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A library for working with phylogenetic and population genetic data.
v0.27.0 |
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A library for working with phylogenetic and population genetic data.
v0.27.0 |
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#include <genesis/population/functions/diversity.hpp>
Data struct to collect all diversity statistics computed by pool_diversity_measures().
This is meant as a simple way to obtain all diversity measures at once. It is slightly inefficient, as the filtering of variants and the traversal of the input iterator is done more than necessary. But it should still be fast enough for most applications.
Definition at line 92 of file diversity.hpp.
Public Attributes | |
| size_t | coverage_count = 0 |
| Out of the variant_count many variants, how many are properly covered, that is, have coverage in between PoolDiversitySettings::min_coverage and PoolDiversitySettings::max_coverage (both inclusive). More... | |
| size_t | snp_count = 0 |
| Out of the variant_count and coverage_count many variants, how many are SNPs, that is, have at least two different counts greater than zero. More... | |
| double | tajima_d = 0 |
| double | theta_pi_absolute = 0 |
| double | theta_pi_relative = 0 |
| double | theta_watterson_absolute = 0 |
| double | theta_watterson_relative = 0 |
| size_t | variant_count = 0 |
| Count of variants in the iterator range that surpass the PoolDiversitySettings::min_allele_count setting. More... | |
| size_t coverage_count = 0 |
Out of the variant_count many variants, how many are properly covered, that is, have coverage in between PoolDiversitySettings::min_coverage and PoolDiversitySettings::max_coverage (both inclusive).
This is the count that is used to compute the relative versions of Theata Pi and Theta Watterson as well.
Definition at line 114 of file diversity.hpp.
| size_t snp_count = 0 |
Out of the variant_count and coverage_count many variants, how many are SNPs, that is, have at least two different counts greater than zero.
Variants that are not SNPs and do not have proper coverage are not considered in the computation of the diversity measures.
Definition at line 123 of file diversity.hpp.
| double tajima_d = 0 |
Definition at line 98 of file diversity.hpp.
| double theta_pi_absolute = 0 |
Definition at line 94 of file diversity.hpp.
| double theta_pi_relative = 0 |
Definition at line 95 of file diversity.hpp.
| double theta_watterson_absolute = 0 |
Definition at line 96 of file diversity.hpp.
| double theta_watterson_relative = 0 |
Definition at line 97 of file diversity.hpp.
| size_t variant_count = 0 |
Count of variants in the iterator range that surpass the PoolDiversitySettings::min_allele_count setting.
Definition at line 104 of file diversity.hpp.
1.8.17