Scaffolding
0.1
This program can assemble genome scaffolds using the pairing information in paired-end reads.
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#include <vector>
#include <queue>
#include <iostream>
#include <boost/graph/graph_traits.hpp>
#include <boost/graph/connected_components.hpp>
#include "graph_typedefs.hpp"
#include "graph_utils.hpp"
#include "low_priority_queue.hpp"
Go to the source code of this file.
Classes | |
struct | scaffold::graph_parameters::degree_less< Graph > |
comparator class, comparing two vertices u,v such that comp(u,v) = true <=> deg(u) < deg(v) More... | |
struct | scaffold::graph_parameters::degree_greater< Graph > |
comparator class, comparing two vertices u,v such that comp(u,v) = true <=> deg(u) > deg(v) More... | |
struct | scaffold::graph_parameters::interval |
an interval consists of a lower & an upper bound More... | |
struct | scaffold::graph_parameters::graph_parameters |
collection of graph parameters that can be computed More... | |
Typedefs | |
template<class Graph > | |
using | scaffold::graph_parameters::vertex_ordering = std::vector< Vertex< Graph > > |
Functions | |
std::ostream & | scaffold::graph_parameters::operator<< (std::ostream &os, const interval &i) |
print intervals | |
std::ostream & | scaffold::graph_parameters::operator<< (std::ostream &os, const graph_parameters ¶ms) |
print all graph parameters | |
template<class Graph > | |
unsigned | scaffold::graph_parameters::num_connected_components (const Graph &g, ComponentMap< Graph > &compMap, graph_parameters *const params=NULL) |
compute a component map and return the number of connected components More... | |
template<class Graph > | |
unsigned | scaffold::graph_parameters::num_connected_components (const Graph &g, graph_parameters *const params=NULL) |
return the number of connected components (see num_connected_components() above) | |
template<class Graph > | |
std::pair< Vertex< Graph >, unsigned > | scaffold::graph_parameters::get_max_degree (const Graph &g, graph_parameters *const params=NULL) |
compute the maximum degree of g and return a vertex that has this degree More... | |
template<class Graph > | |
unsigned | scaffold::graph_parameters::h_index (const Graph &g, graph_parameters *const params=NULL) |
compute the h-index of the graph g More... | |
template<class Graph > | |
unsigned | scaffold::graph_parameters::degeneracy (const Graph &g, vertex_ordering< Graph > *order=NULL, graph_parameters *const params=NULL) |
template<class Graph > | |
unsigned | scaffold::graph_parameters::feedback_vertex_set_greedy (const Graph &g, VertexSet< Graph > *FVS=NULL, graph_parameters *params=NULL) |
compute a greedy feedback vertex set and return the number of vertices therein More... | |
template<class Graph > | |
void | scaffold::graph_parameters::compute_easy_parameters (const Graph &g, graph_parameters ¶ms) |
compute the easy graph parameters More... | |
compute simple graph parameters such as max degree, feedback edge set number, degeneracy, ...
many functions in this class take a pointer to a graph_parameters struct; if this is not NULL, they will store the respective value in the struct as well as returning it