paths_main.cpp File Reference

#include <omp.h>
#include <unistd.h>
#include <getopt.h>
#include <algorithm>
#include <iostream>
#include "subcommand.hpp"
#include "../vg.hpp"
#include "../xg.hpp"
#include "../gbwt_helper.hpp"
#include "../traversal_clusters.hpp"
#include "../io/save_handle_graph.hpp"
#include <bdsg/overlays/overlay_helper.hpp>
#include <vg/io/vpkg.hpp>
#include <vg/io/stream.hpp>
#include <vg/io/alignment_emitter.hpp>
#include <gbwtgraph/utils.h>

Functions
void	help_paths (char **argv)
void	chunk_to_emitter (const Path &path, vg::io::ProtobufEmitter< Graph > &graph_emitter)
int	main_paths (int argc, char **argv)

Variables
unordered_map< PathSense, string >	SENSE_TO_STRING

Detailed Description

Defines the "vg paths" subcommand, which reads paths in the graph.

Function Documentation

chunk_to_emitter()

void chunk_to_emitter	(	const Path &	path,
		vg::io::ProtobufEmitter< Graph > &	graph_emitter
	)

Chunk a path and emit it in Graph messages. Paht must have ranks set.

help_paths()

void help_paths

(

char **

argv

)

main_paths()

int main_paths	(	int	argc,
		char **	argv
	)

Variable Documentation

SENSE_TO_STRING

unordered_map<PathSense, string> SENSE_TO_STRING

Initial value:

{
    {PathSense::REFERENCE, "REFERENCE"},
    {PathSense::GENERIC, "GENERIC"},
    {PathSense::HAPLOTYPE, "HAPLOTYPE"}
}