gbwt_main.cpp File Reference

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

Classes
struct	job_type

Enumerations
enum	build_mode { build_none , build_vcf , build_paths , build_alignments }
enum	merge_mode { merge_none , merge_insert , merge_fast , merge_parallel }
enum	path_cover_mode { path_cover_none , path_cover_augment , path_cover_local , path_cover_greedy }

Functions
void	use_or_save (std::unique_ptr< gbwt::DynamicGBWT > &index, GBWTHandler &gbwts, std::vector< std::string > &filenames, size_t i, bool show_progress)
void	print_metadata (std::ostream &out, const GBWTHandler &gbwts)
void	get_graph (std::unique_ptr< PathHandleGraph > &graph, bool &in_use, const std::string &filename, bool show_progress)
void	clear_graph (std::unique_ptr< PathHandleGraph > &graph, bool &in_use)
std::vector< job_type >	determine_jobs (const std::vector< std::string > &vcf_files, std::unique_ptr< PathHandleGraph > &graph, const std::map< std::string, std::string > &path_to_vcf, bool inputs_as_jobs)
size_t	default_build_jobs ()
size_t	default_merge_jobs ()
void	use_preset (HaplotypeIndexer &haplotype_indexer, std::string preset_name)
void	help_gbwt (char **argv)
int	main_gbwt (int argc, char **argv)

Detailed Description

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

Enumeration Type Documentation

build_mode

enum build_mode

Enumerator
build_none
build_vcf
build_paths
build_alignments

merge_mode

enum merge_mode

Enumerator
merge_none
merge_insert
merge_fast
merge_parallel

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< PathHandleGraph > &	graph,
		bool &	in_use
	)

default_build_jobs()

size_t default_build_jobs

(

)

default_merge_jobs()

size_t default_merge_jobs

(

)

determine_jobs()

std::vector< job_type > determine_jobs	(	const std::vector< std::string > &	vcf_files,
		std::unique_ptr< PathHandleGraph > &	graph,
		const std::map< std::string, std::string > &	path_to_vcf,
		bool	inputs_as_jobs
	)

get_graph()

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

help_gbwt()

void help_gbwt

(

char **

argv

)

main_gbwt()

int main_gbwt	(	int	argc,
		char **	argv
	)

print_metadata()

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

use_or_save()

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

use_preset()

void use_preset	(	HaplotypeIndexer &	haplotype_indexer,
		std::string	preset_name
	)