#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...

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

std::string	sample_haplotypes (const Logger &logger, const std::vector< std::pair< std::string, std::string >> &indexes, const std::unordered_set< std::string > &reference_samples, const std::string &basename, const std::string &sample_name, const std::string &haplotype_file, const std::string &kff_file, bool progress)

void	help_giraffe (char **argv, const BaseOptionGroup &parser, const std::map< std::string, Preset > &presets, bool full_help)

int	main_giraffe (int argc, char **argv)

Detailed Description

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

Function Documentation

◆ help_giraffe()

void help_giraffe	(	char **	argv,
		const BaseOptionGroup &	parser,
		const std::map< std::string, Preset > &	presets,
		bool	full_help
	)

◆ main_giraffe()

int main_giraffe	(	int	argc,
		char **	argv
	)

◆ sample_haplotypes()

std::string sample_haplotypes	(	const Logger &	logger,
		const std::vector< std::pair< std::string, std::string >> &	indexes,
		const std::unordered_set< std::string > &	reference_samples,
		const std::string &	basename,
		const std::string &	sample_name,
		const std::string &	haplotype_file,
		const std::string &	kff_file,
		bool	progress
	)

◆ strip_suffixes()

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