vg::algorithms::Anchor Class Reference

#include <chain_items.hpp>

Public Member Functions
size_t	read_start () const
	Get the start position in the read of this anchor's match. More...
const pos_t &	graph_start () const
	Get the start position in the graph of this anchor's match. More...
size_t	read_exclusion_start () const
size_t	length () const
	Get the length of this anchor's match. More...
int	score () const
	Get the alignment score of the anchor. More...
size_t	read_end () const
	Get the end position in the read of this anchor's match. More...
pos_t	graph_end () const
	Get the end position in the graph of this anchor's match. More...
size_t	read_exclusion_end () const
size_t	seed_start () const
size_t	seed_end () const
ZipCode *	start_hint () const
size_t	start_hint_offset () const
ZipCode *	end_hint () const
size_t	end_hint_offset () const
size_t	base_seed_length () const
bool	is_skippable () const
void	clear_paths ()
void	set_paths (const path_flags_t anchor_paths)
void	set_paths (size_t anchor_start_paths, size_t anchor_end_paths)
void	set_paths (const std::vector< size_t > &anchor_paths)
void	add_paths (const std::vector< size_t > &anchor_paths)
	Add new paths to the supported haplotypes. More...
void	add_path (size_t path)
void	update_paths (const path_flags_t &new_paths)
	Update the paths supported by an anchor. More...
void	update_start_paths (const path_flags_t &new_paths)
void	update_end_paths (const path_flags_t &new_paths)
void	update_paths (const std::vector< size_t > &haplotypes)
const std::pair< path_flags_t, path_flags_t >	anchor_paths () const
	Get the supported paths, as a 64 bit integer, where each bit is set to 1 if the respective path is supported. More...
path_flags_t	anchor_start_paths () const
path_flags_t	anchor_end_paths () const
	Anchor (size_t read_start, const pos_t &graph_start, size_t length, size_t margin_before, size_t margin_after, int score, size_t seed_number=std::numeric_limits< size_t >::max(), ZipCode *hint=nullptr, size_t hint_start=0, bool skippable=false, path_flags_t paths=0)
	Anchor (const Anchor &first, const Anchor &last, size_t extra_margin_before, size_t extra_margin_after, int score)
	Anchor ()=default
	Anchor (const Anchor &other)=default
Anchor &	operator= (const Anchor &other)=default
	Anchor (Anchor &&other)=default
Anchor &	operator= (Anchor &&other)=default

Protected Attributes
size_t	start
size_t	size
size_t	margin_before
size_t	margin_after
pos_t	start_pos
pos_t	end_pos
int	points
size_t	start_seed
size_t	end_seed
ZipCode *	start_zip
ZipCode *	end_zip
size_t	start_offset
size_t	end_offset
size_t	seed_length
bool	skippable
path_flags_t	start_paths
path_flags_t	end_paths

Detailed Description

Represents a piece of a graph node matching to a piece of a read. Can be chained together.

Constructor & Destructor Documentation

Anchor() [1/5]

vg::algorithms::Anchor::Anchor ( size_t  read_start, const pos_t &  graph_start, size_t  length, size_t  margin_before, size_t  margin_after, int  score, size_t  seed_number = std::numeric_limits<size_t>::max(), ZipCode *  hint = nullptr, size_t  hint_start = 0, bool  skippable = false, path_flags_t  paths = 0  )

inline

Compose a read start position, graph start position, and match length into an Anchor. Can also bring along a distance hint and a seed number.

Anchor() [2/5]

vg::algorithms::Anchor::Anchor ( const Anchor &  first, const Anchor &  last, size_t  extra_margin_before, size_t  extra_margin_after, int  score  )

inline

Compose two Anchors into an Anchor that represents coming in through the first one and going out through the second, like a tunnel. Useful for representing chains as chainable items.

Anchor() [3/5]

vg::algorithms::Anchor::Anchor ( )

default

Anchor() [4/5]

vg::algorithms::Anchor::Anchor ( const Anchor &  other )

default

Anchor() [5/5]

vg::algorithms::Anchor::Anchor ( Anchor &&  other )

default

Member Function Documentation

add_path()

void vg::algorithms::Anchor::add_path ( size_t  path )

inline

add_paths()

void vg::algorithms::Anchor::add_paths ( const std::vector< size_t > &  anchor_paths )

inline

Add new paths to the supported haplotypes.

anchor_end_paths()

path_flags_t vg::algorithms::Anchor::anchor_end_paths ( ) const

inline

anchor_paths()

const std::pair<path_flags_t, path_flags_t> vg::algorithms::Anchor::anchor_paths ( ) const

inline

Get the supported paths, as a 64 bit integer, where each bit is set to 1 if the respective path is supported.

anchor_start_paths()

path_flags_t vg::algorithms::Anchor::anchor_start_paths ( ) const

inline

base_seed_length()

size_t vg::algorithms::Anchor::base_seed_length ( ) const

inline

Get the length of the exclusion zone for a primary anchor, or the average such length of the anchors this anchor is made from for a composite anchor. This is used in gap scoring during chaining, to make sure gap scores don't get enormous for long composite anchors.

clear_paths()

void vg::algorithms::Anchor::clear_paths ( )

inline

end_hint()

