nvbio::bowtie2::cuda::ComputeThreadPE Struct Reference

Detailed description

Definition at line 91 of file compute_thread.h.

#include <compute_thread.h>

Inheritance diagram for nvbio::bowtie2::cuda::ComputeThreadPE:

Public Methods
	ComputeThreadPE (const uint32 _thread_id, const uint32 _device_id, const io::SequenceData &_reference_data, const io::FMIndexData &_driver_data, const std::map< std::string, std::string > &_options, const Params &_params, Stats &_stats)
uint32	gauge_batch_size ()
void	set_input (InputThreadPE *_input_thread)
void	set_output (io::OutputFile *_output_file)
void	run ()
void	do_run ()
Public Methods inherited from nvbio::Thread< ComputeThreadPE >
void	create ()
	create the thread More...
void	join ()
	join the thread More...
Public Methods inherited from nvbio::ThreadBase
	ThreadBase ()
	~ThreadBase ()
void	set_id (const uint32 id)
uint32	get_id () const
void	create (void *(*func)(void *), void *arg)
	create the thread More...
void	join ()
	join the thread More...

Public Members
const uint32	thread_id
const uint32	device_id
const io::SequenceData &	reference_data_host
const io::FMIndexData &	driver_data_host
const std::map< std::string, std::string > &	options
InputThreadPE *	input_thread
io::OutputFile *	output_file
Params	params
Stats &	stats
SharedPointer< Aligner >	aligner
SharedPointer < io::SequenceDataDevice >	reference_data_device
SharedPointer < io::FMIndexDataDevice >	driver_data_device

Constructor & Destructor Documentation

nvbio::bowtie2::cuda::ComputeThreadPE::ComputeThreadPE	(	const uint32	_thread_id,
		const uint32	_device_id,
		const io::SequenceData &	_reference_data,
		const io::FMIndexData &	_driver_data,
		const std::map< std::string, std::string > &	_options,
		const Params &	_params,
		Stats &	_stats
	)

constructor

Member Function Documentation

void nvbio::bowtie2::cuda::ComputeThreadPE::do_run

(

)

uint32 nvbio::bowtie2::cuda::ComputeThreadPE::gauge_batch_size

(

)

gauge the favourite batch size

void nvbio::bowtie2::cuda::ComputeThreadPE::run

(

)

void nvbio::bowtie2::cuda::ComputeThreadPE::set_input ( InputThreadPE *  _input_thread)

inline

setup the input thread

Definition at line 110 of file compute_thread.h.

void nvbio::bowtie2::cuda::ComputeThreadPE::set_output ( io::OutputFile *  _output_file)

inline

setup the input thread

Definition at line 114 of file compute_thread.h.

Member Data Documentation

SharedPointer<Aligner> nvbio::bowtie2::cuda::ComputeThreadPE::aligner

Definition at line 129 of file compute_thread.h.

const uint32 nvbio::bowtie2::cuda::ComputeThreadPE::device_id

Definition at line 121 of file compute_thread.h.

SharedPointer<io::FMIndexDataDevice> nvbio::bowtie2::cuda::ComputeThreadPE::driver_data_device

Definition at line 131 of file compute_thread.h.

const io::FMIndexData& nvbio::bowtie2::cuda::ComputeThreadPE::driver_data_host

Definition at line 123 of file compute_thread.h.

InputThreadPE* nvbio::bowtie2::cuda::ComputeThreadPE::input_thread

Definition at line 125 of file compute_thread.h.

const std::map<std::string,std::string>& nvbio::bowtie2::cuda::ComputeThreadPE::options

Definition at line 124 of file compute_thread.h.

io::OutputFile* nvbio::bowtie2::cuda::ComputeThreadPE::output_file

Definition at line 126 of file compute_thread.h.

Params nvbio::bowtie2::cuda::ComputeThreadPE::params

Definition at line 127 of file compute_thread.h.

SharedPointer<io::SequenceDataDevice> nvbio::bowtie2::cuda::ComputeThreadPE::reference_data_device

Definition at line 130 of file compute_thread.h.

const io::SequenceData& nvbio::bowtie2::cuda::ComputeThreadPE::reference_data_host

Definition at line 122 of file compute_thread.h.

Stats& nvbio::bowtie2::cuda::ComputeThreadPE::stats

Definition at line 128 of file compute_thread.h.

const uint32 nvbio::bowtie2::cuda::ComputeThreadPE::thread_id

Definition at line 120 of file compute_thread.h.

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

• E:/git/nvbio/nvBowtie/bowtie2/cuda/compute_thread.h