#include <hts_alignment_emitter.hpp>

Inheritance diagram for vg::SplicedHTSAlignmentEmitter:

Public Member Functions
	SplicedHTSAlignmentEmitter (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, const PathPositionHandleGraph &graph, size_t max_threads)

	~SplicedHTSAlignmentEmitter ()=default

Public Member Functions inherited from 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)

	~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

Public Attributes
size_t	min_splice_length = 20
	The minimum length of a deletion relative to the path that will be coded as a splice junction in the CIGAR. More...

Private Member Functions
void	convert_alignment (const Alignment &aln, vector< pair< int, char >> &cigar, bool &pos_rev, int64_t &pos, string &path_name) const
	Override for convert alignment that converts splices implicitly. More...

vector< pair< int, char > >	spliced_cigar_against_path (const Alignment &aln, const string &path_name, int64_t pos, bool rev) const

Private Attributes
const PathPositionHandleGraph &	graph
	Graph that alignments were aligned against. More...

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...

Constructor & Destructor Documentation

◆ SplicedHTSAlignmentEmitter()

vg::SplicedHTSAlignmentEmitter::SplicedHTSAlignmentEmitter	(	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,
		const PathPositionHandleGraph &	graph,
		size_t	max_threads
	)

◆ ~SplicedHTSAlignmentEmitter()

vg::SplicedHTSAlignmentEmitter::~SplicedHTSAlignmentEmitter ( )

default

Member Function Documentation

◆ convert_alignment()

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

privatevirtual

Override for convert alignment that converts splices implicitly.

Reimplemented from vg::HTSAlignmentEmitter.

◆ spliced_cigar_against_path()

vector< pair< int, char > > vg::SplicedHTSAlignmentEmitter::spliced_cigar_against_path	(	const Alignment &	aln,
		const string &	path_name,
		int64_t	pos,
		bool	rev
	)		const

private

Convert a spliced alignment against a path to a cigar. The alignment must be colinear along a path and contain only mappings on the path, but it can have deletions relative to the path that follow edges in the graph.

Member Data Documentation

◆ graph

const PathPositionHandleGraph& vg::SplicedHTSAlignmentEmitter::graph

private

Graph that alignments were aligned against.

◆ min_splice_length

size_t vg::SplicedHTSAlignmentEmitter::min_splice_length = 20

The minimum length of a deletion relative to the path that will be coded as a splice junction in the CIGAR.

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

src/hts_alignment_emitter.hpp
src/hts_alignment_emitter.cpp

Public Member Functions

Public Attributes

Private Member Functions

Private Attributes

Additional Inherited Members