Splitter part 2#1568
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Itolstoganov
commented
Apr 13, 2026
Itolstoganov
commented
- Adds helper classes in path extend for barcode index-based scaffold graph construction
- Adds splitter tool for repeat resolution of third-party GFA
- Moves mate-pair unrelated functionality from scaffolder2015 to auxiliary_graphs
- Moves IdStorage from GraphCore to enable conjugate GFA links
asl
reviewed
Apr 27, 2026
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| auto vertex_colorer = std::make_shared<ScaffoldVertexSetColorer>(main_edge_set); | ||
| using namespace scaffolder; | ||
| std::set<scaffold_graph::ScaffoldVertex> scaff_vertex_set; |
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can probably be auto scaff_vertex_set = main_edge_set :)
asl
reviewed
Apr 27, 2026
| void BaseScaffoldGraphConstructor::ConstructFromSet(const EdgeSet &edge_set, | ||
| ConnectionConditions &connection_conditions, | ||
| bool use_terminal_vertices_only) { | ||
| graph_->AddVertices(edge_set); |
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what's the problem with AddVertices?
asl
reviewed
Apr 27, 2026
| #pragma omp critical | ||
| { | ||
| if (check_predicate) { | ||
| graph_->AddEdge(edge); |
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Is it ok that edges could be added in arbitrary non-deterministic order?
asl
reviewed
Apr 27, 2026
| ScaffoldGraph::ScaffoldEdge edge = scaffold_edges[i]; | ||
| double score = score_function->GetScore(edge); | ||
| #pragma omp critical | ||
| { |
asl
reviewed
Apr 27, 2026
| { | ||
| TRACE("Success"); | ||
| ScaffoldGraph::ScaffoldEdge new_edge(first, *it, 0, score, 0); | ||
| graph_->AddEdgeSimple(new_edge); |
asl
reviewed
Apr 27, 2026
| if (!is_tellseq) { | ||
| barcode_index_builder.ConstructBarcodeIndex(io::paired_easy_readers(lib, false, 0), barcode_index, lib, is_tellseq); | ||
| } | ||
| if (is_tellseq) { |
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the conditions could probably be combined with previous condition:)
asl
reviewed
Apr 27, 2026
| gfa::GFAReader ReadGraph(const gcfg &cfg, | ||
| debruijn_graph::Graph &graph, | ||
| io::IdMapper<std::string> *id_mapper) { | ||
| gfa::GFAReader gfa(cfg.graph); |
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