describe_main.cpp File Reference

#include "subcommand.hpp"
#include "../recombinator.hpp"
#include "../xg.hpp"
#include "../zip_code.hpp"
#include <gbwt/gbwt.h>
#include <gbwt/fast_locate.h>
#include <gbwtgraph/gbwtgraph.h>
#include <gbwtgraph/gbz.h>
#include <gbwtgraph/minimizer.h>
#include <gcsa/files.h>
#include <bdsg/hash_graph.hpp>
#include <bdsg/packed_graph.hpp>
#include <bdsg/snarl_distance_index.hpp>
#include <fstream>
#include <iostream>
#include <string>
#include <unordered_map>
#include <getopt.h>
#include <arpa/inet.h>

Functions
void	describe_gbwt (std::ifstream &in, const std::string &index_type, std::ostream &out)
void	describe_r_index (std::ifstream &in, const std::string &index_type, std::ostream &out)
void	describe_gbwtgraph (std::ifstream &in, const std::string &index_type, std::ostream &out)
void	describe_gbz (std::ifstream &in, const std::string &index_type, std::ostream &out)
void	describe_minimizer_index (std::ifstream &in, const std::string &index_type, std::ostream &out)
void	describe_gcsa (std::ifstream &in, const std::string &index_type, std::ostream &out)
void	describe_lcp (std::ifstream &in, const std::string &index_type, std::ostream &out)
void	describe_haplotypes (std::ifstream &in, const std::string &index_type, std::ostream &out)
template<typename T >
void	load_value (std::ifstream &in, T &value)
template<typename T >
T	load_and_validate_header (std::ifstream &in)
void	help_describe (char **argv)
void	parse_args (int argc, char **argv)
int	main_describe (int argc, char **argv)
void	list_tags (std::ifstream &in, bool simple_sds, const std::string &index_type, std::ostream &out)

Detailed Description

Defines the "vg describe" subcommand, which attempts to identify and describe a file based on readily available information.

TODO: Try identifying GAM, GAF, GFA, snarls... TODO: Can we get any useful information from graphs? TODO: Could we do this better with vg::io?

Function Documentation

describe_gbwt()

void describe_gbwt	(	std::ifstream &	in,
		const std::string &	index_type,
		std::ostream &	out
	)

describe_gbwtgraph()

void describe_gbwtgraph	(	std::ifstream &	in,
		const std::string &	index_type,
		std::ostream &	out
	)

describe_gbz()

void describe_gbz	(	std::ifstream &	in,
		const std::string &	index_type,
		std::ostream &	out
	)

describe_gcsa()

void describe_gcsa	(	std::ifstream &	in,
		const std::string &	index_type,
		std::ostream &	out
	)

describe_haplotypes()

void describe_haplotypes	(	std::ifstream &	in,
		const std::string &	index_type,
		std::ostream &	out
	)

describe_lcp()

void describe_lcp	(	std::ifstream &	in,
		const std::string &	index_type,
		std::ostream &	out
	)

describe_minimizer_index()

void describe_minimizer_index	(	std::ifstream &	in,
		const std::string &	index_type,
		std::ostream &	out
	)

describe_r_index()

void describe_r_index	(	std::ifstream &	in,
		const std::string &	index_type,
		std::ostream &	out
	)

help_describe()

void help_describe

(

char **

argv

)

list_tags()

void list_tags	(	std::ifstream &	in,
		bool	simple_sds,
		const std::string &	index_type,
		std::ostream &	out
	)

load_and_validate_header()

template<typename T >

T load_and_validate_header

(

std::ifstream &

in

)

load_value()

template<typename T >

void load_value	(	std::ifstream &	in,
		T &	value
	)

main_describe()

int main_describe	(	int	argc,
		char **	argv
	)

parse_args()

void parse_args	(	int	argc,
		char **	argv
	)