Revision 5279176ab4ef97768fe973ca36fb05ff99f07e7a authored by andrewjpage on 26 July 2013, 10:47:07 UTC, committed by andrewjpage on 26 July 2013, 10:47:07 UTC
1 parent 077651b
parse_phylip.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 _PARSE_PHYLIP_H_
#define _PARSE_PHYLIP_H_
typedef struct sample_statistics
{
char * sample_name;
int number_of_recombinations;
int number_of_snps;
int genome_length_without_gaps;
int number_of_blocks;
int bases_in_recombinations;
} sample_statistics;
void get_sequence_for_sample_name(char * sequence_bases, char * sample_name);
int find_sequence_index_from_sample_name( char * sample_name);
void update_sequence_base(char new_sequence_base, int sequence_index, int base_index);
int does_column_contain_snps(int snp_column, char reference_base);
int number_of_samples_from_parse_phylip();
void get_sample_names_from_parse_phylip(char ** sample_names);
char convert_reference_to_real_base_in_column(int snp_column, char reference_base);
void set_genome_length_without_gaps_for_sample(char * sample_name, int genome_length_without_gaps);
void set_number_of_snps_for_sample(char * sample_name, int number_of_snps);
void set_number_of_recombinations_for_sample(char * sample_name, int number_of_recombinations);
void set_number_of_blocks_for_sample(char * sample_name,int num_blocks);
sample_statistics ** get_sample_statistics();
int number_of_snps_in_phylip();
void load_sequences_from_multifasta_file(char filename[]);
void set_internal_node(int internal_node_value,int sequence_index);
void initialise_internal_node();
int get_internal_node(int sequence_index);
void fill_in_unambiguous_bases_in_parent_from_children_where_parent_has_a_gap(int parent_sequence_index, int * child_sequence_indices, int num_children);
void fill_in_unambiguous_gaps_in_parent_from_children(int parent_sequence_index, int * child_sequence_indices, int num_children);
void freeup_memory();
#define MAX_READ_BUFFER 65536
#define MAX_SAMPLE_NAME_SIZE 1024
#endif
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