SelectDetail

Detailed Description

Functions
template<typename BatchType , typename ContextType >
__global__ void	nvbio::bowtie2::cuda::select_kernel (const BatchType read_batch, SeedHitDequeArrayDeviceView hits, const ContextType context, ScoringQueuesDeviceView scoring_queues, const ParamsPOD params)
template<typename ProbTree >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32	nvbio::bowtie2::cuda::randomized_select (ProbTree &prob_tree, SeedHit *hits_data, uint32 *rseeds, const uint32 read_id)
template<typename BatchType , typename ContextType >
__global__ void	nvbio::bowtie2::cuda::rand_select_kernel (const BatchType read_batch, SeedHitDequeArrayDeviceView hits, uint32 *rseeds, const ContextType context, ScoringQueuesDeviceView scoring_queues, const ParamsPOD params)
template<typename BatchType , typename ContextType >
__global__ void	nvbio::bowtie2::cuda::select_multi_kernel (const BatchType read_batch, SeedHitDequeArrayDeviceView hits, const ContextType context, ScoringQueuesDeviceView scoring_queues, const uint32 n_multi, const ParamsPOD params)
template<typename BatchType , typename ContextType >
__global__ void	nvbio::bowtie2::cuda::rand_select_multi_kernel (const BatchType read_batch, SeedHitDequeArrayDeviceView hits, uint32 *rseeds, const ContextType context, ScoringQueuesDeviceView scoring_queues, const uint32 n_multi, const ParamsPOD params)

Function Documentation

template<typename BatchType , typename ContextType >

__global__ void nvbio::bowtie2::cuda::rand_select_kernel	(	const BatchType	read_batch,
		SeedHitDequeArrayDeviceView	hits,
		uint32 *	rseeds,
		const ContextType	context,
		ScoringQueuesDeviceView	scoring_queues,
		const ParamsPOD	params
	)

Prepare for a round of seed extension by selecting the next SA row

Definition at line 182 of file select_inl.h.

template<typename BatchType , typename ContextType >

__global__ void nvbio::bowtie2::cuda::rand_select_multi_kernel	(	const BatchType	read_batch,
		SeedHitDequeArrayDeviceView	hits,
		uint32 *	rseeds,
		const ContextType	context,
		ScoringQueuesDeviceView	scoring_queues,
		const uint32	n_multi,
		const ParamsPOD	params
	)

Prepare for a round of seed extension by selecting a set of up to 'n_multi' next SA rows. For each read in the input queue, this kernel generates:

1. one or zero output reads, in the main output read queue,
2. zero to 'n_multi' SA rows. These are made of three entries, one in 'loc_queue', identifying the corresponding SA index, one in 'seed_queue', storing information about the seed hit, and one in 'parent_queue', storing the index of the "parent" read in the output queue (i.e. the slot where the read is is being stored)

Definition at line 492 of file select_inl.h.

template<typename ProbTree >

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32 nvbio::bowtie2::cuda::randomized_select	(	ProbTree &	prob_tree,
		SeedHit *	hits_data,
		uint32 *	rseeds,
		const uint32	read_id
	)

Definition at line 146 of file select_inl.h.

template<typename BatchType , typename ContextType >

__global__ void nvbio::bowtie2::cuda::select_kernel	(	const BatchType	read_batch,
		SeedHitDequeArrayDeviceView	hits,
		const ContextType	context,
		ScoringQueuesDeviceView	scoring_queues,
		const ParamsPOD	params
	)

Prepare for a round of seed extension by selecting the next SA row

Definition at line 75 of file select_inl.h.

template<typename BatchType , typename ContextType >

__global__ void nvbio::bowtie2::cuda::select_multi_kernel	(	const BatchType	read_batch,
		SeedHitDequeArrayDeviceView	hits,
		const ContextType	context,
		ScoringQueuesDeviceView	scoring_queues,
		const uint32	n_multi,
		const ParamsPOD	params
	)

Prepare for a round of seed extension by selecting a set of up to 'n_multi' next SA rows. For each read in the input queue, this kernel generates:

1. one or zero output reads, in the main output read queue,
2. zero to 'n_multi' SA rows. These are made of three entries, one in 'loc_queue', identifying the corresponding SA index, one in 'seed_queue', storing information about the seed hit, and one in 'parent_queue', storing the index of the "parent" read in the output queue (i.e. the slot where the read is is being stored)

Definition at line 294 of file select_inl.h.