A library for working with phylogenetic 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 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 73 of file diversity.hpp.

Public Attributes

size_t max_coverage = 0
size_t min_allele_count = 0
size_t min_coverage = 0
double min_coverage_fraction = 0.0
size_t min_phred_score = 0
size_t poolsize = 0
size_t window_stride = 0
size_t window_width = 0
bool with_popoolation_bugs = false

Member Data Documentation

◆ max_coverage

size_t max_coverage = 0

Definition at line 82 of file diversity.hpp.

◆ min_allele_count

size_t min_allele_count = 0

Definition at line 80 of file diversity.hpp.

◆ min_coverage

size_t min_coverage = 0

Definition at line 81 of file diversity.hpp.

◆ min_coverage_fraction

double min_coverage_fraction = 0.0

Definition at line 83 of file diversity.hpp.

◆ min_phred_score

size_t min_phred_score = 0

Definition at line 77 of file diversity.hpp.

◆ poolsize

size_t poolsize = 0

Definition at line 79 of file diversity.hpp.

◆ window_stride

size_t window_stride = 0

Definition at line 76 of file diversity.hpp.

◆ window_width

size_t window_width = 0

Definition at line 75 of file diversity.hpp.

◆ with_popoolation_bugs

bool with_popoolation_bugs = false

Definition at line 84 of file diversity.hpp.

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