LocateDetail

Detailed Description

Functions
template<typename FMType , typename rFMType >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32	nvbio::bowtie2::cuda::detail::locate (const FMType &fmi, const rFMType &rfmi, const uint32 dir, const uint32 r)
template<typename FMType , typename rFMType >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint2	nvbio::bowtie2::cuda::detail::locate_init (const FMType &fmi, const rFMType &rfmi, const uint32 dir, const uint32 r)
template<typename FMType , typename rFMType >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32	nvbio::bowtie2::cuda::detail::locate_lookup (const FMType &fmi, const rFMType &rfmi, const uint32 dir, const uint2 it)
template<typename BatchType , typename FMType , typename rFMType >
__global__ void	nvbio::bowtie2::cuda::detail::locate_kernel (const BatchType read_batch, const FMType fmi, const rFMType rfmi, const uint32 in_count, const uint32 *idx_queue, HitQueuesDeviceView hits, const ParamsPOD params)
template<typename BatchType , typename FMType , typename rFMType >
__global__ void	nvbio::bowtie2::cuda::detail::locate_init_kernel (const BatchType read_batch, const FMType fmi, const rFMType rfmi, const uint32 in_count, const uint32 *idx_queue, HitQueuesDeviceView hits, const ParamsPOD params)
template<typename BatchType , typename FMType , typename rFMType >
__global__ void	nvbio::bowtie2::cuda::detail::locate_lookup_kernel (const BatchType read_batch, const FMType fmi, const rFMType rfmi, const uint32 in_count, const uint32 *idx_queue, HitQueuesDeviceView hits, const ParamsPOD params)
template<typename index_iterator , typename flags_iterator >
__global__ void	nvbio::bowtie2::cuda::detail::mark_straddling_kernel (const uint32 in_count, const uint32 *idx_queue, const uint32 reference_count, const index_iterator reference_index, HitQueuesDeviceView hits, flags_iterator flags, const ParamsPOD params)

Function Documentation

template<typename FMType , typename rFMType >

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32 nvbio::bowtie2::cuda::detail::locate	(	const FMType &	fmi,
		const rFMType &	rfmi,
		const uint32	dir,
		const uint32	r
	)

transform an SA index to linear coordinates using either the forward or reverse FM-index

Definition at line 55 of file locate_inl.h.

template<typename FMType , typename rFMType >

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint2 nvbio::bowtie2::cuda::detail::locate_init	(	const FMType &	fmi,
		const rFMType &	rfmi,
		const uint32	dir,
		const uint32	r
	)

first pass of a two pass method to transform an SA index to linear coordinates using either the forward or reverse FM-index

Definition at line 78 of file locate_inl.h.

template<typename BatchType , typename FMType , typename rFMType >

__global__ void nvbio::bowtie2::cuda::detail::locate_init_kernel	(	const BatchType	read_batch,
		const FMType	fmi,
		const rFMType	rfmi,
		const uint32	in_count,
		const uint32 *	idx_queue,
		HitQueuesDeviceView	hits,
		const ParamsPOD	params
	)

Locate the next SA row in the queue. Since the input loc_queue might have been sorted to gather locality, the corresponding entry in seed_queue is now specified by an index (idx_queue).

Definition at line 154 of file locate_inl.h.

template<typename BatchType , typename FMType , typename rFMType >

__global__ void nvbio::bowtie2::cuda::detail::locate_kernel	(	const BatchType	read_batch,
		const FMType	fmi,
		const rFMType	rfmi,
		const uint32	in_count,
		const uint32 *	idx_queue,
		HitQueuesDeviceView	hits,
		const ParamsPOD	params
	)

Locate the next SA row in the queue. Since the input loc_queue might have been sorted to gather locality, the corresponding entry in seed_queue is now specified by an index (idx_queue).

Definition at line 123 of file locate_inl.h.

template<typename FMType , typename rFMType >

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32 nvbio::bowtie2::cuda::detail::locate_lookup	(	const FMType &	fmi,
		const rFMType &	rfmi,
		const uint32	dir,
		const uint2	it
	)

second pass of a two pass method to transform an SA index to linear coordinates using either the forward or reverse FM-index

Definition at line 99 of file locate_inl.h.

template<typename BatchType , typename FMType , typename rFMType >

__global__ void nvbio::bowtie2::cuda::detail::locate_lookup_kernel	(	const BatchType	read_batch,
		const FMType	fmi,
		const rFMType	rfmi,
		const uint32	in_count,
		const uint32 *	idx_queue,
		HitQueuesDeviceView	hits,
		const ParamsPOD	params
	)

Locate the next SA row in the queue. Since the input loc_queue might have been sorted to gather locality, the corresponding entry in seed_queue is now specified by an index (idx_queue).

Definition at line 184 of file locate_inl.h.

template<typename index_iterator , typename flags_iterator >

__global__ void nvbio::bowtie2::cuda::detail::mark_straddling_kernel	(	const uint32	in_count,
		const uint32 *	idx_queue,
		const uint32	reference_count,
		const index_iterator	reference_index,
		HitQueuesDeviceView	hits,
		flags_iterator	flags,
		const ParamsPOD	params
	)

mark seeds straddling the reference boundaries.

Definition at line 214 of file locate_inl.h.