#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 "../flow_caller.hpp"
#include "../legacy_caller.hpp"
#include "../nested_flow_caller.hpp"
#include "../vcf_genotyper.hpp"
#include "../vcf_output_caller.hpp"
#include "../integrated_snarl_finder.hpp"
#include <xg.hpp>
#include "../gbzgraph.hpp"
#include "../gbwtgraph_helper.hpp"
#include "../gref.hpp"
#include <vg/io/stream.hpp>
#include <vg/io/vpkg.hpp>
#include <bdsg/overlays/overlay_helper.hpp>

Functions
void	help_call (char **argv)
int	main_call (int argc, char **argv)

Variables
const string	DEFAULT_SAMPLE_NAME = "SAMPLE"

Detailed Description

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

Function Documentation

◆ help_call()

void help_call ( char ** argv )

◆ main_call()

int main_call	(	int	argc,
		char **	argv )

Variable Documentation

◆ DEFAULT_SAMPLE_NAME

const string DEFAULT_SAMPLE_NAME = "SAMPLE"