traceback_inl.h File Reference

#include <nvBowtie/bowtie2/cuda/alignment_utils.h>

Go to the source code of this file.

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

Namespaces
	nvbio
	Define a vector_view POD type and plain_view() for std::vector.
	nvbio::bowtie2
	nvbio::bowtie2::cuda
	nvbio::bowtie2::cuda::detail

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)
template<uint32 ALN_IDX, typename pipeline_type >
void	nvbio::bowtie2::cuda::banded_traceback_best_t (const uint32 count, const uint32 *idx, io::Alignment *best_data, const uint32 best_stride, const uint32 band_len, const pipeline_type &pipeline, const ParamsPOD params)
template<uint32 ALN_IDX, typename pipeline_type >
void	nvbio::bowtie2::cuda::opposite_traceback_best_t (const uint32 count, const uint32 *idx, io::Alignment *best_data, const uint32 best_stride, const pipeline_type &pipeline, const ParamsPOD params)
template<typename pipeline_type >
void	nvbio::bowtie2::cuda::banded_traceback_all_t (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 ParamsPOD params)
template<uint32 ALN_IDX, typename scoring_scheme_type , typename pipeline_type >
void	nvbio::bowtie2::cuda::finish_alignment_best_t (const uint32 count, const uint32 *idx, io::Alignment *best_data, const uint32 best_stride, const uint32 band_len, const pipeline_type &pipeline, const scoring_scheme_type scoring_scheme, const ParamsPOD params)
template<uint32 ALN_IDX, typename scoring_scheme_type , typename pipeline_type >
void	nvbio::bowtie2::cuda::finish_opposite_alignment_best_t (const uint32 count, const uint32 *idx, io::Alignment *best_data, const uint32 best_stride, const uint32 band_len, const pipeline_type &pipeline, const scoring_scheme_type scoring_scheme, const ParamsPOD params)
template<typename scoring_scheme_type , typename pipeline_type >
void	nvbio::bowtie2::cuda::finish_alignment_all_t (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 scoring_scheme_type scoring_scheme, const ParamsPOD params)