alignment.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:
 *    * 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.
 *    * 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.
 * 
 * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
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 */

#pragma once

#include <nvbio/basic/types.h>
#include <nvbio/basic/numbers.h>

namespace nvbio {
namespace alndiff {

struct Alignment
{
    enum { PAIRED        = 1,
           PROPER_PAIR   = 2,
           UNMAPPED      = 4,
           MATE_UNMAPPED = 8,
           REVERSE       = 16,
           MATE_REVERSE  = 32,
           READ_1        = 64,
           READ_2        = 128,
           SECONDARY     = 256,
           QC_FAILED     = 512,
           DUPLICATE     = 1024
         };

    Alignment() :
        read_id( uint32(-1) ),
        read_len( 0 ),
        mate( 0 ),
        pos( 0 ),
        ref_id( uint32(-1) ),
        flag( UNMAPPED ),
        score( -65536 ),
        mapQ( 0 ),
        ed( 255 ),
        subs( 0 ),
        ins( 0 ),
        dels( 0 ),
        n_mm( 0 ),
        n_gapo( 0 ),
        n_gape( 0 ),
        has_second( 0 ),
        sec_score( -65536 ) {}

    bool is_mapped()    const { return (pos != 0) && ((flag & UNMAPPED) == 0); }
    bool is_rc()        const { return (flag & REVERSE) != 0; }
    bool is_unique()    const { return is_mapped() && (has_second == false); }
    bool is_ambiguous() const { return is_mapped() && has_second && (sec_score == score); }

    uint16 mapped_read_bases() const { return subs + ins; }
    uint16 mapped_ref_bases()  const { return subs + dels; }
    uint16 trimmed()           const { return read_len - subs - ins; }

    uint32 read_id;
    uint32 read_len;
    uint32 mate;
    uint32 pos;
    uint32 ref_id;
    uint32 flag;
     int32 score;
    uint8  mapQ;
    uint8  ed;
    uint16 subs;
    uint16 ins;
    uint16 dels;
    uint8  n_mm;
    uint8  n_gapo;
    uint8  n_gape;
    uint8  has_second;
    int32  sec_score;
};

inline
bool distant(const Alignment& a1, const Alignment& a2)
{
    return (int64(a1.pos) < int64(a2.pos) - a1.read_len) ||
           (int64(a1.pos) > int64(a2.pos) + a1.read_len);
}

struct AlignmentPair
{
    AlignmentPair() {}
    AlignmentPair(const Alignment m1, const Alignment m2) : mate1(m1), mate2(m2) {}

    uint32 read_id()   const { return mate1.read_id; }
    uint32 read_len()  const { return mate1.read_len + mate2.read_len; }
     int32 score()     const { return mate1.score    + mate2.score; }
     uint8 mapQ()      const { return mate1.mapQ; }
     uint8 ed()        const { return mate1.ed       + mate2.ed; }
    uint16 subs()      const { return mate1.subs     + mate2.subs; }
    uint16 ins()       const { return mate1.ins      + mate2.ins; }
    uint16 dels()      const { return mate1.dels     + mate2.dels; }
     uint8 n_mm()      const { return mate1.n_mm     + mate2.n_mm; }
     uint8 n_gapo()    const { return mate1.n_gapo   + mate2.n_gapo; }
     uint8 n_gape()    const { return mate1.n_gape   + mate2.n_gape; }
     bool has_second() const { return mate1.has_second && mate2.has_second; }
     int32 sec_score() const { return mate1.sec_score  +  mate2.sec_score; }

    bool is_mapped()          const { return mate1.is_mapped() && mate2.is_mapped(); }
    bool is_mapped_paired()   const { return mate1.is_mapped() && mate2.is_mapped() && (mate1.flag & Alignment::PROPER_PAIR) && (mate2.flag & Alignment::PROPER_PAIR); }
    bool is_mapped_unpaired() const { return mate1.is_mapped() && mate2.is_mapped() && (((mate1.flag & Alignment::PROPER_PAIR) == 0) || ((mate2.flag & Alignment::PROPER_PAIR) == 0)); }
    bool is_unique_paired()   const { return is_mapped_paired() && mate1.is_unique() && mate2.is_unique(); }
    bool is_ambiguous_paired()const { return is_mapped_paired() && has_second() && (score() == sec_score()); }

    uint16 mapped_read_bases() const { return subs() + ins(); }
    uint16 mapped_ref_bases()  const { return subs() + dels(); }
    uint16 trimmed()           const { return read_len() - subs() - ins(); }

    const Alignment& operator[] (const uint32 i) const { return *(&mate1 + i); }

    Alignment mate1;
    Alignment mate2;
};

struct AlignmentStream
{
    virtual ~AlignmentStream() {}

    virtual bool is_ok() { return false; }

    virtual uint32 next_batch(
        const uint32    count,
        Alignment*      batch) { return 0; }
};

AlignmentStream* open_alignment_file(const char* file_name);

} // alndiff namespace
} // nvbio namespace