/usr/include/snp-sites/alignment-file.h is in libsnp-sites1-dev 2.3.3-2.
This file is owned by root:root, with mode 0o644.
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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 | /*
* 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"
void detect_snps( char filename[], int pure_mode, int output_monomorphic);
void get_bases_for_each_snp(char filename[], char ** bases_for_snps);
int is_unknown(char base);
int get_length_of_genome();
int get_number_of_samples();
int get_number_of_snps();
char ** get_sequence_names();
int * get_snp_locations();
char * get_pseudo_reference_sequence();
int is_pure(char base);
#define MAX_SAMPLE_NAME_SIZE 2048
#define DEFAULT_NUM_SAMPLES 65536
#endif
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