BaseFstPoolCalculator Class Reference

#include <genesis/population/function/fst_pool_calculator.hpp>

Inherited by FstPoolCalculatorKarlsson, FstPoolCalculatorKofler, and FstPoolCalculatorUnbiased.

Detailed Description

Base class to compute FST between two pooled samples, given two instances of SampleCounts.

The class is to be derived from for the actual computation, such as in FstPoolCalculatorKarlsson, FstPoolCalculatorKofler, or FstPoolCalculatorUnbiased, with three virtual methods to override. Then, an instance of such a calculator can be provided to FstPoolProcessor, which processes Variants along a genome, computing FST along the way.

The idea of using classes here instead of simple iterators over Variants, such as VariantInputStream, is that we want to be able to compute FST for many pairs of samples in some input. With input iterators that just read the input files once however, we cannot iterate multiple times over the same input. Hence we would have to keep all Variants in memory to be able to compute FST for multiple pairs - which is not desirable when, e.g., computing FST for the whole genome at once... So instead, we use these classes, which accumulate all needed data along the way, and yield the FST value at the very end when calling get_result().

Definition at line 65 of file fst_pool_calculator.hpp.

Public Member Functions
	BaseFstPoolCalculator ()=default
	BaseFstPoolCalculator (BaseFstPoolCalculator &&)=default
	BaseFstPoolCalculator (BaseFstPoolCalculator const &)=default
virtual	~BaseFstPoolCalculator ()=default
SampleCountsFilterStats	get_filter_stats () const
	Get the sum of filter statistics of all sample pairs processed here. More...
double	get_result () const
BaseFstPoolCalculator &	operator= (BaseFstPoolCalculator &&)=default
BaseFstPoolCalculator &	operator= (BaseFstPoolCalculator const &)=default
void	process (SampleCounts const &p1, SampleCounts const &p2)
void	reset ()

Protected Member Functions
virtual double	get_result_ () const =0
virtual void	process_ (SampleCounts const &p1, SampleCounts const &p2)=0
virtual void	reset_ ()=0

Constructor & Destructor Documentation

BaseFstPoolCalculator() [1/3]

BaseFstPoolCalculator ( )

default

~BaseFstPoolCalculator()

virtual ~BaseFstPoolCalculator ( )

virtualdefault

BaseFstPoolCalculator() [2/3]

BaseFstPoolCalculator ( BaseFstPoolCalculator const &  )

default

BaseFstPoolCalculator() [3/3]

BaseFstPoolCalculator ( BaseFstPoolCalculator &&  )

default

Member Function Documentation

get_filter_stats()

SampleCountsFilterStats get_filter_stats ( ) const

inline

Get the sum of filter statistics of all sample pairs processed here.

With each call to process(), the filter stats are increased according to the filter status of both provided samples. Hence, the counts returned here always have an even sum.

Definition at line 129 of file fst_pool_calculator.hpp.

get_result()

double get_result ( ) const

inline

Definition at line 118 of file fst_pool_calculator.hpp.

get_result_()

virtual double get_result_ ( ) const

protectedpure virtual

operator=() [1/2]

BaseFstPoolCalculator& operator= ( BaseFstPoolCalculator &&  )

default

operator=() [2/2]

BaseFstPoolCalculator& operator= ( BaseFstPoolCalculator const &  )

default

process()

void process ( SampleCounts const &  p1, SampleCounts const &  p2  )

inline

Definition at line 92 of file fst_pool_calculator.hpp.

process_()

virtual void process_ ( SampleCounts const &  p1, SampleCounts const &  p2  )

protectedpure virtual

reset()

void reset ( )

inline

Definition at line 86 of file fst_pool_calculator.hpp.

reset_()

virtual void reset_ ( )

protectedpure virtual

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

• fst_pool_calculator.hpp