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Reduce

Detailed Description

Modules

 ReduceDetail
 

Classes

struct  nvbio::bowtie2::cuda::ReduceBestApproxContext
 
struct  nvbio::bowtie2::cuda::ReduceBestExactContext
 

Functions

void nvbio::bowtie2::cuda::score_reduce (const ReduceBestApproxContext context, const BestApproxScoringPipelineState< EditDistanceScoringScheme > &pipeline, const ParamsPOD &params)
 
void nvbio::bowtie2::cuda::score_reduce (const ReduceBestApproxContext context, const BestApproxScoringPipelineState< SmithWatermanScoringScheme<> > &pipeline, const ParamsPOD &params)
 
void nvbio::bowtie2::cuda::score_reduce_paired (const ReduceBestApproxContext context, const BestApproxScoringPipelineState< EditDistanceScoringScheme > &pipeline, const ParamsPOD &params)
 
void nvbio::bowtie2::cuda::score_reduce_paired (const ReduceBestApproxContext context, const BestApproxScoringPipelineState< SmithWatermanScoringScheme<> > &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)
 

Function Documentation

void nvbio::bowtie2::cuda::score_reduce ( const ReduceBestApproxContext  context,
const BestApproxScoringPipelineState< EditDistanceScoringScheme > &  pipeline,
const ParamsPOD &  params 
)

Reduce the scores associated to each read in the scoring queue to find the best 2 alignments.

void nvbio::bowtie2::cuda::score_reduce ( const ReduceBestApproxContext  context,
const BestApproxScoringPipelineState< SmithWatermanScoringScheme<> > &  pipeline,
const ParamsPOD &  params 
)

Reduce the scores associated to each read in the scoring queue to find the best 2 alignments.

void nvbio::bowtie2::cuda::score_reduce_paired ( const ReduceBestApproxContext  context,
const BestApproxScoringPipelineState< EditDistanceScoringScheme > &  pipeline,
const ParamsPOD &  params 
)

Reduce the scores associated to each paired-end read in the scoring queue to find the best 2 alignments.

void nvbio::bowtie2::cuda::score_reduce_paired ( const ReduceBestApproxContext  context,
const BestApproxScoringPipelineState< SmithWatermanScoringScheme<> > &  pipeline,
const ParamsPOD &  params 
)

Reduce the scores associated to each paired-end read in the scoring queue to find the best 2 alignments.

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

Reduce the scores associated to each paired-end read in the scoring queue to find the best 2 alignments.

Definition at line 524 of file reduce_inl.h.

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

Reduce the scores associated to each read in the scoring queue to find the best 2 alignments.

Definition at line 505 of file reduce_inl.h.