#include <multipath_alignment_emitter.hpp>

Inheritance diagram for vg::MultipathAlignmentEmitter:

Public Member Functions
	MultipathAlignmentEmitter (const string &filename, size_t num_threads, const string out_format="GAMP", const PathPositionHandleGraph graph=nullptr, const SequenceDictionary sequence_dictionary=nullptr)
	~MultipathAlignmentEmitter ()
void	set_read_group (const string &read_group)
	Choose a read group to apply to all emitted alignments.
void	set_sample_name (const string &sample_name)
	Choose a sample name to apply to all emitted alignments.
void	set_min_splice_length (int64_t min_splice_length)
void	emit_pairs (const string &name_1, const string &name_2, vector< pair< multipath_alignment_t, multipath_alignment_t > > &&mp_aln_pairs, vector< pair< tuple< string, bool, int64_t >, tuple< string, bool, int64_t > > > path_positions=nullptr, vector< int64_t > tlen_limits=nullptr)
	Emit paired read mappings as interleaved protobuf messages or HTSLib output.
void	emit_singles (const string &name, vector< multipath_alignment_t > &&mp_alns, vector< tuple< string, bool, int64_t > > *path_positions=nullptr)
	Emit read mappings as protobuf messages or HTSLib output.
void	emit_paired_independent (const string &name_1, const string &name_2, vector< multipath_alignment_t > &&mp_alns_1, vector< multipath_alignment_t > &&mp_alns_2, vector< tuple< string, bool, int64_t > > path_positions_1=nullptr, vector< tuple< string, bool, int64_t > > path_positions_2=nullptr)
	Emit unpaired independent or supplementary alignments for paired reads.
Public Member Functions inherited from vg::HTSWriter
	HTSWriter (const string &filename, const string &format, const SequenceDictionary &sequence_dictionary, const unordered_map< string, size_t > &subpath_to_index, size_t max_threads)
	~HTSWriter ()
	Tear down an HTSWriter and destroy HTSlib structures.
	HTSWriter (const HTSWriter &other)=delete
HTSWriter &	operator= (const HTSWriter &other)=delete
	HTSWriter (HTSWriter &&other)=delete
HTSWriter &	operator= (HTSWriter &&other)=delete

Private Types
enum	output_format_t { GAMP , GAM , GAF , BAM , SAM , CRAM }
	what format are we outputting in More...

Private Member Functions
void	emit_singles_internal (const string &name, vector< multipath_alignment_t > &&mp_alns, vector< tuple< string, bool, int64_t > > path_positions, const string mate_name, bool is_read_1)
	Emit read mappings as protobuf messages or HTSLib output.
void	convert_to_alignment (const multipath_alignment_t &mp_aln, Alignment &aln, const string prev_name=nullptr, const string next_name=nullptr) const
	make a GAM alignment from a multipath alignment
void	create_alignment_shim (const string &name, const multipath_alignment_t &mp_aln, Alignment &shim, const string prev_name=nullptr, const string next_name=nullptr) const
	store the data in an Algnment that is used in the conversion to bam1_t
void	convert_to_hts_unpaired (const string &name, const multipath_alignment_t &mp_aln, const string &ref_name, bool ref_rev, int64_t ref_pos, bam_hdr_t header, vector< bam1_t > &dest, const string *mate_name=nullptr) const
	store a bam1_t object with the indicated data in the dest vector
void	convert_to_hts_paired (const string &name_1, const string &name_2, const multipath_alignment_t &mp_aln_1, const multipath_alignment_t &mp_aln_2, const string &ref_name_1, bool ref_rev_1, int64_t ref_pos_1, const string &ref_name_2, bool ref_rev_2, int64_t ref_pos_2, int64_t tlen_limit, bam_hdr_t header, vector< bam1_t > &dest) const
	store two paired bam1_t objects with the indicated data in the dest vector
void	add_annotations (const multipath_alignment_t &mp_aln, bam1_t *bam) const
	transfer the allelic mapq, group mapq, and secondary annotations to a BAM record
void	canonicalize_subrange (string &path_name, int32_t &pos) const
	take subrange info out of the path name and adjust the position for the subrange start

