vg
tools for working with variation graphs
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#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) |
#define OPT_BUILD_VGI_INDEX 1000 |
#define OPT_RENAME_VARIANTS 1001 |
void help_index | ( | char ** | argv | ) |
int main_index | ( | int | argc, |
char ** | argv | ||
) |
std::vector< std::string > parseGenotypes | ( | const std::string & | vcf_line, |
size_t | num_samples | ||
) |
gbwt::vector_type path_to_gbwt | ( | const Path & | path | ) |
gbwt::vector_type predecessors | ( | const xg::XG & | xg_index, |
const Path & | path | ||
) |