#include <traversal_support.hpp>

Inheritance diagram for vg::NestedCachedPackedTraversalSupportFinder:

Classes
struct	snarl_less

Public Types
typedef map< Snarl, tuple< Support, Support, int >, snarl_less >	SupportMap

Public Member Functions
	NestedCachedPackedTraversalSupportFinder (const Packer &packer, SnarlManager &snarl_manager, size_t cache_size=500000)

virtual	~NestedCachedPackedTraversalSupportFinder ()

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...

Public Member Functions inherited from vg::CachedPackedTraversalSupportFinder
	CachedPackedTraversalSupportFinder (const Packer &packer, SnarlManager &snarl_manager, size_t cache_size=500000)

virtual	~CachedPackedTraversalSupportFinder ()

virtual Support	get_edge_support (id_t from, bool from_reverse, id_t to, bool to_reverse) const
	Support of an edge. More...

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

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

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

Public Member Functions inherited from vg::PackedTraversalSupportFinder
	PackedTraversalSupportFinder (const Packer &packer, SnarlManager &snarl_manager)

virtual	~PackedTraversalSupportFinder ()

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

Public Member Functions inherited from vg::TraversalSupportFinder
	TraversalSupportFinder (const HandleGraph &graph, SnarlManager &snarl_manager)

virtual	~TraversalSupportFinder ()

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_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...

Public Attributes
SupportMap	child_support_map

Additional Inherited Members
Static Public Member Functions inherited from vg::TraversalSupportFinder
static double	support_val (const Support &support)
	Relic from old code. More...

Protected Attributes inherited from vg::CachedPackedTraversalSupportFinder
vector< LRUCache< edge_t, Support > * >	edge_support_cache
	One node cache per threade. More...

vector< LRUCache< nid_t, Support > * >	min_node_support_cache

vector< LRUCache< nid_t, Support > * >	avg_node_support_cache

vector< LRUCache< nid_t, size_t > * >	avg_node_mapq_cache

Protected Attributes inherited from vg::PackedTraversalSupportFinder
const Packer &	packer
	Derive supports from this pack index. More...

Protected Attributes inherited from vg::TraversalSupportFinder
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

Add table to keep track of child snarl support that can be maintained by outside logic

Member Typedef Documentation

◆ SupportMap

typedef map<Snarl, tuple<Support, Support, int>, snarl_less> vg::NestedCachedPackedTraversalSupportFinder::SupportMap

Constructor & Destructor Documentation

◆ NestedCachedPackedTraversalSupportFinder()

vg::NestedCachedPackedTraversalSupportFinder::NestedCachedPackedTraversalSupportFinder	(	const Packer &	packer,
		SnarlManager &	snarl_manager,
		size_t	cache_size = `500000`
	)

◆ ~NestedCachedPackedTraversalSupportFinder()

vg::NestedCachedPackedTraversalSupportFinder::~NestedCachedPackedTraversalSupportFinder ( )

virtual

Member Function Documentation

◆ get_child_support()

tuple< Support, Support, int > vg::NestedCachedPackedTraversalSupportFinder::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 from vg::TraversalSupportFinder.

Member Data Documentation

◆ child_support_map

SupportMap vg::NestedCachedPackedTraversalSupportFinder::child_support_map

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

src/traversal_support.hpp
src/traversal_support.cpp

Classes

Public Types

Public Member Functions

Public Attributes

Additional Inherited Members