/usr/include/pbbam/Cigar.h is in libpbbam-dev 0.7.4+ds-1.
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// File Description
/// \file Cigar.h
/// \brief Defines the Cigar class.
//
// Author: Derek Barnett
#ifndef CIGAR_H
#define CIGAR_H
#include "pbbam/CigarOperation.h"
#include "pbbam/Config.h"
#include <string>
#include <vector>
namespace PacBio {
namespace BAM {
/// \brief The Cigar class represents the CIGAR string used to report alignment
/// charateristics in SAM/BAM.
///
/// \note Use of the 'M' operator is forbidden in PacBio BAMs. See
/// CigarOperationType description for more information.
///
/// \sa https://samtools.github.io/hts-specs/SAMv1.pdf for more information on CIGAR in general.
///
class PBBAM_EXPORT Cigar : public std::vector<CigarOperation>
{
public:
/// \name Constructors & Related Methods
/// \{
/// \brief Creates a Cigar object from SAM/BAM string input
///
/// \param [in] stdString SAM/BAM formatted CIGAR data
/// \returns a Cigar object representing the input data
///
/// \note This class may be removed from the public API in the future,
/// as the constructor taking a std::string accomplishes the same end.
///
static Cigar FromStdString(const std::string& stdString);
/// \brief Creates an empty Cigar.
Cigar(void);
/// \brief Creates a Cigar object from SAM/BAM string input
///
/// \param [in] cigarString SAM/BAM formatted CIGAR data
///
Cigar(const std::string& cigarString);
Cigar(const Cigar& other);
Cigar(Cigar&& other);
Cigar& operator=(const Cigar& other);
Cigar& operator=(Cigar&& other);
~Cigar(void);
/// \}
public:
/// \name Conversion Methods
/// \{
/// Converts Cigar object data to SAM/BAM formatted string
///
/// \returns SAM/BAM formatted std::string
///
std::string ToStdString(void) const;
/// \}
};
} // namespace BAM
} // namespace PacBio
#include "pbbam/internal/Cigar.inl"
#endif // CIGAR_H
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