vg
tools for working with variation graphs
Public Member Functions | Public Attributes | List of all members
vg::Index Class Reference

#include <index.hpp>

Public Member Functions

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

Public Attributes

string name
 
char start_sep
 
char end_sep
 
int threads
 
rocksdb::DB * db
 
rocksdb::Options db_options
 
rocksdb::WriteOptions write_options
 
rocksdb::ColumnFamilyOptions column_family_options
 
bool bulk_load
 
std::atomic< uint64_t > next_nonce
 

Constructor & Destructor Documentation

◆ Index() [1/2]

vg::Index::Index ( void  )

◆ Index() [2/2]

vg::Index::Index ( string &  name)

◆ ~Index()

vg::Index::~Index ( void  )

Member Function Documentation

◆ alignment_entry_to_string()

string vg::Index::alignment_entry_to_string ( const string &  key,
const string &  value 
)

◆ approx_size_of_kmer_matches()

uint64_t vg::Index::approx_size_of_kmer_matches ( const string &  kmer)

◆ approx_sizes_of_kmer_matches()

void vg::Index::approx_sizes_of_kmer_matches ( const vector< string > &  kmers,
vector< uint64_t > &  sizes 
)

◆ base_entry_to_string()

string vg::Index::base_entry_to_string ( const string &  key,
const string &  value 
)

◆ batch_edge()

void vg::Index::batch_edge ( const Edge edge,
rocksdb::WriteBatch &  batch 
)

◆ batch_kmer()

void vg::Index::batch_kmer ( const string &  kmer,
const nid_t  id,
const int32_t  pos,
rocksdb::WriteBatch &  batch 
)

◆ batch_node()

void vg::Index::batch_node ( const Node node,
rocksdb::WriteBatch &  batch 
)

◆ close()

void vg::Index::close ( void  )

◆ compact()

void vg::Index::compact ( void  )

◆ compare_kmers()

pair< uint64_t, uint64_t > vg::Index::compare_kmers ( Index other)

◆ cross_alignment()

void vg::Index::cross_alignment ( int64_t  aln_id,
const Alignment alignment 
)

◆ dump()

void vg::Index::dump ( std::ostream &  out)

◆ entry_to_string()

string vg::Index::entry_to_string ( const string &  key,
const string &  value 
)

◆ expand_context()

void vg::Index::expand_context ( VG graph,
int  steps = 1 
)

◆ first_kmer_key()

string vg::Index::first_kmer_key ( const string &  kmer)

◆ flush()

void vg::Index::flush ( void  )

◆ for_alignment_in_range()

void vg::Index::for_alignment_in_range ( nid_t  id1,
nid_t  id2,
std::function< void(const Alignment &)>  lambda 
)

◆ for_alignment_to_node()

void vg::Index::for_alignment_to_node ( nid_t  node_id,
std::function< void(const Alignment &)>  lambda 
)

◆ for_alignment_to_nodes()

void vg::Index::for_alignment_to_nodes ( const vector< nid_t > &  ids,
std::function< void(const Alignment &)>  lambda 
)

◆ for_all()

void vg::Index::for_all ( std::function< void(string &, string &)>  lambda)

◆ for_base_alignments()

void vg::Index::for_base_alignments ( const set< int64_t > &  aln_ids,
std::function< void(const Alignment &)>  lambda 
)

◆ for_each_alignment()

void vg::Index::for_each_alignment ( function< void(const Alignment &)>  lambda)

◆ for_each_mapping()

void vg::Index::for_each_mapping ( function< void(const Mapping &)>  lambda)

◆ for_graph_range()

void vg::Index::for_graph_range ( nid_t  from_id,
nid_t  to_id,
function< void(string &, string &)>  lambda 
)

◆ for_kmer_range()

void vg::Index::for_kmer_range ( const string &  kmer,
function< void(string &, string &)>  lambda 
)

◆ for_range()

void vg::Index::for_range ( string &  key_start,
string &  key_end,
std::function< void(string &, string &)>  lambda 
)

◆ get_alignments() [1/2]

void vg::Index::get_alignments ( nid_t  id1,
nid_t  id2,
vector< Alignment > &  alignments 
)

