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
_transcript_pathsvg::Transcriptomeprivate
add_exon(Transcript *transcript, const pair< int32_t, int32_t > &exon_pos, const PathIndex &chrom_path_index) constvg::Transcriptomeprivate
add_novel_transcript_junctions(const list< TranscriptPath > &cur_transcript_paths)vg::Transcriptomeprivate
add_paths_to_transcriptome(list< TranscriptPath > *cur_transcript_paths)vg::Transcriptomeprivate
add_transcripts(istream &transcript_stream, const gbwt::GBWT &haplotype_index)vg::Transcriptome
append_transcript_paths(list< TranscriptPath > *cur_transcript_paths, list< TranscriptPath > *new_transcript_paths, const bool add_unqiue_paths_only) constvg::Transcriptomeprivate
collapse_transcript_pathsvg::Transcriptome
compact_ordered()vg::Transcriptome
construct_gbwt(gbwt::GBWTBuilder *gbwt_builder, const bool output_reference_transcripts, const bool add_bidirectional) constvg::Transcriptome
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
num_threadsvg::Transcriptome
project_transcript_embedded(const Transcript &cur_transcript) constvg::Transcriptomeprivate
project_transcript_gbwt(const Transcript &cur_transcript, const gbwt::GBWT &haplotype_index, const float mean_node_length) constvg::Transcriptomeprivate
project_transcripts(const vector< Transcript > &transcripts, const gbwt::GBWT &haplotype_index, const float mean_node_length) constvg::Transcriptomeprivate
project_transcripts_callback(list< TranscriptPath > *proj_transcript_paths, mutex *transcript_paths_mutex, const int32_t thread_idx, const vector< Transcript > &transcripts, 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
transcript_paths() constvg::Transcriptome
transcript_tagvg::Transcriptome
Transcriptome(const string &, const bool)vg::Transcriptome
use_embedded_pathsvg::Transcriptome
use_reference_pathsvg::Transcriptome
write_alignments(ostream *gam_ostream, const bool output_reference_transcripts) constvg::Transcriptome
write_info(ostream *tsv_ostream, const bool output_reference_transcripts) constvg::Transcriptome
write_sequences(ostream *fasta_ostream, const bool output_reference_transcripts)vg::Transcriptome
write_splice_graph(ostream *graph_ostream)vg::Transcriptome