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| | <code>CigarRoller::CigarRoller()</code> | | | <code>CigarRoller::CigarRoller()</code> |
| | Default constructor initializes as a CIGAR with no operations. | | | Default constructor initializes as a CIGAR with no operations. |
| + | |- |
| + | | <code>CigarRoller::CigarRoller(const char *cigarString)</code> |
| + | | Constructor that initializes the object with the specified cigarString. |
| + | |- |
| + | | <code>CigarRoller & CigarRoller::operator += (CigarRoller &rhs)</code> |
| + | | Add the contents of the specified CigarRoller to this object. |
| + | |- |
| + | | <code>CigarRoller & CigarRoller::operator += (CigarOperator &rhs)</code> |
| + | | Append the specified cigar operation to this object. |
| + | |- |
| + | | <code>void CigarRoller::Add(Operation operation, int count)</code> |
| + | | Adds the specified operation with the specified count to this object. |
| + | |- |
| + | | <code>void CigarRoller::Add(const char *cigarString)</code> |
| + | | Adds the specified cigarString to this object. |
| + | |- |
| + | | <code>void CigarRoller::Set(const char *cigarString)</code> |
| + | | Sets this object to the specified cigarString. |
| + | |- |
| + | | ''' DEPRECATED''' <code>int CigarRoller::getMatchPositionOffset()</code> |
| + | | DO NOT USE. |
| + | |- |
| + | | <code>const char * CigarRoller::getString()</code> |
| + | | REturns the string representation of this CIGAR object. |
| + | |- |
| + | | <code>void CigarRoller::getExpandedString(std::string &s)</code> |
| + | | Sets the specified string to a string of characters that represent this cigar with no digits (a CIGAR of "3M" would return "MMM") |
| + | |- |
| + | | <code>void CigarRoller::clear()</code> |
| + | | Clear this object so that it has 0 Cigar Operations. |
| + | |- |
| + | | <code>CigarOperator & CigarRoller::operator [] (int i)</code> |
| + | | Return the Cigar Operation at the specified index (starting at 0). |
| + | |- |
| + | | <code>bool CigarRoller::operator == (CigarRoller &rhs)</code> |
| + | | Returns true if two Cigar Rollers are the same (the same operations of the same sizes) |
| + | |- |
| + | | <code>int CigarRoller::size()</code> |
| + | | Return the number of cigar operations in this object. |
| + | |- |
| + | | <code>void CigarRoller::Dump()</code> |
| + | | Write this object as a string to cout. |
| + | |- |
| + | | <code>int CigarRoller::getExpectedQueryBaseCount()</code> |
| + | | Returns the expected read length |
| + | |- |
| + | | <code>int CigarRoller::getExpectedReferenceBaseCount()</code> |
| + | | Return how many bases in the reference are spanned by the given CIGAR string |
| + | |- |
| + | | <code>int32_t CigarRoller::getRefOffset(int32_t queryIndex)</code> |
| + | |Return the reference offset associated with the specified query index based on this cigar. |
| + | |- |
| + | | <code>int32_t CigarRoller::getQueryIndex(int32_t refOffset)</code> |
| + | | Return the query index associated with the specified reference offset based on this cigar. |
| |} | | |} |
| | | |
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| | <code> std::ostream &operator << (std::ostream &stream, const CigarRoller& roller)</code> | | | <code> std::ostream &operator << (std::ostream &stream, const CigarRoller& roller)</code> |
| | Writes all of the cigar operations contained in this roller to the passed in stream. | | | Writes all of the cigar operations contained in this roller to the passed in stream. |
| + | |- |
| + | | <code> std::ostream &operator << (std::ostream &stream, const CigarRoller::CigarOperator& o)</code> |
| + | | Writes the specified cigar operation to the specified stream as <count><char> (3M). |
| |} | | |} |
| | | |