vg::Recombinator::Statistics Struct Reference

Statistics on the generated haplotypes. More...

#include <recombinator.hpp>

Public Member Functions
void	combine (const Statistics &another)
	Combines the statistics into this object.
std::ostream &	print (std::ostream &out) const
	Prints the statistics and returns the output stream.

Public Attributes
size_t	chains = 0
	Number of top-level chains.
size_t	subchains = 0
	Number of subchains.
size_t	bad_subchains = 0
	Number of subchains exceeding the badness threshold.
size_t	fragments = 0
	Total number of fragments in the generated haplotypes.
size_t	full_haplotypes = 0
size_t	haplotypes = 0
	Number of haplotypes generated.
size_t	extra_fragments = 0
	Number of additional haplotype fragments in bad subchains.
size_t	connections = 0
	Number of times the same haplotype was extended from a subchain to the next subchain.
size_t	ref_paths = 0
	Number of reference paths included.
size_t	copied_paths = 0
	Number of paths copied verbatim from excluded chains.
size_t	kmers = 0
	Number of kmers selected.
double	score = 0.0
	Total score for selected sequences.

Detailed Description

Statistics on the generated haplotypes.

Member Function Documentation

combine()

void vg::Recombinator::Statistics::combine

(

const Statistics &

another

)

Combines the statistics into this object.

print()

std::ostream & vg::Recombinator::Statistics::print

(

std::ostream &

out

)

const

Prints the statistics and returns the output stream.

Member Data Documentation

bad_subchains

size_t vg::Recombinator::Statistics::bad_subchains = 0

Number of subchains exceeding the badness threshold.

chains

size_t vg::Recombinator::Statistics::chains = 0

Number of top-level chains.

connections

size_t vg::Recombinator::Statistics::connections = 0

Number of times the same haplotype was extended from a subchain to the next subchain.

copied_paths

size_t vg::Recombinator::Statistics::copied_paths = 0

Number of paths copied verbatim from excluded chains.

extra_fragments

size_t vg::Recombinator::Statistics::extra_fragments = 0

Number of additional haplotype fragments in bad subchains.

fragments

size_t vg::Recombinator::Statistics::fragments = 0

Total number of fragments in the generated haplotypes.

full_haplotypes

size_t vg::Recombinator::Statistics::full_haplotypes = 0

Number of top-level chains where full haplotypes were taken. These are not counted as fragments.

haplotypes

size_t vg::Recombinator::Statistics::haplotypes = 0

Number of haplotypes generated.

kmers

size_t vg::Recombinator::Statistics::kmers = 0

Number of kmers selected.

ref_paths

size_t vg::Recombinator::Statistics::ref_paths = 0

Number of reference paths included.

score

double vg::Recombinator::Statistics::score = 0.0

Total score for selected sequences.

subchains

size_t vg::Recombinator::Statistics::subchains = 0

Number of subchains.

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

• src/recombinator.hpp
• src/recombinator.cpp