A library for working with phylogenetic and population genetic data.
PoolDiversitySettings Struct Reference

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

Detailed Description

Settings used by different pool-sequencing corrected diversity statistics.

These settings are used for example by theta_pi_pool(), theta_watterson_pool(), and tajima_d_pool(), as well as pool_diversity_measures(), in order to have them in a central place, and avoid ordering confusion of function arguments, that would result from having to provide them individually.

Note in particular the setting with_popoolation_bugs: There are two major bugs (as far as we are aware) in the PoPoolation implementation:

  1. They compute the n_base term based on poolsize alone, and do not take the coverage into account at all.
  2. They do not use alpha star, but set it to be equal to beta star instead.

Using this option, one can voluntarily activate these bugs here as well, in order to get results that are comparable with PoPoolation results.

Definition at line 74 of file diversity.hpp.

Public Attributes

size_t max_coverage = 0
size_t min_allele_count = 0
size_t min_coverage = 0
size_t poolsize = 0
bool with_popoolation_bugs = false

Member Data Documentation

◆ max_coverage

size_t max_coverage = 0

Definition at line 80 of file diversity.hpp.

◆ min_allele_count

size_t min_allele_count = 0

Definition at line 78 of file diversity.hpp.

◆ min_coverage

size_t min_coverage = 0

Definition at line 79 of file diversity.hpp.

◆ poolsize

size_t poolsize = 0

Definition at line 76 of file diversity.hpp.

◆ with_popoolation_bugs

bool with_popoolation_bugs = false

Definition at line 82 of file diversity.hpp.

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