locate.h

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 * nvbio
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#pragma once

#include <nvBowtie/bowtie2/cuda/defs.h>
#include <nvBowtie/bowtie2/cuda/params.h>
#include <nvbio/io/alignments.h>

namespace nvbio {
namespace bowtie2 {
namespace cuda {

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




template <typename BatchType, typename FMType, typename rFMType>
void locate(
    const BatchType             read_batch, const FMType fmi, const rFMType rfmi,
    const uint32                in_count,
    const uint32*               idx_queue,
          HitQueuesDeviceView   hits,
    const ParamsPOD             params);

template <typename BatchType, typename FMType, typename rFMType>
void locate_init(
    const BatchType             read_batch, const FMType fmi, const rFMType rfmi,
    const uint32                in_count,
    const uint32*               idx_queue,
          HitQueuesDeviceView   hits,
    const ParamsPOD             params);

template <typename BatchType, typename FMType, typename rFMType>
void locate_lookup(
    const BatchType             read_batch, const FMType fmi, const rFMType rfmi,
    const uint32                in_count,
    const uint32*               idx_queue,
          HitQueuesDeviceView   hits,
    const ParamsPOD             params);

template <typename ScoringScheme>
void locate_init(
    const BaseScoringPipelineState<ScoringScheme>&  pipeline,
    const ParamsPOD                                 params);

template <typename ScoringScheme>
void locate_lookup(
    const BaseScoringPipelineState<ScoringScheme>&  pipeline,
    const ParamsPOD                                 params);

template <typename index_iterator, typename flags_iterator>
void mark_straddling(
    const uint32                in_count,
    const uint32*               idx_queue,
    const uint32                reference_count,
    const index_iterator        reference_index,
          HitQueuesDeviceView   hits,
          flags_iterator        flags,
    const ParamsPOD             params);


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

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