#!/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/>.
#
# this is a dummy filter
# it just creates a link from *_masked to *
#--- check if environment is ok -----------------
[ "${LOADED_COMMON_PIPELINE_SH+1}" == "" ] && echo "ERROR $0 : main config has not been loaded" 1>&2 && exit 255
#------------------------------------------------
set -u

[ $# -eq 2 ] || fatal_msg "usage: $0 <fasta> <outfile>"

fasta="$1"
check_file "$0" "$fasta" || exit 255

outfile="$2"

fastabase=`basename $fasta`
cd `dirname $fasta`

# create output file name
err=0
rm -f "$outfile"
err=$?

# if the last remove was ok, create the soft link
if [ $err -eq 0 ]; then
    ln -sf "$fastabase" "$outfile"
    err=$?
fi

exit $err
