Scaffolding
0.1
This program can assemble genome scaffolds using the pairing information in paired-end reads.
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This is the complete list of members for scaffold::BridgeInfo< Graph >, including all inherited members.
_get_best_bridge(const Scoring &score) const (defined in scaffold::BridgeInfo< Graph >) | scaffold::BridgeInfo< Graph > | inlineprotected |
_get_cheapest_nonbridge(const EdgePredicate &predicate) const (defined in scaffold::BridgeInfo< Graph >) | scaffold::BridgeInfo< Graph > | inlineprotected |
_get_non_bridges(std::list< WeightedBridge< Graph >> &non_bridges, const EdgePredicate &predicate) const (defined in scaffold::BridgeInfo< Graph >) | scaffold::BridgeInfo< Graph > | inlineprotected |
_has_incident_nonbridge(const Vertex< Graph > &u) const (defined in scaffold::BridgeInfo< Graph >) | scaffold::BridgeInfo< Graph > | inlineprotected |
add_edge(const Vertex< Graph > &u, const Vertex< Graph > &v) (defined in scaffold::BridgeInfo< Graph >) | scaffold::BridgeInfo< Graph > | inline |
delete_edge(const VertexPair< Graph > &uv) (defined in scaffold::BridgeInfo< Graph >) | scaffold::BridgeInfo< Graph > | inline |
g (defined in scaffold::StructuralInfo< Graph, BridgeMap< Graph > >) | scaffold::StructuralInfo< Graph, BridgeMap< Graph > > | protected |
get() (defined in scaffold::StructuralInfo< Graph, BridgeMap< Graph > >) | scaffold::StructuralInfo< Graph, BridgeMap< Graph > > | inline |
get_best_bridge(const Scoring &score=Scoring()) (defined in scaffold::BridgeInfo< Graph >) | scaffold::BridgeInfo< Graph > | inline |
get_best_bridge(const Scoring &score=Scoring()) const (defined in scaffold::BridgeInfo< Graph >) | scaffold::BridgeInfo< Graph > | inline |
get_cheapest_nonbridge(const EdgePredicate &predicate=EdgePredicate()) (defined in scaffold::BridgeInfo< Graph >) | scaffold::BridgeInfo< Graph > | inline |
get_cheapest_nonbridge(const EdgePredicate &predicate=EdgePredicate()) const (defined in scaffold::BridgeInfo< Graph >) | scaffold::BridgeInfo< Graph > | inline |
get_const() const (defined in scaffold::StructuralInfo< Graph, BridgeMap< Graph > >) | scaffold::StructuralInfo< Graph, BridgeMap< Graph > > | inline |
get_non_bridges(std::list< WeightedBridge< Graph >> &non_bridges, const EdgePredicate &predicate=EdgePredicate()) (defined in scaffold::BridgeInfo< Graph >) | scaffold::BridgeInfo< Graph > | inline |
get_non_bridges_const(std::list< WeightedBridge< Graph >> &non_bridges, const EdgePredicate &predicate=EdgePredicate()) const (defined in scaffold::BridgeInfo< Graph >) | scaffold::BridgeInfo< Graph > | inline |
has_incident_nonbridge(const Vertex< Graph > &u) (defined in scaffold::BridgeInfo< Graph >) | scaffold::BridgeInfo< Graph > | inline |
has_incident_nonbridge_const(const Vertex< Graph > &v) const (defined in scaffold::BridgeInfo< Graph >) | scaffold::BridgeInfo< Graph > | inline |
invalidate() (defined in scaffold::StructuralInfo< Graph, BridgeMap< Graph > >) | scaffold::StructuralInfo< Graph, BridgeMap< Graph > > | inline |
is_bridge(const Vertex< Graph > &u, const Vertex< Graph > &v) (defined in scaffold::BridgeInfo< Graph >) | scaffold::BridgeInfo< Graph > | inline |
is_bridge_const(const Vertex< Graph > &u, const Vertex< Graph > &v) const (defined in scaffold::BridgeInfo< Graph >) | scaffold::BridgeInfo< Graph > | inline |
is_valid() const (defined in scaffold::StructuralInfo< Graph, BridgeMap< Graph > >) | scaffold::StructuralInfo< Graph, BridgeMap< Graph > > | inline |
payload (defined in scaffold::StructuralInfo< Graph, BridgeMap< Graph > >) | scaffold::StructuralInfo< Graph, BridgeMap< Graph > > | protected |
read_from_infos(const BridgeInfo< Graph > &infos, const Matching< Graph > &translate) (defined in scaffold::BridgeInfo< Graph >) | scaffold::BridgeInfo< Graph > | inline |
read_from_split_off_component(const BridgeInfo< Graph > &info, const Matching< Graph > &translate) (defined in scaffold::BridgeInfo< Graph >) | scaffold::BridgeInfo< Graph > | inline |
StructuralInfo(const Graph &_g) (defined in scaffold::StructuralInfo< Graph, BridgeMap< Graph > >) | scaffold::StructuralInfo< Graph, BridgeMap< Graph > > | inline |
StructuralInfo(const Graph &_g, const BridgeMap< Graph > &_payload) (defined in scaffold::StructuralInfo< Graph, BridgeMap< Graph > >) | scaffold::StructuralInfo< Graph, BridgeMap< Graph > > | inline |
up_to_date (defined in scaffold::StructuralInfo< Graph, BridgeMap< Graph > >) | scaffold::StructuralInfo< Graph, BridgeMap< Graph > > | protected |
update(const bool force=false) (defined in scaffold::BridgeInfo< Graph >) | scaffold::BridgeInfo< Graph > | inlinevirtual |
update_disjoint_union(const BridgeInfo< Graph > &info, const Matching< Graph > &translate) (defined in scaffold::BridgeInfo< Graph >) | scaffold::BridgeInfo< Graph > | inline |