vg::MinimizerMapper::Minimizer Struct Reference

#include <minimizer_mapper.hpp>

Public Member Functions
bool	operator< (const Minimizer &another) const
size_t	forward_offset () const
size_t	pin_offset () const
size_t	window_size () const
	How many bases are in a window for which a minimizer is chosen? More...
size_t	agglomeration_window_count () const
	How many different windows are in this minimizer's agglomeration? More...
string	forward_sequence () const
	What is the minimizer sequence, in read orientation? More...

Public Attributes
gbwtgraph::DefaultMinimizerIndex::minimizer_type	value
size_t	agglomeration_start
size_t	agglomeration_length
size_t	hits
const gbwtgraph::DefaultMinimizerIndex::value_type *	occs
int32_t	length
int32_t	candidates_per_window
double	score
bool	is_repetitive

Detailed Description

We define our own type for minimizers, to use during mapping and to pass around between our internal functions. Also used to represent syncmers, in which case the only window, the "minimizer", and the agglomeration are all the same region.

Member Function Documentation

agglomeration_window_count()

size_t vg::MinimizerMapper::Minimizer::agglomeration_window_count ( ) const

inline

How many different windows are in this minimizer's agglomeration?

forward_offset()

size_t vg::MinimizerMapper::Minimizer::forward_offset ( ) const

inline

Get the starting position of the given minimizer on the forward strand. Use this instead of value.offset which can really be the last base for reverse strand minimizers.

forward_sequence()

string vg::MinimizerMapper::Minimizer::forward_sequence ( ) const

inline

What is the minimizer sequence, in read orientation?

operator<()

bool vg::MinimizerMapper::Minimizer::operator< ( const Minimizer &  another ) const

inline

pin_offset()

size_t vg::MinimizerMapper::Minimizer::pin_offset ( ) const

inline

Get the position on the read's sequence that corresponds to the located graph positions. For reverse-strand minimizers this will be at the end of the minimizer's interval in the read.

window_size()

size_t vg::MinimizerMapper::Minimizer::window_size ( ) const

inline

How many bases are in a window for which a minimizer is chosen?

Member Data Documentation

agglomeration_length

size_t vg::MinimizerMapper::Minimizer::agglomeration_length

agglomeration_start

size_t vg::MinimizerMapper::Minimizer::agglomeration_start

candidates_per_window

int32_t vg::MinimizerMapper::Minimizer::candidates_per_window

hits

size_t vg::MinimizerMapper::Minimizer::hits

is_repetitive

bool vg::MinimizerMapper::Minimizer::is_repetitive

length

int32_t vg::MinimizerMapper::Minimizer::length

occs

const gbwtgraph::DefaultMinimizerIndex::value_type* vg::MinimizerMapper::Minimizer::occs

score

double vg::MinimizerMapper::Minimizer::score

value

gbwtgraph::DefaultMinimizerIndex::minimizer_type vg::MinimizerMapper::Minimizer::value

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

• src/minimizer_mapper.hpp