A library for working with phylogenetic data.
v0.25.0
base_counts.hpp
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1 #ifndef GENESIS_POPULATION_BASE_COUNTS_H_
2 #define GENESIS_POPULATION_BASE_COUNTS_H_
3 
4 /*
5  Genesis - A toolkit for working with phylogenetic data.
6  Copyright (C) 2014-2020 Lucas Czech
7 
8  This program is free software: you can redistribute it and/or modify
9  it under the terms of the GNU General Public License as published by
10  the Free Software Foundation, either version 3 of the License, or
11  (at your option) any later version.
12 
13  This program is distributed in the hope that it will be useful,
14  but WITHOUT ANY WARRANTY; without even the implied warranty of
15  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
16  GNU General Public License for more details.
17 
18  You should have received a copy of the GNU General Public License
19  along with this program. If not, see <http://www.gnu.org/licenses/>.
20 
21  Contact:
22  Lucas Czech <lucas.czech@h-its.org>
23  Exelixis Lab, Heidelberg Institute for Theoretical Studies
24  Schloss-Wolfsbrunnenweg 35, D-69118 Heidelberg, Germany
25 */
26 
34 #include <string>
35 #include <vector>
36 
37 namespace genesis {
38 namespace population {
39 
40 // =================================================================================================
41 // Base Counts
42 // =================================================================================================
43 
53 struct BaseCounts
54 {
58  size_t a_count = 0;
59 
63  size_t c_count = 0;
64 
68  size_t g_count = 0;
69 
73  size_t t_count = 0;
74 
78  size_t n_count = 0;
79 
83  size_t d_count = 0;
84 };
85 
86 } // namespace population
87 } // namespace genesis
88 
89 #endif // include guard
genesis::population::BaseCounts::d_count
size_t d_count
Count of all deleted (*) nucleotides that are present in the sample.
Definition: base_counts.hpp:83
genesis::population::BaseCounts::t_count
size_t t_count
Count of all T nucleotides that are present in the sample.
Definition: base_counts.hpp:73
genesis::population::BaseCounts::g_count
size_t g_count
Count of all G nucleotides that are present in the sample.
Definition: base_counts.hpp:68
genesis::population::BaseCounts::a_count
size_t a_count
Count of all A nucleotides that are present in the sample.
Definition: base_counts.hpp:58
genesis::population::BaseCounts::n_count
size_t n_count
Count of all N (undetermined/any) nucleotides that are present in the sample.
Definition: base_counts.hpp:78
genesis::population::BaseCounts::c_count
size_t c_count
Count of all C nucleotides that are present in the sample.
Definition: base_counts.hpp:63
genesis
Container namespace for all symbols of genesis in order to keep them separate when used as a library.
Definition: placement/formats/edge_color.cpp:42
genesis::population::BaseCounts
One set of nucleotide base counts, for example for a given sample that represents a pool of sequenced...
Definition: base_counts.hpp:53