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