bnt.h

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/*
 * nvbio
 * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved.
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 *      notice, this list of conditions and the following disclaimer.
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 *    * Neither the name of the NVIDIA CORPORATION nor the
 *      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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//
// NOTE: the code below is a derivative of bntseq.h, originally distributed
// under the MIT License, Copyright (c) 2008 Genome Research Ltd (GRL).
//

#pragma once

#include <nvbio/basic/types.h>
#include <string>
#include <vector>
#include <cstdio>

namespace nvbio {

struct BNTAnnData
{
    BNTAnnData() : offset(0), len(0), n_ambs(0), gi(0) {}

    int64   offset;
        int32   len;
        int32   n_ambs;
        uint32  gi;
};

struct BNTAnnInfo
{
    std::string name;
    std::string anno;
};

struct BNTAmb
{
        int64   offset;
        int32   len;
        char    amb;
};

struct BNTSeq
{
    BNTSeq() : l_pac(0), n_seqs(0), seed(0), n_holes(0) {}

    int64   l_pac;
        int32   n_seqs;
        uint32  seed;
        int32   n_holes;
    std::vector<BNTAnnInfo> anns_info;  // n_seqs elements
    std::vector<BNTAnnData> anns_data;  // n_seqs elements
    std::vector<BNTAmb>     ambs;       // n_holes elements
};

struct BNTInfo
{
    int64   l_pac;
        int32   n_seqs;
        uint32  seed;
        int32   n_holes;
};

struct BNTSeqLoader
{
    virtual void set_info(const BNTInfo info) {}
    virtual void read_ann(const BNTAnnInfo& info, BNTAnnData& data) {}
    virtual void read_amb(const BNTAmb& amb) {}
};

struct bns_fopen_failure {};
struct bns_files_mismatch {};

void save_bns(const BNTSeq& bns, const char *prefix);
void load_bns(BNTSeq& bns, const char *prefix);

void load_bns_info(BNTInfo& bns, const char *prefix);
void load_bns(BNTSeqLoader* bns, const char *prefix);

} // namespace nvbio