vg
tools for working with variation graphs
xg::XG Member List

This is the complete list of members for xg::XG, including all inherited members.

CURRENT_VERSIONxg::XGstatic
deserialize(std::istream &in)handlegraph::SerializableHandleGraphinline
deserialize(const std::string &filename)handlegraph::SerializableHandleGraphinline
deserialize_members(std::istream &in)xg::XGprotectedvirtual
dump_to_stream(std::ostream &out) constxg::XG
edge_countxg::XG
edge_handle(const handle_t &left, const handle_t &right) consthandlegraph::HandleGraph
edge_index(const edge_t &edge) constxg::XGvirtual
edge_orientation(const uint64_t &raw_edge)xg::XGprivatestatic
edge_relative_offset(const uint64_t &raw_edge)xg::XGprivatestatic
encode_edge(const size_t &offest_from, const size_t &offest_to, const bool &to_rev)xg::XGprivatestatic
end_markerxg::XG
flip(const handle_t &handle) constxg::XGvirtual
follow_edges(const handle_t &handle, bool go_left, const Iteratee &iteratee) consthandlegraph::HandleGraph
follow_edges_impl(const handle_t &handle, bool go_left, const std::function< bool(const handle_t &)> &iteratee) constxg::XGvirtual
for_each_edge(const Iteratee &iteratee, bool parallel=false) consthandlegraph::HandleGraph
for_each_handle(const Iteratee &iteratee, bool parallel=false) consthandlegraph::HandleGraph
for_each_handle_impl(const std::function< bool(const handle_t &)> &iteratee, bool parallel=false) constxg::XGvirtual
for_each_path_handle(const Iteratee &iteratee) consthandlegraph::PathHandleGraph
for_each_path_handle_impl(const std::function< bool(const path_handle_t &)> &iteratee) constxg::XGvirtual
for_each_step_in_path(const path_handle_t &path, const Iteratee &iteratee) consthandlegraph::PathHandleGraph
for_each_step_on_handle(const handle_t &handle, const Iteratee &iteratee) consthandlegraph::PathHandleGraph
for_each_step_on_handle_impl(const handle_t &handle, const std::function< bool(const step_handle_t &)> &iteratee) constxg::XGvirtual
for_each_step_position_on_handle(const handle_t &handle, const std::function< bool(const step_handle_t &, const bool &, const size_t &)> &iteratee) consthandlegraph::PathPositionHandleGraphvirtual
for_path_range(const std::string &name, int64_t start, int64_t stop, std::function< void(const handle_t &)> lambda, bool is_rev) constxg::XG
forward(const handle_t &handle) consthandlegraph::HandleGraph
from_enumerators(const std::function< void(const std::function< void(const std::string &seq, const nid_t &node_id)> &)> &for_each_sequence, const std::function< void(const std::function< void(const nid_t &from, const bool &from_rev, const nid_t &to, const bool &to_rev)> &)> &for_each_edge, const std::function< void(const std::function< void(const std::string &path_name, const nid_t &node_id, const bool &is_rev, const std::string &cigar, const bool &is_empty, const bool &is_circular)> &)> &for_each_path_element, bool validate=false, std::string basename="")xg::XG
from_gfa(const std::string &gfa_filename, bool validate=false, std::string basename="")xg::XG
from_handle_graph(const HandleGraph &graph)xg::XG
from_path_handle_graph(const PathHandleGraph &graph)xg::XG
g_bvxg::XGprivate
g_bv_rankxg::XGprivate
g_bv_selectxg::XGprivate
g_ivxg::XGprivate
G_NODE_HEADER_LENGTHxg::XGprivatestatic
G_NODE_ID_OFFSETxg::XGprivatestatic
G_NODE_LEFT_COUNT_OFFSETxg::XGprivatestatic
G_NODE_LENGTH_OFFSETxg::XGprivatestatic
