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.

Classes
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 >