vg
tools for working with variation graphs
|
This is the complete list of members for bdsg::ODGI, including all inherited members.
_deleted_node_count | bdsg::ODGI | private |
_edge_count | bdsg::ODGI | private |
_id_increment | bdsg::ODGI | private |
_max_node_rank | bdsg::ODGI | private |
_min_node_rank | bdsg::ODGI | private |
_node_count | bdsg::ODGI | private |
_path_count | bdsg::ODGI | private |
_path_rank_next | bdsg::ODGI | private |
add_to_number(const handle_t &handle, int64_t offset) const | bdsg::ODGI | private |
append_step(const path_handle_t &path, const handle_t &to_append) | bdsg::ODGI | virtual |
apply_ordering(const std::vector< handle_t > &order, bool compact_ids=false) | bdsg::ODGI | virtual |
apply_orientation(const handle_t &handle) | bdsg::ODGI | virtual |
apply_path_ordering(const std::vector< path_handle_t > &order) | bdsg::ODGI | |
canonicalize_edge(handle_t &left, handle_t &right) const | bdsg::ODGI | inlineprivate |
clear(void) | bdsg::ODGI | virtual |
clear_paths(void) | bdsg::ODGI | |
combine_handles(const std::vector< handle_t > &handles) | bdsg::ODGI | |
create_edge(const handle_t &left, const handle_t &right) | bdsg::ODGI | virtual |
create_edge(const edge_t &edge) | bdsg::ODGI | inline |
create_handle(const std::string &sequence) | bdsg::ODGI | virtual |
create_handle(const std::string &sequence, const nid_t &id) | bdsg::ODGI | virtual |
create_hidden_handle(const std::string &sequence) | bdsg::ODGI | |
create_path_handle(const std::string &name, bool is_circular=false) | bdsg::ODGI | virtual |
create_step(const path_handle_t &path, const handle_t &handle) | bdsg::ODGI | private |
decrement_rank(const step_handle_t &step_handle) | bdsg::ODGI | private |
deleted_node_bv | bdsg::ODGI | private |
deserialize(std::istream &in) | handlegraph::SerializableHandleGraph | inline |
deserialize(const std::string &filename) | handlegraph::SerializableHandleGraph | inline |
deserialize_members(std::istream &in) | bdsg::ODGI | privatevirtual |
destroy_edge(const handle_t &left, const handle_t &right) | bdsg::ODGI | virtual |
destroy_edge(const edge_t &edge) | bdsg::ODGI | inline |
destroy_handle(const handle_t &handle) | bdsg::ODGI | virtual |
destroy_path(const path_handle_t &path) | bdsg::ODGI | virtual |
destroy_path_handle_records(uint64_t i) | bdsg::ODGI | private |
destroy_step(const step_handle_t &step_handle, bool clean_up_empty_path=true) | bdsg::ODGI | private |
display(void) const | bdsg::ODGI | |
divide_handle(const handle_t &handle, const std::vector< size_t > &offsets) | bdsg::ODGI | virtual |
divide_handle(const handle_t &handle, size_t offset) | bdsg::ODGI | inline |
edge_delta_to_id(uint64_t left, uint64_t delta) const | bdsg::ODGI | private |
edge_handle(const handle_t &left, const handle_t &right) const | bdsg::ODGI | |
edge_to_delta(const handle_t &left, const handle_t &right) const | bdsg::ODGI | private |
find_metadata(const path_handle_t &path) | bdsg::ODGI | private |
find_metadata(const path_handle_t &path) const | bdsg::ODGI | private |
flip(const handle_t &handle) const | bdsg::ODGI | 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 | bdsg::ODGI | protectedvirtual |
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 | bdsg::ODGI | protectedvirtual |
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 | bdsg::ODGI | protectedvirtual |
for_each_step_in_path(const path_handle_t &path, const std::function< void(const step_handle_t &)> &iteratee) const | bdsg::ODGI | |
handlegraph::MutablePathDeletableHandleGraph::for_each_step_in_path(const path_handle_t &path, const Iteratee &iteratee) const | handlegraph::PathHandleGraph | |
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 | bdsg::ODGI | protectedvirtual |
forward(const handle_t &handle) const | bdsg::ODGI | |
get_base(const handle_t &handle, size_t index) const | handlegraph::HandleGraph | virtual |
get_degree(const handle_t &handle, bool go_left) const | bdsg::ODGI | virtual |
get_edge_count() const | handlegraph::HandleGraph | virtual |
get_handle(const nid_t &node_id, bool is_reverse=false) const | bdsg::ODGI | virtual |
get_handle_of_step(const step_handle_t &step_handle) const | bdsg::ODGI | virtual |
get_id(const handle_t &handle) const | bdsg::ODGI | virtual |
get_is_circular(const path_handle_t &path_handle) const | bdsg::ODGI | virtual |
get_is_reverse(const handle_t &handle) const | bdsg::ODGI | virtual |
get_length(const handle_t &handle) const | bdsg::ODGI | virtual |
get_magic_number() const | bdsg::ODGI | virtual |
get_next_step(const step_handle_t &step_handle) const | bdsg::ODGI | virtual |
get_node_count(void) const | bdsg::ODGI | virtual |
get_path_count(void) const | bdsg::ODGI | virtual |
get_path_handle(const std::string &path_name) const | bdsg::ODGI | virtual |
get_path_handle_of_step(const step_handle_t &step_handle) const | bdsg::ODGI | virtual |
