gbwt_main.cpp File Reference

#include <omp.h>
#include <unistd.h>
#include <getopt.h>
#include <set>
#include "subcommand.hpp"
#include "../gbwt_helper.hpp"
#include "../gbwtgraph_helper.hpp"
#include "../haplotype_indexer.hpp"
#include "../path.hpp"
#include "../region.hpp"
#include "../algorithms/find_translation.hpp"
#include <vg/io/vpkg.hpp>
#include <gbwt/fast_locate.h>
#include <gbwtgraph/gfa.h>
#include <gbwtgraph/path_cover.h>

Classes
struct	GBWTConfig
struct	GraphHandler
struct	job_type

Functions
GBWTConfig	parse_gbwt_config (int argc, char **argv)
void	validate_gbwt_config (GBWTConfig &config)
void	step_1_build_gbwts (GBWTHandler &gbwts, GraphHandler &graphs, GBWTConfig &config)
void	step_2_merge_gbwts (GBWTHandler &gbwts, GBWTConfig &config)
void	step_3_alter_gbwt (GBWTHandler &gbwts, GraphHandler &graphs, GBWTConfig &config)
void	step_4_path_cover (GBWTHandler &gbwts, GraphHandler &graphs, GBWTConfig &config)
void	step_5_gbwtgraph (GBWTHandler &gbwts, GraphHandler &graphs, GBWTConfig &config)
void	step_6_r_index (GBWTHandler &gbwts, GBWTConfig &config)
void	step_7_metadata (GBWTHandler &gbwts, GBWTConfig &config)
void	step_8_paths (GBWTHandler &gbwts, GBWTConfig &config)
void	report_time_memory (const std::string &what, double start_time, const GBWTConfig &config)
void	print_metadata (std::ostream &out, const GBWTHandler &gbwts)
int	main_gbwt (int argc, char **argv)
void	help_gbwt (char **argv)
void	use_preset (std::string preset_name, GBWTConfig &config)
void	no_multiple_input_types (const GBWTConfig &config)
void	no_multiple_cover_types (const GBWTConfig &config)
void	check_tag_validity (const Logger &logger, const std::string &key, const std::string &value, const std::unordered_set< char > &prohibited, const std::string &description)
std::vector< job_type >	determine_jobs (std::unique_ptr< PathHandleGraph > &graph, const GBWTConfig &config)
void	use_or_save (const Logger &logger, std::unique_ptr< gbwt::DynamicGBWT > &index, GBWTHandler &gbwts, std::vector< std::string > &filenames, size_t i, bool show_progress)
void	remove_samples (GBWTHandler &gbwts, GBWTConfig &config)
void	set_tags (GBWTHandler &gbwts, GraphHandler &graphs, GBWTConfig &config)

Detailed Description

Defines the "vg gbwt" subcommand for building, merging, and manipulating GBWT indexes and GBWTGraphs.

Function Documentation

check_tag_validity()

void check_tag_validity	(	const Logger &	logger,
		const std::string &	key,
		const std::string &	value,
		const std::unordered_set< char > &	prohibited,
		const std::string &	description
	)

determine_jobs()

std::vector<job_type> determine_jobs	(	std::unique_ptr< PathHandleGraph > &	graph,
		const GBWTConfig &	config
	)

help_gbwt()

void help_gbwt

(

char **

argv

)

main_gbwt()

int main_gbwt	(	int	argc,
		char **	argv
	)

no_multiple_cover_types()

void no_multiple_cover_types

(

const GBWTConfig &

config

)

no_multiple_input_types()

void no_multiple_input_types

(

const GBWTConfig &

config

)

parse_gbwt_config()

GBWTConfig parse_gbwt_config	(	int	argc,
		char **	argv
	)

print_metadata()

void print_metadata	(	std::ostream &	out,
		const GBWTHandler &	gbwts
	)

remove_samples()

void remove_samples	(	GBWTHandler &	gbwts,
		GBWTConfig &	config
	)

report_time_memory()

void report_time_memory	(	const std::string &	what,
		double	start_time,
		const GBWTConfig &	config
	)

set_tags()

void set_tags	(	GBWTHandler &	gbwts,
		GraphHandler &	graphs,
		GBWTConfig &	config
	)

step_1_build_gbwts()

void step_1_build_gbwts	(	GBWTHandler &	gbwts,
		GraphHandler &	graphs,
		GBWTConfig &	config
	)

step_2_merge_gbwts()

void step_2_merge_gbwts	(	GBWTHandler &	gbwts,
		GBWTConfig &	config
	)

step_3_alter_gbwt()

void step_3_alter_gbwt	(	GBWTHandler &	gbwts,
		GraphHandler &	graphs,
		GBWTConfig &	config
	)

step_4_path_cover()

void step_4_path_cover	(	GBWTHandler &	gbwts,
		GraphHandler &	graphs,
		GBWTConfig &	config
	)

step_5_gbwtgraph()

void step_5_gbwtgraph	(	GBWTHandler &	gbwts,
		GraphHandler &	graphs,
		GBWTConfig &	config
	)

step_6_r_index()

void step_6_r_index	(	GBWTHandler &	gbwts,
		GBWTConfig &	config
	)

step_7_metadata()

void step_7_metadata	(	GBWTHandler &	gbwts,
		GBWTConfig &	config
	)

step_8_paths()

void step_8_paths	(	GBWTHandler &	gbwts,
		GBWTConfig &	config
	)

use_or_save()

void use_or_save	(	const Logger &	logger,
		std::unique_ptr< gbwt::DynamicGBWT > &	index,
		GBWTHandler &	gbwts,
		std::vector< std::string > &	filenames,
		size_t	i,
		bool	show_progress
	)

use_preset()

void use_preset	(	std::string	preset_name,
		GBWTConfig &	config
	)

validate_gbwt_config()

void validate_gbwt_config

(

GBWTConfig &

config

)