score.h

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/*
 * nvbio
 * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved.
 * 
 * Redistribution and use in source and binary forms, with or without
 * modification, are permitted provided that the following conditions are met:
 *    * Redistributions of source code must retain the above copyright
 *      notice, this list of conditions and the following disclaimer.
 *    * Redistributions in binary form must reproduce the above copyright
 *      notice, this list of conditions and the following disclaimer in the
 *      documentation and/or other materials provided with the distribution.
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 *      names of its contributors may be used to endorse or promote products
 *      derived from this software without specific prior written permission.
 * 
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#pragma once

#include <nvBowtie/bowtie2/cuda/defs.h>
#include <nvBowtie/bowtie2/cuda/string_utils.h>
#include <nvBowtie/bowtie2/cuda/scoring.h>
#include <nvbio/io/utils.h>

namespace nvbio {
namespace bowtie2 {
namespace cuda {

struct ParamsPOD;

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




void score_best(
    const uint32                                                            band_len,
    const BestApproxScoringPipelineState<EditDistanceScoringScheme >&       pipeline,
    const ParamsPOD&                                                        params);

void score_best(
    const uint32                                                            band_len,
    const BestApproxScoringPipelineState<SmithWatermanScoringScheme<> >&    pipeline,
    const ParamsPOD&                                                        params);

uint32 score_all(
    const uint32                                                band_len,
    const AllMappingPipelineState<EditDistanceScoringScheme>&   pipeline,
    const ParamsPOD&                                            params,
    const uint32                                                buffer_offset,
    const uint32                                                buffer_size);

uint32 score_all(
    const uint32                                                    band_len,
    const AllMappingPipelineState<SmithWatermanScoringScheme<> >&   pipeline,
    const ParamsPOD&                                                params,
    const uint32                                                    buffer_offset,
    const uint32                                                    buffer_size);

void anchor_score_best(
    const uint32                                                        band_len,
    const BestApproxScoringPipelineState<EditDistanceScoringScheme>&    pipeline,
    const ParamsPOD&                                                    params);

void anchor_score_best(
    const uint32                                                            band_len,
    const BestApproxScoringPipelineState<SmithWatermanScoringScheme<> >&    pipeline,
    const ParamsPOD&                                                        params);

void opposite_score_best(
    const BestApproxScoringPipelineState<EditDistanceScoringScheme>&    pipeline,
    const ParamsPOD&                                                    params);

void opposite_score_best(
    const BestApproxScoringPipelineState<SmithWatermanScoringScheme<> >&    pipeline,
    const ParamsPOD&                                                        params);


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