vg::io::VGAlignmentEmitter Class Reference

#include <alignment_emitter.hpp>

Inheritance diagram for vg::io::VGAlignmentEmitter:

Public Member Functions
	VGAlignmentEmitter (const string &filename, const string &format, size_t max_threads)
	~VGAlignmentEmitter ()
	Finish and drstroy a VGAlignmentEmitter. More...
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_singles (vector< Alignment > &&aln_batch)
	Emit a batch of Alignments. More...
virtual void	emit_mapped_singles (vector< vector< Alignment >> &&alns_batch)
virtual void	emit_pairs (vector< Alignment > &&aln1_batch, vector< Alignment > &&aln2_batch, vector< int64_t > &&tlen_limit_batch)
	Emit a batch of pairs of Alignments. More...
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_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...

Private Attributes
unique_ptr< ofstream >	out_file
	If we are doing output to a file, this will hold the open file. Otherwise (for stdout) it will be empty. More...
vg::io::StreamMultiplexer	multiplexer
vector< unique_ptr< vg::io::ProtobufEmitter< Alignment > > >	proto
	We also keep ProtobufEmitters, one per thread, if we are doing protobuf output. More...

Detailed Description

Emit Alignments to a stream in GAM or JSON format. Thread safe.

TODO: Split into Protobuf and JSON versions?

Constructor & Destructor Documentation

VGAlignmentEmitter()

vg::io::VGAlignmentEmitter::VGAlignmentEmitter	(	const string &	filename,
		const string &	format,
		size_t	max_threads
	)

Create a VGAlignmentEmitter writing to the given file (or "-") in the given non-HTS format ("JSON", "GAM").

~VGAlignmentEmitter()

vg::io::VGAlignmentEmitter::~VGAlignmentEmitter

(

)

Finish and drstroy a VGAlignmentEmitter.

Member Function Documentation

emit_extra_message()

void vg::io::VGAlignmentEmitter::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::io::VGAlignmentEmitter::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.

Implements vg::io::AlignmentEmitter.

emit_mapped_singles()

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

virtual

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

Implements vg::io::AlignmentEmitter.

emit_pairs()

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

virtual

Emit a batch of pairs of Alignments.

Implements vg::io::AlignmentEmitter.

emit_singles()

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

virtual

Emit a batch of Alignments.

Implements vg::io::AlignmentEmitter.

Member Data Documentation

multiplexer

vg::io::StreamMultiplexer vg::io::VGAlignmentEmitter::multiplexer

private

This holds a StreamMultiplexer on the output stream, for sharing it between threads.

out_file

unique_ptr<ofstream> vg::io::VGAlignmentEmitter::out_file

private

If we are doing output to a file, this will hold the open file. Otherwise (for stdout) it will be empty.

proto

vector<unique_ptr<vg::io::ProtobufEmitter<Alignment> > > vg::io::VGAlignmentEmitter::proto

private

We also keep ProtobufEmitters, one per thread, if we are doing protobuf output.

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

• deps/libvgio/include/vg/io/alignment_emitter.hpp
• deps/libvgio/src/alignment_emitter.cpp