vg::SurjectingAlignmentEmitter Class Reference

#include <surjecting_alignment_emitter.hpp>

Inheritance diagram for vg::SurjectingAlignmentEmitter:

Public Member Functions
	SurjectingAlignmentEmitter (const PathPositionHandleGraph *graph, unordered_set< path_handle_t > paths, unique_ptr< AlignmentEmitter > &&backing, bool prune_suspicious_anchors=false, bool add_graph_alignment_tag=false, bool report_supplementary=false)
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)
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...
Public Member Functions inherited from vg::io::AlignmentEmitter
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...

Public Attributes
bool	surject_subpath_global = true
	Force full length alignment in surjection resolution. More...

Protected Member Functions
void	surject_alignments_in_place (vector< Alignment > &alns) const
	Surject unpaired alignments in place. More...
void	surject_paired_alignments_in_place (vector< Alignment > &alns1, vector< Alignment > &alns2, vector< Alignment > &supplementary_alns) const
	Surject paired alignments in place and separate out supplementary alignments. More...

Protected Attributes
Surjector	surjector
	Surjector used to do the surjection. More...
unordered_set< path_handle_t >	paths
	Paths to surject into. More...
unique_ptr< AlignmentEmitter >	backing
	AlignmentEmitter to emit to once done. More...

Detailed Description

An AlignmentEmitter implementation that surjects alignments before emitting them via a backing AlignmentEmitter, which it owns.

Constructor & Destructor Documentation

SurjectingAlignmentEmitter()

vg::SurjectingAlignmentEmitter::SurjectingAlignmentEmitter	(	const PathPositionHandleGraph *	graph,
		unordered_set< path_handle_t >	paths,
		unique_ptr< AlignmentEmitter > &&	backing,
		bool	prune_suspicious_anchors = false,
		bool	add_graph_alignment_tag = false,
		bool	report_supplementary = false
	)

Surject alignments using the given graph, into the given paths, and send them to the given AlignmentEmitter. Takes ownership of the AlignmentEmitter. Copies the set of paths.

If prune_suspicious_anchors is set, prunes out repetitive-looking anchors when surjecting and lets those parts of reads be realigned.

Member Function Documentation

emit_extra_message()

void vg::SurjectingAlignmentEmitter::emit_extra_message ( const std::string &  tag, std::string &&  data  )

virtual

Emit some extra type-tagged data, if the backing format supports it.

Reimplemented from vg::io::AlignmentEmitter.

emit_mapped_pairs()

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

virtual

Emit a batch of Alignments.

Implements vg::io::AlignmentEmitter.

surject_alignments_in_place()

void vg::SurjectingAlignmentEmitter::surject_alignments_in_place ( vector< Alignment > &  alns ) const

protected

Surject unpaired alignments in place.

surject_paired_alignments_in_place()

void vg::SurjectingAlignmentEmitter::surject_paired_alignments_in_place ( vector< Alignment > &  alns1, vector< Alignment > &  alns2, vector< Alignment > &  supplementary_alns  ) const

protected

Surject paired alignments in place and separate out supplementary alignments.

Member Data Documentation

backing

unique_ptr<AlignmentEmitter> vg::SurjectingAlignmentEmitter::backing

protected

AlignmentEmitter to emit to once done.

paths

unordered_set<path_handle_t> vg::SurjectingAlignmentEmitter::paths

protected

Paths to surject into.

surject_subpath_global

bool vg::SurjectingAlignmentEmitter::surject_subpath_global = true

Force full length alignment in surjection resolution.

surjector

Surjector vg::SurjectingAlignmentEmitter::surjector

protected

Surjector used to do the surjection.

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

• src/surjecting_alignment_emitter.hpp
• src/surjecting_alignment_emitter.cpp