xg::XG Member List

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

ASSEMBLY_OR_NAME_MATCH	handlegraph::PathMetadata	privatestatic
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
CURRENT_VERSION	xg::XG	static
deserialize(std::istream &in)	handlegraph::Serializable	virtual
deserialize(const std::string &filename)	handlegraph::Serializable	virtual
deserialize_members(std::istream &in)	xg::XG	protectedvirtual
dump_to_stream(std::ostream &out) const	xg::XG
edge_count	xg::XG
edge_handle(const handle_t &left, const handle_t &right) const	handlegraph::HandleGraph
edge_index(const edge_t &edge) const	xg::XG	virtual
edge_orientation(const uint64_t &raw_edge)	xg::XG	privatestatic
edge_relative_offset(const uint64_t &raw_edge)	xg::XG	privatestatic
encode_edge(const size_t &offest_from, const size_t &offest_to, const bool &to_rev)	xg::XG	privatestatic
flip(const handle_t &handle) const	xg::XG	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	xg::XG	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	xg::XG	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	xg::XG	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	xg::XG	virtual
for_each_step_position_on_handle(const handle_t &handle, const std::function< bool(const step_handle_t &, const bool &, const size_t &)> &iteratee) const	handlegraph::PathPositionHandleGraph	virtual
for_path_range(const std::string &name, int64_t start, int64_t stop, std::function< void(const handle_t &)> lambda, bool is_rev) const	xg::XG
FORMAT	handlegraph::PathMetadata	privatestatic
forward(const handle_t &handle) const	handlegraph::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_bv	xg::XG	private
g_bv_rank	xg::XG	private
g_bv_select	xg::XG	private
g_iv	xg::XG	private
G_NODE_HEADER_LENGTH	xg::XG	privatestatic
G_NODE_ID_OFFSET	xg::XG	privatestatic
G_NODE_LEFT_COUNT_OFFSET	xg::XG	privatestatic
G_NODE_LENGTH_OFFSET	xg::XG	privatestatic
G_NODE_RIGHT_COUNT_OFFSET	xg::XG	privatestatic
G_NODE_SEQ_START_OFFSET	xg::XG	privatestatic
get_base(const handle_t &handle, size_t index) const	xg::XG	virtual
get_degree(const handle_t &handle, bool go_left) const	handlegraph::HandleGraph	virtual
get_edge_count() const	xg::XG	virtual
get_g_iv_size(void) const	xg::XG
get_handle(const nid_t &node_id, bool is_reverse=false) const	xg::XG	virtual
get_handle_of_step(const step_handle_t &step_handle) const	xg::XG	virtual
get_haplotype(const path_handle_t &handle) const	handlegraph::PathMetadata	virtual
get_id(const handle_t &handle) const	xg::XG	virtual
get_is_circular(const path_handle_t &path_handle) const	xg::XG	virtual
get_is_reverse(const handle_t &handle) const	xg::XG	virtual
get_length(const handle_t &handle) const	xg::XG	virtual
get_locus_name(const path_handle_t &handle) const	handlegraph::PathMetadata	virtual
get_magic_number(void) const	xg::XG	virtual
get_next_step(const step_handle_t &step_handle) const	xg::XG	virtual
get_node_count() const	xg::XG	virtual
get_path(const std::string &name) const	xg::XG
get_path_count(void) const	xg::XG	virtual
get_path_handle(const std::string &path_name) const	xg::XG	virtual
get_path_handle_of_step(const step_handle_t &step_handle) const	xg::XG	virtual
get_path_length(const path_handle_t &path_handle) const	xg::XG	virtual
get_path_name(const path_handle_t &path_handle) const	xg::XG	virtual
get_phase_block(const path_handle_t &handle) const	handlegraph::PathMetadata	virtual
get_position_of_step(const step_handle_t &step) const	xg::XG	virtual
get_previous_step(const step_handle_t &step_handle) const	xg::XG	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	xg::XG	virtual
get_step_at_position(const path_handle_t &path, const size_t &position) const	xg::XG	virtual
get_step_count(const path_handle_t &path_handle) const	xg::XG	virtual
handlegraph::PathPositionHandleGraph::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	xg::XG	virtual
get_total_length() const	xg::XG	virtual
graph_pos_at_path_position(const path_handle_t &path, size_t path_pos) const	xg::XG
graph_pos_at_path_position(const std::string &name, size_t path_pos) const	xg::XG
handle_at_path_position(const path_handle_t &path, size_t pos) const	xg::XG
handle_rank(const handle_t &handle) const	xg::XG
handle_to_rank(const handle_t &handle) const	handlegraph::RankedHandleGraph	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	xg::XG	virtual
has_node(nid_t node_id) const	xg::XG	virtual
has_path(const std::string &path_name) const	xg::XG	virtual
has_previous_step(const step_handle_t &step_handle) const	xg::XG	virtual
id_to_rank(const nid_t &id) const	xg::XG	virtual
index_node_to_path(const std::string &basename)	xg::XG	private
index_path_names()	xg::XG	private
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_id	xg::XG	private
