nvbio::bowtie2::cuda::SeedHitDequeArrayDeviceView Struct Reference

Detailed description

An array containing a priority deque of SeedHit's per read

Definition at line 157 of file seed_hit_deque_array.h.

#include <seed_hit_deque_array.h>

Public Types
typedef device_view_subtype < thrust::device_vector < SeedHit > >::type	hits_storage_type
typedef device_view_subtype < thrust::device_vector < uint32 > >::type	index_storage_type
typedef device_view_subtype < thrust::device_vector< float > >::type	prob_storage_type
typedef vector_view< SeedHit * >	hit_vector_type
typedef priority_deque < SeedHit, hit_vector_type, hit_compare >	hit_deque_type
typedef SeedHitDequeReference < SeedHitDequeArrayDeviceView >	reference

Public Methods
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE	SeedHitDequeArrayDeviceView (index_storage_type counts=index_storage_type(), index_storage_type index=index_storage_type(), hits_storage_type hits=hits_storage_type(), index_storage_type probs_index=index_storage_type(), prob_storage_type probs=prob_storage_type(), index_storage_type pool=index_storage_type(), index_storage_type probs_pool=index_storage_type())
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE reference	operator[] (const uint32 read_id)
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE SeedHit *	alloc_deque (const uint32 read_id, const uint32 size)
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void	resize_deque (const uint32 read_id, const uint32 size)
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32	get_size (const uint32 read_id) const
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE SeedHit *	get_data (const uint32 read_id) const
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE float *	get_probs (const uint32 read_id) const
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void	erase (const uint32 read_id)
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE hit_deque_type	get_deque (const uint32 read_id, bool build_heap=false) const

Public Members
hits_storage_type	m_hits
	global arena of seed hit SA ranges More...
index_storage_type	m_counts
	per-read seed hit counters More...
prob_storage_type	m_probs
	global arena of SA probabilities More...
index_storage_type	m_index
	per-read index marking the beginning of the read's hits vector in the global arena More...
index_storage_type	m_probs_index
	per-read index marking the beginning of the read's hits vector in the global arena More...
index_storage_type	m_pool
	pool counter for the global arena More...
index_storage_type	m_probs_pool
	pool counter for the global arena More...

Member Typedef Documentation

typedef priority_deque<SeedHit, hit_vector_type, hit_compare> nvbio::bowtie2::cuda::SeedHitDequeArrayDeviceView::hit_deque_type

Definition at line 164 of file seed_hit_deque_array.h.

typedef vector_view<SeedHit*> nvbio::bowtie2::cuda::SeedHitDequeArrayDeviceView::hit_vector_type

Definition at line 163 of file seed_hit_deque_array.h.

typedef device_view_subtype< thrust::device_vector<SeedHit> >::type nvbio::bowtie2::cuda::SeedHitDequeArrayDeviceView::hits_storage_type

Definition at line 159 of file seed_hit_deque_array.h.

typedef device_view_subtype< thrust::device_vector<uint32> >::type nvbio::bowtie2::cuda::SeedHitDequeArrayDeviceView::index_storage_type

Definition at line 160 of file seed_hit_deque_array.h.

typedef device_view_subtype< thrust::device_vector<float> >::type nvbio::bowtie2::cuda::SeedHitDequeArrayDeviceView::prob_storage_type

Definition at line 161 of file seed_hit_deque_array.h.

typedef SeedHitDequeReference<SeedHitDequeArrayDeviceView> nvbio::bowtie2::cuda::SeedHitDequeArrayDeviceView::reference

Definition at line 166 of file seed_hit_deque_array.h.

Constructor & Destructor Documentation

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE nvbio::bowtie2::cuda::SeedHitDequeArrayDeviceView::SeedHitDequeArrayDeviceView	(	index_storage_type	counts = index_storage_type(),
		index_storage_type	index = index_storage_type(),
		hits_storage_type	hits = hits_storage_type(),
		index_storage_type	probs_index = index_storage_type(),
		prob_storage_type	probs = prob_storage_type(),
		index_storage_type	pool = index_storage_type(),
		index_storage_type	probs_pool = index_storage_type()
	)

constructor

Definition at line 50 of file seed_hit_deque_array_inl.h.