Private Attributes
output_format_t	format
const PathPositionHandleGraph *	graph
vector< unique_ptr< vg::io::ProtobufEmitter< Alignment > > >	aln_emitters
	an Alignment emitter for each thread
vector< unique_ptr< vg::io::ProtobufEmitter< MultipathAlignment > > >	mp_aln_emitters
	a MultipathAlignment emitter for each thread
string	read_group
	read group applied to alignments
string	sample_name
	sample name applied to alignments
int64_t	min_splice_length = numeric_limits<int64_t>::max()
	the shortest deletion that we will interpret as a splice in the CIGAR string of HTS output

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.
vg::io::StreamMultiplexer	multiplexer
string	format
SequenceDictionary	sequence_dictionary
unordered_map< string, size_t >	subpath_to_index
	This maps from subpath to entry number in the sequence dictionary.
vector< hFILE * >	backing_files
vector< samFile * >	sam_files
atomic< bam_hdr_t * >	atomic_header
	We need a header.
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.
bool	output_is_bgzf
string	hts_mode
	Remember the HTSlib mode string we need to open our files.
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.
static const size_t	HTSLIB_CRAM_THREADS = 8
	For CRAM output, we use a separate pool of compressor threads inside htslib.

Member Enumeration Documentation

◆ output_format_t

enum vg::MultipathAlignmentEmitter::output_format_t

private

what format are we outputting in

Enumerator
GAMP
GAM
GAF
BAM
SAM
CRAM

Constructor & Destructor Documentation

◆ MultipathAlignmentEmitter()

vg::MultipathAlignmentEmitter::MultipathAlignmentEmitter	(	const string &	filename,
		size_t	num_threads,
		const string	out_format = "GAMP",
		const PathPositionHandleGraph *	graph = nullptr,
		const SequenceDictionary *	sequence_dictionary = nullptr )

Initialize with the intended output stream and the maximum number of threads that will be outputting. Allowed formats:

"GAMP"
"GAM", involves conversion to single path
"GAF", involves conversion to single path, requires a graph
"SAM", "BAM", "CRAM:" requires path length map, and all input alignments must already be surjected. If alignments have connections, requires a graph

◆ ~MultipathAlignmentEmitter()

vg::MultipathAlignmentEmitter::~MultipathAlignmentEmitter ( )

Member Function Documentation

◆ add_annotations()

void vg::MultipathAlignmentEmitter::add_annotations	(	const multipath_alignment_t &	mp_aln,
		bam1_t *	bam ) const

private

transfer the allelic mapq, group mapq, and secondary annotations to a BAM record

◆ canonicalize_subrange()

void vg::MultipathAlignmentEmitter::canonicalize_subrange	(	string &	path_name,
		int32_t &	pos ) const

private

take subrange info out of the path name and adjust the position for the subrange start

◆ convert_to_alignment()

void vg::MultipathAlignmentEmitter::convert_to_alignment	(	const multipath_alignment_t &	mp_aln,
		Alignment &	aln,
		const string *	prev_name = nullptr,
		const string *	next_name = nullptr ) const

private

make a GAM alignment from a multipath alignment

◆ convert_to_hts_paired()

void vg::MultipathAlignmentEmitter::convert_to_hts_paired	(	const string &	name_1,
		const string &	name_2,
		const multipath_alignment_t &	mp_aln_1,
		const multipath_alignment_t &	mp_aln_2,
		const string &	ref_name_1,
		bool	ref_rev_1,
		int64_t	ref_pos_1,
		const string &	ref_name_2,
		bool	ref_rev_2,
		int64_t	ref_pos_2,
		int64_t	tlen_limit,
		bam_hdr_t *	header,
		vector< bam1_t * > &	dest ) const

private

store two paired bam1_t objects with the indicated data in the dest vector

◆ convert_to_hts_unpaired()

void vg::MultipathAlignmentEmitter::convert_to_hts_unpaired	(	const string &	name,
		const multipath_alignment_t &	mp_aln,
		const string &	ref_name,
		bool	ref_rev,
		int64_t	ref_pos,
		bam_hdr_t *	header,
		vector< bam1_t * > &	dest,
		const string *	mate_name = nullptr ) const

private

store a bam1_t object with the indicated data in the dest vector

◆ create_alignment_shim()

void vg::MultipathAlignmentEmitter::create_alignment_shim	(	const string &	name,
		const multipath_alignment_t &	mp_aln,
		Alignment &	shim,
		const string *	prev_name = nullptr,
		const string *	next_name = nullptr ) const

private

store the data in an Algnment that is used in the conversion to bam1_t

◆ emit_paired_independent()

void vg::MultipathAlignmentEmitter::emit_paired_independent	(	const string &	name_1,
		const string &	name_2,
		vector< multipath_alignment_t > &&	mp_alns_1,
		vector< multipath_alignment_t > &&	mp_alns_2,
		vector< tuple< string, bool, int64_t > > *	path_positions_1 = nullptr,
		vector< tuple< string, bool, int64_t > > *	path_positions_2 = nullptr )

Emit unpaired independent or supplementary alignments for paired reads.

