/usr/include/snp-sites/vcf.h is in libsnp-sites1-dev 2.3.3-2.
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 | /*
* 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 _VCF_H_
#define _VCF_H_
#include <stdio.h>
void output_vcf_header( FILE * vcf_file_pointer, char ** sequence_names, int number_of_samples, size_t length_of_genome);
void create_vcf_file(char filename[], int snp_locations[], int number_of_snps, char ** bases_for_snps, char ** sequence_names, int number_of_samples, size_t length_of_genome, char pseudo_reference_sequence[]);
void output_vcf_snps(FILE * vcf_file_pointer, char ** bases_for_snps, int * snp_locations, int number_of_snps, int number_of_samples, char pseudo_reference_sequence[]);
void output_vcf_row(FILE * vcf_file_pointer, char * bases_for_snp, int snp_location, int number_of_samples, char pseudo_reference_sequence[]);
void output_vcf_row_samples_bases(FILE * vcf_file_pointer, char reference_base, char * alt_bases, char * bases_for_snp, int number_of_samples);
char * alternative_bases(char reference_base, char * bases_for_snp, int number_of_samples);
char * format_alternative_bases(char *);
char * format_allele_index(char, char, char *);
int check_if_char_in_string(char search_string[], char target_char, int search_string_length);
#define MAXIMUM_NUMBER_OF_ALT_BASES 30
#endif
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