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;
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.
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.
bool Remove(int index)
Remove the operation at the specified index.
bool IncrementCount(int index, int increment)
Increments the count for the operation at the specified index by the specified value,...
void Add(Operation operation, int count)
Append the specified operation with the specified count to this object.
CigarRoller()
Default constructor initializes as a CIGAR with no operations.
CigarRoller(const char *cigarString)
Constructor that initializes the object with the specified cigarString.
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...
void clear()
Clear this object so that it has no Cigar Operations.
void Add(CigarRoller &rhs)
Append the specified Cigar object to this object.
const char * getString()
Get the string reprentation of the Cigar operations in this object, caller must delete the returned v...
void Set(const char *cigarString)
Sets this object to the specified cigarString.
CigarRoller & operator=(CigarRoller &rhs)
Set this object to be equal to the specified CigarRoller.
int getMatchPositionOffset()
DEPRECATED - do not use, there are better ways to accomplish that by using read lengths,...
This class represents the CIGAR without any methods to set the cigar (see CigarRoller for that).
Operation
Enum for the cigar operations.