score.h File Reference

#include <nvBowtie/bowtie2/cuda/defs.h>
#include <nvBowtie/bowtie2/cuda/string_utils.h>
#include <nvBowtie/bowtie2/cuda/scoring.h>
#include <nvbio/io/utils.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::AllMappingPipelineState< ScoringScheme >

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

Functions
void	nvbio::bowtie2::cuda::score_best (const uint32 band_len, const BestApproxScoringPipelineState< EditDistanceScoringScheme > &pipeline, const ParamsPOD &params)
void	nvbio::bowtie2::cuda::score_best (const uint32 band_len, const BestApproxScoringPipelineState< SmithWatermanScoringScheme<> > &pipeline, const ParamsPOD &params)
uint32	nvbio::bowtie2::cuda::score_all (const uint32 band_len, const AllMappingPipelineState< EditDistanceScoringScheme > &pipeline, const ParamsPOD &params, const uint32 buffer_offset, const uint32 buffer_size)
uint32	nvbio::bowtie2::cuda::score_all (const uint32 band_len, const AllMappingPipelineState< SmithWatermanScoringScheme<> > &pipeline, const ParamsPOD &params, const uint32 buffer_offset, const uint32 buffer_size)
void	nvbio::bowtie2::cuda::anchor_score_best (const uint32 band_len, const BestApproxScoringPipelineState< EditDistanceScoringScheme > &pipeline, const ParamsPOD &params)
void	nvbio::bowtie2::cuda::anchor_score_best (const uint32 band_len, const BestApproxScoringPipelineState< SmithWatermanScoringScheme<> > &pipeline, const ParamsPOD &params)
void	nvbio::bowtie2::cuda::opposite_score_best (const BestApproxScoringPipelineState< EditDistanceScoringScheme > &pipeline, const ParamsPOD &params)
void	nvbio::bowtie2::cuda::opposite_score_best (const BestApproxScoringPipelineState< SmithWatermanScoringScheme<> > &pipeline, const ParamsPOD &params)