#include <mapper.hpp>

Public Member Functions
void	record_fragment_configuration (const Alignment &aln1, const Alignment &aln2, Mapper *mapper)

string	fragment_model_str (void)

void	save_frag_lens_to_alns (Alignment &aln1, Alignment &aln2, const unordered_map< path_handle_t, int64_t > &approx_frag_lengths, PathPositionHandleGraph *xindex, bool is_consistent)

double	fragment_length_stdev (void)

double	fragment_length_mean (void)

double	fragment_length_pdf (double length)

double	fragment_length_pval (double length)

bool	fragment_orientation (void)

bool	fragment_direction (void)

Public Attributes
double	cached_fragment_length_mean = 0

double	cached_fragment_length_stdev = 0

bool	cached_fragment_orientation_same = 0

bool	cached_fragment_direction = 1

int64_t	since_last_fragment_length_estimate = 0

int64_t	fragment_model_update_interval = 100

deque< double >	fragment_lengths

deque< bool >	fragment_orientations

deque< bool >	fragment_directions

int64_t	fragment_max = 10000

int64_t	fragment_size = 0

double	fragment_sigma = 10

int64_t	fragment_length_cache_size = 10000

float	perfect_pair_identity_threshold = 0.9

bool	fixed_fragment_model = true

Detailed Description

Keeps track of statistics about fragment length within the Mapper class. Belongs to a single thread.

Member Function Documentation

◆ fragment_direction()

bool vg::FragmentLengthStatistics::fragment_direction ( void )

◆ fragment_length_mean()

double vg::FragmentLengthStatistics::fragment_length_mean ( void )

◆ fragment_length_pdf()

double vg::FragmentLengthStatistics::fragment_length_pdf ( double length )

◆ fragment_length_pval()

double vg::FragmentLengthStatistics::fragment_length_pval ( double length )

◆ fragment_length_stdev()

double vg::FragmentLengthStatistics::fragment_length_stdev ( void )

◆ fragment_model_str()

string vg::FragmentLengthStatistics::fragment_model_str ( void )

◆ fragment_orientation()

bool vg::FragmentLengthStatistics::fragment_orientation ( void )

◆ record_fragment_configuration()

void vg::FragmentLengthStatistics::record_fragment_configuration	(	const Alignment &	aln1,
		const Alignment &	aln2,
		Mapper *	mapper
	)

◆ save_frag_lens_to_alns()

void vg::FragmentLengthStatistics::save_frag_lens_to_alns	(	Alignment &	aln1,
		Alignment &	aln2,
		const unordered_map< path_handle_t, int64_t > &	approx_frag_lengths,
		PathPositionHandleGraph *	xindex,
		bool	is_consistent
	)

Member Data Documentation

◆ cached_fragment_direction

bool vg::FragmentLengthStatistics::cached_fragment_direction = 1

◆ cached_fragment_length_mean

double vg::FragmentLengthStatistics::cached_fragment_length_mean = 0

◆ cached_fragment_length_stdev

double vg::FragmentLengthStatistics::cached_fragment_length_stdev = 0

◆ cached_fragment_orientation_same

bool vg::FragmentLengthStatistics::cached_fragment_orientation_same = 0

◆ fixed_fragment_model

bool vg::FragmentLengthStatistics::fixed_fragment_model = true

◆ fragment_directions

deque<bool> vg::FragmentLengthStatistics::fragment_directions

◆ fragment_length_cache_size

int64_t vg::FragmentLengthStatistics::fragment_length_cache_size = 10000

◆ fragment_lengths

deque<double> vg::FragmentLengthStatistics::fragment_lengths

◆ fragment_max

int64_t vg::FragmentLengthStatistics::fragment_max = 10000

◆ fragment_model_update_interval

int64_t vg::FragmentLengthStatistics::fragment_model_update_interval = 100

◆ fragment_orientations

deque<bool> vg::FragmentLengthStatistics::fragment_orientations

◆ fragment_sigma

double vg::FragmentLengthStatistics::fragment_sigma = 10

◆ fragment_size

int64_t vg::FragmentLengthStatistics::fragment_size = 0

◆ perfect_pair_identity_threshold

float vg::FragmentLengthStatistics::perfect_pair_identity_threshold = 0.9

◆ since_last_fragment_length_estimate

int64_t vg::FragmentLengthStatistics::since_last_fragment_length_estimate = 0

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

src/mapper.hpp
src/mapper.cpp

Public Member Functions

Public Attributes