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nvbio::bowtie2::cuda::BaseScoringPipelineState< ScoringScheme > Struct Template Reference
Pipeline States

Detailed description

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

Base pipeline state object that other scoring pipeline classes will inherit from (see Pipeline States).

Definition at line 42 of file locate.h.

#include <locate.h>

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

Public Types

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

 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

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 Aligner::fmi_type nvbio::bowtie2::cuda::BaseScoringPipelineState< ScoringScheme >::fmi_type

Definition at line 61 of file pipeline_states.h.

template<typename ScoringScheme>
typedef Aligner::genome_iterator nvbio::bowtie2::cuda::BaseScoringPipelineState< ScoringScheme >::genome_iterator

Definition at line 64 of file pipeline_states.h.

template<typename ScoringScheme>
typedef Aligner::read_batch_type nvbio::bowtie2::cuda::BaseScoringPipelineState< ScoringScheme >::read_batch_type

Definition at line 63 of file pipeline_states.h.

template<typename ScoringScheme>
typedef Aligner::rfmi_type nvbio::bowtie2::cuda::BaseScoringPipelineState< ScoringScheme >::rfmi_type

Definition at line 62 of file pipeline_states.h.

template<typename ScoringScheme>
typedef ScoringScheme nvbio::bowtie2::cuda::BaseScoringPipelineState< ScoringScheme >::scheme_type

Definition at line 65 of file pipeline_states.h.

Constructor & Destructor Documentation

template<typename ScoringScheme>
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 
)
inline

Definition at line 67 of file pipeline_states.h.

Member Function Documentation

template<typename ScoringScheme>
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE const read_batch_type& nvbio::bowtie2::cuda::BaseScoringPipelineState< ScoringScheme >::get_reads ( const uint32  mate) const
inline

return the set of reads corresponding to a given mate

Definition at line 97 of file pipeline_states.h.

Member Data Documentation

template<typename ScoringScheme>
const uint32 nvbio::bowtie2::cuda::BaseScoringPipelineState< ScoringScheme >::anchor

Definition at line 99 of file pipeline_states.h.

template<typename ScoringScheme>
uint8* nvbio::bowtie2::cuda::BaseScoringPipelineState< ScoringScheme >::dp_buffer

Definition at line 119 of file pipeline_states.h.

template<typename ScoringScheme>
uint64 nvbio::bowtie2::cuda::BaseScoringPipelineState< ScoringScheme >::dp_buffer_size

Definition at line 120 of file pipeline_states.h.

template<typename ScoringScheme>
const fmi_type nvbio::bowtie2::cuda::BaseScoringPipelineState< ScoringScheme >::fmi

Definition at line 106 of file pipeline_states.h.

template<typename ScoringScheme>
const genome_iterator nvbio::bowtie2::cuda::BaseScoringPipelineState< ScoringScheme >::genome

Definition at line 104 of file pipeline_states.h.

template<typename ScoringScheme>
const uint32 nvbio::bowtie2::cuda::BaseScoringPipelineState< ScoringScheme >::genome_length

Definition at line 103 of file pipeline_states.h.

template<typename ScoringScheme>
SeedHitDequeArrayDeviceView nvbio::bowtie2::cuda::BaseScoringPipelineState< ScoringScheme >::hits

Definition at line 109 of file pipeline_states.h.

template<typename ScoringScheme>
uint32 nvbio::bowtie2::cuda::BaseScoringPipelineState< ScoringScheme >::hits_queue_size

Definition at line 114 of file pipeline_states.h.

template<typename ScoringScheme>
uint32* nvbio::bowtie2::cuda::BaseScoringPipelineState< ScoringScheme >::idx_queue

Definition at line 115 of file pipeline_states.h.

template<typename ScoringScheme>
uint32 nvbio::bowtie2::cuda::BaseScoringPipelineState< ScoringScheme >::n_hits_per_read

Definition at line 113 of file pipeline_states.h.

template<typename ScoringScheme>
uint32* nvbio::bowtie2::cuda::BaseScoringPipelineState< ScoringScheme >::opposite_queue

Definition at line 117 of file pipeline_states.h.

template<typename ScoringScheme>
uint32 nvbio::bowtie2::cuda::BaseScoringPipelineState< ScoringScheme >::opposite_queue_size

Definition at line 116 of file pipeline_states.h.

template<typename ScoringScheme>
const read_batch_type nvbio::bowtie2::cuda::BaseScoringPipelineState< ScoringScheme >::reads

Definition at line 100 of file pipeline_states.h.

template<typename ScoringScheme>
const read_batch_type nvbio::bowtie2::cuda::BaseScoringPipelineState< ScoringScheme >::reads_o

Definition at line 101 of file pipeline_states.h.

template<typename ScoringScheme>
const rfmi_type nvbio::bowtie2::cuda::BaseScoringPipelineState< ScoringScheme >::rfmi

Definition at line 107 of file pipeline_states.h.

template<typename ScoringScheme>
const int32 nvbio::bowtie2::cuda::BaseScoringPipelineState< ScoringScheme >::score_limit

Definition at line 123 of file pipeline_states.h.

template<typename ScoringScheme>
ScoringQueuesDeviceView nvbio::bowtie2::cuda::BaseScoringPipelineState< ScoringScheme >::scoring_queues

Definition at line 111 of file pipeline_states.h.

template<typename ScoringScheme>
const ScoringScheme nvbio::bowtie2::cuda::BaseScoringPipelineState< ScoringScheme >::scoring_scheme

Definition at line 122 of file pipeline_states.h.

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