select_inl.h File Reference

#include <nvBowtie/bowtie2/cuda/defs.h>
#include <nvBowtie/bowtie2/cuda/utils.h>
#include <nvBowtie/bowtie2/cuda/seed_hit.h>
#include <nvBowtie/bowtie2/cuda/pipeline_states.h>
#include <nvbio/io/alignments.h>
#include <nvBowtie/bowtie2/cuda/params.h>
#include <nvbio/basic/cuda/pingpong_queues.h>
#include <nvbio/basic/priority_deque.h>
#include <nvbio/basic/vector_view.h>
#include <nvbio/basic/strided_iterator.h>
#include <nvbio/basic/sum_tree.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

Functions
template<typename ScoringScheme >
void	nvbio::bowtie2::cuda::select_init_t (BestApproxScoringPipelineState< ScoringScheme > &pipeline, const ParamsPOD &params)
template<typename BatchType , typename ContextType >
__global__ void	nvbio::bowtie2::cuda::select_kernel (const BatchType read_batch, SeedHitDequeArrayDeviceView hits, const ContextType context, ScoringQueuesDeviceView scoring_queues, const ParamsPOD params)
template<typename ProbTree >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32	nvbio::bowtie2::cuda::randomized_select (ProbTree &prob_tree, SeedHit *hits_data, uint32 *rseeds, const uint32 read_id)
template<typename BatchType , typename ContextType >
__global__ void	nvbio::bowtie2::cuda::rand_select_kernel (const BatchType read_batch, SeedHitDequeArrayDeviceView hits, uint32 *rseeds, const ContextType context, ScoringQueuesDeviceView scoring_queues, const ParamsPOD params)
template<typename BatchType , typename ContextType >
__global__ void	nvbio::bowtie2::cuda::select_multi_kernel (const BatchType read_batch, SeedHitDequeArrayDeviceView hits, const ContextType context, ScoringQueuesDeviceView scoring_queues, const uint32 n_multi, const ParamsPOD params)
template<typename BatchType , typename ContextType >
__global__ void	nvbio::bowtie2::cuda::rand_select_multi_kernel (const BatchType read_batch, SeedHitDequeArrayDeviceView hits, uint32 *rseeds, const ContextType context, ScoringQueuesDeviceView scoring_queues, const uint32 n_multi, const ParamsPOD params)
template<typename BatchType , typename ContextType >
void	nvbio::bowtie2::cuda::select (const BatchType read_batch, SeedHitDequeArrayDeviceView hits, const ContextType context, ScoringQueuesDeviceView scoring_queues, const ParamsPOD params)
template<typename BatchType , typename ContextType >
void	nvbio::bowtie2::cuda::rand_select (const BatchType read_batch, SeedHitDequeArrayDeviceView hits, uint32 *rseeds, const ContextType context, ScoringQueuesDeviceView scoring_queues, const ParamsPOD params)
template<typename BatchType , typename ContextType >
void	nvbio::bowtie2::cuda::select_multi (const BatchType read_batch, SeedHitDequeArrayDeviceView hits, const ContextType context, ScoringQueuesDeviceView scoring_queues, const uint32 n_multi, const ParamsPOD params)
template<typename BatchType , typename ContextType >
void	nvbio::bowtie2::cuda::rand_select_multi (const BatchType read_batch, SeedHitDequeArrayDeviceView hits, uint32 *rseeds, const ContextType context, ScoringQueuesDeviceView scoring_queues, const uint32 n_multi, const ParamsPOD params)
template<typename BatchType , typename ContextType >
void	nvbio::bowtie2::cuda::select (const BatchType read_batch, SeedHitDequeArrayDeviceView hits, uint32 *rseeds, const ContextType context, ScoringQueuesDeviceView scoring_queues, const uint32 n_multi, const ParamsPOD params)
template<typename ScoringScheme , typename ContextType >
void	nvbio::bowtie2::cuda::select_t (const ContextType context, const BestApproxScoringPipelineState< ScoringScheme > &pipeline, const ParamsPOD params)