eq 2 ] || fatal_msg "usage: $0 <brhclus dumpfile> <output cluster file>"

dumpf=$1
outf=$2

check_file "$0" "$dumpf"           || exit 255
check_file_exe "$0" "$EXE_BRHCLUS" || exit 255

tmpfile=`mktemp /tmp/brhclus_resume.XXXXXXXX`
"$EXE_BRHCLUS" --resume "$dumpf" --og $tmpfile
if [ $? -ne 0 ]; then
	error_msg "Failed resuming brhclus for dump file: $dumpf"
	echo "Output from dumpfile so far: "
	cat $tmpfile
	rm -f $tmpfile
	exit 255
fi
cp -f $tmpfile "$outf"
rm -f $tmpfile
