vg
tools for working with variation graphs
|
#include <omp.h>
#include <unistd.h>
#include <getopt.h>
#include <set>
#include "subcommand.hpp"
#include "../gbwt_helper.hpp"
#include "../haplotype_indexer.hpp"
#include "../path.hpp"
#include "../region.hpp"
#include <vg/io/vpkg.hpp>
#include <gbwt/fast_locate.h>
#include <gbwtgraph/gbwtgraph.h>
#include <gbwtgraph/path_cover.h>
Classes | |
struct | job_type |
Enumerations | |
enum | build_mode { build_none, build_vcf, build_paths, build_alignments } |
enum | merge_mode { merge_none, merge_insert, merge_fast, merge_parallel } |
enum | path_cover_mode { path_cover_none, path_cover_augment, path_cover_local, path_cover_greedy } |
Functions | |
void | use_or_save (std::unique_ptr< gbwt::DynamicGBWT > &index, GBWTHandler &gbwts, std::vector< std::string > &filenames, size_t i, bool show_progress) |
void | print_metadata (std::ostream &out, const GBWTHandler &gbwts) |
void | get_graph (std::unique_ptr< PathHandleGraph > &graph, bool &in_use, const std::string &filename, bool show_progress) |
void | clear_graph (std::unique_ptr< PathHandleGraph > &graph, bool &in_use) |
std::vector< job_type > | determine_jobs (const std::vector< std::string > &vcf_files, std::unique_ptr< PathHandleGraph > &graph, const std::map< std::string, std::string > &path_to_vcf, bool inputs_as_jobs) |
size_t | default_build_jobs () |
size_t | default_merge_jobs () |
void | use_preset (HaplotypeIndexer &haplotype_indexer, std::string preset_name) |
void | help_gbwt (char **argv) |
int | main_gbwt (int argc, char **argv) |
Defines the "vg gbwt" subcommand for building, merging, and manipulating GBWT indexes and GBWTGraphs.
enum build_mode |
enum merge_mode |
enum path_cover_mode |
void clear_graph | ( | std::unique_ptr< PathHandleGraph > & | graph, |
bool & | in_use | ||
) |
size_t default_build_jobs | ( | ) |
size_t default_merge_jobs | ( | ) |
std::vector< job_type > determine_jobs | ( | const std::vector< std::string > & | vcf_files, |
std::unique_ptr< PathHandleGraph > & | graph, | ||
const std::map< std::string, std::string > & | path_to_vcf, | ||
bool | inputs_as_jobs | ||
) |
void get_graph | ( | std::unique_ptr< PathHandleGraph > & | graph, |
bool & | in_use, | ||
const std::string & | filename, | ||
bool | show_progress | ||
) |
void help_gbwt | ( | char ** | argv | ) |
int main_gbwt | ( | int | argc, |
char ** | argv | ||
) |
void print_metadata | ( | std::ostream & | out, |
const GBWTHandler & | gbwts | ||
) |
void use_or_save | ( | std::unique_ptr< gbwt::DynamicGBWT > & | index, |
GBWTHandler & | gbwts, | ||
std::vector< std::string > & | filenames, | ||
size_t | i, | ||
bool | show_progress | ||
) |
void use_preset | ( | HaplotypeIndexer & | haplotype_indexer, |
std::string | preset_name | ||
) |