#include <transcriptome.hpp>

Public Member Functions
	Transcriptome (unique_ptr< MutablePathDeletableHandleGraph > &&graph_in)

int32_t	add_intron_splice_junctions (vector< istream * > intron_streams, unique_ptr< gbwt::GBWT > &haplotype_index, const bool update_haplotypes)

int32_t	add_reference_transcripts (vector< istream * > transcript_streams, unique_ptr< gbwt::GBWT > &haplotype_index, const bool use_haplotype_paths, const bool update_haplotypes)

int32_t	add_haplotype_transcripts (vector< istream * > transcript_streams, const gbwt::GBWT &haplotype_index, const bool proj_emded_paths)

const vector< CompletedTranscriptPath > &	transcript_paths () const
	Returns transcript paths. More...

vector< CompletedTranscriptPath >	reference_transcript_paths () const
	Returns the reference transcript paths. More...

vector< CompletedTranscriptPath >	haplotype_transcript_paths () const
	Returns the haplotype transcript paths. More...

const MutablePathDeletableHandleGraph &	graph () const
	Returns the graph. More...

void	remove_non_transcribed_nodes ()
	Removes non-transcribed (not in transcript paths) nodes. More...

void	chop_nodes (const uint32_t max_node_length)

bool	sort_compact_nodes ()

void	embed_transcript_paths (const bool add_reference_transcripts, const bool add_haplotype_transcripts)

void	add_transcripts_to_gbwt (gbwt::GBWTBuilder *gbwt_builder, const bool add_bidirectional, const bool exclude_reference_transcripts) const

void	write_transcript_sequences (ostream *fasta_ostream, const bool exclude_reference_transcripts) const

void	write_transcript_info (ostream *tsv_ostream, const gbwt::GBWT &haplotype_index, const bool exclude_reference_transcripts) const

void	write_graph (ostream *graph_ostream) const
	Writes the graph to a file. More...

Public Attributes
bool	show_progress = false
	Write progress to stderr. More...

int32_t	num_threads = 1
	Number of threads used for transcript path construction. More...

string	feature_type = "exon"
	Feature type to parse in the gtf/gff file. Parse all types if empty. More...

string	transcript_tag = "transcript_id"
	Attribute tag used to parse the transcript id/name in the gtf/gff file. More...

string	path_collapse_type = "haplotype"

bool	error_on_missing_path = true
	Treat a missing path in the transcripts/introns as a data error. More...

Private Member Functions
void	parse_introns (vector< Transcript > introns, istream intron_stream, const bdsg::PositionOverlay &graph_path_pos_overlay) const
	Parse BED file of introns. More...

int32_t	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
	Parse gtf/gff3 file of transcripts. Returns the number of non-header lines in the parsed file. More...

string	get_base_gbwt_path_name (const gbwt::GBWT &haplotype_index, const size_t path_id, const unordered_set< string > &gbwt_reference_samples) const
	Returns gbwt path name without phaseblock and subrange. More...

string	parse_attribute_value (const string &attribute, const string &name) const
	Parse gtf/gff3 attribute value. More...

float	mean_node_length () const
	Returns the mean node length of the graph. More...

void	add_exon (Transcript *transcript, const pair< int32_t, int32_t > &exon_pos) const
	Adds the exon coordinates to a transcript. More...

void	add_exon (Transcript *transcript, const pair< int32_t, int32_t > &exon_pos, const bdsg::PositionOverlay &graph_path_pos_overlay) const

void	reorder_exons (Transcript *transcript) const

bool	has_overlapping_exons (const vector< Exon > &exons) const
	Checks whether any adjacent exons overlap. More...

list< EditedTranscriptPath >	construct_reference_transcript_paths_embedded (const vector< Transcript > &transcripts, const bdsg::PositionOverlay &graph_path_pos_overlay) const

void	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
	Threaded reference transcript path construction using embedded paths. More...

list< EditedTranscriptPath >	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
	Projects transcripts onto embedded paths in a graph and returns the resulting transcript paths. More...

list< EditedTranscriptPath >	construct_reference_transcript_paths_gbwt (const vector< Transcript > &transcripts, const gbwt::GBWT &haplotype_index) const

void	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
	Threaded reference transcript path construction using GBWT haplotype paths. More...

