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Scaffolding
0.1
This program can assemble genome scaffolds using the pairing information in paired-end reads.
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| ▼Nexcept | |
| Cbad_syntax | Exception for the case that a given file does not conform to expected syntax |
| Cinfo_not_up_to_date | Exception for the case that a graph property is read that is not up to date |
| Cinvalid_assumption | Exception for the case that some assumption that is made is not true |
| Cinvalid_options | Exception for the case that the given program options are not valid |
| Cread_error | Exception for the case that a given file could not be read on a low level |
| ▼Nscaffold | |
| ▼Nfilters | |
| Ccontained_filter | Filter to work with filtered graphs that is based on a set of vertices, passed to the constructor |
| Cmap_filter | Filter to work with filtered graphs that is based on a a mapping of vertices: filter all vertices mapped to some initial X |
| CVP_contained_filter | Filter to work with filtered graphs that is based on a set of VertexPairs, passed to the constructor |
| Cyes_filter | Dummy filter to always say YES |
| ▼Ngraph_infos | |
| CBridgeInfo | Graph property for the set of bridges in g |
| CComponentInfo | Graph property for the number of connected components and a map of vertices to components (represented by unsigneds) |
| CGraphInfos | Accumulator class for different graph properties |
| CMaxDegreeInfo | Graph property for the maximum degree in g |
| CStructuralInfo | Prototype class for structural graph properties |
| ▼Ngraph_parameters | |
| Cdegree_greater | Comparator class, comparing two vertices u,v such that comp(u,v) = true <=> deg(u) > deg(v) |
| Cdegree_less | Comparator class, comparing two vertices u,v such that comp(u,v) = true <=> deg(u) < deg(v) |
| Cgraph_parameters | Collection of graph parameters that can be computed |
| Cinterval | Interval consists of a lower & an upper bound |
| ▼Nio | |
| Cgviz_edge_writer_with_jumps | |
| Cgviz_property_writer | |
| Cgviz_simple_edge_writer | |
| Cgviz_simple_graph_writer | |
| Cgviz_simple_vertex_writer | |
| ▼Npredicates | |
| CContainedPredicate | Predicate that is true iff the given element is (not) contained in a given container |
| CMatchingPredicate | Edge predicate that is true iff the given edge is (not) a matching edge |
| CPredicate | Prototype predicate |
| CTargetContainedPredicate | Edge predicate that is true iff the given edge has its target (not) in a given set |
| CTruePredicate | Predicate that always evaluates to true |
| ▼Nscoring | |
| CDistanceScore | Scoring function returning the distance to a reference score given at construction |
| CIdentityScore | Scoring function for a pair of something and unsigned that just returns the unsigned |
| CPredicatedDistanceScore | Scoring returning the distance to a reference score if a predicate evaluates to true and UINT_MAX otherwise |
| ▼Nsolv | |
| ▼NDP | |
| CCompare_Instance_Size | |
| Cd_to_P_map | |
| CDP_Table | |
| CDynProgSolution | |
| CP_to_pc_map | |
| ▼Nilp | |
| Ccallback_statistics | |
| Cilp_options | |
| CLazyCyclesBlockCallback | |
| CRelaxCallback | |
| Cvar_collection_multi | |
| Cvar_collection_virt | |
| ▼Ntrees | |
| CTreeDPinfos | |
| CBranch | |
| Cpthread_data_block | |
| Ccontig_jump | |
| Cglobal_list | |
| CInstance | Instance is a ScaffoldGraph with given path- & cycle- numbers and a solution to keep track of deleted edges |
| CMatrixEntry | |
| Cnormal_distribution | Normal distribution centered with given mean and standard deviation (makes heavy use of std::erf()) |
| COrientedSequence | |
| CPCMinMatrix | |
| CPermissiveMatching | |
| CPredicated_EdgeIter | Edge iterator that skips over all edges for which the predicate evaluates to false |
| CScafEdgeProperty | |
| CScaffoldGraph | Main graph class |
| CScafGraphProperty | |
| CScafVertexProperty | |
| CSolution | Solution is a list of edge names with weights; it keeps track of the overall weight for O(1) access |
| CTD_Subgraph | |
| CUseCountedOrientedSequence | |
| ▼Nstd | |
| Clow_priority_queue | Low-priority queue of Elements with Priorities |
| Cset_queue | Priority-queue allowing member queries |
| Cunordered_pair | Unordered pair |
| Cdegree_cmp | |
| Cdiagonal_counter | |
| Cedge_component_t | |
| CEdgeHasher | |
| CPathsAndCycles | |
| Ctimer | Simple timer class that can be paused and resumed |
1.8.10