vg
tools for working with variation graphs
vg::Transcriptome Member List

This is the complete list of members for vg::Transcriptome, including all inherited members.

_splice_graphvg::Transcriptomeprivate
_splice_graph_node_updatedvg::Transcriptomeprivate
_transcript_pathsvg::Transcriptomeprivate
add_exon(Transcript *transcript, const pair< int32_t, int32_t > &exon_pos, const bdsg::PositionOverlay &graph_path_pos_overlay) constvg::Transcriptomeprivate
add_intron_splice_junctions(istream &intron_stream, unique_ptr< gbwt::GBWT > &haplotype_index)vg::Transcriptome
add_splice_junction_edges(const list< EditedTranscriptPath > &edited_transcript_paths)vg::Transcriptomeprivate
add_splice_junction_edges(const vector< CompletedTranscriptPath > &completed_transcript_paths)vg::Transcriptomeprivate
add_transcript_splice_junctions(istream &transcript_stream, unique_ptr< gbwt::GBWT > &haplotype_index)vg::Transcriptome
add_transcripts(istream &transcript_stream, const gbwt::GBWT &haplotype_index)vg::Transcriptome
add_transcripts_to_gbwt(gbwt::GBWTBuilder *gbwt_builder, const bool output_reference_transcripts, const bool add_bidirectional) constvg::Transcriptome
append_transcript_paths(list< CompletedTranscriptPath > *completed_transcript_path, list< CompletedTranscriptPath > *new_completed_transcript_paths, const bool add_unqiue_paths_only) constvg::Transcriptomeprivate
augment_splice_graph(list< EditedTranscriptPath > *edited_transcript_paths, unique_ptr< gbwt::GBWT > &haplotype_index, const bool break_at_transcript_ends)vg::Transcriptomeprivate
collapse_transcript_pathsvg::Transcriptome
compact_ordered()vg::Transcriptome
construct_completed_transcript_paths(const list< EditedTranscriptPath > &edited_transcript_paths) constvg::Transcriptomeprivate
construct_edited_transcript_paths(const vector< Transcript > &transcripts, const bdsg::PositionOverlay &graph_path_pos_overlay) constvg::Transcriptomeprivate
construct_edited_transcript_paths_callback(list< EditedTranscriptPath > *edited_transcript_paths, mutex *edited_transcript_paths_mutex, const bdsg::PositionOverlay &graph_path_pos_overlay, const int32_t thread_idx, const vector< Transcript > &transcripts) constvg::Transcriptomeprivate
embed_transcript_paths(const bool add_reference_paths, const bool add_non_reference_paths)vg::Transcriptome
feature_typevg::Transcriptome
get_exon_haplotypes(const vg::id_t start_node, const vg::id_t end_node, const gbwt::GBWT &haplotype_index, const int32_t expected_length) constvg::Transcriptomeprivate
has_novel_exon_boundaries(const list< EditedTranscriptPath > &edited_transcript_paths, const bool include_transcript_ends) constvg::Transcriptomeprivate
mean_node_length() constvg::Transcriptomeprivate
mutex_splice_graphvg::Transcriptomeprivate
mutex_transcript_pathsvg::Transcriptomeprivate
num_threadsvg::Transcriptome
parse_introns(istream &intron_stream, const bdsg::PositionOverlay &graph_path_pos_overlay) constvg::Transcriptomeprivate
parse_transcripts(istream &transcript_stream, const bdsg::PositionOverlay &graph_path_pos_overlay) constvg::Transcriptomeprivate
path_to_handles(const Path &path) constvg::Transcriptomeprivate
project_and_add_transcripts(const vector< Transcript > &transcripts, const gbwt::GBWT &haplotype_index, const bdsg::PositionOverlay &graph_path_pos_overlay, const float mean_node_length)vg::Transcriptomeprivate
project_and_add_transcripts_callback(const int32_t thread_idx, const vector< Transcript > &transcripts, const gbwt::GBWT &haplotype_index, const bdsg::PositionOverlay &graph_path_pos_overlay, const float mean_node_length)vg::Transcriptomeprivate
project_transcript_embedded(const Transcript &cur_transcript, const bdsg::PositionOverlay &graph_path_pos_overlay, const bool reference_only) constvg::Transcriptomeprivate
project_transcript_gbwt(const Transcript &cur_transcript, const gbwt::GBWT &haplotype_index, const float mean_node_length) constvg::Transcriptomeprivate
remove_non_transcribed(const bool new_reference_paths)vg::Transcriptome
reorder_exons(Transcript *transcript) constvg::Transcriptomeprivate
size() constvg::Transcriptome
splice_graph() constvg::Transcriptome
splice_graph_node_updated() constvg::Transcriptome
transcript_paths() constvg::Transcriptome
transcript_tagvg::Transcriptome
Transcriptome(const string &, const bool)vg::Transcriptome
update_haplotype_index(unique_ptr< gbwt::GBWT > &haplotype_index, const vector< Translation > &translation) constvg::Transcriptomeprivate
use_all_pathsvg::Transcriptome
use_reference_pathsvg::Transcriptome
write_info(ostream *tsv_ostream, const gbwt::GBWT &haplotype_index, const bool output_reference_transcripts) constvg::Transcriptome
write_sequences(ostream *fasta_ostream, const bool output_reference_transcripts) constvg::Transcriptome
write_splice_graph(ostream *graph_ostream) constvg::Transcriptome