vg
tools for working with variation graphs
Namespaces | Functions
gbwt_helper.cpp File Reference
#include "gbwt_helper.hpp"
#include "utility.hpp"
#include <sstream>

Namespaces

 vg
 

Functions

std::vector< std::string > vg::parseGenotypes (const std::string &vcf_line, size_t num_samples)
 
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...