#include <traversal_support.hpp>

Inheritance diagram for vg::TraversalSupportFinder:

Public Member Functions
	TraversalSupportFinder (const HandleGraph &graph, SnarlManager &snarl_manager)

virtual	~TraversalSupportFinder ()

virtual Support	get_edge_support (const edge_t &edge) const =0
	Support of an edge. More...

virtual Support	get_edge_support (id_t from, bool from_reverse, id_t to, bool to_reverse) const =0

virtual int64_t	get_edge_length (const edge_t &edge, const unordered_map< id_t, size_t > &ref_offsets) const
	Effective length of an edge. More...

virtual Support	get_min_node_support (id_t node) const =0
	Minimum support of a node. More...

virtual Support	get_avg_node_support (id_t node) const =0
	Average support of a node. More...

virtual size_t	get_avg_node_mapq (id_t node) const =0
	Average MAPQ of reads that map to a node. More...

virtual tuple< Support, Support, int >	get_child_support (const Snarl &snarl) const
	Use node or edge support as proxy for child support (as was done in original calling code) More...

virtual Support	get_traversal_support (const SnarlTraversal &traversal) const

virtual vector< Support >	get_traversal_genotype_support (const vector< SnarlTraversal > &traversals, const vector< int > &genotype, const set< int > &other_trav_subset, int ref_trav_idx=-1, int *max_trav_size=nullptr)

virtual vector< Support >	get_traversal_set_support (const vector< SnarlTraversal > &traversals, const vector< int > &shared_travs, const vector< Support > &shared_support, const set< int > &tgt_travs, bool exclusive_only, const vector< int > &exclusive_count_travs, const vector< Support > &exclusive_count_support, int ref_trav_idx=-1, int *max_trav_size=nullptr) const

virtual vector< int >	get_traversal_sizes (const vector< SnarlTraversal > &traversals) const
	Get the total length of all nodes in the traversal. More...

virtual vector< double >	get_traversal_mapqs (const vector< SnarlTraversal > &traversals) const

virtual size_t	get_average_traversal_support_switch_threshold () const
	Get the average traversal support thresholdek. More...

unordered_map< id_t, size_t >	get_ref_offsets (const SnarlTraversal &ref_trav) const

virtual void	set_support_switch_threshold (size_t trav_thresh, size_t node_thresh)
	set the threshold More...

virtual void	set_min_bp_edge_override (bool bp_override)
	set the breakpoint stricter upper override More...

virtual void	apply_min_bp_edge_override (const vector< SnarlTraversal > &traversals, const set< int > &tgt_travs, vector< Support > &supports, int ref_trav_idx) const
	apply the override to a set of traversals More...

Static Public Member Functions
static double	support_val (const Support &support)
	Relic from old code. More...

Protected Attributes
size_t	average_traversal_support_switch_threshold = 50

size_t	average_node_support_switch_threshold = 50

bool	min_bp_edge_override = false
	If on, always apply minimum edge support for breakpoint (ref->offref) edges. More...

const HandleGraph &	graph

SnarlManager &	snarl_manager

Detailed Description

Get the read support of snarl traversals or sets of snarl traversals

Constructor & Destructor Documentation

◆ TraversalSupportFinder()

vg::TraversalSupportFinder::TraversalSupportFinder	(	const HandleGraph &	graph,
		SnarlManager &	snarl_manager
	)

◆ ~TraversalSupportFinder()

vg::TraversalSupportFinder::~TraversalSupportFinder ( )

virtual

Member Function Documentation

◆ apply_min_bp_edge_override()

void vg::TraversalSupportFinder::apply_min_bp_edge_override	(	const vector< SnarlTraversal > &	traversals,
		const set< int > &	tgt_travs,
		vector< Support > &	supports,
		int	ref_trav_idx
	)		const

virtual

apply the override to a set of traversals

◆ get_average_traversal_support_switch_threshold()

size_t vg::TraversalSupportFinder::get_average_traversal_support_switch_threshold ( ) const

virtual

Get the average traversal support thresholdek.

◆ get_avg_node_mapq()

virtual size_t vg::TraversalSupportFinder::get_avg_node_mapq ( id_t node ) const

pure virtual

Average MAPQ of reads that map to a node.

Implemented in vg::CachedPackedTraversalSupportFinder, and vg::PackedTraversalSupportFinder.

◆ get_avg_node_support()

virtual Support vg::TraversalSupportFinder::get_avg_node_support ( id_t node ) const

pure virtual

Average support of a node.

Implemented in vg::CachedPackedTraversalSupportFinder, and vg::PackedTraversalSupportFinder.

◆ get_child_support()

tuple< Support, Support, int > vg::TraversalSupportFinder::get_child_support ( const Snarl & snarl ) const

virtual

Use node or edge support as proxy for child support (as was done in original calling code)

Reimplemented in vg::NestedCachedPackedTraversalSupportFinder.

◆ get_edge_length()

int64_t vg::TraversalSupportFinder::get_edge_length	(	const edge_t &	edge,
		const unordered_map< id_t, size_t > &	ref_offsets
	)		const

virtual

Effective length of an edge.

◆ get_edge_support() [1/2]

virtual Support vg::TraversalSupportFinder::get_edge_support ( const edge_t & edge ) const

pure virtual

Support of an edge.

Implemented in vg::PackedTraversalSupportFinder.

◆ get_edge_support() [2/2]

virtual Support vg::TraversalSupportFinder::get_edge_support	(	id_t	from,
		bool	from_reverse,
		id_t	to,
		bool	to_reverse
	)		const

pure virtual

Implemented in vg::CachedPackedTraversalSupportFinder, and vg::PackedTraversalSupportFinder.

