index_main.cpp File Reference

#include <omp.h>
#include <unistd.h>
#include <getopt.h>
#include <random>
#include <string>
#include <vector>
#include "subcommand.hpp"
#include "../vg.hpp"
#include "../index.hpp"
#include "xg.hpp"
#include <vg/io/stream.hpp>
#include <vg/io/vpkg.hpp>
#include "../stream_index.hpp"
#include "../vg_set.hpp"
#include "../utility.hpp"
#include "../region.hpp"
#include "../snarls.hpp"
#include "../min_distance.hpp"
#include "../source_sink_overlay.hpp"
#include "../gbwt_helper.hpp"
#include <gcsa/gcsa.h>
#include <gcsa/algorithms.h>
#include <gbwt/variants.h>

Macros
#define	OPT_BUILD_VGI_INDEX   1000
#define	OPT_RENAME_VARIANTS   1001

Functions
void	help_index (char **argv)
gbwt::vector_type	path_to_gbwt (const Path &path)
gbwt::vector_type	predecessors (const xg::XG &xg_index, const Path &path)
std::vector< std::string >	parseGenotypes (const std::string &vcf_line, size_t num_samples)
int	main_index (int argc, char **argv)

Macro Definition Documentation

OPT_BUILD_VGI_INDEX

#define OPT_BUILD_VGI_INDEX   1000

OPT_RENAME_VARIANTS

#define OPT_RENAME_VARIANTS   1001

Function Documentation

help_index()

void help_index

(

char **

argv

)

main_index()

int main_index	(	int	argc,
		char **	argv
	)

parseGenotypes()

std::vector< std::string > parseGenotypes	(	const std::string &	vcf_line,
		size_t	num_samples
	)

path_to_gbwt()

gbwt::vector_type path_to_gbwt

(

const Path &

path

)

predecessors()

gbwt::vector_type predecessors	(	const xg::XG &	xg_index,
		const Path &	path
	)