nvbio::bowtie2::cuda::BestApproxScoringPipelineState< ScoringScheme > Struct Template Reference

Detailed description

template< typename ScoringScheme>
struct nvbio::bowtie2::cuda::BestApproxScoringPipelineState< ScoringScheme >

This object encapsulates the pipeline state for scoring best-approximate alignments (see Pipeline States).

Definition at line 43 of file locate.h.

#include <locate.h>

Inheritance diagram for nvbio::bowtie2::cuda::BestApproxScoringPipelineState< ScoringScheme >:

Public Types
typedef BaseScoringPipelineState < ScoringScheme >	base_type
typedef Aligner::fmi_type	fmi_type
typedef Aligner::rfmi_type	rfmi_type
typedef Aligner::read_batch_type	read_batch_type
typedef Aligner::genome_iterator	genome_iterator
typedef ScoringScheme	scheme_type
Public Types inherited from nvbio::bowtie2::cuda::BaseScoringPipelineState< ScoringScheme >
typedef Aligner::fmi_type	fmi_type
typedef Aligner::rfmi_type	rfmi_type
typedef Aligner::read_batch_type	read_batch_type
typedef Aligner::genome_iterator	genome_iterator
typedef ScoringScheme	scheme_type

Public Methods
	BestApproxScoringPipelineState (const uint32 _anchor, const read_batch_type _reads, const read_batch_type _reads_o, const uint32 _genome_len, const genome_iterator _genome, const fmi_type _fmi, const rfmi_type _rfmi, const ScoringScheme _scoring_scheme, const int32 _score_limit, Aligner &_aligner)
Public Methods inherited from nvbio::bowtie2::cuda::BaseScoringPipelineState< ScoringScheme >
	BaseScoringPipelineState (const uint32 _anchor, const read_batch_type _reads, const read_batch_type _reads_o, const uint32 _genome_len, const genome_iterator _genome, const fmi_type _fmi, const rfmi_type _rfmi, const ScoringScheme _scoring_scheme, const int32 _score_limit, Aligner &_aligner)
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE const read_batch_type &	get_reads (const uint32 mate) const

Public Members
uint32 *	trys
uint32 *	rseeds
io::Alignment *	best_alignments
io::Alignment *	best_alignments_o
uint32	best_stride
Public Members inherited from nvbio::bowtie2::cuda::BaseScoringPipelineState< ScoringScheme >
const uint32	anchor
const read_batch_type	reads
const read_batch_type	reads_o
const uint32	genome_length
const genome_iterator	genome
const fmi_type	fmi
const rfmi_type	rfmi
SeedHitDequeArrayDeviceView	hits
ScoringQueuesDeviceView	scoring_queues
uint32	n_hits_per_read
uint32	hits_queue_size
uint32 *	idx_queue
uint32	opposite_queue_size
uint32 *	opposite_queue
uint8 *	dp_buffer
uint64	dp_buffer_size
const ScoringScheme	scoring_scheme
const int32	score_limit

Member Typedef Documentation

template<typename ScoringScheme>

typedef BaseScoringPipelineState<ScoringScheme> nvbio::bowtie2::cuda::BestApproxScoringPipelineState< ScoringScheme >::base_type

Definition at line 132 of file pipeline_states.h.

template<typename ScoringScheme>

typedef Aligner::fmi_type nvbio::bowtie2::cuda::BestApproxScoringPipelineState< ScoringScheme >::fmi_type

Definition at line 133 of file pipeline_states.h.

template<typename ScoringScheme>

typedef Aligner::genome_iterator nvbio::bowtie2::cuda::BestApproxScoringPipelineState< ScoringScheme >::genome_iterator

Definition at line 136 of file pipeline_states.h.

template<typename ScoringScheme>

typedef Aligner::read_batch_type nvbio::bowtie2::cuda::BestApproxScoringPipelineState< ScoringScheme >::read_batch_type

Definition at line 135 of file pipeline_states.h.

template<typename ScoringScheme>

typedef Aligner::rfmi_type nvbio::bowtie2::cuda::BestApproxScoringPipelineState< ScoringScheme >::rfmi_type

Definition at line 134 of file pipeline_states.h.

template<typename ScoringScheme>

typedef ScoringScheme nvbio::bowtie2::cuda::BestApproxScoringPipelineState< ScoringScheme >::scheme_type

Definition at line 137 of file pipeline_states.h.

Constructor & Destructor Documentation

template<typename ScoringScheme>

nvbio::bowtie2::cuda::BestApproxScoringPipelineState< ScoringScheme >::BestApproxScoringPipelineState ( const uint32  _anchor, const read_batch_type  _reads, const read_batch_type  _reads_o, const uint32  _genome_len, const genome_iterator  _genome, const fmi_type  _fmi, const rfmi_type  _rfmi, const ScoringScheme  _scoring_scheme, const int32  _score_limit, Aligner &  _aligner  )

inline

Definition at line 139 of file pipeline_states.h.

Member Data Documentation

template<typename ScoringScheme>

io::Alignment* nvbio::bowtie2::cuda::BestApproxScoringPipelineState< ScoringScheme >::best_alignments

Definition at line 171 of file pipeline_states.h.

template<typename ScoringScheme>

io::Alignment* nvbio::bowtie2::cuda::BestApproxScoringPipelineState< ScoringScheme >::best_alignments_o

Definition at line 172 of file pipeline_states.h.

template<typename ScoringScheme>

uint32 nvbio::bowtie2::cuda::BestApproxScoringPipelineState< ScoringScheme >::best_stride

Definition at line 173 of file pipeline_states.h.

template<typename ScoringScheme>

uint32* nvbio::bowtie2::cuda::BestApproxScoringPipelineState< ScoringScheme >::rseeds

Definition at line 169 of file pipeline_states.h.

template<typename ScoringScheme>

uint32* nvbio::bowtie2::cuda::BestApproxScoringPipelineState< ScoringScheme >::trys

Definition at line 168 of file pipeline_states.h.

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

• E:/git/nvbio/nvBowtie/bowtie2/cuda/locate.h
• E:/git/nvbio/nvBowtie/bowtie2/cuda/pipeline_states.h