vg
tools for working with variation graphs
Macros | Functions
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
 

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

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 
)