autoindex_main.cpp File Reference

#include <iostream>
#include <sstream>
#include <algorithm>
#include <cctype>
#include <unistd.h>
#include <getopt.h>
#include <htslib/hts.h>
#include <htslib/vcf.h>
#include <gbwt/utils.h>
#include <omp.h>
#include "subcommand.hpp"
#include "index_registry.hpp"
#include "utility.hpp"

Macros
#define	OPT_KEEP_INTERMEDIATE   1000
#define	OPT_FORCE_UNPHASED   1001
#define	OPT_FORCE_PHASED   1002
#define	OPT_GBWT_BUFFER_SIZE   1003
#define	OPT_GCSA_SIZE_LIMIT   1004

Functions
int64_t	parse_memory_usage (const string &mem_arg)
string	mem_usage_string (int64_t mem)
pair< string, vector< string > >	parse_provide_string (const string &str)
void	help_autoindex (char **argv)
int	main_autoindex (int argc, char **argv)

Detailed Description

Defines the "vg autoindex" subcommand, which produces indexes needed for other subcommands

Macro Definition Documentation

OPT_FORCE_PHASED

#define OPT_FORCE_PHASED   1002

OPT_FORCE_UNPHASED

#define OPT_FORCE_UNPHASED   1001

OPT_GBWT_BUFFER_SIZE

#define OPT_GBWT_BUFFER_SIZE   1003

OPT_GCSA_SIZE_LIMIT

#define OPT_GCSA_SIZE_LIMIT   1004

OPT_KEEP_INTERMEDIATE

#define OPT_KEEP_INTERMEDIATE   1000

Function Documentation

help_autoindex()

void help_autoindex

(

char **

argv

)

main_autoindex()

int main_autoindex	(	int	argc,
		char **	argv
	)

mem_usage_string()

string mem_usage_string

(

int64_t

mem

)

parse_memory_usage()

int64_t parse_memory_usage

(

const string &

mem_arg

)

parse_provide_string()

pair<string, vector<string> > parse_provide_string

(

const string &

str

)