7/29/2019 CigarOperation — pbbam 0.13.

2 documentation

CigarOperation

#include <pbbam/CigarOperation.h>

enum PacBio::BAM::CigarOperationType
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 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.

Values:

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]

class PacBio::BAM::CigarOperation
The CigarOperation class represents a single CIGAR operation (consisting of a type & length).

https://pbbam.readthedocs.io/en/latest/api/CigarOperation.html 1/3
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Operation Type Conversion Methods

static char TypeToChar(const CigarOperationType type)

Convert between CigarOperationType enum & SAM/BAM character code.

Return
SAM/BAM character code

Parameters
type: CigarOperationType value

static CigarOperationType CharToType(const char c)

Convert between CigarOperationType enum & SAM/BAM character code.

Return
CigarOperationType value

Parameters
c: SAM/BAM character code

Constructors & Related Methods

CigarOperation()

CigarOperation(char c, uint32_t length)

CigarOperation(CigarOperationType op, uint32_t length)

CigarOperation(const CigarOperation&)

CigarOperation(CigarOperation&&)

CigarOperation &operator=(const CigarOperation&)

CigarOperation &operator=(CigarOperation&&)

~CigarOperation()

Attributes

CigarOperation &Char(const char opChar)

Sets this operation type.

Return
reference to this operation

Parameters
opChar: SAM/BAM character code

CigarOperation &Length(const uint32_t length)

Sets this operation length.

Return
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reference to this operation

Parameters
length:

CigarOperation &Type(const CigarOperationType opType)

Sets this operation type.

Return
reference to this operation

Parameters
opType: CigarOperationType value

Comparison Operators

bool operator==(const CigarOperation &other) const

Return
true if both CIGAR operation type & length match

bool operator!=(const CigarOperation &other) const

Return
true if either CIGAR operation type or length differ

Public Functions

char Char() const

Return
operation type as SAM/BAM char code

uint32_t Length() const

Return
operation length

CigarOperationType Type() const

Return
operation type as CigarOperationType enum value

https://pbbam.readthedocs.io/en/latest/api/CigarOperation.html 3/3