https://github.com/sanger-pathogens/gubbins
Revision 155d08a07dca63f8aad89390933c132eaebda861 authored by andrewjpage on 02 September 2014, 08:29:19 UTC, committed by andrewjpage on 02 September 2014, 08:29:19 UTC
Catch too few sequences
Tip revision: 155d08a07dca63f8aad89390933c132eaebda861 authored by andrewjpage on 02 September 2014, 08:29:19 UTC
Merge pull request #106 from andrewjpage/catch_too_few_sequences
Merge pull request #106 from andrewjpage/catch_too_few_sequences
Tip revision: 155d08a
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[]);
void extract_sequences(char vcf_filename[], char tree_filename[],char multi_fasta_filename[], int min_snps, char original_multi_fasta_filename[]);
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
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