vg::BackTranslatingAlignmentEmitter Class Reference

#include <back_translating_alignment_emitter.hpp>

Inheritance diagram for vg::BackTranslatingAlignmentEmitter:

Public Member Functions
	BackTranslatingAlignmentEmitter (const NamedNodeBackTranslation *translation, unique_ptr< AlignmentEmitter > &&backing)
virtual void	emit_singles (vector< Alignment > &&aln_batch)
	Emit a batch of Alignments. More...
virtual void	emit_mapped_singles (vector< vector< Alignment >> &&alns_batch)
	Emit batch of Alignments with secondaries. All secondaries must have is_secondary set already. More...
virtual void	emit_pairs (vector< Alignment > &&aln1_batch, vector< Alignment > &&aln2_batch, vector< int64_t > &&tlen_limit_batch)
virtual void	emit_mapped_pairs (vector< vector< Alignment >> &&alns1_batch, vector< vector< Alignment >> &&alns2_batch, vector< int64_t > &&tlen_limit_batch)
Public Member Functions inherited from vg::io::AlignmentEmitter
virtual void	emit_extra_message (const std::string &tag, std::string &&data)
	Emit some extra type-tagged data, if the backing format supports it. More...
virtual void	emit_single (Alignment &&aln)
	Emit a single Alignment. More...
virtual void	emit_mapped_single (vector< Alignment > &&alns)
	Emit a single Alignment with secondaries. All secondaries must have is_secondary set already. More...
virtual void	emit_pair (Alignment &&aln1, Alignment &&aln2, int64_t tlen_limit=0)
virtual void	emit_mapped_pair (vector< Alignment > &&alns1, vector< Alignment > &&alns2, int64_t tlen_limit=0)
virtual	~AlignmentEmitter ()=default
	Allow destruction through base class pointer. More...

Protected Member Functions
void	back_translate_alignments_in_place (vector< Alignment > &alns) const
	Back-translate alignments in place. More...

Protected Attributes
const NamedNodeBackTranslation *	translation
	Translation to use to translate node IDs to pieces of named segments. More...
unique_ptr< AlignmentEmitter >	backing
	AlignmentEmitter to emit to once done. More...

Detailed Description

An AlignmentEmitter implementation that translates alignments into named-segment space coordinates before emitting them via a backing AlignmentEmitter, which it owns.

Constructor & Destructor Documentation

BackTranslatingAlignmentEmitter()

vg::BackTranslatingAlignmentEmitter::BackTranslatingAlignmentEmitter	(	const NamedNodeBackTranslation *	translation,
		unique_ptr< AlignmentEmitter > &&	backing
	)

Make an alignment emitter that translates alignments using the given translation and emits them to the given backing AlignmentEmitter. Takes ownership of the AlignmentEmitter.

Member Function Documentation

back_translate_alignments_in_place()

void vg::BackTranslatingAlignmentEmitter::back_translate_alignments_in_place ( vector< Alignment > &  alns ) const

protected

Back-translate alignments in place.

emit_mapped_pairs()

void vg::BackTranslatingAlignmentEmitter::emit_mapped_pairs ( vector< vector< Alignment >> &&  alns1_batch, vector< vector< Alignment >> &&  alns2_batch, vector< int64_t > &&  tlen_limit_batch  )

virtual

Emit the mappings of a batch of pairs of Alignments. All secondaries must have is_secondary set already. The tlen_limit_batch, if specified, is the maximum pairing distance for each pair to flag properly paired, if the output format cares about such things. TODO: Move to a properly paired annotation that runs with the Alignment.

Both ends of each pair must have the same number of mappings.

Implements vg::io::AlignmentEmitter.

emit_mapped_singles()

void vg::BackTranslatingAlignmentEmitter::emit_mapped_singles ( vector< vector< Alignment >> &&  alns_batch )

virtual

Emit batch of Alignments with secondaries. All secondaries must have is_secondary set already.

Implements vg::io::AlignmentEmitter.

emit_pairs()

void vg::BackTranslatingAlignmentEmitter::emit_pairs ( vector< Alignment > &&  aln1_batch, vector< Alignment > &&  aln2_batch, vector< int64_t > &&  tlen_limit_batch  )

virtual

Emit a batch of pairs of Alignments. The tlen_limit_batch, if specified, is the maximum pairing distance for ewch pair to flag properly paired, if the output format cares about such things. TODO: Move to a properly paired annotation that runs with the Alignment.

Implements vg::io::AlignmentEmitter.

emit_singles()

void vg::BackTranslatingAlignmentEmitter::emit_singles ( vector< Alignment > &&  aln_batch )

virtual

Emit a batch of Alignments.

Implements vg::io::AlignmentEmitter.

Member Data Documentation

backing

unique_ptr<AlignmentEmitter> vg::BackTranslatingAlignmentEmitter::backing

protected

AlignmentEmitter to emit to once done.

translation

const NamedNodeBackTranslation* vg::BackTranslatingAlignmentEmitter::translation

protected

Translation to use to translate node IDs to pieces of named segments.

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

• src/back_translating_alignment_emitter.hpp
• src/back_translating_alignment_emitter.cpp