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vg
tools for working with variation graphs
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This is the complete list of members for vg::Transcriptome, including all inherited members.
| _graph | vg::Transcriptome | private |
| _transcript_paths | vg::Transcriptome | private |
| add_edited_transcript_paths(const list< EditedTranscriptPath > &edited_transcript_paths) | vg::Transcriptome | private |
| add_exon(Transcript *transcript, const pair< int32_t, int32_t > &exon_pos) const | vg::Transcriptome | private |
| add_exon(Transcript *transcript, const pair< int32_t, int32_t > &exon_pos, const bdsg::PositionOverlay &graph_path_pos_overlay) const | vg::Transcriptome | private |
| add_haplotype_transcripts(vector< istream * > transcript_streams, const gbwt::GBWT &haplotype_index, const bool proj_emded_paths) | vg::Transcriptome | |
| add_intron_splice_junctions(vector< istream * > intron_streams, unique_ptr< gbwt::GBWT > &haplotype_index, const bool update_haplotypes) | vg::Transcriptome | |
| add_reference_transcripts(vector< istream * > transcript_streams, unique_ptr< gbwt::GBWT > &haplotype_index, const bool use_haplotype_paths, const bool update_haplotypes) | vg::Transcriptome | |
| add_splice_junction_edges(const list< EditedTranscriptPath > &edited_transcript_paths) | vg::Transcriptome | private |
| add_splice_junction_edges(const list< CompletedTranscriptPath > &completed_transcript_paths) | vg::Transcriptome | private |
| add_splice_junction_edges(const vector< CompletedTranscriptPath > &completed_transcript_paths) | vg::Transcriptome | private |
| add_transcripts_to_gbwt(gbwt::GBWTBuilder *gbwt_builder, const bool add_bidirectional, const bool exclude_reference_transcripts) const | vg::Transcriptome | |
| augment_graph(const list< EditedTranscriptPath > &edited_transcript_paths, const bool is_introns, unique_ptr< gbwt::GBWT > &haplotype_index, const bool update_haplotypes, const bool add_reference_transcript_paths) | vg::Transcriptome | private |
| chop_nodes(const uint32_t max_node_length) | vg::Transcriptome | |
| collect_transcribed_nodes(spp::sparse_hash_set< nid_t > *transcribed_nodes) const | vg::Transcriptome | private |
| construct_completed_transcript_paths(const list< EditedTranscriptPath > &edited_transcript_paths) const | vg::Transcriptome | private |
| construct_reference_transcript_paths_embedded(const vector< Transcript > &transcripts, const bdsg::PositionOverlay &graph_path_pos_overlay) const | vg::Transcriptome | private |
| construct_reference_transcript_paths_embedded_callback(list< EditedTranscriptPath > *edited_transcript_paths, spp::sparse_hash_map< handle_t, vector< EditedTranscriptPath * > > *edited_transcript_paths_index, mutex *edited_transcript_paths_mutex, const int32_t thread_idx, const vector< Transcript > &transcripts, const bdsg::PositionOverlay &graph_path_pos_overlay) const | vg::Transcriptome | private |
| construct_reference_transcript_paths_gbwt(const vector< Transcript > &transcripts, const gbwt::GBWT &haplotype_index) const | vg::Transcriptome | private |
| construct_reference_transcript_paths_gbwt_callback(list< EditedTranscriptPath > *edited_transcript_paths, spp::sparse_hash_map< handle_t, vector< EditedTranscriptPath * > > *edited_transcript_paths_index, uint32_t *excluded_transcripts, mutex *edited_transcript_paths_mutex, const int32_t thread_idx, const vector< pair< uint32_t, uint32_t > > &chrom_transcript_sets, const vector< Transcript > &transcripts, const gbwt::GBWT &haplotype_index, const spp::sparse_hash_map< string, map< uint32_t, uint32_t > > &haplotype_name_index) const | vg::Transcriptome | private |
| embed_transcript_paths(const bool add_reference_transcripts, const bool add_haplotype_transcripts) | vg::Transcriptome | |
| error_on_missing_path | vg::Transcriptome | |
| feature_type | vg::Transcriptome | |
| get_base_gbwt_path_name(const gbwt::GBWT &haplotype_index, const size_t path_id, const unordered_set< string > &gbwt_reference_samples) const | vg::Transcriptome | private |
