gbwt_helper.hpp File Reference

#include <vector>
#include "position.hpp"
#include <gbwt/dynamic_gbwt.h>
#include <handlegraph/mutable_path_handle_graph.hpp>

Namespaces
	vg

Functions
std::vector< std::string >	vg::parseGenotypes (const std::string &vcf_line, size_t num_samples)
handle_t	vg::gbwt_to_handle (const HandleGraph &graph, gbwt::node_type node)
	Convert gbwt::node_type to handle_t. More...
pos_t	vg::gbwt_to_pos (gbwt::node_type node, size_t offset)
	Convert gbwt::node_type and an offset as size_t to pos_t. More...
gbwt::node_type	vg::handle_to_gbwt (const HandleGraph &graph, handle_t handle)
	Convert handle_t to gbwt::node_type. More...
gbwt::node_type	vg::pos_to_gbwt (pos_t pos)
	Extract gbwt::node_type from pos_t. More...
gbwt::node_type	vg::mapping_to_gbwt (const Mapping &mapping)
	Convert Mapping to gbwt::node_type. More...
gbwt::vector_type	vg::path_to_gbwt (const Path &path)
	Convert Path to a GBWT path. More...
gbwt::vector_type	vg::path_predecessors (const HandleGraph &graph, const Path &path)
std::string	vg::insert_gbwt_path (MutablePathHandleGraph &graph, const gbwt::GBWT &gbwt_index, gbwt::size_type id)
Path	vg::extract_gbwt_path (const HandleGraph &graph, const gbwt::GBWT &gbwt_index, gbwt::size_type id)
std::string	vg::thread_name (const gbwt::GBWT &gbwt_index, gbwt::size_type id)
gbwt::GBWT	vg::get_gbwt (const std::vector< gbwt::vector_type > &paths)
	Transform the paths into a GBWT index. Primarily for testing. More...

Detailed Description

Utility classes and functions for working with GBWT.