Detailed description

Represents a seed match in the FM-index as an SA range, tracking the direction of the read and that of the FM-index.

Definition at line 54 of file seed_hit.h.

#include <seed_hit.h>

Classes
struct	Flags

Public Methods
NVBIO_HOST_DEVICE NVBIO_FORCEINLINE	SeedHit ()

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE	SeedHit (const ReadType readtype, const DirType indexdir, const uint32 pos, const uint2 &range)

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE	SeedHit (const Flags flags, const uint2 &range)

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void	set_range (const uint2 range)

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint2	get_range () const

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE bool	empty () const

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32	get_range_size () const

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32	front () const

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32	back () const

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32	pop_front ()

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32	pop_front (const uint32 n)

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32	pop_back ()

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32	pop_back (const uint32 n)

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void	set_posinread (const uint32 p)

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void	set_readtype (const ReadType d)

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void	set_indexdir (const DirType d)

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32	get_posinread () const

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE ReadType	get_readtype () const

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE DirType	get_indexdir () const

Static Public Methods
NVBIO_HOST_DEVICE static NVBIO_FORCEINLINE Flags	build_flags (const ReadType readtype, const DirType indexdir, const uint32 pos)

Constructor & Destructor Documentation

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE nvbio::bowtie2::cuda::SeedHit::SeedHit ( )

inline

constructor

Definition at line 76 of file seed_hit.h.

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE nvbio::bowtie2::cuda::SeedHit::SeedHit	(	const ReadType	readtype,
		const DirType	indexdir,
		const uint32	pos,
		const uint2 &	range
	)

inline

constructor

Parameters

readtype	select between forward and reverse-complemented read
indexdir	direction in the FM-index
pos	seed position within the read
range	SA range

Definition at line 85 of file seed_hit.h.

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE nvbio::bowtie2::cuda::SeedHit::SeedHit	(	const Flags	flags,
		const uint2 &	range
	)

inline

constructor

Parameters

flags	compressed seed flags
range	SA range

Definition at line 104 of file seed_hit.h.

Member Function Documentation

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32 nvbio::bowtie2::cuda::SeedHit::back ( ) const

inline

return the back of the SA range

Definition at line 153 of file seed_hit.h.

NVBIO_HOST_DEVICE static NVBIO_FORCEINLINE Flags nvbio::bowtie2::cuda::SeedHit::build_flags	(	const ReadType	readtype,
		const DirType	indexdir,
		const uint32	pos
	)

inlinestatic

build the compressed seed flags for a hit

Definition at line 61 of file seed_hit.h.

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE bool nvbio::bowtie2::cuda::SeedHit::empty ( void ) const

inline

is empty

Definition at line 136 of file seed_hit.h.

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32 nvbio::bowtie2::cuda::SeedHit::front ( ) const

inline

return the front of the SA range

Definition at line 148 of file seed_hit.h.

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE DirType nvbio::bowtie2::cuda::SeedHit::get_indexdir ( ) const

inline

get the FM-index orientation

Definition at line 227 of file seed_hit.h.

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32 nvbio::bowtie2::cuda::SeedHit::get_posinread ( ) const

inline

get the seed position in the read

Definition at line 215 of file seed_hit.h.

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint2 nvbio::bowtie2::cuda::SeedHit::get_range ( ) const

inline

get the SA range

Definition at line 130 of file seed_hit.h.

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32 nvbio::bowtie2::cuda::SeedHit::get_range_size ( ) const

inline

get the size of the SA range

Definition at line 142 of file seed_hit.h.

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE ReadType nvbio::bowtie2::cuda::SeedHit::get_readtype ( ) const

inline

get the read flags

Definition at line 221 of file seed_hit.h.

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32 nvbio::bowtie2::cuda::SeedHit::pop_back ( )

inline

pop the back of the SA range

Definition at line 179 of file seed_hit.h.

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32 nvbio::bowtie2::cuda::SeedHit::pop_back ( const uint32 n)

inline

pop n-elements from the back of the SA range

Definition at line 188 of file seed_hit.h.

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32 nvbio::bowtie2::cuda::SeedHit::pop_front ( )

inline

pop the front of the SA range

Definition at line 158 of file seed_hit.h.

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32 nvbio::bowtie2::cuda::SeedHit::pop_front ( const uint32 n)

inline

pop n-elements from the front of the SA range

Definition at line 168 of file seed_hit.h.

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void nvbio::bowtie2::cuda::SeedHit::set_indexdir ( const DirType d)

inline

set the FM-index orientation

Definition at line 209 of file seed_hit.h.

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void nvbio::bowtie2::cuda::SeedHit::set_posinread ( const uint32 p)

inline

set the seed position in the read

Definition at line 197 of file seed_hit.h.

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void nvbio::bowtie2::cuda::SeedHit::set_range ( const uint2 range)

inline

set the SA range

Definition at line 119 of file seed_hit.h.

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void nvbio::bowtie2::cuda::SeedHit::set_readtype ( const ReadType d)

inline

set the read flags

Definition at line 203 of file seed_hit.h.

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

E:/git/nvbio/nvBowtie/bowtie2/cuda/seed_hit.h

Detailed description

Classes

Public Methods

Static Public Methods

Constructor & Destructor Documentation

Member Function Documentation