Member Function Documentation

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE SeedHit * nvbio::bowtie2::cuda::SeedHitDequeArrayDeviceView::alloc_deque	(	const uint32	read_id,
		const uint32	size
	)

allocate some storage for the deque bound to a given read

Definition at line 78 of file seed_hit_deque_array_inl.h.

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void nvbio::bowtie2::cuda::SeedHitDequeArrayDeviceView::erase ( const uint32  read_id)

inline

erase the set of hits bound to a read. NOTE: this method doesn't release the previously allocated memory!

Definition at line 215 of file seed_hit_deque_array.h.

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE SeedHit* nvbio::bowtie2::cuda::SeedHitDequeArrayDeviceView::get_data ( const uint32  read_id) const

inline

get the storage for the hit vector bound to a given read

Definition at line 204 of file seed_hit_deque_array.h.

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE SeedHitDequeArrayDeviceView::hit_deque_type nvbio::bowtie2::cuda::SeedHitDequeArrayDeviceView::get_deque	(	const uint32	read_id,
		bool	build_heap = false
	)		const

return the deque bound to a given read

Definition at line 105 of file seed_hit_deque_array_inl.h.

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE float* nvbio::bowtie2::cuda::SeedHitDequeArrayDeviceView::get_probs ( const uint32  read_id) const

inline

get the storage for the hit vector bound to a given read

Definition at line 209 of file seed_hit_deque_array.h.

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32 nvbio::bowtie2::cuda::SeedHitDequeArrayDeviceView::get_size ( const uint32  read_id) const

inline

get the size of the hit vector bound to a given read

Definition at line 199 of file seed_hit_deque_array.h.

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE SeedHitDequeArrayDeviceView::reference nvbio::bowtie2::cuda::SeedHitDequeArrayDeviceView::operator[]

(

const uint32

read_id)

return a reference to the given deque

Definition at line 70 of file seed_hit_deque_array_inl.h.

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void nvbio::bowtie2::cuda::SeedHitDequeArrayDeviceView::resize_deque ( const uint32  read_id, const uint32  size  )

inline

resize the deque bound to a given read NOTE: this method doesn't alloc or release any memory! alloc_deque() must have been previously called.

Definition at line 194 of file seed_hit_deque_array.h.

Member Data Documentation

index_storage_type nvbio::bowtie2::cuda::SeedHitDequeArrayDeviceView::m_counts

per-read seed hit counters

Definition at line 224 of file seed_hit_deque_array.h.

hits_storage_type nvbio::bowtie2::cuda::SeedHitDequeArrayDeviceView::m_hits

global arena of seed hit SA ranges

Definition at line 223 of file seed_hit_deque_array.h.

index_storage_type nvbio::bowtie2::cuda::SeedHitDequeArrayDeviceView::m_index

per-read index marking the beginning of the read's hits vector in the global arena

Definition at line 226 of file seed_hit_deque_array.h.

index_storage_type nvbio::bowtie2::cuda::SeedHitDequeArrayDeviceView::m_pool

pool counter for the global arena

Definition at line 228 of file seed_hit_deque_array.h.

prob_storage_type nvbio::bowtie2::cuda::SeedHitDequeArrayDeviceView::m_probs

global arena of SA probabilities

Definition at line 225 of file seed_hit_deque_array.h.

index_storage_type nvbio::bowtie2::cuda::SeedHitDequeArrayDeviceView::m_probs_index

per-read index marking the beginning of the read's hits vector in the global arena

Definition at line 227 of file seed_hit_deque_array.h.

index_storage_type nvbio::bowtie2::cuda::SeedHitDequeArrayDeviceView::m_probs_pool

pool counter for the global arena

Definition at line 229 of file seed_hit_deque_array.h.

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

• E:/git/nvbio/nvBowtie/bowtie2/cuda/seed_hit_deque_array.h
• E:/git/nvbio/nvBowtie/bowtie2/cuda/seed_hit_deque_array_inl.h