nvbio::bowtie2::cuda::HitQueues Struct Reference

Detailed description

The collection of queues defining the set of hits - each queue holds one element/attribute per hit

Definition at line 220 of file scoring_queues.h.

#include <scoring_queues.h>

Public Types
typedef thrust::device_vector < uint32 >	index_storage_type
typedef thrust::device_vector < packed_seed >	seed_storage_type
typedef thrust::device_vector < uint32 >	ssa_storage_type
typedef thrust::device_vector < uint32 >	loc_storage_type
typedef thrust::device_vector < int32 >	score_storage_type
typedef thrust::device_vector < uint32 >	sink_storage_type
typedef HitQueuesDeviceView	device_view_type
	view subtype More...
typedef HitReference< HitQueues >	reference
	reference subtype More...

Public Methods
uint64	resize (const uint32 size, const bool do_alloc)
HitQueuesDeviceView	device_view ()

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::HitQueues::device_view_type

view subtype

Definition at line 229 of file scoring_queues.h.

typedef thrust::device_vector<uint32> nvbio::bowtie2::cuda::HitQueues::index_storage_type

Definition at line 222 of file scoring_queues.h.

typedef thrust::device_vector<uint32> nvbio::bowtie2::cuda::HitQueues::loc_storage_type

Definition at line 225 of file scoring_queues.h.

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

reference subtype

Definition at line 230 of file scoring_queues.h.

typedef thrust::device_vector<int32> nvbio::bowtie2::cuda::HitQueues::score_storage_type

Definition at line 226 of file scoring_queues.h.

typedef thrust::device_vector<packed_seed> nvbio::bowtie2::cuda::HitQueues::seed_storage_type

Definition at line 223 of file scoring_queues.h.

typedef thrust::device_vector<uint32> nvbio::bowtie2::cuda::HitQueues::sink_storage_type

Definition at line 227 of file scoring_queues.h.

typedef thrust::device_vector<uint32> nvbio::bowtie2::cuda::HitQueues::ssa_storage_type

Definition at line 224 of file scoring_queues.h.

Member Function Documentation

HitQueuesDeviceView nvbio::bowtie2::cuda::HitQueues::device_view ( )

inline

return a view of the data structure

Definition at line 102 of file scoring_queues_inl.h.

uint64 nvbio::bowtie2::cuda::HitQueues::resize ( const uint32  size, const bool  do_alloc  )

inline

resize all queues

Definition at line 82 of file scoring_queues_inl.h.

Member Data Documentation

loc_storage_type nvbio::bowtie2::cuda::HitQueues::loc

hit locations

Definition at line 243 of file scoring_queues.h.

loc_storage_type nvbio::bowtie2::cuda::HitQueues::opposite_loc

hit locations, opposite mate

Definition at line 246 of file scoring_queues.h.

score_storage_type nvbio::bowtie2::cuda::HitQueues::opposite_score

hit scores, opposite mate

Definition at line 247 of file scoring_queues.h.

score_storage_type nvbio::bowtie2::cuda::HitQueues::opposite_score2

hit scores, opposite mate

Definition at line 249 of file scoring_queues.h.

sink_storage_type nvbio::bowtie2::cuda::HitQueues::opposite_sink

hit sinks, opposite mate

Definition at line 248 of file scoring_queues.h.

sink_storage_type nvbio::bowtie2::cuda::HitQueues::opposite_sink2

hit sinks, opposite mate

Definition at line 250 of file scoring_queues.h.

index_storage_type nvbio::bowtie2::cuda::HitQueues::read_id

hit -> read mapping

Definition at line 240 of file scoring_queues.h.

score_storage_type nvbio::bowtie2::cuda::HitQueues::score

hit scores

Definition at line 244 of file scoring_queues.h.

seed_storage_type nvbio::bowtie2::cuda::HitQueues::seed

hit info

Definition at line 241 of file scoring_queues.h.

sink_storage_type nvbio::bowtie2::cuda::HitQueues::sink

hit sinks

Definition at line 245 of file scoring_queues.h.

ssa_storage_type nvbio::bowtie2::cuda::HitQueues::ssa

hit ssa info

Definition at line 242 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