nvbio::bowtie2::cuda::ReadHitsIndexDeviceView Struct Reference

Detailed description

This data structure represents a collection of hit arrays bound to a set of reads. For each read it stores an array of hits of arbitrary length.

Definition at line 135 of file scoring_queues.h.

#include <scoring_queues.h>

Classes
struct	HitArray

Public Types
typedef device_view_subtype < ReadHitsIndex::links_storage_type > ::type	links_storage_type
typedef HitArray	reference

Public Methods
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE	ReadHitsIndexDeviceView (links_storage_type links=links_storage_type(), const uint32 stride=0u)
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32	hit_count (const uint32 read_index) const
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void	set_hit_count (const uint32 read_index, const uint32 count)
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32 &	operator() (const uint32 read_index, const uint32 slot)
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32	operator() (const uint32 read_index, const uint32 slot) const
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE HitArray	operator[] (const uint32 read_index)

Public Members
links_storage_type	m_links
uint32	m_stride

Friends
struct	HitArray

Member Typedef Documentation

typedef device_view_subtype<ReadHitsIndex::links_storage_type>::type nvbio::bowtie2::cuda::ReadHitsIndexDeviceView::links_storage_type

Definition at line 137 of file scoring_queues.h.

typedef HitArray nvbio::bowtie2::cuda::ReadHitsIndexDeviceView::reference

Definition at line 175 of file scoring_queues.h.

Constructor & Destructor Documentation

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE nvbio::bowtie2::cuda::ReadHitsIndexDeviceView::ReadHitsIndexDeviceView ( links_storage_type  links = links_storage_type(), const uint32  stride = 0u  )

inline

constructor

Definition at line 181 of file scoring_queues.h.

Member Function Documentation

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32 nvbio::bowtie2::cuda::ReadHitsIndexDeviceView::hit_count ( const uint32  read_index) const

inline

return the number of hits bound to a read

Definition at line 188 of file scoring_queues.h.

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32& nvbio::bowtie2::cuda::ReadHitsIndexDeviceView::operator() ( const uint32  read_index, const uint32  slot  )

inline

return the i-th hit link bound to a given read

Definition at line 198 of file scoring_queues.h.

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32 nvbio::bowtie2::cuda::ReadHitsIndexDeviceView::operator() ( const uint32  read_index, const uint32  slot  ) const

inline

return the i-th hit link bound to a given read

Definition at line 203 of file scoring_queues.h.

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE HitArray nvbio::bowtie2::cuda::ReadHitsIndexDeviceView::operator[] ( const uint32  read_index)

inline

return the hit array bound to a given read

Definition at line 208 of file scoring_queues.h.

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void nvbio::bowtie2::cuda::ReadHitsIndexDeviceView::set_hit_count ( const uint32  read_index, const uint32  count  )

inline

setup the number of hits

Definition at line 193 of file scoring_queues.h.

Friends And Related Function Documentation

friend struct HitArray

friend

Definition at line 214 of file scoring_queues.h.

Member Data Documentation

links_storage_type nvbio::bowtie2::cuda::ReadHitsIndexDeviceView::m_links

Definition at line 211 of file scoring_queues.h.

uint32 nvbio::bowtie2::cuda::ReadHitsIndexDeviceView::m_stride

Definition at line 212 of file scoring_queues.h.

---

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

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