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.
_splice_graph | vg::Transcriptome | private |
_splice_graph_node_updated | vg::Transcriptome | private |
_transcript_paths | 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_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::Transcriptome | private |
add_splice_junction_edges(const vector< CompletedTranscriptPath > &completed_transcript_paths) | vg::Transcriptome | private |
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) const | vg::Transcriptome | |
append_transcript_paths(list< CompletedTranscriptPath > *completed_transcript_path, list< CompletedTranscriptPath > *new_completed_transcript_paths, const bool add_unqiue_paths_only) const | vg::Transcriptome | private |
augment_splice_graph(list< EditedTranscriptPath > *edited_transcript_paths, unique_ptr< gbwt::GBWT > &haplotype_index, const bool break_at_transcript_ends) | vg::Transcriptome | private |
collapse_transcript_paths | vg::Transcriptome | |
compact_ordered() | vg::Transcriptome | |
construct_completed_transcript_paths(const list< EditedTranscriptPath > &edited_transcript_paths) const | vg::Transcriptome | private |
construct_edited_transcript_paths(const vector< Transcript > &transcripts, const bdsg::PositionOverlay &graph_path_pos_overlay) const | vg::Transcriptome | private |
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) const | vg::Transcriptome | private |
embed_transcript_paths(const bool add_reference_paths, const bool add_non_reference_paths) | vg::Transcriptome | |
feature_type | vg::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) const | vg::Transcriptome | private |
has_novel_exon_boundaries(const list< EditedTranscriptPath > &edited_transcript_paths, const bool include_transcript_ends) const | vg::Transcriptome | private |
mean_node_length() const | vg::Transcriptome | private |
mutex_splice_graph | vg::Transcriptome | private |
mutex_transcript_paths | vg::Transcriptome | private |
num_threads | vg::Transcriptome | |
parse_introns(istream &intron_stream, const bdsg::PositionOverlay &graph_path_pos_overlay) const | vg::Transcriptome | private |
parse_transcripts(istream &transcript_stream, const bdsg::PositionOverlay &graph_path_pos_overlay) const | vg::Transcriptome | private |
path_to_handles(const Path &path) const | vg::Transcriptome | private |
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::Transcriptome | private |
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::Transcriptome | private |
project_transcript_embedded(const Transcript &cur_transcript, const bdsg::PositionOverlay &graph_path_pos_overlay, const bool reference_only) const | vg::Transcriptome | private |
project_transcript_gbwt(const Transcript &cur_transcript, const gbwt::GBWT &haplotype_index, const float mean_node_length) const | vg::Transcriptome | private |
remove_non_transcribed(const bool new_reference_paths) | vg::Transcriptome | |
reorder_exons(Transcript *transcript) const | vg::Transcriptome | private |
size() const | vg::Transcriptome | |
splice_graph() const | vg::Transcriptome | |
splice_graph_node_updated() const | vg::Transcriptome | |
transcript_paths() const | vg::Transcriptome | |
transcript_tag | vg::Transcriptome | |
Transcriptome(const string &, const bool) | vg::Transcriptome | |
update_haplotype_index(unique_ptr< gbwt::GBWT > &haplotype_index, const vector< Translation > &translation) const | vg::Transcriptome | private |
use_all_paths | vg::Transcriptome | |
use_reference_paths | vg::Transcriptome | |
write_info(ostream *tsv_ostream, const gbwt::GBWT &haplotype_index, const bool output_reference_transcripts) const | vg::Transcriptome | |
write_sequences(ostream *fasta_ostream, const bool output_reference_transcripts) const | vg::Transcriptome | |
write_splice_graph(ostream *graph_ostream) const | vg::Transcriptome |