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
#define	OPT_REF_PATHS   1009
#define	OPT_SHOW_WORK   1010

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_REF_PATHS

#define OPT_REF_PATHS   1009

OPT_REPORT_NAME

#define OPT_REPORT_NAME   1002

OPT_RESCUE_STDEV

#define OPT_RESCUE_STDEV   1008

OPT_SHOW_WORK

#define OPT_SHOW_WORK   1010

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
	)