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Scoring Queues

Detailed Description

This module contains a set of classes used to represent the scoring queues employed throughout all of nvBowtie in best mapping mode. Conceptually, the queues (ScoringQueues) represent a set of "active" reads, and a nested sequence of variable length seed hit lists bound to the active reads.

The hits (HitQueues) in turn are represented by a set of attributes that are computed during different pipeline stages: the hit location, its RC flags, its alignment score, its alignment sink, and so on.

In order to achieve maximum access performance, all of these attributes are stored in SOA layout: the classes in this module serve the purpose of providing a structured AOS-like view over the raw data.


struct  nvbio::bowtie2::cuda::HitReference< HitQueuesType >
struct  nvbio::bowtie2::cuda::ReadHitReference< ScoringQueuesType >
struct  nvbio::bowtie2::cuda::ReadHitBinder< ScoringQueuesType >
struct  nvbio::bowtie2::cuda::ReadHitsIndex
struct  nvbio::bowtie2::cuda::ReadHitsIndexDeviceView
struct  nvbio::bowtie2::cuda::HitQueues
struct  nvbio::bowtie2::cuda::HitQueuesDeviceView
struct  nvbio::bowtie2::cuda::ScoringQueues
struct  nvbio::bowtie2::cuda::ScoringQueuesDeviceView
struct  nvbio::bowtie2::cuda::ReadHitsReference< ScoringQueuesType >
struct  nvbio::bowtie2::cuda::ReadHitsBinder< ScoringQueuesType >