select.h File Reference

#include <nvBowtie/bowtie2/cuda/defs.h>
#include <nvBowtie/bowtie2/cuda/seed_hit.h>
#include <nvBowtie/bowtie2/cuda/seed_hit_deque_array.h>
#include <nvBowtie/bowtie2/cuda/scoring_queues.h>
#include <nvBowtie/bowtie2/cuda/params.h>
#include <nvbio/basic/cuda/pingpong_queues.h>
#include <nvbio/io/alignments.h>

Go to the source code of this file.

Classes
struct	nvbio::bowtie2::cuda::BaseScoringPipelineState< ScoringScheme >
struct	nvbio::bowtie2::cuda::BestApproxScoringPipelineState< ScoringScheme >
struct	nvbio::bowtie2::cuda::SelectBestApproxContext

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

Functions
void	nvbio::bowtie2::cuda::select_init (const uint32 count, const char *read_names, const uint32 *read_names_idx, const SeedHitDequeArrayDeviceView hits, uint32 *trys, uint32 *rseeds, const ParamsPOD params)
void	nvbio::bowtie2::cuda::select_init (BestApproxScoringPipelineState< EditDistanceScoringScheme > &pipeline, const ParamsPOD &params)
void	nvbio::bowtie2::cuda::select_init (BestApproxScoringPipelineState< SmithWatermanScoringScheme<> > &pipeline, const ParamsPOD &params)
__global__ void	nvbio::bowtie2::cuda::select_n_from_top_range_kernel (const uint32 begin, const uint32 count, const uint32 n_reads, const SeedHit *hit_data, const uint32 *hit_range_scan, uint32 *loc_queue, uint32 *seed_queue, uint32 *read_info)
void	nvbio::bowtie2::cuda::select (const SelectBestApproxContext context, const BestApproxScoringPipelineState< EditDistanceScoringScheme > &pipeline, const ParamsPOD params)
void	nvbio::bowtie2::cuda::select (const SelectBestApproxContext context, const BestApproxScoringPipelineState< SmithWatermanScoringScheme<> > &pipeline, const ParamsPOD params)
void	nvbio::bowtie2::cuda::select_all (const uint64 begin, const uint32 count, const uint32 n_reads, const uint32 n_hit_ranges, const uint64 n_hits, const SeedHitDequeArrayDeviceView hits, const uint32 *hit_count_scan, const uint64 *hit_range_scan, HitQueuesDeviceView scoring_queues)