gbwtgraph_helper.hpp File Reference

#include <gbwtgraph/gfa.h>
#include <gbwtgraph/gbz.h>
#include <gbwtgraph/minimizer.h>
#include "position.hpp"
#include "snarl_distance_index.hpp"
#include "zip_code.hpp"
#include <vector>
#include <unordered_map>

Classes
struct	vg::MinimizerIndexParameters
	Minimizer index construction parameters. More...

Namespaces
	vg

Functions
gbwtgraph::GFAParsingParameters	vg::get_best_gbwtgraph_gfa_parsing_parameters ()
void	vg::load_gbwtgraph (gbwtgraph::GBWTGraph &graph, const std::string &filename, bool show_progress)
void	vg::load_gbz (gbwtgraph::GBZ &gbz, const std::string &filename, bool show_progress=false)
	Load GBZ from the file. More...
void	vg::load_gbz (gbwtgraph::GBZ &gbz, const std::string &gbwt_name, const std::string &graph_name, bool show_progress=false)
	Load GBZ from separate GBWT / GBWTGraph files. More...
void	vg::load_gbz (gbwt::GBWT &index, gbwtgraph::GBWTGraph &graph, const std::string &filename, bool show_progress=false)
	Load GBWT and GBWTGraph from the GBZ file. More...
void	vg::load_minimizer (gbwtgraph::DefaultMinimizerIndex &index, const std::string &filename, bool show_progress)
void	vg::save_gbwtgraph (const gbwtgraph::GBWTGraph &graph, const std::string &filename, bool show_progress=false)
	Save GBWTGraph to the file. More...
void	vg::save_gbz (const gbwtgraph::GBZ &gbz, const std::string &filename, bool show_progress=false)
	Save GBZ to the file. More...
void	vg::save_gbz (const gbwt::GBWT &index, gbwtgraph::GBWTGraph &graph, const std::string &filename, bool show_progress=false)
	Save GBWT and GBWTGraph to the GBZ file. More...
void	vg::save_gbz (const gbwtgraph::GBZ &gbz, const std::string &gbwt_name, const std::string &graph_name, bool show_progress=false)
	Save GBZ to separate GBWT / GBWTGraph files. More...
void	vg::save_minimizer (const gbwtgraph::DefaultMinimizerIndex &index, const std::string &filename, bool show_progress=false)
	Save a minimizer index to the file. More...
gbwtgraph::DefaultMinimizerIndex	vg::build_minimizer_index (const gbwtgraph::GBZ &gbz, const SnarlDistanceIndex *distance_index, ZipCodeCollection *oversized_zipcodes, const MinimizerIndexParameters &params)
void	vg::require_payload (const gbwtgraph::DefaultMinimizerIndex &index, MinimizerIndexParameters::PayloadType expected_payload)
void	vg::require_payload (const gbwtgraph::DefaultMinimizerIndex &index, const std::vector< MinimizerIndexParameters::PayloadType > &expected_payload)
unordered_map< string, vector< nid_t > >	vg::load_translation_map (const gbwtgraph::GBWTGraph &graph)
	Return a mapping of the original segment ids to a list of chopped node ids. More...
unordered_map< nid_t, pair< string, size_t > >	vg::load_translation_back_map (const gbwtgraph::GBWTGraph &graph)
	Return a backwards mapping of chopped node to original segment position (id,offset pair) More...
handle_t	vg::empty_gbwtgraph_handle ()
	Returns an empty GBWTGraph handle corresponding to the GBWT endmarker. More...
std::string	vg::to_string_gbwtgraph (handle_t handle)
	Returns a string representation of a GBWTGraph handle. More...
std::string	vg::to_string_gbwtgraph (gbwt::node_type node)
	Returns a string representation of a GBWTGraph node. More...

Detailed Description

Utility classes and functions for working with GBWTGraph.