void	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)

void	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)
	Threaded haplotype transcript projecting. More...

list< EditedTranscriptPath >	project_transcript_gbwt (const Transcript &cur_transcript, const gbwt::GBWT &haplotype_index, const unordered_set< string > &reference_samples, const float mean_node_length) const
	Projects transcripts onto haplotypes in a GBWT index and returns the resulting transcript paths. More...

vector< pair< exon_nodes_t, thread_ids_t > >	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

template<class T >
void	remove_redundant_transcript_paths (list< T > new_transcript_paths, spp::sparse_hash_map< handle_t, vector< T > > *transcript_paths_index) const
	Remove redundant transcript paths and update index. More...

list< CompletedTranscriptPath >	construct_completed_transcript_paths (const list< EditedTranscriptPath > &edited_transcript_paths) const

void	add_edited_transcript_paths (const list< EditedTranscriptPath > &edited_transcript_paths)

bool	has_novel_exon_boundaries (const list< EditedTranscriptPath > &edited_transcript_paths, const bool include_transcript_ends) const

void	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)

void	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
	Update threads in gbwt index using graph translations. More...

void	update_transcript_paths (const spp::sparse_hash_map< handle_t, vector< pair< int32_t, handle_t > > > &update_index)
	Update/split node handles in transcriptome transcript paths according to index. More...

void	add_splice_junction_edges (const list< EditedTranscriptPath > &edited_transcript_paths)
	Adds transcript path splice-junction edges to the graph. More...

void	add_splice_junction_edges (const list< CompletedTranscriptPath > &completed_transcript_paths)

void	add_splice_junction_edges (const vector< CompletedTranscriptPath > &completed_transcript_paths)

void	collect_transcribed_nodes (spp::sparse_hash_set< nid_t > *transcribed_nodes) const
	Collects all unique nodes in transcriptome transcript paths. More...

void	sort_transcript_paths_update_copy_id ()

Private Attributes
vector< CompletedTranscriptPath >	_transcript_paths
	Transcript paths representing the transcriptome. More...

mutex	mutex_transcript_paths

unique_ptr< MutablePathDeletableHandleGraph >	_graph
	Spliced pangenome graph. More...

mutex	mutex_graph

Detailed Description

Class that defines a transcriptome represented by a set of transcript paths.

Constructor & Destructor Documentation

◆ Transcriptome()

vg::Transcriptome::Transcriptome ( unique_ptr< MutablePathDeletableHandleGraph > && graph_in )

Member Function Documentation

◆ add_edited_transcript_paths()

void vg::Transcriptome::add_edited_transcript_paths ( const list< EditedTranscriptPath > & edited_transcript_paths )

private

Adds edited transcript paths to transcriptome Checks that the paths contain no edits compared to the graph.

◆ add_exon() [1/2]

void vg::Transcriptome::add_exon	(	Transcript *	transcript,
		const pair< int32_t, int32_t > &	exon_pos
	)		const

private

Adds the exon coordinates to a transcript.

◆ add_exon() [2/2]

void vg::Transcriptome::add_exon	(	Transcript *	transcript,
		const pair< int32_t, int32_t > &	exon_pos,
		const bdsg::PositionOverlay &	graph_path_pos_overlay
	)		const

private

Adds the exon coordinates to a transcript and finds the position of each end of a exon on the contig path in the graph.

◆ add_haplotype_transcripts()

int32_t vg::Transcriptome::add_haplotype_transcripts	(	vector< istream * >	transcript_streams,
		const gbwt::GBWT &	haplotype_index,
		const bool	proj_emded_paths
	)

Adds haplotype-specific transcript paths by projecting transcripts in gtf/gff3 files onto either non-reference embedded paths and/or haplotypes in a GBWT index. Returns the number of haplotype transcript paths projected.

◆ add_intron_splice_junctions()

int32_t vg::Transcriptome::add_intron_splice_junctions	(	vector< istream * >	intron_streams,
		unique_ptr< gbwt::GBWT > &	haplotype_index,
		const bool	update_haplotypes
	)

Adds splice-junstions from intron BED files to the graph. Optionally update haplotype GBWT index with new splice-junctions. Returns the number of introns parsed.

