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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
typedef thrust::device_vector
< packed_seed
typedef thrust::device_vector
< uint32
typedef thrust::device_vector
< uint32
typedef thrust::device_vector
< int32
typedef thrust::device_vector
< uint32
typedef HitQueuesDeviceView device_view_type
 view subtype More...
typedef HitReference< HitQueuesreference
 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

view subtype

Definition at line 229 of file scoring_queues.h.

Definition at line 222 of file scoring_queues.h.

Definition at line 225 of file scoring_queues.h.

reference subtype

Definition at line 230 of file scoring_queues.h.

Definition at line 226 of file scoring_queues.h.

Definition at line 223 of file scoring_queues.h.

Definition at line 227 of file scoring_queues.h.

Definition at line 224 of file scoring_queues.h.

Member Function Documentation

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

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 

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.

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