◆ emit_pairs()

void vg::MultipathAlignmentEmitter::emit_pairs	(	const string &	name_1,
		const string &	name_2,
		vector< pair< multipath_alignment_t, multipath_alignment_t > > &&	mp_aln_pairs,
		vector< pair< tuple< string, bool, int64_t >, tuple< string, bool, int64_t > > > *	path_positions = nullptr,
		vector< int64_t > *	tlen_limits = nullptr )

Emit paired read mappings as interleaved protobuf messages or HTSLib output.

◆ emit_singles()

void vg::MultipathAlignmentEmitter::emit_singles	(	const string &	name,
		vector< multipath_alignment_t > &&	mp_alns,
		vector< tuple< string, bool, int64_t > > *	path_positions = nullptr )

Emit read mappings as protobuf messages or HTSLib output.

◆ emit_singles_internal()

void vg::MultipathAlignmentEmitter::emit_singles_internal	(	const string &	name,
		vector< multipath_alignment_t > &&	mp_alns,
		vector< tuple< string, bool, int64_t > > *	path_positions,
		const string *	mate_name,
		bool	is_read_1 )

private

Emit read mappings as protobuf messages or HTSLib output.

◆ set_min_splice_length()

void vg::MultipathAlignmentEmitter::set_min_splice_length ( int64_t min_splice_length )

Set the length deletion (at a node boundary) that will be considered an unaligned splicing event in HTSLib output

◆ set_read_group()

void vg::MultipathAlignmentEmitter::set_read_group ( const string & read_group )

Choose a read group to apply to all emitted alignments.

◆ set_sample_name()

void vg::MultipathAlignmentEmitter::set_sample_name ( const string & sample_name )

Choose a sample name to apply to all emitted alignments.

Member Data Documentation

◆ aln_emitters

vector<unique_ptr<vg::io::ProtobufEmitter<Alignment> > > vg::MultipathAlignmentEmitter::aln_emitters

private

an Alignment emitter for each thread

◆ format

output_format_t vg::MultipathAlignmentEmitter::format

private

◆ graph

const PathPositionHandleGraph* vg::MultipathAlignmentEmitter::graph

private

◆ min_splice_length

int64_t vg::MultipathAlignmentEmitter::min_splice_length = numeric_limits<int64_t>::max()

private

the shortest deletion that we will interpret as a splice in the CIGAR string of HTS output

◆ mp_aln_emitters

vector<unique_ptr<vg::io::ProtobufEmitter<MultipathAlignment> > > vg::MultipathAlignmentEmitter::mp_aln_emitters

private

a MultipathAlignment emitter for each thread

◆ read_group

string vg::MultipathAlignmentEmitter::read_group

private

read group applied to alignments

◆ sample_name

string vg::MultipathAlignmentEmitter::sample_name

private

sample name applied to alignments

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

Public Member Functions

Private Types

Private Member Functions

Private Attributes

Additional Inherited Members

Member Enumeration Documentation

◆ output_format_t

Constructor & Destructor Documentation

◆ MultipathAlignmentEmitter()

◆ ~MultipathAlignmentEmitter()

Member Function Documentation

◆ add_annotations()

◆ canonicalize_subrange()

◆ convert_to_alignment()

◆ convert_to_hts_paired()

◆ convert_to_hts_unpaired()

◆ create_alignment_shim()

◆ emit_paired_independent()

◆ emit_pairs()

◆ emit_singles()

◆ emit_singles_internal()

◆ set_min_splice_length()

◆ set_read_group()

◆ set_sample_name()

Member Data Documentation

◆ aln_emitters

◆ format

◆ graph

◆ min_splice_length

◆ mp_aln_emitters

◆ read_group

◆ sample_name