Scaffolding
0.1
This program can assemble genome scaffolds using the pairing information in paired-end reads.
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| Instance (scaffold) |
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| graph_parameters (scaffold::graph_parameters) | |||
| gviz_edge_writer_with_jumps (scaffold::io) | ||||||
Branch (scaffold::solv) | RelaxCallback (scaffold::solv::ilp) | bad_syntax (except) | gviz_property_writer (scaffold::io) | ||||
BridgeInfo (scaffold::graph_infos) | LazyCyclesBlockCallback (scaffold::solv::ilp) |
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| gviz_simple_edge_writer (scaffold::io) | |||
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| gviz_simple_graph_writer (scaffold::io) | |||||
ScafEdgeProperty (scaffold) | callback_statistics (scaffold::solv::ilp) | gviz_simple_vertex_writer (scaffold::io) | |||||
Compare_Instance_Size (scaffold::solv::DP) | MatchingPredicate (scaffold::predicates) | ScaffoldGraph (scaffold) | contained_filter (scaffold::filters) |
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ComponentInfo (scaffold::graph_infos) | MatrixEntry (scaffold) | ScafGraphProperty (scaffold) | contig_jump (scaffold) | ||||
ContainedPredicate (scaffold::predicates) | MaxDegreeInfo (scaffold::graph_infos) | ScafVertexProperty (scaffold) |
| ilp_options (scaffold::solv::ilp) | |||
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| Solution (scaffold) | info_not_up_to_date (except) | ||||
StructuralInfo (scaffold::graph_infos) | d_to_P_map (scaffold::solv::DP) | interval (scaffold::graph_parameters) | |||||
DistanceScore (scaffold::scoring) | OrientedSequence (scaffold) |
| degree_cmp | invalid_assumption (except) | |||
DP_Table (scaffold::solv::DP) |
| degree_greater (scaffold::graph_parameters) | invalid_options (except) | ||||
DynProgSolution (scaffold::solv::DP) | TargetContainedPredicate (scaffold::predicates) | degree_less (scaffold::graph_parameters) |
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| P_to_pc_map (scaffold::solv::DP) | TD_Subgraph (scaffold) | diagonal_counter | ||||
PathsAndCycles | TreeDPinfos (scaffold::solv::trees) |
| low_priority_queue (std) | ||||
EdgeHasher | PCMinMatrix (scaffold) | TruePredicate (scaffold::predicates) |
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| PermissiveMatching (scaffold) |
| edge_component_t | ||||
Predicate (scaffold::predicates) |
| map_filter (scaffold::filters) | |||||
GraphInfos (scaffold::graph_infos) | Predicated_EdgeIter (scaffold) | UseCountedOrientedSequence (scaffold) |
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| PredicatedDistanceScore (scaffold::scoring) |
| global_list (scaffold) | ||||
normal_distribution (scaffold) | |||||||
IdentityScore (scaffold::scoring) | VP_contained_filter (scaffold::filters) | ||||||