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vg
tools for working with variation graphs
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This is the complete list of members for vg::AugRefCover, including all inherited members.
| add_interval(vector< pair< step_handle_t, step_handle_t >> &thread_augref_intervals, unordered_map< nid_t, int64_t > &thread_node_to_interval, const pair< step_handle_t, step_handle_t > &new_interval, bool global=false, vector< pair< nid_t, nid_t >> *snarl_bounds_vec=nullptr, pair< nid_t, nid_t > snarl_bounds={0, 0}) | vg::AugRefCover | protected |
| apply(MutablePathMutableHandleGraph *mutable_graph) | vg::AugRefCover | |
| augref_intervals | vg::AugRefCover | protected |
| augref_sample_name | vg::AugRefCover | protected |
| augref_suffix | vg::AugRefCover | static |
| base_path_augref_counter | vg::AugRefCover | mutableprotected |
| clear(MutablePathMutableHandleGraph *graph) | vg::AugRefCover | |
| compute(const PathHandleGraph *graph, SnarlManager *snarl_manager, const unordered_set< path_handle_t > &reference_paths, int64_t minimum_length) | vg::AugRefCover | |
| compute_snarl(const Snarl &snarl, PathTraversalFinder &path_trav_finder, int64_t minimum_length, vector< pair< step_handle_t, step_handle_t >> &thread_augref_intervals, unordered_map< nid_t, int64_t > &thread_node_to_interval, nid_t top_snarl_start, nid_t top_snarl_end, vector< pair< nid_t, nid_t >> &thread_snarl_bounds) | vg::AugRefCover | protected |
| copy_base_paths_to_sample(MutablePathMutableHandleGraph *mutable_graph, const unordered_set< path_handle_t > &reference_paths) | vg::AugRefCover | protected |
| defragment_intervals() | vg::AugRefCover | protected |
| fill_uncovered_nodes(int64_t minimum_length) | vg::AugRefCover | protected |
| filter_short_intervals(int64_t minimum_length) | vg::AugRefCover | protected |
| forwardize_augref_paths(MutablePathMutableHandleGraph *mutable_graph) | vg::AugRefCover | protected |
| get_augref_sample() const | vg::AugRefCover | |
| get_coverage(const vector< step_handle_t > &trav, const pair< int64_t, int64_t > &uncovered_interval) | vg::AugRefCover | protected |
| get_interval(nid_t node_id) const | vg::AugRefCover | |
| get_intervals() const | vg::AugRefCover | |
| get_num_ref_intervals() const | vg::AugRefCover | |
| get_rank(nid_t node_id) const | vg::AugRefCover | |
| get_reference_nodes(nid_t node_id, bool first) const | vg::AugRefCover | protected |
| get_uncovered_intervals(const vector< step_handle_t > &trav, const unordered_map< nid_t, int64_t > &thread_node_to_interval) | vg::AugRefCover | protected |
| get_verbose() const | vg::AugRefCover | |
| graph | vg::AugRefCover | protected |
| interval_snarl_bounds | vg::AugRefCover | protected |
| is_augref_name(const string &path_name) | vg::AugRefCover | static |
| load(const PathHandleGraph *graph, const unordered_set< path_handle_t > &reference_paths) | vg::AugRefCover | |
| make_augref_name(const string &base_path_name, int64_t augref_index) | vg::AugRefCover | static |
| node_to_interval | vg::AugRefCover | protected |
| num_ref_intervals | vg::AugRefCover | protected |
| parse_augref_index(const string &augref_name) | vg::AugRefCover | static |
| parse_base_path(const string &augref_name) | vg::AugRefCover | static |
| rank_by_name | vg::AugRefCover | protected |
| set_augref_sample(const string &sample_name) | vg::AugRefCover | |
| set_verbose(bool verbose) | vg::AugRefCover | |
| try_extend_backward(step_handle_t start_step, path_handle_t path, const pair< step_handle_t, step_handle_t > &other_interval) | vg::AugRefCover | protected |
| try_extend_forward(step_handle_t start_step, path_handle_t path, const pair< step_handle_t, step_handle_t > &other_interval) | vg::AugRefCover | protected |
| verbose | vg::AugRefCover | protected |
| verify_cover() const | vg::AugRefCover | protected |
| write_augref_segments(ostream &os) | vg::AugRefCover |
1.9.1