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std::vector< std::string > | vg::parseGenotypes (const std::string &vcf_line, size_t num_samples) |
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handle_t | vg::gbwt_to_handle (const HandleGraph &graph, gbwt::node_type node) |
| Convert gbwt::node_type to handle_t. More...
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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...
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gbwt::node_type | vg::handle_to_gbwt (const HandleGraph &graph, handle_t handle) |
| Convert handle_t to gbwt::node_type. More...
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gbwt::node_type | vg::pos_to_gbwt (pos_t pos) |
| Extract gbwt::node_type from pos_t. More...
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gbwt::node_type | vg::mapping_to_gbwt (const Mapping &mapping) |
| Convert Mapping to gbwt::node_type. More...
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gbwt::vector_type | vg::path_to_gbwt (const Path &path) |
| Convert Path to a GBWT path. More...
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gbwt::vector_type | vg::extract_as_gbwt_path (const PathHandleGraph &graph, const std::string &path_name) |
| Extract a path as a GBWT path. If the path does not exist, it is treated as empty. More...
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gbwt::vector_type | vg::path_predecessors (const PathHandleGraph &graph, const std::string &path_name) |
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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...
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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, const std::string &header="GBWT") |
| Finish GBWT construction and optionally print the metadata. More...
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void | vg::load_gbwt (gbwt::GBWT &index, const std::string &filename, bool show_progress=false) |
| Load a compressed GBWT from the file. More...
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void | vg::load_gbwt (gbwt::DynamicGBWT &index, const std::string &filename, bool show_progress=false) |
| Load a dynamic GBWT from the file. More...
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void | vg::load_r_index (gbwt::FastLocate &index, const std::string &filename, bool show_progress=false) |
| Load an r-index from the file. More...
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void | vg::save_gbwt (const gbwt::GBWT &index, const std::string &filename, bool show_progress=false) |
| Save a compressed GBWT to the file. More...
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void | vg::save_gbwt (const gbwt::DynamicGBWT &index, const std::string &filename, bool show_progress=false) |
| Save a dynamic GBWT to the file. More...
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void | vg::save_r_index (const gbwt::FastLocate &index, const std::string &filename, bool show_progress=false) |
| Save an r-index to the file. More...
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gbwt::GBWT | vg::rebuild_gbwt (const gbwt::GBWT &gbwt_index, const std::vector< RebuildJob > &jobs, const std::unordered_map< nid_t, size_t > &node_to_job, const RebuildParameters ¶meters) |
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gbwt::GBWT | vg::rebuild_gbwt (const gbwt::GBWT &gbwt_index, const std::vector< RebuildJob::mapping_type > &mappings) |
| As the general rebuild_gbwt , but always using a single job with default parameters. More...
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std::vector< gbwt::size_type > | vg::threads_for_sample (const gbwt::GBWT &gbwt_index, const std::string &sample_name) |
| Return the list of thread ids / gbwt path ids for the given sample. More...
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std::vector< gbwt::size_type > | vg::threads_for_contig (const gbwt::GBWT &gbwt_index, const std::string &contig_name) |
| Return the list of thread ids / gbwt path ids for the given contig. More...
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std::string | vg::insert_gbwt_path (MutablePathHandleGraph &graph, const gbwt::GBWT &gbwt_index, gbwt::size_type id, std::string path_name) |
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Path | vg::extract_gbwt_path (const HandleGraph &graph, const gbwt::GBWT &gbwt_index, gbwt::size_type id) |
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std::string | vg::compose_short_path_name (const gbwt::GBWT &gbwt_index, gbwt::size_type id) |
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void | vg::copy_reference_samples (const gbwt::GBWT &source, gbwt::GBWT &destination) |
| Copies the reference sample tag from the source GBWT index to the destination GBWT index. More...
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void | vg::copy_reference_samples (const PathHandleGraph &source, gbwt::GBWT &destination) |
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gbwt::GBWT | vg::get_gbwt (const std::vector< gbwt::vector_type > &paths) |
| Transform the paths into a GBWT index. Primarily for testing. More...
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unordered_map< string, vector< nid_t > > | vg::load_translation_map (ifstream &input_stream) |
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unordered_map< nid_t, pair< string, size_t > > | vg::load_translation_back_map (HandleGraph &graph, ifstream &input_stream) |
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Utility classes and functions for working with GBWT.