#include "subcommand.hpp"
#include "../gbwt_helper.hpp"
#include "../snarl_distance_index.hpp"
#include "../snarls.hpp"
#include <sdsl/int_vector.hpp>
#include <vg/io/vpkg.hpp>
#include <fstream>
#include <iostream>
#include <tuple>
#include <vector>
#include <getopt.h>

Classes
struct	ChainsConfig

Functions
void	write_binary (const std::vector< sdsl::int_vector<> > &chains, std::ostream &out)
void	write_gfa_paths (const std::vector< sdsl::int_vector<> > &chains, std::ostream &out)
gbwt::vector_type	extract_chain (const SnarlDistanceIndex &distance_index, const HandleGraph &graph, net_handle_t chain, size_t chain_id)
gbwt::vector_type	extract_chain (const SnarlManager &snarls, const HandleGraph &graph, const Chain &chain, size_t chain_id)
sdsl::int_vector	normalize_chain (gbwt::vector_type &chain)
int	main_chains (int argc, char **argv)
void	help_chains (char **argv)
net_handle_t	follow_chain (const SnarlDistanceIndex &distance_index, const HandleGraph &graph, size_t chain_id, net_handle_t curr)
void	try_append (gbwt::vector_type &chain, gbwt::node_type start, gbwt::node_type end)

Detailed Description

Defines the "vg chains" subcommand, which extracts the handles in top-level chains from a distance index or a snarl file.

NOTE: If a component (~chromosome) does not start with a shared node, the top-level chain is not unique. For example, if the component starts with edges (u, w) and (v, w), the chain may start with either u or v.

TODO: Option to get chain (~contig, chromosome) names from a graph.

TODO: Full GFA format with segments and jumps.

Function Documentation

◆ extract_chain() [1/2]

gbwt::vector_type extract_chain	(	const SnarlDistanceIndex &	distance_index,
		const HandleGraph &	graph,
		net_handle_t	chain,
		size_t	chain_id )

◆ extract_chain() [2/2]

gbwt::vector_type extract_chain	(	const SnarlManager &	snarls,
		const HandleGraph &	graph,
		const Chain &	chain,
		size_t	chain_id )

◆ follow_chain()

net_handle_t follow_chain	(	const SnarlDistanceIndex &	distance_index,
		const HandleGraph &	graph,
		size_t	chain_id,
		net_handle_t	curr )

◆ help_chains()

void help_chains ( char ** argv )

◆ main_chains()

int main_chains	(	int	argc,
		char **	argv )

◆ normalize_chain()

sdsl::int_vector normalize_chain ( gbwt::vector_type & chain )

◆ try_append()

void try_append	(	gbwt::vector_type &	chain,
		gbwt::node_type	start,
		gbwt::node_type	end )

◆ write_binary()

void write_binary	(	const std::vector< sdsl::int_vector<> > &	chains,
		std::ostream &	out )

◆ write_gfa_paths()

void write_gfa_paths	(	const std::vector< sdsl::int_vector<> > &	chains,
		std::ostream &	out )

Classes

Functions