vg
tools for working with variation graphs
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#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... | |
Utility classes and functions for working with GBWT.