◆ add_reference_transcripts()

int32_t vg::Transcriptome::add_reference_transcripts	(	vector< istream * >	transcript_streams,
		unique_ptr< gbwt::GBWT > &	haplotype_index,
		const bool	use_haplotype_paths,
		const bool	update_haplotypes
	)

Adds splice-junstions from transcript gtf/gff3 files to the graph and creates reference transcript paths. Optionally update haplotype GBWT index with new splice-junctions. Returns the number of transcripts parsed.

◆ add_splice_junction_edges() [1/3]

void vg::Transcriptome::add_splice_junction_edges ( const list< CompletedTranscriptPath > & completed_transcript_paths )

private

◆ add_splice_junction_edges() [2/3]

void vg::Transcriptome::add_splice_junction_edges ( const list< EditedTranscriptPath > & edited_transcript_paths )

private

Adds transcript path splice-junction edges to the graph.

◆ add_splice_junction_edges() [3/3]

void vg::Transcriptome::add_splice_junction_edges ( const vector< CompletedTranscriptPath > & completed_transcript_paths )

private

◆ add_transcripts_to_gbwt()

void vg::Transcriptome::add_transcripts_to_gbwt	(	gbwt::GBWTBuilder *	gbwt_builder,
		const bool	add_bidirectional,
		const bool	exclude_reference_transcripts
	)		const

Adds transcriptome transcript paths as threads to a GBWT index. Returns the number of added threads.

◆ augment_graph()

void 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
	)

private

Augments the graph with transcript path exon boundaries and splice-junctions. Updates threads in gbwt index to match the augmented graph. Optinally adds transcript paths to the transcriptome.

◆ chop_nodes()

void vg::Transcriptome::chop_nodes ( const uint32_t max_node_length )

Chop nodes so that they are not longer than the supplied maximum node length. Returns number of chopped nodes.

◆ collect_transcribed_nodes()

void vg::Transcriptome::collect_transcribed_nodes ( spp::sparse_hash_set< nid_t > * transcribed_nodes ) const

private

Collects all unique nodes in transcriptome transcript paths.

◆ construct_completed_transcript_paths()

list< CompletedTranscriptPath > vg::Transcriptome::construct_completed_transcript_paths ( const list< EditedTranscriptPath > & edited_transcript_paths ) const

private

Constructs completed transcripts paths from edited transcript paths. Checks that the paths contain no edits compared to the graph.

◆ construct_reference_transcript_paths_embedded()

list< EditedTranscriptPath > vg::Transcriptome::construct_reference_transcript_paths_embedded	(	const vector< Transcript > &	transcripts,
		const bdsg::PositionOverlay &	graph_path_pos_overlay
	)		const

private

Constructs edited reference transcript paths from a set of transcripts using embedded graph paths.

◆ construct_reference_transcript_paths_embedded_callback()

void vg::Transcriptome::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

private

Threaded reference transcript path construction using embedded paths.

◆ construct_reference_transcript_paths_gbwt()

list< EditedTranscriptPath > vg::Transcriptome::construct_reference_transcript_paths_gbwt	(	const vector< Transcript > &	transcripts,
		const gbwt::GBWT &	haplotype_index
	)		const

private

Constructs edited reference transcript paths from a set of transcripts using haplotype paths in a GBWT index.

◆ construct_reference_transcript_paths_gbwt_callback()

void vg::Transcriptome::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

private

Threaded reference transcript path construction using GBWT haplotype paths.

◆ embed_transcript_paths()

void vg::Transcriptome::embed_transcript_paths	(	const bool	add_reference_transcripts,
		const bool	add_haplotype_transcripts
	)

Embeds transcriptome transcript paths in the graph.
Returns the number of paths embedded.

◆ get_base_gbwt_path_name()

string 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

private

Returns gbwt path name without phaseblock and subrange.

◆ get_exon_haplotypes()

vector< pair< exon_nodes_t, thread_ids_t > > vg::Transcriptome::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

private

Extracts all unique haplotype paths between two nodes from a GBWT index and returns the resulting paths and the corresponding haplotype ids for each path.

◆ graph()

const MutablePathDeletableHandleGraph & vg::Transcriptome::graph ( ) const

Returns the graph.

