TracebackDetail

Detailed Description

Classes
struct	nvbio::bowtie2::cuda::detail::BestTracebackStream< ALN_IDX, AlignerType, PipelineType >
struct	nvbio::bowtie2::cuda::detail::AllTracebackStream< AlignerType, PipelineType >

Functions
template<uint32 ALN_IDX, typename aligner_type , typename pipeline_type >
void	nvbio::bowtie2::cuda::detail::banded_traceback_best (const MateType mate_type, const uint32 count, const uint32 *idx, io::Alignment *best_data, const uint32 best_stride, const uint32 band_len, const pipeline_type &pipeline, const aligner_type aligner, const ParamsPOD params)
template<uint32 ALN_IDX, typename aligner_type , typename pipeline_type >
void	nvbio::bowtie2::cuda::detail::traceback_best (const MateType mate_type, const uint32 count, const uint32 *idx, io::Alignment *best_data, const uint32 best_stride, const pipeline_type &pipeline, const aligner_type aligner, const ParamsPOD params)
template<typename aligner_type , typename pipeline_type >
void	nvbio::bowtie2::cuda::detail::banded_traceback_all (const uint32 count, const uint32 *idx, const uint32 buffer_offset, const uint32 buffer_size, io::Alignment *alignments, const uint32 band_len, const pipeline_type &pipeline, const aligner_type aligner, const ParamsPOD params)
template<typename stream_type , typename scheme_type , typename pipeline_type >
__global__ void	nvbio::bowtie2::cuda::detail::finish_alignment_kernel (stream_type stream, pipeline_type pipeline, const scheme_type scoring_scheme, const ParamsPOD params)
template<uint32 ALN_IDX, typename scheme_type , typename pipeline_type >
void	nvbio::bowtie2::cuda::detail::finish_alignment_best (const MateType mate_type, const uint32 count, const uint32 *idx, io::Alignment *best_data, const uint32 best_stride, const uint32 band_len, const pipeline_type &pipeline, const scheme_type scoring_scheme, const ParamsPOD params)
template<typename scheme_type , typename pipeline_type >
void	nvbio::bowtie2::cuda::detail::finish_alignment_all (const uint32 count, const uint32 *idx, const uint32 buffer_offset, const uint32 buffer_size, io::Alignment *alignments, const uint32 band_len, const pipeline_type &pipeline, const scheme_type scoring_scheme, const ParamsPOD params)

Function Documentation

template<typename aligner_type , typename pipeline_type >

void nvbio::bowtie2::cuda::detail::banded_traceback_all	(	const uint32	count,
		const uint32 *	idx,
		const uint32	buffer_offset,
		const uint32	buffer_size,
		io::Alignment *	alignments,
		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 traceback calculations

Definition at line 461 of file traceback_inl.h.

template<uint32 ALN_IDX, typename aligner_type , typename pipeline_type >

void nvbio::bowtie2::cuda::detail::banded_traceback_best	(	const MateType	mate_type,
		const uint32	count,
		const uint32 *	idx,
		io::Alignment *	best_data,
		const uint32	best_stride,
		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 traceback calculations

Definition at line 205 of file traceback_inl.h.

template<typename scheme_type , typename pipeline_type >

void nvbio::bowtie2::cuda::detail::finish_alignment_all	(	const uint32	count,
		const uint32 *	idx,
		const uint32	buffer_offset,
		const uint32	buffer_size,
		io::Alignment *	alignments,
		const uint32	band_len,
		const pipeline_type &	pipeline,
		const scheme_type	scoring_scheme,
		const ParamsPOD	params
	)

finish computing the final alignments, i.e. computing the MD strings and the final scores (given the CIGARs)

Definition at line 778 of file traceback_inl.h.

template<uint32 ALN_IDX, typename scheme_type , typename pipeline_type >

void nvbio::bowtie2::cuda::detail::finish_alignment_best	(	const MateType	mate_type,
		const uint32	count,
		const uint32 *	idx,
		io::Alignment *	best_data,
		const uint32	best_stride,
		const uint32	band_len,
		const pipeline_type &	pipeline,
		const scheme_type	scoring_scheme,
		const ParamsPOD	params
	)

finish computing the final alignments, i.e. computing the MD strings and the final scores (given the CIGARs)

Definition at line 729 of file traceback_inl.h.

template<typename stream_type , typename scheme_type , typename pipeline_type >

__global__ void nvbio::bowtie2::cuda::detail::finish_alignment_kernel	(	stream_type	stream,
		pipeline_type	pipeline,
		const scheme_type	scoring_scheme,
		const ParamsPOD	params
	)

finish computing the final alignments, i.e. computing the MD strings and the final scores (given the CIGARs)

Definition at line 524 of file traceback_inl.h.

template<uint32 ALN_IDX, typename aligner_type , typename pipeline_type >

void nvbio::bowtie2::cuda::detail::traceback_best	(	const MateType	mate_type,
		const uint32	count,
		const uint32 *	idx,
		io::Alignment *	best_data,
		const uint32	best_stride,
		const pipeline_type &	pipeline,
		const aligner_type	aligner,
		const ParamsPOD	params
	)

dispatch the execution of a batch of full DP alignment traceback calculations

Definition at line 267 of file traceback_inl.h.