◆ get_alignments() [2/2]

void vg::Index::get_alignments ( nid_t  node_id,
vector< Alignment > &  alignments 
)

◆ get_connected_nodes()

void vg::Index::get_connected_nodes ( VG graph)

◆ get_context()

void vg::Index::get_context ( nid_t  id,
VG graph 
)

◆ get_edge()

rocksdb::Status vg::Index::get_edge ( nid_t  from,
bool  from_start,
nid_t  to,
bool  to_end,
Edge edge 
)

◆ get_edges_of()

void vg::Index::get_edges_of ( nid_t  node,
vector< Edge > &  edges 
)

◆ get_edges_on_end()

void vg::Index::get_edges_on_end ( nid_t  node,
vector< Edge > &  edges 
)

◆ get_edges_on_start()

void vg::Index::get_edges_on_start ( nid_t  node,
vector< Edge > &  edges 
)

◆ get_kmer_positions() [1/2]

void vg::Index::get_kmer_positions ( const string &  kmer,
map< nid_t, vector< int32_t > > &  positions 
)

◆ get_kmer_positions() [2/2]

void vg::Index::get_kmer_positions ( const string &  kmer,
map< string, vector< pair< nid_t, int32_t > > > &  positions 
)

◆ get_kmer_subgraph()

void vg::Index::get_kmer_subgraph ( const string &  kmer,
VG graph 
)

◆ get_mappings()

void vg::Index::get_mappings ( nid_t  node_id,
vector< Mapping > &  mappings 
)

◆ get_max_path_id()

int64_t vg::Index::get_max_path_id ( void  )

◆ get_metadata()

rocksdb::Status vg::Index::get_metadata ( const string &  key,
string &  data 
)

◆ get_nearest_node_next_path_member()

pair< list< pair< nid_t, bool > >, pair< nid_t, bool > > 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 
)

◆ get_nearest_node_prev_path_member()

pair< list< pair< nid_t, bool > >, pair< nid_t, bool > > 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 
)

◆ get_node()

rocksdb::Status vg::Index::get_node ( nid_t  id,
Node node 
)

◆ get_node_path()

int vg::Index::get_node_path ( nid_t  node_id,
int64_t  path_id,
int64_t &  path_pos,
bool &  backward,
Mapping mapping 
)

◆ get_node_path_relative_position()

bool 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 
)

◆ get_nodes_next()

void vg::Index::get_nodes_next ( nid_t  node,
bool  backward,
vector< pair< nid_t, bool >> &  destinations 
)

◆ get_nodes_prev()

void vg::Index::get_nodes_prev ( nid_t  node,
bool  backward,
vector< pair< nid_t, bool >> &  destinations 
)

◆ get_path()

void vg::Index::get_path ( VG graph,
const string &  name,
int64_t  start,
int64_t  end 
)

◆ get_path_id()

int64_t vg::Index::get_path_id ( const string &  name)

◆ get_path_name()

string vg::Index::get_path_name ( int64_t  id)

◆ get_range()

void vg::Index::get_range ( nid_t  from_id,
nid_t  to_id,
VG graph 
)

◆ GetOptions()

rocksdb::Options vg::Index::GetOptions ( bool  read_only)

◆ graph_entry_to_string()

string vg::Index::graph_entry_to_string ( const string &  key,
const string &  value 
)

◆ graph_key_type()

char vg::Index::graph_key_type ( const string &  key)

◆ key_for_alignment()

const string vg::Index::key_for_alignment ( const Alignment alignment)

◆ key_for_alignment_prefix()

const string vg::Index::key_for_alignment_prefix ( nid_t  node_id)

◆ key_for_base()

const string vg::Index::key_for_base ( int64_t  aln_id)

◆ key_for_edge_on_end()

const string vg::Index::key_for_edge_on_end ( nid_t  node_id,
nid_t  other,
bool  backward 
)

◆ key_for_edge_on_start()

const string vg::Index::key_for_edge_on_start ( nid_t  node_id,
nid_t  other,
bool  backward 
)

◆ key_for_kmer()

const string vg::Index::key_for_kmer ( const string &  kmer,
nid_t  id 
)

