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vg
tools for working with variation graphs
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This is the complete list of members for handlegraph::MutablePathMutableHandleGraph, including all inherited members.
| append_step(const path_handle_t &path, const handle_t &to_append)=0 | handlegraph::MutablePathHandleGraph | pure virtual |
| apply_ordering(const std::vector< handle_t > &order, bool compact_ids=false)=0 | handlegraph::MutableHandleGraph | pure virtual |
| apply_orientation(const handle_t &handle)=0 | handlegraph::MutableHandleGraph | pure virtual |
| ASSEMBLY_OR_NAME_MATCH | handlegraph::PathMetadata | privatestatic |
| create_edge(const handle_t &left, const handle_t &right)=0 | handlegraph::MutableHandleGraph | pure virtual |
| create_edge(const edge_t &edge) | handlegraph::MutableHandleGraph | inline |
| create_handle(const std::string &sequence)=0 | handlegraph::MutableHandleGraph | pure virtual |
| create_handle(const std::string &sequence, const nid_t &id)=0 | handlegraph::MutableHandleGraph | pure virtual |
| create_path(const PathSense &sense, const std::string &sample, const std::string &locus, const size_t &haplotype, const size_t &phase_block, const subrange_t &subrange, bool is_circular=false) | handlegraph::MutablePathMetadata | virtual |
| create_path_handle(const std::string &name, bool is_circular=false)=0 | handlegraph::MutablePathHandleGraph | pure virtual |
| create_path_name(const PathSense &sense, const std::string &sample, const std::string &locus, const size_t &haplotype, const size_t &phase_block, const subrange_t &subrange) | handlegraph::PathMetadata | static |
| destroy_path(const path_handle_t &path_handle)=0 | handlegraph::MutablePathHandleGraph | pure virtual |
| destroy_paths(const std::vector< path_handle_t > &paths) | handlegraph::MutablePathHandleGraph | virtual |
| divide_handle(const handle_t &handle, const std::vector< size_t > &offsets)=0 | handlegraph::MutableHandleGraph | pure virtual |
| divide_handle(const handle_t &handle, size_t offset) | handlegraph::MutableHandleGraph | inline |
| edge_handle(const handle_t &left, const handle_t &right) const | handlegraph::HandleGraph | |
| flip(const handle_t &handle) const =0 | handlegraph::HandleGraph | pure virtual |
| follow_edges(const handle_t &handle, bool go_left, const Iteratee &iteratee) const | handlegraph::HandleGraph | |
| follow_edges_impl(const handle_t &handle, bool go_left, const std::function< bool(const handle_t &)> &iteratee) const =0 | handlegraph::HandleGraph | protectedpure virtual |
| for_each_edge(const Iteratee &iteratee, bool parallel=false) const | handlegraph::HandleGraph | |
| for_each_handle(const Iteratee &iteratee, bool parallel=false) const | handlegraph::HandleGraph | |
| for_each_handle_impl(const std::function< bool(const handle_t &)> &iteratee, bool parallel=false) const =0 | handlegraph::HandleGraph | protectedpure virtual |
| for_each_path_handle(const Iteratee &iteratee) const | handlegraph::PathHandleGraph | |
| for_each_path_handle_impl(const std::function< bool(const path_handle_t &)> &iteratee) const =0 | handlegraph::PathHandleGraph | protectedpure virtual |
| for_each_path_matching(const std::unordered_set< PathSense > *senses, const std::unordered_set< std::string > *samples, const std::unordered_set< std::string > *loci, const Iteratee &iteratee) const | handlegraph::PathMetadata | |
| for_each_path_matching(const std::unordered_set< PathSense > &senses, const std::unordered_set< std::string > &samples, const std::unordered_set< std::string > &loci, const Iteratee &iteratee) const | handlegraph::PathMetadata | |
| for_each_path_matching_impl(const std::unordered_set< PathSense > *senses, const std::unordered_set< std::string > *samples, const std::unordered_set< std::string > *loci, const std::function< bool(const path_handle_t &)> &iteratee) const | handlegraph::PathMetadata | protectedvirtual |
| for_each_path_of_sample(const std::string &sample, const Iteratee &iteratee) const | handlegraph::PathMetadata | |
| for_each_path_of_sense(const PathSense &sense, const Iteratee &iteratee) const | handlegraph::PathMetadata | |
