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

enum 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
	)