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
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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]
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REFERENCE_SKIP¶ skipped region from the reference [N]
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SOFT_CLIP¶ soft clipping (clipped sequences present in SEQ) [S]
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HARD_CLIP= 5¶ hard clipping (clipped sequences NOT present in SEQ) [H]
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PADDING¶ padding (silent deletion from padded reference) [P]
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SEQUENCE_MATCH¶ sequence match [=]
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SEQUENCE_MISMATCH¶ sequence mismatch [X]
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class
PacBio::BAM::CigarOperation¶ The CigarOperation class represents a single CIGAR operation (consisting of a type & length).
Operation Type Conversion Methods
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static char
TypeToChar(const CigarOperationType type)¶ Convert between CigarOperationType enum & SAM/BAM character code.
- Return
- SAM/BAM character code
- Parameters
type: CigarOperationType value
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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
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CigarOperation()¶
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CigarOperation(char c, uint32_t length)¶
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CigarOperation(CigarOperationType op, uint32_t length)¶
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CigarOperation(const CigarOperation&)¶
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CigarOperation(CigarOperation&&)¶
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CigarOperation &
operator=(const CigarOperation&)¶
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CigarOperation &
operator=(CigarOperation&&)¶
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~CigarOperation()¶
Attributes
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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
- 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
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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
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CigarOperationType
Type() const¶ - Return
- operation type as CigarOperationType enum value
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static char