vg::FragmentLengthDistribution Class Reference

#include <mapper.hpp>

Public Member Functions
	FragmentLengthDistribution (size_t maximum_sample_size, size_t reestimation_frequency, double robust_estimation_fraction)
	FragmentLengthDistribution (void)
	~FragmentLengthDistribution ()
void	force_parameters (double mean, double stddev)
	Instead of estimating anything, just use these parameters.
void	register_fragment_length (int64_t length)
	Record an observed fragment length.
double	mean () const
	Robust mean of the distribution observed so far.
double	std_dev () const
	Robust standard deviation of the distribution observed so far.
bool	is_finalized () const
size_t	max_sample_size () const
size_t	curr_sample_size () const
	Returns the number of samples that have been collected so far.
multiset< double >::const_iterator	measurements_begin () const
multiset< double >::const_iterator	measurements_end () const

Private Member Functions
void	estimate_distribution ()

Private Attributes
multiset< double >	lengths
bool	is_fixed = false
double	robust_estimation_fraction
size_t	maximum_sample_size
size_t	reestimation_frequency
double	mu = 0.0
double	sigma = 1.0

Constructor & Destructor Documentation

FragmentLengthDistribution() [1/2]

vg::FragmentLengthDistribution::FragmentLengthDistribution	(	size_t	maximum_sample_size,
		size_t	reestimation_frequency,
		double	robust_estimation_fraction )

Initialize distribution

Args: maximum_sample_size sample size at which reestimation stops reestimation_frequency update running estimate after this many samples robust_estimation_fraction robustly estimate using this fraction of samples

FragmentLengthDistribution() [2/2]

vg::FragmentLengthDistribution::FragmentLengthDistribution

(

void

)

~FragmentLengthDistribution()

vg::FragmentLengthDistribution::~FragmentLengthDistribution

(

)

Member Function Documentation

curr_sample_size()

size_t vg::FragmentLengthDistribution::curr_sample_size

(

)

const

Returns the number of samples that have been collected so far.

estimate_distribution()

void vg::FragmentLengthDistribution::estimate_distribution ( )

private

force_parameters()

void vg::FragmentLengthDistribution::force_parameters	(	double	mean,
		double	stddev )

Instead of estimating anything, just use these parameters.

is_finalized()

bool vg::FragmentLengthDistribution::is_finalized

(

)

const

Returns true if the maximum sample size has been reached, which finalizes the distribution estimate

max_sample_size()

size_t vg::FragmentLengthDistribution::max_sample_size

(

)

const

Returns the max sample size up to which the distribution will continue to reestimate parameters

mean()

double vg::FragmentLengthDistribution::mean

(

)

const

Robust mean of the distribution observed so far.

measurements_begin()

multiset< double >::const_iterator vg::FragmentLengthDistribution::measurements_begin

(

)

const

Begin iterator to the measurements that the distribution has used to estimate the parameters

measurements_end()

multiset< double >::const_iterator vg::FragmentLengthDistribution::measurements_end

(

)

const

End iterator to the measurements that the distribution has used to estimate the parameters

register_fragment_length()

void vg::FragmentLengthDistribution::register_fragment_length

(

int64_t

length

)

Record an observed fragment length.

std_dev()

double vg::FragmentLengthDistribution::std_dev

(

)

const

Robust standard deviation of the distribution observed so far.

Member Data Documentation

is_fixed

bool vg::FragmentLengthDistribution::is_fixed = false

private

lengths

multiset<double> vg::FragmentLengthDistribution::lengths

private

maximum_sample_size

size_t vg::FragmentLengthDistribution::maximum_sample_size

private

mu

double vg::FragmentLengthDistribution::mu = 0.0

private

reestimation_frequency

size_t vg::FragmentLengthDistribution::reestimation_frequency

private

robust_estimation_fraction

double vg::FragmentLengthDistribution::robust_estimation_fraction

private

sigma

double vg::FragmentLengthDistribution::sigma = 1.0

private

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

• src/mapper.hpp
• src/mapper.cpp