vg
tools for working with variation graphs
Namespaces | Functions
gbwt_helper.hpp File Reference
#include <vector>
#include "position.hpp"
#include "xg.hpp"
#include <gbwt/dynamic_gbwt.h>

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::node_type vg::xg_path_to_gbwt (const xg::XGPath &path, size_t i)
 Convert a node on XGPath 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::thread_name (const gbwt::GBWT &gbwt_index, size_t i)
 Get a string representation of a thread name stored in GBWT metadata. More...
 
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.