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| void | vg::trace_haplotypes_and_paths (const PathHandleGraph &source, const gbwt::GBWT &haplotype_database, vg::id_t start_node, int extend_distance, Graph &out_graph, map< string, int > &out_thread_frequencies, bool expand_graph) |
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| Path | vg::path_from_thread_t (thread_t &t, const HandleGraph &source) |
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| vector< pair< vector< gbwt::node_type >, gbwt::SearchState > > | vg::list_haplotypes (const HandleGraph &graph, const gbwt::GBWT &gbwt, handle_t start, function< bool(const vector< gbwt::node_type > &)> stop_fn) |
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| void | vg::output_graph_with_embedded_paths (ostream &subgraph_ostream, vector< pair< thread_t, int >> &haplotype_list, const HandleGraph &source, bool json) |
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| Graph | vg::output_graph_with_embedded_paths (vector< pair< thread_t, int >> &haplotype_list, const HandleGraph &source) |
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| void | vg::output_haplotype_counts (ostream &annotation_ostream, vector< pair< thread_t, int >> &haplotype_list) |
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| void | vg::thread_to_graph_spanned (thread_t &t, Graph &g, const HandleGraph &source) |
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| void | vg::add_thread_nodes_to_set (thread_t &t, set< int64_t > &nodes) |
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| void | vg::add_thread_edges_to_set (thread_t &t, set< pair< int, int > > &edges) |
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| void | vg::construct_graph_from_nodes_and_edges (Graph &g, const HandleGraph &source, set< int64_t > &nodes, set< pair< int, int > > &edges) |
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