giraffe_main.cpp File Reference

#include <omp.h>
#include <unistd.h>
#include <getopt.h>
#include <iostream>
#include <cassert>
#include <cstring>
#include <ctime>
#include <map>
#include <vector>
#include <unordered_set>
#include <chrono>
#include <mutex>
#include "subcommand.hpp"
#include "options.hpp"
#include "../snarl_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 "../minimizer_mapper.hpp"
#include "../index_registry.hpp"
#include "../watchdog.hpp"
#include "../crash.hpp"
#include <bdsg/overlays/overlay_helper.hpp>
#include "../gbwtgraph_helper.hpp"
#include "../recombinator.hpp"
#include <gbwtgraph/gbz.h>
#include <gbwtgraph/minimizer.h>
#include <sys/ioctl.h>

Classes
struct	GiraffeMainOptions
	Options struct for options for the Giraffe driver (i.e. this file) More...
struct	ScoringOptions
	Options struct for scoring-related parameters. Defaults are in aligner.hpp. More...

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_REF_PATHS   1010
#define	OPT_SHOW_WORK   1011
#define	OPT_NAMED_COORDINATES   1012

Functions
std::string	strip_suffixes (std::string filename, const std::vector< std::string > &suffixes)
string	sample_haplotypes (const vector< pair< string, string >> &indexes, string &basename, string &sample_name, string &haplotype_file, string &kff_file, bool progress)
void	help_giraffe (char **argv, const BaseOptionGroup &parser, bool full_help)
int	main_giraffe (int argc, char **argv)

Detailed Description

: G(ir)AF (Graph Alignment Format) Fast Emitter: a fast short-read-to-haplotypes mapper

Macro Definition Documentation

OPT_FRAGMENT_MEAN

#define OPT_FRAGMENT_MEAN   1005

OPT_FRAGMENT_STDEV

#define OPT_FRAGMENT_STDEV   1006

OPT_NAMED_COORDINATES

#define OPT_NAMED_COORDINATES   1012

OPT_OUTPUT_BASENAME

#define OPT_OUTPUT_BASENAME   1001

OPT_REF_PATHS

#define OPT_REF_PATHS   1010

OPT_REPORT_NAME

#define OPT_REPORT_NAME   1002

OPT_SHOW_WORK

#define OPT_SHOW_WORK   1011

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,
		const BaseOptionGroup &	parser,
		bool	full_help
	)

main_giraffe()

int main_giraffe	(	int	argc,
		char **	argv
	)

sample_haplotypes()

string sample_haplotypes	(	const vector< pair< string, string >> &	indexes,
		string &	basename,
		string &	sample_name,
		string &	haplotype_file,
		string &	kff_file,
		bool	progress
	)

strip_suffixes()

std::string strip_suffixes	(	std::string	filename,
		const std::vector< std::string > &	suffixes
	)