mapping_impl.h

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 * nvbio
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#pragma once

#include <nvBowtie/bowtie2/cuda/defs.h>
#include <nvBowtie/bowtie2/cuda/utils.h>
#include <nvBowtie/bowtie2/cuda/params.h>
#include <nvBowtie/bowtie2/cuda/seed_hit.h>
#include <nvBowtie/bowtie2/cuda/seed_hit_deque_array.h>
#include <nvBowtie/bowtie2/cuda/reads_def.h>
#include <nvBowtie/bowtie2/cuda/fmindex_def.h>
#include <nvbio/io/utils.h>
#include <nvbio/basic/cuda/pingpong_queues.h>
#include <nvbio/basic/cached_iterator.h>
#include <nvbio/basic/packedstream.h>
#include <nvbio/basic/priority_deque.h>
#include <nvbio/basic/strided_iterator.h>
#include <nvbio/basic/algorithms.h>

namespace nvbio {
namespace bowtie2 {
namespace cuda {




template <typename BatchType, typename FMType, typename rFMType>
void map_whole_read_t(
    const BatchType&                                read_batch, const FMType fmi, const rFMType rfmi,
    const nvbio::cuda::PingPongQueuesView<uint32>   queues,
    uint8*                                          reseed,
    SeedHitDequeArrayDeviceView                     hits,
    const ParamsPOD                                 params,
    const bool                                      fw,
    const bool                                      rc);

template <typename BatchType, typename FMType, typename rFMType>
void map_exact_t(
    const BatchType&                                read_batch, const FMType fmi, const rFMType rfmi,
    const uint32                                    retry,
    const nvbio::cuda::PingPongQueuesView<uint32>   queues,
    uint8*                                          reseed,
    SeedHitDequeArrayDeviceView                     hits,
    const ParamsPOD                                 params,
    const bool                                      fw,
    const bool                                      rc);

template <typename BatchType, typename FMType, typename rFMType>
void map_exact_t(
    const BatchType&                                read_batch, const FMType fmi, const rFMType rfmi,
    SeedHitDequeArrayDeviceView                     hits,
    const uint2                                     seed_range,
    const ParamsPOD                                 params,
    const bool                                      fw,
    const bool                                      rc);

template <typename BatchType, typename FMType, typename rFMType>
void map_case_pruning_t(
    const BatchType&                                read_batch, const FMType fmi, const rFMType rfmi,
    const uint32                                    retry,
    const nvbio::cuda::PingPongQueuesView<uint32>   queues,
    uint8*                                          reseed,
    SeedHitDequeArrayDeviceView                     hits,
    const ParamsPOD                                 params,
    const bool                                      fw,
    const bool                                      rc);

template <typename BatchType, typename FMType, typename rFMType>
void map_approx_t(
    const BatchType&                                read_batch, const FMType fmi, const rFMType rfmi,
    const uint32                                    retry,
    const nvbio::cuda::PingPongQueuesView<uint32>   queues,
    uint8*                                          reseed,
    SeedHitDequeArrayDeviceView                     hits,
    const ParamsPOD                                 params,
    const bool                                      fw,
    const bool                                      rc);

template <typename BatchType, typename FMType, typename rFMType>
void map_approx_t(
    const BatchType&                                read_batch, const FMType fmi, const rFMType rfmi,
    SeedHitDequeArrayDeviceView                     hits,
    const uint2                                     seed_range,
    const ParamsPOD                                 params,
    const bool                                      fw,
    const bool                                      rc);

template <typename BatchType, typename FMType, typename rFMType>
void map_t(
    const BatchType&                                read_batch, const FMType fmi, const rFMType rfmi,
    const uint32                                    retry,
    const nvbio::cuda::PingPongQueuesView<uint32>   queues,
    uint8*                                          reseed,
    SeedHitDequeArrayDeviceView                     hits,
    const ParamsPOD                                 params,
    const bool                                      fw,
    const bool                                      rc);


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

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