vg
tools for working with variation graphs
|
#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) |
Defines the "vg gbwt" subcommand, which wraps up access for commands we'd otherwise find in the gbwt submodule.
enum index_type |
enum merge_mode |
enum path_cover_mode |
void clear_graph | ( | std::unique_ptr< HandleGraph > & | graph, |
bool & | in_use | ||
) |
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 help_gbwt | ( | char ** | argv | ) |
void load_gbwt | ( | const std::string & | filename, |
gbwt::DynamicGBWT & | index, | ||
bool | show_progress | ||
) |
void load_gbwt | ( | const std::string & | filename, |
gbwt::GBWT & | index, | ||
bool | show_progress | ||
) |
int main_gbwt | ( | int | argc, |
char ** | argv | ||
) |