Cigar

#include <pbbam/Cigar.h>

class PacBio::BAM::Cigar

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.

See

https://samtools.github.io/hts-specs/SAMv1.pdf for more information on CIGAR in general.

Inherits from std::vector< CigarOperation >

Constructors & Related Methods

static Cigar FromStdString(const std::string &stdString)

Creates a Cigar object from SAM/BAM string input.

Return

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.

Parameters

• stdString: SAM/BAM formatted CIGAR data

Cigar()

Creates an empty Cigar.

Cigar(const std::string &cigarString)

Creates a Cigar object from SAM/BAM string input.

Parameters

• cigarString: SAM/BAM formatted CIGAR data

Cigar(const Cigar &other)

Cigar(Cigar &&other)

Cigar &operator=(const Cigar &other)

Cigar &operator=(Cigar &&other)

~Cigar()

Conversion Methods

std::string ToStdString() const

Converts Cigar object data to SAM/BAM formatted string

Return

SAM/BAM formatted std::string