|
| ostream & | vg::operator<< (ostream &out, mapping_t mapping) |
| | Allow a mapping_t to be printed, for debugging purposes. More...
|
| |
| Path & | vg::append_path (Path &a, const Path &b) |
| |
| int | vg::path_to_length (const Path &path) |
| |
| int | vg::path_from_length (const Path &path) |
| |
| int | vg::mapping_to_length (const Mapping &m) |
| |
| int | vg::mapping_from_length (const Mapping &m) |
| |
| int | vg::softclip_start (const Mapping &mapping) |
| |
| int | vg::softclip_end (const Mapping &mapping) |
| |
| Position | vg::first_path_position (const Path &path) |
| |
| Position | vg::last_path_position (const Path &path) |
| |
| int | vg::to_length (const Mapping &m) |
| |
| int | vg::from_length (const Mapping &m) |
| |
| Path & | vg::extend_path (Path &path1, const Path &path2) |
| |
| Path | vg::concat_paths (const Path &path1, const Path &path2) |
| |
| Path | vg::simplify (const Path &p, bool trim_internal_deletions) |
| |
| Mapping | vg::concat_mappings (const Mapping &m, const Mapping &n, bool trim_internal_deletions) |
| |
| Mapping | vg::simplify (const Mapping &m, bool trim_internal_deletions) |
| |
| bool | vg::edits_are_compatible (const Edit &e, const Edit &f) |
| | Return true if two edits could be combined into one (assuming adjacency). More...
|
| |
| void | vg::merge_edits_in_place (Edit &e, const Edit &f) |
| | Glom the second edit into the first, assuming adjacency. More...
|
| |
| Mapping | vg::merge_adjacent_edits (const Mapping &m) |
| | Merge adjacent edits of the same type. More...
|
| |
| Path | vg::trim_hanging_ends (const Path &p) |
| |
| bool | vg::mappings_equivalent (const Mapping &m1, const Mapping &m2) |
| |
| bool | vg::mapping_ends_in_deletion (const Mapping &m) |
| |
| bool | vg::mapping_starts_in_deletion (const Mapping &m) |
| |
| bool | vg::mapping_is_total_deletion (const Mapping &m) |
| |
| bool | vg::mapping_is_total_insertion (const Mapping &m) |
| |
| bool | vg::mapping_is_simple_match (const Mapping &m) |
| |
| bool | vg::path_is_simple_match (const Path &p) |
| |
| const string | vg::mapping_sequence (const Mapping &mp, const string &node_seq) |
| |
| const string | vg::mapping_sequence (const Mapping &mp, const Node &n) |
| |
| string | vg::path_sequence (const HandleGraph &graph, const Path &path) |
| |
| Mapping | vg::reverse_complement_mapping (const Mapping &m, const function< int64_t(id_t)> &node_length) |
| |
| void | vg::reverse_complement_mapping_in_place (Mapping *m, const function< int64_t(id_t)> &node_length) |
| |
| Path | vg::reverse_complement_path (const Path &path, const function< int64_t(id_t)> &node_length) |
| |
| void | vg::reverse_complement_path_in_place (Path *path, const function< int64_t(id_t)> &node_length) |
| |
| pair< Mapping, Mapping > | vg::cut_mapping (const Mapping &m, const Position &pos) |
| |
| pair< mapping_t, mapping_t > | vg::cut_mapping (const mapping_t &m, const Position &pos) |
| |
| pair< Mapping, Mapping > | vg::cut_mapping_offset (const Mapping &m, size_t offset) |
| |
| pair< mapping_t, mapping_t > | vg::cut_mapping_offset (const mapping_t &m, size_t offset) |
| |
| pair< Mapping, Mapping > | vg::cut_mapping (const Mapping &m, size_t offset) |
| |
| pair< mapping_t, mapping_t > | vg::cut_mapping (const mapping_t &m, size_t offset) |
| |
| pair< Path, Path > | vg::cut_path (const Path &path, const Position &pos) |
| |
| pair< Path, Path > | vg::cut_path (const Path &path, size_t offset) |
| |
| bool | vg::maps_to_node (const Path &p, id_t id) |
| |
| Position | vg::path_start_position (const Path &path) |
| |
| string | vg::path_to_string (Path p) |
| |
| Position | vg::path_end_position (const Path &path) |
| |
| bool | vg::adjacent_mappings (const Mapping &m1, const Mapping &m2) |
| |
| bool | vg::mapping_is_match (const Mapping &m) |
| |
| double | vg::divergence (const Mapping &m) |
| |
| double | vg::identity (const Path &path) |
| |
| void | vg::decompose (const Path &path, map< pos_t, int > &ref_positions, map< pos_t, Edit > &edits) |
| |
| double | vg::overlap (const Path &p1, const Path &p2) |
| |
| void | vg::translate_node_ids (Path &path, const unordered_map< id_t, id_t > &translator) |
| | Switches the node ids in the path to the ones indicated by the translator. More...
