BamRead.h

#ifndef theplu_yat_omic_bam_read
#define theplu_yat_omic_bam_read

// $Id: BamRead.h 3055 2013-06-16 00:21:30Z peter $

/*
  Copyright (C) 2012, 2013 Peter Johansson

  This file is part of the yat library, http://dev.thep.lu.se/yat

  The yat library is free software; you can redistribute it and/or
  modify it under the terms of the GNU General Public License as
  published by the Free Software Foundation; either version 3 of the
  License, or (at your option) any later version.

  The yat library is distributed in the hope that it will be useful,
  but WITHOUT ANY WARRANTY; without even the implied warranty of
  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
  General Public License for more details.

  You should have received a copy of the GNU General Public License
  along with this program. If not, see <http://www.gnu.org/licenses/>.
*/

#include "config_bam.h"

#include YAT_BAM_HEADER
#include YAT_SAM_HEADER

#include <functional>
#include <string>
#include <vector>

// backport #defines from samtools 0.1.19
#ifndef BAM_CIGAR_STR
#define BAM_CIGAR_STR "MIDNSHP=XB"
// lookup table used in bam_cigar_type
#define BAM_CIGAR_TYPE 0x3C1A7

#define bam_cigar_op(c) ((c)&BAM_CIGAR_MASK)
// length of the operation
#define bam_cigar_oplen(c) ((c)>>BAM_CIGAR_SHIFT)
// char describing the operation, see column 2 in table below
#define bam_cigar_opchr(c) (BAM_CIGAR_STR[bam_cigar_op(c)])
// Create a cigar element with length l and operation o
#define bam_cigar_gen(l, o) ((l)<<BAM_CIGAR_SHIFT|(o))
// Returns a two-bits number describing the type of operation. The
// first bit, bam_cigar_type & 1, (4th column in table below) is 1 iff
// operation consumes query sequence. The second bit, bam_cigar_type &
// 2, (3rd column below) is 1 iff operation consumes reference
// sequence.
#define bam_cigar_type(o) (BAM_CIGAR_TYPE>>((o)<<1)&3)
#endif

/*
  CIGAR
0 M 1 1 match
1 I 0 1 insert
2 D 1 0 deletion
3 N 1 0 spliced (rna)
4 S 0 1 soft clipped
5 H 0 0 hard clipped
6 P 0 0 padded
7 = 1 1 equal
8 X 1 1 mismatch
9 B 0 0

3rd column: consumes reference sequence
4th column: consumes query sequence
 */

namespace theplu {
namespace yat {
namespace omic {

  class BamRead
  {
  public:
    BamRead(void);

    BamRead(const BamRead& other);

    virtual ~BamRead(void);

    const BamRead& operator=(const BamRead& rhs);

    const uint8_t* aux(void) const;

    const uint8_t* aux(const char tag[2]) const;

    void aux_append(const char tag[2], char type, int len, uint8_t* data);

    void aux_del(const char tag[2]);

    int aux_size(void) const;

    const bam1_core_t& core(void) const;

    bam1_core_t& core(void);

    const uint32_t* cigar(void) const;

    uint32_t cigar(size_t i) const;

    uint32_t cigar_op(size_t i) const;

    uint32_t cigar_oplen(size_t i) const;

    std::string cigar_str(void) const;

    void cigar(const std::vector<uint32_t>& c);

    uint8_t qual(size_t i) const;

    void qual(size_t i, uint8_t q);

    const char* name(void) const;

    void name(const std::string& n);

    int32_t tid(void) const;

    int32_t pos(void) const;

    int32_t end(void) const;

    int32_t mtid(void) const;

    int32_t mpos(void) const;

    std::string sequence(void) const;

    uint8_t sequence(size_t index) const;

    void sequence(size_t i, uint8_t x);

    void sequence(const std::string& seq, const std::vector<uint8_t>& qual);

    uint32_t sequence_length(void) const;

    uint16_t flag(void) const;

    void swap(BamRead& other);

  private:
    // ensure capacity of data pointer is (at least) n
    void reserve(int n);

    bam1_t* bam_;

    friend class InBamFile;
    friend class OutBamFile;
    friend class BamReadIterator;
  };

  void swap(BamRead& lhs, BamRead& rhs);

  bool soft_clipped(const BamRead& bam);

  uint32_t left_soft_clipped(const BamRead& bam);

  uint32_t right_soft_clipped(const BamRead& bam);

  bool same_query_name(const BamRead& lhs, const BamRead& rhs);

  struct BamLessPos
    : public std::binary_function<const BamRead&, const BamRead&, bool>
  {
    bool operator()(const BamRead& lhs, const BamRead& rhs) const;
  };


  struct BamLessEnd
    : public std::binary_function<const BamRead&, const BamRead&, bool>
  {
    bool operator()(const BamRead& lhs, const BamRead& rhs) const;
  };

}}}
#endif