18 #if !defined(_CIGAR_ROLLER_H)
19 #define _CIGAR_ROLLER_H
81 clearQueryAndReferenceIndexes();
103 void Add(
char operation,
int count);
106 void Add(
const char *cigarString);
129 void Set(
const char *cigarString);
133 void Set(
const uint32_t* cigarBuffer, uint16_t bufferLen);
169 stream << roller.cigarOperations;
void Add(Operation operation, int count)
Append the specified operation with the specified count to this object.
This class represents the CIGAR without any methods to set the cigar (see CigarRoller for that).
CigarRoller()
Default constructor initializes as a CIGAR with no operations.
Operation
Enum for the cigar operations.
void clear()
Clear this object so that it has no Cigar Operations.
void Set(const char *cigarString)
Sets this object to the specified cigarString.
CigarRoller(const char *cigarString)
Constructor that initializes the object with the specified cigarString.
bool Remove(int index)
Remove the operation at the specified index.
bool Update(int index, Operation op, int count)
Updates the operation at the specified index to be the specified operation and have the specified cou...
friend std::ostream & operator<<(std::ostream &stream, const CigarRoller &roller)
Writes all of the cigar operations contained in this roller to the passed in stream.
void Add(CigarRoller &rhs)
Append the specified Cigar object to this object.
int getMatchPositionOffset()
DEPRECATED - do not use, there are better ways to accomplish that by using read lengths,...
const char * getString()
Get the string reprentation of the Cigar operations in this object, caller must delete the returned v...
CigarRoller & operator=(CigarRoller &rhs)
Set this object to be equal to the specified CigarRoller.
The purpose of this class is to provide accessors for setting, updating, modifying the CIGAR object....
CigarRoller & operator+=(CigarRoller &rhs)
Add the contents of the specified CigarRoller to this object.
bool IncrementCount(int index, int increment)
Increments the count for the operation at the specified index by the specified value,...