ReduceDetail

Detailed Description

Functions
template<typename ScoringScheme , typename PipelineType , typename ReduceContext >
__global__ void	nvbio::bowtie2::cuda::detail::score_reduce_kernel (const ReduceContext context, PipelineType pipeline, const ParamsPOD params)
template<typename ReduceContext >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void	nvbio::bowtie2::cuda::detail::update_best (const uint32 read_id, io::BestPairedAlignments &best_pairs, const io::PairedAlignments &pair, ReduceContext &context, const ParamsPOD params)
template<typename ReduceContext >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void	nvbio::bowtie2::cuda::detail::replace_best (const uint32 read_id, io::BestPairedAlignments &best_pairs, const io::PairedAlignments &pair, ReduceContext &context, const ParamsPOD params)
template<typename ReduceContext >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void	nvbio::bowtie2::cuda::detail::update_second (const uint32 read_id, io::BestPairedAlignments &best_pairs, const io::PairedAlignments &pair, ReduceContext &context, const ParamsPOD params)
template<typename ReduceContext >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE bool	nvbio::bowtie2::cuda::detail::try_update (const uint32 read_id, io::BestPairedAlignments &best_pairs, const io::PairedAlignments &pair, const uint32 min_distance, ReduceContext &context, const ParamsPOD params)
template<typename ReduceContext >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void	nvbio::bowtie2::cuda::detail::update_best (const uint32 read_id, io::Alignment &a1, io::Alignment &a2, const io::Alignment &a, ReduceContext &context, const ParamsPOD params)
template<typename ReduceContext >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void	nvbio::bowtie2::cuda::detail::replace_best (const uint32 read_id, io::Alignment &a1, io::Alignment &a2, const io::Alignment &a, ReduceContext &context, const ParamsPOD params)
template<typename ReduceContext >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void	nvbio::bowtie2::cuda::detail::update_second (const uint32 read_id, io::Alignment &a1, io::Alignment &a2, const io::Alignment &a, ReduceContext &context, const ParamsPOD params)
template<typename ReduceContext >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE bool	nvbio::bowtie2::cuda::detail::try_update (const uint32 read_id, io::Alignment &a1, io::Alignment &a2, const io::Alignment &a, const uint32 min_distance, ReduceContext &context, const ParamsPOD params)
template<typename ScoringScheme , typename PipelineType , typename ReduceContext >
__global__ void	nvbio::bowtie2::cuda::detail::score_reduce_paired_kernel (const ReduceContext context, PipelineType pipeline, const ParamsPOD params)

Function Documentation

template<typename ReduceContext >

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void nvbio::bowtie2::cuda::detail::replace_best	(	const uint32	read_id,
		io::BestPairedAlignments &	best_pairs,
		const io::PairedAlignments &	pair,
		ReduceContext &	context,
		const ParamsPOD	params
	)

Definition at line 175 of file reduce_inl.h.

template<typename ReduceContext >

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void nvbio::bowtie2::cuda::detail::replace_best	(	const uint32	read_id,
		io::Alignment &	a1,
		io::Alignment &	a2,
		const io::Alignment &	a,
		ReduceContext &	context,
		const ParamsPOD	params
	)

Definition at line 275 of file reduce_inl.h.

template<typename ScoringScheme , typename PipelineType , typename ReduceContext >

__global__ void nvbio::bowtie2::cuda::detail::score_reduce_kernel	(	const ReduceContext	context,
		PipelineType	pipeline,
		const ParamsPOD	params
	)

Reduce the list of scores associated to each read in the input queue to find the best 2 alignments.

this kernel takes a batch of extension results (one per active read, indexed by a sorting id) and 'reduces' them with best 2 results found so far. The kernel is parameterized by a templated context which can take further actions upon updates to the best or second best scores, as well as bailing-out on failures.

Parameters

context	the template context
pipeline	the pipeline state
params	algorithm parameters

Definition at line 74 of file reduce_inl.h.

template<typename ScoringScheme , typename PipelineType , typename ReduceContext >

__global__ void nvbio::bowtie2::cuda::detail::score_reduce_paired_kernel	(	const ReduceContext	context,
		PipelineType	pipeline,
		const ParamsPOD	params
	)

Reduce the list of scores associated to each read in the input queue to find the best 2 alignments.

this kernel takes a batch of extension results (one per active read, indexed by a sorting id) and 'reduces' them with best 2 results found so far. The kernel is parameterized by a templated context which can take further actions upon updates to the best or second best scores, as well as bailing-out on failures.

Parameters

context	the template context
pipeline	the pipeline state
params	algorithm parameters

Definition at line 369 of file reduce_inl.h.

template<typename ReduceContext >

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE bool nvbio::bowtie2::cuda::detail::try_update	(	const uint32	read_id,
		io::BestPairedAlignments &	best_pairs,
		const io::PairedAlignments &	pair,
		const uint32	min_distance,
		ReduceContext &	context,
		const ParamsPOD	params
	)

Definition at line 207 of file reduce_inl.h.

template<typename ReduceContext >

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE bool nvbio::bowtie2::cuda::detail::try_update	(	const uint32	read_id,
		io::Alignment &	a1,
		io::Alignment &	a2,
		const io::Alignment &	a,
		const uint32	min_distance,
		ReduceContext &	context,
		const ParamsPOD	params
	)

Definition at line 307 of file reduce_inl.h.

template<typename ReduceContext >

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void nvbio::bowtie2::cuda::detail::update_best	(	const uint32	read_id,
		io::BestPairedAlignments &	best_pairs,
		const io::PairedAlignments &	pair,
		ReduceContext &	context,
		const ParamsPOD	params
	)

Definition at line 156 of file reduce_inl.h.

template<typename ReduceContext >

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void nvbio::bowtie2::cuda::detail::update_best	(	const uint32	read_id,
		io::Alignment &	a1,
		io::Alignment &	a2,
		const io::Alignment &	a,
		ReduceContext &	context,
		const ParamsPOD	params
	)

Definition at line 258 of file reduce_inl.h.

template<typename ReduceContext >

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void nvbio::bowtie2::cuda::detail::update_second	(	const uint32	read_id,
		io::BestPairedAlignments &	best_pairs,
		const io::PairedAlignments &	pair,
		ReduceContext &	context,
		const ParamsPOD	params
	)

Definition at line 191 of file reduce_inl.h.

template<typename ReduceContext >

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void nvbio::bowtie2::cuda::detail::update_second	(	const uint32	read_id,
		io::Alignment &	a1,
		io::Alignment &	a2,
		const io::Alignment &	a,
		ReduceContext &	context,
		const ParamsPOD	params
	)

Definition at line 291 of file reduce_inl.h.