vg
tools for working with variation graphs
Classes | Enumerations | Functions
gbwt_main.cpp File Reference
#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_typedetermine_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)
 

Detailed Description

Defines the "vg gbwt" subcommand for building, merging, and manipulating GBWT indexes and GBWTGraphs.

Enumeration Type Documentation

◆ build_mode

enum build_mode
Enumerator
build_none 
build_vcf 
build_paths 
build_alignments 

◆ merge_mode

enum merge_mode
Enumerator
merge_none 
merge_insert 
merge_fast 
merge_parallel 

◆ path_cover_mode

Enumerator
path_cover_none 
path_cover_augment 
path_cover_local 
path_cover_greedy 

Function Documentation

◆ clear_graph()

void clear_graph ( std::unique_ptr< PathHandleGraph > &  graph,
bool &  in_use 
)

◆ default_build_jobs()

size_t default_build_jobs ( )

◆ default_merge_jobs()

size_t default_merge_jobs ( )

◆ determine_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 
)

◆ get_graph()

void get_graph ( std::unique_ptr< PathHandleGraph > &  graph,
bool &  in_use,
const std::string &  filename,
bool  show_progress 
)

◆ help_gbwt()

void help_gbwt ( char **  argv)

◆ main_gbwt()

int main_gbwt ( int  argc,
char **  argv 
)

◆ print_metadata()

void print_metadata ( std::ostream &  out,
const GBWTHandler gbwts 
)

◆ use_or_save()

void use_or_save ( std::unique_ptr< gbwt::DynamicGBWT > &  index,
GBWTHandler gbwts,
std::vector< std::string > &  filenames,
size_t  i,
bool  show_progress 
)

◆ use_preset()

void use_preset ( HaplotypeIndexer haplotype_indexer,
std::string  preset_name 
)