vg
tools for working with variation graphs
vg::Index Member List

This is the complete list of members for vg::Index, including all inherited members.

alignment_entry_to_string(const string &key, const string &value)vg::Index
approx_size_of_kmer_matches(const string &kmer)vg::Index
approx_sizes_of_kmer_matches(const vector< string > &kmers, vector< uint64_t > &sizes)vg::Index
base_entry_to_string(const string &key, const string &value)vg::Index
batch_edge(const Edge *edge, rocksdb::WriteBatch &batch)vg::Index
batch_kmer(const string &kmer, const nid_t id, const int32_t pos, rocksdb::WriteBatch &batch)vg::Index
batch_node(const Node *node, rocksdb::WriteBatch &batch)vg::Index
bulk_loadvg::Index
close(void)vg::Index
column_family_optionsvg::Index
compact(void)vg::Index
compare_kmers(Index &other)vg::Index
cross_alignment(int64_t aln_id, const Alignment &alignment)vg::Index
dbvg::Index
db_optionsvg::Index
dump(std::ostream &out)vg::Index
end_sepvg::Index
entry_to_string(const string &key, const string &value)vg::Index
expand_context(VG &graph, int steps)vg::Index
first_kmer_key(const string &kmer)vg::Index
flush(void)vg::Index
for_alignment_in_range(nid_t id1, nid_t id2, std::function< void(const Alignment &)> lambda)vg::Index
for_alignment_to_node(nid_t node_id, std::function< void(const Alignment &)> lambda)vg::Index
for_alignment_to_nodes(const vector< nid_t > &ids, std::function< void(const Alignment &)> lambda)vg::Index
for_all(std::function< void(string &, string &)> lambda)vg::Index
for_base_alignments(const set< int64_t > &aln_ids, std::function< void(const Alignment &)> lambda)vg::Index
for_each_alignment(function< void(const Alignment &)> lambda)vg::Index
for_each_mapping(function< void(const Mapping &)> lambda)vg::Index
for_graph_range(nid_t from_id, nid_t to_id, function< void(string &, string &)> lambda)vg::Index
for_kmer_range(const string &kmer, function< void(string &, string &)> lambda)vg::Index
for_range(string &key_start, string &key_end, std::function< void(string &, string &)> lambda)vg::Index
get_alignments(nid_t node_id, vector< Alignment > &alignments)vg::Index
get_alignments(nid_t id1, nid_t id2, vector< Alignment > &alignments)vg::Index
get_connected_nodes(VG &graph)vg::Index
get_context(nid_t id, VG &graph)vg::Index
get_edge(nid_t from, bool from_start, nid_t to, bool to_end, Edge &edge)vg::Index
get_edges_of(nid_t node, vector< Edge > &edges)vg::Index
get_edges_on_end(nid_t node, vector< Edge > &edges)vg::Index
get_edges_on_start(nid_t node, vector< Edge > &edges)vg::Index
get_kmer_positions(const string &kmer, map< nid_t, vector< int32_t > > &positions)vg::Index
get_kmer_positions(const string &kmer, map< string, vector< pair< nid_t, int32_t > > > &positions)vg::Index
get_kmer_subgraph(const string &kmer, VG &graph)vg::Index
get_mappings(nid_t node_id, vector< Mapping > &mappings)vg::Index
get_max_path_id(void)vg::Index
get_metadata(const string &key, string &data)vg::Index
get_nearest_node_next_path_member(nid_t node_id, bool backward, int64_t path_id, int64_t &path_pos, bool &relative_orientation, int max_steps=4)vg::Index
get_nearest_node_prev_path_member(nid_t node_id, bool backward, int64_t path_id, int64_t &path_pos, bool &relative_orientation, int max_steps=4)vg::Index
get_node(nid_t id, Node &node)vg::Index
get_node_path(nid_t node_id, int64_t path_id, int64_t &path_pos, bool &backward, Mapping &mapping)vg::Index
get_node_path_relative_position(nid_t node_id, bool backward, int64_t path_id, list< pair< nid_t, bool >> &path_prev, int64_t &prev_pos, bool &prev_orientation, list< pair< nid_t, bool >> &path_next, int64_t &next_pos, bool &next_orientation)vg::Index
get_nodes_next(nid_t node, bool backward, vector< pair< nid_t, bool >> &destinations)vg::Index
get_nodes_prev(nid_t node, bool backward, vector< pair< nid_t, bool >> &destinations)vg::Index
get_path(VG &graph, const string &name, int64_t start, int64_t end)vg::Index
get_path_id(const string &name)vg::Index
get_path_name(int64_t id)vg::Index
get_range(nid_t from_id, nid_t to_id, VG &graph)vg::Index
GetOptions(bool read_only)vg::Index
graph_entry_to_string(const string &key, const string &value)vg::Index
graph_key_type(const string &key)vg::Index
Index(void)vg::Index
Index(string &name)vg::Index
key_for_alignment(const Alignment &alignment)vg::Index
key_for_alignment_prefix(nid_t node_id)vg::Index
key_for_base(int64_t aln_id)vg::Index
key_for_edge_on_end(nid_t node_id, nid_t other, bool backward)vg::Index
key_for_edge_on_start(nid_t node_id, nid_t other, bool backward)vg::Index
key_for_kmer(const string &kmer, nid_t id)vg::Index
