nvbio::bowtie2::cuda::HitQueuesDeviceView Struct Reference

Detailed description

A view of the HitQueues class

Definition at line 255 of file scoring_queues.h.

#include <scoring_queues.h>

Public Types
typedef device_view_subtype < HitQueues::index_storage_type > ::type	index_storage_type
typedef device_view_subtype < HitQueues::seed_storage_type > ::type	seed_storage_type
typedef device_view_subtype < HitQueues::ssa_storage_type > ::type	ssa_storage_type
typedef device_view_subtype < HitQueues::loc_storage_type > ::type	loc_storage_type
typedef device_view_subtype < HitQueues::score_storage_type > ::type	score_storage_type
typedef device_view_subtype < HitQueues::sink_storage_type > ::type	sink_storage_type
typedef HitQueuesDeviceView	device_view_type
	view subtype More...
typedef HitReference < HitQueuesDeviceView >	reference
	reference subtype More...

Public Methods
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE	HitQueuesDeviceView (index_storage_type _read_id=index_storage_type(), seed_storage_type _seed=seed_storage_type(), ssa_storage_type _ssa=ssa_storage_type(), loc_storage_type _loc=loc_storage_type(), score_storage_type _score=score_storage_type(), sink_storage_type _sink=sink_storage_type(), loc_storage_type _opposite_loc=loc_storage_type(), score_storage_type _opposite_score=score_storage_type(), sink_storage_type _opposite_sink=sink_storage_type(), score_storage_type _opposite_score2=score_storage_type(), sink_storage_type _opposite_sink2=sink_storage_type())
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE HitReference < HitQueuesDeviceView >	operator[] (const uint32 i)
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE HitReference < HitQueuesDeviceView >	operator[] (const uint32 i) const

Public Members
index_storage_type	read_id
	hit -> read mapping More...
seed_storage_type	seed
	hit info More...
ssa_storage_type	ssa
	hit ssa info More...
loc_storage_type	loc
	hit locations More...
score_storage_type	score
	hit scores More...
sink_storage_type	sink
	hit sinks More...
loc_storage_type	opposite_loc
	hit locations, opposite mate More...
score_storage_type	opposite_score
	hit scores, opposite mate More...
sink_storage_type	opposite_sink
	hit sinks, opposite mate More...
score_storage_type	opposite_score2
	hit scores, opposite mate More...
sink_storage_type	opposite_sink2
	hit sinks, opposite mate More...

Member Typedef Documentation

typedef HitQueuesDeviceView nvbio::bowtie2::cuda::HitQueuesDeviceView::device_view_type

view subtype

Definition at line 264 of file scoring_queues.h.

typedef device_view_subtype<HitQueues::index_storage_type>::type nvbio::bowtie2::cuda::HitQueuesDeviceView::index_storage_type

Definition at line 257 of file scoring_queues.h.

typedef device_view_subtype<HitQueues::loc_storage_type>::type nvbio::bowtie2::cuda::HitQueuesDeviceView::loc_storage_type

Definition at line 260 of file scoring_queues.h.

typedef HitReference<HitQueuesDeviceView> nvbio::bowtie2::cuda::HitQueuesDeviceView::reference

reference subtype

Definition at line 265 of file scoring_queues.h.

typedef device_view_subtype<HitQueues::score_storage_type>::type nvbio::bowtie2::cuda::HitQueuesDeviceView::score_storage_type

Definition at line 261 of file scoring_queues.h.

typedef device_view_subtype<HitQueues::seed_storage_type>::type nvbio::bowtie2::cuda::HitQueuesDeviceView::seed_storage_type

Definition at line 258 of file scoring_queues.h.

typedef device_view_subtype<HitQueues::sink_storage_type>::type nvbio::bowtie2::cuda::HitQueuesDeviceView::sink_storage_type

Definition at line 262 of file scoring_queues.h.

typedef device_view_subtype<HitQueues::ssa_storage_type>::type nvbio::bowtie2::cuda::HitQueuesDeviceView::ssa_storage_type

Definition at line 259 of file scoring_queues.h.

Constructor & Destructor Documentation

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE nvbio::bowtie2::cuda::HitQueuesDeviceView::HitQueuesDeviceView	(	index_storage_type	_read_id = index_storage_type(),
		seed_storage_type	_seed = seed_storage_type(),
		ssa_storage_type	_ssa = ssa_storage_type(),
		loc_storage_type	_loc = loc_storage_type(),
		score_storage_type	_score = score_storage_type(),
		sink_storage_type	_sink = sink_storage_type(),
		loc_storage_type	_opposite_loc = loc_storage_type(),
		score_storage_type	_opposite_score = score_storage_type(),
		sink_storage_type	_opposite_sink = sink_storage_type(),
		score_storage_type	_opposite_score2 = score_storage_type(),
		sink_storage_type	_opposite_sink2 = sink_storage_type()
	)

constructor

Definition at line 121 of file scoring_queues_inl.h.

Member Function Documentation

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE HitReference< HitQueuesDeviceView > nvbio::bowtie2::cuda::HitQueuesDeviceView::operator[]

(

const uint32

i)

return a reference to a given hit

Definition at line 161 of file scoring_queues_inl.h.

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE HitReference< HitQueuesDeviceView > nvbio::bowtie2::cuda::HitQueuesDeviceView::operator[]

(

const uint32

i)

const

return a reference to a given hit

Definition at line 169 of file scoring_queues_inl.h.

Member Data Documentation

loc_storage_type nvbio::bowtie2::cuda::HitQueuesDeviceView::loc

hit locations

Definition at line 296 of file scoring_queues.h.

loc_storage_type nvbio::bowtie2::cuda::HitQueuesDeviceView::opposite_loc

hit locations, opposite mate

Definition at line 299 of file scoring_queues.h.

score_storage_type nvbio::bowtie2::cuda::HitQueuesDeviceView::opposite_score

hit scores, opposite mate

Definition at line 300 of file scoring_queues.h.

score_storage_type nvbio::bowtie2::cuda::HitQueuesDeviceView::opposite_score2

hit scores, opposite mate

Definition at line 302 of file scoring_queues.h.

sink_storage_type nvbio::bowtie2::cuda::HitQueuesDeviceView::opposite_sink

hit sinks, opposite mate

Definition at line 301 of file scoring_queues.h.

sink_storage_type nvbio::bowtie2::cuda::HitQueuesDeviceView::opposite_sink2

hit sinks, opposite mate

Definition at line 303 of file scoring_queues.h.

index_storage_type nvbio::bowtie2::cuda::HitQueuesDeviceView::read_id

hit -> read mapping

Definition at line 293 of file scoring_queues.h.

score_storage_type nvbio::bowtie2::cuda::HitQueuesDeviceView::score

hit scores

Definition at line 297 of file scoring_queues.h.

seed_storage_type nvbio::bowtie2::cuda::HitQueuesDeviceView::seed

hit info

Definition at line 294 of file scoring_queues.h.

sink_storage_type nvbio::bowtie2::cuda::HitQueuesDeviceView::sink

hit sinks

Definition at line 298 of file scoring_queues.h.

ssa_storage_type nvbio::bowtie2::cuda::HitQueuesDeviceView::ssa

hit ssa info

Definition at line 295 of file scoring_queues.h.

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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