vg::io Namespace Reference

Classes
class	ConvertedHashGraph
class	JSONStreamHelper

Functions
void	json2graph (const std::string &json, MutablePathMutableHandleGraph *dest)
	Load a JSON string into a graph. The string must be a single JSON object.
void	load_proto_to_graph (vg::MutablePathMutableHandleGraph *destination, const vg::io::message_sender_function_t &for_each_message)
void	load_proto_to_graph (vg::MutablePathMutableHandleGraph *destination, const function< void(const function< void(Graph &)> &)> &chunk_sender)
bool	register_libvg_io ()
void	register_loader_gfaz ()
void	register_loader_params_json ()
void	register_loader_saver_distance_index ()
void	register_loader_saver_gbwt ()
void	register_loader_saver_gbwtgraph ()
void	register_loader_saver_gbz ()
void	register_loader_saver_gbzgraph ()
void	register_loader_saver_gcsa ()
void	register_loader_saver_gfa ()
void	register_loader_saver_hash_graph ()
void	register_loader_saver_lcp ()
void	register_loader_saver_minimizer ()
void	register_loader_saver_packed_graph ()
void	register_loader_saver_r_index ()
void	register_loader_saver_snarl_manager ()
void	register_loader_saver_vg ()
void	register_loader_saver_xg ()
void	register_loader_saver_zip_codes ()
void	save_handle_graph (HandleGraph *graph, ostream &os)
void	save_handle_graph (HandleGraph *graph, const string &dest_path)
bool	valid_output_format (const string &fmt_string)
template<class T>
unique_ptr< T >	new_output_graph (const string &fmt_string)

Function Documentation

json2graph()

void vg::io::json2graph ( const std::string & json, MutablePathMutableHandleGraph * dest )

inline

Load a JSON string into a graph. The string must be a single JSON object.

load_proto_to_graph() [1/2]

void vg::io::load_proto_to_graph	(	vg::MutablePathMutableHandleGraph *	destination,
		const function< void(const function< void(Graph &)> &)> &	chunk_sender )

Call the given function with a callback which it can call with a series of Protobuf Graph objects, possibly in multiple threads. The Protobuf Graph objects may have dangling edges.

Resolves all the dangling edges and writes all the graph data into the given MutablePathMutableHandleGraph, with the destination graph being protected from concurrent modification.

load_proto_to_graph() [2/2]

void vg::io::load_proto_to_graph	(	vg::MutablePathMutableHandleGraph *	destination,
		const vg::io::message_sender_function_t &	for_each_message )

Read all string messages supplied by the given message sender as Protobuf Graph objects, and create the specified graph in the destination graph.

Paths need to be cached until the end for ranks to be respected.

new_output_graph()

template<class T>

unique_ptr< T > vg::io::new_output_graph

(

const string &

fmt_string

)

register_libvg_io()

bool vg::io::register_libvg_io

(

)

Register libvg types with libvgio. Must be called by library users before doing IO. Does not magically statically call itself. TODO: work out a way it can. Returns true on success.

register_loader_gfaz()

void vg::io::register_loader_gfaz

(

)

register_loader_params_json()

void vg::io::register_loader_params_json

(

)

register_loader_saver_distance_index()

void vg::io::register_loader_saver_distance_index

(

)

register_loader_saver_gbwt()

void vg::io::register_loader_saver_gbwt

(

)

register_loader_saver_gbwtgraph()

void vg::io::register_loader_saver_gbwtgraph

(

)

register_loader_saver_gbz()

void vg::io::register_loader_saver_gbz

(

)

register_loader_saver_gbzgraph()

void vg::io::register_loader_saver_gbzgraph

(

)

register_loader_saver_gcsa()

void vg::io::register_loader_saver_gcsa

(

)

register_loader_saver_gfa()

void vg::io::register_loader_saver_gfa

(

)

register_loader_saver_hash_graph()

void vg::io::register_loader_saver_hash_graph

(

)

register_loader_saver_lcp()

void vg::io::register_loader_saver_lcp

(

)

register_loader_saver_minimizer()

void vg::io::register_loader_saver_minimizer

(

)

register_loader_saver_packed_graph()

void vg::io::register_loader_saver_packed_graph

(

)

register_loader_saver_r_index()

void vg::io::register_loader_saver_r_index

(

)

register_loader_saver_snarl_manager()

void vg::io::register_loader_saver_snarl_manager

(

)

register_loader_saver_vg()

void vg::io::register_loader_saver_vg

(

)

register_loader_saver_xg()

void vg::io::register_loader_saver_xg

(

)

register_loader_saver_zip_codes()

void vg::io::register_loader_saver_zip_codes

(

)

save_handle_graph() [1/2]

void vg::io::save_handle_graph ( HandleGraph * graph, const string & dest_path )

inline

save_handle_graph() [2/2]

void vg::io::save_handle_graph ( HandleGraph * graph, ostream & os )

inline

Save a handle graph. Todo: should this be somewhere else (ie in vgio with new types registered?)

valid_output_format()

bool vg::io::valid_output_format ( const string & fmt_string )

inline