https://github.com/jttoivon/MODER
Tip revision: c485231e5b468ae509306e1aaeebaa0f3004572d authored by Jarkko Toivonen on 31 March 2020, 18:10:18 UTC
Fixed indexing bug.
Fixed indexing bug.
Tip revision: c485231
parameters.hpp
/*
MODER is a program to learn DNA binding motifs from SELEX datasets.
Copyright (C) 2016, 2017 Jarkko Toivonen,
Department of Computer Science, University of Helsinki
MODER 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 2 of the License, or
(at your option) any later version.
MODER 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 this program; if not, write to the Free Software Foundation, Inc.,
51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
*/
#ifndef PARAMETERS_HPP
#define PARAMETERS_HPP
extern bool use_markov_background;
extern bool use_positional_background;
extern bool use_two_strands;
extern bool use_pseudo_counts;
extern bool use_submotif;
extern bool use_em;
extern bool reestimate_error_rate;
extern bool use_logodds_score;
extern bool use_permutation_test;
extern bool use_bernoulli_read_method;
extern bool print_alignment;
extern bool count_palindromes_twice;
const int min_matrix_len=3;
const int max_matrix_len=20;
#endif // PARAMETERS_HPP