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

Detailed description

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

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

Definition at line 180 of file pipeline_states.h.

#include <pipeline_states.h>

Inheritance diagram for nvbio::bowtie2::cuda::AllMappingPipelineState< 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
	AllMappingPipelineState (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 *	output_read_info
uint32 *	buffer_read_info
io::Alignment *	buffer_alignments
nvbio::VectorArrayView< io::Cigar >	cigar
	cigar arena More...
uint2 *	cigar_coords
	cigar coords More...
nvbio::VectorArrayView< uint8 >	mds
	mds arena More...
uint8 *	dp_buffer
	DP buffer. More...
uint64	dp_buffer_size
	DP buffer size. More...
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::AllMappingPipelineState< ScoringScheme >::base_type

Definition at line 182 of file pipeline_states.h.

template<typename ScoringScheme>

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

Definition at line 183 of file pipeline_states.h.

template<typename ScoringScheme>

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

Definition at line 186 of file pipeline_states.h.

template<typename ScoringScheme>

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

Definition at line 185 of file pipeline_states.h.

template<typename ScoringScheme>

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

Definition at line 184 of file pipeline_states.h.

template<typename ScoringScheme>

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

Definition at line 187 of file pipeline_states.h.

Constructor & Destructor Documentation

template<typename ScoringScheme>

nvbio::bowtie2::cuda::AllMappingPipelineState< ScoringScheme >::AllMappingPipelineState ( 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 189 of file pipeline_states.h.

Member Data Documentation

template<typename ScoringScheme>

io::Alignment* nvbio::bowtie2::cuda::AllMappingPipelineState< ScoringScheme >::buffer_alignments

Definition at line 223 of file pipeline_states.h.

template<typename ScoringScheme>

uint32* nvbio::bowtie2::cuda::AllMappingPipelineState< ScoringScheme >::buffer_read_info

Definition at line 222 of file pipeline_states.h.

template<typename ScoringScheme>

nvbio::VectorArrayView<io::Cigar> nvbio::bowtie2::cuda::AllMappingPipelineState< ScoringScheme >::cigar

cigar arena

Definition at line 225 of file pipeline_states.h.

template<typename ScoringScheme>

uint2* nvbio::bowtie2::cuda::AllMappingPipelineState< ScoringScheme >::cigar_coords

cigar coords

Definition at line 226 of file pipeline_states.h.

template<typename ScoringScheme>

uint8* nvbio::bowtie2::cuda::AllMappingPipelineState< ScoringScheme >::dp_buffer

DP buffer.

Definition at line 229 of file pipeline_states.h.

template<typename ScoringScheme>

uint64 nvbio::bowtie2::cuda::AllMappingPipelineState< ScoringScheme >::dp_buffer_size

DP buffer size.

Definition at line 230 of file pipeline_states.h.

template<typename ScoringScheme>

nvbio::VectorArrayView<uint8> nvbio::bowtie2::cuda::AllMappingPipelineState< ScoringScheme >::mds

mds arena

Definition at line 227 of file pipeline_states.h.

template<typename ScoringScheme>

uint32* nvbio::bowtie2::cuda::AllMappingPipelineState< ScoringScheme >::output_read_info

Definition at line 221 of file pipeline_states.h.

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

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