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
alignment_file.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 _ALIGNMENT_FILE_H_
#define _ALIGNMENT_FILE_H_
#include "kseq.h"
int detect_snps(char reference_sequence[], char filename[], int length_of_genome, int exclude_gaps);
int line_length(FILE * alignment_file_pointer);
int build_reference_sequence(char reference_sequence[], char filename[]);
void advance_to_sequence(FILE * alignment_file_pointer);
void advance_to_sequence_name(FILE * alignment_file_pointer);
int genome_length(char filename[]);
char * read_line(char sequence[], FILE * pFilePtr);
int number_of_sequences_in_file(char filename[]);
void get_sample_names_for_header(char filename[], char ** sequence_names, int number_of_samples);
char filter_invalid_characters(char input_char);
void get_bases_for_each_snp(char filename[], int snp_locations[], char ** bases_for_snps, int length_of_genome, int number_of_snps);
#define MAX_READ_BUFFER 65536
#define MAX_READ_BUFFER_SMALL 1024
#define MAX_SAMPLE_NAME_SIZE 1024
#endif
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