|
| |
| void | vg::translate_node_ids (Path &path, const unordered_map< id_t, id_t > &translator, id_t cut_node, size_t bases_removed, bool from_right) |
| |
| void | vg::translate_oriented_node_ids (Path &path, const unordered_map< id_t, pair< id_t, bool >> &translator) |
| | Switches the node ids and orientations in the path to the ones indicated by the translator. More...
|
| |
| void | vg::translate_oriented_node_ids (Path &path, const function< pair< id_t, bool >(id_t)> &translator) |
| | Switches node ids and orientations in the path to the ones indicated by the translator. More...
|
| |
| void | vg::translate_node_ids (path_t &path, const unordered_map< id_t, id_t > &translator) |
| |
| void | vg::translate_oriented_node_ids (path_t &path, const unordered_map< id_t, pair< id_t, bool >> &translator) |
| |
| void | vg::translate_oriented_node_ids (path_t &path, const function< pair< id_t, bool >(id_t)> &translator) |
| |
| pos_t | vg::initial_position (const Path &path) |
| |
| pos_t | vg::final_position (const Path &path) |
| |
| Path | vg::path_from_node_traversals (const list< NodeTraversal > &traversals) |
| |
| void | vg::remove_paths (Graph &graph, const function< bool(const string &)> &paths_to_take, std::list< Path > *matching) |
| |
| Path | vg::path_from_path_handle (const PathHandleGraph &graph, path_handle_t path_handle) |
| |
| Alignment | vg::alignment_from_path (const HandleGraph &graph, const Path &path) |
| |
| void | vg::from_proto_edit (const Edit &proto_edit, edit_t &edit) |
| |
| void | vg::to_proto_edit (const edit_t &edit, Edit &proto_edit) |
| |
| void | vg::from_proto_mapping (const Mapping &proto_mapping, path_mapping_t &mapping) |
| |
| void | vg::to_proto_mapping (const path_mapping_t &mapping, Mapping &proto_mapping) |
| |
| void | vg::from_proto_path (const Path &proto_path, path_t &path) |
| |
| void | vg::to_proto_path (const path_t &path, Path &proto_path) |
| |
| int | vg::mapping_from_length (const path_mapping_t &mapping) |
| |
| int | vg::path_from_length (const path_t &path) |
| |
| int | vg::mapping_to_length (const path_mapping_t &mapping) |
| |
| int | vg::path_to_length (const path_t &path) |
| |
| void | vg::reverse_complement_mapping_in_place (path_mapping_t *m, const function< int64_t(id_t)> &node_length) |
| |
| path_mapping_t | vg::reverse_complement_mapping (const path_mapping_t &m, const function< int64_t(id_t)> &node_length) |
| |
| path_t | vg::reverse_complement_path (const path_t &path, const function< int64_t(id_t)> &node_length) |
| |
| void | vg::reverse_complement_path_in_place (path_t *path, const function< int64_t(id_t)> &node_length) |
| |
| pos_t | vg::initial_position (const path_t &path) |
| |
| pos_t | vg::final_position (const path_t &path) |
| |
| string | vg::debug_string (const path_t &path) |
| |
| string | vg::debug_string (const path_mapping_t &mapping) |
| |
| string | vg::debug_string (const edit_t &edit) |
| |
| int | vg::corresponding_length_internal (const path_t &path, int given_length, bool is_from_length, bool from_end) |
| |
| int | vg::corresponding_to_length (const path_t &path, int from_length, bool from_end) |
| |
| int | vg::corresponding_from_length (const path_t &path, int to_length, bool from_end) |
| |
