nvbio::bowtie2::cuda::ScoringQueues Struct Reference

Detailed description

The collection of queues needed by the scoring pipeline. Particularly:

• a ping-pong set of input/output active-read queues, storing information about the read-id and some flags representing their pipeline state.
• a set of hits, and a read->hits index these can essentially be seen as forming a nested sequence of hits, with a variable length set of hits bound to each read.

The scoring pipeline is essentially a two-stage self-feeding loop:

In the first stage, a certain amount of hits are selected for scoring for each input active-read. Reads for which no hits are selected become inactive, and reads which stay active are output to the output queue together with their hits.

In the second stage, the queues are swapped, the output queue becomes the input, and the hits bound ot each active read gets scored.

This class provides two accessors to represent:

• "references" to the reads in the input queue (ReadHitsReference), and
• "binders" to reads in the output queue (ReadHitsBinder), useful for binding output reads in the first stage.

Definition at line 335 of file scoring_queues.h.

#include <scoring_queues.h>

Public Types
typedef nvbio::cuda::PingPongQueues < packed_read >	active_reads_storage_type
typedef HitQueues	hits_storage_type
typedef ReadHitsIndex	read_hits_index_type
typedef thrust::device_vector < uint32 >	pool_type
typedef ScoringQueuesDeviceView	device_view_type

Public Methods
	ScoringQueues ()
uint64	resize (const uint32 n_reads, const uint32 n_hits, const bool do_alloc)
void	clear_output ()
uint32	hits_count ()
ScoringQueuesDeviceView	device_view ()

Public Members
active_reads_storage_type	active_reads
	set of active reads More...
hits_storage_type	hits
	nested sequence More...
read_hits_index_type	hits_index
	read -> hits mapping More...
pool_type	hits_pool
	pool counter More...

Member Typedef Documentation

typedef nvbio::cuda::PingPongQueues<packed_read> nvbio::bowtie2::cuda::ScoringQueues::active_reads_storage_type

Definition at line 337 of file scoring_queues.h.

typedef ScoringQueuesDeviceView nvbio::bowtie2::cuda::ScoringQueues::device_view_type

Definition at line 342 of file scoring_queues.h.

typedef HitQueues nvbio::bowtie2::cuda::ScoringQueues::hits_storage_type

Definition at line 338 of file scoring_queues.h.

typedef thrust::device_vector<uint32> nvbio::bowtie2::cuda::ScoringQueues::pool_type

Definition at line 340 of file scoring_queues.h.

typedef ReadHitsIndex nvbio::bowtie2::cuda::ScoringQueues::read_hits_index_type

Definition at line 339 of file scoring_queues.h.

Constructor & Destructor Documentation

nvbio::bowtie2::cuda::ScoringQueues::ScoringQueues ( )

inline

constructor

Definition at line 346 of file scoring_queues.h.

Member Function Documentation

void nvbio::bowtie2::cuda::ScoringQueues::clear_output ( )

inline

clear output queues

Definition at line 354 of file scoring_queues.h.

ScoringQueuesDeviceView nvbio::bowtie2::cuda::ScoringQueues::device_view ( )

inline

return a view of the data structure

Definition at line 198 of file scoring_queues_inl.h.

uint32 nvbio::bowtie2::cuda::ScoringQueues::hits_count ( )

inline

return the number of allocated hits

Definition at line 358 of file scoring_queues.h.

uint64 nvbio::bowtie2::cuda::ScoringQueues::resize ( const uint32  n_reads, const uint32  n_hits, const bool  do_alloc  )

inline

resize

Definition at line 149 of file scoring_queues_inl.h.

Member Data Documentation

active_reads_storage_type nvbio::bowtie2::cuda::ScoringQueues::active_reads

set of active reads

Definition at line 364 of file scoring_queues.h.

hits_storage_type nvbio::bowtie2::cuda::ScoringQueues::hits

nested sequence

Definition at line 365 of file scoring_queues.h.

read_hits_index_type nvbio::bowtie2::cuda::ScoringQueues::hits_index

read -> hits mapping

Definition at line 366 of file scoring_queues.h.

pool_type nvbio::bowtie2::cuda::ScoringQueues::hits_pool

pool counter

Definition at line 367 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