cufmi::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 67 of file proposal.h.

#include <proposal.h>

Classes
struct	HitArray

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

Public Methods
CUFMI_FORCEINLINE CUFMI_HOST_DEVICE	ReadHitsIndexDeviceView (uint32 *links=NULL, const uint32 links_stride=0u)
CUFMI_FORCEINLINE CUFMI_HOST_DEVICE uint32	hit_count (const uint32 read_idx) const
CUFMI_FORCEINLINE CUFMI_HOST_DEVICE void	set_hit_count (const uint32 read_index, const uint32 count)
CUFMI_FORCEINLINE CUFMI_HOST_DEVICE uint32 &	operator() (const uint32 read_index, const uint32 slot)
CUFMI_FORCEINLINE CUFMI_HOST_DEVICE uint32	operator() (const uint32 read_index, const uint32 slot) const
CUFMI_FORCEINLINE CUFMI_HOST_DEVICE HitArray	operator[] (const uint32 read_index) const

Friends
struct	HitArray

Member Typedef Documentation

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

Definition at line 69 of file proposal.h.

Constructor & Destructor Documentation

CUFMI_FORCEINLINE CUFMI_HOST_DEVICE cufmi::bowtie2::cuda::ReadHitsIndexDeviceView::ReadHitsIndexDeviceView	(	uint32 *	links = NULL,
		const uint32	links_stride = 0u
	)

constructor

Member Function Documentation

CUFMI_FORCEINLINE CUFMI_HOST_DEVICE uint32 cufmi::bowtie2::cuda::ReadHitsIndexDeviceView::hit_count ( const uint32  read_idx) const

inline

return the number of hits bound to a read

Definition at line 106 of file proposal.h.

CUFMI_FORCEINLINE CUFMI_HOST_DEVICE uint32& cufmi::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 116 of file proposal.h.

CUFMI_FORCEINLINE CUFMI_HOST_DEVICE uint32 cufmi::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 121 of file proposal.h.

CUFMI_FORCEINLINE CUFMI_HOST_DEVICE HitArray cufmi::bowtie2::cuda::ReadHitsIndexDeviceView::operator[] ( const uint32  read_index) const

inline

return the hit array bound to a given read

Definition at line 126 of file proposal.h.

CUFMI_FORCEINLINE CUFMI_HOST_DEVICE void cufmi::bowtie2::cuda::ReadHitsIndexDeviceView::set_hit_count ( const uint32  read_index, const uint32  count  )

inline

setup the number of hits

Definition at line 111 of file proposal.h.

Friends And Related Function Documentation

friend struct HitArray

friend

Definition at line 132 of file proposal.h.

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

• E:/git/nvbio/vs/proposal.h