get_path_name(const path_handle_t &path_handle) const | bdsg::ODGI | virtual |
get_previous_step(const step_handle_t &step_handle) const | bdsg::ODGI | virtual |
get_sequence(const handle_t &handle) const | bdsg::ODGI | virtual |
get_step_count(const path_handle_t &path_handle) const | bdsg::ODGI | virtual |
get_step_count(const handle_t &handle) const | bdsg::ODGI | |
get_subsequence(const handle_t &handle, size_t index, size_t size) const | handlegraph::HandleGraph | virtual |
get_total_length() const | handlegraph::HandleGraph | virtual |
graph_id_hidden_set | bdsg::ODGI | private |
has_edge(const handle_t &left, const handle_t &right) const | bdsg::ODGI | virtual |
handlegraph::MutablePathDeletableHandleGraph::has_edge(const edge_t &edge) const | handlegraph::HandleGraph | inline |
has_linear_next_step(const step_handle_t &step_handle) const | bdsg::ODGI | protected |
has_linear_previous_step(const step_handle_t &step_handle) const | bdsg::ODGI | protected |
has_next_step(const step_handle_t &step_handle) const | bdsg::ODGI | virtual |
has_node(nid_t node_id) const | bdsg::ODGI | virtual |
has_path(const std::string &path_name) const | bdsg::ODGI | virtual |
has_previous_step(const step_handle_t &step_handle) const | bdsg::ODGI | virtual |
id_to_rank(const nid_t &node_id) const | bdsg::ODGI | private |
increment_node_ids(nid_t increment) | bdsg::ODGI | virtual |
insert_step(const step_handle_t &before, const step_handle_t &after, const handle_t &to_insert) | bdsg::ODGI | |
is_empty(const path_handle_t &path_handle) const | bdsg::ODGI | virtual |
is_path_end(const step_handle_t &step_handle) const | bdsg::ODGI | |
is_path_front_end(const step_handle_t &step_handle) const | bdsg::ODGI | |
link_steps(const step_handle_t &from, const step_handle_t &to) | bdsg::ODGI | private |
load(std::istream &in) | bdsg::ODGI | |
max_node_id(void) const | bdsg::ODGI | virtual |
min_node_id(void) const | bdsg::ODGI | virtual |
node_v | bdsg::ODGI | private |
ODGI(void) | bdsg::ODGI | inline |
optimize(bool allow_id_reassignment=true) | bdsg::ODGI | virtual |
path_back(const path_handle_t &path_handle) const | bdsg::ODGI | virtual |
path_begin(const path_handle_t &path_handle) const | bdsg::ODGI | virtual |
path_end(const path_handle_t &path_handle) const | bdsg::ODGI | virtual |
path_front_end(const path_handle_t &path_handle) const | bdsg::ODGI | virtual |
path_metadata_v | bdsg::ODGI | private |
path_name_map | bdsg::ODGI | private |
path_to_rank(const path_handle_t &path) const | bdsg::ODGI | private |
prepend_step(const path_handle_t &path, const handle_t &to_append) | bdsg::ODGI | virtual |
rank_to_id(const uint64_t &rank) const | bdsg::ODGI | private |
rank_to_path(size_t rank) const | bdsg::ODGI | private |
reassign_node_ids(const std::function< nid_t(const nid_t &)> &get_new_id) | bdsg::ODGI | virtual |
rewrite_segment(const step_handle_t &segment_begin, const step_handle_t &segment_end, const std::vector< handle_t > &new_segment) | bdsg::ODGI | virtual |
scan_path(const path_handle_t &path) const | handlegraph::PathHandleGraph | |
serialize(std::ostream &out) const | handlegraph::SerializableHandleGraph | inline |
serialize(const std::string &filename) const | handlegraph::SerializableHandleGraph | inline |
serialize_and_measure(std::ostream &out) const | bdsg::ODGI | |
serialize_members(std::ostream &out) const | bdsg::ODGI | privatevirtual |
set_circularity(const path_handle_t &path_handle, bool circular) | bdsg::ODGI | virtual |
set_handle_of_step(step_handle_t &step_handle, const handle_t &handle) const | bdsg::ODGI | private |
set_handle_sequence(const handle_t &handle, const std::string &seq) | bdsg::ODGI | private |
set_id_increment(const nid_t &min_id) | bdsg::ODGI | virtual |
set_step(const step_handle_t &step_handle, const handle_t &handle) | bdsg::ODGI | |
steps_of_handle(const handle_t &handle, bool match_orientation=false) const | bdsg::ODGI | virtual |
swap_handles(const handle_t &a, const handle_t &b) | bdsg::ODGI | |
to_gfa(std::ostream &out) const | bdsg::ODGI | |
to_gfa(const string &filename) const | bdsg::ODGI | |
to_gfa() const | bdsg::ODGI | |
traverse_edge_handle(const edge_t &edge, const handle_t &left) const | bdsg::ODGI | |
~DeletableHandleGraph()=default | handlegraph::DeletableHandleGraph | virtual |
~HandleGraph()=default | handlegraph::HandleGraph | virtual |
~MutableHandleGraph()=default | handlegraph::MutableHandleGraph | virtual |
~MutablePathDeletableHandleGraph()=default | handlegraph::MutablePathDeletableHandleGraph | virtual |
~MutablePathHandleGraph()=default | handlegraph::MutablePathHandleGraph | virtual |
~MutablePathMutableHandleGraph()=default | handlegraph::MutablePathMutableHandleGraph | virtual |
~ODGI(void) | bdsg::ODGI | inline |
~PathHandleGraph()=default | handlegraph::PathHandleGraph | virtual |
~SerializableHandleGraph()=default | handlegraph::SerializableHandleGraph | virtual |