Revision 1c3f3b1324e5a8588a4fcc99f4e4ce35005abdaf authored by andrewjpage on 01 September 2014, 09:47:51 UTC, committed by andrewjpage on 01 September 2014, 09:47:51 UTC
1 parent 7404620
snp_searching.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 _SNP_SEARCHING_H_
#define _SNP_SEARCHING_H_
int advance_window_start_to_next_snp(int window_start_coordinate, int * snp_locations, char * child_sequence, int number_of_branch_snps);
int find_starting_index(int window_start_coordinate, int * snp_locations, int start_index, int end_index);
int rewind_window_end_to_last_snp(int window_end_coordinate, int * snp_locations, char * child_sequence, int number_of_branch_snps);
int get_window_end_coordinates_excluding_gaps(int window_start_coordinate, int window_size, int * snp_locations, char * child_sequence, int number_of_snps);
int find_number_of_snps_in_block(int window_start_coordinate, int window_end_coordinate, int * snp_locations, char * child_sequence, int number_of_snps);
int calculate_block_size_without_gaps(char * child_sequence, int * snp_locations, int starting_coordinate, int ending_coordinate, int length_of_original_genome);
int calculate_size_of_genome_without_gaps(char * child_sequence, int start_index, int length_of_sequence, int length_of_original_genome);
int calculate_number_of_snps_excluding_gaps(char * ancestor_sequence, char * child_sequence, int child_sequence_size, int * branch_snp_coords, int * snp_locations, char * branch_snp_sequence, char * branch_snp_ancestor_sequence);
int flag_recombinations_in_window(int window_start_coordinate, int window_end_coordinate, int number_of_snps, int * branch_snp_sites, int * recombinations, int number_of_recombinations,int * snp_locations, int total_num_snps);
int find_matching_coordinate_index(int window_start_coordinate, int * snp_sites, int number_of_snps, int starting_index);
int advance_window_start_to_next_snp_with_start_index(int window_start_coordinate, int * snp_locations, char * child_sequence, int number_of_branch_snps, int start_index);
int rewind_window_end_to_last_snp_with_start_end_index(int window_end_coordinate, int * snp_locations, char * child_sequence, int number_of_branch_snps, int start_index,int end_index);
int find_number_of_snps_in_block_with_start_end_index(int window_start_coordinate, int window_end_coordinate, int * snp_locations, char * child_sequence, int number_of_snps, int start_index,int end_index);
int get_window_end_coordinates_excluding_gaps_with_start_end_index(int window_start_coordinate, int window_size, int * snp_locations, char * child_sequence, int number_of_snps, int start_index,int end_index);
#endif
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