select_impl.h

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#pragma once

#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/io/alignments.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>

namespace nvbio {
namespace bowtie2 {
namespace cuda {

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



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

template <typename BatchType, typename ContextType>
void select(
    const BatchType                         read_batch,
    SeedHitDequeArrayDeviceView             hits,
    const ContextType                       context,
          ScoringQueuesDeviceView           scoring_queues,
    const ParamsPOD                         params);

template <typename BatchType, typename ContextType>
void 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 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 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 select_t(
    const ContextType                                       context,
    const BestApproxScoringPipelineState<ScoringScheme>&    pipeline,
    const ParamsPOD                                         params);


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

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