|
| 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. If the path does not exist, it is treated as empty. 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::load_gbwt (gbwt::GBWT &index, const std::string &filename, bool show_progress=false) |
| | Load a compressed GBWT from the file. More...
|
| |
| void | vg::load_gbwt (gbwt::DynamicGBWT &index, const std::string &filename, bool show_progress=false) |
| | Load a dynamic GBWT from the file. More...
|
| |
| void | vg::load_r_index (gbwt::FastLocate &index, const std::string &filename, bool show_progress=false) |
| | Load an r-index from the file. More...
|
| |
| void | vg::save_gbwt (const gbwt::GBWT &index, const std::string &filename, bool show_progress=false) |
| | Save a compressed GBWT to the file. More...
|
| |
| void | vg::save_gbwt (const gbwt::DynamicGBWT &index, const std::string &filename, bool show_progress=false) |
| | Save a dynamic GBWT to the file. More...
|
| |
| 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...
|
| |
| std::vector< std::vector< gbwt::size_type > > | vg::partition_gbwt_sequences (const gbwt::GBWT &gbwt_index, const std::unordered_map< nid_t, size_t > &node_to_job, size_t num_jobs) |
| |
| gbwt::GBWT | vg::rebuild_gbwt_job (const gbwt::GBWT &gbwt_index, const RebuildJob &job, size_t job_id, const std::vector< gbwt::size_type > &sequences, const RebuildParameters ¶meters) |
| |
| void | vg::copy_metadata (const gbwt::GBWT &source, gbwt::GBWT &target, const std::vector< std::vector< gbwt::size_type >> &jobs, const std::vector< size_t > &job_order) |
| |
| 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) |
| |
| 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...
|
| |
| 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...
|
| |
| 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...
|
| |
| std::string | vg::insert_gbwt_path (MutablePathHandleGraph &graph, const gbwt::GBWT &gbwt_index, gbwt::size_type id, std::string path_name) |
| |
| Path | vg::extract_gbwt_path (const HandleGraph &graph, const gbwt::GBWT &gbwt_index, gbwt::size_type id) |
| |
| std::string | vg::compose_short_path_name (const gbwt::GBWT &gbwt_index, gbwt::size_type id) |
| |
| 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...
|
| |
| void | vg::copy_reference_samples (const PathHandleGraph &source, gbwt::GBWT &destination) |
| |
| gbwt::GBWT | vg::get_gbwt (const std::vector< gbwt::vector_type > &paths) |
| | Transform the paths into a GBWT index. Primarily for testing. More...
|
| |
| unordered_map< string, vector< nid_t > > | vg::load_translation_map (ifstream &input_stream) |
| |
| unordered_map< nid_t, pair< string, size_t > > | vg::load_translation_back_map (HandleGraph &graph, ifstream &input_stream) |
| |
