gbwtgraph_helper.cpp File Reference

#include "gbwtgraph_helper.hpp"
#include "gbwt_helper.hpp"
#include "gbzgraph.hpp"
#include <gbwtgraph/index.h>
#include <vg/io/alignment_io.hpp>

Namespaces
	vg

Typedefs
using	vg::key_type = gbwtgraph::DefaultMinimizerIndex::key_type
using	vg::code_type = gbwtgraph::KmerEncoding::code_type
using	vg::payload_t = ZipCode::payload_type

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 (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_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_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)
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...
GraphCompatibilityFlags	vg::operator| (GraphCompatibilityFlags a, GraphCompatibilityFlags b)
GraphCompatibilityFlags &	vg::operator|= (GraphCompatibilityFlags &a, GraphCompatibilityFlags b)
void	vg::require_compatible_graphs_impl (const gbwtgraph::GraphName &first_name, const std::string &first_decription, const gbwtgraph::GraphName &second_name, const std::string &second_description, GraphCompatibilityFlags flags)
	Implementation of require_compatible_graphs(). More...
void	vg::require_compatible_reference (const std::string &gaf_filename, const HandleGraph *handle_graph, const gbwtgraph::GBZ *gbz, bool strict)
size_t	vg::trailing_zeros (size_t value)
size_t	vg::estimate_hash_table_size (const gbwtgraph::GBZ &gbz, bool progress)
std::vector< key_type >	vg::find_frequent_kmers (const gbwtgraph::GBZ &gbz, const MinimizerIndexParameters &params)
void	vg::cache_payloads (const gbwtgraph::GBZ &gbz, const SnarlDistanceIndex &distance_index, hash_map< nid_t, payload_t > &node_id_to_payload, ZipCodeCollection *oversized_zipcodes, bool progress)
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_payloads)
bool	vg::has_payload (const gbwtgraph::DefaultMinimizerIndex &index, MinimizerIndexParameters::PayloadType payload)
bool	vg::has_payload (const gbwtgraph::DefaultMinimizerIndex &index, const std::vector< MinimizerIndexParameters::PayloadType > &payloads)
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...
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...