key_for_mapping(const Mapping &mapping)vg::Index
key_for_mapping_prefix(nid_t node_id)vg::Index
key_for_metadata(const string &tag)vg::Index
key_for_node(nid_t id)vg::Index
key_for_node_path_position(nid_t node_id, int64_t path_id, int64_t path_pos, bool backward)vg::Index
key_for_path_position(int64_t path_id, int64_t path_pos, bool backward, nid_t node_id)vg::Index
key_for_traversal(int64_t aln_id, const Mapping &mapping)vg::Index
key_prefix_for_edges_on_node_end(nid_t node)vg::Index
key_prefix_for_edges_on_node_start(nid_t node)vg::Index
key_prefix_for_kmer(const string &kmer)vg::Index
key_prefix_for_node_path(nid_t node_id, int64_t path_id)vg::Index
key_prefix_for_traversal(nid_t node_id)vg::Index
kmer_entry_to_string(const string &key, const string &value)vg::Index
kmer_matches(std::string &kmer, std::set< nid_t > &node_ids, std::set< int64_t > &edge_ids)vg::Index
load_graph(VG &graph)vg::Index
load_paths(VG &graph)vg::Index
mapping_entry_to_string(const string &key, const string &value)vg::Index
metadata_entry_to_string(const string &key, const string &value)vg::Index
namevg::Index
new_path_id(const string &name)vg::Index
next_noncevg::Index
node_path_position(nid_t id, string &path_name, int64_t &position, bool &backward, int64_t &offset)vg::Index
node_path_to_string(const string &key, const string &value)vg::Index
open(const std::string &dir, bool read_only=false)vg::Index
open_for_bulk_load(string &dir)vg::Index
open_for_write(string &dir)vg::Index
open_read_only(string &dir)vg::Index
parse_alignment(const string &key, const string &value, nid_t &node_id, uint64_t &nonce, Alignment &alignment)vg::Index
parse_base(const string &key, const string &value, int64_t &aln_id, Alignment &alignment)vg::Index
parse_edge(const string &key, const string &value, char &type, nid_t &id1, nid_t &id2, Edge &edge)vg::Index
parse_edge(const string &key, char &type, nid_t &node_id, nid_t &other_id, bool &backward)vg::Index
parse_kmer(const string &key, const string &value, string &kmer, nid_t &id, int32_t &pos)vg::Index
parse_mapping(const string &key, const string &value, nid_t &node_id, uint64_t &nonce, Mapping &mapping)vg::Index
parse_node(const string &key, const string &value, nid_t &id, Node &node)vg::Index
parse_node_path(const string &key, const string &value, nid_t &node_id, int64_t &path_id, int64_t &path_pos, bool &backward, Mapping &mapping)vg::Index
parse_path_position(const string &key, const string &value, int64_t &path_id, int64_t &path_pos, bool &backward, nid_t &node_id, Mapping &mapping)vg::Index
parse_traversal(const string &key, const string &value, nid_t &node_id, int16_t &rank, bool &backward, int64_t &aln_id)vg::Index
path_first_node(int64_t path_id)vg::Index
path_id_prefix(int64_t id)vg::Index
path_last_node(int64_t path_id, int64_t &path_length)vg::Index
path_layout(map< string, pair< pair< nid_t, bool >, pair< nid_t, bool >> > &layout, map< string, int64_t > &lengths)vg::Index
path_name_prefix(const string &name)vg::Index
path_position_to_string(const string &key, const string &value)vg::Index
path_relative_mapping(nid_t node_id, bool backward, int64_t path_id, list< pair< nid_t, bool >> &path_prev, int64_t &prev_pos, bool &prev_orientation, list< pair< nid_t, bool >> &path_next, int64_t &next_pos, bool &next_orientation)vg::Index
paths_by_id(void)vg::Index
position_entry_to_string(const string &key, const string &value)vg::Index
prune_kmers(int max_kb_on_disk)vg::Index
put_alignment(const Alignment &alignment)vg::Index
put_base(int64_t aln_id, const Alignment &alignment)vg::Index
put_edge(const Edge *edge)vg::Index
put_kmer(const string &kmer, const nid_t id, const int32_t pos)vg::Index
put_mapping(const Mapping &mapping)vg::Index
put_max_path_id(int64_t id)vg::Index
put_metadata(const string &tag, const string &data)vg::Index
put_node(const Node *node)vg::Index
put_node_path(nid_t node_id, int64_t path_id, int64_t path_pos, bool backward, const Mapping &mapping)vg::Index
put_path_id_to_name(int64_t id, const string &name)vg::Index
put_path_name_to_id(int64_t id, const string &name)vg::Index
put_path_position(int64_t path_id, int64_t path_pos, bool backward, nid_t node_id, const Mapping &mapping)vg::Index
put_traversal(int64_t aln_id, const Mapping &mapping)vg::Index
remember_kmer_size(int size)vg::Index
reset_options(void)vg::Index
start_sepvg::Index
store_batch(map< string, string > &items)vg::Index
store_path(VG &graph, const Path &path)vg::Index
store_paths(VG &graph)vg::Index
stored_kmer_sizes(void)vg::Index
threadsvg::Index
traversal_entry_to_string(const string &key, const string &value)vg::Index
write_optionsvg::Index
~Index(void)vg::Index