augment_main.cpp File Reference

#include <omp.h>
#include <unistd.h>
#include <getopt.h>
#include <list>
#include <fstream>
#include "subcommand.hpp"
#include "../option.hpp"
#include "../xg.hpp"
#include "../vg.hpp"
#include "../augment.hpp"
#include "../packer.hpp"
#include "../io/save_handle_graph.hpp"
#include <vg/io/stream.hpp>
#include <vg/io/vpkg.hpp>
#include <handlegraph/mutable_path_mutable_handle_graph.hpp>
#include "bdsg/packed_graph.hpp"
#include "bdsg/hash_graph.hpp"
#include <bdsg/overlays/overlay_helper.hpp>

Functions
void	help_augment (char **argv, ConfigurableParser &parser)
int	main_augment (int argc, char **argv)

Detailed Description

Defines the "vg augment" subcommand, which augments a graph using a GAM as a first step before computing sites and calling variants.

It presently only supports augmentation via pileup (as originally used by vg call).

vg mod -i is an alternative, but as currently implemented it is too expensive. Ideally, a more heuristic/fast implementation would get added as an option here.

The new vg count structure, provided edge/edit/strand/quality is supported, may be an interesting replacement for the current protobuf pileups which ought to go, one way or the other.

Function Documentation

help_augment()

void help_augment	(	char **	argv,
		ConfigurableParser &	parser
	)

main_augment()

int main_augment	(	int	argc,
		char **	argv
	)