#include <genesis/population/functions/diversity.hpp>
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:
n_base
term based on poolsize alone, and do not take the coverage into account at all.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 |
size_t max_coverage = 0 |
Definition at line 80 of file diversity.hpp.
size_t min_allele_count = 0 |
Definition at line 78 of file diversity.hpp.
size_t min_coverage = 0 |
Definition at line 79 of file diversity.hpp.
size_t poolsize = 0 |
Definition at line 76 of file diversity.hpp.
bool with_popoolation_bugs = false |
Definition at line 82 of file diversity.hpp.