https://github.com/sanger-pathogens/gubbins
Tip revision: 75e5a846f77b7c110269ca333a32aad622b027c1 authored by andrewjpage on 16 April 2015, 15:10:13 UTC
Merge pull request #140 from andrewjpage/window_size_self_error
Merge pull request #140 from andrewjpage/window_size_self_error
Tip revision: 75e5a84
gubbins.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 _GUBBINS_H_
#define _GUBBINS_H_
#include "seqUtil.h"
#include "Newickform.h"
void run_gubbins(char vcf_filename[], char tree_filename[], char multi_fasta_filename[], int min_snps, char original_multi_fasta_filename[], int window_min, int window_max);
void extract_sequences(char vcf_filename[], char tree_filename[],char multi_fasta_filename[], int min_snps, char original_multi_fasta_filename[], int window_min, int window_max);
char find_first_real_base(int base_position, int number_of_child_sequences, char ** child_sequences);
#define MAX_EDGES_IN_TREE 20000
#define MAX_SAMPLE_NAME_SIZE 1024
#endif