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

Detailed description

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

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:

Definition at line 335 of file scoring_queues.h.

#include <scoring_queues.h>

Public Types

< packed_read
typedef HitQueues hits_storage_type
typedef ReadHitsIndex read_hits_index_type
typedef thrust::device_vector
< uint32
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

Definition at line 337 of file scoring_queues.h.

Definition at line 342 of file scoring_queues.h.

Definition at line 338 of file scoring_queues.h.

Definition at line 340 of file scoring_queues.h.

Definition at line 339 of file scoring_queues.h.

Constructor & Destructor Documentation

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


Definition at line 346 of file scoring_queues.h.

Member Function Documentation

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

clear output queues

Definition at line 354 of file scoring_queues.h.

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

return a view of the data structure

Definition at line 198 of file scoring_queues_inl.h.

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

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 


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.

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