◆ haplotype_transcript_paths()

vector< CompletedTranscriptPath > vg::Transcriptome::haplotype_transcript_paths ( ) const

Returns the haplotype transcript paths.

◆ has_novel_exon_boundaries()

bool vg::Transcriptome::has_novel_exon_boundaries	(	const list< EditedTranscriptPath > &	edited_transcript_paths,
		const bool	include_transcript_ends
	)		const

private

Checks whether transcript path only consist of whole nodes (complete).

◆ has_overlapping_exons()

bool vg::Transcriptome::has_overlapping_exons ( const vector< Exon > & exons ) const

private

Checks whether any adjacent exons overlap.

◆ mean_node_length()

float vg::Transcriptome::mean_node_length ( ) const

private

Returns the mean node length of the graph.

◆ parse_attribute_value()

string vg::Transcriptome::parse_attribute_value	(	const string &	attribute,
		const string &	name
	)		const

private

Parse gtf/gff3 attribute value.

◆ parse_introns()

void vg::Transcriptome::parse_introns	(	vector< Transcript > *	introns,
		istream *	intron_stream,
		const bdsg::PositionOverlay &	graph_path_pos_overlay
	)		const

private

Parse BED file of introns.

◆ parse_transcripts()

int32_t vg::Transcriptome::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

private

Parse gtf/gff3 file of transcripts. Returns the number of non-header lines in the parsed file.

◆ project_haplotype_transcripts()

void 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
	)

private

Constructs haplotype transcript paths by projecting transcripts onto embedded paths in a graph and/or haplotypes in a GBWT index. Adds haplotype transcript to transcriptome.

◆ project_haplotype_transcripts_callback()

void vg::Transcriptome::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
	)

private

Threaded haplotype transcript projecting.

◆ project_transcript_embedded()

list< EditedTranscriptPath > vg::Transcriptome::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

private

Projects transcripts onto embedded paths in a graph and returns the resulting transcript paths.

◆ project_transcript_gbwt()

list< EditedTranscriptPath > vg::Transcriptome::project_transcript_gbwt	(	const Transcript &	cur_transcript,
		const gbwt::GBWT &	haplotype_index,
		const unordered_set< string > &	reference_samples,
		const float	mean_node_length
	)		const

private

Projects transcripts onto haplotypes in a GBWT index and returns the resulting transcript paths.

◆ reference_transcript_paths()

vector< CompletedTranscriptPath > vg::Transcriptome::reference_transcript_paths ( ) const

Returns the reference transcript paths.

◆ remove_non_transcribed_nodes()

void vg::Transcriptome::remove_non_transcribed_nodes ( )

Removes non-transcribed (not in transcript paths) nodes.

◆ remove_redundant_transcript_paths()

template<class T >

void vg::Transcriptome::remove_redundant_transcript_paths	(	list< T > *	new_transcript_paths,
		spp::sparse_hash_map< handle_t, vector< T * > > *	transcript_paths_index
	)		const

private

Remove redundant transcript paths and update index.

◆ reorder_exons()

void vg::Transcriptome::reorder_exons ( Transcript * transcript ) const

private

Reverses exon order if the transcript is on the reverse strand and the exons are ordered in reverse.

◆ sort_compact_nodes()

bool vg::Transcriptome::sort_compact_nodes ( )

Topological sorts graph and compacts node ids. Only works for graphs in the PackedGraph format. Return false if not sorted.

◆ sort_transcript_paths_update_copy_id()

void vg::Transcriptome::sort_transcript_paths_update_copy_id ( )

private

Sort transcriptome transcript paths by name and is reference, and update their copy ids.

◆ transcript_paths()

const vector< CompletedTranscriptPath > & vg::Transcriptome::transcript_paths ( ) const

Returns transcript paths.

◆ update_haplotype_index()

void 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

private

Update threads in gbwt index using graph translations.

◆ update_transcript_paths()

void vg::Transcriptome::update_transcript_paths ( const spp::sparse_hash_map< handle_t, vector< pair< int32_t, handle_t > > > & update_index )

private

Update/split node handles in transcriptome transcript paths according to index.