◆ key_for_mapping()

const string vg::Index::key_for_mapping ( const Mapping mapping)

◆ key_for_mapping_prefix()

const string vg::Index::key_for_mapping_prefix ( nid_t  node_id)

◆ key_for_metadata()

const string vg::Index::key_for_metadata ( const string &  tag)

◆ key_for_node()

const string vg::Index::key_for_node ( nid_t  id)

◆ key_for_node_path_position()

const string vg::Index::key_for_node_path_position ( nid_t  node_id,
int64_t  path_id,
int64_t  path_pos,
bool  backward 
)

◆ key_for_path_position()

const string vg::Index::key_for_path_position ( int64_t  path_id,
int64_t  path_pos,
bool  backward,
nid_t  node_id 
)

◆ key_for_traversal()

const string vg::Index::key_for_traversal ( int64_t  aln_id,
const Mapping mapping 
)

◆ key_prefix_for_edges_on_node_end()

const string vg::Index::key_prefix_for_edges_on_node_end ( nid_t  node)

◆ key_prefix_for_edges_on_node_start()

const string vg::Index::key_prefix_for_edges_on_node_start ( nid_t  node)

◆ key_prefix_for_kmer()

const string vg::Index::key_prefix_for_kmer ( const string &  kmer)

◆ key_prefix_for_node_path()

const string vg::Index::key_prefix_for_node_path ( nid_t  node_id,
int64_t  path_id 
)

◆ key_prefix_for_traversal()

const string vg::Index::key_prefix_for_traversal ( nid_t  node_id)

◆ kmer_entry_to_string()

string vg::Index::kmer_entry_to_string ( const string &  key,
const string &  value 
)

◆ kmer_matches()

void vg::Index::kmer_matches ( std::string &  kmer,
std::set< nid_t > &  node_ids,
std::set< int64_t > &  edge_ids 
)

◆ load_graph()

void vg::Index::load_graph ( VG graph)

◆ load_paths()

void vg::Index::load_paths ( VG graph)

◆ mapping_entry_to_string()

string vg::Index::mapping_entry_to_string ( const string &  key,
const string &  value 
)

◆ metadata_entry_to_string()

string vg::Index::metadata_entry_to_string ( const string &  key,
const string &  value 
)

◆ new_path_id()

int64_t vg::Index::new_path_id ( const string &  name)

◆ node_path_position()

void vg::Index::node_path_position ( nid_t  id,
string &  path_name,
int64_t &  position,
bool &  backward,
int64_t &  offset 
)

◆ node_path_to_string()

string vg::Index::node_path_to_string ( const string &  key,
const string &  value 
)

◆ open()

void vg::Index::open ( const std::string &  dir,
bool  read_only = false 
)

◆ open_for_bulk_load()

void vg::Index::open_for_bulk_load ( string &  dir)

◆ open_for_write()

void vg::Index::open_for_write ( string &  dir)

◆ open_read_only()

void vg::Index::open_read_only ( string &  dir)

◆ parse_alignment()

void vg::Index::parse_alignment ( const string &  key,
const string &  value,
nid_t node_id,
uint64_t &  nonce,
Alignment alignment 
)

◆ parse_base()

void vg::Index::parse_base ( const string &  key,
const string &  value,
int64_t &  aln_id,
Alignment alignment 
)

◆ parse_edge() [1/2]

void vg::Index::parse_edge ( const string &  key,
char &  type,
nid_t node_id,
nid_t other_id,
bool &  backward 
)

◆ parse_edge() [2/2]

void vg::Index::parse_edge ( const string &  key,
const string &  value,
char &  type,
nid_t id1,
nid_t id2,
Edge edge 
)

◆ parse_kmer()

void vg::Index::parse_kmer ( const string &  key,
const string &  value,
string &  kmer,
nid_t id,
int32_t &  pos 
)

◆ parse_mapping()

void vg::Index::parse_mapping ( const string &  key,
const string &  value,
nid_t node_id,
uint64_t &  nonce,
Mapping mapping 
)

◆ parse_node()

void vg::Index::parse_node ( const string &  key,
const string &  value,
nid_t id,
Node node 
)

◆ parse_node_path()

void 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 
)

