#include <omp.h>
#include <unistd.h>
#include <getopt.h>
#include <list>
#include <fstream>
#include "subcommand.hpp"
#include "../utility.hpp"
#include "../handle.hpp"
#include "../path.hpp"
#include "../split_strand_graph.hpp"
#include "../dagified_graph.hpp"
#include "../ssw_aligner.hpp"
#include "../aligner.hpp"
#include <vg/io/stream.hpp>
#include <vg/io/vpkg.hpp>

Macros
#define	OPT_SCORE_MATRIX 1000

Functions
void	help_align (char **argv)

int	main_align (int argc, char **argv)

Detailed Description

Defines the "vg align" subcommand, which aligns a read against an entire graph.

Macro Definition Documentation

◆ OPT_SCORE_MATRIX

#define OPT_SCORE_MATRIX 1000

Function Documentation

◆ help_align()

void help_align ( char ** argv )

◆ main_align()

int main_align	(	int	argc,
		char **	argv
	)