A library for working with phylogenetic data.
v0.25.0
BaseCountsStatus Struct Reference

#include <genesis/population/functions/base_counts.hpp>

Detailed Description

Definition at line 49 of file functions/base_counts.hpp.

Public Attributes

bool is_biallelic = false
 Is the Sample biallelic? More...
 
bool is_covered = false
 Is the Sample covered by enough reads/nucleotides? More...
 
bool is_ignored = false
 Is the Sample ignored due to high deletions count? More...
 
bool is_snp = false
 Does the Sample have two or more alleles? More...
 

Member Data Documentation

◆ is_biallelic

bool is_biallelic = false

Is the Sample biallelic?

This is closely related to Sample::is_snp, but only true iff the number of nucleotide counts above zero is exactly two - that is, if there are only reads of two of A, C, G, T in the sample.

This value is also false if the amount of deletions (Sample::d_count) is too high (using min_count() as the inclusive threshold), unless tolerate_deletions() is true.

Definition at line 88 of file functions/base_counts.hpp.

◆ is_covered

bool is_covered = false

Is the Sample covered by enough reads/nucleotides?

This value is set to true iff the total Sample::nucleotide_count (sum of Sample::a_count, Sample::c_count, Sample::g_count, and Sample::t_count after testing that they are at least min_count()) is in between the min_coverage() and max_coverage() values (inclusive), and iff the amount of deletions (Sample::d_count) is not higher than min_count() as well (unless, tolerate_deletions() is also set to true).

That was a mouthful. Basically, a Sample is covered, if the sum of A, C, G, T is in between min_coverage() and max_coverage(), and (unless we tolerate that) the amount of deletions is not too high.

Definition at line 64 of file functions/base_counts.hpp.

◆ is_ignored

bool is_ignored = false

Is the Sample ignored due to high deletions count?

This value is only set to true iff the Sample is well covered (as determined by Sample::is_covered), but also has a high amount of deletions (at least min_count() many), and if not also tolerate_deletions() is true.

It is hence an indicator that there are too many deletions in the sample (if we decide not to tolerate them).

Definition at line 100 of file functions/base_counts.hpp.

◆ is_snp

bool is_snp = false

Does the Sample have two or more alleles?

That is the case if at least two of the A, C, G, T counts (Sample::a_count, Sample::c_count, Sample::g_count, and Sample::t_count ) are above zero, after testing that they are at least min_count().

This value is also false if the amount of deletions (Sample::d_count) is too high (using min_count() as the inclusive threshold), unless tolerate_deletions() is true.

Definition at line 76 of file functions/base_counts.hpp.


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