ZipCode* vg::algorithms::Anchor::end_hint ( ) const

inline

Get the distance-finding hint information (i.e. "zip code") for accelerating distance queries from the end of this anchor, or null if none is set.

end_hint_offset()

size_t vg::algorithms::Anchor::end_hint_offset ( ) const

inline

Get the graph distance from wherever the end hint is positioned forward to the actual end of the anchor.

graph_end()

pos_t vg::algorithms::Anchor::graph_end ( ) const

inline

Get the end position in the graph of this anchor's match.

graph_start()

const pos_t& vg::algorithms::Anchor::graph_start ( ) const

inline

Get the start position in the graph of this anchor's match.

is_skippable()

bool vg::algorithms::Anchor::is_skippable ( ) const

inline

Can this anchor be skipped when constructing an alignment? This will be true if the anchor is in a repetitive region of the read

length()

size_t vg::algorithms::Anchor::length ( ) const

inline

Get the length of this anchor's match.

operator=() [1/2]

Anchor& vg::algorithms::Anchor::operator= ( Anchor &&  other )

default

operator=() [2/2]

Anchor& vg::algorithms::Anchor::operator= ( const Anchor &  other )

default

read_end()

size_t vg::algorithms::Anchor::read_end ( ) const

inline

Get the end position in the read of this anchor's match.

read_exclusion_end()

size_t vg::algorithms::Anchor::read_exclusion_end ( ) const

inline

Get the end position in the read of the part of the read that you can't have another anchor in if you take this one.

read_exclusion_start()

size_t vg::algorithms::Anchor::read_exclusion_start ( ) const

inline

Get the start position in the read of the part of the read that you can't have another anchor in if you take this one.

We trimmed the anchors down from the minimizers to avoid having to deal with the tail ends of the minimizers going multiple places in the graph. But we don't want to let you take anchors from minimizers that overlapped.

read_start()

size_t vg::algorithms::Anchor::read_start ( ) const

inline

Get the start position in the read of this anchor's match.

score()

int vg::algorithms::Anchor::score ( ) const

inline

Get the alignment score of the anchor.

seed_end()

size_t vg::algorithms::Anchor::seed_end ( ) const

inline

Get the number of the seed at the end of the chain, or std::numeric_limits<size_t>::max() if not set.

seed_start()

size_t vg::algorithms::Anchor::seed_start ( ) const

inline

Get the number of the seed at the start of the anchor, or std::numeric_limits<size_t>::max() if not set.

set_paths() [1/3]

void vg::algorithms::Anchor::set_paths ( const path_flags_t  anchor_paths )

inline

Set the haplotypes supported by this anchor Maximum number limited to 64 for now

set_paths() [2/3]

void vg::algorithms::Anchor::set_paths ( const std::vector< size_t > &  anchor_paths )

inline

set_paths() [3/3]

void vg::algorithms::Anchor::set_paths ( size_t  anchor_start_paths, size_t  anchor_end_paths  )

inline

start_hint()

ZipCode* vg::algorithms::Anchor::start_hint ( ) const

inline

Get the distance-finding hint information (i.e. "zip code") for accelerating distance queries to the start of this anchor, or null if none is set.

start_hint_offset()

size_t vg::algorithms::Anchor::start_hint_offset ( ) const

inline

Get the graph distance from wherever the start hint is positioned back to the actual start of the anchor.

update_end_paths()

void vg::algorithms::Anchor::update_end_paths ( const path_flags_t &  new_paths )

inline

update_paths() [1/2]

void vg::algorithms::Anchor::update_paths ( const path_flags_t &  new_paths )

inline

Update the paths supported by an anchor.

update_paths() [2/2]

void vg::algorithms::Anchor::update_paths ( const std::vector< size_t > &  haplotypes )

inline

update_start_paths()

void vg::algorithms::Anchor::update_start_paths ( const path_flags_t &  new_paths )

inline

Member Data Documentation

end_offset

size_t vg::algorithms::Anchor::end_offset

protected

end_paths

path_flags_t vg::algorithms::Anchor::end_paths

protected

end_pos

pos_t vg::algorithms::Anchor::end_pos

protected

end_seed

size_t vg::algorithms::Anchor::end_seed

protected

end_zip

ZipCode* vg::algorithms::Anchor::end_zip

protected

margin_after

size_t vg::algorithms::Anchor::margin_after

protected

margin_before

size_t vg::algorithms::Anchor::margin_before

protected

points

int vg::algorithms::Anchor::points

protected

seed_length

size_t vg::algorithms::Anchor::seed_length

protected

size

size_t vg::algorithms::Anchor::size

protected

skippable

bool vg::algorithms::Anchor::skippable

protected

start

size_t vg::algorithms::Anchor::start

protected

start_offset

size_t vg::algorithms::Anchor::start_offset

protected

start_paths

path_flags_t vg::algorithms::Anchor::start_paths

protected

start_pos

pos_t vg::algorithms::Anchor::start_pos

protected

start_seed

size_t vg::algorithms::Anchor::start_seed

protected

start_zip

ZipCode* vg::algorithms::Anchor::start_zip

protected

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

• src/algorithms/chain_items.hpp