debruijn_graph Struct Reference

Detailed description

Definition at line 35 of file assembly_graph.h.

#include <assembly_graph.h>

Classes
struct	view

Public Methods
	operator view ()
bool	construct_graph (const D_SequenceSet &sequence_set, const D_VectorU32 &d_active_region_ids, const uint32 kmer_size, const bool allow_low_complexity)
void	compute_edge_weights ()
void	compute_in_degrees ()
void	compute_in_adjacencies ()
void	compute_subgraph_n_nodes ()
void	compute_complexity ()
bool	is_low_complexity (const uint32 subgraph_id)
bool	has_cycles (const uint32 subgraph_id)
void	topological_sort ()
void	find_k_best_paths (const uint32 k)
void	print_dot_graph (const D_SequenceSet &sequence_set)

Public Members
uint32	kmer_size
uint32	n_nodes
uint32	n_edges
uint32	n_subgraphs
D_VectorSetKmerCoord	nodes
D_VectorU32	node_adjancency_map
D_VectorU32	node_adj_offests
D_VectorU32	node_out_degrees
D_VectorU32	node_in_degrees
D_VectorU32	edge_counts
D_VectorU32	edge_weights
D_VectorU8	edge_ref_flags
D_VectorU32	node_in_adjancency_map
D_VectorU32	node_in_adj_offests
D_VectorU32	subgraph_source_ids
D_VectorU32	subgraph_sink_ids
D_VectorU32	subgraph_n_nodes
D_VectorU32	topo_sorted_uids
D_VectorU32	topo_sorted_offsets
D_VectorU8	low_complexity
D_VectorU8	cycle_presence

Member Function Documentation

void debruijn_graph::compute_complexity

(

)

Definition at line 576 of file assembly_graph_inl.h.

void debruijn_graph::compute_edge_weights

(

)

Definition at line 480 of file assembly_graph_inl.h.

void debruijn_graph::compute_in_adjacencies

(

)

Definition at line 525 of file assembly_graph_inl.h.

void debruijn_graph::compute_in_degrees

(

)

Definition at line 492 of file assembly_graph_inl.h.

void debruijn_graph::compute_subgraph_n_nodes

(

)

Definition at line 537 of file assembly_graph_inl.h.

bool debruijn_graph::construct_graph	(	const D_SequenceSet &	sequence_set,
		const D_VectorU32 &	d_active_region_ids,
		const uint32	kmer_size,
		const bool	allow_low_complexity
	)

Definition at line 280 of file assembly_graph_inl.h.

void debruijn_graph::find_k_best_paths

(

const uint32

k)

Definition at line 596 of file assembly_graph_inl.h.

bool debruijn_graph::has_cycles ( const uint32  subgraph_id)

inline

Definition at line 124 of file assembly_graph.h.

bool debruijn_graph::is_low_complexity ( const uint32  subgraph_id)

inline

Definition at line 123 of file assembly_graph.h.

debruijn_graph::operator view ( )

inline

Definition at line 92 of file assembly_graph.h.

void debruijn_graph::print_dot_graph

(

const D_SequenceSet &

sequence_set)

Definition at line 610 of file assembly_graph_inl.h.

void debruijn_graph::topological_sort

(

)

Definition at line 583 of file assembly_graph_inl.h.

Member Data Documentation

D_VectorU8 debruijn_graph::cycle_presence

Definition at line 66 of file assembly_graph.h.

D_VectorU32 debruijn_graph::edge_counts

Definition at line 48 of file assembly_graph.h.

D_VectorU8 debruijn_graph::edge_ref_flags

Definition at line 50 of file assembly_graph.h.

D_VectorU32 debruijn_graph::edge_weights

Definition at line 49 of file assembly_graph.h.

uint32 debruijn_graph::kmer_size

Definition at line 37 of file assembly_graph.h.

D_VectorU8 debruijn_graph::low_complexity

Definition at line 65 of file assembly_graph.h.

uint32 debruijn_graph::n_edges

Definition at line 39 of file assembly_graph.h.

uint32 debruijn_graph::n_nodes

Definition at line 38 of file assembly_graph.h.

uint32 debruijn_graph::n_subgraphs

Definition at line 40 of file assembly_graph.h.

D_VectorU32 debruijn_graph::node_adj_offests

Definition at line 45 of file assembly_graph.h.

D_VectorU32 debruijn_graph::node_adjancency_map

Definition at line 44 of file assembly_graph.h.

D_VectorU32 debruijn_graph::node_in_adj_offests

Definition at line 53 of file assembly_graph.h.

D_VectorU32 debruijn_graph::node_in_adjancency_map

Definition at line 52 of file assembly_graph.h.

D_VectorU32 debruijn_graph::node_in_degrees

Definition at line 47 of file assembly_graph.h.

D_VectorU32 debruijn_graph::node_out_degrees

Definition at line 46 of file assembly_graph.h.

D_VectorSetKmerCoord debruijn_graph::nodes

Definition at line 43 of file assembly_graph.h.

D_VectorU32 debruijn_graph::subgraph_n_nodes

Definition at line 58 of file assembly_graph.h.

D_VectorU32 debruijn_graph::subgraph_sink_ids

Definition at line 57 of file assembly_graph.h.

D_VectorU32 debruijn_graph::subgraph_source_ids

Definition at line 56 of file assembly_graph.h.

D_VectorU32 debruijn_graph::topo_sorted_offsets

Definition at line 62 of file assembly_graph.h.

D_VectorU32 debruijn_graph::topo_sorted_uids

Definition at line 61 of file assembly_graph.h.

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

• E:/git/nvbio/nvMicroAssembly/assembly_graph.h
• E:/git/nvbio/nvMicroAssembly/assembly_graph_inl.h