nvbio::bowtie2::cuda::SeedHitDequeArray Struct Reference

Detailed description

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

Definition at line 116 of file seed_hit_deque_array.h.

#include <seed_hit_deque_array.h>

Inheritance diagram for nvbio::bowtie2::cuda::SeedHitDequeArray:

Public Types
typedef SeedHitDequeArrayDeviceStorage::hits_storage_type	hits_storage_type
typedef SeedHitDequeArrayDeviceStorage::index_storage_type	index_storage_type
typedef SeedHitDequeArrayDeviceStorage::prob_storage_type	prob_storage_type
typedef SeedHitDequeArrayDeviceView	device_view_type
Public Types inherited from nvbio::bowtie2::cuda::SeedHitDequeArrayDeviceStorage
typedef thrust::device_vector < SeedHit >	hits_storage_type
typedef thrust::device_vector < uint32 >	index_storage_type
typedef thrust::device_vector < float >	prob_storage_type

Public Methods
uint64	resize (const uint32 n_reads, const uint32 max_hits, const bool do_alloc=true)
void	clear_deques ()
SeedHitDequeArrayDeviceView	device_view ()
hits_storage_type &	hits ()
index_storage_type &	counts ()
index_storage_type &	index ()
prob_storage_type &	probs ()

Additional Inherited Members
Public Members inherited from nvbio::bowtie2::cuda::SeedHitDequeArrayDeviceStorage
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 SeedHitDequeArrayDeviceView nvbio::bowtie2::cuda::SeedHitDequeArray::device_view_type

Definition at line 122 of file seed_hit_deque_array.h.

typedef SeedHitDequeArrayDeviceStorage::hits_storage_type nvbio::bowtie2::cuda::SeedHitDequeArray::hits_storage_type

Definition at line 118 of file seed_hit_deque_array.h.

typedef SeedHitDequeArrayDeviceStorage::index_storage_type nvbio::bowtie2::cuda::SeedHitDequeArray::index_storage_type

Definition at line 119 of file seed_hit_deque_array.h.

typedef SeedHitDequeArrayDeviceStorage::prob_storage_type nvbio::bowtie2::cuda::SeedHitDequeArray::prob_storage_type

Definition at line 120 of file seed_hit_deque_array.h.

Member Function Documentation

void nvbio::bowtie2::cuda::SeedHitDequeArray::clear_deques

(

)

clear all deques

index_storage_type& nvbio::bowtie2::cuda::SeedHitDequeArray::counts ( )

inline

return the counts vector

Definition at line 143 of file seed_hit_deque_array.h.

SeedHitDequeArrayDeviceView nvbio::bowtie2::cuda::SeedHitDequeArray::device_view ( )

inline

return the device view

Definition at line 35 of file seed_hit_deque_array_inl.h.

hits_storage_type& nvbio::bowtie2::cuda::SeedHitDequeArray::hits ( )

inline

return the hits vector

Definition at line 139 of file seed_hit_deque_array.h.

index_storage_type& nvbio::bowtie2::cuda::SeedHitDequeArray::index ( )

inline

return the index vector

Definition at line 147 of file seed_hit_deque_array.h.

prob_storage_type& nvbio::bowtie2::cuda::SeedHitDequeArray::probs ( )

inline

return the probs vector

Definition at line 151 of file seed_hit_deque_array.h.

uint64 nvbio::bowtie2::cuda::SeedHitDequeArray::resize	(	const uint32	n_reads,
		const uint32	max_hits,
		const bool	do_alloc = true
	)

resize the arena

Returns

# of allocated bytes

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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