mapping.h

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/*
 * nvbio
 * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved.
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 * modification, are permitted provided that the following conditions are met:
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 *      notice, this list of conditions and the following disclaimer.
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 *      names of its contributors may be used to endorse or promote products
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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 {




void gather_ranges(
    const uint32                    count,
    const uint32                    n_reads,
    SeedHitDequeArrayDeviceView     hits,
    const uint32*                   hit_counts_scan,
          uint64*                   out_ranges);

void map_whole_read(
    const ReadsDef::type&                           read_batch,
    const FMIndexDef::type                          fmi,
    const FMIndexDef::type                          rfmi,
    const nvbio::cuda::PingPongQueuesView<uint32>   queues,
    uint8*                                          reseed,
    SeedHitDequeArrayDeviceView                     hits,
    const ParamsPOD                                 params,
    const bool                                      fw,
    const bool                                      rc);

void map_exact(
    const ReadsDef::type&                           read_batch,
    const FMIndexDef::type                          fmi,
    const FMIndexDef::type                          rfmi,
    const uint32                                    retry,
    const nvbio::cuda::PingPongQueuesView<uint32>   queues,
    uint8*                                          reseed,
    SeedHitDequeArrayDeviceView                     hits,
    const ParamsPOD                                 params,
    const bool                                      fw,
    const bool                                      rc);

void map_exact(
    const ReadsDef::type&                           read_batch,
    const FMIndexDef::type                          fmi,
    const FMIndexDef::type                          rfmi,
    SeedHitDequeArrayDeviceView                     hits,
    const uint2                                     seed_range,
    const ParamsPOD                                 params,
    const bool                                      fw,
    const bool                                      rc);

void map_approx(
    const ReadsDef::type&                           read_batch,
    const FMIndexDef::type                          fmi,
    const FMIndexDef::type                          rfmi,
    const uint32                                    retry,
    const nvbio::cuda::PingPongQueuesView<uint32>   queues,
    uint8*                                          reseed,
    SeedHitDequeArrayDeviceView                     hits,
    const ParamsPOD                                 params,
    const bool                                      fw,
    const bool                                      rc);

void map_approx(
    const ReadsDef::type&                           read_batch,
    const FMIndexDef::type                          fmi,
    const FMIndexDef::type                          rfmi,
    SeedHitDequeArrayDeviceView                     hits,
    const uint2                                     seed_range,
    const ParamsPOD                                 params,
    const bool                                      fw,
    const bool                                      rc);

void map(
    const ReadsDef::type&                           read_batch,
    const FMIndexDef::type                          fmi,
    const FMIndexDef::type                          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