vg::HTSAlignmentEmitter Class Reference

#include <hts_alignment_emitter.hpp>

Inheritance diagram for vg::HTSAlignmentEmitter:

Public Member Functions
	HTSAlignmentEmitter (const string &filename, const string &format, const vector< pair< string, int64_t >> &path_order_and_length, const unordered_map< string, int64_t > &subpath_to_length, size_t max_threads)
	~HTSAlignmentEmitter ()=default
	Tear down an HTSAlignmentEmitter and destroy HTSlib structures. More...
	HTSAlignmentEmitter (const HTSAlignmentEmitter &other)=delete
HTSAlignmentEmitter &	operator= (const HTSAlignmentEmitter &other)=delete
	HTSAlignmentEmitter (HTSAlignmentEmitter &&other)=delete
HTSAlignmentEmitter &	operator= (HTSAlignmentEmitter &&other)=delete
void	emit_singles (vector< Alignment > &&aln_batch)
	Emit a batch of Alignments. More...
void	emit_mapped_singles (vector< vector< Alignment >> &&alns_batch)
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...
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...
Public Member Functions inherited from vg::HTSWriter
	HTSWriter (const string &filename, const string &format, const vector< pair< string, int64_t >> &path_order_and_length, const unordered_map< string, int64_t > &subpath_to_length, size_t max_threads)
	~HTSWriter ()
	Tear down an HTSWriter and destroy HTSlib structures. More...
	HTSWriter (const HTSWriter &other)=delete
HTSWriter &	operator= (const HTSWriter &other)=delete
	HTSWriter (HTSWriter &&other)=delete
HTSWriter &	operator= (HTSWriter &&other)=delete

Private Member Functions
virtual void	convert_alignment (const Alignment &aln, vector< pair< int, char >> &cigar, bool &pos_rev, int64_t &pos, string &path_name) const
void	convert_unpaired (Alignment &aln, bam_hdr_t *header, vector< bam1_t * > &dest)
void	convert_paired (Alignment &aln1, Alignment &aln2, bam_hdr_t *header, int64_t tlen_limit, vector< bam1_t * > &dest)

Additional Inherited Members
Protected Member Functions inherited from vg::HTSWriter
void	save_records (bam_hdr_t *header, vector< bam1_t * > &records, size_t thread_number)
bam_hdr_t *	ensure_header (const string &read_group, const string &sample_name, size_t thread_number)
void	initialize_sam_file (bam_hdr_t *header, size_t thread_number, bool keep_header=false)
Protected Attributes inherited from vg::HTSWriter
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
string	format
	This holds our format name, for later error messages. More...
vector< pair< string, int64_t > >	path_order_and_length
	Store the path names and lengths in the order to put them in the header. More...
unordered_map< string, int64_t >	subpath_to_length
vector< hFILE * >	backing_files
vector< samFile * >	sam_files
atomic< bam_hdr_t * >	atomic_header
	We need a header. More...
string	sam_header
mutex	header_mutex
	If the header isn't present when we want to write, we need a mutex to control creating it. More...
bool	output_is_bgzf
string	hts_mode
	Remember the HTSlib mode string we need to open our files. More...
Static Protected Attributes inherited from vg::HTSWriter
static const size_t	BGZF_FOOTER_LENGTH = 28
	We hack about with htslib's BGZF EOF footers, so we need to know how long they are. More...

Detailed Description

Emit Alignments to a stream in SAM/BAM/CRAM format. Thread safe.

Constructor & Destructor Documentation

HTSAlignmentEmitter() [1/3]

vg::HTSAlignmentEmitter::HTSAlignmentEmitter	(	const string &	filename,
		const string &	format,
		const vector< pair< string, int64_t >> &	path_order_and_length,
		const unordered_map< string, int64_t > &	subpath_to_length,
		size_t	max_threads
	)

Create an HTSAlignmentEmitter writing to the given file (or "-") in the given HTS format ("SAM", "BAM", "CRAM"). path_order_and_length must give contig names and lengths to include in the header, in order. Sample names and read groups for the header will be guessed from the first reads. HTSlib positions will be read from the alignments' refpos, and the alignments must be surjected.

~HTSAlignmentEmitter()

vg::HTSAlignmentEmitter::~HTSAlignmentEmitter ( )

default

Tear down an HTSAlignmentEmitter and destroy HTSlib structures.

HTSAlignmentEmitter() [2/3]

vg::HTSAlignmentEmitter::HTSAlignmentEmitter ( const HTSAlignmentEmitter &  other )

delete

HTSAlignmentEmitter() [3/3]

vg::HTSAlignmentEmitter::HTSAlignmentEmitter ( HTSAlignmentEmitter &&  other )

delete

Member Function Documentation

convert_alignment()

void vg::HTSAlignmentEmitter::convert_alignment ( const Alignment &  aln, vector< pair< int, char >> &  cigar, bool &  pos_rev, int64_t &  pos, string &  path_name  ) const

privatevirtual

Reimplemented in vg::SplicedHTSAlignmentEmitter.

convert_paired()

void vg::HTSAlignmentEmitter::convert_paired ( Alignment &  aln1, Alignment &  aln2, bam_hdr_t *  header, int64_t  tlen_limit, vector< bam1_t * > &  dest  )

private

Convert a paired alignment to HTS format. Header must have been created already.

convert_unpaired()

void vg::HTSAlignmentEmitter::convert_unpaired ( Alignment &  aln, bam_hdr_t *  header, vector< bam1_t * > &  dest  )

private

Convert an unpaired alignment to HTS format. Header must have been created already.

emit_mapped_pairs()

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

virtual

Emit a batch of Alignments.

Implements vg::io::AlignmentEmitter.

operator=() [1/2]

HTSAlignmentEmitter& vg::HTSAlignmentEmitter::operator= ( const HTSAlignmentEmitter &  other )

delete

operator=() [2/2]

HTSAlignmentEmitter& vg::HTSAlignmentEmitter::operator= ( HTSAlignmentEmitter &&  other )

delete

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

• src/hts_alignment_emitter.hpp
• src/hts_alignment_emitter.cpp