◆ parse_path_position()

void 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 
)

◆ parse_traversal()

void vg::Index::parse_traversal ( const string &  key,
const string &  value,
nid_t node_id,
int16_t &  rank,
bool &  backward,
int64_t &  aln_id 
)

◆ path_first_node()

pair< nid_t, bool > vg::Index::path_first_node ( int64_t  path_id)

◆ path_id_prefix()

string vg::Index::path_id_prefix ( int64_t  id)

◆ path_last_node()

pair< nid_t, bool > vg::Index::path_last_node ( int64_t  path_id,
int64_t &  path_length 
)

◆ path_layout()

void vg::Index::path_layout ( map< string, pair< pair< nid_t, bool >, pair< nid_t, bool >> > &  layout,
map< string, int64_t > &  lengths 
)

◆ path_name_prefix()

string vg::Index::path_name_prefix ( const string &  name)

◆ path_position_to_string()

string vg::Index::path_position_to_string ( const string &  key,
const string &  value 
)

◆ path_relative_mapping()

Mapping 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 
)

◆ paths_by_id()

map< string, int64_t > vg::Index::paths_by_id ( void  )

◆ position_entry_to_string()

string vg::Index::position_entry_to_string ( const string &  key,
const string &  value 
)

◆ prune_kmers()

void vg::Index::prune_kmers ( int  max_kb_on_disk)

◆ put_alignment()

void vg::Index::put_alignment ( const Alignment alignment)

◆ put_base()

void vg::Index::put_base ( int64_t  aln_id,
const Alignment alignment 
)

◆ put_edge()

void vg::Index::put_edge ( const Edge edge)

◆ put_kmer()

void vg::Index::put_kmer ( const string &  kmer,
const nid_t  id,
const int32_t  pos 
)

◆ put_mapping()

void vg::Index::put_mapping ( const Mapping mapping)

◆ put_max_path_id()

void vg::Index::put_max_path_id ( int64_t  id)

◆ put_metadata()

void vg::Index::put_metadata ( const string &  tag,
const string &  data 
)

◆ put_node()

void vg::Index::put_node ( const Node node)

◆ put_node_path()

void vg::Index::put_node_path ( nid_t  node_id,
int64_t  path_id,
int64_t  path_pos,
bool  backward,
const Mapping mapping 
)

◆ put_path_id_to_name()

void vg::Index::put_path_id_to_name ( int64_t  id,
const string &  name 
)

◆ put_path_name_to_id()

void vg::Index::put_path_name_to_id ( int64_t  id,
const string &  name 
)

◆ put_path_position()

void vg::Index::put_path_position ( int64_t  path_id,
int64_t  path_pos,
bool  backward,
nid_t  node_id,
const Mapping mapping 
)

◆ put_traversal()

void vg::Index::put_traversal ( int64_t  aln_id,
const Mapping mapping 
)

◆ remember_kmer_size()

void vg::Index::remember_kmer_size ( int  size)

◆ reset_options()

void vg::Index::reset_options ( void  )

◆ store_batch()

void vg::Index::store_batch ( map< string, string > &  items)

◆ store_path()

void vg::Index::store_path ( VG graph,
const Path path 
)

◆ store_paths()

void vg::Index::store_paths ( VG graph)

◆ stored_kmer_sizes()

set< int > vg::Index::stored_kmer_sizes ( void  )

◆ traversal_entry_to_string()

string vg::Index::traversal_entry_to_string ( const string &  key,
const string &  value 
)

Member Data Documentation

◆ bulk_load

bool vg::Index::bulk_load

◆ column_family_options

rocksdb::ColumnFamilyOptions vg::Index::column_family_options

◆ db

rocksdb::DB* vg::Index::db

◆ db_options

rocksdb::Options vg::Index::db_options

◆ end_sep

char vg::Index::end_sep

◆ name

string vg::Index::name

◆ next_nonce

std::atomic<uint64_t> vg::Index::next_nonce

◆ start_sep

char vg::Index::start_sep

◆ threads

int vg::Index::threads

◆ write_options

rocksdb::WriteOptions vg::Index::write_options

The documentation for this class was generated from the following files: