#include <omp.h>
#include <unistd.h>
#include <getopt.h>
#include <regex>
#include <list>
#include <fstream>
#include "subcommand.hpp"
#include "../path.hpp"
#include "../graph_caller.hpp"
#include "../integrated_snarl_finder.hpp"
#include "../xg.hpp"
#include "../gbzgraph.hpp"
#include "../gbwtgraph_helper.hpp"
#include <vg/io/stream.hpp>
#include <vg/io/vpkg.hpp>
#include <bdsg/overlays/overlay_helper.hpp>

Typedefs
typedef bdsg::PairOverlayHelper< PathPositionHandleGraph, bdsg::PackedReferencePathOverlay, PathHandleGraph, VectorizableHandleGraph, bdsg::PathPositionVectorizableOverlay, PathPositionHandleGraph >	ReferencePathVectorizableOverlayHelper
	Helper to ensure that a PathHandleGraph has the VectorizableHandleGraph and PathPositionHandleGraph interfaces. More...

Functions
void	help_call (char **argv)

int	main_call (int argc, char **argv)

Detailed Description

Defines the "vg call" subcommand, which calls variation from an augmented graph

Typedef Documentation

◆ ReferencePathVectorizableOverlayHelper

typedef bdsg::PairOverlayHelper<PathPositionHandleGraph, bdsg::PackedReferencePathOverlay, PathHandleGraph, VectorizableHandleGraph, bdsg::PathPositionVectorizableOverlay, PathPositionHandleGraph> ReferencePathVectorizableOverlayHelper

Helper to ensure that a PathHandleGraph has the VectorizableHandleGraph and PathPositionHandleGraph interfaces.

Function Documentation

◆ help_call()

void help_call ( char ** argv )

◆ main_call()

int main_call	(	int	argc,
		char **	argv
	)