vg
tools for working with variation graphs
Classes | Namespaces | Macros | Functions
giraffe_main.cpp File Reference
#include <omp.h>
#include <unistd.h>
#include <getopt.h>
#include <iostream>
#include <cassert>
#include <cstring>
#include <map>
#include <vector>
#include <unordered_set>
#include <chrono>
#include <mutex>
#include "subcommand.hpp"
#include "../seed_clusterer.hpp"
#include "../mapper.hpp"
#include "../annotation.hpp"
#include <vg/io/vpkg.hpp>
#include <vg/io/stream.hpp>
#include "../hts_alignment_emitter.hpp"
#include "../gapless_extender.hpp"
#include "../minimizer_mapper.hpp"
#include "../index_manager.hpp"
#include <bdsg/overlays/overlay_helper.hpp>
#include <gbwtgraph/minimizer.h>

Classes

struct  vg::Range< Number >
 This defines a range of values to test, from start to <=end, going up by step. More...
 
struct  vg::is_instantiation_of< Subject, Predicate >
 
struct  vg::is_instantiation_of< Predicate< PredicateArgs... >, Predicate >
 

Namespaces

 vg
 

Macros

#define OPT_OUTPUT_BASENAME   1001
 
#define OPT_REPORT_NAME   1002
 
#define OPT_TRACK_PROVENANCE   1003
 
#define OPT_TRACK_CORRECTNESS   1004
 
#define OPT_FRAGMENT_MEAN   1005
 
#define OPT_FRAGMENT_STDEV   1006
 
#define OPT_CLUSTER_STDEV   1007
 
#define OPT_RESCUE_STDEV   1008
 

Functions

template<typename Result >
bool vg::parse (const string &arg, typename enable_if< is_instantiation_of< Result, Range >::value, Result >::type &dest)
 Parse a range as start[:end[:step]]. More...
 
void help_giraffe (char **argv)
 
int main_giraffe (int argc, char **argv)
 

Detailed Description

: G(ir)AF (Graph Alignment Format) Fast Emitter: a new mapper that will be extremely fast once we actually write it

Macro Definition Documentation

◆ OPT_CLUSTER_STDEV

#define OPT_CLUSTER_STDEV   1007

◆ OPT_FRAGMENT_MEAN

#define OPT_FRAGMENT_MEAN   1005

◆ OPT_FRAGMENT_STDEV

#define OPT_FRAGMENT_STDEV   1006

◆ OPT_OUTPUT_BASENAME

#define OPT_OUTPUT_BASENAME   1001

◆ OPT_REPORT_NAME

#define OPT_REPORT_NAME   1002

◆ OPT_RESCUE_STDEV

#define OPT_RESCUE_STDEV   1008

◆ OPT_TRACK_CORRECTNESS

#define OPT_TRACK_CORRECTNESS   1004

◆ OPT_TRACK_PROVENANCE

#define OPT_TRACK_PROVENANCE   1003

Function Documentation

◆ help_giraffe()

void help_giraffe ( char **  argv)

◆ main_giraffe()

int main_giraffe ( int  argc,
char **  argv 
)