NVBIO
 All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Macros Groups Pages
Namespaces | Functions
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)