max_node_id() const	xg::XG	virtual
max_node_rank(void) const	xg::XG
max_path_rank(void) const	xg::XG
min_approx_path_distance(const nid_t &id1, const nid_t &id2) const	xg::XG
min_id	xg::XG	private
min_node_id() const	xg::XG	virtual
nearest_offsets_in_paths(const pos_t &pos, int64_t max_search) const	xg::XG
nearest_path_node(const nid_t &id, int64_t max_steps=16) const	xg::XG
next_path_position(const pos_t &pos, const int64_t &max_search) const	xg::XG
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
node_at_vector_offset(const size_t &offset) const	xg::XG	virtual
node_count	xg::XG
node_graph_idx(const nid_t &id) const	xg::XG
node_start_at_path_position(const path_handle_t &path, size_t pos) const	xg::XG
node_vector_offset(const nid_t &id) const	xg::XG	virtual
np_bv	xg::XG	private
np_bv_select	xg::XG	private
np_iv	xg::XG	private
nr_iv	xg::XG	private
nx_iv	xg::XG	private
offsets_in_paths(const pos_t &gpos) const	xg::XG
OLD_EDGE_TYPE_END_END	xg::XG	privatestatic
OLD_EDGE_TYPE_END_START	xg::XG	privatestatic
OLD_EDGE_TYPE_MAX	xg::XG	privatestatic
OLD_EDGE_TYPE_MIN	xg::XG	privatestatic
OLD_EDGE_TYPE_START_END	xg::XG	privatestatic
OLD_EDGE_TYPE_START_START	xg::XG	privatestatic
OLD_G_EDGE_LENGTH	xg::XG	privatestatic
OLD_G_EDGE_OFFSET_OFFSET	xg::XG	privatestatic
OLD_G_EDGE_TYPE_OFFSET	xg::XG	privatestatic
OLD_G_NODE_FROM_COUNT_OFFSET	xg::XG	privatestatic
OLD_G_NODE_TO_COUNT_OFFSET	xg::XG	privatestatic
old_version_path_name_end	xg::XG	static
old_version_path_name_start	xg::XG	static
operator=(const XG &other)=delete	xg::XG
operator=(XG &&other)=delete	xg::XG
orientation_from_old_edge_type(int type, bool &from_rev, bool &to_rev) const	xg::XG	private
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	xg::XG	virtual
path_begin(const path_handle_t &path_handle) const	xg::XG	virtual
path_contains_handle(const std::string &name, const handle_t &handle) const	xg::XG
path_count	xg::XG
path_end(const path_handle_t &path_handle) const	xg::XG	virtual
path_front_end(const path_handle_t &path_handle) const	xg::XG	virtual
path_name(const size_t &rank) const	xg::XG
path_name_csa_delim	xg::XG	static
path_names_by_prefix(const std::string &prefix) const	xg::XG
path_ranks_by_prefix(const std::string &prefix) const	xg::XG
paths	xg::XG	private
paths_of_handle(const handle_t &handle) const	xg::XG
PHASE_BLOCK_MATCH	handlegraph::PathMetadata	privatestatic
pi_iv	xg::XG	private
pn_bv	xg::XG	private
pn_bv_rank	xg::XG	private
pn_bv_select	xg::XG	private
pn_csa	xg::XG	private
pn_iv	xg::XG	private
pos_char(nid_t id, bool is_rev, size_t off) const	xg::XG
pos_substr(nid_t id, bool is_rev, size_t off, size_t len) const	xg::XG
position_in_path(const handle_t &handle, const path_handle_t &path) const	xg::XG
position_in_paths(const handle_t &handle, const size_t &offset) const	xg::XG
print_graph() const	xg::XG	private
r_iv	xg::XG	private
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
rank_to_handle(const size_t &rank) const	handlegraph::RankedHandleGraph	virtual
rank_to_id(const size_t &rank) const	xg::XG	virtual
reencode_old_g_vector(const sdsl::int_vector<> &old_g_iv, const sdsl::rank_support_v< 1 > &old_g_bv_rank)	xg::XG	private
s_bv	xg::XG	private
s_bv_rank	xg::XG	private
s_bv_select	xg::XG	private
s_iv	xg::XG	private
scan_path(const path_handle_t &path) const	handlegraph::PathHandleGraph
SEPARATOR	handlegraph::PathMetadata	privatestatic
seq_length	xg::XG
serialize(std::ostream &out) const	handlegraph::Serializable	virtual
serialize(const std::string &filename) const	handlegraph::Serializable	virtual
serialize(std::ostream &out)	handlegraph::Serializable	virtual
serialize(const std::string &filename)	handlegraph::Serializable	virtual
serialize_and_measure(std::ostream &out, sdsl::structure_tree_node *s=nullptr, std::string name="") const	xg::XG
serialize_members(std::ostream &out) const	xg::XG	protectedvirtual
serialize_members_and_measure(std::ostream &out, sdsl::structure_tree_node *s=nullptr, std::string name="") const	xg::XG	protected
steps_of_handle(const handle_t &handle, bool match_orientation=false) const	handlegraph::PathHandleGraph	virtual
to_gfa(std::ostream &out) const	xg::XG
traverse_edge_handle(const edge_t &edge, const handle_t &left) const	handlegraph::HandleGraph
XG(void)=default	xg::XG
XG(const XG &other)=delete	xg::XG
XG(XG &&other)=delete	xg::XG
~HandleGraph()=default	handlegraph::HandleGraph	virtual
~PathHandleGraph()=default	handlegraph::PathHandleGraph	virtual
~PathMetadata()=default	handlegraph::PathMetadata	virtual
~PathPositionHandleGraph()=default	handlegraph::PathPositionHandleGraph	virtual
~Serializable()=default	handlegraph::Serializable	virtual
~VectorizableHandleGraph()=default	handlegraph::VectorizableHandleGraph	virtual
~XG(void)	xg::XG