/usr/include/pbbam/internal/CigarOperation.inl is in libpbbam-dev 0.7.4+ds-1build2.
This file is owned by root:root, with mode 0o644.
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// File Description
/// \file CigarOperation.inl
/// \brief Inline implemenations for the CigarOperation class.
//
// Author: Derek Barnett
#include "pbbam/CigarOperation.h"
namespace PacBio {
namespace BAM {
inline CigarOperation::CigarOperation(void)
: type_(CigarOperationType::UNKNOWN_OP)
, length_(0)
{ }
inline CigarOperation::CigarOperation(char c, uint32_t length)
: type_(CigarOperation::CharToType(c))
, length_(length)
{
if (type_ == CigarOperationType::ALIGNMENT_MATCH)
throw std::runtime_error("CIGAR operation 'M' is not allowed in PacBio BAM files. Use 'X/=' instead.");
}
inline CigarOperation::CigarOperation(CigarOperationType op, uint32_t length)
: type_(op)
, length_(length)
{
if (type_ == CigarOperationType::ALIGNMENT_MATCH)
throw std::runtime_error("CIGAR operation 'M' is not allowed in PacBio BAM files. Use 'X/=' instead.");
}
inline CigarOperation::CigarOperation(const CigarOperation& other)
: type_(other.type_)
, length_(other.length_)
{ }
inline CigarOperation::CigarOperation(CigarOperation&& other)
: type_(std::move(other.type_))
, length_(std::move(other.length_))
{ }
inline CigarOperation::~CigarOperation(void) { }
inline uint32_t CigarOperation::Length(void) const
{ return length_; }
inline CigarOperation& CigarOperation::Length(const uint32_t length)
{ length_ = length; return *this; }
inline CigarOperationType CigarOperation::Type(void) const
{ return type_; }
inline CigarOperation &CigarOperation::Type(const CigarOperationType opType)
{ type_ = opType; return *this; }
inline char CigarOperation::Char(void) const
{ return CigarOperation::TypeToChar(type_); }
inline CigarOperation &CigarOperation::Char(const char opChar)
{ type_ = CigarOperation::CharToType(opChar);return *this; }
inline CigarOperation& CigarOperation::operator=(const CigarOperation& other)
{ type_ = other.type_; length_ = other.length_; return *this; }
inline CigarOperation& CigarOperation::operator=(CigarOperation&& other)
{ type_ = std::move(other.type_); length_ = std::move(other.length_); return *this; }
inline bool CigarOperation::operator==(const CigarOperation& other) const
{ return type_ == other.type_ && length_ == other.length_; }
inline bool CigarOperation::operator!=(const CigarOperation& other) const
{ return !(*this == other); }
} // namespace BAM
} // namespace PacBio
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