map_main.cpp File Reference

#include "subcommand.hpp"
#include "../vg.hpp"
#include "../xg.hpp"
#include "../utility.hpp"
#include "../mapper.hpp"
#include "../hts_alignment_emitter.hpp"
#include <vg/io/stream.hpp>
#include <vg/io/vpkg.hpp>
#include <bdsg/overlays/overlay_helper.hpp>
#include <unistd.h>
#include <getopt.h>
#include <chrono>

Macros
#define	OPT_SCORE_MATRIX   1000
#define	OPT_RECOMBINATION_PENALTY   1001
#define	OPT_EXCLUDE_UNALIGNED   1002
#define	OPT_REF_PATHS   1003
#define	OPT_REF_NAME   1004
#define	OPT_COMMENTS_AS_TAGS   1005

Functions
void	help_map (char **argv)
int	main_map (int argc, char **argv)

Macro Definition Documentation

OPT_COMMENTS_AS_TAGS

#define OPT_COMMENTS_AS_TAGS   1005

OPT_EXCLUDE_UNALIGNED

#define OPT_EXCLUDE_UNALIGNED   1002

OPT_RECOMBINATION_PENALTY

#define OPT_RECOMBINATION_PENALTY   1001

OPT_REF_NAME

#define OPT_REF_NAME   1004

OPT_REF_PATHS

#define OPT_REF_PATHS   1003

OPT_SCORE_MATRIX

#define OPT_SCORE_MATRIX   1000

Function Documentation

help_map()

void help_map

(

char **

argv

)

main_map()

int main_map	(	int	argc,
		char **	argv
	)