Detailed description

The output file interface.

This class is the base class for all file output classes. By itself, it implements a "null" output, which discards all data sent into it. Other classes derive from this to implement various file output formats.

After each alignment pass in the pipeline, the aligner should call OutputFile::process. This call takes a handle to the alignment buffers in GPU memory (a DeviceOutputBatchSE structure). The implementation ensures that any data required is copied out before the call returns, allowing the caller to invalidate the GPU memory immediately.

Sequence alignment is generally done in batches of reads; for each batch multiple OutputFile::process calls can be made. Two extra enum parameters serve to identify which alignment pass we're handling at each call. Each batch should be preceded by a OutputFile::start_batch call; at the end of each batch, OutputFile::end_batch should be called. In most cases, data is only written to disk after OutputFile::end_batch is called.

The factory method OutputFile::open is used to create OutputFile objects. It parses the file name extension to determine the file format for the output.

Definition at line 71 of file output_file.h.

#include <output_file.h>

Inheritance diagram for nvbio::io::OutputFile:

Public Methods
virtual	~OutputFile ()

void	set_program (const char _pg_id, const char _pg_name, const char _pg_version, const char _pg_args)

void	set_rg (const char _rg_id, const char _rg_string)

virtual void	header ()

virtual void	configure_mapq_evaluator (int mapq_filter)

virtual void	process (struct HostOutputBatchSE &batch)

virtual void	process (struct HostOutputBatchPE &batch)

virtual void	close (void)
	Flush and close the output file. More...

virtual IOStats &	get_aggregate_statistics (void)
	Returns aggregate I/O statistics for this object. More...

Static Public Methods
static OutputFile *	open (const char *file_name, AlignmentType aln_type, BNT bnt)

Proteced Methods
	OutputFile (const char *file_name, AlignmentType alignment_type, BNT bnt)

Protected Members
const char *	file_name
	Name of the file we're writing. More...

AlignmentType	alignment_type
	The type of alignment we're running (single or paired-end) More...

BNT	bnt
	Reference genome data handle. More...

int	mapq_filter
	The current mapping quality filter: reads with a mapq below this value will be marked as not aligned. More...

IOStats	iostats
	I/O statistics. More...

std::string	pg_id

std::string	pg_name

std::string	pg_version

std::string	pg_args

std::string	rg_id

std::string	rg_string

Constructor & Destructor Documentation

nvbio::io::OutputFile::OutputFile	(	const char *	file_name,
		AlignmentType	alignment_type,
		BNT	bnt
	)

protected

Definition at line 36 of file output_file.cpp.

nvbio::io::OutputFile::~OutputFile ( )

virtual

Definition at line 44 of file output_file.cpp.

Member Function Documentation

void nvbio::io::OutputFile::close ( void )

virtual

Flush and close the output file.

Reimplemented in nvbio::io::SamOutput, nvbio::io::DebugOutput, and nvbio::io::BamOutput.

Definition at line 53 of file output_file.cpp.

void nvbio::io::OutputFile::configure_mapq_evaluator ( int mapq_filter)

virtual

Configure the MapQ evaluator. Must be called prior to any batch processing.

Definition at line 48 of file output_file.cpp.

IOStats & nvbio::io::OutputFile::get_aggregate_statistics ( void )

virtual

Returns aggregate I/O statistics for this object.

Definition at line 57 of file output_file.cpp.

virtual void nvbio::io::OutputFile::header ( )

inlinevirtual

write the header out

Reimplemented in nvbio::io::SamOutput, and nvbio::io::BamOutput.

Definition at line 102 of file output_file.h.

OutputFile * nvbio::io::OutputFile::open	(	const char *	file_name,
		AlignmentType	aln_type,
		BNT	bnt
	)

static

Factory method to create OutputFile objects

Parameters

[in]	file_name	The name of the file to create (will be silently overwritten if it already exists). This method parses out the extension from the file name to determine what kind of file format to write.
[in]	aln_type	The type of alignment (single or paired-end)
[in]	bnt	A handle to the reference genome

Returns: A pointer to an OutputFile object, or NULL if an error occurs.

Definition at line 62 of file output_file.cpp.

virtual void nvbio::io::OutputFile::process ( struct HostOutputBatchSE & batch)

inlinevirtual

Process a set of alignment results for the current batch.

Parameters

batch Handle to the buffers containing the alignment results

Reimplemented in nvbio::io::SamOutput, nvbio::io::DebugOutput, and nvbio::io::BamOutput.

Definition at line 112 of file output_file.h.

virtual void nvbio::io::OutputFile::process ( struct HostOutputBatchPE & batch)

inlinevirtual

Process a set of alignment results for the current batch.

Parameters

batch Handle to the buffers containing the alignment results

Reimplemented in nvbio::io::SamOutput, nvbio::io::DebugOutput, and nvbio::io::BamOutput.

Definition at line 118 of file output_file.h.

void nvbio::io::OutputFile::set_program	(	const char *	_pg_id,
		const char *	_pg_name,
		const char *	_pg_version,
		const char *	_pg_args
	)

inline

Definition at line 80 of file output_file.h.

void nvbio::io::OutputFile::set_rg	(	const char *	_rg_id,
		const char *	_rg_string
	)

inline

Definition at line 92 of file output_file.h.

Member Data Documentation

AlignmentType nvbio::io::OutputFile::alignment_type

protected

The type of alignment we're running (single or paired-end)

Definition at line 130 of file output_file.h.

BNT nvbio::io::OutputFile::bnt

protected

Reference genome data handle.

Definition at line 132 of file output_file.h.

const char* nvbio::io::OutputFile::file_name

protected

Name of the file we're writing.

Definition at line 128 of file output_file.h.

IOStats nvbio::io::OutputFile::iostats

protected

I/O statistics.

Definition at line 138 of file output_file.h.

int nvbio::io::OutputFile::mapq_filter

protected

The current mapping quality filter: reads with a mapq below this value will be marked as not aligned.

Definition at line 135 of file output_file.h.

std::string nvbio::io::OutputFile::pg_args

protected

Definition at line 143 of file output_file.h.

std::string nvbio::io::OutputFile::pg_id

protected

Definition at line 140 of file output_file.h.

std::string nvbio::io::OutputFile::pg_name

protected

Definition at line 141 of file output_file.h.

std::string nvbio::io::OutputFile::pg_version

protected

Definition at line 142 of file output_file.h.

std::string nvbio::io::OutputFile::rg_id

protected

Definition at line 145 of file output_file.h.

std::string nvbio::io::OutputFile::rg_string

protected

Definition at line 146 of file output_file.h.

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

E:/git/nvbio/nvbio/io/output/output_file.h
E:/git/nvbio/nvbio/io/output/output_file.cpp

Detailed description

Public Methods

Static Public Methods

Proteced Methods

Protected Members

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation