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nvbio::bowtie2::cuda::HitReference< HitQueuesType > Struct Template Reference

Detailed description

template< typename HitQueuesType>
struct nvbio::bowtie2::cuda::HitReference< HitQueuesType >

A reference to a hit

Template Parameters
HitQueuesTypecan be either HitQueues or HitQueuesView.

Definition at line 65 of file scoring_queues.h.

#include <scoring_queues.h>

Public Types

typedef reference_subtype
< typename
HitQueuesType::index_storage_type >
::type 
index_type
 
typedef reference_subtype
< typename
HitQueuesType::seed_storage_type >
::type 
seed_type
 
typedef reference_subtype
< typename
HitQueuesType::ssa_storage_type >
::type 
ssa_type
 
typedef reference_subtype
< typename
HitQueuesType::loc_storage_type >
::type 
loc_type
 
typedef reference_subtype
< typename
HitQueuesType::score_storage_type >
::type 
score_type
 
typedef reference_subtype
< typename
HitQueuesType::sink_storage_type >
::type 
sink_type
 

Public Methods

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE HitReference (HitQueuesType &hits, const uint32 hit_index)
 

Public Members

index_type read_id
 parent read index More...
 
seed_type seed
 seed reference More...
 
ssa_type ssa
 ssa reference More...
 
loc_type loc
 loc reference More...
 
score_type score
 score reference More...
 
sink_type sink
 sink reference More...
 
loc_type opposite_loc
 opposite mate's loc reference More...
 
score_type opposite_score
 opposite mate's score reference More...
 
sink_type opposite_sink
 opposite mate's sink reference More...
 
score_type opposite_score2
 opposite mate's score reference More...
 
sink_type opposite_sink2
 opposite mate's sink reference More...
 

Member Typedef Documentation

template<typename HitQueuesType>
typedef reference_subtype<typename HitQueuesType::index_storage_type>::type nvbio::bowtie2::cuda::HitReference< HitQueuesType >::index_type

Definition at line 417 of file scoring_queues.h.

template<typename HitQueuesType>
typedef reference_subtype<typename HitQueuesType::loc_storage_type>::type nvbio::bowtie2::cuda::HitReference< HitQueuesType >::loc_type

Definition at line 420 of file scoring_queues.h.

template<typename HitQueuesType>
typedef reference_subtype<typename HitQueuesType::score_storage_type>::type nvbio::bowtie2::cuda::HitReference< HitQueuesType >::score_type

Definition at line 421 of file scoring_queues.h.

template<typename HitQueuesType>
typedef reference_subtype<typename HitQueuesType::seed_storage_type>::type nvbio::bowtie2::cuda::HitReference< HitQueuesType >::seed_type

Definition at line 418 of file scoring_queues.h.

template<typename HitQueuesType>
typedef reference_subtype<typename HitQueuesType::sink_storage_type>::type nvbio::bowtie2::cuda::HitReference< HitQueuesType >::sink_type

Definition at line 422 of file scoring_queues.h.

template<typename HitQueuesType>
typedef reference_subtype<typename HitQueuesType::ssa_storage_type>::type nvbio::bowtie2::cuda::HitReference< HitQueuesType >::ssa_type

Definition at line 419 of file scoring_queues.h.

Constructor & Destructor Documentation

template<typename HitQueuesType >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE nvbio::bowtie2::cuda::HitReference< HitQueuesType >::HitReference ( HitQueuesType &  hits,
const uint32  hit_index 
)

constructor

Parameters
hitshits container
hit_indexindex of this hit

Definition at line 181 of file scoring_queues_inl.h.

Member Data Documentation

template<typename HitQueuesType>
loc_type nvbio::bowtie2::cuda::HitReference< HitQueuesType >::loc

loc reference

Definition at line 434 of file scoring_queues.h.

template<typename HitQueuesType>
loc_type nvbio::bowtie2::cuda::HitReference< HitQueuesType >::opposite_loc

opposite mate's loc reference

Definition at line 437 of file scoring_queues.h.

template<typename HitQueuesType>
score_type nvbio::bowtie2::cuda::HitReference< HitQueuesType >::opposite_score

opposite mate's score reference

Definition at line 438 of file scoring_queues.h.

template<typename HitQueuesType>
score_type nvbio::bowtie2::cuda::HitReference< HitQueuesType >::opposite_score2

opposite mate's score reference

Definition at line 440 of file scoring_queues.h.

template<typename HitQueuesType>
sink_type nvbio::bowtie2::cuda::HitReference< HitQueuesType >::opposite_sink

opposite mate's sink reference

Definition at line 439 of file scoring_queues.h.

template<typename HitQueuesType>
sink_type nvbio::bowtie2::cuda::HitReference< HitQueuesType >::opposite_sink2

opposite mate's sink reference

Definition at line 441 of file scoring_queues.h.

template<typename HitQueuesType>
index_type nvbio::bowtie2::cuda::HitReference< HitQueuesType >::read_id

parent read index

Definition at line 431 of file scoring_queues.h.

template<typename HitQueuesType>
score_type nvbio::bowtie2::cuda::HitReference< HitQueuesType >::score

score reference

Definition at line 435 of file scoring_queues.h.

template<typename HitQueuesType>
seed_type nvbio::bowtie2::cuda::HitReference< HitQueuesType >::seed

seed reference

Definition at line 432 of file scoring_queues.h.

template<typename HitQueuesType>
sink_type nvbio::bowtie2::cuda::HitReference< HitQueuesType >::sink

sink reference

Definition at line 436 of file scoring_queues.h.

template<typename HitQueuesType>
ssa_type nvbio::bowtie2::cuda::HitReference< HitQueuesType >::ssa

ssa reference

Definition at line 433 of file scoring_queues.h.


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