reduce_impl.h

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#pragma once

#include <nvBowtie/bowtie2/cuda/defs.h>
#include <nvbio/io/alignments.h>
#include <nvBowtie/bowtie2/cuda/seed_hit.h>
#include <nvBowtie/bowtie2/cuda/params.h>
#include <nvbio/io/utils.h>
#include <nvbio/basic/exceptions.h>

namespace nvbio {
namespace bowtie2 {
namespace cuda {

template <typename ScoringScheme> struct BaseScoringPipelineState;
template <typename ScoringScheme> struct BestApproxScoringPipelineState;



template <typename ScoringScheme, typename ReduceContext>
void score_reduce_t(
    const ReduceContext                                     context,
    const BestApproxScoringPipelineState<ScoringScheme>&    pipeline,
    const ParamsPOD                                         params);

template <typename ScoringScheme, typename ReduceContext>
void score_reduce_paired_t(
    const ReduceContext                                     context,
    const BestApproxScoringPipelineState<ScoringScheme>&    pipeline,
    const ParamsPOD                                         params);


} // namespace cuda
} // namespace bowtie2
} // namespace nvbio

#include <nvBowtie/bowtie2/cuda/reduce_inl.h>