vg
tools for working with variation graphs
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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_load | vg::Index | |
close(void) | vg::Index | |
column_family_options | vg::Index | |
compact(void) | vg::Index | |
compare_kmers(Index &other) | vg::Index | |
cross_alignment(int64_t aln_id, const Alignment &alignment) | vg::Index | |
db | vg::Index | |
db_options | vg::Index | |
dump(std::ostream &out) | vg::Index | |
end_sep | vg::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 | |
name | vg::Index | |
new_path_id(const string &name) | vg::Index | |
next_nonce | vg::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_sep | vg::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 | |
threads | vg::Index | |
traversal_entry_to_string(const string &key, const string &value) | vg::Index | |
write_options | vg::Index | |
~Index(void) | vg::Index |