◆ write_graph()

void vg::Transcriptome::write_graph ( ostream * graph_ostream ) const

Writes the graph to a file.

◆ write_transcript_info()

void vg::Transcriptome::write_transcript_info	(	ostream *	tsv_ostream,
		const gbwt::GBWT &	haplotype_index,
		const bool	exclude_reference_transcripts
	)		const

Writes info on transcriptome transcript paths to tsv file. Returns the number of written transcripts.

◆ write_transcript_sequences()

void vg::Transcriptome::write_transcript_sequences	(	ostream *	fasta_ostream,
		const bool	exclude_reference_transcripts
	)		const

Writes transcriptome transcript path sequences to a fasta file.
Returns the number of written sequences.

Member Data Documentation

◆ _graph

unique_ptr<MutablePathDeletableHandleGraph> vg::Transcriptome::_graph

private

Spliced pangenome graph.

◆ _transcript_paths

vector<CompletedTranscriptPath> vg::Transcriptome::_transcript_paths

private

Transcript paths representing the transcriptome.

◆ error_on_missing_path

bool vg::Transcriptome::error_on_missing_path = true

Treat a missing path in the transcripts/introns as a data error.

◆ feature_type

string vg::Transcriptome::feature_type = "exon"

Feature type to parse in the gtf/gff file. Parse all types if empty.

◆ mutex_graph

mutex vg::Transcriptome::mutex_graph

private

◆ mutex_transcript_paths

mutex vg::Transcriptome::mutex_transcript_paths

private

◆ num_threads

int32_t vg::Transcriptome::num_threads = 1

Number of threads used for transcript path construction.

◆ path_collapse_type

string vg::Transcriptome::path_collapse_type = "haplotype"

Speicifies which paths should be compared when collapsing identical paths. Can be no, haplotype or all.

◆ show_progress

bool vg::Transcriptome::show_progress = false

Write progress to stderr.

◆ transcript_tag

string vg::Transcriptome::transcript_tag = "transcript_id"

Attribute tag used to parse the transcript id/name in the gtf/gff file.

The documentation for this class was generated from the following files:

src/transcriptome.hpp
src/transcriptome.cpp

Public Member Functions

Public Attributes

Private Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ Transcriptome()

Member Function Documentation

◆ add_edited_transcript_paths()

◆ add_exon() [1/2]

◆ add_exon() [2/2]

◆ add_haplotype_transcripts()

◆ add_intron_splice_junctions()

◆ add_reference_transcripts()

◆ add_splice_junction_edges() [1/3]

◆ add_splice_junction_edges() [2/3]

◆ add_splice_junction_edges() [3/3]

◆ add_transcripts_to_gbwt()

◆ augment_graph()

◆ chop_nodes()

◆ collect_transcribed_nodes()

◆ construct_completed_transcript_paths()

◆ construct_reference_transcript_paths_embedded()

◆ construct_reference_transcript_paths_embedded_callback()

◆ construct_reference_transcript_paths_gbwt()

◆ construct_reference_transcript_paths_gbwt_callback()

◆ embed_transcript_paths()

◆ get_base_gbwt_path_name()

◆ get_exon_haplotypes()

◆ graph()

◆ haplotype_transcript_paths()

◆ has_novel_exon_boundaries()

◆ has_overlapping_exons()

◆ mean_node_length()

◆ parse_attribute_value()

◆ parse_introns()

◆ parse_transcripts()

◆ project_haplotype_transcripts()

◆ project_haplotype_transcripts_callback()

◆ project_transcript_embedded()

◆ project_transcript_gbwt()

◆ reference_transcript_paths()

◆ remove_non_transcribed_nodes()

◆ remove_redundant_transcript_paths()

◆ reorder_exons()

◆ sort_compact_nodes()

◆ sort_transcript_paths_update_copy_id()

◆ transcript_paths()

◆ update_haplotype_index()

◆ update_transcript_paths()

◆ write_graph()

◆ write_transcript_info()

◆ write_transcript_sequences()

Member Data Documentation

◆ _graph

◆ _transcript_paths

◆ error_on_missing_path

◆ feature_type

◆ mutex_graph

◆ mutex_transcript_paths

◆ num_threads

◆ path_collapse_type

◆ show_progress

◆ transcript_tag