vg
tools for working with variation graphs
Namespaces | Functions
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::extract_as_gbwt_path (const PathHandleGraph &graph, const std::string &path_name)
 Extract a path as a GBWT path. More...
 
gbwt::vector_type vg::path_predecessors (const PathHandleGraph &graph, const std::string &path_name)
 
gbwt::size_type vg::gbwt_node_width (const HandleGraph &graph)
 Determine the node width in bits for the GBWT nodes based on the given graph. More...
 
void vg::finish_gbwt_constuction (gbwt::GBWTBuilder &builder, const std::vector< std::string > &sample_names, const std::vector< std::string > &contig_names, size_t haplotype_count, bool print_metadata)
 Finish GBWT construction and optionally print the metadata. More...
 
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.