| for_each_step_in_path(const path_handle_t &path, const Iteratee &iteratee) const | handlegraph::PathHandleGraph | |
| for_each_step_of_sense(const handle_t &visited, const PathSense &sense, const Iteratee &iteratee) const | handlegraph::PathMetadata | |
| for_each_step_of_sense_impl(const handle_t &visited, const PathSense &sense, const std::function< bool(const step_handle_t &)> &iteratee) const | handlegraph::PathMetadata | protectedvirtual |
| for_each_step_on_handle(const handle_t &handle, const Iteratee &iteratee) const | handlegraph::PathHandleGraph | |
| for_each_step_on_handle_impl(const handle_t &handle, const std::function< bool(const step_handle_t &)> &iteratee) const =0 | handlegraph::PathHandleGraph | protectedpure virtual |
| FORMAT | handlegraph::PathMetadata | privatestatic |
| forward(const handle_t &handle) const | handlegraph::HandleGraph | |
| get_base(const handle_t &handle, size_t index) const | handlegraph::HandleGraph | virtual |
| get_degree(const handle_t &handle, bool go_left) const | handlegraph::HandleGraph | virtual |
| get_edge_count() const | handlegraph::HandleGraph | virtual |
| get_handle(const nid_t &node_id, bool is_reverse=false) const =0 | handlegraph::HandleGraph | pure virtual |
| get_handle_of_step(const step_handle_t &step_handle) const =0 | handlegraph::PathHandleGraph | pure virtual |
| get_haplotype(const path_handle_t &handle) const | handlegraph::PathMetadata | virtual |
| get_id(const handle_t &handle) const =0 | handlegraph::HandleGraph | pure virtual |
| get_is_circular(const path_handle_t &path_handle) const =0 | handlegraph::PathHandleGraph | pure virtual |
| get_is_reverse(const handle_t &handle) const =0 | handlegraph::HandleGraph | pure virtual |
| get_length(const handle_t &handle) const =0 | handlegraph::HandleGraph | pure virtual |
| get_locus_name(const path_handle_t &handle) const | handlegraph::PathMetadata | virtual |
| get_next_step(const step_handle_t &step_handle) const =0 | handlegraph::PathHandleGraph | pure virtual |
| get_node_count() const =0 | handlegraph::HandleGraph | pure virtual |
| get_path_count() const =0 | handlegraph::PathHandleGraph | pure virtual |
| get_path_handle(const std::string &path_name) const =0 | handlegraph::PathHandleGraph | pure virtual |
| get_path_handle_of_step(const step_handle_t &step_handle) const =0 | handlegraph::PathHandleGraph | pure virtual |
| get_path_name(const path_handle_t &path_handle) const =0 | handlegraph::PathHandleGraph | pure virtual |
| get_phase_block(const path_handle_t &handle) const | handlegraph::PathMetadata | virtual |
| get_previous_step(const step_handle_t &step_handle) const =0 | handlegraph::PathHandleGraph | pure virtual |
| get_sample_name(const path_handle_t &handle) const | handlegraph::PathMetadata | virtual |
| get_sense(const path_handle_t &handle) const | handlegraph::PathMetadata | virtual |
| get_sequence(const handle_t &handle) const =0 | handlegraph::HandleGraph | pure virtual |
| get_step_count(const path_handle_t &path_handle) const =0 | handlegraph::PathHandleGraph | pure virtual |
| get_step_count(const handle_t &handle) const | handlegraph::PathHandleGraph | virtual |
| get_subrange(const path_handle_t &handle) const | handlegraph::PathMetadata | virtual |
| get_subsequence(const handle_t &handle, size_t index, size_t size) const | handlegraph::HandleGraph | virtual |
| get_total_length() const | handlegraph::HandleGraph | virtual |
| HAPLOTYPE_MATCH | handlegraph::PathMetadata | privatestatic |
| has_edge(const handle_t &left, const handle_t &right) const | handlegraph::HandleGraph | virtual |
| has_edge(const edge_t &edge) const | handlegraph::HandleGraph | inline |
| has_next_step(const step_handle_t &step_handle) const =0 | handlegraph::PathHandleGraph | pure virtual |
| has_node(nid_t node_id) const =0 | handlegraph::HandleGraph | pure virtual |
| has_path(const std::string &path_name) const =0 | handlegraph::PathHandleGraph | pure virtual |
| has_previous_step(const step_handle_t &step_handle) const =0 | handlegraph::PathHandleGraph | pure virtual |
| increment_node_ids(nid_t increment) | handlegraph::MutableHandleGraph | virtual |
| increment_node_ids(long increment) | handlegraph::MutableHandleGraph | virtual |