G_NODE_RIGHT_COUNT_OFFSETxg::XGprivatestatic
G_NODE_SEQ_START_OFFSETxg::XGprivatestatic
get_base(const handle_t &handle, size_t index) constxg::XGvirtual
get_degree(const handle_t &handle, bool go_left) consthandlegraph::HandleGraphvirtual
get_edge_count() constxg::XGvirtual
get_g_iv_size(void) constxg::XG
get_handle(const nid_t &node_id, bool is_reverse=false) constxg::XGvirtual
get_handle_of_step(const step_handle_t &step_handle) constxg::XGvirtual
get_id(const handle_t &handle) constxg::XGvirtual
get_is_circular(const path_handle_t &path_handle) constxg::XGvirtual
get_is_reverse(const handle_t &handle) constxg::XGvirtual
get_length(const handle_t &handle) constxg::XGvirtual
get_magic_number(void) constxg::XGvirtual
get_next_step(const step_handle_t &step_handle) constxg::XGvirtual
get_node_count() constxg::XGvirtual
get_path(const std::string &name) constxg::XG
get_path_count(void) constxg::XGvirtual
get_path_handle(const std::string &path_name) constxg::XGvirtual
get_path_handle_of_step(const step_handle_t &step_handle) constxg::XGvirtual
get_path_length(const path_handle_t &path_handle) constxg::XGvirtual
get_path_name(const path_handle_t &path_handle) constxg::XGvirtual
get_position_of_step(const step_handle_t &step) constxg::XGvirtual
get_previous_step(const step_handle_t &step_handle) constxg::XGvirtual
get_sequence(const handle_t &handle) constxg::XGvirtual
get_step_at_position(const path_handle_t &path, const size_t &position) constxg::XGvirtual
get_step_count(const path_handle_t &path_handle) constxg::XGvirtual
get_subsequence(const handle_t &handle, size_t index, size_t size) constxg::XGvirtual
get_total_length() constxg::XGvirtual
graph_pos_at_path_position(const path_handle_t &path, size_t path_pos) constxg::XG
graph_pos_at_path_position(const std::string &name, size_t path_pos) constxg::XG
handle_at_path_position(const path_handle_t &path, size_t pos) constxg::XG
handle_rank(const handle_t &handle) constxg::XG
handle_to_rank(const handle_t &handle) consthandlegraph::RankedHandleGraphvirtual
has_edge(const handle_t &left, const handle_t &right) consthandlegraph::HandleGraphvirtual
has_edge(const edge_t &edge) consthandlegraph::HandleGraphinline
has_next_step(const step_handle_t &step_handle) constxg::XGvirtual
has_node(nid_t node_id) constxg::XGvirtual
has_path(const std::string &path_name) constxg::XGvirtual
has_previous_step(const step_handle_t &step_handle) constxg::XGvirtual
id_to_rank(const nid_t &id) constxg::XGvirtual
index_node_to_path(const std::string &basename)xg::XGprivate
is_empty(const path_handle_t &path_handle) consthandlegraph::PathHandleGraphvirtual
max_idxg::XGprivate
max_node_id() constxg::XGvirtual
max_node_rank(void) constxg::XG
max_path_rank(void) constxg::XG
min_approx_path_distance(const nid_t &id1, const nid_t &id2) constxg::XG
min_idxg::XGprivate
min_node_id() constxg::XGvirtual
nearest_offsets_in_paths(const pos_t &pos, int64_t max_search) constxg::XG
nearest_path_node(const nid_t &id, int64_t max_steps=16) constxg::XG
next_path_position(const pos_t &pos, const int64_t &max_search) constxg::XG
node_at_vector_offset(const size_t &offset) constxg::XGvirtual
node_countxg::XG
node_graph_idx(const nid_t &id) constxg::XG
node_start_at_path_position(const path_handle_t &path, size_t pos) constxg::XG
node_vector_offset(const nid_t &id) constxg::XGvirtual
np_bvxg::XGprivate
np_bv_selectxg::XGprivate