| get_exon_haplotypes(const vg::id_t start_node, const vg::id_t end_node, const gbwt::GBWT &haplotype_index, const unordered_set< string > &reference_samples, const int32_t expected_length) const | vg::Transcriptome | private |
| graph() const | vg::Transcriptome | |
| haplotype_transcript_paths() const | vg::Transcriptome | |
| has_novel_exon_boundaries(const list< EditedTranscriptPath > &edited_transcript_paths, const bool include_transcript_ends) const | vg::Transcriptome | private |
| has_overlapping_exons(const vector< Exon > &exons) const | vg::Transcriptome | private |
| mean_node_length() const | vg::Transcriptome | private |
| mutex_graph | vg::Transcriptome | private |
| mutex_transcript_paths | vg::Transcriptome | private |
| num_threads | vg::Transcriptome | |
| parse_attribute_value(const string &attribute, const string &name) const | vg::Transcriptome | private |
| parse_introns(vector< Transcript > *introns, istream *intron_stream, const bdsg::PositionOverlay &graph_path_pos_overlay) const | vg::Transcriptome | private |
| parse_transcripts(vector< Transcript > *transcripts, uint32_t *number_of_excluded_transcripts, istream *transcript_stream, const bdsg::PositionOverlay &graph_path_pos_overlay, const gbwt::GBWT &haplotype_index, const bool use_haplotype_paths) const | vg::Transcriptome | private |
| path_collapse_type | vg::Transcriptome | |
| project_haplotype_transcripts(const vector< Transcript > &transcripts, const gbwt::GBWT &haplotype_index, const bdsg::PositionOverlay &graph_path_pos_overlay, const bool proj_emded_paths, const float mean_node_length) | vg::Transcriptome | private |
| project_haplotype_transcripts_callback(list< CompletedTranscriptPath > *completed_transcript_paths, spp::sparse_hash_map< handle_t, vector< CompletedTranscriptPath * > > *completed_transcript_paths_index, mutex *completed_transcript_paths_mutex, const int32_t thread_idx, const vector< Transcript > &transcripts, const gbwt::GBWT &haplotype_index, const bdsg::PositionOverlay &graph_path_pos_overlay, const bool proj_emded_paths, const float mean_node_length) | vg::Transcriptome | private |
| project_transcript_embedded(const Transcript &cur_transcript, const bdsg::PositionOverlay &graph_path_pos_overlay, const bool use_reference_paths, const bool use_haplotype_paths) const | vg::Transcriptome | private |
| project_transcript_gbwt(const Transcript &cur_transcript, const gbwt::GBWT &haplotype_index, const unordered_set< string > &reference_samples, const float mean_node_length) const | vg::Transcriptome | private |
| reference_transcript_paths() const | vg::Transcriptome | |
| remove_non_transcribed_nodes() | vg::Transcriptome | |
| remove_redundant_transcript_paths(list< T > *new_transcript_paths, spp::sparse_hash_map< handle_t, vector< T * > > *transcript_paths_index) const | vg::Transcriptome | private |
| reorder_exons(Transcript *transcript) const | vg::Transcriptome | private |
| show_progress | vg::Transcriptome | |
| sort_compact_nodes() | vg::Transcriptome | |
| sort_transcript_paths_update_copy_id() | vg::Transcriptome | private |
| transcript_paths() const | vg::Transcriptome | |
| transcript_tag | vg::Transcriptome | |
| Transcriptome(unique_ptr< MutablePathDeletableHandleGraph > &&graph_in) | vg::Transcriptome | |
| update_haplotype_index(unique_ptr< gbwt::GBWT > &haplotype_index, const spp::sparse_hash_map< handle_t, vector< pair< int32_t, handle_t > > > &update_index) const | vg::Transcriptome | private |
| update_transcript_paths(const spp::sparse_hash_map< handle_t, vector< pair< int32_t, handle_t > > > &update_index) | vg::Transcriptome | private |
| write_graph(ostream *graph_ostream) const | vg::Transcriptome | |
| write_transcript_info(ostream *tsv_ostream, const gbwt::GBWT &haplotype_index, const bool exclude_reference_transcripts) const | vg::Transcriptome | |
| write_transcript_sequences(ostream *fasta_ostream, const bool exclude_reference_transcripts) const | vg::Transcriptome |
1.8.17