Parameters for generate_haplotypes(). More...

#include <recombinator.hpp>

Public Types
enum	preset_t { preset_default, preset_haploid, preset_diploid }
	Preset parameters for common use cases. More...

Public Member Functions
	Parameters (preset_t preset=preset_default)

void	print (std::ostream &out) const
	Print a description of the parameters. More...

Public Attributes
size_t	num_haplotypes = NUM_HAPLOTYPES

size_t	coverage = COVERAGE
	Kmer coverage. Use 0 to estimate from kmer counts. More...

gbwt::size_type	buffer_size = gbwt::DynamicGBWT::INSERT_BATCH_SIZE
	Buffer size (in nodes) for GBWT construction. More...

double	present_discount = PRESENT_DISCOUNT

double	het_adjustment = HET_ADJUSTMENT

double	absent_score = ABSENT_SCORE

bool	haploid_scoring = false

bool	diploid_sampling = false

bool	include_reference = false
	Include named and reference paths. More...

Detailed Description

Parameters for generate_haplotypes().

Member Enumeration Documentation

◆ preset_t

enum vg::Recombinator::Parameters::preset_t

Preset parameters for common use cases.

Enumerator
preset_default	Default parameters.
preset_haploid	Best practices for haploid sampling.
preset_diploid	Best practices for diploid sampling.

Constructor & Destructor Documentation

◆ Parameters()

vg::Recombinator::Parameters::Parameters ( preset_t preset = preset_default )

explicit

Member Function Documentation

◆ print()

void vg::Recombinator::Parameters::print ( std::ostream & out ) const

Print a description of the parameters.

Member Data Documentation

◆ absent_score

double vg::Recombinator::Parameters::absent_score = ABSENT_SCORE

Score for absent kmers. This should be less than 1 if we assume that having the right variants in the graph is more important than keeping the wrong variants out.

◆ buffer_size

gbwt::size_type vg::Recombinator::Parameters::buffer_size = gbwt::DynamicGBWT::INSERT_BATCH_SIZE

Buffer size (in nodes) for GBWT construction.

◆ coverage

size_t vg::Recombinator::Parameters::coverage = COVERAGE

Kmer coverage. Use 0 to estimate from kmer counts.

◆ diploid_sampling

bool vg::Recombinator::Parameters::diploid_sampling = false

After selecting the initial num_haplotypes haplotypes, choose the highest-scoring pair out of them.

◆ haploid_scoring

bool vg::Recombinator::Parameters::haploid_scoring = false

Use the haploid scoring model. The most common kmer count is used as the coverage estimate. Kmers that would be classified as heterozygous are treated as homozygous.

◆ het_adjustment

double vg::Recombinator::Parameters::het_adjustment = HET_ADJUSTMENT

Additive term for adjusting the scores for heterozygous kmers after each haplotype to encourage even sampling of haplotypes with and without that kmer.

◆ include_reference

bool vg::Recombinator::Parameters::include_reference = false

Include named and reference paths.

◆ num_haplotypes

size_t vg::Recombinator::Parameters::num_haplotypes = NUM_HAPLOTYPES

Number of haplotypes to be generated, or the number of candidates for diploid sampling.

◆ present_discount

double vg::Recombinator::Parameters::present_discount = PRESENT_DISCOUNT

Multiplicative factor for discounting the scores for present kmers after selecting a haplotype with that kmer.

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

src/recombinator.hpp
src/recombinator.cpp

Public Types

Public Member Functions

Public Attributes