| is_empty(const path_handle_t &path_handle) const | handlegraph::PathHandleGraph | virtual |
| LOCUS_MATCH_ANY | handlegraph::PathMetadata | privatestatic |
| LOCUS_MATCH_NUMERICAL_WITHOUT_HAPLOTYPE | handlegraph::PathMetadata | privatestatic |
| max_node_id() const =0 | handlegraph::HandleGraph | pure virtual |
| min_node_id() const =0 | handlegraph::HandleGraph | pure virtual |
| NO_END_POSITION | handlegraph::PathMetadata | static |
| NO_HAPLOTYPE | handlegraph::PathMetadata | static |
| NO_LOCUS_NAME | handlegraph::PathMetadata | static |
| NO_PHASE_BLOCK | handlegraph::PathMetadata | static |
| NO_SAMPLE_NAME | handlegraph::PathMetadata | static |
| NO_SUBRANGE | handlegraph::PathMetadata | static |
| optimize(bool allow_id_reassignment=true)=0 | handlegraph::MutableHandleGraph | pure virtual |
| parse_haplotype(const std::string &path_name) | handlegraph::PathMetadata | static |
| parse_locus_name(const std::string &path_name) | handlegraph::PathMetadata | static |
| parse_path_name(const std::string &path_name, PathSense &sense, std::string &sample, std::string &locus, size_t &haplotype, size_t &phase_block, subrange_t &subrange) | handlegraph::PathMetadata | static |
| parse_phase_block(const std::string &path_name) | handlegraph::PathMetadata | static |
| parse_sample_name(const std::string &path_name) | handlegraph::PathMetadata | static |
| parse_sense(const std::string &path_name) | handlegraph::PathMetadata | static |
| parse_subrange(const std::string &path_name) | handlegraph::PathMetadata | static |
| path_back(const path_handle_t &path_handle) const =0 | handlegraph::PathHandleGraph | pure virtual |
| path_begin(const path_handle_t &path_handle) const =0 | handlegraph::PathHandleGraph | pure virtual |
| path_end(const path_handle_t &path_handle) const =0 | handlegraph::PathHandleGraph | pure virtual |
| path_front_end(const path_handle_t &path_handle) const =0 | handlegraph::PathHandleGraph | pure virtual |
| PHASE_BLOCK_MATCH | handlegraph::PathMetadata | privatestatic |
| pop_back_step(const path_handle_t &path_handle) | handlegraph::MutablePathHandleGraph | virtual |
| pop_front_step(const path_handle_t &path_handle) | handlegraph::MutablePathHandleGraph | virtual |
| prepend_step(const path_handle_t &path, const handle_t &to_prepend)=0 | handlegraph::MutablePathHandleGraph | pure virtual |
| RANGE_END_MATCH | handlegraph::PathMetadata | privatestatic |
| RANGE_END_SEPARATOR | handlegraph::PathMetadata | privatestatic |
| RANGE_START_MATCH | handlegraph::PathMetadata | privatestatic |
| RANGE_START_SEPARATOR | handlegraph::PathMetadata | privatestatic |
| RANGE_TERMINATOR | handlegraph::PathMetadata | privatestatic |
| reassign_node_ids(const std::function< nid_t(const nid_t &)> &get_new_id)=0 | handlegraph::MutableHandleGraph | pure virtual |
| rename_path(const path_handle_t &path_handle, const std::string &new_name) | handlegraph::MutablePathHandleGraph | virtual |
| rewrite_segment(const step_handle_t &segment_begin, const step_handle_t &segment_end, const std::vector< handle_t > &new_segment)=0 | handlegraph::MutablePathHandleGraph | pure virtual |
| scan_path(const path_handle_t &path) const | handlegraph::PathHandleGraph | |
| SEPARATOR | handlegraph::PathMetadata | privatestatic |
| set_circularity(const path_handle_t &path, bool circular)=0 | handlegraph::MutablePathHandleGraph | pure virtual |
| set_id_increment(const nid_t &min_id)=0 | handlegraph::MutableHandleGraph | pure virtual |
| steps_of_handle(const handle_t &handle, bool match_orientation=false) const | handlegraph::PathHandleGraph | virtual |
| traverse_edge_handle(const edge_t &edge, const handle_t &left) const | handlegraph::HandleGraph | |
| ~HandleGraph()=default | handlegraph::HandleGraph | virtual |
| ~MutableHandleGraph()=default | handlegraph::MutableHandleGraph | virtual |
| ~MutablePathHandleGraph()=default | handlegraph::MutablePathHandleGraph | virtual |
| ~MutablePathMetadata()=default | handlegraph::MutablePathMetadata | virtual |
| ~MutablePathMutableHandleGraph()=default | handlegraph::MutablePathMutableHandleGraph | virtual |
| ~PathHandleGraph()=default | handlegraph::PathHandleGraph | virtual |
| ~PathMetadata()=default | handlegraph::PathMetadata | virtual |
1.8.17