libpbbam-dev 0.7.4+ds-1 / usr / include / pbbam / CigarOperation.h

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// File Description
/// \file CigarOperation.h
/// \brief Defines the CigarOperationType enum & CigarOperation class.
//
// Author: Derek Barnett

#ifndef CIGAROPERATION_H
#define CIGAROPERATION_H

#include "pbbam/Config.h"
#include <stdexcept>

namespace PacBio {
namespace BAM {

/// \brief Describes a CIGAR operation.
///
/// Bracketed character is the corresponding SAM/BAM character code.
///
/// \warning ALIGNMENT_MATCH ('M') is included in this enum to maintain
///          consistency with htslib. However, as of PacBio BAM spec version
///          3.0b7, this CIGAR operation \b forbidden. Any attempt to read or
///          write a record containing this operation will trigger a
///          std::runtime_error. SEQUENCE_MATCH('=) or SEQUENCE_MISMATCH('X')
///          should be used instead.
///
enum class CigarOperationType
{
    UNKNOWN_OP        = -1 ///< unknown/invalid CIGAR operator
  , ALIGNMENT_MATCH   = 0  ///< alignment match (can be a sequence match or mismatch) [M]
  , INSERTION              ///< insertion to the reference [I]
  , DELETION               ///< deletion from the reference [D]
  , REFERENCE_SKIP         ///< skipped region from the reference [N]
  , SOFT_CLIP              ///< soft clipping (clipped sequences present in SEQ) [S]
  , HARD_CLIP         = 5  ///< hard clipping (clipped sequences NOT present in SEQ) [H]
  , PADDING                ///< padding (silent deletion from padded reference) [P]
  , SEQUENCE_MATCH         ///< sequence match [=]
  , SEQUENCE_MISMATCH      ///< sequence mismatch [X]
};

/// \brief The CigarOperation class represents a single CIGAR operation
///        (consisting of a type & length).
///
class PBBAM_EXPORT CigarOperation
{
public:

    /// \name Operation Type Conversion Methods
    /// \{

    /// Convert between CigarOperationType enum & SAM/BAM character code.
    ///
    /// \param[in] type CigarOperationType value
    /// \returns SAM/BAM character code
    static char TypeToChar(const CigarOperationType type);

    /// Convert between CigarOperationType enum & SAM/BAM character code.
    ///
    /// \param[in] c SAM/BAM character code
    /// \returns CigarOperationType value
    static CigarOperationType CharToType(const char c);

    /// \}

public:
    /// \name Constructors & Related Methods
    /// \{

    CigarOperation(void);
    CigarOperation(char c, uint32_t length);
    CigarOperation(CigarOperationType op, uint32_t length);
    CigarOperation(const CigarOperation& other);
    CigarOperation(CigarOperation&& other);
    CigarOperation& operator=(const CigarOperation& other);
    CigarOperation& operator=(CigarOperation&& other);
    ~CigarOperation(void);

    /// \}

public:

    /// \returns operation type as SAM/BAM char code
    inline char Char(void) const;

    /// \returns operation length
    inline uint32_t Length(void) const;

    /// \returns operation type as CigarOperationType enum value
    inline CigarOperationType Type(void) const;

    /// \}

public:
    /// \name Attributes
    /// \{

    /// Sets this operation type.
    ///
    /// \param[in] opChar SAM/BAM character code
    /// \returns reference to this operation
    inline CigarOperation& Char(const char opChar);

    /// Sets this operation length.
    ///
    /// \param[in] length
    /// \returns reference to this operation
    inline CigarOperation& Length(const uint32_t length);

    /// Sets this operation type.
    ///
    /// \param[in] opType CigarOperationType value
    /// \returns reference to this operation
    inline CigarOperation& Type(const CigarOperationType opType);

    /// \}

public:
    /// \name Comparison Operators
    /// \{

    /// \returns true if both CIGAR operation type & length match
    inline bool operator==(const CigarOperation& other) const;

    /// \returns true if either CIGAR operation type or length differ
    inline bool operator!=(const CigarOperation& other) const;

    /// \}

private:
    CigarOperationType type_;
    uint32_t length_;
};

} // namespace BAM
} // namespace PacBio

#include "pbbam/internal/CigarOperation.inl"

#endif // CIGAROPERATION_H