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 |
_transcript_paths | vg::Transcriptome | private |
add_exon(Transcript *transcript, const pair< int32_t, int32_t > &exon_pos, const PathIndex &chrom_path_index) const | vg::Transcriptome | private |
add_novel_transcript_junctions(const list< TranscriptPath > &cur_transcript_paths) | vg::Transcriptome | private |
add_paths_to_transcriptome(list< TranscriptPath > *cur_transcript_paths) | vg::Transcriptome | private |
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) const | vg::Transcriptome | private |
collapse_transcript_paths | vg::Transcriptome | |
compact_ordered() | vg::Transcriptome | |
construct_gbwt(gbwt::GBWTBuilder *gbwt_builder, const bool output_reference_transcripts, const bool add_bidirectional) const | vg::Transcriptome | |
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 |
num_threads | vg::Transcriptome | |
project_transcript_embedded(const Transcript &cur_transcript) 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 |
project_transcripts(const vector< Transcript > &transcripts, const gbwt::GBWT &haplotype_index, const float mean_node_length) const | vg::Transcriptome | private |
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) 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 | |
transcript_paths() const | vg::Transcriptome | |
transcript_tag | vg::Transcriptome | |
Transcriptome(const string &, const bool) | vg::Transcriptome | |
use_embedded_paths | vg::Transcriptome | |
use_reference_paths | vg::Transcriptome | |
write_alignments(ostream *gam_ostream, const bool output_reference_transcripts) const | vg::Transcriptome | |
write_info(ostream *tsv_ostream, const bool output_reference_transcripts) const | vg::Transcriptome | |
write_sequences(ostream *fasta_ostream, const bool output_reference_transcripts) | vg::Transcriptome | |
write_splice_graph(ostream *graph_ostream) | vg::Transcriptome |