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vg
tools for working with variation graphs
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This is the complete list of members for vg::GrefCover, including all inherited members.
| add_interval(vector< pair< step_handle_t, step_handle_t >> &thread_gref_intervals, unordered_map< nid_t, int64_t > &thread_node_to_interval, const pair< step_handle_t, step_handle_t > &new_interval, vector< pair< nid_t, nid_t >> *snarl_bounds_vec=nullptr, pair< nid_t, nid_t > snarl_bounds={0, 0}) | vg::GrefCover | protected |
| apply(MutablePathMutableHandleGraph *mutable_graph) | vg::GrefCover | |
| assign_nesting(const bdsg::SnarlDistanceIndex &distance_index) | vg::GrefCover | |
| assign_top_level_snarls(const bdsg::SnarlDistanceIndex &distance_index) | vg::GrefCover | |
| base_path_gref_counter | vg::GrefCover | protected |
| clear(MutablePathMutableHandleGraph *graph) | vg::GrefCover | |
| compute(const PathHandleGraph *graph, const bdsg::SnarlDistanceIndex *distance_index, const unordered_set< path_handle_t > &reference_paths, int64_t minimum_length) | vg::GrefCover | |
| copy_base_paths_to_gref(MutablePathMutableHandleGraph *mutable_graph, const unordered_set< path_handle_t > &reference_paths) | vg::GrefCover | protected |
| enforce_top_level_anchoring(const bdsg::SnarlDistanceIndex &distance_index) | vg::GrefCover | |
| excluded_bp | vg::GrefCover | protected |
| excluded_nodes | vg::GrefCover | protected |
| excluded_units | vg::GrefCover | protected |
| fill_uncovered_nodes(int64_t minimum_length) | vg::GrefCover | protected |
| filter_short_intervals(int64_t minimum_length) | vg::GrefCover | protected |
| get_reference_nodes(nid_t node_id, bool first) const | vg::GrefCover | protected |
| graph | vg::GrefCover | protected |
| gref_intervals | vg::GrefCover | protected |
| gref_prefix | vg::GrefCover | static |
| gref_suffix | vg::GrefCover | static |
| interval_level | vg::GrefCover | protected |
| interval_parent | vg::GrefCover | protected |
| interval_snarl_bounds | vg::GrefCover | protected |
| is_gref_derived(const string &name) | vg::GrefCover | static |
| is_gref_name(const string &path_name) | vg::GrefCover | static |
| make_gref_base_name(const string &base_path_name) | vg::GrefCover | static |
| make_gref_copy_name(const string &path_name) | vg::GrefCover | static |
| make_gref_name(const string &base_path_name, int64_t gref_index) | vg::GrefCover | static |
| node_to_interval | vg::GrefCover | protected |
| num_ref_intervals | vg::GrefCover | protected |
| parse_base_path(const string &gref_name) | vg::GrefCover | static |
| parse_gref_index(const string &gref_name) | vg::GrefCover | static |
| resolve_base_path_name(int64_t interval_index, path_handle_t *out_ref_path=nullptr, nid_t *out_ref_node=nullptr) const | vg::GrefCover | protected |
| set_verbose(bool verbose) | vg::GrefCover | |
| top_level_snarl_stats | vg::GrefCover | protected |
| verbose | vg::GrefCover | protected |
| verify_cover(int64_t minimum_length) const | vg::GrefCover | protected |
| verify_disjoint() const | vg::GrefCover | protected |
| write_gref_segments(ostream &os) | vg::GrefCover |
1.9.1