vg::PairedEndMapper Class Reference

#include <mapper.hpp>

Inheritance diagram for vg::PairedEndMapper:

Public Member Functions
void	set_fragment_length_distr_params (size_t maximum_sample_size=1000, size_t reestimation_frequency=1000, double robust_estimation_fraction=0.95)
bool	has_fixed_fragment_length_distr ()
	Returns true if fragment length distribution has been fixed. More...
void	force_fragment_length_distr (double mean, double stddev)

Protected Attributes
FragmentLengthDistribution	fragment_length_distr
	Holds the actual fragment length distribution and estimation information. More...

Detailed Description

A class trait/mixin which defines a mapper's paired end distribution support.

Doesn't actually define the paired-end mapping methods.

Member Function Documentation

force_fragment_length_distr()

void vg::PairedEndMapper::force_fragment_length_distr	(	double	mean,
		double	stddev
	)

Use the given fragment length distribution parameters instead of estimating them.

has_fixed_fragment_length_distr()

bool vg::PairedEndMapper::has_fixed_fragment_length_distr

(

)

Returns true if fragment length distribution has been fixed.

set_fragment_length_distr_params()

void vg::PairedEndMapper::set_fragment_length_distr_params	(	size_t	maximum_sample_size = 1000,
		size_t	reestimation_frequency = 1000,
		double	robust_estimation_fraction = 0.95
	)

Set parameters for estimating fragment length distribution. TODO: setting alignment threads after this could mess up the internal memory for how many threads to reset to

Member Data Documentation

fragment_length_distr

FragmentLengthDistribution vg::PairedEndMapper::fragment_length_distr

protected

Holds the actual fragment length distribution and estimation information.

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

• src/mapper.hpp
• src/mapper.cpp