#include <genesis/population/sample_counts.hpp>

Detailed Description

One set of nucleotide sample 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 56 of file sample_counts.hpp.

Public Types
using	size_type = size_t
	Public alias for the size type that the class uses to store its counts. More...

Public Attributes
size_type	a_count = 0
	Count of all `A` nucleotides that are present in the sample. More...

size_type	c_count = 0
	Count of all `C` nucleotides that are present in the sample. More...

size_type	d_count = 0
	Count of all deleted (`*`) nucleotides that are present in the sample. More...

size_type	g_count = 0
	Count of all `G` nucleotides that are present in the sample. More...

size_type	n_count = 0
	Count of all `N` (undetermined/any) nucleotides that are present in the sample. More...

FilterStatus	status
	Status to indicate whether any applied filters failed to pass. More...

size_type	t_count = 0
	Count of all `T` nucleotides that are present in the sample. More...

Member Typedef Documentation

◆ size_type

using size_type = size_t

Public alias for the size type that the class uses to store its counts.

Definition at line 61 of file sample_counts.hpp.

Member Data Documentation

◆ a_count

size_type a_count = 0

Count of all A nucleotides that are present in the sample.

Definition at line 66 of file sample_counts.hpp.

◆ c_count

size_type c_count = 0

Count of all C nucleotides that are present in the sample.

Definition at line 71 of file sample_counts.hpp.

◆ d_count

size_type d_count = 0

Count of all deleted (*) nucleotides that are present in the sample.

Definition at line 91 of file sample_counts.hpp.

◆ g_count

size_type g_count = 0

Count of all G nucleotides that are present in the sample.

Definition at line 76 of file sample_counts.hpp.

◆ n_count

size_type n_count = 0

Count of all N (undetermined/any) nucleotides that are present in the sample.

Definition at line 86 of file sample_counts.hpp.

◆ status

FilterStatus status

Status to indicate whether any applied filters failed to pass.

Definition at line 96 of file sample_counts.hpp.

◆ t_count

size_type t_count = 0

Count of all T nucleotides that are present in the sample.

Definition at line 81 of file sample_counts.hpp.

The documentation for this struct was generated from the following file:

sample_counts.hpp