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

HitQueuesType

can 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

hits	hits container
hit_index	index 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.

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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