18 #include "extract_kmers.h" 22 #define V_NOT_VISITED 0 Interface containing all functions to use a BFT.
size_t extract_dispensable_kmers(BFT_kmer *kmer, BFT *graph, va_list args)
Function of type BFT_func_ptr extracting a dispensable k-mer to disk.
Definition: snippets.c:35
size_t extract_core_kmers(BFT_kmer *kmer, BFT *graph, va_list args)
Function of type BFT_func_ptr extracting a core k-mer to disk.
Definition: snippets.c:10
void extract_simple_core_paths_to_disk(BFT *graph, double core_ratio, char *filename_output)
Function extracting from a colored de Bruijn graph stored as a BFT all simple (non branching) core pa...
Definition: snippets.c:560
void get_nb_connected_component(BFT *graph,...)
Compute the number of connected components in a colored de-Bruijn graph.
Definition: snippets.c:925
size_t DFS_subgraph(BFT_kmer *kmer, BFT *graph, va_list args)
Function of type BFT_func_ptr starting a Depth-First Search traversal from a k-mer that is part of a ...
Definition: snippets.c:761
void extract_pangenome_kmers_to_disk(BFT *graph, char *filename_output, BFT_func_ptr f)
Function extracting pan-genome (core/dispensable/singleton) k-mers from a BFT to disk.
Definition: snippets.c:86
size_t(* BFT_func_ptr)(BFT_kmer *bft_kmer, BFT *bft, va_list args)
Pointer on function used by iterate_over_kmers() and v_iterate_over_kmers().
Definition: bft.h:51
size_t DFS(BFT_kmer *kmer, BFT *graph, va_list args)
Function of type BFT_func_ptr starting a Depth-First Search traversal from a k-mer.
Definition: snippets.c:731
void extract_simple_paths_to_disk(BFT *graph, char *filename_output)
Function extracting from a colored de Bruijn graph stored as a BFT all simple (non branching) paths...
Definition: snippets.c:310
bool is_in_subgraph(BFT_kmer *kmer, BFT *graph, int nb_id_genomes, const va_list args)
Function computing if a k-mer is part of a subgraph.
Definition: snippets.c:812
K-mer stored in a BFT_Root.
Definition: Node.h:124
size_t extract_core_simple_paths(BFT_kmer *kmer, BFT *graph, va_list args)
Function of type BFT_func_ptr extracting from a non-branching core k-mer the simple (non branching) p...
Definition: snippets.c:346
void cdbg_traversal(BFT *graph, BFT_func_ptr f,...)
Function traversing a colored de Bruijn graph stored as a BFT.
Definition: snippets.c:871
size_t BFS_subgraph(BFT_kmer *kmer, BFT *graph, va_list args)
Function of type BFT_func_ptr starting a Breadth-First Search traversal from a k-mer that is part of ...
Definition: snippets.c:655
size_t BFS(BFT_kmer *kmer, BFT *graph, va_list args)
Function of type BFT_func_ptr starting a Breadth-First Search traversal from a k-mer.
Definition: snippets.c:593
size_t nb_connected_components(BFT_kmer *kmer, BFT *graph, va_list args)
Function of type BFT_func_ptr calling a traversal method (DFS/BFS, DFS_subgraph/BFS_subgraph) on a k-...
Definition: snippets.c:903
Root vertex of a BFT.
Definition: Node.h:91
size_t extract_simple_paths(BFT_kmer *kmer, BFT *graph, va_list args)
Function of type BFT_func_ptr extracting from a non-branching k-mer the simple (non branching) path i...
Definition: snippets.c:115
size_t extract_singleton_kmers(BFT_kmer *kmer, BFT *graph, va_list args)
Function of type BFT_func_ptr extracting a singleton k-mer to disk.
Definition: snippets.c:60