/*
 *  Wellcome Trust Sanger Institute
 *  Copyright (C) 2011  Wellcome Trust Sanger Institute
 *  
 *  This program 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.
 *  
 *  This program 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 _SNP_SITES_H_
#define _SNP_SITES_H_

void build_snp_locations(int snp_locations[], char reference_sequence[]);
int generate_snp_sites(char filename[],  int exclude_gaps, char suffix[]);
int refilter_existing_snps(char * reference_bases, int number_of_snps, int * snp_locations, int * filtered_snp_locations, int internal_nodes[]);
void remove_filtered_snp_locations(int * filtered_snp_locations, int * snp_locations, int number_of_snps);
void strip_directory_from_filename(char * input_filename, char * output_filename);

#define MAX_FILENAME_SIZE 1024
#define MAX_SAMPLE_NAME_SIZE 1024

#endif