nvbio::bowtie2::cuda::ReadHitsBinder< ScoringQueuesType > Struct Template Reference

Detailed description

template< typename ScoringQueuesType>
struct nvbio::bowtie2::cuda::ReadHitsBinder< ScoringQueuesType >

A class used to bind a read and its hits to the output queue

Definition at line 499 of file scoring_queues.h.

#include <scoring_queues.h>

Public Types
typedef ScoringQueuesType::read_hits_index_type	read_hits_index_type
typedef ScoringQueuesType::hits_storage_type	hits_storage_type
typedef HitReference < hits_storage_type >	reference

Public Methods
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE	ReadHitsBinder (ScoringQueuesType &queues, const uint32 read_index=uint32(-1))
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void	bind (const uint32 read_index)
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void	resize (const uint32 size)
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32	size () const
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE HitReference < hits_storage_type >	operator[] (const uint32 i) const
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE packed_read	read_info () const
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void	set_read_info (const packed_read info)
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void	bind_hit (const uint32 i, const uint32 slot)

Member Typedef Documentation

template<typename ScoringQueuesType>

typedef ScoringQueuesType::hits_storage_type nvbio::bowtie2::cuda::ReadHitsBinder< ScoringQueuesType >::hits_storage_type

Definition at line 502 of file scoring_queues.h.

template<typename ScoringQueuesType>

typedef ScoringQueuesType::read_hits_index_type nvbio::bowtie2::cuda::ReadHitsBinder< ScoringQueuesType >::read_hits_index_type

Definition at line 501 of file scoring_queues.h.

template<typename ScoringQueuesType>

typedef HitReference<hits_storage_type> nvbio::bowtie2::cuda::ReadHitsBinder< ScoringQueuesType >::reference

Definition at line 503 of file scoring_queues.h.

Constructor & Destructor Documentation

template<typename ScoringQueuesType >

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE nvbio::bowtie2::cuda::ReadHitsBinder< ScoringQueuesType >::ReadHitsBinder	(	ScoringQueuesType &	queues,
		const uint32	read_index = uint32(-1)
	)

constructor

Parameters

queues	scoring queues
read_index	index of this read
selector	input/output queue selector

Definition at line 292 of file scoring_queues_inl.h.

Member Function Documentation

template<typename ScoringQueuesType >

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void nvbio::bowtie2::cuda::ReadHitsBinder< ScoringQueuesType >::bind

(

const uint32

read_index)

bind this object to a given index

Parameters

read_index

output index of this read

Definition at line 302 of file scoring_queues_inl.h.

template<typename ScoringQueuesType >

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void nvbio::bowtie2::cuda::ReadHitsBinder< ScoringQueuesType >::bind_hit	(	const uint32	i,
		const uint32	slot
	)

bind the i-th hit to a given location

Parameters

i	index of the hit to bind relative to this read
slot	address of the bound hit in the HitQueues

Definition at line 362 of file scoring_queues_inl.h.

template<typename ScoringQueuesType >

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE ReadHitsBinder< ScoringQueuesType >::reference nvbio::bowtie2::cuda::ReadHitsBinder< ScoringQueuesType >::operator[]

(

const uint32

i)

const

return the i-th element NOTE: this method is only valid after the i-th hit has been bound.

Definition at line 331 of file scoring_queues_inl.h.

template<typename ScoringQueuesType >

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE packed_read nvbio::bowtie2::cuda::ReadHitsBinder< ScoringQueuesType >::read_info

(

)

const

access the packed_read info in the selected queue

Definition at line 341 of file scoring_queues_inl.h.

template<typename ScoringQueuesType >

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void nvbio::bowtie2::cuda::ReadHitsBinder< ScoringQueuesType >::resize

(

const uint32

size)

resize the hits vector

Definition at line 311 of file scoring_queues_inl.h.

template<typename ScoringQueuesType >

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void nvbio::bowtie2::cuda::ReadHitsBinder< ScoringQueuesType >::set_read_info

(

const packed_read

info)

set the read info

Parameters

read_index

output index of this read

Definition at line 351 of file scoring_queues_inl.h.

template<typename ScoringQueuesType >

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32 nvbio::bowtie2::cuda::ReadHitsBinder< ScoringQueuesType >::size

(

void

)

const

size of the hits vector

Definition at line 320 of file scoring_queues_inl.h.

---

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

• E:/git/nvbio/nvBowtie/bowtie2/cuda/scoring_queues.h
• E:/git/nvbio/nvBowtie/bowtie2/cuda/scoring_queues_inl.h