Detailed description

Definition at line 43 of file output_sam.h.

#include <output_sam.h>

Inheritance diagram for nvbio::io::SamOutput:

Public Methods
	SamOutput (const char *file_name, AlignmentType alignment_type, BNT bnt)

	~SamOutput ()

void	header ()

void	process (struct HostOutputBatchSE &batch)

void	process (struct HostOutputBatchPE &batch)

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

template<>
void	write_tag (const char name, const char value)

Public Methods inherited from nvbio::io::OutputFile
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	configure_mapq_evaluator (int mapq_filter)

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

Additional Inherited Members
Static Public Methods inherited from nvbio::io::OutputFile
static OutputFile *	open (const char *file_name, AlignmentType aln_type, BNT bnt)

Proteced Methods inherited from nvbio::io::OutputFile
	OutputFile (const char *file_name, AlignmentType alignment_type, BNT bnt)

Protected Members inherited from nvbio::io::OutputFile
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::SamOutput::SamOutput	(	const char *	file_name,
		AlignmentType	alignment_type,
		BNT	bnt
	)

Definition at line 37 of file output_sam.cpp.

nvbio::io::SamOutput::~SamOutput ( )

Definition at line 53 of file output_sam.cpp.

void nvbio::io::SamOutput::close ( void )

virtual

Flush and close the output file.

Definition at line 574 of file output_sam.cpp.

void nvbio::io::SamOutput::header ( )

inlinevirtual

write the header out

Definition at line 96 of file output_sam.h.

void nvbio::io::SamOutput::process ( struct HostOutputBatchSE & batch)

virtual

Process a set of alignment results for the current batch.

Parameters

batch Handle to the buffers containing the alignment results

Definition at line 535 of file output_sam.cpp.

void nvbio::io::SamOutput::process ( struct HostOutputBatchPE & batch)

virtual

Process a set of alignment results for the current batch.

Parameters

batch Handle to the buffers containing the alignment results

Definition at line 554 of file output_sam.cpp.

template<>

void nvbio::io::SamOutput::write_tag	(	const char *	name,
		const char *	value
	)

Definition at line 148 of file output_sam.cpp.

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