snp_sites.h
/*
* 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