Detailed Description

Classes
struct	nvbio::bowtie2::cuda::detail::AllScoreStream< AlignerType, PipelineType >

struct	nvbio::bowtie2::cuda::detail::BestScoreStream< AlignerType, PipelineType >

struct	nvbio::bowtie2::cuda::detail::BestOppositeScoreStream< AlignerType, PipelineType >

struct	nvbio::bowtie2::cuda::detail::BestAnchorScoreStream< AlignerType, PipelineType >

Functions
template<typename aligner_type , typename pipeline_type >
void	nvbio::bowtie2::cuda::detail::banded_score_all (const uint32 band_len, const pipeline_type &pipeline, const aligner_type aligner, const ParamsPOD params, const uint32 buffer_offset, const uint32 buffer_size, uint32 *counter)

template<typename aligner_type , typename pipeline_type >
void	nvbio::bowtie2::cuda::detail::banded_score_best (const uint32 band_len, const pipeline_type &pipeline, const aligner_type aligner, const ParamsPOD params)

template<typename aligner_type , typename pipeline_type >
void	nvbio::bowtie2::cuda::detail::opposite_score_best (const pipeline_type &pipeline, const aligner_type aligner, const ParamsPOD params)

template<typename aligner_type , typename pipeline_type >
void	nvbio::bowtie2::cuda::detail::banded_anchor_score_best (const uint32 band_len, const pipeline_type &pipeline, const aligner_type aligner, const ParamsPOD params)

Function Documentation

template<typename aligner_type , typename pipeline_type >

void nvbio::bowtie2::cuda::detail::banded_anchor_score_best	(	const uint32	band_len,
		const pipeline_type &	pipeline,
		const aligner_type	aligner,
		const ParamsPOD	params
	)

dispatch the execution of a batch of banded-alignment score calculations for the anchor mates

Definition at line 192 of file score_paired_inl.h.

template<typename aligner_type , typename pipeline_type >

void nvbio::bowtie2::cuda::detail::banded_score_all	(	const uint32	band_len,
		const pipeline_type &	pipeline,
		const aligner_type	aligner,
		const ParamsPOD	params,
		const uint32	buffer_offset,
		const uint32	buffer_size,
		uint32 *	counter
	)

dispatch the execution of a batch of single-ended banded-alignment score calculations

Definition at line 168 of file score_all_inl.h.

template<typename aligner_type , typename pipeline_type >

void nvbio::bowtie2::cuda::detail::banded_score_best	(	const uint32	band_len,
		const pipeline_type &	pipeline,
		const aligner_type	aligner,
		const ParamsPOD	params
	)

dispatch the execution of a batch of single-ended banded-alignment score calculations

Definition at line 154 of file score_best_inl.h.

template<typename aligner_type , typename pipeline_type >

void nvbio::bowtie2::cuda::detail::opposite_score_best	(	const pipeline_type &	pipeline,
		const aligner_type	aligner,
		const ParamsPOD	params
	)

dispatch the execution of a batch of alignment score calculations for the opposite mates

Definition at line 254 of file score_opposite_inl.h.