vg
tools for working with variation graphs
Enumerations | Functions
gbwt_main.cpp File Reference
#include <omp.h>
#include <unistd.h>
#include <getopt.h>
#include <list>
#include <fstream>
#include "subcommand.hpp"
#include "../gbwt_helper.hpp"
#include <vg/io/vpkg.hpp>
#include <bdsg/overlays/overlay_helper.hpp>
#include <gbwt/fast_locate.h>
#include <gbwtgraph/gbwtgraph.h>
#include <gbwtgraph/path_cover.h>

Enumerations

enum  merge_mode { merge_none, merge_insert, merge_fast }
 
enum  path_cover_mode { path_cover_none, path_cover_augment, path_cover_local, path_cover_greedy }
 
enum  index_type { index_none, index_compressed, index_dynamic }
 

Functions

void load_gbwt (const std::string &filename, gbwt::GBWT &index, bool show_progress)
 
void load_gbwt (const std::string &filename, gbwt::DynamicGBWT &index, bool show_progress)
 
void get_compressed (gbwt::GBWT &compressed_index, gbwt::DynamicGBWT &dynamic_index, index_type &in_use, const std::string &filename, bool show_progress)
 
void get_dynamic (gbwt::GBWT &compressed_index, gbwt::DynamicGBWT &dynamic_index, index_type &in_use, const std::string &filename, bool show_progress)
 
void get_graph (std::unique_ptr< HandleGraph > &graph, bool &in_use, const std::string &filename, bool show_progress)
 
void clear_graph (std::unique_ptr< HandleGraph > &graph, bool &in_use)
 
void help_gbwt (char **argv)
 
int main_gbwt (int argc, char **argv)
 

Detailed Description

Defines the "vg gbwt" subcommand, which wraps up access for commands we'd otherwise find in the gbwt submodule.

Enumeration Type Documentation

◆ index_type

enum index_type
Enumerator
index_none 
index_compressed 
index_dynamic 

◆ merge_mode

enum merge_mode
Enumerator
merge_none 
merge_insert 
merge_fast 

◆ path_cover_mode

Enumerator
path_cover_none 
path_cover_augment 
path_cover_local 
path_cover_greedy 

Function Documentation

◆ clear_graph()

void clear_graph ( std::unique_ptr< HandleGraph > &  graph,
bool &  in_use 
)

◆ get_compressed()

void get_compressed ( gbwt::GBWT &  compressed_index,
gbwt::DynamicGBWT &  dynamic_index,
index_type in_use,
const std::string &  filename,
bool  show_progress 
)

◆ get_dynamic()

void get_dynamic ( gbwt::GBWT &  compressed_index,
gbwt::DynamicGBWT &  dynamic_index,
index_type in_use,
const std::string &  filename,
bool  show_progress 
)

◆ get_graph()

void get_graph ( std::unique_ptr< HandleGraph > &  graph,
bool &  in_use,
const std::string &  filename,
bool  show_progress 
)

◆ help_gbwt()

void help_gbwt ( char **  argv)

◆ load_gbwt() [1/2]

void load_gbwt ( const std::string &  filename,
gbwt::DynamicGBWT &  index,
bool  show_progress 
)

◆ load_gbwt() [2/2]

void load_gbwt ( const std::string &  filename,
gbwt::GBWT &  index,
bool  show_progress 
)

◆ main_gbwt()

int main_gbwt ( int  argc,
char **  argv 
)