#include <omp.h>
#include <unistd.h>
#include <getopt.h>
#include <random>
#include <string>
#include <vector>
#include "subcommand.hpp"
#include "../vg.hpp"
#include "../haplotype_indexer.hpp"
#include "xg.hpp"
#include <vg/io/stream.hpp>
#include <vg/io/vpkg.hpp>
#include "../io/save_handle_graph.hpp"
#include "../stream_index.hpp"
#include "../vg_set.hpp"
#include "../utility.hpp"
#include "../region.hpp"
#include "../integrated_snarl_finder.hpp"
#include "../snarl_distance_index.hpp"
#include "../source_sink_overlay.hpp"
#include "../gbwt_helper.hpp"
#include "../gbwtgraph_helper.hpp"
#include "../gcsa_helper.hpp"
#include <gcsa/algorithms.h>
#include <gbwt/variants.h>
#include <bdsg/overlays/packed_subgraph_overlay.hpp>
#include <handlegraph/algorithms/weakly_connected_components.hpp>

Macros
#define	OPT_BUILD_VGI_INDEX 1000

#define	OPT_RENAME_VARIANTS 1001

#define	OPT_DISTANCE_SNARL_LIMIT 1002

Functions
void	help_index (char **argv)

void	multiple_thread_sources ()

int	main_index (int argc, char **argv)

Macro Definition Documentation

◆ OPT_BUILD_VGI_INDEX

#define OPT_BUILD_VGI_INDEX 1000

◆ OPT_DISTANCE_SNARL_LIMIT

#define OPT_DISTANCE_SNARL_LIMIT 1002

◆ 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
	)

◆ multiple_thread_sources()

void multiple_thread_sources ( )

Macros

Functions