reduce_inl.h File Reference

#include <nvBowtie/bowtie2/cuda/defs.h>
#include <nvBowtie/bowtie2/cuda/seed_hit.h>
#include <nvBowtie/bowtie2/cuda/params.h>
#include <nvBowtie/bowtie2/cuda/alignment_utils.h>
#include <nvBowtie/bowtie2/cuda/pipeline_states.h>
#include <nvbio/io/alignments.h>
#include <nvbio/io/utils.h>
#include <nvbio/basic/exceptions.h>

Go to the source code of this file.

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<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)
template<typename ScoringScheme , typename ReduceContext >
void	nvbio::bowtie2::cuda::score_reduce_t (const ReduceContext context, const BestApproxScoringPipelineState< ScoringScheme > &pipeline, const ParamsPOD params)
template<typename ScoringScheme , typename ReduceContext >
void	nvbio::bowtie2::cuda::score_reduce_paired_t (const ReduceContext context, const BestApproxScoringPipelineState< ScoringScheme > &pipeline, const ParamsPOD params)