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 |