◆ get_min_node_support()

virtual Support vg::TraversalSupportFinder::get_min_node_support ( id_t node ) const

pure virtual

Minimum support of a node.

Implemented in vg::CachedPackedTraversalSupportFinder, and vg::PackedTraversalSupportFinder.

◆ get_ref_offsets()

unordered_map< id_t, size_t > vg::TraversalSupportFinder::get_ref_offsets ( const SnarlTraversal & ref_trav ) const

get a map of the beginning of a node (in forward orientation) on a traversal used for up-weighting large deletion edges in complex snarls with average support

◆ get_traversal_genotype_support()

vector< Support > vg::TraversalSupportFinder::get_traversal_genotype_support	(	const vector< SnarlTraversal > &	traversals,
		const vector< int > &	genotype,
		const set< int > &	other_trav_subset,
		int	ref_trav_idx = `-1`,
		int *	max_trav_size = `nullptr`
	)

virtual

wrapper for using get_traversal_set_support to get the support for some alleles in a genotype, where everything is split evently among them anything not in the genotype gets a support using "exclusive_count" where nodes taken by the genotype are counted as 0 stuff not in the genotype is limited to other_trav_subset (or all if empty)

◆ get_traversal_mapqs()

vector< double > vg::TraversalSupportFinder::get_traversal_mapqs ( const vector< SnarlTraversal > & traversals ) const

virtual

Get the average MAPQ in each traversal Only consider nodes Normalize by base coverage (ie avg coverage / node by node length)

◆ get_traversal_set_support()

vector< Support > vg::TraversalSupportFinder::get_traversal_set_support	(	const vector< SnarlTraversal > &	traversals,
		const vector< int > &	shared_travs,
		const vector< Support > &	shared_support,
		const set< int > &	tgt_travs,
		bool	exclusive_only,
		const vector< int > &	exclusive_count_travs,
		const vector< Support > &	exclusive_count_support,
		int	ref_trav_idx = `-1`,
		int *	max_trav_size = `nullptr`
	)		const

virtual

traversals: get support for each traversal in this set shared_travs: if a node appears N times in shared_travs, then it will count as 1 / (N+1) support shared_support: optional supports for shared_travs. used to weight support split by traversal support. tgt_travs: if not empty, only compute support for these traversals (remaining slots in output vector left 0) eclusive_only: shared_travs are completely ignored exclusive_count_travs: these traversals get subtracted from supports in the target traversals exclusive_count_support: used with above, to determine amount of support to subtract ref_trav_idx: index of reference traversal if known max_trav_size: optional input of max trav size. useful when longest traversral is outside target set

◆ get_traversal_sizes()

vector< int > vg::TraversalSupportFinder::get_traversal_sizes ( const vector< SnarlTraversal > & traversals ) const

virtual

Get the total length of all nodes in the traversal.

◆ get_traversal_support()

Support vg::TraversalSupportFinder::get_traversal_support ( const SnarlTraversal & traversal ) const

virtual

Get the support of a traversal Child snarls are handled as in the old call code: their maximum support is used

◆ set_min_bp_edge_override()

void vg::TraversalSupportFinder::set_min_bp_edge_override ( bool bp_override )

virtual

set the breakpoint stricter upper override

◆ set_support_switch_threshold()

void vg::TraversalSupportFinder::set_support_switch_threshold	(	size_t	trav_thresh,
		size_t	node_thresh
	)

virtual

set the threshold

◆ support_val()

static double vg::TraversalSupportFinder::support_val ( const Support & support )

inlinestatic

Relic from old code.

Member Data Documentation

◆ average_node_support_switch_threshold

size_t vg::TraversalSupportFinder::average_node_support_switch_threshold = 50

protected

Use average instead of minimum support when determining a node's support its position supports.

◆ average_traversal_support_switch_threshold

size_t vg::TraversalSupportFinder::average_traversal_support_switch_threshold = 50

protected

◆ graph

const HandleGraph& vg::TraversalSupportFinder::graph

protected

◆ min_bp_edge_override

bool vg::TraversalSupportFinder::min_bp_edge_override = false

protected

If on, always apply minimum edge support for breakpoint (ref->offref) edges.

◆ snarl_manager

SnarlManager& vg::TraversalSupportFinder::snarl_manager

protected

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

src/traversal_support.hpp
src/traversal_support.cpp

Public Member Functions

Static Public Member Functions

Protected Attributes

Detailed Description

Constructor & Destructor Documentation

◆ TraversalSupportFinder()

◆ ~TraversalSupportFinder()

Member Function Documentation

◆ apply_min_bp_edge_override()

◆ get_average_traversal_support_switch_threshold()

◆ get_avg_node_mapq()

◆ get_avg_node_support()

◆ get_child_support()

◆ get_edge_length()

◆ get_edge_support() [1/2]

◆ get_edge_support() [2/2]

◆ get_min_node_support()

◆ get_ref_offsets()

◆ get_traversal_genotype_support()

◆ get_traversal_mapqs()

◆ get_traversal_set_support()

◆ get_traversal_sizes()

◆ get_traversal_support()

◆ set_min_bp_edge_override()

◆ set_support_switch_threshold()

◆ support_val()

Member Data Documentation

◆ average_node_support_switch_threshold

◆ average_traversal_support_switch_threshold

◆ graph

◆ min_bp_edge_override

◆ snarl_manager