np_ivxg::XGprivate
nr_ivxg::XGprivate
nx_ivxg::XGprivate
offsets_in_paths(const pos_t &gpos) constxg::XG
OLD_EDGE_TYPE_END_ENDxg::XGprivatestatic
OLD_EDGE_TYPE_END_STARTxg::XGprivatestatic
OLD_EDGE_TYPE_MAXxg::XGprivatestatic
OLD_EDGE_TYPE_MINxg::XGprivatestatic
OLD_EDGE_TYPE_START_ENDxg::XGprivatestatic
OLD_EDGE_TYPE_START_STARTxg::XGprivatestatic
OLD_G_EDGE_LENGTHxg::XGprivatestatic
OLD_G_EDGE_OFFSET_OFFSETxg::XGprivatestatic
OLD_G_EDGE_TYPE_OFFSETxg::XGprivatestatic
OLD_G_NODE_FROM_COUNT_OFFSETxg::XGprivatestatic
OLD_G_NODE_TO_COUNT_OFFSETxg::XGprivatestatic
operator=(const XG &other)=deletexg::XG
operator=(XG &&other)=deletexg::XG
orientation_from_old_edge_type(int type, bool &from_rev, bool &to_rev) constxg::XGprivate
path_back(const path_handle_t &path_handle) constxg::XGvirtual
path_begin(const path_handle_t &path_handle) constxg::XGvirtual
path_contains_handle(const std::string &name, const handle_t &handle) constxg::XG
path_countxg::XG
path_end(const path_handle_t &path_handle) constxg::XGvirtual
path_front_end(const path_handle_t &path_handle) constxg::XGvirtual
path_name(const size_t &rank) constxg::XG
path_names_by_prefix(const std::string &prefix) constxg::XG
path_ranks_by_prefix(const std::string &prefix) constxg::XG
pathsxg::XGprivate
paths_of_handle(const handle_t &handle) constxg::XG
pi_ivxg::XGprivate
pn_bvxg::XGprivate
pn_bv_rankxg::XGprivate
pn_bv_selectxg::XGprivate
pn_csaxg::XGprivate
pn_ivxg::XGprivate
pos_char(nid_t id, bool is_rev, size_t off) constxg::XG
pos_substr(nid_t id, bool is_rev, size_t off, size_t len) constxg::XG
position_in_path(const handle_t &handle, const path_handle_t &path) constxg::XG
position_in_paths(const handle_t &handle, const size_t &offset) constxg::XG
print_graph() constxg::XGprivate
r_ivxg::XGprivate
rank_to_handle(const size_t &rank) consthandlegraph::RankedHandleGraphvirtual
rank_to_id(const size_t &rank) constxg::XGvirtual
reencode_old_g_vector(const sdsl::int_vector<> &old_g_iv, const sdsl::rank_support_v< 1 > &old_g_bv_rank)xg::XGprivate
s_bvxg::XGprivate
s_bv_rankxg::XGprivate
s_bv_selectxg::XGprivate
s_ivxg::XGprivate
scan_path(const path_handle_t &path) consthandlegraph::PathHandleGraph
seq_lengthxg::XG
serialize(std::ostream &out) consthandlegraph::SerializableHandleGraphinline
serialize(const std::string &filename) consthandlegraph::SerializableHandleGraphinline
serialize_and_measure(std::ostream &out, sdsl::structure_tree_node *s=nullptr, std::string name="") constxg::XG
serialize_members(std::ostream &out) constxg::XGprotectedvirtual
serialize_members_and_measure(std::ostream &out, sdsl::structure_tree_node *s=nullptr, std::string name="") constxg::XGprotected
start_markerxg::XG
steps_of_handle(const handle_t &handle, bool match_orientation=false) consthandlegraph::PathHandleGraphvirtual
to_gfa(std::ostream &out) constxg::XG
traverse_edge_handle(const edge_t &edge, const handle_t &left) consthandlegraph::HandleGraph
XG(void)=defaultxg::XG
XG(const XG &other)=deletexg::XG
XG(XG &&other)=deletexg::XG
~HandleGraph()=defaulthandlegraph::HandleGraphvirtual
~PathHandleGraph()=defaulthandlegraph::PathHandleGraphvirtual
~PathPositionHandleGraph()=defaulthandlegraph::PathPositionHandleGraphvirtual
~SerializableHandleGraph()=defaulthandlegraph::SerializableHandleGraphvirtual
~VectorizableHandleGraph()=defaulthandlegraph::VectorizableHandleGraphvirtual
~XG(void)xg::XG