/usr/include/snp-sites/alignment-file.h is in libsnp-sites1-dev 1.5.0-1ubuntu1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 | /*
* Wellcome Trust Sanger Institute
* Copyright (C) 2013 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 3
* 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[], size_t length_of_genome);
int line_length(FILE * alignment_file_pointer);
int build_reference_sequence(char reference_sequence[], char filename[]);
int build_reference_sequence_and_truncate(char reference_sequence[], char filename[], size_t buffer_length);
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, size_t length_of_genome, int number_of_snps);
#define MAX_READ_BUFFER 65536
#define MAX_SAMPLE_NAME_SIZE 1024
#endif
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