#include <genesis/population/base_counts.hpp>
One set of nucleotide base counts, for example for a given sample that represents a pool of sequenced individuals.
This class is a general representation of the read counts (frequencies) contained in the variants/SNPs of (a pool of) individuals at a certain chromosome position. The class only stores theses counts; for the additional container that also captures the chromosome and position, see Variant.
Definition at line 54 of file base_counts.hpp.
Public Member Functions | |
void | clear () |
Reset all counts to 0. More... | |
Public Attributes | |
size_t | a_count = 0 |
Count of all A nucleotides that are present in the sample. More... | |
size_t | c_count = 0 |
Count of all C nucleotides that are present in the sample. More... | |
size_t | d_count = 0 |
Count of all deleted (* ) nucleotides that are present in the sample. More... | |
size_t | g_count = 0 |
Count of all G nucleotides that are present in the sample. More... | |
size_t | n_count = 0 |
Count of all N (undetermined/any) nucleotides that are present in the sample. More... | |
size_t | t_count = 0 |
Count of all T nucleotides that are present in the sample. More... | |
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inline |
Reset all counts to 0.
Definition at line 89 of file base_counts.hpp.
size_t a_count = 0 |
Count of all A
nucleotides that are present in the sample.
Definition at line 59 of file base_counts.hpp.
size_t c_count = 0 |
Count of all C
nucleotides that are present in the sample.
Definition at line 64 of file base_counts.hpp.
size_t d_count = 0 |
Count of all deleted (*
) nucleotides that are present in the sample.
Definition at line 84 of file base_counts.hpp.
size_t g_count = 0 |
Count of all G
nucleotides that are present in the sample.
Definition at line 69 of file base_counts.hpp.
size_t n_count = 0 |
Count of all N
(undetermined/any) nucleotides that are present in the sample.
Definition at line 79 of file base_counts.hpp.
size_t t_count = 0 |
Count of all T
nucleotides that are present in the sample.
Definition at line 74 of file base_counts.hpp.