subsample.cpp File Reference

#include "genesis/population/function/subsample.hpp"
#include "genesis/population/function/functions.hpp"
#include "genesis/utils/core/algorithm.hpp"
#include "genesis/utils/core/logging.hpp"
#include "genesis/utils/math/distribution.hpp"
#include <cassert>
#include <cmath>
#include <stdexcept>

Go to the source code of this file.

Namespaces
	genesis
	Container namespace for all symbols of genesis in order to keep them separate when used as a library.
	genesis::population

Functions
void	resample_counts (SampleCounts &sample, size_t target_depth)
	Resample all counts in a SampleCounts sample to a new target_depth. More...
void	resample_counts (Variant &variant, size_t target_depth)
	Resample all counts in a SampleCounts sample to a new target_depth. More...
template<typename Distribution >
void	resample_counts_ (SampleCounts &sample, size_t max_depth, Distribution distribution, bool skip_if_below_target_depth)
	Local helper function to avoid code duplication. Takes the distribution (with or without replacement) and performs the resampling of base counts. More...
void	rescale_counts (SampleCounts &sample, size_t target_depth)
	Transform a SampleCounts sample by re-scaling the base counts (A, C, G, T, as well as N and D) to sum up to max if max_depth is exceeded for the sample. More...
void	rescale_counts (Variant &variant, size_t target_depth)
	Transform a SampleCounts sample by re-scaling the base counts (A, C, G, T, as well as N and D) to sum up to max if max_depth is exceeded for the sample. More...
void	rescale_counts_ (SampleCounts &sample, size_t target_depth, bool skip_if_below_target_depth)
void	subsample_counts_with_replacement (SampleCounts &sample, size_t max_depth)
	Transform a SampleCounts sample by subsampling the nucleotide counts (A, C, G, T, as well as N and D) with replacement to sum up to max if max_depth is exceeded for the sample. More...
void	subsample_counts_with_replacement (Variant &variant, size_t max_depth)
	Transform a SampleCounts sample by subsampling the nucleotide counts (A, C, G, T, as well as N and D) with replacement to sum up to max if max_depth is exceeded for the sample. More...
void	subsample_counts_without_replacement (SampleCounts &sample, size_t max_depth)
	Transform a SampleCounts sample by subsampling the nucleotide counts (A, C, G, T, as well as N and D) without replacement to sum up to max if max_depth is exceeded for the sample. More...
void	subsample_counts_without_replacement (Variant &variant, size_t max_depth)
	Transform a SampleCounts sample by subsampling the nucleotide counts (A, C, G, T, as well as N and D) without replacement to sum up to max if max_depth is exceeded for the sample. More...
void	subscale_counts (SampleCounts &sample, size_t max_depth)
	Transform a SampleCounts sample by sub-scaling the base counts (A, C, G, T, as well as N and D) to sum up to max_depth if max_depth is exceeded for the sample. More...
void	subscale_counts (Variant &variant, size_t max_depth)
	Transform a SampleCounts sample by sub-scaling the base counts (A, C, G, T, as well as N and D) to sum up to max_depth if max_depth is exceeded for the sample. More...